2-d-colocalisation-cells
type: software
has author: Christian "Tischi" Tischer
has documentation: CellProfiler 2D Coloc PerCell
has documentation: Github tischi/ImageAnalysisWorkflows
has function: operation Image colocalization
has function: operation Colocalisation analysis
has location: CellProfiler 2D Coloc PerCell
has location: 2-D colocalisation in cells using CellProfiler
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2014-12-09T12:49:48
modified: 2019-02-05T09:39:29
title: 2-D Colocalisation in Cells
comment: The workflow computes cell-based colocalisation of two stainings in 2-D images. Both pixel- and object-based readouts are provided and some pros and cons are discussed. Please read here for more information: https://github.com/tischi/ImageAnalysisWorkflows/blob/master/CellProfiler_2D_Coloc_PerCell/README.md Input data type: images Output data type: processed images, numbers, text file, csv files

2d-3d-distributed-parallel-region-competition-segmentation
type: software
has author: MOSAIC Group, Dresden
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has location: PPM RC
has reference publication: journal.pone.0152528
has reference publication: A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-07T16:26:00
modified: 2019-10-18T17:07:01
title: 2D-3D distributed parallel region competition segmentation
comment: This is the source code and data page of a distributed parallel algorithm 2683 for segmentation of large fluorescence microscopy images.

2d-and-3d-mitochondrial-shape-analysis-and-network-properties
type: software
has author: Julie Nikolaisen, Linn I. H. Nilsson, Ina K. N. Pettersen, Peter H. G. M. Willems, James B. Lorens, Werner J. H. Koopman, Karl J. Tronstad
has function: operation 2945
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has reference publication: journal.pone.0101365#s2
has reference publication: Publication
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/118
created: 2014-12-08T14:39:57
modified: 2023-04-26T13:43:13
title: 2D and 3D mitochondrial shape analysis and network properties
comment: The original paper describes a method to analyze mitochondrial morphology in 2D and 3D.

2d-and-3d-tracking-based-global-cost-function-optimization
type: software
has author: Perrine Paul-Gilloteaux
has function: operation Image tracking
has function: operation Particle tracking
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: MacroBatchForOnedirectorytif2.0.ijm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: nmeth.2808
has reference publication: Chenouard et al.(2014) Objective comparison of particle tracking methods
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1040
requires: http://biii.eu/node/1309
requires: http://biii.eu/node/1310
requires: http://biii.eu/node/1311
requires: http://biii.eu/node/38
created: 2014-12-15T11:19:23
modified: 2023-04-27T15:15:32
title: 2D and 3D tracking based on global cost function optimization
comment: The workflow consists of firstly identifying spot (which can be also gravity center of cells identified by another method), and then secondly compute trajectories by linking these spots by global optimisation with a cost function. This method is part of the methods evaluated in Chanouard et al (2014) as "method 9" and is described in detail in its supplementary PDF (page 65). ## Dependencies Following plugins are required. 1. [JAR to be placed under IJ plugin directory](http://xfer.curie.fr/get/192esfJKxA1/Trackingv2.0.zip) 1. A pdf file with instructions and output description is also available in the zip . 1. [MTrackJ](https://imagescience.org/meijering/software/mtrackj/) : Used for visualization of tracks. Preinstalled in Fiji. 2. [Imagescience.jar](http://www.imagescience.org/meijering/software/download/imagescience.jar): This library is used by MTrackJ. Use update site to install this plugin. 3. [jama.jar](http://math.nist.gov/javanumerics/jama/). Preinstalled in Fiji. ##Advantages: - support blinking (with a parameters allowing it or not) - fast, - can be used in batch, some analysis results provided. - No dynamic model. - The tracking part is not dependent of ImageJ. ## Pitfalls: - does not support division - the optimization algorithm used is a simulated annealing, so results can be slightly different between two runs. - No Dynamic model (so less good results but can be used for a first study of the kind of movements) ##The sample data The parameters used for this example data Beads, were 1. detection: 150 2. the max distance in pixels: 20 3. max allowed disappearance in frame: 1

2d-brain-slice-region-annotation-slicemap
type: software
has author: Barbier Michaël
has author: Bottelbergs Astrid
has author: De Vos Winnok H.
has author: Ebneth Andreas
has author: Nuydens Rony
has documentation: user manual.pdf
has function: operation Image registration
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has license: MIT
has location: SliceMap
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btx658/4557183
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic Widefield microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-28T11:37:30
modified: 2023-05-02T16:19:55
title: 2D brain slice region annotation: SliceMap
comment: SliceMap Whole brain tissue slices are commonly used in neurobiological research for analyzing pathological features in an anatomically defined manner. However, since many pathologies are expressed in specific regions of the brain, it is necessary to have an annotation of the regions in the brain slices. Such an annotation can be done by manual delineation, as done most often, or by an automated region annotation tool. SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of fluorescent brain slices. The plugin uses a reference library of pre-annotated brain slices (the brain region templates) to annotate brain regions of unknown samples. To perform the region annotation, SliceMap registers the reference slices to the sample slice (using elastic registration plugin BUnwarpJ) and uses the resulting image transformations to morph the template regions towards the anatomical brain regions of the sample. The resulting brain regions are saved as FIJI/ImageJ ROI’s (Regions Of Interest) as a single zip-file for each sample slice. More information can also be found in "SliceMap: an algorithm for automated brain region annotation", Michaël Barbier, Astrid Bottelbergs, Rony Nuydens, Andreas Ebneth, Winnok H De Vos, Bioinformatics, btx658, https://doi.org/10.1093/bioinformatics/btx658

2d-cell-tracking-and-analysis-morphological-dynamics
type: software
has author: R.A. Tyson, D.B.A. Epstein, K.I. Anderson and T. Bretschneider
has function: operation Active contours
has function: operation Cell segmentation
has function: operation Cell tracking
has location: quimp
has location: Home Page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://doi.org/10.1051/mmnp/20105102
has reference publication: Tyson et al (2010) High Resolution Tracking of Cell Membrane Dynamics in Moving Cells: an Electrifying Approach
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
requires: http://biii.eu/node/61
created: 2014-12-09T10:02:20
modified: 2019-02-05T09:55:57
title: 2D cell tracking and analysis of morphological dynamics
comment: The QuimP software from Bretschneider group is deployed as ImageJ plugin and includes model-based cell segmentation, cell outline tracking and quantification of the spatially resolved speed of protrusions and retractions. The algorithm to calculate morphological dynamics is faster compared to other approaches (e.g. [Machacek and Danuser, 2006](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367294/)). The reference paper describes the workflow for these analyses.

2d-gaussian-fitting-macro-fijiimagej-multiple-signals
type: software
has author: Waithe dominic orcid.org/0000-0003-2685-4226
has documentation: Gaussian function
has documentation: Related Wikipedia article.
has function: operation 3443
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has location: IJ1 macro script.
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2018-10-17T17:13:31
modified: 2021-03-16T21:06:27
title: 2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals.
comment: This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. This implementation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated).

2d-spots-counting-using-knime
type: software
has author: Juergen Reymann
has documentation: Training material
has function: operation Spot extraction
has location: Session3b SpotsInNucleiSurroundings
has location: download workflow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4543
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2014-12-09T11:35:33
modified: 2018-05-14T21:26:17
title: 2D spots counting using KNIME
comment: These two KNIME workflow solutions are similar: first one detects nuclei and spots inside the nuclei without taking care of surrounding regions, i.e. mitochondria. The second one provides the full solution including spots in mitochondria. see section 2.4 for KNIME workflow. Section 2.3 is also available, using Fiji. Sample image: hela-cells.tif (674k x 3)

2d-tracking-using-knime-and-fiji
type: software
has author: Juergen Reymann
has documentation: Chapter 3 2D+time tracking
has function: operation Image tracking
has location: Session4 Tracking
has location: Session4_Tracking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4543
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
requires: http://biii.eu/node/79
created: 2014-12-09T11:47:49
modified: 2018-05-14T21:16:25
title: 2D tracking using KNIME and Fiji
comment: This simple KNIME workflow solution tracks 2D objects/cells in time series. After a few intensity based preprocessing steps, objects/cells are segmented first, then it uses Fiji TrackMate LAP method for the tracking task. Documentation starts from p23 of the linked PDF. Example Image: mitocheck_small.tif (2.9M)

3-d-density-kernel-estimation
type: software
has author: Waithe dominic orcid.org/0000-0003-2685-4226
has DOI: 1284027#.W8he6xO2nfY
has DOI: https://zenodo.org/record/1284027#.W8he6xO2nfY
has function: operation 2423
has function: operation Cell counting
has function: operation Pixel classification
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v2.0
has location: 3-D Density Kernel Estimation.ipynb
has location: link to ipython github.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: submissionFinal.pdf
has reference publication: 978-3-319-46604-0 18
has reference publication: conference proceedings
has reference publication: pdf version
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1369
requires: http://biii.eu/node/1376
requires: http://biii.eu/node/73
created: 2018-10-18T10:18:22
modified: 2018-10-18T10:29:30
title: 3-D Density Kernel Estimation
comment: 3-D density kernel estimation (DKE-3-D) method, utilises an ensemble of random decision trees for counting objects in 3D images. DKE-3-D avoids the problem of discrete object identification and segmentation, common to many existing 3-D counting techniques, and outperforms other methods when quantification of densely packed and heterogeneous objects is desired.

3d-active-meshes-icy
type: software
has author: Alexandre Dufour
has documentation: 3D-Active-Meshes
has function: operation Cell segmentation
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: 3D-Active-Meshes
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/21193379
has reference publication: 3-D Active Meshes: Fast Discrete Deformable Models for Cell Tracking in 3-D Time-Lapse Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/741
requires: http://biii.eu/node/780
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2023-04-29T14:36:45
title: 3D Active Meshes (Icy)

3d-affine-transformation-based-paired-points
type: software
has author: Kota Miura
has function: operation R8ANfLkuHu47r739AkhxrId
has location: affinetransform3Dv3.js
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4668
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-09T15:28:50
modified: 2018-05-30T08:10:34
title: 3D affine transformation based on paired points
comment: Using a text file containing 3D point coordinates as reference pairs, 3D image stack is transformed.

3d-area
type: software
has location: 3D Area
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/463
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:47
modified: 2017-09-13T10:11:03
title: 3D Area

3d-cell-tracking-and-quantification-shape-changes
type: software
has author: Du CJ, Hawkins PT, Stephens LR, Bretschneider T
has function: operation Cell tracking
has reference publication: http://doi.org/10.1186/1471-2105-14-296
has reference publication: Du et al (2013) 3D time series analysis of cell shape using Laplacian approaches
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2014-12-08T12:08:18
modified: 2018-05-31T20:10:08
title: 3D cell tracking and quantification of shape changes
comment: The workflow includes segmentation, tracking and quantifying morphological dynamics of moving cells in 3D. The authors have implemented the workflow in Matlab, but so far there is no download link provided. To apply this workflow, we recommend to contact the authors or to implement the worflow based on the detailed description in the original paper.

3d-cell-tracking-using-gaussian-mixture-model-tgmm
type: software
has author: Amat Fernando
has author: Branson Kristin
has author: Keller J Philipp
has author: Lemon William
has author: McDole Katie
has author: Mossing P Daniel
has author: Myers W Eugene
has author: Wan Yinan
has function: operation Cell tracking
has location: bin
has location: Download executables from Git
has reference publication: nmeth.3036
has reference publication: Article in Nature Methods
has topic: topic Light-sheet microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/3568
has usage example: tgmm-docker
has usage example: TGMM docker
openess: http://biii.eu/taxonomy/term/3575
created: 2019-12-19T13:48:13
modified: 2020-10-19T15:07:15
title: 3D cell tracking using Gaussian Mixture Model (TGMM)
comment: TGMM is a cell tracking solution for large 3D volume (typically lightsheet). It detects cell nuclei by fitting gaussians on their fluorescent intensity. It can run on GPU using CUDA and is called via the command line.

3d-confocal-noise-simulator
type: software
has author: David ROUSSEAU
has documentation: UserManual.pdf
has location: MicroTools
has type: http://biii.eu/taxonomy/term/8
has usage example: document
openess: http://biii.eu/taxonomy/term/3577
created: 2018-05-20T17:49:05
modified: 2018-05-20T17:59:40
title: 3D confocal noise simulator
comment: This Matlab code simulates the noise of the confocal laser scanning microscope depending on the depth in the image stack (serial sections). Using the stack of binary images, it applies different levels of noise in the signal and background parts of the images to simulate confocal images. This is useful for generating "virtual ground truth" images with known values of sample rotation and distortion.

3d-daostorm
type: software
has author: Hazen Babcock
has author: Xiaowei Zhuang
has author: Yaron M. Sigal
has comparison: http://bigwww.epfl.ch/smlm/challenge2016/index.html%3Fp%3Dresults
has comparison: Challenge in SUper Resolution 2016
has DOI: 10.1186/2192-2853-1-6
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has implementation: http://biii.eu/taxonomy/term/4341
has location: stable
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: 10.1186/2192-2853-1-6
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Super-resolution microscopy
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-09-21T11:52:58
modified: 2023-05-02T10:11:55
title: 3D-DAOSTORM
comment: Stochastic optical reconstruction microscopy (STORM) and related methods achieves sub-diffraction-limit image resolution through sequential activation and localization of individual fluorophores. The analysis of image data from these methods has typically been confined to the sparse activation regime where the density of activated fluorophores is sufficiently low such that there is minimal overlap between the images of adjacent emitters. Recently several methods have been reported for analyzing higher density data, allowing partial overlap between adjacent emitters. However, these methods have so far been limited to two-dimensional imaging, in which the point spread function (PSF) of each emitter is assumed to be identical. In this work, we present a method to analyze high-density super-resolution data in three dimensions, where the images of individual fluorophores not only overlap, but also have varying PSFs that depend on the z positions of the fluorophores.

3d-estimation-synaptic-vesicle-distribution-serial-section-tem-sstem
type: software
has author: A Great Guy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
created: 2014-12-08T17:29:35
modified: 2017-09-12T18:04:01
title: 3D estimation of synaptic vesicle distribution in serial section TEM (ssTEM)
comment: An estimate of the shortest distance of vesicles to synaptic cleft is computed in 3D for serial section TEM. Unfortunately the the authors do not provide an implementation. Method: 1. Bias correction for inhomogene lighting 2. Image registration of TEM sections / stacks 3. Detection of vesicles & synaptic cleft (semi-automatic) 4. Compute distances in 3D

3d-fill-holes-mcib3d
type: software
has author: Boudier, Thomas
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4340
has location: IntImage3D.java
has location: mcib3d Github repository linking to Fill Holes method
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/781
created: 2019-02-26T15:15:10
modified: 2019-02-26T15:21:31
title: 3D Fill holes (mcib3d)
comment: Runs fill holes operation on 3D images.

3d-generalized-riesz-wavelet-toolbox-matlab
type: software
has author: Dimitri Van De Ville
has author: Michael Unser
has author: Nicolas Chenouard
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: steerable-wavelets-3d
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:43
modified: 2020-03-03T08:40:59
title: 3D Generalized Riesz-Wavelet Toolbox for Matlab
comment: This Matlab code is the 3D extension of the Generalized Riesz-Wavelet Toolbox for Matlab.

3d-imagej-suite
type: software
has author: Boudier, Thomas
has author: Ollion, Jean
has function: operation_0337
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Morphological operations
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: #download
has location: 3D ImageJ Suite webpage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: btt276
has reference publication: J. Ollion, J. Cochennec, F. Loll, C. Escudé, T. Boudier. (2013) TANGO: A Generic Tool for High-throughput 3D Image Analysis for Studying Nuclear Organization. Bioinformatics 2013 Jul 15;29(14):1840-1.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: https://www.youtube.com/watch%3Fv%3DOPC2kP-5By4
has usage example: Youtube Lecture and Hands-On, NEUBIAS Academy
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1309
requires: http://biii.eu/node/38
created: 2019-02-05T13:55:55
modified: 2023-04-27T12:27:22
title: 3D ImageJ Suite
comment: This suite provides plugins to enhance 3D capabilities of ImageJ. 3D Filters (mean, median, max, min, tophat, max local, …) and edge and symmetry filter 3D Segmentation (iterative thresholding, spots segmentation, watershed, …) 3D hysteresis thresholding with two thresholds (see 2D hysteresis for explanation). 3D simple segmentation with thresholding to label 3D objects (similar to 3D objects counter). 3D iterative thresholding (find optimal threshold for each object). 3D spot segmentation with various local threshold estimations. 3D Maxima Finder (with noise parameter) 3D seeds-based watershed with automatic local maxima detection for seeds. 3D Mathematical Morphology tools (fill holes, binary closing, distance map, …) 3D RoiManager (3D display and analysis of 3D objects) 3D Analysis (Geometrical measurements, Mesh measurements, Convex hull, …) 3D Geometrical measurements (volume, surface, …) for each labelled object. 3D Centroid, to compute centroids of labelled objects. 3D Intensity measurements (mean, integrated density, …) in a opened image for each labelled object. 3D Shape measurements (compactness, elongation, …) for each labelled object. 3D Mesh Measurements after triangulation (see 3D Viewer for surface mesh computation). 3D fitting by an ellipsoid and main direction computation (details here). 3D convex hull (see http://rsbweb.nih.gov/ij/plugins/3d-convex-hull/index.html). 3D Radial Distance Area Ratio (RDAR) 3D Density, to compute density of dots, based on closest distance analysis (details here). 3D MereoTopology (Relationship between objects) 3D Tools (Drawing ellipsoids and lines, cropping, …) Drawing 3D line Drawing 3D ellipsoids in any direction Drawing in stacks as volumes Drawing in 3D viewer as surfaces

3d-intensity-profile
type: software
has author: Kota Miura
has documentation: 3dintensityprofile
has location: 3DdiscV3.js
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-09T13:06:54
modified: 2018-05-16T02:07:30
title: 3D intensity profile
comment: This Javascript works in ImageJ to measure 3D intensity profile along cylindrical space with variable radius.

3d-nuclei-clustering-tool
type: software
has author: Bäcker Volker orcid.org/0000-0002-9129-6403
has documentation: 3D Nuclei Clustering Tool
has documentation: 3D_Nuclei_Clustering_Tool documentation
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT
has location: 3D Nuclei Clustering Tool
has location: Download 3D_Nuclei_Clustering_Tool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has programming language: http://biii.eu/taxonomy/term/4525
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2020-09-22T15:59:35
modified: 2020-09-22T16:40:57
title: 3D Nuclei Clustering Tool
comment: Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a different channel. The clustering is done with the density based algorithm DBSCAN. The nearest neighbor distances between all nuclei and those outside and inside of the clusters are calculated.

3d-object-based-colocalization-using-knime
type: software
has author: Juergen Reymann
has function: operation Image colocalization
has function: operation Colocalisation analysis
has location: Session5 Colocalisation NonPointLike
has location: colocalization based on overlapping
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4543
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/71
created: 2014-12-09T12:04:21
modified: 2018-11-16T08:46:57
title: 3D object based colocalization using KNIME
comment: These two similar KNIME workflow solutions take 3D data stacks to segment the spots first, using local thresholding with subsequent morphological operations in order to remove noise. Colocalization is then defined by overlapping or center point distance between segmented objects. Further filtering such as overlapping ratio or distance range is done through KNIME table processing. Two different types are available. colocalization based on overlapping colocalization based on distance between object centers Sample images: Smapp_Ori files Chapter 4 in the documentation.

3d-objects-counter
type: software
has author: Daniel James White
has author: Fabrice Cordelires
has author: Jonathan Jackson
has documentation: 3D Objects Counter
has documentation: wiki
has function: operation Cell counting
has function: operation Feature extraction
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4340
has location: 3D Objects Counter
has location: Contained in Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:44
modified: 2018-08-07T13:43:36
title: 3D Objects Counter
comment: Counts the number of 3D objects in a stack. quantifies for each found object the following parameters: 3D intensity related measurement (with possible redirection to an image with the actual intensity value to be measured, for example for two channels measurements) Volume and shape factors measurements, surface etc... generates results representations such as: Objects' map; Surface voxels' map; Centroids' map; Centres of masses' map. As ImageJ's “Analyze Particles” function, 3D-OC also has a “redirect to” option, allowing one image to be taken as a mask to quantify intensity related parameters on a second image. But unlike the Analyze particle, it include a thresholding option, meaning that you can start from a gray level stack, not necessarily a binary mask. To use it, first set the list of measurements by editing 3D OC Options. Both (3D Object counter and 3D OC Options are now in the default Fiji "Analyze" menu.

3d-orthoviewer-icy
type: software
has author: Alexandre Dufour
has documentation: 3D-OrthoViewer
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: 3D-OrthoViewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-03T09:12:20
title: 3D OrthoViewer (Icy)

3d-psf-estimator
type: software
has author: Jannick Cardinale
has author: Mosaic group
has documentation: PSF measurement 3D.pdf
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-15T10:45:51
modified: 2023-04-27T15:00:44
title: 3D PSF estimator
comment: This ImageJ plugin creates high resolution PSF images by averaging many bead im- ages as well as exploiting the assumption that the point spread function is rotationally symmetric with respect to the axial axis (z-direction).

3d-segmentation-reconstruction-and-modeling-using-free-d
type: software
has function: operation 2945
has function: operation Image registration
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
created: 2016-10-05T08:31:46
modified: 2023-04-29T11:43:53
title: 3D segmentation (reconstruction) and modeling using Free-D
comment: Free-D (http://free-d.versailles.inra.fr/) is a 3D reconstruction and modeling software. It is multiplatform, free (but not open source) tool for academic research and teaching. Here is how to proceed, using Free-D: 1. Segmentation: * load (a collection of) individual 3d stacks * (optional for serial sections) perform a 2D registration to align image slices * segment/reconstruct 3D contours using snakes * segment 3D spots 2. Construct average cell: * normalize the contours to compute a average cell, by registering/warping 3D contours/surfaces 3. Quantification: * project each individual cell to the average one * build density maps to analyze (cartography) A few notes for current software version (till 10/2016): * input file format: tiff (not able to import bioformats) * currently results are saved in customized format, but there is an exportor to convert this format into fiji readable one * import already generated contours is on the software's TODO list

3d-segmentation-visualization-nanoparticles-attached-surface-red-blood-cells
type: software
has author: André Dias, Marco Werner, Kevin R. Ward, Jean-Baptiste Fleuryd and Vladimir A. Baulin
has function: operation Feature extraction
has location: c8nr09960j3.zip
has location: ImageJ macro files
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: c8nr09960j
has reference publication: High-throughput 3D visualization of nanoparticles attached to the surface of red blood cells
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-06-21T11:59:15
modified: 2023-04-29T21:12:45
title: 3D Segmentation & visualization of nanoparticles attached to the surface of red blood cells

3d-slicer
type: software
has author: Steve Pieper, Ron Kikinis
has license: a BSD-style open source license
has location: www.slicer.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/601
requires: http://biii.eu/node/92
created: 2013-10-23T14:25:10
modified: 2017-09-13T10:12:53
title: 3D Slicer
comment: Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.

3d-surface-plot
type: software
has author: Kai Uwe Barthel
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: surface-plot-3d.html
has location: Interactive 3D Surface Plot
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has training material: http://biii.eu/node/1407
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2018-12-17T00:21:51
title: 3D Surface Plot

3d-vessel-segmentation-synchrotron-phase-contrast-tomography
type: software
has function: operation 3443
has function: operation Interactive segmentation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: journal.pone.0218192
has reference publication: Structural coronary artery remodelling in the rabbit fetus as a result of intrauterine growth restriction
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3452
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/79
requires: http://biii.eu/node/88
created: 2019-02-04T10:07:58
modified: 2023-05-03T08:25:58
title: 3D vessel segmentation of synchrotron phase contrast tomography
comment: This workflow describes a semi-automatic image segmentation procedure for 3D reconstructions of the coronary arterial tree, after which how different morphometric features are automatically extracted, including vessel lumen diameter of the three main coronaries.

3d-viewer
type: software
has author: Schindelin Johannes
has author: Schmid Benjamin
has documentation: 3D Viewer: User FAQs
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: 3D Viewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://doi.org/10.1186/1471-2105-11-274
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/601
created: 2013-10-11T13:08:43
modified: 2020-03-01T15:03:54
title: 3D Viewer
comment: 3D viewer provides hardware-accelerated 3D visualization of image stacks as volumes, surfaces and orthoslices.

3dscript
type: software
has author: Schmid, Benjamin
has documentation: Manual.pdf
has function: operation Image visualisation
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD 2-Clause License
has location: 3Dscript
has location: Benjamin Schmid 3Dscript Github repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
has usage example: gallery.html
has usage example: 3Dscripts demonstrations gallery
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-12-09T18:45:53
modified: 2019-02-06T22:33:00
title: 3Dscript
comment: 3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope data. In contrast to existing 3D visualization packages, animations are not keyframe-based, but are described by a natural language-based syntax.

3view-import-list
type: software
has documentation: 3View import list
has documentation: Fiji wiki: 3View import list
has function: operation 2409
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: 3View import list
has location: download instruction in the documentation page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RByvmgDpAo4FOrMdvTm1gwR
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/663
created: 2013-10-11T13:08:43
modified: 2019-10-16T18:12:46
title: 3View import list
comment: The purpose of this plugin is to create a text file with a list of files from Gatan’s 3View montage image stacks. This text file can then be used to automatically import all the images into TrakEM2, as they are, stored in the original directories.

absnake
type: software
has author: P. Andrey
has author: T. Boudier
has function: operation Active contours
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: ABSnake
has location: GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-07-12T14:44:00
modified: 2023-05-03T15:11:18
title: ABSnake
comment: ABSnake can segment complex structures in 2D images as well as 3D or temporal images. It uses a new active contour model based on a geometrical approach for correctly following invaginated structures.

acquiarium
type: software
has author: Michal Kozubek
has documentation: acquiarium.html#
has documentation: Download link broken Oct.2018
has function: operation Illumination correction
has function: operation Spot extraction
has function: operation R3BGvVm77d5vFMF6f28ZiW
has function: operation RDr8xcZEa4L3mZsslmhhee8
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL
has location: acquiarium.html
has location: Download link on main page
has platform: http://biii.eu/taxonomy/term/30
has reference publication: ISBI.2009.5193258
has reference publication: Acquiarium: Free software for the acquisition and analysis of 3D images of cells in fluorescence microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic High content screening
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-10-04T09:20:38
modified: 2018-10-04T09:47:18
title: acquiarium
comment: Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

actionbar-imagej
type: software
has author: Jérôme Mutterer
has documentation: action-bar
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: action-bar
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: m9.figshare.3397603.v3
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T11:58:19
modified: 2023-04-29T09:49:01
title: ActionBar (ImageJ)
comment: An ActionBar is a simple annotated text document that has snippets of Imagej macros or Beanshell arranged into buttons. This tool is very useful when creating custom work flows integrating multiple components. Each component can be linked to a button for a more streamlined and accessible workflow.

active-cells-3d
type: software
has author: Biomedical Imaging Group
has author: Nicolas Chenouard
has author: Ricard Delgado-Gonzalo
has author: Virginie
has documentation: Active-Cells-3D
has function: operation Active contours
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Active-Cells-3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/454
requires: http://biii.eu/node/736
requires: http://biii.eu/node/8
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:40
modified: 2020-03-03T08:58:09
title: Active Cells 3D

active-cells-3d-0
type: software
has location: Active Cells 3D
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:40
modified: 2017-09-12T09:03:43
title: Active Cells 3D

active-contours
type: software
has author: Dallongeville Stephane
has author: Dufour Alexandre
has author: González Obando Daniel Felipe
has author: Vannary
has function: operation Active contours
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: active-contours
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: TIP.2010.2099125
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:43
modified: 2020-03-02T11:37:23
title: Active Contours
comment: Automatically segment the boundary of a nucleus or cell starting from an approximate ROI. Supports 2D and 3D images and tracking of slowly moving cells. Ideal to study cell morphodynamics.

adapt
type: software
has author: Dave Barry
has documentation: Adapt
has function: operation 2945
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: Adapt
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-02-15T10:18:00
modified: 2023-04-29T21:23:03
title: ADAPT
comment: ADAPT is capable of rapid, automated analysis of migration and membrane protrusions, together with associated fluorescently labeled proteins, across multiple cells. ADAPT can detect and morphologically profile filopodia. ADAPT (Automated Detection and Analysis of ProTrusions) is a plug-in developed for the ImageJ/Fiji platform to automatically detect and analyse cell migration and morphodynamics. The program provides whole-cell analysis of multiple cells, while also returning data on individual membrane protrusion events. The plug-in accepts as input one or two image stacks and outputs a variety of data. ADAPT may also be run in batch mode.

adaptive-histogram-equalization
type: software
has author: Dufour Alexandre
has author: Pop Sorin
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Adaptive histogram equalization
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://portal.acm.org/citation.cfm%3Fid%3D180940
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/671
requires: http://biii.eu/node/759
requires: http://biii.eu/node/787
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:49:51
title: Adaptive histogram equalization

adaptive-pixel-representation
type: software
has author: Bevan L. Cheeseman http://orcid.org/0000-0002-9248-5118
has author: Ivo F. Sbalzarini http://orcid.org/0000-0003-4414-4340
has author: Krzysztof Gonciarz http://orcid.org/0000-0001-9054-8341
has author: Mateusz Susik
has author: Ulrik Günther http://orcid.org/0000-0002-1179-8228
has DOI: s41467-018-07390-9
has DOI: nature communications 2018
has documentation: LibAPR
has function: operation 3434
has location: LibAPR
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: LibAPR
openess: http://biii.eu/taxonomy/term/3578
created: 2019-10-16T15:43:50
modified: 2019-10-16T16:01:35
title: Adaptive Pixel Representation
comment: A content-adaptive representation of fluorescence microscopy images called Adaptive Particle Representation (APR), which replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels.

adaptive-thresholding-ebimage
type: software
has documentation: EBImage.pdf
has documentation: package EBImage
has function: operation Adaptative thresholding
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: btq046
has reference publication: Pau et. al. (2010)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
has usage example: thresh.html
has usage example: thresh: Adaptive thresholding
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/86
created: 2013-10-11T13:08:40
modified: 2018-05-09T19:57:52
title: Adaptive Thresholding (EBImage)

adipocyte-quantification-imagej-baecker
type: software
has author: Volker Baecker
has documentation: Adipocytes Tool
has function: operation Cell segmentation
has location: Adipocytes Tool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: 273769192 ImageJ Macro Tool Sets for Biological Image Analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
has usage example: Adipocytes Tool
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-13T10:35:45
modified: 2018-05-20T22:38:42
title: Adipocyte quantification ImageJ by Baecker
comment: The Adipocytes Tools help to analyze fat cells in images from histological section. This is a rather general cell segmentation approach. It can be adapted to different situations via the parameters. This means that you have to find the right parameters for your application. Sample Image: [0178_x5_3.tif](http://dev.mri.cnrs.fr/attachments/190/0178_x5_3.tif)

adipocyte-quantification-matlab
type: software
has author: Claire J Stocker
has author: Jacqueline F O’Dowd
has author: Joanne L Selway
has author: Jonathan RS Arch
has author: Kenneth Langlands
has author: Małgorzata A Kępczyńska
has author: Michael A Cawthorne
has author: Osman S Osman
has author: Sabah Jassim
has function: operation Cell segmentation
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: adip.24652
has reference publication: Osman et. al. (2013) A novel automated image analysis method for accurate adipocyte quantification
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/101
created: 2017-09-13T10:29:08
modified: 2018-05-20T22:34:51
title: Adipocyte quantification MATLAB
comment: Analysis of adipocyte number and size. The original code and example images supposed to be discovered at <http://webspace.buckingham.ac.uk/klanglands/> but currently the webpage is missing the code and sample images.

adiposoft
type: software
has author: Arrate Muñoz-Barrutia
has author: Carlos Ortiz-de-Solórzano
has author: Fermín Milagro
has author: Haritz Moreno
has author: Javier Campión
has author: José Alfredo Martínez
has author: Miguel Galarraga
has author: Noemí Boqué
has documentation: Adiposoft
has function: operation Cell segmentation
has function: operation Image thresholding
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has location: Adiposoft
has location: IJ wiki: Adiposoft
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: jlr.D023788
has reference publication: Galarraga et. al. (2012), Adiposoft: automated software for the analysis of white adipose tissue cellularity in histological sections
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-01-03T23:37:14
modified: 2018-05-20T22:14:16
title: Adiposoft
comment: >Adiposoft is an automated Open Source software for the analysis of adipose tissue cellularity in histological sections. Example data can be found on the plugin description page in ImageJ wiki ([download link](https://dl.dropboxusercontent.com/u/4235078/SW/Dataset.zip)). There is also a link to a MATLAB version of the workflow.

advanced-cell-classifier
type: software
has author: Peter Horvath
has documentation: about-acc
has function: operation 3443
has function: operation 3553
has function: operation Image classification
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU
has location: download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1117
requires: http://biii.eu/node/89
created: 2017-02-15T09:53:55
modified: 2020-03-03T16:20:54
title: Advanced Cell Classifier
comment: Advanced Cell Classifier is a data analyzer program to evaluate cell-based high-content screens and tissue section images developed at the Biological Research Centre, Szeged and FIMM, Helsinki (formerly at ETH Zurich). The basic aim is to provide a very accurate analysis with minimal user interaction using advanced machine learning methods.

affine-ebimage
type: software
has documentation: EBImage.pdf
has function: operation R8ANfLkuHu47r739AkhxrId
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2020-03-03T18:07:12
title: affine (EBImage)

affine-transformation-software
type: software
has documentation: affine
has function: operation Image processing
has function: operation R8ANfLkuHu47r739AkhxrId
has implementation: http://biii.eu/taxonomy/term/4339
has location: affine
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:43
modified: 2018-10-18T15:32:45
title: Affine transformation software
comment: This C routine is based on the following two papers: - M. Unser, A. Aldroubi and M. Eden, "B-Spline Signal Processing: Part I--Theory," IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 821-832, February 1993. - M. Unser, A. Aldroubi and M. Eden, "B-Spline Signal Processing: Part II--Efficient Design and Applications," IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 834-848, February 1993. It implements the resampling of an image/volume under an affine transformation. The continuous model is based on splines of degree 0 (nearest neighbours), degree 1 (linear interpolation), degree 2 (quadratic), 3 (cubic), 4 (quartic), 5 (quintic), 6 and 7. By convention, the affine transformation is given by an homogenous matrix; the operation performed is output(A x) = input(x). In other words, a matrix given by ``` A = { {2,0,0,0}, {0,2,0,0}, {0,0,2,0}, {0,0,0,1} } ``` will result in a magnification by a factor 2 in linear dimensions. In case the desired operation would be `output(x) = input(A x)`, it should be easy to modify the code (mainly: remove the call to `invertTrsf()` and assign `invTRsf = trsf)`. The origin relative to which the transformation is performed is given with respect to the center of the top-upper-left voxel; the coordinate system is right-handed. Output values in need of extrapolation are set to the value background. The input volume (the volume to transform) is given by `inPtr`, a pointer to an array of float values in raster order. More precisely, the values are ordered such that the x values are incremented first, then the y values, finally the z values. The size of the volume is given by nx, ny and nz, respectively. The output volume has necessarily the same size and follows the same organization. Its memory space cannot be shared with the input, and is supposed to be already allocated when the `affineTransform()` routine is called. All routines are local, with the exception of the routine to call, named `affineTransform()`, and the…

air-tools-ii
type: software
has documentation: AIRtoolsManual.pdf
has function: operation Image reconstruction
has implementation: http://biii.eu/taxonomy/term/4339
has location: AIRtools
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: 10.1007/s11075-017-0430-x
has reference publication: AIR Tools II: Algebraic Iterative Reconstruction Methods, Improved Implementation
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-06-02T08:41:20
modified: 2020-03-05T17:12:44
title: AIR tools II
comment: AIR Tools is a MATLAB software package for tomographic reconstruction (and other imaging problems) consisting of a number of algebraic iterative reconstruction methods.

aivia-aivia-cloud-aivia-web
type: software
has documentation: overview
has documentation: Aivia Wiki
has function: operation_0226
has function: operation_0337
has function: operation 2945
has function: operation 2990
has function: operation 3096
has function: operation 3441
has function: operation 3443
has function: operation Cell counting
has function: operation Cell segmentation
has function: operation Cell tracking
has function: operation Image colocalization
has function: operation Image deconvolution
has function: operation Image segmentation
has function: operation Image tracking
has function: operation Image visualisation
has function: operation Neuron image analysis
has function: operation Object detection
has function: operation Particle tracking
has function: operation Pixel classification
has function: operation Texture extraction
has function: operation Volume rendering
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has function: operation Colocalisation analysis
has function: operation Pixel-based colocalisation
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: demo
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/3568
has usage example: overview
has usage example: Aivia Wiki
openess: http://biii.eu/taxonomy/term/3577
created: 2018-06-28T00:10:51
modified: 2023-04-28T13:30:03
title: Aivia - Aivia Cloud - Aivia Web

align-image-line-roi
type: software
has author: Johannes Schindelin
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: Align Image by line ROI
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:43
modified: 2018-12-18T03:43:31
title: Align Image by line ROI
comment: Manually selecting line ROIs and align two images.

align-slices-stack
type: software
has documentation: tuto2
has documentation: Tutorial for Align slices in stack
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: template-matching-ij-plugin
has location: Template Matching and Slice Alignment--- ImageJ Plugins
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: C0LC00641F
has reference publication: Tseng et. al. (2011) A new micropatterning method of soft substrates reveals that different tumorigenic signals can promote or reduce cell contraction levels
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-05-09T01:53:52
modified: 2018-05-09T02:04:03
title: Align slices in stack
comment: **Align_slices** in stack utilized the template matching function **cvMatch_Template** to do slice registration(alignment) based on a selected landmark. This function will try to find the landmark or the most similar image pattern in every slice and translate each slice so that the landmark pattern will be the same position throughout the whole stack. It could be used to fix the drift of a time-lapse image stacks. Source code: [link](https://sites.google.com/site/fileqzt/file/Align_slices.java?attredirects=0) Input data: image stack output data: image stack

alignment-fibsem-or-sbfsem-images
type: software
has type: http://biii.eu/taxonomy/term/8
requires: http://biii.eu/node/1206
requires: http://biii.eu/node/1207
requires: http://biii.eu/node/1208
requires: http://biii.eu/node/663
requires: http://biii.eu/node/79
requires: http://biii.eu/node/870
created: 2018-01-30T16:25:14
modified: 2018-06-05T01:49:16
title: Alignment of FIBSEM or SBFSEM images

allen-cell-structure-segmenter
type: software
has author: Irina A. Mueller
has author: Jianxu Chen https://orcid.org/0000-0002-8500-1357
has author: Liya Ding
has author: Matheus P. Viana https://orcid.org/0000-0001-9288-2108
has author: Melissa C. Hendershott
has author: Ruian Yang
has author: Susanne M. Rafelski
has DOI: https://doi.org/10.1101/491035
has DOI: The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
has documentation: full doc.md
has documentation: Documentation for Developers
has function: operation Image segmentation
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: 2-clause BSD license plus clause a third clause that prohibits redistribution for commercial purposes without further permission.
has location: segmenter.html
has location: ​The Allen Cell Structure Segmenter: Project Page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://www.biorxiv.org/content/early/2018/12/08/491035
has reference publication: The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images (biorxiv)
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1413
created: 2019-01-02T09:09:35
modified: 2019-01-02T17:15:39
title: ​The Allen Cell Structure Segmenter
comment: ​The Allen Cell Structure Segmenter is a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images. It consists of two complementary elements: Classic image segmentation workflows for 20 distinct intracellular structure localization patterns. A visual “lookup table” is outlining the modular algorithmic steps for each segmentation workflow. This provides an intuitive guide for selection or construction of new segmentation workflows for a user’s particular segmentation task. Human-in-the-loop iterative deep learning segmentation workflow trained on ground truth manually curated data from the images segmented with the segmentation workflow. Importantly, this module was not released yet.

amira
type: software
has documentation: amira-avizo-technical-resources-and-support
has documentation: Amira technical ressources and support
has function: operation_0337
has function: operation 2945
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: overview
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
has usage example: JCS181842supp.pdf
has usage example: usage example in multimodal imaging
openess: http://biii.eu/taxonomy/term/3577
created: 2013-11-07T19:55:56
modified: 2021-05-19T19:27:08
title: Amira
comment: Amira is 3D visualization and analysis software for life sciences. " Amira software is a powerful, multifaceted 3D platform for visualizing, manipulating, and understanding life sciences data from computed tomography, microscopy, MRI, and many other imaging modalities. With incredible speed and flexibility, Amira software enables advanced 3D imaging workflows for specialists in research areas ranging from molecular and cellular biology to neuroscience and bioengineering. "

amira-avizo-xtra-library
type: software
has author: Zuse Institute Berlin (ZIB) and Thermo Fisher Scientific
has implementation: http://biii.eu/taxonomy/term/4339
has location: xtras.amira-avizo.com
has location: Amira / Avizo Xtra
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/109
created: 2019-11-22T09:33:39
modified: 2020-10-19T15:07:49
title: Amira / Avizo Xtra library
comment: Collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency. Use the Search field to look for specific keywords related to your domain of interest. The different filters also help you target specific resources.

anaglyph-red-cyan-glasses
type: software
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Anaglyph for Red Cyan glasses
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-15T15:50:24
title: Anaglyph for Red Cyan glasses
comment: JRuby script that will take an image stack and generate from it an image that should appear in 3D when viewed through red and cyan glasses. All that this does is to do two maximum intensity projections from two slightly different angles and merges them together.

analyze-120
type: software
has documentation: Analyze Training Guide.pdf
has location: www.analyzedirect.com
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:44
modified: 2018-05-14T20:16:23
title: Analyze 12.0
comment: Analyze 12.0 is a set of image processing, visualization and analysis tools that provides users access to a breadth of essential post-processing functions critical for innovative research. Analyze 12.0 provides users with all the key display, editing, processing, registration, and measurement tools needed to realize their research goals in a single multifaceted software package. Analyze 12.0 is open-ended, allowing for the application of its tools to novel and emerging research.

analyze-complex-roots-tool
type: software
has author: Bäcker Volker orcid.org/0000-0002-9129-6403
has documentation: Analyze Complex Roots Tool
has documentation: Documetation of the Analyze Complex Roots Tool
has function: operation 3443
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT
has location: Analyze Complex Roots Tool
has location: Download Analyze Complex Roots Tool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: s191777
has reference publication: Root developmental responses to nutrient shortage and biotic conditions in wheat: identification of beneficial bacteria from wheat rhizosphere and new procedures for phenotyping root and root hair development
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
has usage example: s191777
has usage example: Root developmental responses to nutrient shortage and biotic conditions in wheat: identification of beneficial bacteria from wheat rhizosphere and new procedures for phenotyping root and root hair development
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2021-05-13T14:41:58
modified: 2021-05-13T15:13:52
title: Analyze Complex Roots Tool
comment: This tool allows to analyze morphological characteristics of complex roots. While for young roots the root system architecture can be analyzed automatically, this is often not possible for more developed roots. The tool is inspired by the Sholl analysis used in neuronal studies. The tool creates a binary mask and the Euclidean Distance Transform from the input image. It then allows to draw concentric circles around a base point and to extract measures on or within the circles. Instead of circles, which present the distance from the base point, horizontal lines can be used, which present the distance in the soil from the base-line. The following features are currently implemented: The area of the root per distance/depth. The number of border pixel per distance/depth, giving an idea of the surface in contact with the soil. The maximum radius per distance/depth of a root, measured at the crossing points with the circles or lines. The number of crossings of roots with the circles or lines. The maximum distance to the left and the right from the vertical axis at crossing points with the circles or lines.

analyze-particles
type: software
has documentation: 146-30.html#toc-Subsection-30.2
has documentation: ImageJ documentation
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: download.html
has location: Download ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2016-10-24T13:46:16
modified: 2023-04-25T17:55:43
title: Analyze Particles
comment: An object detection function in ImageJ. [Analyze > Analyze Particles...]. It could simply be used for counting number of cells, but could also do more complex stuffs. ## Jython Snippet Here is a snippet of how to use Particle Analysis in Jython script.

analyze-skeleton-2d-time-series
type: software
has documentation: Analyze Skeleton 2D time series
has function: operation Skeletonization
has location: Analyze Skeleton 2D time series
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Analyze Skeleton 2D time series
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1072
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2023-04-27T10:53:19
title: Analyze Skeleton 2D time series
comment: This is a scripting example to process stack of images using AnalyzeSkeleton.

analyze-spheroid-cell-invasion-3d-matrix
type: software
has author: Bäcker Volker orcid.org/0000-0002-9129-6403
has documentation: Analyze-Spheroid-Cell-Invasion-In-3D-Matrix
has documentation: Analyze-Spheroid-Cell-Invasion-In-3D-Matrix Documentation
has function: operation Cell counting
has function: operation Cell segmentation
has location: Analyze-Spheroid-Cell-Invasion-In-3D-Matrix
has location: Download Analyze-Spheroid-Cell-Invasion-In-3D-Matrix
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic Widefield microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/3568
has usage example: journal.pone.0204976
has usage example: CRISPR deletion of MIEN1 in breast cancer cells
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1057
created: 2021-05-13T16:05:28
modified: 2023-04-29T20:40:32
title: Analyze Spheroid Cell Invasion In 3D Matrix
comment: The tool allows to measure the area of the invading spheroïd in a 3D cell invasion assay. It can also count and measure the area of the nuclei within the spheroïd.

analyzing-gels-and-western-blots-imagej
type: software
has author: Luke Miller (contact@lukemiller.org)
has documentation: analyzing-gels-and-western-blots-with-image-j
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T11:56:06
modified: 2018-05-25T22:06:55
title: Analyzing gels and western blots with ImageJ
comment: It explains how to use ImageJ to compare the density (aka intensity) of bands on an agar gel or western blot. Some notes can be found here: <http://cellnetmcweb.bioquant.uni-heidelberg.de/image-analysis/ShortTutorials/Fiji_GelAnalyzer.pdf>

anamorf
type: software
has author: David J. Barry
has DOI: s10295-009-0552-9
has DOI: 10.1007/s10295-009-0552-9
has documentation: Home
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: 10.1007/s10295-009-0552-9
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2017-09-12T13:18:28
modified: 2017-09-12T15:43:15
title: AnaMorf
comment: AnaMorf is a plug-in developed for the ImageJ platform (rsb.info.nih.gov/ij) to analyse the microscopic morphology of filamentous microbes. The program returns average data on a population of mycelial elements, using the descriptors projected area, circularity, total hyphal length, number of hyphal tips, hyphal growth unit, lacunarity and fractal dimension. The plug-in accepts as input a user-specified directory of images, analysing each and outputing tabulated results.

angiogenesis-analyzer-imagej
type: software
has author: Gilles Carpentier
has function: operation 3443
has location: http://image.bio.methods.free.fr/ImageJ/%3FAngiogenesis-Analyzer-for-ImageJ%3D%26lang%3Den
has location: Angiogenesis Analyzer for ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-05-25T19:37:32
modified: 2023-04-26T13:24:25
title: Angiogenesis Analyzer for ImageJ
comment: Quote: The "Angiogenesis Analyzer" allows analysis of cellular networks. Typically, it can detect and analyze the pseudo vascular organization of endothelial cells cultured in gel medium ...a simple tool to quantify the ETFA (Endothelial Tube Formation Assay) experiment images by extracting characteristic information of the network. The outputs are network feature parameters. Sample images http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Pseudo-Phase-Contrast.tif.zip http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Fluo.tif.zip Source code https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt

angiogenesis-sprout-analyzer-imagej
type: software
has author: Jan Ellinger
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: Sprout Morphology
has location: description and download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: s41232-016-0033-2
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-05-16T10:01:34
modified: 2023-04-27T14:56:09
title: Angiogenesis / Sprout Analyzer (ImageJ)
comment: The Sprout Morphology plugin measures sprout number, length, width and cell density of endothelial cell (EC) sprouts grown in a bead sprouting assay. It optionally includes measuring the coverage of these sprouts with pericytes included in the assay, as well as the endothelial cell/pericyte ratio.

angle-helper
type: software
has author: Fabrice de Chaumont
has implementation: http://biii.eu/taxonomy/term/4340
has location: Angle Helper
has location: Angle_Helper@ICY website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2018-12-17T00:15:35
title: Angle Helper
comment: Manual angle measurements. No javadoc accessible, but can be downloaded from the webpage.

animated-overlay-tutorial
type: software
has location: Animated overlay tutorial
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:05:59
title: Animated overlay tutorial

animation-3d
type: software
has author: Provoost Thomas
has author: de Chaumont Fabrice
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: animation-3d
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/527
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:43
modified: 2020-03-03T11:24:10
title: Animation 3D
comment: This plugin allows the creation of custom animations for 3D viewing. It will generate a new sequence that can be edited in Icy, and saved. The animation is based on key framing, as in most of 3D rendering software projects.

anisotropic-diffusion-2d
type: software
has author: Jiri Janacek
has author: Johannes Schindelin
has author: Vladimir Pilny
has documentation: anisotropic-diffusion-2d.html
has function: operation Image smoothing
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Anisotropic Diffusion 2D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: TPAMI.2005.87
has reference publication: Vector-valued image regularization with PDEs: a common framework for different applications
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2018-12-18T03:30:34
title: Anisotropic Diffusion 2D
comment: >Anisotropic filters are a class of filter that reduces noise in an image while trying to preserve sharp edges There are two implementations of Tschumperle/ R. Deriche filter ("anisotropic diffusion") for ImageJ Plugin 1. in the "imaging book" codes: [see the javadoc here](https://imagingbook.github.io/imagingbook-common/javadoc/imagingbook/pub/edgepreservingfilters/TschumperleDericheFilter.html). 2. in [Xlib](https://imagej.net/Xlib#Anisotropic_Diffusion)

annotatorj
type: software
has author: Peter Horvath
has author: Réka Hollandi
has documentation: annotatorj
has documentation: Git HUB
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: Spreka
has location: Fiji Update Site to add
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: mbc.E20-02-0156
has reference publication: AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2021-07-09T07:49:35
modified: 2021-07-09T08:03:42
title: AnnotatorJ
comment: AnnotatorJ is a Fiji Plugin to ease annotation of images, particulrly useful for Deep Learning or to validate an alogorithm. Interestingly, it allows annotation for instance segmentation, semantic segmentation, or bounding box annotations. It includes toolssuch as active contours to ease these annotations.

ants-advanced-normalization-tools
type: software
has author: Avants Brian
has author: Johnson Hans
has author: Tustison Nicholas
has documentation: Documentation
has function: operation Illumination correction
has function: operation Image registration
has function: operation Image segmentation
has function: operation Pixel classification
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has location: ANTs
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/17659998
has reference publication: Avants et al. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/92
created: 2018-01-30T14:29:40
modified: 2018-01-30T14:37:21
title: ANTs: Advanced Normalization Tools
comment: ANTs computes high-dimensional mappings to capture the statistics of brain structure and function. Image Registration Diffeomorphisms: SyN, Independent Evaluation: Klein, Murphy, Template Construction (2004)(2010), Similarity Metrics, Multivariate registration, Multiple modality analysis and statistical bias Image Segmentation Atropos Multivar-EM Segmentation (link), Multi-atlas methods (link) and JLF, Bias Correction (link), DiReCT cortical thickness (link), DiReCT in chimpanzees

apeer
type: software
has author: Carl Zeiss Microscopy GmbH
has function: operation_0226
has function: operation 2409
has function: operation 2945
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation Pixel classification
has function: operation RDyyXyhf1oHK93opXhEnRND
has function: operation Model-based segmentation
has location: home
has location: APEER
has topic: topic 3382
has topic: topic 3474
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3577
created: 2021-07-01T10:46:57
modified: 2021-07-01T10:52:45
title: APEER
comment: Machine Learning made easy APEER ML provides an easy way to train your own machine learning models and segment your microscopy images. No expertise or coding required.

aphelion
type: software
has author: ADCIS
has function: operation 3443
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: Image-Processing-And-Analysis-Software-And-Custom-Engineering-Developments.html
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2014-12-08T13:44:51
modified: 2020-03-02T20:51:51
title: Aphelion
comment: A commercial image analysis software. It's interface allows to easily perform measurements and image analysis. Your actions can be recorded and a macro (in a basic script language) can then be created. Almost no knowledge in programming is needed. You can also use python. A SDK is also available to develop stand alone applications in c++. Additional modules allow to use specific operations (3D operators... Examples of available categories of operators : filtering, edge detection, mathematical morphology, segmentation, Frequency operations, mathematical/logical operations, measurements...

app-all-path-pruning
type: software
has author: Long, Fuhui
has author: Myers, Gene
has author: Peng, Hanchuan (http://orcid.org/0000-0002-3478-3942)
has function: operation Image thresholding
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT License
has location: app1
has location: APP Plugin Github repository in Vaa3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: btr237
has reference publication: Automatic 3D neuron tracing using all-path pruning
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2017-09-11T23:23:19
modified: 2018-04-11T10:51:48
title: APP (All-path pruning)
comment: "We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal- covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly)" This plugin can be used with default parameters or user-defined parameters.

app2
type: software
has author: Peng, Hanchuan (http://orcid.org/0000-0002-3478-3942)
has author: Xiao, Hang
has comparison: btt170
has comparison: APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
has function: operation Distance transform
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: neurontracing vn2
has location: APP2 Plugin Github repository in Vaa3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: btt170
has reference publication: APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/8
has usage example: btt170
has usage example: APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2017-09-12T00:18:47
modified: 2018-10-16T13:07:34
title: APP2
comment: All-path-pruning 2.0 (APP2) is a component of Vaa3D. APP2 prunes an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search process in APP. APP2 computes the distance transform of all image voxels directly for a gray-scale image, without the need to binarize the image before invoking the conventional distance transform. APP2 uses a fast-marching algorithm-based method to compute the initial reconstruction trees without pre-computing a large graph. This method allows to trace large images. This method can be used with default parameters or user-defined parameters.

aquiarium
type: software
has author: Matula
has author: kozubek
has function: operation Image segmentation
has function: operation R7MFwdgojfmkZ07yWbdcda0
has function: operation RDr8xcZEa4L3mZsslmhhee8
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL
has location: acquiarium.html
has location: Download link
has platform: http://biii.eu/taxonomy/term/31
has reference publication: ISBI.2009.5193258
has reference publication: Acquiarium: Free Software for Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. ISBI 2009
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
has usage example: https://www.youtube.com/watch%3Fv%3DwsXP51WfGsw
has usage example: Tutorial: How to count DNA double strand breaks
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-24T12:41:02
modified: 2019-08-26T10:57:45
title: Aquiarium
comment: Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

arabidopsis-seedlings-tool
type: software
has author: Volker Baecker
has documentation: Arabidopsis Seedlings Tool
has documentation: Arabidopsis_Seedlings_Tool
has function: operation Image thresholding
has license: CeCILL-C
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: image analysis.pdf
has reference publication: ImageJ macro tool sets for biological image analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: IJHTS.S40565
has usage example: Simple system using natural mineral water for high-throughput phenotyping of Arabidopsis thaliana seedlings in liquid culture
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-30T19:00:38
modified: 2023-05-03T13:07:24
title: Arabidopsis Seedlings Tool
comment: The Arabidopsis Seedlings Tool allows to analyze the germination and seedling growth of Arabidopsis (Arabidopsis thaliana) in liquid culture. It measures the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well. See http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Arabidopsis_Seedlings_Tool Test images can be found here.

arivis-vision4d
type: software
has function: operation 2409
has function: operation 3443
has function: operation 3553
has function: operation Image processing
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: arivis-vision4d
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2016-10-05T15:52:48
modified: 2020-03-05T12:11:05
title: arivis Vision4D
comment: arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. Many imaging systems, such as high speed confocal, Light Sheet/ SPIM and 2 Photon systems, can produce a huge amount of multi-channel data, which arivis Vision4D handles without constraints. Terabyte ready arivis Vision4D main functionality: Easy import of most image formats from microsopes as well as biological formats High performance interactive 3D / 4D rendering on standard PCs and laptops with 3D Graphics Support Intuitive tools for stitching and alignment to create large multi-dimensional image stacks Immediate 2D, 3D and 4D visualization, annotation and analysis regardless of image size Creation, import, and export of 4D Iso-surfaces Powerful Analysis Pipeline for 3D /4D image analysis (cell segmentation, tracking, annotation, quantitative measurement and statistics, etc) Semi-automatic/manual segmentation and tracking with interactive Track Editor Easy design and export of 3D / 4D High Resolution Movies Seamless integration of custom workflows via Matlab API and Python scripting Data sharing for collaboration A user friendly software, easy to learn and use for any life scientist

arrow
type: software
has author: Jean-Yves Tinevez
has function: operation_0226
has location: Arrow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/321
requires: http://biii.eu/node/38
requires: http://biii.eu/node/618
created: 2013-10-11T13:08:43
modified: 2023-05-02T11:10:37
title: Arrow
comment: This version replaces the old Arrow_.class tool that was present in Fiji before. The main changes are the ability to draw the arrow as a floating selection, and to tune its shape. Warning: Since ImageJ version 1.43n, a similar tool, made by Wayne Rasband, does a similar thing from the ImageJ core, see here.

artemia-color-analysis
type: software
has author: Volker Baecker
has DOI: ele.12074
has documentation: Artemia Tools
has function: operation Feature extraction
has license: CeCILL-C
has location: Artemia Tools
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: https://www.ncbi.nlm.nih.gov/pubmed/23351125
has usage example: Why join groups? Lessons from parasite-manipulated Artemia.
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T15:49:16
modified: 2017-09-13T14:02:03
title: Artemia color analysis
comment: The Artemia Tools help to calculate the normalized redness of Artemia in color images. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Artemia_Tools Test images: http://biii.eu/node/1139

asap
type: software
has author: Geert Litjens
has documentation: ASAP
has function: operation 2409
has function: operation 3553
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL2
has location: ASAP
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-13T14:34:24
modified: 2020-03-03T20:30:29
title: ASAP
comment: ASAP is an open source platform for visualizing, annotating and automatically analyzing whole-slide histopathology images. It consists of several key-components (slide input/output, image processing, viewer) which can be used seperately. It is built on top of several well-developed open source packages like OpenSlide, Qt and OpenCV but also tries to extend them in several meaningful ways.

assayscope
type: software
has author: QuantaCell
has function: operation 2945
has function: operation Cell segmentation
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2019-01-09T11:36:32
modified: 2019-01-09T11:36:32
title: AssayScope
comment: AssayScope is an intuitive application dedicated to large scale image processing and data analysis. It is meant for histology, cell culture (2D, 3D, 2D+t) and phenotypic analysis.

astec
type: software
has author: Grégoire Malandain
has author: Léo Guignard
has documentation: astec
has documentation: documentation
has function: operation Cell segmentation
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has implementation: http://biii.eu/taxonomy/term/4341
has location: astec
has location: Gitlab source code and installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: tel-01278725
has reference publication: Léo Guignard. Quantitative analysis of animal morphogenesis: from high-throughput laser imaging to 4D virtual embryo in ascidians. Theses, Université Montpellier, December 2015.
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/3568
has usage example: science.aar5663
has usage example: Léo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Julien Laussu, Emmanuel Faure, Gaël Michelin, Kilian Biasuz, Lars Hufnagel, Grégoire Malandain, Christophe Godin, and Patrick Lemaire. Contact area-dependent cell communication and the morphological invariance o
openess: http://biii.eu/taxonomy/term/3575
created: 2022-05-18T06:44:04
modified: 2022-05-18T07:35:07
title: ASTEC
comment: ASTEC stands for Adaptive Segmentation and Tracking of Embryonic Cells. It proposes a full workflow for time lapse light sheet imaging analysis, including drift/motion compensation before the segmentation itself, and the capacity to correct for it. It was used to process 3D+t movies acquired by the MuViSPIM light-sheet microscope in particular.

atlas-vesicle-segmentation-method
type: software
has author: Antoine Basset
has author: Jean Salamero
has author: Jérôme Boulanger
has author: Patrick Bouthemy
has function: operation Spot extraction
has function: operation RBNng13hEB0CJD5VzSKqrfB
has location: portal.py#forms::ATLAS
has location: ATLAS Vesicle segmentation method
has reference publication: 269272445 SLT-LoG A Vesicle Segmentation Method with Automatic Scale Selection and Local Thresholding Applied to TIRF Microscopy
has reference publication: SLT-LoG: A Vesicle Segmentation Method with Automatic Scale Selection and Local Thresholding Applied to TIRF Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
created: 2017-09-13T16:35:50
modified: 2018-05-27T16:58:26
title: ATLAS Vesicle segmentation method
comment: Part of ATLAS software Comment / Instructions: You can upload your image at the Mobyle@SERPICO portal and download the result. The workflow is only available online, i.e. no download possible.

auto-bayes
type: software
has author: Johnny Hendriks
has author: Junbai Li
has author: Luru Dai
has author: Thomas Gensch
has author: Yunqing Tang
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD and LGPL
has location: t20150504 146858.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Statistics
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-12T22:46:30
modified: 2020-03-05T11:59:22
title: Auto-Bayes
comment: Auto-Bayes is a software package based on Bayesian statistics and requires no user dependent parameters for molecule detection and image reconstruction for Single-Molecule Localization Microscopy (SMLM), including photoactivated localization microscope (PALM), stochastic optical reconstruction microscope (STORM), and direct stochastic optical reconstruction microscopy (dSTORM), etc.

auto-local-threshold
type: software
has author: Gabriel Landini
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Auto Local Threshold
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-29T17:14:41
title: Auto Local Threshold

auto-threshold
type: software
has author: Gabriel Landini
has documentation: auto-threshold
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Auto Threshold
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: auto-threshold
has usage example: see slide 21
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2023-04-25T17:22:05
title: Auto Threshold
comment: Bundled with Fiji. "Do all" is the great feature...

autofocus
type: software
has author: Richard Mort
has function: operation Object detection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: jemt.20118
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/195
requires: http://biii.eu/node/38
created: 2014-12-08T14:05:07
modified: 2023-05-03T15:32:35
title: Autofocus
comment: Autofocus hyperstack macro: Select the in focus frame from each slice of a hyperstack and create a new stack of just the in focus frames. Based on algorithm F-11 "Normalized Variance". Original macro by Andy Weller.

automated-structures-analysis-program-asap
type: software
has documentation: Guides
has implementation: http://biii.eu/taxonomy/term/4341
has license: MIT
has location: ASAP
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: s41592-019-0472-1
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
has usage example: Examples
openess: http://biii.eu/taxonomy/term/3575
created: 2019-10-18T11:01:43
modified: 2019-10-18T11:10:49
title: automated structures analysis program (ASAP)
comment: ASAP allows to automatically detect, classify and quantify structures acquired by super resolution microscopy.

automated-velocity-mapping-migrating-cell-populations-avemap
type: software
has author: Maxime Deforet, Maria Carla Parrini, Laurence Petitjean, Marco Biondini, Axel Buguin, Jacques Camonis, Pascal Silberzan
has function: operation Feature extraction
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has location: avemap
has location: Download AVeMap
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: AVeMap Tutorial.pdf
has usage example: Tutorial
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1117
created: 2014-12-08T17:13:15
modified: 2023-05-02T17:04:37
title: Automated velocity mapping of migrating cell populations (AVeMap)
comment: Requires Matlab Runtime Environment or Matlab. Source code (m-files) are downloaded. Software availability: AVeMap was developed under MATLAB (MathWorks). It is available as an executable, multiplatform program, together with source codes and documentation here, and the source code is also available as Supplementary Software. For practical reasons, this executable version, which does not require MATLAB, runs on a single processor. For users who want to customize the software and/or need the power of parallel computing, an installation of MATLAB with its 'parallel' and 'image processing' toolboxes is needed. Note that, even with the executable version, the velocity fields are stored for further analysis. The add-on AVeMap+ uses these AVeMap-computed velocity fields to generate heat map tables. It is available with the same link.

automated-workflow-parallel-multiview-reconstruction
type: software
has author: Christopher Schmied
has author: Pavel Tomancak
has author: Peter Steinbach
has author: Stephan Preibisch
has author: Tobias Pietzsch
has documentation: Automated workflow for parallel Multiview Reconstruction
has function: operation Image deconvolution
has function: operation Image processing
has function: operation Image registration
has function: operation RBPObKBKIMwjdLygBOlvojW
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has license: MIT
has location: spim registration
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://academic.oup.com/bioinformatics/article/32/7/1112/1744153
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1491
requires: http://biii.eu/node/79
created: 2019-03-25T16:00:02
modified: 2019-03-25T16:23:49
title: Automated workflow for parallel Multiview Reconstruction
comment: Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation.

automatic-2d3d-tracking-using-ilastik
type: software
has author: ilastik team
has function: operation Image segmentation
has function: operation Image tracking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 978-1-4939-9686-5 20
has reference publication: Book chapter
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: 978-1-4939-9686-5 20
has usage example: Book chapter
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/88
created: 2014-12-08T16:18:37
modified: 2023-04-28T13:22:42
title: Automatic 2D/3D Tracking using ilastik
comment: This workflow is used to track multiple (appear/disappear, dividing and merging) objects in presumably big 2D+t or 3D+t datasets. It is best suitable for roundish objects or spots. Tracking is done through segmentation, which can be obtained from ilastik pixel classification, or imported from other tools. Users should provide a few object level labels, and the software predicts results on the rest of the image or new images with similar image characteristics. As a result, all objects get assigned random IDs at the first frame of the image sequence and all descendants in the same track (also children objects such as daughter cells) inherit this ID.

autoqc
type: software
has author: Erick Martins Ratamero orcid.org/0000-0002-7545-3675
has DOI: https://zenodo.org/badge/latestdoi/169840753
has DOI: DOI
has location: auto qc
has location: AutoQC
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2019-02-14T15:06:51
modified: 2019-02-14T15:14:23
title: autoQC
comment: autoQC encapsulates a number of routines for performing microscope quality controls. From a few input images, it generates computer-friendly (i.e. CSV) data with numerical parameters for quality measures (resolution, field of view illumination, chromatic shift, stage reproducibility).

autoquant
type: software
has function: operation Image deconvolution
has license: -
has location: http://www.mediacy.com/index.aspx%3Fpage%3DAutoQuant
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2013-11-07T19:57:02
modified: 2017-09-12T18:05:49
title: AutoQuant
comment: Deconvolution software

avemap
type: software
has author: Maxime Deforet
has function: operation 3443
has function: operation Optical flow analysis
has function: operation Wound-healing analysis
has location: avemap
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: nmeth.2209.html
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3382
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/420
created: 2017-09-12T16:22:47
modified: 2023-03-10T22:13:03
title: AVEMAP
comment: Measures wound-healing assay videos, For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.

avizo
type: software
has license: commercial
has location: overview
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-11-07T20:00:14
modified: 2017-09-12T18:05:48
title: Avizo
comment: Wherever three-dimensional data sets need to be processed, in materials science, geosciences, environmental or engineering applications, Avizo offers abundant state-of-the-art features within an intuitive workflow and easy-to-use graphical user interface. Avizo is packaged in different Editions, with optional eXtension modules. Each Avizo Edition delivers tailored user interface and specific feature-set for each application area: [Avizo Standard](http://www.vsg3d.com/avizo/standard) [Avizo Earth](http://www.vsg3d.com/avizo/earth) [Avizo Wind](http://www.vsg3d.com/avizo/wind) [Avizo Green](http://www.vsg3d.com/avizo/green) [Avizo Fire](http://www.vsg3d.com/avizo/fire)

background-subtractor
type: software
has author: Janick Cardinale
has author: MOSAIC Group
has documentation: BGS manual.pdf
has function: operation Illumination correction
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/79
created: 2013-10-15T10:45:49
modified: 2019-10-17T12:31:20
title: Background Subtractor
comment: Histogram-based background subtractor for ImageJ. The implemented algorithm is based on the assumption that, compared to the background region, object (foreground) regions are small. The plugin builds local histograms and assumes the most occuring intensity to be part of the background.

balanced-sofi
type: software
has author: Marcel Leutenegger
has function: operation Image enhancement
has implementation: http://biii.eu/taxonomy/term/4339
has license: GNU General Public License version 3
has location: index.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://dx.doi.org/10.1186/2192-2853-1-4
has reference publication: bSOFI publication 2012
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Super-resolution microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2016-10-06T13:15:51
modified: 2023-05-03T09:51:11
title: Balanced SOFI
comment: Super-resolution optical fluctuation imaging (SOFI) achieves 3D super-resolution by computing temporal cumulants or spatio-temporal cross-cumulants of stochastically blinking fluorophores. In contrast to localization microscopy, SOFI is compatible with weakly emitting fluorophores and a wider range of blinking conditions. Balanced SOFI analyses several cumulant orders for extracting molecular parameter maps, such as the bright and dark state lifetimes, the concentration and the brightness distributions of fluorophores within biological samples. In combination with a deconvolution of the cumulant images, the estimated parameter maps proved useful to balance the image contrast and to linearize the brightness and blinking response. Thereby, the image quality and the resolution were improved significantly.

basic
type: software
has author: Carsten Marr
has author: Tingying Peng
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has license: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License
has location: BaSiC
has location: BaSiC GitHub page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: ncomms14836
has reference publication: A BaSiC tool for background and shading correction of optical microscopy images, Nat. Comm.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3385
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2022-04-21T13:49:31
modified: 2023-04-29T13:15:55
title: BaSiC
comment: BaSiC is a software tool for Background and Shading correction of Optical Microscopy Images. It implements an image correction method based on low-rank and sparse decomposition to solve both shading in space and background variation in time. It can correct temporal drift in time-lapse microscopy data and thus improve continuous single-cell quantification. BaSiC is available as a Fiji/ImageJ plugin.

batch-spot-detection-custom-output
type: software
has author: Fabrice de Chaumont
has function: operation Spot extraction
has location: Batch spot detection with custom output
has location: Download protocol
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-09T09:38:22
modified: 2018-04-11T10:51:24
title: Batch spot detection with custom output
comment: Download the protocol,use and modify in Icy. It permits to detect spot with wavelet spot detector block. Input : loop on a folder Outputs: excel, binary, and detection screenshot

bayesian-tracker-btrack
type: software
has author: Kristina Ulicna
has documentation: index.html
has documentation: User guide
has function: operation 2945
has function: operation Cell segmentation
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4339
has location: installation.html
has location: Installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: full
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic Fluorescent microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2023-05-12T15:31:54
modified: 2023-05-12T15:41:14
title: Bayesian Tracker (btrack)
comment: btrack is a Python library for multi object tracking, used to reconstruct trajectories in crowded fields. btrack implemented a residual U-Net model coupledd with a classification CNN to allow accurate instance segmentation of the cell nuclei. To track the cells over time and through cell divisions, btrack developed a Bayesian cell tracking methodology that uses input features from the images to enable the retrieval of multi-generational lineage information from a corpus of thousands of hours of live-cell imaging data.

beeps-bi-exponential-edge-preserving-smoother
type: software
has documentation: beeps
has function: operation Image processing
has function: operation Image smoothing
has implementation: http://biii.eu/taxonomy/term/4340
has location: beeps
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2018-10-18T15:32:45
title: BEEPS (Bi-Exponential Edge-Preserving Smoother)
comment: The smoothing is applied by the way of a bi-exponential filter, itself realized by a pair of one-tap recursions. It is therefore very fast; moreover, its computational cost is truly independent of the amount of smoothing. Meanwhile, the preservation of edges is obtained by a range filter akin to the range filter found in a bilateral filter. More technical details are available here. The plugin allows one to control the amount of smoothing, the type of range filter, its broadness, and to iterate the filter several times if desired. We illustrate in Figure 2 a possible outcome of this filter. Here, we iterated the BEEPS 10 times with a Gaussian range filter, σ = 10, and the spatial decay λ = 0.1.

best-threshold
type: software
has author: Dufour, Alexandre
has author: Provoost, Thomas
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: best-threshold
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: Huang E016529624.pdf
has reference publication: Huang, L-K & Wang, M-J J (1995), "Image thresholding by minimizing the measure of fuzziness", Pattern Recognition 28(1): 41-51
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/393
requires: http://biii.eu/node/82
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:30:21
title: Best Threshold
comment: Choose the best auto thresholding technique for your data.

bftools
type: software
created: 2018-05-31T19:58:47
modified: 2018-05-31T19:58:47
title: bftools

biapy-bioimage-analysis-pipelines-python
type: software
has author: Daniel Franco-Barranco
has function: operation Cell segmentation
has function: operation Image classification
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4339
has location: BiaPy
has location: github
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
has usage example: s12021-021-09556-1
has usage example: Stable Deep Neural Network Architectures for Mitochondria Segmentation on Electron Microscopy Volumes
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2023-05-12T16:04:58
modified: 2023-05-12T16:14:54
title: BiaPy: Bioimage analysis pipelines in Python
comment: BiaPy is an open source Python library for building bioimage analysis pipelines. BiaPy contains ready-to-use solutions for the tasks of semantic segmentation, instance segmentation, object detection, image denoising, single image super-resolution, self-supervised learning and image classification.

bidifuse
type: software
has author: Jan Detrez et al
has function: operation 2928
has implementation: http://biii.eu/taxonomy/term/4340
has location: BiDiFuse
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2016-09-15T18:48:14
modified: 2019-10-21T08:48:51
title: BiDiFuse
comment: to be completed

bigdataviewer
type: software
has author: Pietzsch Tobias
has author: Preibisch Stephan orcid.org/0000-0002-0276-494X
has author: Saalfeld Stephan orcid.org/0000-0002-4106-1761
has documentation: BigDataViewer#Usage
has function: operation_0337
has function: operation Image registration
has function: operation Image visualisation
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: BigDataViewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.3392
has reference publication: Pietzsch et al. (2015), "BigDataViewer: visualization and processing for large image data sets", Nature Methods 12(6): 481-483,
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/80
created: 2018-01-28T11:24:07
modified: 2018-01-30T11:34:23
title: BigDataViewer
comment: The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline.

bigstitcher
type: software
has author: Hörl David orcid.org/0000-0003-1710-1708
has author: Preibisch Stephan orcid.org/0000-0002-0276-494X
has documentation: BigStitcher#Documentation
has function: operation_0337
has function: operation 2409
has function: operation Image deconvolution
has function: operation Image registration
has function: operation Image stitching
has function: operation R8ANfLkuHu47r739AkhxrId
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RBPObKBKIMwjdLygBOlvojW
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL-2.0
has location: BigStitcher
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1171
requires: http://biii.eu/node/38
requires: http://biii.eu/node/80
created: 2018-01-28T09:50:47
modified: 2018-01-28T11:42:37
title: BigStitcher
comment: The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy.

bigwarp
type: software
has author: John Bogovic
has function: operation Image registration
has function: operation Warping
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: BigWarp
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: ISBI.2016.7493463
has reference publication: Bogovic et al Robust registration of calcium images by learned contrast synthesis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-28T10:29:20
modified: 2023-03-06T14:02:28
title: Bigwarp
comment: Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.

bilateral-filter-knime
type: software
has documentation: org.knime.knip.base.nodes.filter.nonlinear.BilateralFilterNodeFactory#Bilateral Filter
has function: operation Image enhancement
has function: operation Edge detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:43
modified: 2020-03-03T17:18:56
title: Bilateral Filter (KNIME)

binary-image-operations
type: software
has documentation: org.knime.knip.base.nodes.proc.binary.BinaryArithmeticNodeFactory#Binary Image Operations
has location: org.knime.knip.feature.feature.group
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:43
modified: 2018-12-18T04:07:42
title: Binary Image Operations

bio-formats
type: software
has author: The OME Consortium, http://www.openmicroscopy.org/site/about/who-ome
has function: operation 2409
has location: bio-formats
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:41
modified: 2019-10-29T17:36:36
title: Bio-Formats
comment: Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. The primary goal of Bio-Formats is to facilitate the exchange of microscopy data between different software packages and organizations. It achieves this by converting proprietary microscopy data into an open standard called the OME Data Model, particularly into the OME-TIFF file format. ### Command Line Tools Bioformats could also be used as stand alone application from command line. See [Bioformats command line tools introduction.](http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/)

bio7
type: software
has author: Dr. Marcel Austenfeld
has license: EPL, an OSI approved OpenSource license
has location: bio7.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-22T23:55:56
modified: 2017-09-13T10:12:50
title: Bio7
comment: Quote The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

biocat
type: software
has author: Hanchuan Peng orcid.org/0000-0002-3478-3942
has author: Lamichhane Santosh orcid.org/0000-0002-9292-3595
has author: Zhou Jie orcid.org/0000-0003-2176-6366
has DOI: https://doi.org/10.1186/1471-2105-14-291
has DOI: DOI
has documentation: UserGuide.pdf
has documentation: User guide
has function: operation 3553
has function: operation Image classification
has function: operation RDetoixS3xEu0agR2CebaoB
has implementation: http://biii.eu/taxonomy/term/4341
has location: index.php
has location: Download page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-291
has reference publication: Publication
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/60
created: 2018-10-08T17:31:45
modified: 2023-04-28T12:33:48
title: BioCat
comment: Biocat is a java based software that allows to perform image classification or segmentation using machine learning. Several algorithm for the classification are available.

bioconductor
type: software
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4341
has location: install
has location: Install BioConductor
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/4236
has topic: topic High content screening
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-05-08T13:24:48
modified: 2018-10-18T15:35:57
title: Bioconductor
comment: Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.

bioimage-model-zoo
type: software
has function: operation Cell segmentation
has function: operation Image classification
has function: operation RDyyXyhf1oHK93opXhEnRND
has location: bioimage.io
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3385
has topic: topic 3474
has topic: topic Digital histology
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
created: 2020-03-05T08:39:34
modified: 2023-04-30T15:13:52
title: BioImage Model Zoo
comment: BioImage.IO -- a collaborative effort to bring AI models to the bioimaging community. Integrated with Fiji, ilastik, ImJoy and more Try model instantly with BioEngine Contribute your models via Github This is a database of pretrained deep Learning models.

bioimagexd
type: software
has function: operation 3443
has function: operation Image processing
has function: operation Image visualisation
has license: GPL2
has location: bioimagexd.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nmeth.2047
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-15T10:41:23
modified: 2020-03-03T17:03:12
title: BioImageXD
comment: BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It's a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.

birl
type: software
has author: Arrate Muñoz Barrutia
has author: Jiří Borovec
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD-3
has location: BIRL
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: ICIP.2018.8451040
has reference publication: Benchmarking of image registration methods for differently stained histological slides.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2019-03-08T10:37:07
modified: 2023-03-10T23:13:03
title: BIRL
comment: BIRL stands for "Benchmark on Image Registration methods with Landmark validation". BIRL is a cross-platform framework for comparison of image registration methods with landmark validation (registration precision is measured by user landmarks). The project contains a set of sample images with related landmark annotations and experimental evaluation of state-of-the-art image registration methods. Some key features of the framework: automatic execution of image registration of a sequence of image pairs integrated evaluation of registration performances using Target Registration Error (TRE) integrated visualization of performed registration running several image registration experiment in parallel resuming unfinished sequence of registration benchmark handling around dataset and creating own experiments rerun evaluation and visualisation for finished experiments

bisque
type: software
has author: USCB center for bio-image informatics
has documentation: bisque
has documentation: documentation
has function: operation 2409
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4342
has location: bisqueUCSB
has location: source code
has platform: http://biii.eu/taxonomy/term/30
has reference publication: btp699
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
has usage example: client service
has usage example: demo website
openess: http://biii.eu/taxonomy/term/3575
created: 2018-08-17T14:53:34
modified: 2023-04-30T15:44:27
title: BisQue
comment: Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud. It also allow to run workflows using a set of deployed tools, such as CellProfiler, RootTipMultin Nuclear Tracker, Microtubule tracker etc... Bisque was developed for the exchange and exploration of biological images. The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. Bisque is free and open-source Flexible textual and graphical annotations Cloud scalability: PBs of images, millions of annotations Distributed storage: local, iRODS, S3 Integrated image analysis, high-throughput with Condor Analysis in MATLAB, Python, Java+ImageJ 100+ biological image formats Very large 5D images (100+ GB)

bleach-correction
type: software
has author: Jens Rietdorf
has author: Kota Miura
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has location: Bleach Correction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: f1000research.27171.1
has reference publication: Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2021-02-16T12:57:45
title: Bleach Correction
comment: Three different methods for correcting fluorescence bleaching. 1. Simple (framewise ratio based) 2. Exponential (curve fitting with exponential decay model) 3. Histogram matching (register histogram shape. with 16 bit, it takes long time... it should be improved).

bleb-dynamics
type: software
has author: Garcia Arcos Juan Manuel
has author: Maurin Mathieu
has function: operation Cell tracking
has function: operation Shape features
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1215
requires: http://biii.eu/node/1216
requires: http://biii.eu/node/1217
requires: http://biii.eu/node/532
created: 2018-02-01T19:00:56
modified: 2018-02-01T19:07:57
title: bleb dynamics
comment: The purpose of the workflow is .... First you need

blend-two-images-fiji-scripting-example
type: software
has author: Albert Cardona
has implementation: http://biii.eu/taxonomy/term/4340
has location: Blend two images
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4801
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2018-12-20T17:31:33
title: Blend two images (Fiji scripting example)
comment: This is a Fiji scripting demo using Clojure.

blender
type: software
has documentation: support
has function: operation Image visualisation
has function: operation Volume rendering
has function: operation Surface rendering
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU GPL Version 2 or later
has location: www.blender.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-11-07T13:24:26
modified: 2019-02-03T14:58:11
title: Blender
comment: Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

blob-segmentation
type: software
has author: Ignacio Arganda-Carreras
has function: operation Image segmentation
has location: MarieLaureB
has location: Gist: MarieLaureB / Morphological_Segmentation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1057
requires: http://biii.eu/node/79
created: 2014-12-08T12:04:24
modified: 2018-05-14T22:59:51
title: Blob segmentation
comment: Simple macro to separates blobs. - Load the ImageJ sample image "Blobs" - Run the plugin Morphological Segmentation - Display the overlaid This macro depends on "Morphological Segmentation" component of the MorphoLibJ library, which should be installed via update sites.

blood-vessel-segmentation-and-network-analysis
type: software
has author: Sébastien Tosi
has function: operation Image segmentation
has location: image-j-fiji#h.p ID 525
has location: ImageJ Macro: Blood vessel segmentation and network analysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3568
has usage example: image-j-fiji#h.p ID 525
has usage example: User guide - Blood vessel segmentation and network analysis
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-08T14:09:51
modified: 2023-04-28T14:16:36
title: Blood vessel segmentation and network analysis
comment: This macro segments blood vessels in a 3D stack. It is suited for well-contrasted images (low background) and works better if the width of the vessels of interest is reasonably uniform. Sample image: 1 sample image: 2

bm3d-denoising
type: software
has location: l bm3d
has type: http://biii.eu/taxonomy/term/8
created: 2018-05-20T18:43:23
modified: 2018-05-20T18:52:37
title: BM3D denoising
comment: BM3D is a recent denoising method based on the fact that an image has a locally sparse representation in transform domain. This sparsity is enhanced by grouping similar 2D image patches into 3D groups. In this paper we propose an open-source implementation of the method. We discuss the choice of all parameter methods and confirm their actual optimality. The description of the method is rewritten with a a more transparent notation that in the original paper. A final index gives nonetheless the correspondence between the new notation and the original notation.

bonej
type: software
has author: Michael Doube
has documentation: #provides
has documentation: BoneJ user guide
has function: operation Skeletonization
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU General Public License version 3
has location: bonej.org
has location: BoneJ homepage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: Doube 2010UKPMC.pdf
has reference publication: Doube M, Kłosowski MM, Arganda-Carreras I, Cordeliéres F, Dougherty RP, Jackson J, Schmid B, Hutchinson JR, Shefelbine SJ. (2010) BoneJ: free and extensible bone image analysis in ImageJ. Bone 47:1076-9. doi: 10.1016/j.bone.2010.08.023
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-01-29T20:47:57
modified: 2019-01-29T20:59:02
title: BoneJ

bounding-box-3d
type: software
has author: Provoost, Thomas
has author: de Chaumont, Fabrice
has implementation: http://biii.eu/taxonomy/term/4340
has location: bounding-box-3D
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
requires: http://biii.eu/node/835
created: 2013-10-11T13:08:44
modified: 2019-10-17T10:26:43
title: Bounding Box 3D
comment: Layer for 3D View that displays a Bounding Box around the object.

bsif-binarized-statistical-image-features
type: software
has author: Bordallo López M.
has function: operation Image processing
has function: operation Object detection
has function: operation Texture extraction
has location: index.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: Paper JRTIP14.pdf
has reference publication: Evaluation of real-time LBP computing in multiple architectures
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/89
created: 2017-02-13T14:19:56
modified: 2019-10-18T16:23:30
title: BSIF (Binarized Statistical Image Features)
comment: This is a software toolbox that extends the original BSIF code allowing the utilization of a GPU in Matlab to compute the features. It contains: -Matlab function to calculate BSIF in CPU -Matlab function extension to calculate BSIF in GPU -Pre-learnt filters -Usage instructions

btrackmate
type: software
has author: Varun Kapoor
has location: BTrackMate
has location: Update site Fiji MTrack
has type: http://biii.eu/taxonomy/term/3568
has type: http://biii.eu/taxonomy/term/8
has usage example: https://twitter.com/EntraCod/status/1354786723016925184
openess: http://biii.eu/taxonomy/term/3575
created: 2021-01-28T13:46:05
modified: 2021-01-28T13:50:51
title: BTrackMate
comment: TrackMate based tracker to be used when uploading integer labelled segmentation images, coming from a Deep Learning tool such as stardist. To use this tool efficiently we provide a python notebook to collect/localize the position of cells, this step creates a CSV file which can then be loaded into the Fiji tracker to do particle tracking with TrackMate interface.

bunwarpj
type: software
has author: Ignacio Arganda-Carreras
has documentation: BUnwarpJ
has function: operation Warping
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has implementation: http://biii.eu/taxonomy/term/4340
has location: BUnwarpJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2020-03-02T20:19:32
title: BUnwarpJ
comment: 2D Image registration method based on elastic deformations represented by B-splines.

calculateimageoverlap
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html%3Fhighlight%3Dimageoverlap%23module-cellprofiler.modules.measureimageoverlap
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-17T15:15:51
title: CalculateImageOverlap

calculatemath
type: software
has implementation: http://biii.eu/taxonomy/term/4340
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.0.0/modules/datatools.html%3Fhighlight%3Dcalculatemath%23module-cellprofiler.modules.calculatemath
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-17T15:22:38
title: CalculateMath
comment: This module can perform addition, subtraction, multiplication, division, or averaging of two or more image intensities, as well as inversion, log transform, or scaling by a constant for individual image intensities.

calculatestatistics
type: software
has documentation: cp2 manual 9978.pdf
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: gb-2006-7-10-r100
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-02T16:55:37
title: CalculateStatistics
comment: Calculate Statistics calculates measures of assay quality (V and Z' factors) and dose response data (EC50) for all measured features made from images.

cancer-imaging-phenomics-toolkit-captk
type: software
has author: Center for Biomedical Image Computing and Analytics (CBICA)
has documentation: captk.projects.nitrc.org
has documentation: CaPTk
has function: operation 3443
has function: operation Feature extraction
has function: operation Image enhancement
has function: operation Image registration
has function: operation Image segmentation
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has license: SBIA Contribution and Software License Agreement
has location: captk
has location: CaPTk
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/29340286
has reference publication: Cancer imaging phenomics toolkit
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: the CaPTk Playlist on YouTube
openess: http://biii.eu/taxonomy/term/3575
created: 2018-04-06T00:30:33
modified: 2023-04-30T16:20:00
title: Cancer Imaging Phenomics Toolkit (CaPTk)
comment: CaPTk is a software platform for analysis of radiographic cancer images, currently focusing on brain, breast, and lung cancer. CaPTk integrates advanced, validated tools performing various aspects of medical image analysis, that have been developed in the context of active clinical research studies and collaborations toward addressing real clinical needs. With emphasis given in its use as a very lightweight and efficient viewer, and with no prerequisites for substantial computational background, CaPTk aims to facilitate the swift translation of advanced computational algorithms into routine clinical quantification, analysis, decision making, and reporting workflow. Its long-term goal is providing widely used technology that leverages the value of advanced imaging analytics in cancer prediction, diagnosis and prognosis, as well as in better understanding the biological mechanisms of cancer development.

careless
type: software
has author: csommer
has documentation: careless
has function: operation Image deconvolution
has function: operation Image enhancement
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v2.0
has location: careless
has location: Installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3567
has usage example: careless
has usage example: How to use
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/38
created: 2020-03-09T12:51:29
modified: 2023-04-27T10:26:53
title: CAREless
comment: Deep learning based image restoration methods have recently been made available to restore images from under-exposed imaging conditions, increase spatio-temporal resolution (CARE) or self-supervised image denoising (Noise2Void). These powerful methods outperform conventional state-of-the-art methods and leverage down-stream analyses significantly such as segmentation and quantification. To bring these new tools to a broader platform in the image analysis community, we developed a simple Jupyter based graphical user interface for CARE and Noise2Void, which lowers the burden for non-programmers and biologists to access these powerful methods in their daily routine. CARE-less supports temporal, multi-channel image and volumetric data and many file formats by using the bioformats library. The user is guided through the different computation steps via inline documentation. For standard use cases, the graphical user interface exposes the most relevant parameters such as patch size and number of training iterations, while expert users still have access to advanced parameters such as U-net depth and kernel sizes. In addition, CARE-less provides visual outputs for training convergence and restoration quality. Any project settings can be stored and reused from command line for processing on compute clusters. The generated output files preserve important meta-data such as pixel sizes, axial spacing and time intervals.

catmaid
type: software
has author: Cardona Albert
has author: Hartenstein Volker / orcid.org/0000-0001-9676-7393
has author: Saalfeld Stephan / orcid.org/0000-0002-4106-1761
has author: Tomacák Pavel / orcid.org/0000-0002-2222-9370
has documentation: index.html
has documentation: CATMAID documentation
has function: operation_0337
has function: operation 2409
has function: operation 3553
has function: operation Image segmentation
has function: operation Image visualisation
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: GPLv3
has location: CATMAID
has location: github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic Light-sheet microscopy
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-11-07T20:03:07
modified: 2023-04-29T13:23:11
title: CATMAID
comment: **Collaborative Annotation Toolkit for Massive Amounts of Image Data** CATMAID is a Collaborative Annotation Toolkit for Massive Amounts of Image Data. It is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation.

cbiretrieval
type: software
has author: Loïc Rollus, Raphaël Marée
has implementation: http://biii.eu/taxonomy/term/4341
has location: wiki
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2017-02-13T14:15:04
modified: 2019-03-08T02:14:58
title: CBIRetrieval
comment: This is a Java content-based image retrieval software components. It can be runned independantly or connected to a Cytomine server. Content-based image retrieval (CBIR), also known as query by image content (QBIC) and content-based visual information retrieval (CBVIR) is the application of computer vision techniques to the image retrieval problem, that is, the problem of searching for digital images in large databases. Content-based" means that the search algorithm analyzes the contents of the image rather than the metadata such as keywords, tags, or descriptions associated with the image. The term "content" in this context might refer to colors, shapes, textures, or any other information that can be derived from the image itself. The CBIRetrieval library is: Incremental: You can add new images all over the time. Scalable: Run as many server as you want. Client performs search on all servers. Flexible: Run as a simple app (command line) or use the JAR in your own JVM app/server (java import) Opensource/Free: Apache 2.0 CBIRetrieval is a java library for CBIR, CBIRest is a server with a REST HTTP API with CBIRetrieval embedded. If you want to connect a software/webapp with a CBIR engine, you should use CBIRest. This is a fast multi-threaded and noSQL implementation of the algorithm published in: Incremental Indexing and Distributed Image Search using Shared Randomized Vocabularies Marée, Raphaël; Denis, Philippe; Wehenkel, Louis; Geurts, Pierre,in ACM Proceedings MIR 2010 (2010, March). It was applied on histology images and radiology images.

cell-counter-imagej
type: software
has author: Kurt De Vos
has documentation: cell-counter.html
has function: operation Cell counting
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: cell-counter.html
has location: Cell Counter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2018-05-25T23:10:57
title: Cell Counter ImageJ
comment: An ImageJ plugin (author: Kurt De Vos) for counting multiple cell classes manually, which overlays already-counted cells on the image. It is controlled via its own graphical user interface, and can export and load results.

cell-or-particle-counting-and-scoring-percentage-stained-objects
type: software
has author: Cell Profiler Team
has function: operation Cell counting
has function: operation Cell segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has location: ExamplePercentPositive.zip
has location: CP Pipeline and example data set
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
has usage example: 1337
has usage example: ITR notebook example
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2018-08-16T11:20:25
modified: 2023-04-26T17:18:17
title: Cell or particle counting and scoring the percentage of stained objects
comment: This one example workflow from the Cell Profiler(CP) Examples . CP is commonly used to count cells or other objects as well as percent-positives, by measuring the per-cell staining intensity. This pipeline shows how to do both of these tasks, and demonstrates how various modules may be used to accomplish the same result. In a few words, it used the IdentifyPrimaryObject module of CellProfiler to detect nuclei from a channel (e.g DAPI), then again the same module on another channel to detect another probe (e.g some particular histone) . Then objects (nuclei) are related to the second object (Histone), to create a parent child-relation ship: where nuclei can have histone has child. Nuclei are then filtered according to the property of having histone (positive) or not having histone (negtiveobject) related to them. If needed, nuclei can be expanded in order to include touching object rather than object inside only. The percentage of positive nuclei vs total number of nuclei can then be computed using the CalculateMath Module.

cell-or-particle-counting-and-scoring-stained-objects-using-cellprofiler
type: software
has author: Open Microscopy Environment
has function: operation 2945
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4342
has location: idr0002.ipynb
has location: Jupyter Notebook from ITR
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1338
requires: http://biii.eu/node/1344
created: 2018-08-16T11:11:50
modified: 2018-10-18T15:35:57
title: Cell or particle Counting and scoring stained objects using CellProfiler
comment: This is a Jupyter notebook demonstrating the run of a code from IDR data sets by loading a CellProfiler Pipeline The example here is applied on real data set, but does not correspond to a biological question. It aims to demonstrate how to create a jupyter notebook to process online plates hosted in the IDR. It reads the plate images from the IDR. It loads the CellProfiler Pipeline and replace the reading modules used to read local files from this defaults pipeline by module allowing to read data remotely accessible. It creates a CSV file and displays it in the notebook. It makes some plot with Matplotlib.

cell-segmentation-and-measurements
type: software
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/286
requires: http://biii.eu/node/31
created: 2013-10-20T15:32:41
modified: 2017-09-13T10:12:44
title: Cell segmentation and measurements
comment: Human HT29 cells are fairly smooth and elliptical. This CellProfiler workflow demonstrates how to accurately identify these cells and how to measurements cellular parameters such as morphology, count, intensity and texture.

cell-segmentation-and-quantification-cellx
type: software
has author: Christian Mayer
has author: Fabian Rudolf
has author: Jorg Stelling
has author: Sotiris Dimopoulos
has documentation: CellX
has function: operation Cell tracking
has function: operation Image segmentation
has license: BSD
has location: cellx.html
has location: cellx website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: btu302
has reference publication: 0471142727.mb1422s101
has reference publication: Dimopoulos et al. (2014) Accurate cell segmentation in microscopy images using membrane patterns.
has reference publication: Mayer et al (2013) Using CellX to quantify intracellular events.
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/89
created: 2014-12-09T11:11:04
modified: 2023-04-27T15:43:25
title: Cell segmentation and quantification with CellX
comment: CellX is an open-source software package of workflow template for cell segmentation, intensity quantification, and cell tracking on a variety of microscopy images with distinguishable cell boundary. Installation and step-by-step usage details are described in Mayer et al (2013). After users provide a few annotations of cell sizes and cell boundary profiles, it tries to match boundary profile pattern on cells thus provide segmentation and further tracking. It works the best on cells without extreme shapes and with a rather homogeneous boundary pattern. It may not work well on images with cells of sizes only a few pixels. Its output comprises control images for visual validation, text files for post-processing statistics, and MATLAB objects for advanced subsequent analysis.

cell-segmentation-ebimage-r
type: software
has author: takeo katsuki
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/286
requires: http://biii.eu/node/826
requires: http://biii.eu/node/86
created: 2013-10-30T00:56:41
modified: 2017-09-13T10:13:00
title: Cell segmentation by EBImage, R

cell-segmentation-phase-contrast-images
type: software
has author: Chunming Li
has documentation: MATLAB level set for image segmentation
has function: operation Active contours
has function: operation Cell segmentation
has function: operation Cell tracking
has function: operation Image tracking
has location: Matlab code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-09T16:23:54
modified: 2023-04-28T15:13:51
title: Cell segmentation in phase contrast images
comment: This Matlab code demonstrates an edge-based active contour model as an application of the Distance Regularized Level Set Evolution (DRLSE) formulation.

cellcognition
type: software
has author: Held Michael, Thomas Walter, Sommer Christoph, Rudolf Hoefler
has license: GPLv3
has location: www.cellcognition.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/286
requires: http://biii.eu/node/321
created: 2013-10-14T12:13:32
modified: 2023-04-25T18:06:02
title: CellCognition
comment: ## Introduction CellCognition is a computational framework dedicated to the automatic analysis of live cell imaging data in the context of High-Content Screening (HCS). It contains algorithms for segmentation of cells and cellular compartments based on various fluorescent markers, features to describe cellular morphology by both texture and shape, tools for visualizing and annotating the phenotypes, classification, tracking and error correction. Events such as mitosis can be automatically identified and aligned to study the temporal kinetics of various cellular processes during cell cycle. CellCognition can be used by novices in the field of image analysis and is applicable to hundreds of thousands of images by parallelization on compute clusters with minimal effort. The tool has been successfully applied to quantitative phenotypic profiling of cell division, yet machine learning enables CellCognition to be used for the analysis of other dynamic processes. ## Backends Following libraries are used: * numpy * VIGRA * PyQT * hdf5 * matplotlib * sklearn * Machine Learning in Python

cellpose
type: software
has author: Carsen Stringer
has author: Marius Pachitariu
has documentation: latest
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: BSD 3-Clause "New" or "Revised" License
has location: cellpose
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: 2020.02.02.931238v1
has reference publication: s41592-020-01018-x
has reference publication: Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021).
has reference publication: bioarxiv
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
has usage example: Cellpose 2D ZeroCostDL4Mic.ipynb
has usage example: ZeroCostDL4Mic notebook
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2020-03-03T14:19:48
modified: 2021-10-18T04:09:55
title: cellpose
comment: Summary Deep learning-based segmentation of cells, both fluorescence, and bright-field images ("a generalist algorithm for cellular segmentation"). The tool can be used either online or local or via notebooks (e.g. ZeroCostDL4Mic). How to use it cellpose can be used online via ready-to-use Jyupyter notebooks with very good documentation. These notebooks are listed here. Local Installation The general local installation procedure can be found here. ... Installing to Silicon Mac (M1 processor) needs some tricks, and as of October 2021, the following sequence of commands works. numba should be conda-installed before pip-installing the cellpose. conda create --name cellpose python=3.8 conda activate cellpose conda install numba git clone https://github.com/MouseLand/cellpose.git cd cellpose pip install -e .

cellprofiler
type: software
has author: Anne Carpenter
has author: Lee Kamentsky
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-15T11:14:13
modified: 2019-10-17T14:24:49
title: CellProfiler
comment: CellProfiler is free, open-source software for quantitative analysis of biological images. CellProfiler is designed to enable biologists without training in computer vision or programming to quantitatively measure cell or whole-organism phenotypes from thousands of images automatically. The researcher creates an analysis pipeline from modules that find cells and cell compartments, measure features of those cells to form a rich, quantitative dataset that characterizes the imaged site in all of its heterogeneity. CellProfiler is structured so that the most general and successful methods and strategies are the ones that are automatically suggested, but the user can override these defaults and pull from many of the basic algorithms and techniques of image analysis to solve harder problems. CellProfiler is extensible through plugins written in Python or for ImageJ. Strengths: Cells, Neurons, C. Elegans, 2D Fluorescent images, high-throughput screening, phenotype classification, multiple stains/site, interoperability, extensibility, machine learning, segmentation Limitations: largely limited to 2D, not well suited to manually-guided analysis or content review, image size limitations

cellprofiler-align
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.0.0/modules/imageprocessing.html%3Fhighlight%3Dalign%23module-cellprofiler.modules.align
has documentation: CellProfiler Image Processing Align
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has location: align.py
has location: Source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-15T09:54:42
modified: 2018-05-14T16:09:20
title: CellProfiler Align
comment: **Align** aligns images relative to each other, for example, to correct shifts in the optical path of a microscope in each channel of a multi-channel set of images. For two or more input images, this module determines the optimal alignment among them. Aligning images is useful to obtain proper measurements of the intensities in one channel based on objects identified in another channel, for example. Alignment is often needed when the microscope is not perfectly calibrated. It can also be useful to align images in a time-lapse series of images. The module stores the amount of shift between images as a measurement, which can be useful for quality control purposes. Note that the second image (and others following) is always aligned with respect to the first image. That is, the X/Y offsets indicate how much the second image needs to be shifted by to match the first. This module does not perform warping or rotation, it simply shifts images in X and Y. For more complex registration tasks, you might preprocess images using a plugin for that purpose in FIJI/ImageJ. | Supports 2D? | Supports 3D? | Respects masks? | |--------------|--------------|-----------------| | Yes | No | Yes | ### Measurements made by this module - *Xshift, Yshift:* The pixel shift in X and Y of the aligned image with respect to the original image. ### References - Lewis JP. (1995) “Fast normalized cross-correlation.” *Vision Interface*, 1-7.

cellprofiler-analyst-cpa
type: software
has author: Broad Institute Imaging Platform
has documentation: CellProfiler-Analyst
has documentation: Code
has function: operation_0337
has function: operation 3443
has function: operation Image classification
has implementation: http://biii.eu/taxonomy/term/4341
has location: releases
has location: CellProfilerAnalyst download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: btw390
has reference publication: CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic High content screening
has topic: topic Statistics
has training material: http://biii.eu/node/1526
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2019-04-08T10:26:56
modified: 2019-04-14T14:10:45
title: CellProfiler Analyst CPA
comment: CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CPA provides tools for exploring and analyzing multidimensional data, particularly data from high-throughput, image-based experiments analyzed by its companion image analysis software, CellProfiler.

cellprofiler-comet-assaydna-damage-assay
type: software
has author: CellProfiler team
has documentation: #Comet
has location: ExampleCometAssay.zip
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2014-12-08T17:02:11
modified: 2018-05-16T19:56:54
title: CellProfiler Comet assay/DNA damage assay
comment: quote This is a simple example of a DNA damage assay using single cell gel electrophoresis. Here, the measurement of interest is the length and intensity of the comet tail. Also, illumination correction is used to reduce background fluorescence prior to measurement. Also shown is a silver-stained comet example in which the percentage of DNA contained in the tail is calculated. Example Images: Packaged together with the cellprofiler pipeline file.

cellprofiler-crop
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.0.0/modules/imageprocessing.html%3F%23crop
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-16T11:49:03
title: CellProfiler Crop
comment: Crop crops or masks an image. This module crops images into a rectangle, ellipse, an arbitrary shape provided by you, the shape of object(s) identified by an Identify module, or a shape created using a previous Crop module in the pipeline.

cellprofiler-examples-colocalization
type: software
has author: Cellprofiler Developers
has documentation: #Colocalization
has function: operation Image colocalization
has function: operation Colocalisation analysis
has location: ExampleColocalization.zip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2014-12-08T13:28:39
modified: 2023-04-29T12:22:44
title: CellProfiler Examples - Colocalization
comment: Quote: Measuring the colocalization between fluorescently labeled molecules is a widely used approach to measure the degree of spatial coincidence and potential interactions among subcellular species (e.g., proteins). This example shows how the object identification and RelateObjects modules are used to measure the degree of overlap between two fluorescent channels. Sample image is included in the download package.

cellprofiler-examples-speckle-counting
type: software
has author: Cellprofiler team
has documentation: #Speckles
has function: operation Image segmentation
has function: operation Spot extraction
has location: ExampleSpeckles.zip
has location: ExampleSpeckles zip file
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2014-12-08T13:34:39
modified: 2023-04-29T12:55:54
title: CellProfiler Examples - Speckle Counting
comment: Quote: This pipeline shows how to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a relationship between the two as well as perform per-object aggregate measurements (such as number of foci per nucleus). Sample images are included in the download package.

cellprofiler-smooth
type: software
has documentation: imageprocessing.html#smooth
has function: operation Image processing
has function: operation Image smoothing
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-21T12:25:38
title: CellProfiler Smooth
comment: This CellProfiler module allows smoothen the image with a choice from various algorithms: - Fit Polynomial - Gaussian Filter - Median Filter - Bilateral Filter - Circular averaging - "Smooth to Average" filter.

cellprofiler-threshold
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.0.0/modules/imageprocessing.html%3Fhighlight%3Dthreshold%23threshold
has documentation: Threshold (3.0)
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:40
modified: 2018-06-06T17:40:13
title: CellProfiler Threshold
comment: in CP 2.1, it was "ApplyThreshold". Renamed to "Threshold" from 3.0.

cellprofiler-unmixcolors
type: software
has documentation: imageprocessing.html
has function: operation 3443
has location: UnmixColors.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:40
modified: 2019-10-18T14:28:28
title: Cellprofiler UnmixColors

cells-tracking-tissue
type: software
has author: Sébastien Tosi
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
requires: http://biii.eu/node/826
created: 2014-12-08T14:41:14
modified: 2017-09-13T10:14:05
title: Cells tracking in tissue
comment: Plot the centroid tracks and area evolution of the cells of a tissue with membrane labelling.

cellsegm
type: software
has author: Erlend Hodneland
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has license: GNU General Public License
has location: cellsegm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-8-16
has reference publication: CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: examples
has usage example: gihub examples
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-09T14:43:23
modified: 2023-04-28T15:19:20
title: CellSegm
comment: An automated MATLAB tool for segmentation of surface stained cells

celltrack
type: software
has documentation: software
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4341
has location: CellTrack
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: btn247
has reference publication: CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-15T09:48:52
modified: 2020-03-03T16:29:38
title: CellTrack
comment: A standalone cell tracking software for single cell migration. Tracking of cells in tissue was also done in Drosophila germband.

celltracker
type: software
has author: Chengjin Du
has author: Douglas Kell
has author: Hailin Shen
has author: Mike White
has author: Till Bretschneider
has function: operation Cell tracking
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4341
has location: celltracker
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
has usage example: PMC2785900
has usage example: 10.1126/science.1164860
openess: http://biii.eu/taxonomy/term/3576
created: 2013-10-15T10:45:49
modified: 2019-10-17T16:12:14
title: CellTracker
comment: CellTracker software is a platform for tracking nuclear and cytoplasmic fluorescence intensities from live cell microscopy time series data. Requires visual C++

celsius-fahrenheit
type: software
has function: operation 3434
has implementation: http://biii.eu/taxonomy/term/4339
has location: Celsius to fahrenheit
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4801
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:41
modified: 2020-03-03T17:07:18
title: Celsius to fahrenheit

cem
type: software
has documentation: cem
has documentation: User Manual is included in the compressed file
has function: operation Dilation
has function: operation Neuron image analysis
has function: operation Object detection
has function: operation Colocalisation analysis
has function: operation Pixel-based colocalisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: cem
has location: Download from Kerman Lab
has reference publication: 2213.long
has reference publication: 10.1242/dev.116517
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic High content screening
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-02-07T07:30:01
modified: 2018-11-16T08:47:48
title: CEM
comment: Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents. CEM runs as an imageJ plugin with an optional Matlab extension to remove cell bodies. More details are published at Kerman et al. 2015 Development. Supplemental Material includes a detailed user manual and the download link.

centromere-recognition-and-quantification
type: software
has author: A Great Guy
has documentation: microscopy-macros.php#craq
has documentation: CRaQ
has function: operation Spot extraction
has location: CRaQ v1.12.ijm
has location: CRaQ_v1.12.ijm
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: 0471143030.cb0808s55
has reference publication: Bodor, Gómez-Rodriguez, Moreno & Jansen (2012) Analysis of Protein Turnover by Quantitative SNAP‐Based Pulse‐Chase Imaging
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/726
created: 2013-11-08T18:10:58
modified: 2023-04-26T11:53:46
title: Centromere Recognition and Quantification
comment: Particle detection is based on "Analyze Particles" in ImageJ. It probably could also be used in spot detection, not limited to centromere. >This macro is described in Bodor et al. (2012). The macro recognizes centromere or kinetochore foci in Delta Vision or TIFF images and determines their centroid position. Fluorescent intensities are then measured for each centromere by placing a small box around the centroid position of the centromere. The peak intensity value within the box is corrected for local background by subtraction of the minimum pixel value. This process results in an accurate measurement of large numbers of centromere or kinetochore-specific signals. Following papers uses CRaQ (picked up, maybe more): - [Fachinetti et al. (2017)](https://www.cell.com/developmental-cell/pdf/S1534-5807(16)30909-1.pdf), Developmental Cell 40, 104–113, - [Guo et al. (2017)](https://www.nature.com/articles/ncomms15775) Nature Communications volume 8, Article number: 15775 (2017) doi:10.1038/ncomms15775 - [Lgosdon et. al. (2015)](http://jcb.rupress.org/content/208/5/521) J Cell Biol Mar 2015, 208 (5) 521-531; DOI: 10.1083/jcb.201412011 - [Bodor et al. (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091408/), eLife. 2014; 3: e02137

chainer
type: software
has documentation: chainer.org
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-06-04T13:13:43
modified: 2023-04-28T12:23:58
title: Chainer
comment: Chainer is a Python-based deep learning framework aiming at flexibility. It provides automatic differentiation APIs based on the define-by-run approach (a.k.a. dynamic computational graphs) as well as object-oriented high-level APIs to build and train neural networks. It also supports CUDA/cuDNN using CuPy for high performance training and inference. For more details of Chainer, see the documents and resources listed above and join the community in Forum, Slack, and Twitter.

channel-montage
type: software
has author: Dufour, Alexandre
has function: operation 2409
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: channel-montage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
requires: http://biii.eu/node/852
requires: http://biii.eu/node/970
created: 2013-10-11T13:08:46
modified: 2023-04-29T20:05:04
title: Channel Montage
comment: View your multi-channel data as a montage with one image per channel plus a merged, color channel (useful to create figures for communication). This viewer plugin will split all N channels of the active sequence into a montage of N+1 images, with one image for each channel, plus an additionnal color (merge) rendering.

chart-tutorial-1
type: software
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Chart-tutorial-1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2023-04-29T15:33:40
title: Chart tutorial 1
comment: Tutorial explaining how to display a JFreeChart graph in Icy.

chart-tutorial-2
type: software
has author: Dallongeville, Stephane
has location: chart-tutorial-2
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:41
modified: 2019-10-17T11:43:24
title: Chart tutorial 2
comment: This tutorial explain how to use a deviation renderer JFreeChart chart in Icy.

chart1dcanvas
type: software
has author: Ouyang, Wei
has implementation: http://biii.eu/taxonomy/term/4340
has location: chart1dcanvas
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:43
modified: 2019-10-17T10:20:56
title: Chart1DCanvas
comment: A canvas plugin using JFreeChart to show intensity profile of a specific row or column. Initially used in a 1-row image of 1D signal representation. Can also used with Micro-Manager for Icy Plugin to show 1D signal from hardware like data acquisition device as waveform. Common 2D+ sequence is also supported. Using it by select the plugin icon in the canvas type combobox of the sequence window, a JFreeChart line chart will show up. As an alternative plugin to Intensity Profile, this plugin is modified from "Intensity Profile" by fab, special thanks to him for giving me the idea to make such a plugin.

chess
type: software
has implementation: http://biii.eu/taxonomy/term/4340
has location: Chess
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-15T16:00:39
title: Chess
comment: This Jython script illustrates how to make an image interactive. It let you play chess within Fiji!

chromagnon
type: software
has author: Atsushi Matsuda
has DOI: s41598-018-25922-7
has DOI: 10.1038/s41598-018-25922-7
has documentation: ChromagnonDocumentV065.pdf
has documentation: How it works
has function: operation RDr8xcZEa4L3mZsslmhhee8
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL-2.0
has location: releases
has location: Chromagnon packages
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41598-018-25922-7
has reference publication: Matsuda et. al. Scientific Reports 2018
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
created: 2019-02-03T12:44:43
modified: 2019-02-05T11:08:43
title: Chromagnon
comment: Image correction software for chromatic shifts in fluorescence microscopy

chronometer
type: software
has author: Provoost, Thomas
has implementation: http://biii.eu/taxonomy/term/4340
has location: Chronometer
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:40
modified: 2019-10-17T11:27:50
title: Chronometer
comment: Simple chronometer for Icy.

cicardian-gene-expression
type: software
has author: Daniel Sage
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: circadian
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://doi.org/10.1186/1747-1028-5-17
has reference publication: A software solution for recording circadian oscillator features in time-lapse live cell microscopy.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2018-12-18T04:13:18
title: Cicardian Gene Expression
comment: "This ImageJ plugin (CGE) is a semi-automatic tool to detect and track moving cell, and to measure the fluorescent protein expression level. CGE extracts the trajectory of the cells by tracking their displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level, cell displacement."

cidre
type: software
has author: Kevin Smith
has comparison: nmeth.3323.html
has DOI: nmeth.3323
has DOI: 10.1038/nmeth.3323
has function: operation Illumination correction
has license: GNU GPL2
has location: cidre
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth.3323
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3385
has topic: topic High content screening
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/38
created: 2017-09-12T07:53:59
modified: 2023-04-29T12:27:21
title: CIDRE
comment: CIDRE is a retrospective illumination correction method for optical microscopy. It is designed to correct collections of images by building a model of the illumination distortion directly from the image data. Larger image collections provide more robust corrections. Details of the method are described in K. Smith, Y. Li, F. Ficcinini, G. Csucs, A. Bevilacqua, and P. Horvath CIDRE: An Illumination Correction Method for Optical Microscopy, Nature Methods 12(5), 2015, doi:10.1038/NMETH.3323

clahe
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/787
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:08:26
title: CLAHE

classification-hemp-fibers-based-morphological-features
type: software
has author: David Legland
has function: operation Feature extraction
has function: operation Morphological operations
has function: operation Object detection
has function: operation Watershed
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1057
requires: http://biii.eu/node/38
created: 2016-10-01T18:11:30
modified: 2018-08-16T15:37:52
title: classification of hemp fibers based on morphological features
comment: In this workflow, you can use MorphoLibJ to generate accurate morphometric measurements First the fibers are segmented by mathematical morphology: for example by using MorphoLibJ: Create a marker image by creating a rough mask with extended regional maxima (similar to Find Max), such that you have one max per fiber Use the marker controlled watershed (in MorpholLibJ/ Segmentation/ marker controlled watershed) : indicate the original grayscale image as the input, Marker will be your maxima image, select None for mask it will create a label mask of your fibers In MorphoLibJ /analyze/ select Region Morphometry: this will compute different shape factors which are more robust than the ones implemented by default in ImageJ Export the result table created to a csv file Then for example in Matlab or R, you can apply a PCA analysis (Principal component analysis) followed by a k-means with the number of class (clusters) (different fibers type) you want to separate. You can then add this class as a new feature to your csv file. From this you can sort your labelled fibers into these clusters for a visual feedback or further spatial analysis

classifyobjects
type: software
has location: objectprocessing.html
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
requires: http://biii.eu/node/88
created: 2013-10-11T13:08:43
modified: 2019-10-17T15:18:14
title: ClassifyObjects
comment: This module classifies objects into a number of different bins according to the value of a measurement (e.g., by size, intensity, shape). It reports how many objects fall into each class as well as the percentage of objects that fall into each class. The module asks you to select the measurement feature to be used to classify your objects and specify the bins to use. It also requires you to have run a measurement or CalculateMath previous to this module in the pipeline so that the measurement values can be used to classify the objects.

classifypixels-cellprofiler
type: software
has documentation: predict.py
has documentation: github
has function: operation 2409
has function: operation Pixel classification
has implementation: http://biii.eu/taxonomy/term/4340
has location: predict.py
has location: CellProfiler-plugins - predict (python)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Supervised learning
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
requires: http://biii.eu/node/88
created: 2013-10-11T13:08:46
modified: 2023-05-02T11:49:38
title: ClassifyPixels (CellProfiler)
comment: This originally came from this module. Currently it is available as the ilastik CellProfiler plugin (see this image.sc post for details).

clearcl
type: software
has author: Royer Loic orcid.org/0000-0002-9991-9724
has documentation: resources
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: ClearCL
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: demo
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1186
requires: http://biii.eu/node/60
created: 2018-01-28T11:40:58
modified: 2018-01-28T15:54:59
title: ClearCL
comment: ClearCL is a Multi-backend Java Object Oriented Facade API for OpenCL. OpenCL libraries come and go in Java, some are great but then one day the lead developper goes on to greener pastures and you are left with code that needs to be rewritten to take advantage of a new up-to-date library with better support. Maybe a particular library has a bug or does not support the function you need? or it does not give you access to the underlying native pointers, making difficult to process large buffers/images or interoperate with hardware? or maybe it just does not support your exotic OS of choice. To protect your code from complete rewrites ClearCL offers a very clean and complete API to write your code against. Changing backend requires just changing one line of code.

cleargl
type: software
has author: Gunther Ulrik
has author: Pietzsch Tobias
has author: Royer Loic orcid.org/0000-0002-9991-9724
has author: Weigert Martin
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4339
has location: ClearGL
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.3372
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: ClearGLDemo.java
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/60
created: 2018-01-28T12:11:08
modified: 2018-01-28T12:16:26
title: ClearGL
comment: Facade API on top of JOGL (http://jogamp.org/jogl/www/) offering a simple interface for creating OpenGL contexts/windows, GLSL shader programs, and textures. Use it in your favourite JVM-based language.

clearmap
type: software
has author: Christoph Kirst
has documentation: ClearMap2
has documentation: Source code
has function: operation_0337
has function: operation 2409
has function: operation 2928
has function: operation 3443
has function: operation Cell segmentation
has function: operation Image registration
has function: operation Image stitching
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL 3.0
has location: installation.html
has location: Installation from Anaconda or source
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: j.cell.2016.05.007
has reference publication: j.cell.2020.01.028
has reference publication: Mapping of brain activity by automated volume analysis of immediate early genes.
has reference publication: Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature.
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
requires: http://biii.eu/node/128
created: 2022-05-17T08:49:59
modified: 2023-05-03T13:28:50
title: ClearMap
comment: ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues. It was initially developed to map brain activity at cellular resolution in whole mouse brains using immediate early gene expression. It has since then been extended as a tool for the qunatification of whole mouse brain vascualtur networks at capilary resolution. It is composed of sevral specialized modules or scripts: tubemap, cellmap, WobblyStitcher. ClearMap has been designed to analyze O(TB) 3d datasets obtained via light sheet microscopy from iDISCO+ cleared tissue samples immunolabeled for proteins. The ClearMap tools may also be useful for data obtained with other types of microscopes, types of markers, clearing techniques, as well as other species, organs, or samples.

clearvolume
type: software
has author: Gunther Ulrik
has author: Jug Florian
has author: Maghelli Nicola
has author: Myers Eugene
has author: Royer Loic orcid.org/0000-0002-9991-9724
has author: Sbalzarini Ivo
has author: Weigert Martin
has documentation: wiki
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4339
has location: clearvolume.github.io
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.3372
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3385
has topic: topic Light-sheet microscopy
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: Integration-in-Java
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1180
requires: http://biii.eu/node/1185
requires: http://biii.eu/node/60
created: 2018-01-28T11:58:08
modified: 2018-01-28T12:20:07
title: ClearVolume
comment: ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data. The biologists can immediately decide whether a sample is worth imaging. ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks with ClearVolume from within these popular frameworks for offline viewing.

clij2
type: software
has author: Robert Haase 0000-0001-5949-2327
has documentation: reference
has documentation: Methods reference
has function: operation Cell counting
has function: operation Closing
has function: operation Dilation
has function: operation Erosion
has function: operation Image deconvolution
has function: operation Image smoothing
has function: operation Image thresholding
has function: operation Local thresholding
has function: operation Opening
has function: operation Projection
has function: operation Rotation
has function: operation Spot extraction
has function: operation Volume rendering
has function: operation R8ANfLkuHu47r739AkhxrId
has function: operation RDyyXyhf1oHK93opXhEnRND
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD3
has location: clij
has location: ImageJ update site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3594
has programming language: http://biii.eu/taxonomy/term/4223
has programming language: http://biii.eu/taxonomy/term/4525
has programming language: http://biii.eu/taxonomy/term/4668
has reference publication: clij2-docs
has reference publication: User guide
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has training material: http://biii.eu/node/1840
has type: http://biii.eu/taxonomy/term/3567
has usage example: macro
has usage example: Example ImageJ macros
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/79
requires: http://biii.eu/node/82
created: 2019-02-03T14:32:21
modified: 2023-04-29T09:03:24
title: clij2
comment: CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java. It comes with hundreds of operations for filtering, binarizing, labeling, measuring in images, projections, transformations and mathematical operations for images. While most of these are classical image processing operations, CLIJ2 also allows performing operations on matrices potentially representing neighborhood relationships between cells and pixels. CLIJ2 was developed to process images from fluorescence microscopy data of developing cells, tissues, organoids and organisms.

clojure-icy
type: software
has author: Dallongeville, Stephane
has author: Provoost, Thomas
has implementation: http://biii.eu/taxonomy/term/4340
has location: Clojure
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:51:37
title: Clojure (ICY)
comment: Library used by Micro-Manager for fast acquisition.

clus-doc
type: software
has author: Sophie V. Pageon, Philip R. Nicovich, Mahdie Mollazade, Thibault Tabarin, Katharina Gaus
has license: Unknown
has location: ClusDoC
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: 3627.short
has reference publication: 10.1091/mbc.E16-07-0478
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2016-10-08T00:09:57
modified: 2017-09-13T13:17:26
title: Clus-Doc
comment: Clus-Doc is a software that quantifies both the spatial distribution of a protein as well as its colocalization status. It may be used to quantify signaling activity and protein colocalization at the level of individual proteins.

cmake
type: software
created: 2019-02-28T09:00:21
modified: 2019-02-28T09:00:21
title: CMake

cmtk
type: software
has author: Rohlfing Torsten
has documentation: https://www.nitrc.org/docman/index.php%3Fgroup_id%3D212%26selected_doc_group_id%3D-1%26language_id%3D1%23folder
has function: operation 3443
has function: operation Image classification
has function: operation Image processing
has function: operation Image registration
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL
has location: cmtk
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/12670015
has reference publication: Rohlfing et al. Nonrigid image registration in shared-memory multiprocessor environments with application to brains, breasts, and bees.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3444
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-30T12:27:24
modified: 2021-05-19T18:50:24
title: CMTK
comment: A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model).

cmyk-exporter
type: software
has author: Dufour, Alexandre
has implementation: http://biii.eu/taxonomy/term/4340
has location: CMYK-exporter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:19
title: CMYK exporter
comment: Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for high-fidelity color printing).

coloc-2
type: software
has author: Johannes Schindelin
has function: operation Pixel-based colocalisation
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Coloc 2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:46
modified: 2018-12-18T04:05:10
title: Coloc 2
comment: " Coloc 2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing. Coloc 2 does NOT perform object based colocalization measurements, where objects are first segmented from the image, then their spatial relationships like overlap etc. are measured. This complementary approach is implemented in many ways elsewhere. "

colocalization-test
type: software
has author: Daniel James White
has location: Colocalization Test
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2018-12-20T17:39:58
title: Colocalization Test
comment: DEPRECATED Use coloc 2!

colocalizer
type: software
has author: de Chaumont, Fabrice
has function: operation Colocalisation analysis
has location: Colocalizer
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/49
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:43
modified: 2019-10-17T12:43:19
title: Colocalizer
comment: Colocalizer block.

colony-blob-count-tool
type: software
has author: Volker Baecker
has documentation: Colony Blob Count Tool
has function: operation Cell counting
has location: Colony Blob Count Tool.txt
has location: Colony_Blob_Count_Tool.txt
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T16:46:23
modified: 2018-05-29T00:35:37
title: Colony Blob Count Tool
comment: Count bacterial colonies on agar plates and measure the occupied surfaces. The user has to provide a selection (roi) of the area that will be analyzed. He can than run the segmentation and if necessary correct the results. In a third step he can run the counting and measurement.

color-inspector-3d
type: software
has author: Kai Uwe Barthel
has implementation: http://biii.eu/taxonomy/term/4340
has location: Color Inspector 3D
has location: imageJ.net page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2018-12-18T23:21:00
title: Color Inspector 3D
comment: This plugin shows the color distribution within a 3D-color-space. Extensive documentation is available atwww.f4.fhtw-berlin.de/~barthel/ImageJ/ColorInspector/help.htm. Color Inspector 3D is also available as a stand-alone program that uses ImageJ as a library. To run it, download ColorInspector3D.jar and double click on it. On Windows, Java 5.0 or later must be installed

color-normalization-he-stains
type: software
has author: Mitko Veta
has function: operation Image deconvolution
has location: staining-normalization
has location: GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: Quantification of histochemical staining.pdf
has reference publication: macenko2009.pdf
has reference publication: ISBI.2009.5193250
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/11531144
has reference publication: Macenko et al. (2009) A method for normalizing histology slides for quantitative analysis.
has reference publication: Quantification_of_histochemical_staining.pdf
has reference publication: Ruifrok and Johnston (2001) Quantification of histochemical staining by color deconvolution.
has reference publication: same, PDF
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2014-12-09T11:56:53
modified: 2018-06-05T01:06:57
title: Color normalization of H&E stains
comment: The overall colors seen in H&E stained slides can vary widely, influenced by factors such as the precise stains and scanner used. This MATLAB function implements the color normalization strategy described in Macenko et al (2009) in order to match stain colors in an image more closely to 'reference' stains. This may help when comparing images visually, or when applying an automated analysis algorithm. The function may also be useful to understand the functioning of the color deconvolution described in Ruifork and Johnston (2001).

color-picker-threshold
type: software
has author: Dallongeville, Stephane
has author: Dufour, Alexandre
has author: Hervé, Nicolas
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: color-picker-threshold
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic 3382
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/467
requires: http://biii.eu/node/537
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:19
title: Color Picker Threshold
comment: Image segmentation by representative colors selection. Two versions are available : thresholding positive and negative colors selection and SVM learning

colorlab
type: software
has author: Jesús Malo
has author: Maria José Luque
has documentation: colorlab.html#download
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: colorlab.html#download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2017-02-13T15:39:27
modified: 2019-10-18T16:15:54
title: ColorLab
comment: COLORLAB is a component for processing, representing and reproducing color in a MATLAB environment. Among others, some of the functionalities it makes able to: -Represent the color content of any image in chromatic diagrams and tristimulus spaces in any system of primaries. -Compute advanced color descriptions of any image using several color appearance models (CIELab, CIEluv, ATD, Rlab, LLab, SVF and CIECAM). An userguide is provided.

colormine
type: software
has author: ColorMine.org
has documentation: ColorMine
has function: operation 3434
has license: MIT
has location: colormine
has platform: http://biii.eu/taxonomy/term/29
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2017-02-13T12:17:34
modified: 2020-03-05T10:35:23
title: Colormine
comment: Nuget package for conversion between color spaces and calculation of color differences. Color spaces available: -CMY -CMYK -HSL -HSB -HSV -CIE L*a*b* -Hunter LAB -L*C*h* -L*u*v* -RGB -XYZ -YXY Color differences available: -CIE76 -CMC l:c -CIE94 -CIE2000. Online example at http://colormine.org/color-converter

colortogray
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.0.0/modules/imageprocessing.html%3Fhighlight%3Dcolortogray%23module-cellprofiler.modules.colortogray
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
requires: http://biii.eu/node/970
created: 2013-10-11T13:08:44
modified: 2019-10-17T15:21:38
title: ColorToGray
comment: Converts an image with multiple color channels to one or more grayscale images.

colour-deconvolution
type: software
has author: Gabriel Landini
has documentation: Colour Deconvolution
has function: operation R7qn3VpJyCAPGqdW6ia3h2d
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:40
modified: 2018-06-07T23:01:48
title: Colour Deconvolution
comment: This plugin is bundled with Fiji. For installation in ImageJ1, download from the link below and manually install the class file. Quote: The colour deconvolution plugin (java and class files) for ImageJ and Fiji implements stain separation using Ruifrok and Johnston's method described in [1]. The code is based on a NIH Image macro kindly provided by A.C. Ruifrok. The plugin assumes images generated by colour subtraction (i.e. light-absorbing dyes such as those used in bright field histology or ink on printed paper). However, the dyes should not be neutral grey (most histological stains are not so). If you intend to work with this plugin, it is important to read the original paper to understand how new vectors are determined and how the procedure works. The plugin works correctly when the background is neutral (white to grey), so background subtraction with colour correction must be applied to the images before processing. The plugin provides a number of "built in" stain vectors some of which were determined experimentally in our lab (marked in the source with GL), but you should determine your own vectors to achieve an accurate stain separation, depending on the stains and methods you use. See the note below. The built-in vectors are : Haematoxylin and Eosin (H&E) x2 Haematoxylin and DAB (H DAB) Feulgen Light Green Giemsa Fast Red, Fast Blue and DAB Methyl green and DAB Haematoxylin, Eosin and DAB (H&E DAB) Haematoxylin and AEC (H AEC) Azan-Mallory Masson Trichrome Alcian blue & Haematoxylin Haematoxylin and Periodic Acid - Schiff (PAS) RGB subtractive CMY subtractive User values entered by hand Values interactively determined from rectangular ROIs

colour-merge
type: software
has location: Colour merge
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2018-12-20T17:37:00
title: Colour merge
comment: DEPRECATED (as of Dec. 2018)

columbus-image-data-storage-and-analysis-system
type: software
has author: PerkinElmer
has license: commercial
has location: columbus.xhtml
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-24T08:04:33
modified: 2017-09-12T18:06:07
title: Columbus Image Data Storage and Analysis System
comment: Columbus is a combination of an image database (based on Omero, OME) and an image analysis engine based on Acapella (PerkinElmer). It is dedicated to cell culture based high content screening data and is used via a web interface. It provides a set importers for automated microscopes such as Yokogawa CellVoyager, PerkinElmer Operetta, PerkinElmer Opera and data in Metamorph format. After login, Images can be explored in a standard web browser by clicking on a well plate view. Image analysis workflows can be developed by combining modules like "find nuclei", "find cytoplasm", "find spots" for object detection. Objects can have a hierarchical structure, e.g. spot objects can be part of a cell object. The approach of workflow design is similar to the freeware cell profiler, but more restricted (less functions and less parameters to tweak) and easier to use. Mutliple intensity- and shape based features can be calculated from detected objects (e.g. texture: haralick, Garbor, SER). Objects can be classified by these features by using hard thresholds or by supervised machine learning. Analysis workflows and results are stored in the database and can be exprted as csv tables for secondary analysis. Simple secondary analysis workflows can be also applied in Columbus directly. Results can be visualized as heatmaps on the plate view. The HCS statistics software Genedata Screener Assay Analyzer can be directly connected to the database.

combine-ebimage
type: software
has documentation: EBImage.pdf
has function: operation 2409
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2020-03-03T09:32:59
title: combine (EBImage)

compaction-profiler
type: software
has author: Lagache, Thibault
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: compaction-profiler
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: S1931312812002697
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2023-04-29T13:59:11
title: Compaction Profiler
comment: This plugin permit to measure the signal spread of a molecule with respect to the cell area.

compucell3d
type: software
has author: contact team: compucell3d.iu@gmail.com
has author: http://www.indiana.edu/~bioc/jglazier/
has documentation: Tutorials
has function: operation 3441
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has location: www.compucell3d.org
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://www.sciencedirect.com/science/article/pii/B9780123884039000138
has reference publication: https://doi.org/10.1016/B978-0-12-388403-9.00013-8
has topic: topic R96toeNl9iMp8oqv9augU84
has type: http://biii.eu/taxonomy/term/3567
has usage example: Simulation Movies
openess: http://biii.eu/taxonomy/term/3575
created: 2018-04-11T14:17:59
modified: 2018-05-06T14:07:59
title: CompuCell3D
comment: CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience. It uses Cellular Potts Model to model cell behavior.

confocalcheck
type: software
has author: Dormann Dirk orcid.org/0000-0001-6309-7522
has author: Hng Keng Imm
has documentation: journal.pone.0079879.s013
has documentation: System configuration
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL-3
has location: pone.0079879.s015.txt
has location: ConfocalCheck
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: pone.0079879.pdf
has reference publication: 10.1371/journal.pone.0079879
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has training material: http://biii.eu/node/1426
has type: http://biii.eu/taxonomy/term/8
has usage example: journal.pone.0079879.s020
has usage example: Example with standardised data set
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-03T10:33:33
modified: 2019-02-05T11:16:16
title: ConfocalCheck
comment: Assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation.

connected-components
type: software
has author: Dufour, Alexandre
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: connected-components
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:19
title: Connected Components
comment: This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works on both binary and gray-scale data. Output can be pushed to the swimming pool for other plug-ins to further exploit the extracted objects.

connected-components-xls-export-block
type: software
has author: de Chaumont, Fabrice
has implementation: http://biii.eu/taxonomy/term/4340
has location: connected-components-XLS-export-block
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:43
modified: 2019-10-17T10:29:53
title: Connected components XLS export Block
comment: Exports connected components data in XLS. Exports All, by T or by ROI

continuous-time-arma-identification
type: software
has location: gaussian-maximum-likelihood
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:09:33
title: Continuous-Time ARMA Identification

contour-plot
type: software
has author: Timothée Lecomte, Alexandre Dufour
has documentation: contour-plot
has function: operation 3441
has function: operation Overlay
has implementation: http://biii.eu/taxonomy/term/4340
has location: contour-plot
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/977
created: 2013-10-11T13:08:40
modified: 2020-03-02T13:30:21
title: Contour Plot
comment: Draws a contour plot on top of a sequence.

contourlines
type: software
has author: Eugene Katrukha
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT
has location: ContourLines
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2019-03-14T22:42:35
modified: 2019-03-14T22:52:03
title: ContourLines
comment: > ImageJ/FIJI plugin generating contour lines with equal spacing on top of an image (using overlay).

convertobjectstoimage
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/objectprocessing.html%3Fhighlight%3Dconvertobjectstoimage%23module-cellprofiler.modules.convertobjectstoimage
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2019-10-17T15:14:48
title: ConvertObjectsToImage
comment: Converts objects you have identified into an image.

convolve-2d-bessel-function
type: software
has documentation: BesselPSFConvolver manual.pdf
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-15T10:45:49
modified: 2019-10-18T16:03:49
title: Convolve with 2D Bessel function

convolver
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/593
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:33
title: Convolver

copy-pixel-size
type: software
has author: J. Anthony Parker
has documentation: Copy Pixel Size
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Copy Pixel Size.java
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T10:56:04
title: Copy Pixel Size
comment: This plugin copies the pixel size from the calibration of one image or stack to a second image or stack. This allows one to copy the spatial calibration from one stack to another. A second dialog allows to enter the scale factors.

correct-3d-drift
type: software
has author: Albert Cardona
has author: Robert Bryson-Richardson
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Correct 3D drift
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 10.3791/51086
has reference publication: sample-drift-correction-following-4d-confocal-time-lapse-imaging
has reference publication: Sample Drift Correction Following 4D Confocal Time-lapse Imaging
has reference publication: publication
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T16:31:21
modified: 2020-03-03T11:30:14
title: Correct 3D drift
comment: Rigid registration of time series in 3D. A video tutorial is available (be careful of sounds, the video automatically starts!): [Sample Drift Correction Following 4D Confocal Time-lapse Imaging](http://www.jove.com/video/51086/sample-drift-correction-following-4d-confocal-time-lapse-imaging)

correctilluminationapply
type: software
has author: Bengtsson E
has author: Lindblad J
has documentation: imageprocessing.html
has function: operation Illumination correction
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: http://citeseerx.ist.psu.edu/viewdoc/summary%3Fdoi%3D10.1.1.468.2915
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-03T08:08:04
title: CorrectIlluminationApply
comment: CorrectIlluminationCalculate calculates an illumination function that is used to correct uneven illumination/lighting/shading or to reduce uneven background in images.

correctilluminationcalculate
type: software
has location: CorrectIlluminationCalculate.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:09:29
title: CorrectIlluminationCalculate

correlia
type: software
has author: Rohde Florens orcid.org/0000-0001-7114-1669
has author: Schmidt Matthias orcid.org/0000-0002-0161-8326
has author: Ulf-Dietrich Braumann orcid.org/0000-0002-0987-4498
has documentation: https://www.ufz.de/index.php%3Fen%3D47216
has documentation: Documentation
has function: operation_0337
has function: operation Image registration
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL 3.0
has location: correlia
has location: GitHUB
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: jmi.12928
has reference publication: Correlia: an ImageJ plug-in to co-register and visualise multimodal correlative micrographs FLORENS ROHDE, ULF-DIETRICH BRAUMANN, MATTHIAS SCHMIDT. Journal of Microscopy 2020
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
has usage example: acs.est.2c07340
has usage example: Correlative Imaging of the Rhizosphere: A Multimethod Workflow for Targeted Mapping of Chemical Gradients
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2023-03-06T14:04:44
modified: 2023-03-06T14:17:29
title: Correlia
comment: Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The software is developed at ProVIS - Centre for Correlative Microscopy and is specifically designed for the needs of chemical microscopy involving various micrographs as well as chemical maps at different resolutions and field-of-views.

count-chromosomes
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/427
created: 2013-10-11T13:08:41
modified: 2017-09-13T10:03:47
title: Count Chromosomes

counting-clumped-cells
type: software
has author: [kaye11](http://stackoverflow.com/users/2307398/kaye11), Curtis Ruden
has documentation: imagej-counting-clumped-cells
has function: operation Cell counting
has function: operation Cell segmentation
has location: imagej-counting-clumped-cells
has location: Stackoverflow: ImageJ counting clumped cells
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-11-09T00:41:10
modified: 2018-05-14T20:52:28
title: Counting Clumped Cells
comment: A workflow combining ImageJ macro and manually using Trainable Weka Segmentation plugin for counting clumped cells.

counting-foci-imagej
type: software
has author: Peter Bankhead
has documentation: Find-maxima-algorithm-discription-td3683914.html
has documentation: Algorithm of Find Maxima (ImageJ mailing list)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T17:38:28
modified: 2018-06-09T00:41:40
title: Counting foci in ImageJ
comment: Various ways are proposed in different websites for example: - [Count the number of foci](https://microscopy.duke.edu/guides/count-nuclear-foci-ImageJ) - [IJ Forum: How to utilize ImageJ to count foci per nucleus](http://forum.imagej.net/t/how-to-utilize-imagej-to-count-foci-per-nucleus/9257) - [PDF: Two Ways to Count Cells with ImageJ](https://www.researchgate.net/profile/Alexander_Chockley3/post/How_to_count_gamma_H2AX_foci_in_cells_with_the_help_of_imageJ_software/attachment/59d652df79197b80779aafbf/AS%3A514570208935936%401499694506877/download/cell+counting+automated+and+manual.pdf) Here, a workflow template using ImageJ's build-in `Find Maxima` ( `Process -> Find Maxima`) is explained. It can be used for many 2D counting-related tasks. For counting small, bright foci (dots), set Output type to be Point Selection. If too many points are detected, the number may be reduced using one or more of the following methods: Apply a filter to reduce noise, e.g. Process -> Filters -> Gaussian Blur... prior to running Find Maxima Set a minimum threshold with Image -> Adjust -> Threshold... prior to running Find Maxima, then use the Above lower threshold option within the dialog box Increase the Noise tolerance value (which effectively acts as a local threshold) The resulting point selection can be modified (points added/removed) by the Multi-Point tool. After the points are available, final measurements can be made using Analyze -> Measure.

cover-maker
type: software
has author: Schindelin, Johannes
has author: Tomancak, Pavel
has implementation: http://biii.eu/taxonomy/term/4340
has location: Cover Maker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-15T16:27:39
title: Cover Maker
comment: This plugin explores the algorithms for reconstructing scientific images as a combination of other scientific images drawing from a large database of scientific imagery.

create-new-trakem-project-fiji
type: software
has type: http://biii.eu/taxonomy/term/8
created: 2018-01-30T16:32:31
modified: 2018-01-30T16:33:33
title: Create new TrakEM project in Fiji

createbatchfiles
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/fileprocessing.html%3Fhighlight%3Dcreatebatchfiles%23module-cellprofiler.modules.createbatchfiles
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-03T08:11:52
title: CreateBatchFiles
comment: Produces files that allow individual batches of images to be processed separately on a cluster of computers.

creating-imagej-plugin-command
type: software
has author: Curtis Rueden
has documentation: https://www.youtube.com/watch%3Fv%3DYIWpoBnnLio
has documentation: Online video tutorial
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has license: Simplified BSD
has location: example-imagej-command
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1377
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2018-10-18T13:27:00
modified: 2018-10-18T13:34:19
title: Creating an ImageJ plugin / command
comment: The best way to start writing an ImageJ2 plugin (ImageJ2 developers call it command and not plugin) is to download the example command from github and modify it. There is a video tutorial on the whole workflow on how to do this on youtube.

creatools
type: software
has author: Cervenansky, Frederic
has author: Davila, Eduardo
has author: Mouton, Claire
has author: Orkisz, Maciej
has author: Pop, Sorina Caramasu
has author: Roux, Jean-Pierre
has implementation: http://biii.eu/taxonomy/term/4339
has location: CreaTools home
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/92
created: 2013-10-11T13:08:46
modified: 2019-10-17T15:57:49
title: CreaTools
comment: The CreaTools are a suite of medical image processing and visualization software and development tools. They are developed by CREATIS, a research unit with extensive experience in the medical image processing field.

crimage
type: software
has author: Henrik Failmezger, Yinyin Yuan, Oscar Rueda, Florian Markowetz
has DOI: B9.bioc.CRImage
has DOI: CRimage package doi
has documentation: CRImage.pdf
has documentation: Reference manual
has function: operation 2990
has implementation: http://biii.eu/taxonomy/term/4340
has location: CRImage
has location: Home Page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has topic: topic High content screening
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1152
created: 2019-02-03T17:14:01
modified: 2019-02-03T18:41:52
title: CRImage
comment: CRImage a package to classify cells and calculate tumour cellularity CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

crop-5d
type: software
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has location: crop-5d
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/835
created: 2013-10-11T13:08:44
modified: 2019-10-17T14:34:47
title: Crop 5D
comment: Select a portion of a sequence in all 5 dimensions.

csbdeep-toolbox-content-aware-image-restoration-care-fiji
type: software
has author: Jug, Florian orcid.org/0000-0002-8499-5812
has author: Schmidt, Uwe orcid.org/0000-0003-1649-2057
has author: Weigert, Martin
has DOI: s41592-018-0216-7
has DOI: 10.1038/s41592-018-0216-7
has documentation: csbdeep.bioimagecomputing.com
has documentation: general website for csbdeep
has function: operation Image deconvolution
has function: operation Image reconstruction
has function: operation Projection
has function: operation RBPObKBKIMwjdLygBOlvojW
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD 3-Clause License
has location: CSBDeep-in-Fiji
has location: CSBDeep in Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41592-018-0216-7
has reference publication: Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3385
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-05-07T16:11:35
modified: 2023-04-27T10:26:11
title: CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji
comment: Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.

csbdeep-toolbox-content-aware-image-restoration-care-knime
type: software
has function: operation Image deconvolution
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has topic: topic 3385
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
requires: http://biii.eu/node/1130
created: 2018-05-07T16:21:56
modified: 2021-05-19T17:49:27
title: CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Knime
comment: Deep learning based restoration, with guidelines for training. See also the Fiji plugin.

ctrax-caltech-multiple-fly-tracker
type: software
has author: Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson
has license: ?
has location: ctrax.sourceforge.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2014-12-08T17:16:55
modified: 2017-09-12T18:04:02
title: Ctrax - Caltech Multiple Fly Tracker
comment: Well maintained and documented project that includes a core tracking incl. GUI as well as Matlab toolboxes to (1) correct tracking results and (2) analyze fly behavior. >Ctrax is an open-source, freely available, machine vision program for estimating the positions and orientations of many walking flies, maintaining their individual identities over long periods of time. It was designed to allow high-throughput, quantitative analysis of behavior in freely moving flies. Our primary goal in this project is to provide quantitative behavior analysis tools to the neuroethology community, thus we've endeavored to make the system adaptable to other labs' setups. We have assessed the quality of the tracking results for our setup, and found that it can maintain fly identities indefinitely with minimal supervision, and on average for 1.5 fly-hours automatically.

cvmatchtemplate
type: software
has documentation: tuto1
has documentation: Tutorial for cvMatch_Template
has function: operation Image segmentation
has function: operation RDetoixS3xEu0agR2CebaoB
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: template-matching-ij-plugin
has location: Template Matching and Slice Alignment--- ImageJ Plugins
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: C0LC00641F
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic_0611
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
requires: http://biii.eu/node/38
created: 2018-05-08T03:12:52
modified: 2018-05-09T02:06:17
title: cvMatch_Template
comment: It implements the template matching function from the OpenCV library. The java interface of OpenCV was done through the javacv library. It is quite similar as the existing template matching plugin but runs much faster and users could choose among six matching methods: 1.Squared difference 2.Normalized squared difference 3.Cross-correlation 4.Normalized cross-correlation 5.Correlation coefficient 6.Normalized correlation coefficient The detailed algorithms could be found here. The cvMatch_Template will search a specific object (image pattern) over an image of interest by the user-specified method.

cython
type: software
has documentation: #documentation
has location: #download
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: index.html
has usage example: Getting Started
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-09-09T20:49:25
modified: 2023-04-26T15:20:36
title: cython
comment: The Cython language is a superset of the Python language that additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, embedding CPython into existing applications, and for fast C modules that speed up the execution of Python code.

cytomine
type: software
has author: Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel
has documentation: doc.cytomine.be
has documentation: Cytomine documentation
has function: operation 2409
has function: operation 3553
has license: Apache2
has location: www.cytomine.be
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: btw013
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
has usage example: #publications
openess: http://biii.eu/taxonomy/term/3575
created: 2016-06-01T13:16:16
modified: 2018-10-18T15:38:19
title: Cytomine
comment: Cytomine is a rich internet application using modern web and distributed technologies (Grails, HTML/CSS/Javascript, Docker), databases (spatial SQL and NoSQL), and machine learning (tree-based approaches with random subwindows) to foster active and distributed collaboration and ease large-scale image exploitation. It provides remote and collaborative principles, rely on data models that allow to easily organize and semantically annotate imaging datasets in a standardized way (using user-defined ontologies associated to regions of interest), efficiently support high-resolution multi-gigapixel images (incl. major digital scanner image formats), and provide mechanisms to readily proofread and share image quantifications produced by any image recognition algorithms. By emphasizing collaborative principles, the aim of Cytomine is to accelerate scientific progress and to significantly promote image data accessibility and reusability. Cytomine allows to break common practices in this domain where imaging datasets, quantification results, and associated knowledge are still often stored and analyzed within the restricted circle of a specific laboratory. This software is e.g. being used by life scientists in to help them better evaluate drug treatments or understand biological processes directly from whole-slide tissue images (digital histology), by pathologists to share and ease their diagnosis, and by teachers and students for pathology training purposes. It is also used in various microscopy applications. Cytomine can be used as a stand-alone application (e.g. on a laptop) or on larger servers for collaborative works. Cytomine implements object classification, image segmentation, content-based image retrieval, object counting, and interest point detection algorithms using machine learning.

cytoochip-analysis
type: software
has author: Sébastien
has documentation: cytoochip-analysis-macro
has documentation: Online documentation
has location: cytoochip-analysis-macro
has location: CytooChip Analysis site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T14:21:29
modified: 2023-05-02T11:26:49
title: CytooChip Analysis
comment: This macro is a plugin macro to the "Intelligent Imaging" workflow. It detects the Cytoo patterns (specific fluorsecence channel) and computes the occupancy (number of cells) of each pattern by analyzing the images of the DAPI channel. The analysis function can be easily extended to, for instance, only select the cells that are well spread on the patterns (by analyzing a third channel with a properly chosen marker of the cytoplasm).

cytopacq
type: software
has author: MICHAL KOZUBEK
has documentation: simulator.html
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4342
has location: simulator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:25:15
title: CytoPacq

daman
type: software
has author: E. Labruyère
has author: J. -C. Olivo-Marin
has author: R. Sarkar
has author: S. Mukherjee
has comparison: tmi.2022.3203022
has comparison: results are compared against two unsupervised methods used in cell segmentation (L2S and CellStar ), and two supervised techniques ANCIS and MultiCell-Net (MCN)
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL
has location: DAMAN-Release
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: tmi.2022.3203022
has reference publication: Mukherjee S, Sarkar R, Manich M, Labruyere E, Olivo-Marin JC. Domain Adapted Multitask Learning for Segmenting Amoeboid Cells in Microscopy. IEEE Trans Med Imaging. 2023 Jan;42(1):42-54. doi: 10.1109/TMI.2022.3203022.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has topic: topic Fluorescent microscopy
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/8
has usage example: test data
has usage example: Some test data
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1476
created: 2023-05-04T21:32:35
modified: 2023-05-05T10:36:36
title: DAMAN
comment: The method proposed in this paper is a robust combination of multi-task learning and unsupervised domain adaptation for segmenting amoeboid cells in microscopy. This end-to-end framework provides a consolidated mechanism to harness the potential of multi-task learning to isolate and segment clustered cells from low contrast brightfield images, and it simultaneously leverages deep domain adaptation to segment fluorescent cells without explicit pixel-level re- annotation of the data. The entry-point to the codebase is the main.py file. The user has the option to Train the network on their own dataset Load a pre-trained model and use that for inference on their own data Note: The provided pretrained model was trained on 256x256 images. Results on different resolutions could require fine-tuning This model is trained (supervised) on brightfield, and domain adapted to fluorescence data. The results are saved as 'inference.png'

data-analysis-strategies-image-based-cell-profiling
type: software
has function: operation 2945
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Shape features
has function: operation R7MFwdgojfmkZ07yWbdcda0
has location: nmeth.4397.html
has reference publication: nmeth.4397.html
has reference publication: wiki
has reference publication: Wiki
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic High content screening
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
created: 2017-09-13T07:39:31
modified: 2023-05-03T13:53:41
title: Data-analysis strategies for image-based cell profiling
comment: Workflow of data-analysis strategies for image-based cell profiling. Image analysis (image correction, image segmentation, feature extraction) Image quality control Preprocessing extracted features Dimensionality reduction Single-cell data aggregation Measuring profile similarity Assay quality assessment Downstream analysis Examples of publications where the workflow has been used at least partly: Image-based multivariate profiling of drug responses from single cells Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Cell shape and the microenvironment regulate nuclear translocation of NF‐κB in breast epithelial and tumor cells Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes Systematic morphological profiling of human gene and allele function via Cell Painting

daybook2
type: software
has author: Argolight
has implementation: http://biii.eu/taxonomy/term/4341
has location: daybook-2
has location: Daybook2
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2019-02-03T11:29:24
modified: 2019-02-05T11:17:51
title: Daybook2
comment: Daybook 2 is the analysis software linked to argoligth slides. It tests the performance of microscopes on various levels: illumination homogeneity, field distortion, lateral resolving power, stage drift, chromatic aberrations, intensity response... It works with various file formats but requires the use of an argolight test slide.

dbscan-clustering-using-palmsiever
type: software
has author: Seamus Holden
has function: operation Cell segmentation
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/76
created: 2014-12-09T14:42:42
modified: 2018-10-19T13:28:52
title: DBSCAN clustering using PALMsiever
comment: DBSCAN (Density-based spatial clustering of applications with noise) performs multi-dimensional clustering based on the local density of points. This plugin is implemented for 2-3 dimensions.

debleach
type: software
has author: Thibault Lagache
has documentation: Debleach
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has location: Debleach
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2023-04-29T14:20:47
title: Debleach
comment: This plugins allows debleaching of time sequences of fluorescence images.

deconvolutionlab
type: software
has author: Daniel Sage
has location: deconvolution
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2018-12-20T17:45:43
title: DeconvolutionLab
comment: Released in 2007, there is a newer "remastered" version "DeconvolutionLab2" (2017)

deconvolutionlab2
type: software
has author: Donati, Lauréne
has author: Fortun, Denis
has author: Guiet, Romain
has author: Sage, Daniel
has author: Schmit, Guillaume
has author: Seitz, Arne
has author: Soulez, Ferréol
has author: Unser, Michael
has author: Vonesch, Cédric
has documentation: deconvolutionlab2
has function: operation Image deconvolution
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL 3
has location: deconvolutionlab2
has location: DeconvolutionLab2 at Bioimedical Imaging Group @ EPFL
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.ymeth.2016.12.015
has reference publication: DeconvolutionLab2: An open-source software for deconvolution microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
has usage example: microtubules-challenge.zip
has usage example: Synthetic microtubules - Small 3D data and 3D Theoretical PSF of a realistic specimen
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-12-20T18:09:36
modified: 2019-02-05T12:28:50
title: DeconvolutionLab2
comment: DeconvolutionLab2 includes a friendly user interface to run the following deconvolution algortihms: Regularized Inverse Filter, Tikhonov Inverse Filter, Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), Non-negative Least Squares, Bounded-Variable Least Squares, Van Cittert, Tikhonov-Miller, Iterative Constraint Tikhonov-Miller, FISTA, ISTA. The backbone of our software architecture is a library that contains the number-crunching elements of the deconvolution task. It includes the tool for a complete validation pipeline. Inquisitive minds inclined to peruse the code will find it fosters the understanding of deconvolution.

deepcell
type: software
has author: Covert Markus
has author: Van Valen David
has documentation: readme link.html
has documentation: Cloud usage
has function: operation Cell segmentation
has function: operation Cell tracking
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: https://simtk.org/frs/%3Fgroup_id%3D1052
has location: Deep Cell Source code and Docker image
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://doi.org/10.1101/505032
has reference publication: journal.pcbi.1005177
has reference publication: Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. Plos computational Biology 2016
has reference publication: DeepCell 2.0: Automated cloud deployment of deep learning models for large-scale cellular image analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/8
has usage example: Watershed Transform 2D Fully Convolutional.ipynb
has usage example: Fully Convolutional Watershed Distance Transform for 2D Data
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1201
requires: http://biii.eu/node/1202
created: 2019-08-26T10:09:13
modified: 2020-10-19T15:09:45
title: DeepCell
comment: DeepCell is neural network library for single cell analysis, written in Python and built using TensorFlow and Keras. DeepCell aids in biological analysis by automatically segmenting and classifying cells in optical microscopy images. This framework consumes raw images and provides uniquely annotated files as an output. The jupyter session in the read docs are broken, but the one from the GitHub are functional (see usage example )

deepclem
type: software
has author: Christian Stigloher
has author: Christoph Erbacher
has author: Philip Kollmannsberger orcid.org/0000-0002-8049-61861
has author: Rick Seifert
has author: Sebastian Britz orcid.org/0000-0002-7566-005X2
has author: Sebastian M. Markert orcid.org/0000-0001-9069-156X2
has author: Veronika Perschin
has DOI: zenodo.4095247
has DOI: Version used for the reference publication
has documentation: Deep CLEM#readme
has documentation: Installation and usage instructions
has function: operation Image registration
has function: operation R8ANfLkuHu47r739AkhxrId
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT license
has location: Deep CLEM
has location: Git Hub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: f1000research.27158.1
has reference publication: DeepCLEM: automated registration for correlative light and electron microscopy using deep learning
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3568
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1291
requires: http://biii.eu/node/428
requires: http://biii.eu/node/79
created: 2021-05-19T17:26:19
modified: 2021-05-19T17:52:10
title: DeepCLEM
comment: This Fiji plugin is a python script for CLEM registration using deep learning, but it could be applied in principle to other modalities. The pretrained model was learned on chromatin SEM images and fluorescent staining, but a script is also provided to train an new model, based on CSBDeep. The registration is then performed as a feature based registration, using register virtual stack plugin (which extract features and then perform RANSAc. Editing the script in python gives access to more option (such as the transformation model to be used, similarity by default. Images need to be prepared such that they contain only one channel, but channel of ineterst (to be transformed with the same transformation) can be given as input, and Transform Virtual Stack plugin can be used as well.

deepimagej
type: software
has author: Estibaliz Gómez de Mariscal
has documentation: tutorials.html
has documentation: tutorials
has function: operation Cell segmentation
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: download.html
has location: Download and installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41592-021-01262-9
has reference publication: Gómez-de-Mariscal, E. et al. DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nat Methods 18, 1192–1195 (2021)
has topic: topic 3474
has training material: http://biii.eu/node/1842
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1201
requires: http://biii.eu/node/38
created: 2020-03-03T14:08:47
modified: 2023-04-27T11:25:18
title: DeepImageJ
comment: DeepImageJ is a user-friendly plugin that enables the use of a variety of pre-trained deep learning models in ImageJ and Fiji. The plugin bridges the gap between deep learning and standard life-science applications. DeepImageJ runs image-to-image operations on a standard CPU-based computer and does not require any deep learning expertise. Training developper constructs and upload trained model, and made them available to users. Models are available in a repository here. It is macro recordable. It is advised to use DeepImageJ on a computer with GPU (CPU will likely be 20x slower)

defcon-imagej
type: software
has author: Baptiste Ottino
has author: Kyle Douglass
has documentation: latest
has function: operation Cell counting
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNUv3
has location: Kmdouglass
has location: Fiji update site, add Kmdouglass
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-05-18T10:14:09
modified: 2023-04-28T13:04:05
title: DEFCoN-ImageJ
comment: An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks

definegrid
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/other.html%3Fhighlight%3Ddefinegrid%23module-cellprofiler.modules.definegrid
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2019-10-17T15:32:58
title: DefineGrid
comment: Produces a grid of desired specifications either manually, or automatically based on previously identified objects.

definiens-developer
type: software
has license: commercial
has location: developer.definiens.com
has platform: http://biii.eu/taxonomy/term/31
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-15T18:21:22
modified: 2017-09-12T18:06:28
title: Definiens Developer
comment: Definiens is a commercial image segmentation and classification tool. The user designs a signal processing workflow by combining built-in filtering, thresholding and object classification modules. Object detection is typically done on hierarchical object levels, e.g cell level for cell objects and organelle level Nucleus and ER obejcts inside a cell object. For each object, a huge set of features (shape-based, intensity based, relations to neighbor objects...) is available and can be used for object classification or merging with neighboring objects. The classical definiens workflow is the so called bottom-up approach: In a first step, the image is segmented in numerous small objects, resulting in a heavy oversegmentation of of the target objects. Objects are then fused step by step on basis of features like relative border to neighbor object or elliptic fit of resulting (fused) object. Objects can assigned to different classes (like nucleus or cancer cell), based on their features. Weaknesses: -complex to use -closed (no API) -very expensive -relatively slow (you have to buy one license for each core) -bad 3D-visualization -time lapse analysis is possible but complicated Strengths: -powerful method to classify objects based on multiple features -2D data, especially histological data -good training material to learn software usage -detailed documentation

delaunay-voronoi
type: software
has author: Johannes Schindelin
has author: L. Paul Chew
has documentation: Delaunay Voronoi
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: Delaunay Voronoi.java
has reference publication: Source code
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:43
modified: 2019-03-08T00:55:40
title: Delaunay Voronoi
comment: >Plugin to perform Delaunay Triangulation, or draw the Voronoi Diagram for a given point ROI. This plugin comes with Fiji.

delayed-snapshot
type: software
has author: Albert Cardona
has documentation: Delayed Snapshot
has implementation: http://biii.eu/taxonomy/term/4340
has location: Delayed Snapshot
has location: Bundled with Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:46
modified: 2019-03-10T02:44:25
title: Delayed Snapshot
comment: A Jython scripting example (but is included as a menu item in Fiji) for screen capturing with certain time delay.

densitoquant
type: software
has author: The Digital Pathology Company
has function: operation 3443
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4341
has location: DensitoQuant module
has platform: http://biii.eu/taxonomy/term/30
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-11T13:08:43
modified: 2020-03-03T11:16:55
title: DensitoQuant
comment: DensitoQuant is a simple and fast, yet effective tool for IHC measurements. It measures the density of immunostain on the digital slides by distributing pixels to negative and 3 grades of positive classes by their RGB values. DensitoQuant is especially suitable for quick TMA evaluation. Analyzing a whole digital slide takes only a couple of minutes.

detection-molecules-dom
type: software
has author: Eugene Katrukha
has documentation: wiki
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has function: operation RDr8xcZEa4L3mZsslmhhee8
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: How-to-install-plugin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic Super-resolution microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-06-29T10:22:13
modified: 2018-06-29T10:27:08
title: Detection of Molecules - DoM
comment: A collection of components for super resolution image data: - Detect Molecules - Reconstruct Image - Results table - Drift correction - Chromatic correction

difference-gaussians-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.dogdetector.DoGDetector3NodeFactory#DoG Spot Detection
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2020-03-03T11:05:54
title: Difference of Gaussians (KNIME)

differentials
type: software
has author: Philippe Thévenaz
has documentation: differentials
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: differentials
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-29T18:00:11
title: Differentials
comment: Six 2D differential operations are implemented in this ImageJ plugin. - Gradient Magnitude - Gradient Direction - Laplacian - Largest Hessian - Smallest Hessian - Hessian Orientation

diffraction-psf-3d
type: software
has author: Bob Dougherty
has documentation: Diffraction-PSF-3D.htm
has implementation: http://biii.eu/taxonomy/term/4340
has license: original
has location: Diffraction PSF 3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-03-08T01:17:44
title: Diffraction PSF 3D
comment: >This plugin generates theoretical PSFs, assuming they arise only from diffraction.

diffusion-filters-tool
type: software
has author: Sorin Pop, Alexandre Dufour
has documentation: diffusion-filters-tool
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: diffusion-filters-tool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:30:21
title: Diffusion Filters Tool
comment: Some functions for PDE filtering.

dimension-swapper-knime
type: software
has documentation: org.knime.knip.base.nodes.misc.dimswap.DimensionSwapperNodeFactory#Dimension Swapper
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2020-03-03T17:09:41
title: Dimension Swapper (KNIME)

dipimage
type: software
has author: Bernd Rieger
has author: Cris Luengo
has documentation: documentation
has license: free for non-profit use, licensed for profit use
has location: dipimage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T09:04:57
modified: 2018-06-06T18:27:11
title: DIPimage
comment: DIPimage is a MATLAB toolbox for scientific image processing and analysis build on the DIPlib image library. It is a tool for teaching and research in image processing. Most operations are independent of dimensionality, and are defined for any data type that MATLAB can store. Many functions are available through a GUI, which makes them more accessible to novices. The interactive image display windows, to which images can be automatically displayed after each operation, provide great insight into the image data.DIPlib is a platform independent scientific image processing library written in C. It consists of a large number of functions for processing and analysing multi-dimensional image data. The library provides functions for performing transforms, filter operations, object generation, local structure analysis, object measurements and statistical analysis of images. Key design features include ample support for different data types (binary, integer, floating point, complex) and dimensionalities.

directionality
type: software
has author: Jan Eglinger 0000-0001-7234-1435
has author: Jean-Yves Tinevez orcid.org/0000-0002-0998-4718
has author: Johannes Schindelin
has author: Mark Hiner
has documentation: Directionality
has license: GPLv3
has location: Directionality -2.0.2
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-13T10:09:39
modified: 2017-09-13T10:45:47
title: Directionality
comment: This plugin is used to infer the preferred orientation of structures present in the input image. It computes a histogram indicating the amount of structures in a given direction. Images with completely isotropic content are expected to give a flat histogram, whereas images in which there is a preferred orientation are expected to give a histogram with a peak at that orientation. On top of the histogram, the plugin tries to generate statistics on the highest peak found. The plugin offers the possibility to generate an orientation map, where the image is colored according to its local directionality, or location orientation. The plugin is part of Fiji, can be launched through the menu: Analyze > Directionality

displaydataonimage
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/datatools.html%3Fhighlight%3Ddisplaydataonimage%23module-cellprofiler.modules.displaydataonimage
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2019-10-17T14:43:28
title: DisplayDataOnImage
comment: Produces an image with measured data on top of identified objects.

displaydensityplot
type: software
has documentation: datatools.html#displaydensityplot
has function: operation 3441
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2019-10-16T11:40:48
title: DisplayDensityPlot
comment: DisplayDensityPlot plots measurements as a two-dimensional density plot.

displayhistogram
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/datatools.html%3Fhighlight%3Ddisplayhistogram%23module-cellprofiler.modules.displayhistogram
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:44
modified: 2019-10-17T15:13:51
title: DisplayHistogram
comment: Plots a histogram of the desired measurement.

displayplatemap
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/datatools.html%3Fhighlight%3Dplatemap%23module-cellprofiler.modules.displayplatemap
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-17T15:51:37
title: DisplayPlatemap
comment: DisplayPlatemap displays a desired measurement in a plate map view.

displayscatterplot
type: software
has documentation: datatools.html#displayscatterplot
has function: operation 3441
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-16T12:40:00
title: DisplayScatterPlot
comment: DisplayScatterPlot plots the values for two measurements.

distance-analysis-diana
type: software
has author: Jean-Francois Gilles
has author: Thomas Boudier
has documentation: distance-analysis
has documentation: ImageJ DiAna
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: distance-analysis
has location: ImageJ DiAna
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: j.ymeth.2016.11.016
has reference publication: DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2016-10-07T23:43:33
modified: 2023-05-03T15:17:42
title: Distance Analysis (DiAna)
comment: This plugin allows : Calculating co-localization between objects in 3D Measuring 3D distances between nearest object, co-localized or not Getting some 3D measurements about each objects The plugin can be used with labelled images, but it also integrates tools for the segmentation of the objects. Programming language: JAVA Processes: Denoise filter Segmentation of the objects Object based co-localization and distance analysis Counting and measurements on objects

distance-map
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/710
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:51
title: Distance Map

distortion-correction
type: software
has author: Verena Kaynig
has documentation: DistortionCorrectionPlugin Manual.pdf
has documentation: PDF (Manual)
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has location: Distortion Correction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: 10.1016/j.jsb.2010.04.012
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2019-03-08T01:29:27
title: Distortion Correction
comment: This plugin comes with Fiji >This plugin can be used to estimate nonlinear distortions induced by the image acquisition process[1] . It does not require special calibration samples, but needs sufficient overlapping image areas with preferably high contrast. For further information on how to best arrange calibration images please see the documentation.

dithering
type: software
has author: Gabriel Landini
has documentation: Dithering
has function: operation 3434
has location: Dithering
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-01-10T14:00:50
title: Dithering
comment: Dithering is a type of half tone thresholding where greyscale (or RGB channel) intensity is converted into a local density of binary pixels. This is ideal for rendering images in devices with a binary output such as printers (greyscale) or with a small number of colours (colour dithering). The following methods have been implemented (there are several more): - Floyd-Steinberg - Atkinson - Jarvis-Judice-Ninke - Stucki - Bayer_2x2 - Bayer_4x4 - Bayer_8x8 - Clustered_4x4 - Random [Here is a good text explaining various dithering algorithm. ](http://www.tannerhelland.com/4660/dithering-eleven-algorithms-source-code/)

dna-microarray-image-processing-case-study
type: software
has author: Robert Bemis
has documentation: 2573-dna-microarray-image-processing-case-study
has documentation: MathWorks File Exchange: DNA MicroArray Image Processing Case Study
has function: operation Image segmentation
has function: operation Spot extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1318
requires: http://biii.eu/node/89
created: 2014-12-09T16:34:58
modified: 2018-05-29T22:36:39
title: DNA MicroArray Image Processing Case Study
comment: In this case study, MATLAB, the Image Processing and Signal Processing toolboxes were used to determine the green intensities from a small portion of a microarray image containing 4,800 spots. A 10x10 pattern of spots was detected by averaging rows and columns to produce horizontal and vertical profiles. Periodicity was determined automatically by autocorrelation and used to form an optimal length filter for morphological background removal. A rectangular grid of bounding boxes was defined. Each spot was individually addressed and segmented by thresholding to form a mask. The mask was used to isolate each spot from surrounding background. Individual spot intensity was determined by integrating pixel intensities. Finally, integrated intensities were tabulated and saved to a data file for subsequent statistical analysis to determine which genes matter most.

docker-paraviewweb
type: software
has author: Biomedical Computer Vision (BMCV)
has function: operation_0337
has function: operation Image visualisation
has location: docker-paraviewweb
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1270
requires: http://biii.eu/node/1272
created: 2018-03-16T11:51:57
modified: 2018-03-16T11:55:58
title: Docker ParaViewWeb
comment: This ParaViewWeb Docker container is used by the Galaxy Project. Paraview is an VTK based visualization server, for 3D.

dragonfly
type: software
has author: Object Research Systems Montreal
has function: operation_0337
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Image visualisation
has function: operation Interactive segmentation
has function: operation Object detection
has function: operation Shape features
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4341
has location: get-non-commercial-license.php
has location: Request a non commercial license, download link sent by representatives
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3385
has topic: topic 3474
has topic: topic Digital histology
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
has usage example: showcase-publications.html
has usage example: List of publications (including image processing publications)
openess: http://biii.eu/taxonomy/term/3576
openess: http://biii.eu/taxonomy/term/3577
created: 2019-08-13T08:32:36
modified: 2019-10-17T10:18:09
title: DragonFly
comment: Dragonfly is a software platform for the intuitive inspection of multi-scale multi-modality image data. Its user-friendly experience translates into powerful quantitative findings with high-impact visuals, driven by nuanced easy-to-learn controls. For segmentation: It provides an engine fior machine Learning, Watershed and superpixel methods, support histological data . It offers a 3D viewer, and python scripting capacities . It is free for reserach use, but not for commercial usage.

drift-correction-using-palmsiever
type: software
has author: Seamus Holden
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has location: palm-siever
has location: Github for the palm-siever plugin for drift correction
has topic: topic Super-resolution microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/76
created: 2014-12-09T14:39:00
modified: 2018-05-09T20:39:10
title: Drift correction using PALMsiever
comment: Two workflows are proposed here: one based on fiducials, the other one on cross-correlation.

drishti
type: software
has author: Limaye Ajay
has documentation: features.shtml
has documentation: Website with gallery and features
has function: operation_0337
has function: operation 2409
has function: operation Image visualisation
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4341
has location: drishti
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3452
has topic: topic R9O3HmIAjoN5IqXXXRukzzr
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-02-01T10:00:37
modified: 2018-02-01T10:08:36
title: Drishti
comment: Drishti (from Sanskrit word for "vision" or "insight") is a multi-platform, open-source volume-exploration and presentation tool. Written for visualizing tomography data, electron-microscopy data and the like.

drop-shape-analysis
type: software
has author: Aurélien Stalder
has documentation: dropanalysis
has function: operation Image processing
has function: operation Image segmentation
has location: dropanalysis
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T11:14:50
title: Drop Shape Analysis
comment: Drop Shape Analysis is a collection of two methods (DropSnake and LBADSA) for high-accuracy measure of contact angles for drop measurement.

dropsnake
type: software
has author: Aurélien Stalder
has DOI: j.colsurfa.2006.03.008
has documentation: dropanalysis
has function: operation Active contours
has implementation: http://biii.eu/taxonomy/term/4340
has location: dropanalysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: S0927775706002214
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-10-16T11:16:50
modified: 2020-10-19T15:09:57
title: DropSnake
comment: DropSnake is based on B-spline snakes (active contours) to shape and measure a drop.

dynamic-reslice
type: software
has author: Albert Cardona
has author: Jean-Yves Tinevez
has documentation: Dynamic Reslice
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Dynamic Reslice#Scripting
has usage example: Scripting
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2019-03-09T02:12:43
title: Dynamic Reslice
comment: > a dynamic version of the Reslice command. Bundled with Fiji.

dynamic-roi-profiler
type: software
has author: Albert Cardona
has documentation: Dynamic ROI Profiler
has implementation: http://biii.eu/taxonomy/term/4340
has location: Dynamic ROI Profiler
has location: Bundled with Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4801
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2019-03-11T15:57:20
title: Dynamic ROI Profiler
comment: GUI tool, to view intensity profile dynamically as the position of ROI is changed by mouse-dragging a ROI. In more recent ImageJ, the native plot-profile window is equipped with "Live" mode, so this plugin function became a part of ImageJ. This plugin is a good scripting example using Clojure (see [source code](https://github.com/fiji/fiji/blob/master/plugins/Analyze/Dynamic_ROI_Profiler.clj)).

e-snake
type: software
has author: Ricard Delgado-Gonzalo
has documentation: esnake
has function: operation Active contours
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: esnake
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: j.cagd.2011.10.005
has reference publication: j.irbm.2013.04.002
has reference publication: TIP.2011.2169975
has reference publication: Exponential splines and minimal-support bases for curve representation
has reference publication: Snakes with an Ellipse-Reproducing Property
has reference publication: Spline-based framework for interactive segmentation in biomedical imaging
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-03-09T02:50:09
title: E-Snake
comment: >This software implements an active contour (a.k.a. snake) segmentation method using exponential splines as basis functions to represent the outline of the shape. While the snake is versatile enough to provide a good approximation of any closed curve in the plane, its most important feature is that it perfectly reproduces circular and elliptical shapes. These features are very appropriate to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.

e-splines
type: software
has documentation: Esplines
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: Esplines
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1586
created: 2013-10-11T13:08:41
modified: 2019-10-16T13:02:18
title: E-splines
comment: A Mathematica package available for the symbolic computation of exponential spline related quantities: B-splines, Gram sequence, Green function, and localization filter.

easyfrap
type: software
has author: Panagiotis Kotsantis
has author: Ioanna-Eleni Symeonidou
has author: Maria Anna Rapsomaniki
has author: Nickolaos-Nikiforos Giakoumakis
has author: Stavros Taraviras
has author: Zoi Lygerou
has documentation: easyfrap quick guide.pdf
has documentation: Quick guide
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv3
has location: http://ccl.med.upatras.gr/index.php%3Fid%3Deasyfrap
has location: easyFRAP website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: bts241
has reference publication: Rapsomaniki et. al. (2012)
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T11:26:04
modified: 2023-04-29T12:02:04
title: easyFRAP
comment: Very simple application that lets you load your time-lapse intensity data to generate the normalized FRAP recovery curve and perform exponential curve fitting. Quote: The user can handle simultaneously large data sets of raw data, visualize fluorescence recovery curves, exclude low quality data, perform data normalization, extract quantitative parameters, perform batch analysis and save the resulting data and figures for further use. Our tool is implemented as a single-screen Graphical User Interface (GUI) and is highly interactive, as it permits parameterization and visual data quality assessment at various points during the analysis.

ebimage
type: software
has DOI: B9.bioc.EBImage
has DOI: EBimage package doi
has documentation: EBImage-introduction.html
has documentation: Tutorials
has function: operation 3443
has function: operation Geometrical transform
has function: operation Image processing
has function: operation Image segmentation
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4339
has license: LGPL
has location: EBImage
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: btq046
has reference publication: EBImage—an R package for image processing with applications to cellular phenotypes
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic High content screening
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1297
created: 2017-09-13T07:41:00
modified: 2023-05-02T16:48:13
title: EBImage
comment: EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data. EBImage is available through the Bioconductor software project (www.bioconductor.org). Strengths Lightweight Suitable for automated, scripted analyses All functions are documented with examples Modular links to R and Bioconductor software, notably imageHTS and cellHTS2 Community support via the Bioconductor mailing list Reproducible (image) analysis using the Sweave report-writing system

ebimage-blacktophat
type: software
has documentation: EBImage.pdf
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T11:13:41
title: EBImage blackTopHat

ebimage-bwlabel
type: software
has documentation: EBImage.pdf
has function: operation Cell counting
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T11:49:08
title: EBImage bwlabel

ebimage-channel
type: software
has documentation: EBImage.pdf
has function: operation 2409
has function: operation 3434
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1006
created: 2013-10-15T10:45:51
modified: 2019-11-14T12:09:56
title: EBImage channel

ebimage-closing
type: software
has documentation: EBImage.pdf
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T13:10:20
title: EBImage closing

ebimage-colour-mode-conversion
type: software
has author: Sklyar, Oleg
has implementation: http://biii.eu/taxonomy/term/4340
has location: EBImage.pdf
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1152
created: 2013-10-11T13:08:43
modified: 2019-10-17T10:32:14
title: EBImage Colour Mode Conversion
comment: Color space conversions between image modes.

ebimage-computefeatures
type: software
has documentation: EBImage.pdf
has function: operation Feature extraction
has function: operation Texture extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T11:45:56
title: EBImage computeFeatures

ebimage-dilate
type: software
has documentation: EBImage.pdf
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:09:20
title: EBImage dilate
comment: A function to perform morphological operation on binary and grayscale images.

ebimage-display
type: software
has documentation: EBImage.pdf
has function: operation Image visualisation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T10:26:35
title: EBImage display

ebimage-distance-map-transform
type: software
has author: Pau, Gregoire
has location: EBImage.pdf
has programming language: http://biii.eu/taxonomy/term/4236
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/710
created: 2013-10-11T13:08:44
modified: 2019-10-17T13:29:50
title: EBImage Distance Map Transform
comment: Computes the distance map transform of a binary image. The distance map is a matrix which contains for each pixel the distance to its nearest background pixel.

ebimage-distmap
type: software
has documentation: EBImage.pdf
has function: operation Distance transform
has programming language: http://biii.eu/taxonomy/term/4236
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T10:59:09
title: EBImage distmap

ebimage-erode
type: software
has documentation: EBImage.pdf
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T11:26:07
title: EBImage erode

ebimage-fill-holes
type: software
has author: Pau, Gregoire
has author: Sklyar, Oleg
has documentation: fillHull.html
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4340
has location: EBImage.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2019-10-16T14:37:23
title: EBImage Fill Holes
comment: Fill holes in objects Included into EBImage Image processing and analysis toolbox for R

ebimage-fillhull
type: software
has documentation: EBImage.pdf
has documentation: pdf
has function: operation R7MFwdgojfmkZ07yWbdcda0
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T13:03:25
title: EBImage fillHull
comment: Fill holes in objects.

ebimage-filter2
type: software
has documentation: EBImage.pdf
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has function: operation Image convolution
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T14:49:53
title: EBImage filter2
comment: Filters an image using the fast 2D FFT convolution product.

ebimage-flop
type: software
has documentation: EBImage.pdf
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T11:52:47
title: EBImage flop
comment: flop mirrors x around the image vertical axis (horizontal reflection).

ebimage-gblur
type: software
has documentation: EBImage.pdf
has function: operation Image smoothing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:17:03
title: EBImage gblur

ebimage-makebrush
type: software
has documentation: EBImage.pdf
has function: operation_0226
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T11:38:01
title: EBImage makeBrush

ebimage-median-filter
type: software
has author: Joseph Barry
has documentation: EBImage.pdf
has function: operation Image processing
has license: GNU General Public License
has location: EBImage.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:43
modified: 2019-10-16T14:55:16
title: EBImage Median Filter
comment: Process an image using Perreault’s modern constant-time median filtering algorithm.

ebimage-medianfilter
type: software
has documentation: EBImage.pdf
has documentation: pdf
has function: operation Image smoothing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:00:46
title: EBImage medianFilter

ebimage-ocontour
type: software
has documentation: EBImage.pdf
has function: operation Feature extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:21:41
title: EBImage ocontour
comment: Computes the oriented contour of objects.

ebimage-opening
type: software
has author: Andrzej Oles
has author: Ilia Kats
has documentation: EBImage.pdf
has documentation: pdf
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T10:03:19
title: EBImage opening
comment: Function to perform an erosion followed by a dilation morphological operation on binary and grayscale images.

ebimage-paintobjects
type: software
has documentation: EBImage.pdf
has function: operation_0337
has function: operation RBNng13hEB0CJD5VzSKqrfB
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T11:46:47
title: EBImage paintObjects

ebimage-propagate
type: software
has documentation: EBImage.pdf
has function: operation Image segmentation
has location: propagate.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: propagate.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/170
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:58:56
title: EBImage propagate

ebimage-rgbimage
type: software
has documentation: EBImage.pdf
has documentation: pdf
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T11:41:14
title: EBImage rgbImage
comment: rgbImage combines Grayscale images into a Color one.

ebimage-rmobjects
type: software
has author: Oleg Sklyar
has documentation: EBImage.pdf
has documentation: pdf
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:07:04
title: EBImage rmObjects
comment: deletes objects from an image by setting their pixel intensity values to 0.

ebimage-rotate
type: software
has documentation: EBImage.pdf
has function: operation Geometrical transform
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:25:40
title: EBImage rotate

ebimage-selfcomplementarytophat
type: software
has documentation: EBImage.pdf
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T10:22:36
title: EBImage selfComplementaryTopHat

ebimage-stackobjects
type: software
has documentation: EBImage.pdf
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T10:57:17
title: EBImage stackObjects

ebimage-thresh
type: software
has author: Oleg Sklyar
has documentation: EBImage.pdf
has function: operation Adaptative thresholding
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/346
created: 2013-10-15T10:45:51
modified: 2019-11-14T11:22:24
title: EBImage thresh

ebimage-tile
type: software
has documentation: EBImage.pdf
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: EBImage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-10-17T11:13:25
title: EBImage tile

ebimage-translate
type: software
has documentation: EBImage.pdf
has function: operation Geometrical transform
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T13:01:13
title: EBImage translate

ebimage-transpose
type: software
has author: Oles Andrzej
has documentation: transpose.html
has function: operation Geometrical transform
has location: transpose.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: transpose.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:43
modified: 2019-10-17T12:04:43
title: EBImage Transpose

ebimage-transpose-0
type: software
has documentation: EBImage.pdf
has documentation: pdf
has function: operation Geometrical transform
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-14T14:47:21
title: EBImage transpose
comment: Transposes an image by swapping its spatial dimensions.

ebimage-watershed-segmentation
type: software
has documentation: EBImage.pdf
has documentation: pdf
has function: operation Watershed
has location: packages
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/170
created: 2013-10-11T13:08:43
modified: 2019-10-18T14:07:51
title: EBImage Watershed Segmentation

ebimage-writeimage
type: software
has documentation: EBImage.pdf
has documentation: pdf
has function: operation 2409
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-11-13T12:13:47
title: EBImage writeImage

ec-clem
type: software
has author: Perrine Paul-Gilloteaux orcid.org/0000-0003-3903-4841
has author: Xavier Heiligenstein
has function: operation 2928
has function: operation Image registration
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2017-01-26T16:55:32
modified: 2021-05-19T17:25:34
title: eC-CLEM
comment: This plugin allows to compute a similarity (translation/rotation/scaling and flipping) transform from pair of points. It is updating the transformed image interactively such that the user get immediate feedback. The transformation is saved and can be applied to any other stack/image. Non rigid deformation can also be applied in 2D or 3D. 3D/3D,2D/3D or 3D /2D can be handled . 3D ROI are enabled, and can be checked with the 3D vtk view (size of ROI can be changed using the ROI stroke width). Some prealignment by rotating in 3D the volume is possible. Transformations can be applied directly or combined through Block Protocols (search for apply transformation). It's also provide information about the predicted Error (based on statistical prediction), either as a full color mapping, either on each points used as landmarks, and error on the discrepancy in position between points. There are video tutorials available in the web.

ec-clem-autofinder
type: software
has author: Perrine Paul-Gilloteaux orcid.org/0000-0003-3903-4841
has function: operation Image registration
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RLtOI0poPsYRHzgXbAcr2E
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has type: http://biii.eu/taxonomy/term/8
has usage example: http://biii.eu/node/50
has usage example: workflow using it
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2017-01-26T17:05:15
modified: 2017-05-05T15:15:55
title: ec-clem autofinder
comment: Automatic registration in 2D or 3D based on detection or binary mask. Takes images with detections already done on it.

eclipse
type: software
created: 2018-10-18T13:17:55
modified: 2018-10-18T13:17:55
title: Eclipse

edge-detection
type: software
has author: vannary
has implementation: http://biii.eu/taxonomy/term/4340
has location: edge-detection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2019-10-17T15:40:49
title: Edge Detection
comment: Edge detection by Deriche's method.

editobjectsmanually
type: software
has location: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/objectprocessing.html%3Fhighlight%3Deditobjectsmanually%23module-cellprofiler.modules.editobjectsmanually
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2019-10-17T14:44:31
title: EditObjectsManually
comment: The interface will show the image that you selected as the guiding image, overlaid with colored outlines of the selected objects (or filled objects if you choose). This module allows you to remove or edit specific objects by pointing and clicking to select objects for removal or editing. Once editing is complete, the module displays the objects as originally identified (left) and the objects that remain after this module (right). More detailed Help is provided in the editing window via the ‘?’ button. The pipeline pauses once per processed image when it reaches this module. You must press the Done button to accept the selected objects and continue the pipeline.

effective-image-visualization-publications-workflow-using-open-access-tools-and-concepts
type: software
has author: Christoher Schmied https://orcid.org/0000-0003-2058-1124
has author: Helena Klara Jambor https://orcid.org/0000-0003-3397-1842
has DOI: f1000research.27140.2
has documentation: https://f1000research.com/articles/9-1373
has location: DF3MQ
has reference publication: https://f1000research.com/articles/9-1373
has type: http://biii.eu/taxonomy/term/3568
has usage example: hela-cells.zip
openess: http://biii.eu/taxonomy/term/3575
created: 2021-03-04T14:56:31
modified: 2021-03-04T15:16:08
title: Effective image visualization for publications – a workflow using open access tools and concepts
comment: Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization. Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible “cheat sheet”-style format, enabling wide distribution, use, and adoption to more specific needs.

elastic-alignment-and-montage
type: software
has author: Stephan Saalfeld
has documentation: Elastic Alignment and Montage
has function: operation Image registration
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4340
has location: Elastic Alignment and Montage
has location: Bundled with Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.2072
has reference publication: S. Saalfeld, R. Fetter, A. Cardona and P. Tomancak (2012) "Elastic volume reconstruction from series of ultra-thin microscopy sections, Nature Methods, 9(7), 717-720
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:43
modified: 2023-04-26T17:15:37
title: Elastic Alignment and Montage
comment: This plugin has two components: - Elastic Montage - montaging mosaics from overlapping tiles where the tiles have non-linear relative deformation - Elastic Stack Alignment - alignment of deformed section series from serially sectioned volumes

elastix
type: software
has author: Marius Staring
has author: Stefan Klein
has documentation: wiki
has documentation: Elastix wiki
has function: operation Image registration
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4341
has location: elastix
has location: github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: TMI.2009.2035616
has reference publication: full
has reference publication: 10.1109/TMI.2009.2035616
has reference publication: 10.3389/fninf.2013.00050
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3444
has topic: topic RxfmHE99gOkUOOML5krfsJ
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-04-11T10:11:30
modified: 2023-04-30T16:12:47
title: elastix
comment: Elastix is a toolbox for rigid and nonrigid registration of (medical) images. Elastix is based on the ITK library, and provides additional algorithms for image registration. The software can be run as a single-line command, making it easy to include in larger scripts or workflows. The user needs to edit a configuration file that contains all relevant parameters for registration: transformation model, metric used to comapre images, optimization algorithm, mutliscale pyramidal representation of images... Nowadays elastix is accompanied by SimpleElastix, making it available in other languages like C++, Python, Java, R, Ruby, C# and Lua.

elevation-map
type: software
has author: Alexandre Dufour
has documentation: elevation-map
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: elevation-map
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-16T10:27:00
title: Elevation Map
comment: View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).

empanada-napari
type: software
has author: Conrad Ryan
has author: Narayan Kedar
has documentation: index.html
has documentation: Documentation
has function: operation Cell segmentation
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: empanada-napari
has location: Source Code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: j.cels.2022.12.006
has reference publication: Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1594
created: 2023-01-25T14:17:26
modified: 2023-01-25T14:51:17
title: empanada-napari
comment: The empanada-napari plugin is built to democratize deep learning image segmentation for researchers in electron microscopy (EM). It ships with MitoNet, a generalist model for the instance segmentation of mitochondria. There are also tools to quickly build and annotate training datasets, train generic panoptic segmentation models, finetune existing models, and scalably run inference on 2D or 3D data. To make segmentation model training faster and more robust, CEM pre-trained weights are used by default. These weights were trained using an unsupervised learning algorithm on over 1.5 million EM images from hundreds of unique EM datasets making them remarkably general.

endrov
type: software
has author: Johan Henriksson
has license: BSD 3-Clause, GPL
has location: www.endrov.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/321
requires: http://biii.eu/node/463
requires: http://biii.eu/node/77
requires: http://biii.eu/node/80
created: 2013-10-23T00:47:18
modified: 2017-09-13T10:12:52
title: Endrov
comment: Endrov started development in 2007 by Johan Henriksson in the group of Thomas Bürglin group / Karolinska insitutet. At that time it was merely a tool to support the analysis of C. elegans embryogenesis. It was decided to not base it on ImageJ because little of it could be reused, many of the problems came from the core design. Since then the scope of Endrov has expanded to be useful for all image processing and be able to replace ImageJ.

enhance-local-contrast-clahe
type: software
has author: Stephan Saalfeld
has function: operation Contrast enhancement
has implementation: http://biii.eu/taxonomy/term/4340
has location: Enhance Local Contrast (CLAHE)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-29T17:29:22
title: Enhance Local Contrast (CLAHE)

enhanceedges
type: software
has documentation: imageprocessing.html#enhanceedges
has function: operation R7MFwdgojfmkZ07yWbdcda0
has function: operation Contrast enhancement
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageprocessing.html#enhanceedges
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:47
modified: 2019-10-16T13:11:02
title: EnhanceEdges
comment: EnhanceEdges enhances or identifies edges in an image, which can improve object identification or other downstream image processing.

enhanceorsuppressfeatures
type: software
has documentation: imageprocessing.html#enhanceorsuppressfeatures
has function: operation R7MFwdgojfmkZ07yWbdcda0
has function: operation Contrast enhancement
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageprocessing.html#enhanceorsuppressfeatures
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:40
modified: 2019-10-16T13:13:42
title: EnhanceOrSuppressFeatures
comment: EnhanceOrSuppressFeatures enhances or suppresses certain image features (such as speckles, ring shapes, and neurites), which can improve subsequent identification of objects.

epina-image-lab
type: software
has function: operation 2928
has function: operation 3443
has function: operation Image processing
has function: operation Image registration
has location: en download.html
has location: download (test version)
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2019-11-22T05:09:27
modified: 2020-10-19T15:08:06
title: Epina Image Lab
comment: Epina ImageLab is a Microsoft Windows-based multisensor imaging tool for processing and analyzing hyperspectral images. It is a modular system consisting of a basic engine, a graphical user interface, a chemometrics toolbox and optional user-supplied modules. It supports the most important spectroscopic imaging techniques, such as UV/Vis, infrared, Raman, THz, optical emission/absorption, and mass spectrometry. On top of that Epina ImageLab enables the user to merge hyperspectral images with maps of physical properties and conventional high-resolution color photos.

erodegreyscale
type: software
has location: EBImage.pdf
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/332
requires: http://biii.eu/node/86
created: 2013-10-15T10:45:51
modified: 2017-09-13T10:11:56
title: erodeGreyScale

evaluate-3d-data-bead-calibration-sample
type: software
has author: RapidSTORM authors
has documentation: manual.pdf.gz
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/130
created: 2014-12-09T14:19:29
modified: 2023-05-03T14:34:24
title: Evaluate 3D data with a bead calibration sample
comment: as of 20180529, links are not working due to web defacement.

evaluate-spectral-demixing-measurement
type: software
has author: RapidSTORM authors
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/130
created: 2014-12-09T14:22:39
modified: 2018-05-16T01:22:53
title: Evaluate spectral demixing measurement
comment: (from the webpage) >This usage example shows how to produce two-color images from spectrally unmixed data sets. It was written for an Alexa647/Alexa700 measurement on the Würzburg 1 biplane setup as documented in [Aufmkolk2012]. The first two tasks in this example produce prerequisite knowledge for the image generation, the alignment information (Produce linear alignment matrix) and the F2 ratios, i.e. the relative intensity of fluorophores between the channels. [Aufmkolk2012] Hochauflösende Mehrfarben-Fluoeszenzmikroskopie. Sarah Aufmkolk. Julius-Maximilians-Universität Würzburg. 2012-mar.

evaluatesegmentation-tool
type: software
has author: Abdel Aziz Taha
has documentation: EvaluateSegmentation
has implementation: http://biii.eu/taxonomy/term/4339
has license: Apache License, Version 2.0
has location: EvaluateSegmentation
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4680
has reference publication: s12880-015-0068-x
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1468
requires: http://biii.eu/node/92
created: 2019-03-25T16:34:49
modified: 2019-03-25T16:39:43
title: EvaluateSegmentation Tool
comment: A command line tool that allows to quantitatively compare two volumes of binary segmentations. Implements 22 different metrics for comparing segmentations such as Dice Coefficient, Hausdorff Distance and average Distance.

event-tutorial-1
type: software
has author: Dallongeville, Stephane
has location: event-tutorial-1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:51:37
title: Event tutorial 1
comment: Details how to listen and use events provided by the main interface.

event-tutorial-2
type: software
has author: Dallongeville, Stephane
has location: event-tutorial-2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:51:37
title: Event tutorial 2
comment: Shows how to listen active sequence / viewer events.

ever-imagej-plugin
type: software
has author: Hongqiang Ma
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: EVER-ImageJ-Plugin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: s41598-021-00066-3
has reference publication: Ma, H., Jiang, W., Xu, J. et al. Enhanced super-resolution microscopy by extreme value based emitter recovery. Sci Rep 11, 20417 (2021)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2021-10-18T05:19:13
modified: 2023-04-25T17:45:39
title: EVER-ImageJ-Plugin
comment: Removal of heterogeneous background from image data of single-molecule localization microscopy, using extreme value-based emitter recovery (EVER). Quote: EVER requires no manual adjustment of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of reconstructed super-resolution images. This method is validated as an efficient way for robust nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

excel
type: software
created: 2018-05-07T16:29:29
modified: 2018-05-07T16:29:29
title: Excel

expandorshrinkobjects
type: software
has documentation: objectprocessing.html#expandorshrinkobjects
has function: operation Dilation
has function: operation Erosion
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2019-10-16T14:46:05
title: ExpandOrShrinkObjects
comment: ExpandOrShrinkObjects expands or shrinks objects by a defined distance.

exporttodatabase
type: software
has location: ExportToDatabase.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:08:42
title: ExportToDatabase

exporttospreadsheet
type: software
has location: ExportToSpreadsheet.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:10:24
title: ExportToSpreadsheet

extended-depth-field
type: software
has author: Prudencio, Alex
has author: Sage, Daniel
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: edf
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: aguet0802.html
has reference publication: forster0404.html
has reference publication: Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy Images
has reference publication: Model-based 2.5-D deconvolution for extended depth-of-field in brightfield microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:19:03
title: Extended Depth of Field
comment: This plugin provides an extended depth of field algorithm to obtain in focus microscopic images of 3D objects and organisms using different algorithms: Sobel, variance, real and complex wavelets.

extended-depth-focus
type: software
has author: B. Forster
has author: D. Sage
has author: D. Van De Ville
has author: J. Berent
has author: M. Unser
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: edf
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: aguet0802.html
has reference publication: forster0404.html
has reference publication: "Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy Images," Microsc. Res. Tech., 65(1-2), pp. 33-42, September 2004.
has reference publication: "Model-based 2.5-D deconvolution for extended depth-of-field in brightfield microscopy," IEEE Trans. Image Process., 17(7), pp. 1144-1153, July 2008.
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:43
modified: 2019-10-16T17:36:37
title: Extended Depth of Focus
comment: Wavelet-based method to merge a stack of micrographs taken at different focal positions (aligned along the optical axis) into a single, entirely focused composite image.

extract-images-pdf
type: software
has author: Gregory Jefferis
has documentation: Extract Images From PDF...
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Extract Images From PDF...
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T13:26:20
title: Extract Images From PDF
comment: This plugin allows to open images embedded in PDFs.

extractimages
type: software
has author: Christophe ????Leterrier
has location: Extract Images.ijm
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1299
requires: http://biii.eu/node/38
created: 2014-12-09T09:51:37
modified: 2018-05-19T23:31:55
title: Extract_Images
comment: A utility macro for the specified use of BioFormats plugin. Takes a folder of proprietary images formats (Zeiss zvi, lsm, czi or Nikon nd2) and extracts them to .tif images The extracted images are located in a folder defined in the menu. Other options: reset spatial scales, reads ROIs, split channels, add stage position in the name. **note**: The old name of the macro was "ZVI Extractor" and the data format was limited to ZVI, but the upgraded version includes more formats. Requires Bio-Formats plugin

ezplug-sdk
type: software
has author: Alexandre Dufour
has documentation: ezplug-sdk
has implementation: http://biii.eu/taxonomy/term/4340
has location: ezplug-sdk
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:19
title: EzPlug SDK
comment: The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive user interaction based on your algorithm’s parameters.

ezplug-tutorial
type: software
has documentation: EzPlug-Tutorial
has function: operation 3429
has location: EzPlug-Tutorial
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2023-04-29T20:18:01
title: EzPlug Tutorial
comment: The EzPlug library is meant to help developers write plug-ins fast and efficiently. This tutorial shows EzPlug's features.

fairsim
type: software
has author: Marcel Müller
has function: operation Image reconstruction
has license: GPL
has location: fairsim.github.io
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: ncomms10980
has topic: topic Super-resolution microscopy
has topic: topic RC91JqkkQnsmvg8zuG6Td7q
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-01T17:44:06
modified: 2019-01-11T11:14:35
title: fairSIM
comment: An easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses. 2662

fandplimittool
type: software
has author: Abraham, A.V, Ram, S., Chao, J, Ward, E. S, Ober, R. J.
has documentation: FandPLimitToolUserManual.pdf
has documentation: User's Manual
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has location: fandplimittool
has location: FandPLimitTool Webpage
has reference publication: https://www.osapublishing.org/oe/abstract.cfm%3Furi%3Doe-17-26-23352
has reference publication: Reference Publication
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
has usage example: O7wh41LNWJA
has usage example: Usage Video
openess: http://biii.eu/taxonomy/term/3578
created: 2019-02-23T19:48:30
modified: 2023-04-25T17:50:39
title: FandPLimitTool
comment: Software for computing single molecule localization accuracies and resolution measures The FandPLimitTool is a GUI based software module that allows users to calculate the limits to the accuracy with which parameters can be estimated from single molecule imaging data. The software supports calculation of limits for the 2D/3D location estimation problem and the 2D/3D distance-estimation/resolution problem. The location estimation problem is concerned with the task of determining the position of a single molecule and the distance-estimation/resolution problem is concerned with the task of determining the distance of separation between two single molecules. The user can calculate limits for a variety of imaging scenarios.

farsight
type: software
has license: GPLv2, and Apache 2.0
has location: www.farsight-toolkit.org
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/286
created: 2013-10-15T18:23:47
modified: 2017-09-13T10:12:36
title: FARSIGHT
comment: A General purpose image processing toolkit written in C++ based on ITK, VTK, Qt, and Boost. Main features: algorithms for cell segmentation, cell tracing, cell tracking, and vessel tracing. Registration and mosaicing algorithms for large scale datasets. Visualization tools actively linked to inspect and edit results. Strengths: - Open-source, free, multi platform, code is highly parallelized, uses git for version control - Large scale processing, also efficient visualization of such datasets. - Active learning module for classification - Most of the algorithms have been extended to handle 16-bit images, and 3D Images. - Possibility to create complex pipelines thanks to its modular architecture - Editing tools are designed to save the editing operation which can later be used to validate the algorithms performance - Advance preprocessing algorithms like curvelets, tensor voting, and wrappers around ITK-algorithms - Multiple viewers included to inspect results such as: Histograms, scatter plots, tables, kymograph, all of them linked together. - Strong emphasis to work on multichannel images (up to 40 channels) - Rich number of cell features included Weakness: - GUI is suboptimal compared to commercial packages. - Tracking module requires an external library CPLEX. - No support for brightfield images - No native interoperability with other software packages - More documentation needed / tutorial needed

fast-fourier-transform
type: software
has author: Praveen Pankajakshan, Timothée Lecomte, Stephane Dallongeville
has documentation: fast-fourier-transform
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: fast-fourier-transform
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2020-03-02T13:51:08
title: Fast Fourier Transform
comment: Fast Fourier Transform (FFT) for 2D/3D images.

fast-multilevel-thresholded-landweber-deconvolution-algorithm
type: software
has author: Unser, M.
has author: Vonesch, C.
has function: operation Image deconvolution
has location: mltldeconvolution
has reference publication: vonesch0801.html
has reference publication: vonesch0901.html
has reference publication: A Fast Multilevel Algorithm for Wavelet-Regularized Image Restoration
has reference publication: A Fast Thresholded Landweber Algorithm for Wavelet-Regularized Multidimensional Deconvolution
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:46
modified: 2019-10-16T10:17:56
title: Fast Multilevel Thresholded-Landweber Deconvolution Algorithm
comment: MultiLevel Thresholded Landweber (MLTL) algorithm is an accelerated version of the TL algorithm that was specifically developped for deconvolution problems with a wavelet-domain regularization

fastfilters3d
type: software
has author: Thomas Boudier
has documentation: http://web.archive.org/web/20160911003855/http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Afilter%253A3d_filters_with_jni%253Astart
has documentation: Online documentatoin (Archived old website image)
has function: operation Image processing
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: http://web.archive.org/web/20160911003855/http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Afilter%253A3d_filters_with_jni%253Astart
has location: Download (Archived old website image)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2023-05-03T15:41:28
title: FastFilters3D
comment: This plugin perform various 3D filters on 8-bits or 16-bits gray-levels stacks : 3D median 3D mean 3D minimum 3D maximum 3D maximum local 3D tophat (detect bright spots, TH=I-max(min(I)) )

fastsme
type: software
has author: Asm Shihavuddin orcid.org/0000-0002-4137-9374
has function: operation Projection
has implementation: http://biii.eu/taxonomy/term/4341
has location: FastSME
has location: MATLAB code on Github.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: Basu FastSME Faster and CVPR 2018 paper.html
has reference publication: FastSME: Faster and Smoother Manifold Extraction From 3D Stack.
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2019-10-15T11:03:13
modified: 2019-10-15T13:47:03
title: FastSME
comment: FastSME: Faster and Smoother Manifold Extraction From 3D Stack. 3D image stacks are routinely acquired to capture data that lie on undulating 3D manifolds yet processed in 2D by biologists. Algorithms to reconstruct the specimen morphology into a 2D representation from the 3D image volume are employed in such scenarios. In this paper, we present FastSME, which offers several improvements on the baseline SME algorithm which enables accurate 2D representation of data on a manifold from 3D volumes, however is computationally expensive. The improvements are achieved in terms of processing speed (3X-10X speed-up depending on image size), minimizing sensitivity to initialization, and also increases local smoothness of the recovered manifold resulting in better reconstructed 2D composite image. We compare the proposed FastSME against the baseline SME as well as other accessible state-of-the-art tools on synthetic and real microscopy data. Our evaluation on multiple metrics demonstrates the efficiency of the presented method in maintaining fidelity of manifold shape and hence specimen morphology.

feature-calculation-knime
type: software
has documentation: 06 Feature Calculation
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: 06 Feature Calculation:data
has location: download workflow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:46
modified: 2020-03-03T17:53:57
title: Feature Calculation (KNIME)

feature-detector
type: software
has author: Ricard Delgado-Gonzalo
has implementation: http://biii.eu/taxonomy/term/4340
has location: feature-detector
has reference publication: TPAMI.2004.44
has reference publication: 10.1109/TPAMI.2004.44
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/410
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:46
modified: 2019-10-15T16:54:54
title: Feature Detector
comment: The tool implements a series of optimized contour and ridge detectors. The filters are steerable and are based on the optimization of a Canny-like criterion. They have a better orientation selectivity than the classical gradient or Hessian-based detectors.

featurej-derivatives
type: software
has author: Erik Meijering
has documentation: derivatives
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: derivatives
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://dx.doi.org/10.1007/BF00318371
has reference publication: Representation of Local Geometry in the Visual System
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-02-25T01:34:23
modified: 2019-10-21T12:08:50
title: FeatureJ Derivatives
comment: ## Algorithm See .

featurej-hessian
type: software
has author: Meijering, Erik
has documentation: hessian
has documentation: FeatureJ Hessian page
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2020-01-23T13:01:45
modified: 2020-01-23T13:05:01
title: FeatureJ Hessian
comment: This plugin computes for each image element (pixel/voxel) the eigenvalues of the Hessian, which can be used for example to discriminate locally between plate-like, line-like, and blob-like image structures

featurej-laplacian
type: software
has author: Erik Meijering
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: laplacian
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-19T22:07:55
modified: 2023-04-25T17:19:58
title: FeatureJ Laplacian
comment: An often used Laplacian filter for enhancing signals at object boundaries and dots. It works with XY, XYZ, XYZ-T, XYZ-T-Ch1, XYZT-C1-C2 images. Distributed as a part of ImageJ plugin FeatureJ, and included in Fiji. The second URL above is the link to its Javadoc. (imagescience.feature.Laplacian). A primer for using this class in Jython script is in CMCI Jython/Fiji cookbook: FeatureJ.

ffmpeg
type: software
has function: operation 3434
has location: www.ffmpeg.org
has location: FFmpeg website
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-09-13T15:43:54
modified: 2019-03-11T16:34:20
title: FFmpeg
comment: A complete, cross-platform solution to record, convert and stream audio and video. An ImageJ plugin is available for using FFMPEG in ImageJ. Add its update sites ([see the listing here](https://imagej.github.io/list-of-update-sites/)) For handling video files in ImageJ/Fiji, [see also here](https://imagej.net/Video).

fibriltool
type: software
has author: Arezki Boudaoud
has function: operation Interactive segmentation
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: 41596 2014 BFnprot2014024 MOESM377 ESM.txt
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: nprot.2014.024
has reference publication: FibrilTool, an ImageJ plug-in to quantify fibrillar structures in raw microscopy images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-04-13T13:59:42
modified: 2023-04-26T13:30:55
title: FibrilTool
comment: Evaluates the orientation of fiber orientation pattern and plots the results in the image. It calculates gradient in x and y direction. - then calculates the eigenvector of nematic tensor, which is the orientation of the pattern.

figurej
type: software
has author: Edda Zinck
has author: Jerome Mutterer
has DOI: jmi.12069
has documentation: figurej
has documentation: FigureJ documentation
has function: operation_0337
has function: operation Montage
has implementation: http://biii.eu/taxonomy/term/4340
has location: figurej
has location: FigureJ github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: jmi.12069
has reference publication: Mutterer J., Zinck E., J. Microscopy, 2013
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-12T08:16:47
modified: 2023-04-29T09:34:50
title: FigureJ
comment: This plugin achieves easy creation of image figures for publications, reports, projects. Easy-to-design interactive figure layout. Visually assign image content to panels. High-quality image scaling and rotation. Easy and consistent panel labels and scale bars. Each panel has it's original datasource's properties and tracks achieved image processing. Save and re-open editable figures. Export as standard image formats with textual description of each panel history. Compared to Make montage, the plugin adds more flexibility to montage creation: Easy-to-design interactive figure layout. Visually assign image content to panels. High-quality image scaling and rotation. Easy and consistent panel labels and scale bars. Each panel has it's original data source's properties and tracks achieved image processing. Save and re-open editable figures. Export as standard image formats with textual description of each panel history.

fiji
type: software
has license: GPL v2 (and others: http://fiji.sc/Fiji:About)
has location: fiji.sc
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-15T18:05:47
modified: 2018-10-19T07:01:17
title: Fiji
comment: Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

fiji-cmtk-gui
type: software
has author: Jefferis Gregory orcid.org/0000-0002-0587-9355
has function: operation Image registration
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4340
has location: fiji-cmtk-gui
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1196
requires: http://biii.eu/node/79
created: 2018-01-30T16:13:18
modified: 2021-05-19T18:52:10
title: Fiji CMTK GUI
comment: Working version of a simple GUI frontend for CMTK image registration tools in Fiji

fiji-logo-3d
type: software
has location: Fiji Logo 3D
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:33
title: Fiji Logo 3D

fijiarchipelago
type: software
has author: Larry Lindsey
has documentation: FijiArchipelago
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv2
has location: FijiArchipelago
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:32:15
title: FijiArchipelago
comment: Fiji Archipelago is a tool designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other computers.

filament-tracing-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS Vessel Tracing 3D project
has function: operation Image smoothing
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has location: W FilamentTracing3D-ImageJ
has location: Neubias BIAFLOWS workflow of Filament Tracing 3D with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-25T11:49:12
modified: 2023-05-01T17:03:45
title: Filament Tracing (ImageJ)

filament-tracing-locthresh-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: VESSEL-TRACING-3D
has function: operation Local thresholding
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: W FilamentTracing3D-LocThr-IJ
has location: Neubias BIAFLOWS workflow of Filament Tracing with LocThresh ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2020-01-23T16:30:05
modified: 2023-05-01T17:01:52
title: Filament Tracing LocThresh (ImageJ)
comment: Blood vessels tracing in 3D image from 3D Gaussian blurring (user defined radius), local thresholding (user defined radius and offset) and 3D skeletonization. Dockerized version for BIAFLOWS,

filament-tracing-tubeness-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: VESSEL-TRACING-3D
has function: operation Edge detection
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: W FilamentTracing3D-Tub-IJ
has location: Neubias BIAFLOWS workflow of Filament Tracing with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1140
requires: http://biii.eu/node/38
created: 2020-01-23T16:22:13
modified: 2023-05-01T17:02:55
title: Filament Tracing Tubeness (ImageJ)
comment: Blood vessels tracing in 3D image from Tubeness filtering (user defined scale), 3D opening (radius set to 2), thresholding (user defined level) and 3D skeletonization.

file-extension
type: software
has location: File extension
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:54
title: File Extension

file-import
type: software
has location: File Import
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-03-10T02:45:54
title: File Import

fill-regions
type: software
has author: Andrzej Oles
has DOI: btq046
has documentation: EBImage.pdf
has function: operation Closing
has implementation: http://biii.eu/taxonomy/term/4341
has location: EBImage.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: https://academic.oup.com/bioinformatics/article/26/7/979/211835
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1152
created: 2013-10-11T13:08:44
modified: 2019-10-16T14:43:26
title: Fill Regions
comment: Fill regions in images.

filopodyan
type: software
has author: Butler Richard
has documentation: Filopodyan
has documentation: Git Hub
has function: operation 3443
has function: operation Image tracking
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: http://jcb.rupress.org/content/216/10/3405
has reference publication: Filopodyan: An open-source pipeline for the analysis of filopodia in JCB 2017
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has training material: http://biii.eu/node/1552
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2019-04-08T12:28:50
modified: 2019-04-19T15:01:19
title: Filopodyan
comment: Fiji plugin for detecting, tracking and quantifying filopodia

filter-toolbox-icy
type: software
has author: Alexandre Dufour
has documentation: filter-toolbox
has function: operation Image smoothing
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: filter-toolbox
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:46
modified: 2023-04-29T14:48:28
title: Filter Toolbox (Icy)
comment: Provides a selection of spatial, separable and customizable filters in 1D and 2D, with OpenCL implementation if supported.

filterobjects
type: software
has documentation: objectprocessing.html#filterobjects
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2019-10-16T13:38:24
title: FilterObjects
comment: FilterObjects eliminates objects based on their measurements (e.g., area, shape, texture, intensity).

find-cells-using-nuclear-and-membrane-fluorescence
type: software
has author: Alexandre Dufour
has function: operation Active contours
has function: operation Cell segmentation
has location: find-cells-using-nuclear-and-membrane-fluorescence
has location: Find cells using nuclear and membrane fluorescence
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-08T14:43:59
modified: 2023-04-29T13:29:21
title: Find cells using nuclear and membrane fluorescence
comment: This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and grows a contour from each nucleus to extract the cell edge in another fluorescence channel (membrane-labeling).

find-dimension-raw-image-imagej
type: software
has author: Johannes Schindelin
has documentation: Find Dimension of Raw Image
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: Find Dimension of Raw Image
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2020-03-03T17:34:04
title: Find Dimension of Raw Image (ImageJ)

find-draw-and-measure-wells-multi-well-plate-picture
type: software
has author: Laurent Gelman
has function: operation Image segmentation
has location: Gist
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T11:10:48
modified: 2018-06-05T00:48:20
title: Find, Draw and Measure Wells in a Multi-Well Plate Picture
comment: This macro recognizes wells in a picture from a multi-well plate (it works also on a picture of a single well). It is used to segment a picture to determine the number of "Colony Forming Units" in each individual well of a plate. The steps are the following: 1. Makes a 8-bit B&W picture, inverts it (=> borders will look white instead of black), resizes it (optional, this is to speed-up convolution thereafter) and find edges. 2. Convolves the obtained picture with a kernel corresponding to a thick white circle of the size of the wells. The resulting image has big "blobs" or "particles" corresponding roughly to the centers of the well. 3. The image is thresholded to remove particles not corresponding to strong hits and "Analyze particle" is run. 4. The measured parameter is the center of mass of the particles which gives the center of the well. These are saved in an array. 5. Circles are drawn and added to the ROI manager. The centers of the circles are the identified centers of mass of the particles and their radius is the expected radius of the wells in the original image.

find-focused-slices
type: software
has author: Qingzong TSENG
has documentation: find-focus
has function: operation Object detection
has function: operation Image validation
has implementation: http://biii.eu/taxonomy/term/4340
has location: find-focus
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-11-07T18:48:58
modified: 2020-03-03T09:17:25
title: Find Focused Slices
comment: An ImageJ plugin for selecting a plane in focus among multiple slices image stack. The algorithm uses normalized variance. A short tutorial is available in the plugin web page (above).

find-maxima
type: software
has author: Michael Schmid
has comparison: 1367
has documentation: 146-29.html#toc-Subsection-29.4
has function: operation Feature extraction
has function: operation Object detection
has location: 146-29.html#toc-Subsection-29.4
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-01-03T23:12:52
modified: 2019-10-29T17:33:23
title: Find Maxima

find-maxima-python
type: software
has author: Waithe, Dominic orcid.org/0000-0003-2685-4226
has comparison: 1042
has documentation: MaximaFinder
has documentation: Link to README text.
has function: operation 3443
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v3.0
has location: MaximaFinder
has location: link to jupyter notebook in Github.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1287
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1368
requires: http://biii.eu/node/1369
created: 2018-10-17T17:47:03
modified: 2021-05-26T08:05:03
title: Find Maxima (Python)
comment: Maxima finding algorithm implemented in Python recreated from implementation in Fiji(ImageJ) This is a re-implementation of the java plugin written by Michael Schmid and Wayne Rasband for ImageJ. The original java code source can be found in: https://imagej.nih.gov/ij/developer/source/ij/plugin/filter/MaximumFinder.java.html This implementation remains faithful to the original implementation but is not 100% optimised. The java version is faster but this could be alleviated by compiling c code for parts of the code. This script is simply to provide the functionality of the ImageJ find maxima algorithm to individuals writing pure python script. The algorithm works as follows: The first stage in the maxima finding algorithm is to find the local maxima. This involves processing the image with a 3x3 neighbourhood maximum filter. Once filtered this image is compared back to the original, where the pixels are the same value represents the locations of the local maxima. Typically there are far too many local maxima to be meaningful so the goal is then to merge and prune this maxima using some kind of measure of quality. In the case of algorithm a single parameter is used, the noise tolerance (Prominence). If a maxima is close to another then the maxima will be merged or removed based on the below criteria. Starting with the brightest maxima and working down the intensities: Expand out (‘flood fill’) from each maxima location. Neighbouring pixels within a noise tolerance (notl) of the maxima are scanned until the region within tolerance is exhausted. If the pixels are equal to the maxima, mark this as equal. If a greater maxima is met, ignore the active maxima. If the pixels are less than maxima, but greater than maxima minus the noise tolerance, mark as listed. Mark all ‘listed’ pixels 'processed' if they are included within a valid peak region, otherwise reset them. From the regions containing a peak, calculate the best pixel to be considered as maxima based on minimum dis…

findfoci
type: software
has author: Alex Herbert
has documentation: FindFoci.pdf
has documentation: pdf
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: findfoci
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: journal.pone.0114749
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/726
created: 2014-12-19T12:42:13
modified: 2019-10-28T11:19:42
title: FindFoci
comment: The FindFoci plugins allow the identification of peak intensity regions within 2D and 3D images. The algorithm is highly configurable and parameters can be optimised using reference images and then applied to multiple images using the batch mode. Details of the benefits of training an algorithm on multiple images can be found in the FindFoci paper: 2591

fish-quant
type: software
has author: Florian Mueller
has documentation: fish quant
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4339
has location: fish quant
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: nmeth.2406
has reference publication: FISH-quant: automatic counting of transcripts in 3D FISH images
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: fish-quant-the-sequel
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1289
requires: http://biii.eu/node/1290
requires: http://biii.eu/node/89
created: 2014-12-09T14:34:40
modified: 2020-03-03T10:36:47
title: FISH-quant
comment: Matlab toolbox to analyze single molecule mRNA FISH data. Allows counting the number of mature and nascent transcripts in 3D images. See 2513. Following toolboxes are required: - Optimization toolbox - Statistics toolbox - Image processing toolbox - (Optional) Parallel processing toolbox Input data type: 3D image Output data type: CSV

fish-signals-detection
type: software
has author: Sébastien Tosi
has function: operation Spot extraction
has location: image-j-fiji#h.p ID 228
has location: FISH Signals detection in Human Spermatozoids macro
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p ID 228
has usage example: User guide - FISH Signals detection in Human Spermatozoids
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-08T14:00:58
modified: 2023-04-28T14:03:40
title: FISH signals detection
comment: The macro segments and classifies human spermatozoids nuclei (DAPI) based on the number of FISH signals (spots) they contain. It reports the percentage of occurrences of user defined classes (combinations of spot multiplicity in the FISH channels) as well as the position (point selections) of the detected nuclei falling in these classes. The input image should be an hyperstack with 4 channels: DAPI (first channel) and three FISH channels. The images are typically obtained as a maximum intensity projection of few channels (confocal) or a single z slice acquisition (widefield). Example image available in the linked page.

fishfinder
type: software
has documentation: fishfinder
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv3
has location: downloads
has location: FISHfinder downloads
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-09T14:12:57
modified: 2018-06-01T23:00:51
title: FISHfinder
comment: Quote: > Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus extraction. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual extraction and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus extraction as a classification problem, compound Bayesian Classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters.

fishinspector
type: software
has author: Arantza Muriana
has author: Celia Quevedo
has author: Eckart Krupp
has author: Tobias R. Kießling
has author: Elisabet Teixidó
has author: Stefan Scholz
has DOI: kfy250
has DOI: DOI
has function: operation 3553
has function: operation Feature extraction
has function: operation Object detection
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RDetoixS3xEu0agR2CebaoB
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has function: operation Edge detection
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU GENERAL PUBLIC LICENSE
has location: releases
has location: Download last windows version from GitHub
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has programming language: http://biii.eu/taxonomy/term/4543
has reference publication: https://academic.oup.com/toxsci/advance-article/doi/10.1093/toxsci/kfy250/5123521
has reference publication: Original publication
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3385
has topic: topic High content screening
has topic: topic Microscopy
has topic: topic Widefield microscopy
has topic: topic R8XUtD89JCyeUaaVebe9Mkw
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/51
created: 2018-10-19T08:39:35
modified: 2018-10-19T08:56:54
title: FishInspector
comment: The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed). The recent version requires images of a lateral position. It is important that the position is precise since deviation may confound with feature annotations. Images from any source can be used. However, depending on the image properties parameters may have to be adjusted. Furthermore, images obtained with normal microscope and not using an automated position system with embryos in glass capillaries require conversion using a KNIME workflow (the workflow is available as well). As a result of the analysis the software provides JSON files that contain the coordinates of the features. Coordinates are provided for eye, fish contour, notochord , otoliths, yolk sac, pericard and swimbladder. Furthermore, pigment cells in the notochord area are detected. Additional features can be manually annotated. It is the aim of the software to provide the coordinates, which may then be analysed subsequently to identify and quantify changes in the morphology of zebrafish embryos.

fishquant
type: software
has location: fishquant module
has location: (not public?!)
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:32:58
title: FishQuant

fit-model-growth-yeast-cells
type: software
has author: Open Microscopy Environment
has function: operation 2945
has function: operation Cell counting
has implementation: http://biii.eu/taxonomy/term/4342
has location: Yeast cell growth.ipynb
has location: Jupyter Notebook from ITR
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic High content screening
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
requires: http://biii.eu/node/1343
created: 2018-08-16T12:39:47
modified: 2023-05-03T13:55:38
title: Fit a model for the growth of yeast cells
comment: This notebook uses the rOMERO-gateway and EBImage to process an Image associated to the paper 'Timing of gene expression in a cell-fate decision system'. The Image "Pos22" is taken from the dataset idr0040-aymoz-singlecell/experimentA/YDA306_AGA1y_PRM1r_Mating. It is a timelapse Image with 42 timepoints separated by 5 minutes. This Image is used to fit a model for the growth of the yeast cells. The notebook does not replicate any of the analysis of the above mentioned paper. Its purpose is mainly to demonstrate the use of Jupyter, rOMERO-gateway and EBimage. What it does: For each time point of one movie: Read the image for this time point from the IDR Threshold the images and count the cells using EBimage functions Fit an exponential model to the count of cells against time to get a coefficient of grow (exponential factor)

flagimage
type: software
has author: Carpenter, Anne
has function: operation 2990
has implementation: http://biii.eu/taxonomy/term/4340
has location: flagimage.py
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: journal.pbio.2005970
has reference publication: CellProfiler 3.0: Next-generation image processing for biology
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic High content screening
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:44
modified: 2019-10-16T15:47:34
title: FlagImage
comment: CellProfiler FlagImage module allows to assign a flag if an image meets certain measurement criteria that you specify (for example, if the image fails a quality control measurement). The value of the flag is 1 if the image meets the selected criteria (for example, if it fails QC), and 0 if it does not meet the criteria (if it passes QC).

flickrimageretrieve
type: software
has author: Nicolas Hervé
has documentation: FlickrImageRetrieve
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: FlickrImageRetrieve
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-16T13:52:25
title: FlickrImageRetrieve
comment: Grab random images from Flickr : in recent uploads in interestingness stream from tags search

flim-slim-analysis
type: software
has author: Paul Barber
has location: SLIM Curve
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3593
has programming language: http://biii.eu/taxonomy/term/4241
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T11:47:51
modified: 2018-06-09T22:41:30
title: FLIM / SLIM Analysis
comment: An exponential curve fitting library used for Fluorescence Lifetime Imaging (FLIM) and Spectral Lifetime Imaging (SLIM), available as: * [Source code as C/C++ and Java library](https://github.com/slim-curve) * [ImageJ plugin](http://fiji.sc/SLIM_Curve) * [Standalone Open-Source Windows application](https://www.assembla.com/spaces/ATD_TRI/wiki/Home) Publications: * [Barber, P.R., Proc. SPIE, 5700, 2005.pdf](http://users.ox.ac.uk/~atdgroup/publications/Barber,%20P.R.,%20Proc.%20SPIE,%205700,2005.pdf) * [Barber, P.R., J. R. Soc. Interface, 6, 2009.pdf](http://users.ox.ac.uk/%7Eatdgroup/publications/Barber,%20P.R.,%20J.%20R.%20Soc.%20Interface,%206,%202009.pdf)

flip-ebimage
type: software
has documentation: EBImage.pdf
has function: operation Geometrical transform
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2020-03-03T10:09:19
title: flip (EBImage)

flipandrotate
type: software
has documentation: imageprocessing.html#flipandrotate
has function: operation Rotation
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2019-10-16T14:05:59
title: FlipAndRotate
comment: FlipAndRotate flips (mirror image) and/or rotates an image

floodfill
type: software
has documentation: floodFill.html
has documentation: online link
has function: operation 3553
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: floodFill.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2019-10-30T12:31:19
title: floodFill

flow-display-icy
type: software
has author: Alexandre Dufour
has author: Timothée Lecomte
has documentation: Flow-Display
has function: operation_0337
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: Flow-Display
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:46
modified: 2023-04-29T14:08:20
title: Flow Display (Icy)
comment: This plugin provides a painter to visualize 2D flows. 2D Flows are couples of two sequences, one for the horizontal displacements, the other for the vertical displacements. This plugin provides a painter that draws flow arrows on top of another sequence.

flowj
type: software
has author: Jean-Yves Tinevez
has author: Michael Abràmoff
has documentation: FlowJ
has documentation: Fiji page
has function: operation Optical flow analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: flowj.htm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://doi.org/10.1109/42.887614
has reference publication: IEEE Transactions in Medical Imaging , M.D. Abràmoff, W.J. Niessen and M.A. Viergever: Objective Quantification of the Motion of Soft Tissues. IEEE TMI. 2000; 19 (10): 986-995.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:44
modified: 2019-03-11T01:02:25
title: FlowJ
comment: FlowJ is a collection of popular 2D optical flow algorithms, Lucas and Kanade, Uras, Fleet and Jepson, and Singh, in Java. Bundled with Fiji, but can also be simply installed to ImageJ as well.

fluogan
type: software
has author: Blanc-Ferraud Laure
has author: Cachia Mayeul
has documentation: FluoGAN
has documentation: Readme from github
has function: operation Image deconvolution
has function: operation Image reconstruction
has implementation: http://biii.eu/taxonomy/term/4341
has location: FluoGAN
has location: GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: hal-03790156v1
has reference publication: Preprint to appear in Inverse Problem
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Widefield microscopy
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1476
created: 2023-03-31T08:00:32
modified: 2023-03-31T08:44:02
title: FluoGAN
comment: FluoGAN is a fluorescence image deconvolution software combining the knowledge of acquisition physical model with gan. It takes a fluctuating sequence of blurred, undersampled and noisy images of the sample of interest fixed sample as input from wide field or confocal and returns a super resolved image.

fluorender
type: software
has author: Wan Yong
has documentation: fluorender.html
has function: operation Image visualisation
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4341
has license: MIT License
has location: fluorender
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has training material: http://biii.eu/node/1401
has type: http://biii.eu/taxonomy/term/8
has usage example: fluorender.html
openess: http://biii.eu/taxonomy/term/3575
created: 2018-12-09T18:48:01
modified: 2018-12-09T18:55:28
title: FluoRender
comment: FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the rendering of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples.

flying-camera
type: software
has author: Thomas Provoost, Fabrice de Chaumont
has documentation: flying-camera
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: flying-camera
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:39:31
title: Flying Camera
comment: Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.

flylimbtracker
type: software
has author: Delgado-Gonzalo Ricardo
has author: Ramdya Pavan
has author: Uhlman Virginie
has documentation: FlyLimbTracker
has documentation: Documentation page
has function: operation Active contours
has function: operation Image tracking
has function: operation Interactive segmentation
has function: operation RDsrmC9l0bZw9kGJzGMCyY8
has implementation: http://biii.eu/taxonomy/term/4340
has location: icy with flylimbtracker.zip
has location: Download flyLimbTracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: journal.pone.0173433
has reference publication: V. Uhlmann, P. Ramdya, R. Delgado-Gonzalo, R. Benton, M. Unser, FlyLimbTracker: An Active Contour Based Approach for Leg Segment Tracking in Unmarked, Freely Behaving Drosophila," PLoS ONE, vol. 12, no. 4, pp. 1-21, April 28, 2017.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3568
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/8
created: 2018-02-01T09:38:57
modified: 2018-02-01T09:59:19
title: FlyLimbTracker
comment: FlyLimbTracker is a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving Drosophila flies. This approach can be used to measure leg segment motions during a variety of locomotor and grooming behaviors. For now the plugin have to be downlaoded directly from the EPFL website (see link), not from the search bar as usual in ICY.

fmribs-linear-image-registration-tool-flirt
type: software
has author: Analysis Group, FMRIB, Oxford, UK
has documentation: FLIRT
has documentation: Flirt documentation
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4341
has location: fsldownloads registration
has location: Formular to get access to download
has platform: http://biii.eu/taxonomy/term/30
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3444
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2018-10-04T15:01:58
modified: 2018-10-04T15:14:11
title: FMRIB's Linear Image Registration Tool FLIRT
comment: FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration. FLIRT comes with a main GUI as well as three supporting guis: ApplyXFM - for applying saved transformations and changing FOVs InvertXFM - for inverting saved transformations ConcatXFM - for concatenating saved transformations

fnirt
type: software
has author: Analysis Group, FMRIB, Oxford, UK
has documentation: UserGuide
has documentation: User Guide
has function: operation Image registration
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has implementation: http://biii.eu/taxonomy/term/4341
has location: fsldownloads registration
has location: Formular to get access to download
has platform: http://biii.eu/taxonomy/term/30
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3444
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1354
created: 2018-10-04T15:14:27
modified: 2018-10-04T15:19:51
title: FNIRT
comment: Non linear registration intensity based for MRI brain exams. To be applied after FLIRT

focal
type: software
has author: A. Mazouchi, JN. Milstein
has license: Unknown
has location: focal-cluster-analysis-for-super-resolved-microscopy.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: btv630
has reference publication: 10.1093/bioinformatics/btv630
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2016-10-09T17:26:30
modified: 2017-09-13T13:22:52
title: FOCAL
comment: FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets.

focal-adhesion-analysis-server
type: software
has author: Eric A. Vitriol
has author: Klaus M. Hahn
has author: Mathew E. Berginski
has author: Shawn M. Gomez
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4342
has location: faas.bme.unc.edu
has location: Focal Adhesion Analysis Server
has reference publication: j.cell.2011.12.034
has reference publication: journal.pone.0022025
has reference publication: f1000research.2-68.v1
has reference publication: Arp2/3 Is Critical for Lamellipodia and Response to Extracellular Matrix Cues but Is Dispensable for Chemotaxis
has reference publication: High-Resolution Quantification of Focal Adhesion Spatiotemporal Dynamics in Living Cells
has reference publication: The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
created: 2014-12-09T12:56:56
modified: 2018-05-16T17:54:00
title: Focal Adhesion Analysis Server
comment: The website implements a set of computer vision algorithms designed to automatically process time-lapse images of fluorescently labeled focal adhesion proteins in motile cells. The methods associated with the processing have been published in PLOS One and Cell. The publication describes a quantitative analysis of focal adhesion dynamics that have been imaged using TIRF. All image processing steps are well explained or referenced. > To better understand the dynamic regulation of focal adhesions, we have developed an analysis system for the automated detection, tracking, and data extraction of these structures in living cells. This analysis system was used to quantify the dynamics of fluorescently tagged Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). High content time series included the size, shape, intensity, and position of every adhesion present in a living cell. These properties were followed over time, revealing adhesion lifetime and turnover rates, and segregation of properties into distinct zones.

focus-point
type: software
has author: Waithe dominic orcid.org/0000-0003-2685-4226
has comparison: 1033
has DOI: https://zenodo.org/badge/latestdoi/29305715
has documentation: releases
has documentation: Link to manual (please select for latest release).
has function: operation 2945
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v2.0
has location: releases
has location: FoCuS-point download page (please select for latest release).
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/26589275
has reference publication: FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting.
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic Statistics
has topic: topic R7Vn7GbwtqVvGWNAMGdcNW1
has topic: topic Fluctuation based microscopy
has topic: topic Fluorescence correlative spectroscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-10-17T14:59:34
modified: 2018-10-18T16:43:04
title: FoCuS-point
comment: FoCuS-point is stand-alone software for TCSPC correlation and analysis. FoCuS-point utilizes advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualization. The software has been designed to be highly user-friendly and is tailored to handle batches of data with tools designed to process files in bulk. FoCuS-point also includes advanced diffusion curve fitting algorithms which allow the parameters of the correlation functions and thus the kinetics of diffusion to be established quickly and efficiently.

focus-scan
type: software
has author: Waithe dominic orcid.org/0000-0003-2685-4226
has comparison: 1173
has DOI: zenodo.1292334
has function: operation 2945
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v3.0
has location: releases
has location: FoCuS-scan download page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://www.sciencedirect.com/science/article/pii/S1046202317302554%3Fvia%253Dihub
has reference publication: Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic Microscopy
has topic: topic RBfI2XgIsxcfKonPPluKAhK
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-10-17T10:46:16
modified: 2018-10-18T15:35:57
title: FoCuS-scan
comment: FoCuS-scan is software for processing and analysis of large-scale scanning fluorescence correlation spectroscopy (FCS) data. FoCuS-scan can correlate data acquired on conventional turn-key confocal systems and in the form of xt image carpets.

fourier-bandpass-filter
type: software
has author: Joachim Walter
has documentation: fft-filter.html
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
requires: http://biii.eu/node/38
created: 2018-06-05T01:22:18
modified: 2018-06-05T01:32:55
title: Fourier Bandpass Filter
comment: This is a plugin bundled with native ImageJ. See IJ reference for more details > [Link](https://imagej.nih.gov/ij/docs/guide/146-29.html#toc-Subsection-29.10)

fourier-ring-correlation
type: software
has author: Alex Herbert
has author: Olivier Burri
has function: operation 3443
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: Fourier Ring Correlation Plugin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth.2448
has topic: topic Super-resolution microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-10-01T16:13:54
modified: 2019-10-21T08:44:45
title: Fourier Ring Correlation
comment: Calculate the Fourier ring correlation (FRC). The FRC can be used as a resolution criterion for super resolution microscopy. The Plugin can display a plot of the FRC curve, along with the LOESS smoothed version of the curve. Finally it displays the threshold method used and the intersection of the FRC with the threshold, providing the FIRE number. It can be used on two open images or on pairs of images in batch mode. 2654 2655

fpbioimage
type: software
has author: Clemens F. Kaminski
has author: Marcus Fantham
has documentation: fpb.ceb.cam.ac.uk
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: Creative Commons Attribution - ShareAlike 4.0 International license
has location: downloads
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4728
has reference publication: nphoton.2016.273
has reference publication: Fantham, Marcus, and Clemens F. Kaminski. “A New Online Tool for Visualization of Volumetric Data.” Nature Photonics 11, no. 2 (February 2017): 69. https://doi.org/10.1038/nphoton.2016.273.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: demo
openess: http://biii.eu/taxonomy/term/3575
created: 2019-04-18T12:46:49
modified: 2020-10-19T15:09:10
title: FPBioimage
comment: >FPBioimage is a volumetric visualization tool which runs in all modern web browsers. Try the tool yourself at our example site [here](https://fpb.ceb.cam.ac.uk/).

fraclac
type: software
has author: A. Karperien, Charles Sturt University, Australia/Canada, Earth 2007-2012
has implementation: http://biii.eu/taxonomy/term/4340
has location: Introduction.htm
has location: FracLac site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-11-10T15:41:54
modified: 2019-10-30T13:18:01
title: FracLac
comment: FracLac is for digital image analysis. Use it to measure difficult to describe morphological features. FracLac is a plugin for ImageJ. It is freely available software developed and maintained by our lab at the School of Community Health, Faculty of Science, Charles Sturt University, Australia. The author of the software and project lead is also the author of this document (me, Audrey Karperien). The basic box counting algorithm was originally modified from ImageJ's box counting algorithm and H. Jelinek's NIH Image plugin, and was further elaborated based on extensive research and development. The convex hull algorithm was provided by Thomas Roy, University of Alberta, Canada. As open source software, with the continuing help of a host of users and collaborators, FracLac has evolved to a suite of fractal analysis and morphology functions.

fractal
type: software
has author: Gustavo de Medeiros
has author: Jacopo Nespolo
has author: Joel Lüthi
has author: Marco Franzon
has author: Prisca Liberali
has author: Tommaso Comparin
has documentation: fractal-analytics-platform.github.io
has documentation: github
has function: operation_0337
has function: operation 2409
has function: operation 3443
has function: operation Illumination correction
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: BSD 3-Clause
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic High content screening
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: fractal-analytics-platform.github.io
has usage example: github
openess: http://biii.eu/taxonomy/term/3575
created: 2023-04-29T07:48:41
modified: 2023-04-29T12:45:01
title: Fractal
comment: Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization. Fractal provides distributed workflows that convert TBs of image data into OME-Zarr files. The platform then processes the 3D image data by applying tasks like illumination correction, maximum intensity projection, 3D segmentation using cellpose and measurements using napari workflows. The pyramidal OME-Zarr files enable interactive visualization in the napari viewer.

fractional-splines-and-fractals
type: software
has author: M. Unser, T. Blu
has DOI: S0036144598349435
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: fractsplines-fractals
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:59:06
title: Fractional Splines and Fractals
comment: A MATLAB package is made available for computing the fractional smoothing spline estimator of a 1D signal, and for generating fBms (fractional Brownian motion).

fractional-splines-wavelets
type: software
has author: Blu, Thierry
has author: Sage, Daniel
has author: Unser, Michael
has author: Van De Ville, Dimitri
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: fractsplines
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: unser9901.html
has reference publication: "Fractional Splines and Wavelets," SIAM Review, vol. 42, no. 1, pp. 43-67, March 2000
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: demoprep.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T17:02:00
title: Fractional Splines Wavelets
comment: The fractional splines are an extension of the polynomial splines for all fractional degrees α > -1. Their basic constituents are piecewise power functions of degree α. One constructs the corresponding B-splines through a localization process similar to the classical one, replacing finite differences by fractional differences. The fractional B-splines share virtually all the properties of the classical B-splines, including the two-scale relation, and can therefore be used to define new wavelet bases with a continuously-varying order parameter

freed
type: software
has author: Andrey P
has author: Maurin Y
has function: operation 2945
has function: operation Image segmentation
has function: operation R9EjejimBB0tmnQRmZt0RhA
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4341
has license: Free but not open source
has location: free-d.versailles.inra.fr
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: 312
has usage example: 3D segmentation using free-D
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/286
created: 2016-10-05T19:56:34
modified: 2018-10-18T15:39:39
title: FreeD
comment: Free-D is a three-dimensional (3D) reconstruction and modeling software. It allows to generate, process and analyze 3D point and surface models from stacks of 2D images. Free-D is an integrated software, offering in a single graphical user interface all the functionalities required for 3D modeling. It runs on Linux, Windows, and MacOS. Free-D is developed by the Modeling and Digital Imaging team of the Institut Jean-Pierre Bourgin, INRA Versailles, France.

galaxy-image-analysis-tools
type: software
has author: Biomedical Computer Vision (BMCV)
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4339
has location: galaxy-image-analysis
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: j.jbiotec.2017.07.019
has reference publication: Publication about imaging workflows in Galaxy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1270
requires: http://biii.eu/node/1271
created: 2018-03-16T11:48:11
modified: 2018-08-07T11:43:29
title: Galaxy Image Analysis Tools
comment: Image analysis tools to be used within Galaxy

galaxy-workbench-image-analysis
type: software
has author: Bjoern Gruening
has author: Greg von Kuster
has author: Thomas Wollmann
has implementation: http://biii.eu/taxonomy/term/4341
has location: docker-galaxy-imaging
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-03-16T11:42:15
modified: 2018-03-16T11:47:36
title: Galaxy Workbench for Image Analysis
comment: Galaxy instance with tools for Image analyses shipped in a Docker container.

gaussfit-onspot
type: software
has author: Nico Stuurman
has author: Peter Haub
has author: Tobias Meckel
has documentation: GaussFit OnSpot.pdf
has documentation: GaussFit On Spot PDF
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: index.html
has location: NIH plugin page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-12-18T23:05:47
modified: 2018-12-18T23:11:54
title: GaussFit OnSpot
comment: quote: GaussFit_OnSpot is an ImageJ plugin for fitting Gaussian profiles onto selected positions in diffraction-limited images (e.g. single molecules, protein clusters, vesicles, or stars). The plugin performs a function fit in regions of interest (ROI) around spots marked by point selections in grayscale images. Single or multiple spots can be either selected manually with the Multi-point tool or automatically with the Find Maxima function. There is a PDF with more information, and also an example image.

gaussian-blur-3d-imagej
type: software
has author: Rasband, Waine
has function: operation Image smoothing
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: index.html
has location: Gaussian Blur 3D ImageJ java code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-05T13:50:28
modified: 2019-02-05T13:53:38
title: Gaussian Blur 3D (ImageJ)
comment: Performs 3D Gaussian blurring.

gaussian-blur-imagej
type: software
has author: Wayne Rasband
has documentation: process.html
has documentation: Gaussian Blur Filter
has function: operation Image processing
has location: download.html
has location: Download ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-02-01T19:07:57
modified: 2023-05-02T09:44:27
title: Gaussian blur in ImageJ
comment: This filter uses convolution with a Gaussian function for smoothing. Sigma is the radius of decay to exp(-0.5) ~ 61%, i.e. the standard deviation sigma of the Gaussian (this is the same as in Photoshop, but different from earlier versions of ImageJ, where a value 2.5 times as much had to be entered. Like all ImageJ convolution operations, it assumes that out-of-image pixels have a value equal to the nearest edge pixel. This gives higher weight to edge pixels than pixels inside the image, and higher weight to corner pixels than non-corner pixels at the edge. Thus, when smoothing with very high blur radius, the output will be dominated by the edge pixels and especially the corner pixels (in the extreme case, with a blur radius of e.g. 1e20, the image will be raplaced by the average of the four corner pixels). For increased speed, except for small blur radii, the lines (rows or columns of the image) are downscaled before convolution and upscaled to their original length thereafter.

gaussian-convolution-ebimage
type: software
has location: EBImage.pdf
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:41
modified: 2017-09-13T09:53:46
title: Gaussian Convolution (EBImage)

gaussian-noise-estimator
type: software
has author: Yoann Le Montagner
has documentation: gaussian-noise-estimator
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: gaussian-noise-estimator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/852
requires: http://biii.eu/node/880
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:46
modified: 2023-04-29T15:29:53
title: Gaussian noise estimator
comment: Automatic detection of the variance (i.e. standard deviation, power) of the noise that affects a sequence, assuming that it is a white additive Gaussian noise.

gdsc-plugins
type: software
has author: Alex Herbert
has documentation: FindFoci.pdf
has documentation: FindFoci manual (PDF)
has function: operation Spot extraction
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: gdsc plugins
has location: GDSC ImageJ Plugins
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2017-09-13T15:08:30
modified: 2018-12-16T15:47:35
title: GDSC plugins
comment: Quote: "The GDSC ImageJ plugins are a collection of analysis programs for microscopy images including colocalisation analysis and peak finding (FindFoci)." Many types of analysis besides simply finding foci detection (spot detection) is bundled in this plugin. One prominent function is "FindFoci Optimizer". This allows feeding images with spot annotation by the user (multi-point selection tool) and scans through various parameter combinations to find the best parameter set that gives the results similar to the annotation. This is almost like machine learning... but with well-established parameter types that allows you to fully understand what is going on.

gdsc-single-molecule-localisation-microscopy
type: software
has author: Alex Herbert
has DOI: wellcomeopenres.18327.1
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has implementation: http://biii.eu/taxonomy/term/4340
has location: latest
has location: GDSC-SMLM ImageJ Plugins
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-06-10T10:49:00
modified: 2023-05-02T10:19:56
title: GDSC Single Molecule Localisation Microscopy
comment: The GDSC Single Molecule Light Microscopy (SMLM) plugins is a package of tools for single molecule localisation analysis. - Fitting Plugins: get point cloud from super resolution image. - Results Plugins: organize results. - Analysis plugins - Model plugins

gelbandfitter
type: software
has author: Kenneth S. Campbell and Mihail I. Mitov, University of Kentucky
has function: operation 2945
has license: N/A (available at no cost to academic users)
has location: Gelbandfitter home.html
has platform: http://biii.eu/taxonomy/term/31
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2017-03-02T13:58:03
modified: 2018-10-18T15:35:57
title: GelBandFitter
comment: GelBandFitter is a user-friendly software specific for analysis of protein gels and estimation of relative protein content. Using non-linear regression methods to fit mathematical functions to densitometry profiles, it is able to estimate content from protein bands that partially overlap. The software is available either as Matlab code (Optimization toolbox required) or a Windows executable. Reference: Mitov, M. I., Greaser, M. L., & Campbell, K. S. (2009). GelBandFitter A computer program for analysis of closely spaced electrophoretic and immunoblotted bands. Electrophoresis, 30(5), 848851. http://doi.org/10.1002/elps.200800583

generalized-daubechies-wavelets
type: software
has author: C. Vonesch
has DOI: TSP.2007.896255
has documentation: generalized-daubechies
has function: operation Object detection
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: generalized-daubechies
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: vonesch0702.pdf
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:44
modified: 2019-10-16T14:25:32
title: Generalized Daubechies wavelets
comment: This is a set of Matlab routines for computing generalized Daubechies wavelet filters.

generalized-riesz-wavelet-toolbox-matlab
type: software
has author: Nicolas, Chenouard
has author: Unser, Michael
has author: Van De Ville, Dimitri
has documentation: steerable-wavelets
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: steerable-wavelets
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:43
modified: 2020-03-03T08:42:49
title: Generalized Riesz-Wavelet Toolbox for Matlab
comment: A toolbox that contains Matlab routines for computing the forward and backward generalized Riesz-wavelet transform of high order is provided. It includes utilities for orientation computation, coefficients steering, basic denoising, frame learning.

generate-animations-image-data
type: software
has author: Bitplane
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2014-12-09T14:45:06
modified: 2017-09-13T10:15:38
title: Generate animations from image data
comment: Imaris is a commercial 3D image visualisation and analysis tool. It can be used to produce complex 3D animations that include multiple volume and surface elements in several channels, as well as clipping planes and annotations such as text and arrows. Movies interpolate seamlessly between user-defined key frames, and properties such as viewing angle, zoom and visibility of each element can be changed during the animation. These features allow effective communication of results based on image data.

generate-bug
type: software
has location: Generate-a-bug
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2023-04-29T20:20:15
title: Generate a bug

gimp
type: software
has author: The GIMP Team
has documentation: docs
has function: operation 3434
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4341
has license: Creative Commons Attribution-ShareAlike 4.0 International License
has location: downloads
has location: GIMP > Downloads
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-05-27T14:22:52
modified: 2018-05-27T14:31:50
title: GIMP
comment: >This is the official website of the GNU Image Manipulation Program (GIMP). >GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems. It is free software, you can change its source code and distribute your changes. >Whether you are a graphic designer, photographer, illustrator, or scientist, GIMP provides you with sophisticated tools to get your job done. You can further enhance your productivity with GIMP thanks to many customization options and 3rd party plugins. ### CLI example ``` gimp -i -b '(simple-unsharp-mask "foo.png" 5.0 0.5 0)' -b '(gimp-quit 0)' ``` More details, see here: **[GIMP Batch Mode](https://www.gimp.org/tutorials/Basic_Batch/)**

global-thresholder-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.ThresholderNodeFactory3#Global Thresholder
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:41
modified: 2020-03-03T13:52:01
title: Global Thresholder (KNIME)

globals-images-simfcs-4
type: software
has author: Gratton Enrico orcid.org/0000-0002-6450-7391
has comparison: 1032
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4341
has location: globals
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic Fluorescent microscopy
has topic: topic Microscopy
has topic: topic RBfI2XgIsxcfKonPPluKAhK
has type: http://biii.eu/taxonomy/term/3567
has usage example: tutorials
has usage example: Link to tutorials
openess: http://biii.eu/taxonomy/term/3577
created: 2018-01-28T11:36:44
modified: 2018-10-17T16:47:13
title: Globals for Images SimFCS 4
comment: Software for analysis, visualization, simulation, and acquisition of data from spectroscopy and fluorescence microscopy. Fluorescence Correlation Spectroscopy (FCS) Fluorescence Lifetime Imaging (FLIM) and Phasor plots Förster Resonance Energy Transfer (FRET) Generalized Polarization (GP) and Spectral Phasors Number and Brightness (N&B) Photon Counting Histogram (PCH) Raster and Spatio-temporal Image Correlation Spectroscopy (RICS and STICS) Single Particle and Modulation Tracking (SPT, MT) Image Mean Square Displacement (iMSD) Pair correlation function (pCF)

gnu-octave
type: software
has license: GNU
has location: octave
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-11-07T20:06:26
modified: 2017-09-13T10:13:09
title: GNU Octave
comment: "GNU Octave is a high-level language, primarily intended for numerical computations."* It can also be used for image processing, statistics and plotting as well as Matlab. "GNU Octave is also freely redistributable software. You may redistribute it and/or mod- ify it under the terms of the GNU General Public License as published by the Free Software Foundation."* *

gnu-parallel
type: software
created: 2018-05-31T19:58:47
modified: 2018-05-31T19:58:47
title: GNU Parallel

golgi-segmentation-active-mask-framework
type: software
has author: G. Srinivasa, M. C. Fickus, Y. Guo, A. D. Linstedt and J. Kova?evi?
has documentation: 08 SrinivasaFGLK.html
has documentation: Documentation in zip file
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: 08 SrinivasaFGLK.html
has location: Active mask segmentation of fluorescence microscope images
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: TIP.2009.2021081
has reference publication: PMC2765110
has reference publication: Full text
has reference publication: IEEE page
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/89
created: 2013-10-24T13:59:17
modified: 2023-05-03T15:03:48
title: Golgi Segmentation by Active Mask framework
comment: Segmentation of Golgi. Sample Images can be found here.

gradient-philippe-thevenaz
type: software
has author: Philippe Thévenaz
has function: operation Image enhancement
has license: see http://bigwww.epfl.ch/thevenaz/differentials/index.html#LegalBlurb
has location: differentials
has location: Image Differentials
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-12T14:57:27
modified: 2017-09-12T15:14:21
title: gradient by Philippe Thévenaz
comment: Computes image gradient Based on the algorithm below. Splines: A Perfect Fit for Signal and Image Processing M. Unser IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999. DOI: 10.1109/79.799930 http://ieeexplore.ieee.org/document/799930/

granulometric-filtering-imagej
type: software
has author: Dimiter Prodanov
has documentation: Granulometric Filtering
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: Granulometric Filtering
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-03T11:57:22
title: Granulometric Filtering (ImageJ)

graph-cut
type: software
has author: Funke Jan
has documentation: Graph Cut
has function: operation Image segmentation
has function: operation Image smoothing
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Graph Cut
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://dl.acm.org/doi/10.5555/646596.698262
has reference publication: Based on this publication
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/326
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2020-03-03T10:28:58
title: Graph Cut
comment: The Graph Cut plugin provides a way to obtain a globally smooth binary segmentation. As input, you have to provide a gray-scale image that represents the pixel affinities for belonging to the foreground. Via a single parameter you can adjust the smoothness of the segmentation.

graph-cut-library
type: software
has author: Ondrej Danek
has documentation: index.html
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has location: graph-cut-library.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-15T10:45:51
modified: 2019-11-14T09:57:29
title: graph cut library

graphcut-2d-knime
type: software
has documentation: org.knime.knip.base.nodes.seg.graphcuts.GraphCutNodeFactory#GraphCut 2D
has function: operation Image segmentation
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-03T11:50:26
title: GraphCut 2D (KNIME)

graylevel-watershed-imagej
type: software
has author: Daniel Sage
has documentation: watershed
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has location: watershed
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: watershed
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-18T12:29:51
title: Graylevel Watershed for ImageJ
comment: The grayscale watershed segmentation is useful to segment particles in contact when the model of shape is unknown a priori.

grayscale-granulometry
type: software
has author: David Legland
has function: operation 2945
has function: operation Morphological operations
has location: ijGranulometry
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2016-10-01T17:33:29
modified: 2018-10-18T15:35:57
title: Grayscale granulometry
comment: This imageJ/Fiji plugin provides an analysis of the granulometry inside an image by mathematical morphology. It has sevral option for the structuring element to be used, and the size domain to be tested. The output will be both a curve of the remaining content of the image against the growing size of the structuring element, and the corresponding results table that could be then exported. It can deal with grayscale images directly, no need to segment the image first. This plugin can then be used to compare different texture based on some statistical analysis of the produced curve (for exemple comparison of the geometrical means to discriminate 2 textures). It is macro recordable as well. Programming Language: java Processes: successive erosion, dilation, closing or opening -> ANALYSIS User skills: Life Scientist, developers, analysts

grayscale-reconstruction-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.GrayscaleReconstructionNodeFactory#Grayscale Reconstruction
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:41
modified: 2020-03-03T13:48:15
title: Grayscale Reconstruction (KNIME)

graytocolor
type: software
has documentation: imageprocessing.html#graytocolor
has documentation: manual version 3.1.9
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: gb-2006-7-10-r100
has reference publication: journal.pbio.2005970
has reference publication: CellProfiler 3.0: Next-generation image processing for biology.
has reference publication: CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-02T16:16:51
title: GrayToColor
comment: GrayToColor takes grayscale images as input and assigns them to colors in a red, green, blue (RGB) image or a cyan, magenta, yellow, black (CMYK) image. Each color’s brightness can be adjusted independently by using relative weights.

grid
type: software
has author: Wayne Rasband
has function: operation_0226
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: Grid
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: S0165-0270(00)00228-4
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/783
created: 2013-10-11T13:08:46
modified: 2020-03-03T09:18:33
title: Grid
comment: This plugin creates a non-destructive grid of lines, crosses or points on the current image or stack. You can specify the grid type (lines, crosses or points), the area per point (in pixels or physical units), and the color.

gui-tutorial-1
type: software
has location: GUI tutorial 1
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2017-09-13T10:03:17
title: GUI tutorial 1

gui-tutorial-2
type: software
has location: GUI tutorial 2
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2017-09-13T10:02:29
title: GUI tutorial 2

h-dome-extraction
type: software
has documentation: org.knime.knip.base.nodes.proc.HDomeNodeFactory#h-Dome Extraction
has function: operation Morphological operations
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:40
modified: 2019-10-18T14:24:09
title: h-dome Extraction

h2-database-icy-plugin
type: software
has author: Hervé, Nicolas
has documentation: main.html
has documentation: H2 Database Engine
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:43
modified: 2019-10-17T11:36:24
title: H2 database Icy plugin
comment: H2 database packaged as an Icy plugin See http://www.h2database.com

hawk
type: software
has author: Cox Susan
has author: Marsh Richard
has comparison: 41592 2018 72 MOESM1 ESM.pdf
has comparison: Comparison with other methods (from the same authors)
has documentation: plugin
has documentation: Source code as zip
has function: operation Image processing
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU AFFERO
has location: 41592 2018 72 MOESM3 ESM.zip
has location: Dowload Hawk
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: s41592-018-0072-5
has reference publication: Nature Methods 2018
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic Super-resolution microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-06T08:45:27
modified: 2019-02-06T09:14:08
title: HAWK
comment: Preprocessing step for high-density analysis methods in super resolution localisation microscopy: it aims at correcting artefacts due to these approaches with based on Haar Wavelet Kernel Analysis.

hdf5-plugin-fiji-and-imagej
type: software
has author: Olaf Ronneberger
has documentation: hdf5.html
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv2
has location: hdf5.html
has location: HDF5 Plugin for ImageJ and Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2014-12-09T16:47:33
modified: 2018-05-25T16:34:22
title: HDF5 plugin for Fiji and ImageJ
comment: HDF5 is a data format for storing extremely large and complex data collections. This Fiji/ImageJ HDF5 plugin saves and loads 2D - 5D datasets with flexible options. In Fiji, the plugin is downloadable via update site "HDF5".

hdometransform3d
type: software
has author: Oliver Greß
has documentation: HDomeTransform3D.html
has documentation: Javadoc
has function: operation Morphological operations
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: Main Page
has location: MiToBo - A microscope image analysis toolbox
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: jors.103
has reference publication: A Toolbox for Image Processing and Analysis, Journal of Open Research Software, 2016, 4:e17
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: python imagej cookbook#pluginmitobo h-dome transformation
has usage example: Plugin: MiToBo h-dome transformation
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1404
requires: http://biii.eu/node/79
created: 2018-12-10T22:58:27
modified: 2018-12-11T01:00:35
title: HDomeTransform3D
comment: h-Dome transformation, useful for spot detection. Jython code example: ```python from de.unihalle.informatik.MiToBo.core.datatypes.images import MTBImage from de.unihalle.informatik.MiToBo.morphology import HDomeTransform3D from ij import IJ imp = IJ.getImage() mtb = MTBImage.createMTBImage( imp.duplicate() ) hdome = HDomeTransform3D(mtb, 10.0) hdome.runOp() mtbdone = hdome.getResultImage() imp2 = mtbdone.getImagePlus() imp2.show() ```

hello-world-tutorial
type: software
has location: Hello world tutorial
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:08:20
title: Hello world tutorial

helmholtz-analysis
type: software
has author: Dougherty Bob
has author: Schindelin Johannes
has DOI: https://doi.org/10.1117/1.2967536
has documentation: helmholtz.pdf
has documentation: Explanation of the Helmholtz Analysis ImageJ Plugin
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Helmholtz Analysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://doi.org/10.1117/1.2967536
has reference publication: Measurement of muscle disease by quantitative second-harmonic generation imaging
has topic: topic 3382
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:46
modified: 2023-05-03T10:23:14
title: Helmholtz Analysis
comment: This plugin allows to analyze the local direction and frequency of sinusoidal waves, for example muscle repetitive stripy pattern. The output are optionally smoothed lambda (inversely proportional to the frequency) and phi (direction in degrees).

hessian-philippe-thevenaz
type: software
has author: Philippe Thévenaz
has function: operation Image enhancement
has license: see http://bigwww.epfl.ch/thevenaz/differentials/index.html#LegalBlurb
has location: index.html
has location: Image Differentials
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: http://ieeexplore.ieee.org/document/799930/
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-12T15:49:05
modified: 2017-09-12T15:53:56
title: Hessian by Philippe Thévenaz
comment: Computes image Hessian Based on the algorithm described in the paper below. Splines: A Perfect Fit for Signal and Image Processing M. Unser IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999. DOI: 10.1109/79.799930 http://ieeexplore.ieee.org/document/799930/

hex-splines
type: software
has location: hexsplines
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:43
modified: 2020-03-03T12:56:24
title: Hex-splines

high-content-screening-knime
type: software
has documentation: com.knime.hub/Users/knime/Examples/99 Community/01 Image Processing/03 Applications/06 High Content Screening
has function: operation 2945
has function: operation Feature extraction
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has location: com.knime.hub/Users/knime/Examples/99 Community/01 Image Processing/03 Applications/06 High Content Screening
has location: download workflow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic High content screening
has type: http://biii.eu/taxonomy/term/3568
has usage example: com.knime.hub/Users/knime/Examples/99 Community/01 Image Processing/03 Applications/06 High Content Screening
has usage example: tutorial
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:46
modified: 2020-03-03T17:53:15
title: High-Content Screening (KNIME)

hipnat
type: software
has author: orcid.org/0000-0001-6866-1540
has documentation: Neuroanatomy
has function: operation Feature extraction
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU General Public License v3.0
has location: hIPNAT
has location: github page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-12T08:12:34
modified: 2020-03-03T16:55:35
title: hIPNAT
comment: hIPNAT (hIPNAT: Image Processing for NeuroAnatomy and Tree-like structures) is a set of tools for the analysis of images of neurons and other tree-like morphologies. It is written for ImageJ, the de facto standard in scientific image processing. It is available through the ImageJ Neuroanatomy update site.

histocat
type: software
has author: Denis Shapiro
has author: bernd Bodenmiller
has documentation: histoCAT
has documentation: Short doc, how to install
has function: operation 2945
has function: operation Cell segmentation
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4341
has location: histoCAT 1.761
has location: download latest release
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2020-12-09T13:38:41
modified: 2020-12-09T13:52:08
title: HistoCAT
comment: Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse multiplexed image cytometry data interactively. It can also export data in.fcs data for further analysis using a specialized cytometry sofwtare such as Flowjo. It can be run as a compiled standalone or from matlab.

histogram
type: software
has author: Le Montagner, Yoann
has documentation: histogram
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:44
modified: 2019-10-17T11:29:26
title: Histogram
comment: Compute and display the histogram of a sequence, with a more accurate control on the histogram parameters (such as the number of bins) than the built-in Icy widget. In particular, the histogram can be computed either over a whole sequence or over a sub-region defined by a ROI.

histogram-equalization
type: software
has author: Dufour, Alexandre
has author: Lecomte, Timothée
has documentation: histogram-equalization
has function: operation Image enhancement
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2019-10-16T17:14:52
title: Histogram Equalization
comment: Enhances the global contrast by equalizing the histogram. This plugin transforms pixel intensities so that they are uniformly distributed over the gray-scale range. It operates on the selected channel of each image of a sequence. This operation is also called "histogram flattening".

histoquant
type: software
has location: HistoQuant module
has location: not public
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-11T13:08:44
modified: 2020-03-03T20:25:46
title: HistoQuant

histosurfaces
type: software
has author: [Fabrice Duprat](https://www.ipmc.cnrs.fr/~duprat/ipmcgb.htm#debut)
has documentation: ImageJ 0histo surfaces.pdf
has documentation: Macro for calculating empty surfaces on histological slices (ex: tubules in a kidney).
has location: ImageJ 0histo arteries.txt
has location: histo_arteries ImageJ macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-11-09T00:28:39
modified: 2023-04-29T12:28:52
title: Histo_surfaces
comment: An ImageJ macro for calculating empty surfaces on histological slices (ex: tubules in a kidney).

holovibes
type: software
has author: Atlan, Michael https://scholar.google.fr/citations?user=e_K90MoAAAAJ&hl=en
has documentation: holovibes.com
has function: operation 3429
has function: operation Image reconstruction
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4341
has location: installer
has platform: http://biii.eu/taxonomy/term/31
has reference publication: https://www.osapublishing.org/abstract.cfm%3Furi%3DDH-2018-DM5F.4
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3385
has topic: topic Microscopy
has topic: topic Widefield microscopy
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has training material: http://biii.eu/node/1448
has type: http://biii.eu/taxonomy/term/3567
has usage example: https://www.youtube.com/watch%3Fv%3DAy2b1aP8_HQ%26feature%3Dyoutu.be
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/1449
created: 2019-02-19T12:47:48
modified: 2019-02-19T15:43:55
title: Holovibes
comment: Holovibes is a free software dedicated to the calculation of holograms in real-time. Input interferogram data can be grabbed from a digital camera or loaded from files recorded beforehand. Massive amounts of data can be handled robustly at high throughput, saved to disk, and visualized in real-time without any risk of frame dropping thanks to the use of several configurable input and output memory buffers. Main features Image acquisition from several digital cameras or from data files Choice of hologram rendering method Blazing-fast hologram rendering Real-time computation of spectrograms Hologram autofocus Image and video post-processing High throughput saving to disc of massive datasets Batch recording and communication with remote instruments via GPIB Requirements A PC with at least 8 GB of RAM Microsoft Windows 7/10 64-bit operating system A NVidia graphics card (GeForce GTX 700+ series) NVidia CUDA 9 A supported digital camera, or raw interferogram files Use case examples Holographic microscopy Holographic OCT Holographic vibrometry Holographic angiography Holographic plethysmography

hot-knife
type: software
has author: Saalfed lab
has function: operation 2409
has function: operation 2928
has function: operation Image stitching
has function: operation R3BGvVm77d5vFMF6f28ZiW
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL-2.0
has location: hot-knife
has location: Github Page
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic R9zg34pnGmTyzPidJj9vfJt
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2022-03-16T06:26:27
modified: 2022-03-16T06:38:14
title: hot-knife
comment: Hot-Knife is a library specifically designed for FIB-SEM data and thick sections, which includes code for flattening, deformable alignment with features and a more robust kind of block-matching, and some visualization, manual correction, and import and export tools (n5).

hough-circles
type: software
has author: Hemerson Pistori, Eduardo Rocha Costa
has function: operation Feature extraction
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: hough-circles.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-07-12T14:47:54
modified: 2019-10-21T08:59:44
title: Hough Circles
comment: This plugin applies the Hough Transform for Circles to an 8-Bit image, shows the resulting Hough Space in a new window and marks the centers of the found circles.

human-cytoplasm-nucleus-translocation-assay-using-cellprofiler
type: software
has author: Cellprofiler team
has implementation: http://biii.eu/taxonomy/term/4339
has location: #human-cytoplasm-nucleus-translocation-assay-sbs-vitra
has location: download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2014-12-08T14:46:08
modified: 2020-03-03T19:45:43
title: Human cytoplasm-nucleus translocation assay using CellProfiler
comment: In this human cytoplasm-nucleus translocation assay, learn how to load a previously calculated illumination correction function for two separate channels, measure protein content in the nucleus and cytoplasm, and calculate the ratio as a measure of translocation. This is a clumpy cell type, so studying the settings in primary object identification may be helpful for users interested in the more advanced options that module offers. More about these images can be found at the BBBC.

huygens
type: software
has function: operation Image colocalization
has function: operation Image deconvolution
has function: operation Image tracking
has function: operation Image visualisation
has function: operation Volume rendering
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has function: operation RDr8xcZEa4L3mZsslmhhee8
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: HomePage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic Light-sheet microscopy
has topic: topic Super-resolution microscopy
has topic: topic Widefield microscopy
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-11-07T20:08:25
modified: 2019-10-15T10:25:54
title: Huygens
comment: The Huygens Software Suite consists of different image processing packages with functionalities that include deconvolution, interactive analysis, and volume visualization of 2D-3D multi-channel and time series images from fluorescence microscopes such as widefield, confocal, multi-photon, spinning disk, Array Detector, STED, and Light Sheet

huygens-remote-manager
type: software
has author: Alessandra Griffa
has author: Aaron Ponti
has author: Asheesh Gulati
has author: Daniel Sevilla
has author: José Viña
has author: Niko Ehrenfeuchter
has author: Olivier Burri
has author: Torsten Stöter
has author: Volker Baecker
has documentation: www.huygens-rm.org
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4342
has license: CeCILL license
has location: www.huygens-rm.org
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-24T13:46:16
modified: 2020-03-05T10:43:31
title: Huygens Remote Manager
comment: The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.

hyphatracker
type: software
has author: Sebastian van de Linde
has documentation: 41598 2017 19103 MOESM3 ESM.pdf
has documentation: Detailed explanation of GUI and example
has function: operation 3443
has function: operation Image processing
has function: operation Image segmentation
has function: operation Image tracking
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has implementation: http://biii.eu/taxonomy/term/4340
has location: 41598 2017 19103 MOESM2 ESM.zip
has location: v1.0
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: s41598-017-19103-1
has reference publication: HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3385
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3568
has type: http://biii.eu/taxonomy/term/8
has usage example: 41598 2017 19103 MOESM3 ESM.pdf
has usage example: Example, data sets available from the paper
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-02-22T13:28:06
modified: 2018-10-18T15:32:45
title: HyphaTracker
comment: HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.

iceimarisconnector
type: software
has author: Aaron Ponti
has license: GNU Public License version 2.0
has location: http://www.scs2.net/next/index.php%3Fid%3D110
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/87
created: 2016-10-24T13:46:16
modified: 2017-09-13T10:16:45
title: IceImarisConnector
comment: IceImarisConnector is a simple commodity class that eases communication between Bitplane Imaris and MATLAB or python using the Imaris XT interface.

ics-tools
type: software
has author: Fitz Elliott
has function: operation 3443
has function: operation Optical flow analysis
has function: operation Particle tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: ICS Tools-0.5.16.zip
has location: ICS_Tools-0.5.16 zip file
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Fluctuation based microscopy
has topic: topic Fluorescence correlative spectroscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-15T11:47:39
modified: 2023-05-02T11:23:31
title: ICS tools
comment: Implementation of some image correlation spectroscopy tools

icy-0
type: software
has author: Dallongeville, Stephane
has author: de Chaumont, Fabrice orcid.org/0000-0001-7613-7204
has license: GPLv3
has location: icy.bioimageanalysis.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.2075
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-15T18:19:13
modified: 2019-02-26T10:53:53
title: Icy
comment: Reproducing an experiment doesnt stop at the bench when images are concerned. Icy is an open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope. Icy was released in April 2011 and is being developed at the Quantitative Image Analysis Unit at the Pasteur Institute in France by Jean-Christophe Olivo-Marin and his team. The goal is to provide standardized software architecture, with a visual programming framework and online repository of plugins and protocols, brought together with sophisticated content-management and communication systems for such extended reproducible research. Icy provides intuitive user interfaces for graphical protocol development for image acquisition, analysis and storage that are easy to use for biologists and developers alike. Developers should find that Icys EzPlug API library, versioning, and auditing tools make creating a custom plugin from most any source easy. Users will find the automatic error reporting, central repository and on-line community hub great for storing and sharing plugins and protocols. Icy is even developing a cloud-computing framework to address the scalability issues of high-content screening. As of this writing there are 207 plug-ins 50 scripts and 14 protocols available for download, including those for microscope control, particle tracking, three dimensional segmentation, and even spot detection using wavelets. Published in Nature Methods (Nat Methods 9(7):690-6 (2012)). Icy can be downloaded at http://icy.bioimageanalysis.org/ Strength: Open-source. Centralized repository of 205 plugins, 50 scripts and 14 protocols Rate and comment plugins 5D Search and install features directly from Icy Graphical programming with protocols Write scripts in javascript or python Automatic bug reports Native ImageJ integration 100% compatible Native Micro-Manager integration Share your plugins and protocols online Can run headl…

icy-3d-rotation
type: software
has author: Alexandre Dufour
has function: operation_0337
has function: operation Rotation
has function: operation Volume rendering
has location: 3D Rotation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2020-03-02T13:30:19
title: ICY 3D Rotation
comment: The 3D Rotation plug-in allows you to record a 360 degree rotation of the current focused 3D VTK viewer about the vertical screen axis. The 'angle step' parameter indicates the deviation in degrees between two consecutive snapshots. Increasing the angle will increase rotation speed (up to a point where it might look like jumping more than rotating) and reduce the final movie length.

icy-active-cells
type: software
has author: Nicolas Chenouard
has author: Ricard Delgado-Gonzalo
has author: Virginie Uhlmann
has documentation: active-cells
has function: operation Active contours
has function: operation Interactive segmentation
has location: active-cells
has reference publication: delgadogonzalo1501.pdf
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: active-cells
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/286
requires: http://biii.eu/node/517
requires: http://biii.eu/node/658
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-16T17:37:10
title: ICY Active Cells
comment: This plug-in implements fast active contours for image segmentation. Their representation in terms of spline curves allows for a natural and intuitive manipulation of the active contour through control points. Based on Delgado-Gonzalo et al. "Snakes on a Plane: A Perfect Snap for Bioimage Analysis"

icy-active-cells-sdk
type: software
has author: Biomedical Imaging Group
has function: operation Active contours
has function: operation Image segmentation
has function: operation Image tracking
has location: active-cells-sdk
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.irbm.2013.04.002
has reference publication: Spline-based framework for interactive segmentation in biomedical imaging
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/517
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-16T17:52:08
title: ICY Active Cells SDK
comment: This is an icy package that encapsulates tools to design and implement parametric active contours. The package provides fast 2D and 3D filters for image preprocessing, and a framework to create and evolve snakes defined by a set of control points.

icy-anisotropic-filter
type: software
has author: Alexandre Dufour
has author: Sorin Pop
has documentation: book.pdf
has documentation: a book by Weickert about anisotropic diffusion, theoretical basis of this filter
has function: operation Edge detection
has location: anisotropic-filter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/502
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:17
title: ICY Anisotropic Filter
comment: Anisotropic filter implements the classical Coherence Enhancing Diffusion Filter [Weickert]. The plugins works on the first band of a 2D, 3D and 4D sequence. 2D and 3D algorithms are proposed. For the 3D case 2 options are available: CED 1D option is the classical filter that acts mainly on the most homogeneous structure direction; CED 2D option acts on the tangential plane of the structure.

icy-annotation
type: software
has author: Stéphane Dallongeville
has author: Thomas Provoost
has function: operation_0226
has implementation: http://biii.eu/taxonomy/term/4340
has location: Annotation
has location: ICY Annotation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2020-03-02T13:51:37
title: ICY Annotation
comment: This plugin (Icy Tool) allows the user to create and edit annotations. Annotations are blocks of text that the user can put anywhere in the sequence. Run the plugin to get the GUI with all the features. Once a note is added to a sequence, left click on it to edit this one. If you closed your GUI and you have some notes on your sequence, right click and select "edit" to display the GUI. As of now, the annotations are saved when the sequence is closed, but you have to run the plugin at least once to be able to see all the annotations in the image.

icy-batch-pixel-density-measurement
type: software
has author: Fabrice de Chaumont
has documentation: Pixel-density-batch-mode
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: Pixel-density-batch-mode
has location: Pixel density (batch mode)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-09T11:30:39
modified: 2023-04-29T19:58:09
title: ICY batch pixel density measurement
comment: For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.

icy-colocalization-scatter-plot
type: software
has author: Fabrice de Chaumont
has function: operation Pixel-based colocalisation
has location: colocalization-scatter-plot
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-18T12:43:33
title: ICY Colocalization Scatter Plot
comment: ICY Plugin, creates a colocalization scatter plot based on 2 channels. This plugin can take 1 ROI as input, and provides the data to build the bubble excel graph.

icy-complex-toolbox
type: software
has author: Yoann Le Montagner
has function: operation 3443
has location: complex-toolbox
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-18T13:00:34
title: ICY Complex toolbox
comment: This plugin provides some useful functions to work with complex-valued sequences. It provides the base operation to deal with complex-valued sequences, such as real-part, imaginary-part, modulus and argument extraction, and conversion between Cartesian and polar representation.

icy-connected-component-painter
type: software
has author: Fabrice de Chaumont
has function: operation 3553
has location: connected-component-painter
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2023-05-02T16:38:32
title: ICY Connected Component Painter
comment: Add a layer on an image to display the detections

icy-context-menu
type: software
has author: Stéphane Dallongeville
has author: Thomas Provoost
has documentation: context-menu
has function: operation 3434
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has location: context-menu
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2020-03-02T13:51:08
title: ICY Context Menu
comment: ICY plugin, the right click on sequences and ROIs will open a menu with various features, such as image and ROI copy, data conversion and extraction. See documentation for more information.

icy-diagnose
type: software
has author: Fabrice de Chaumont
has implementation: http://biii.eu/taxonomy/term/4340
has location: icy-diagnose
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2020-03-03T11:16:12
title: Icy diagnose
comment: Diagnose bugs in Icy

icy-fill-holes-2d
type: software
has author: Alexandre Dufour
has function: operation Closing
has implementation: http://biii.eu/taxonomy/term/4340
has location: fill-holes-2d
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:19
title: Icy Fill Holes 2D
comment: Fills holes below a given threshold. 3D data is currently processed slice per slice.

icy-fill-holes-roi
type: software
has author: Alexandre Dufour
has documentation: fill-holes-in-roi
has function: operation Closing
has implementation: http://biii.eu/taxonomy/term/4340
has location: fill-holes-in-roi
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2023-04-29T14:26:07
title: ICY Fill holes in ROI
comment: Fills the holes in all the ROI of the active sequence (also works in Protocols).

icy-hk-means
type: software
has author: Alexandre Dufour
has function: operation 3443
has function: operation Image classification
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: HK-Means
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://ieeexplore.ieee.org/document/4761748/
has reference publication: Automated Quantification of Cell Endocytosis Using Active Contours and Wavelet
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/393
requires: http://biii.eu/node/741
requires: http://biii.eu/node/8
requires: http://biii.eu/node/819
requires: http://biii.eu/node/852
requires: http://biii.eu/node/880
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:46
modified: 2019-10-18T17:19:05
title: Icy HK-Means
comment: This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then extracts objects in a bottom-up manner using user-defined minimum and maximum object sizes. Very useful to detect clustered objects in fluorescence microscopy.

icy-label-extractor
type: software
has author: Dufour Alexandre
has documentation: label-extractor
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has location: label-extractor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2019-10-17T14:52:39
modified: 2019-10-17T14:56:27
title: Icy Label Extractor

icy-matlab-blocks
type: software
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Matlab-blocks
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/367
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2020-03-01T10:37:58
title: Icy Matlab blocks
comment: This plugin provides import and export Icy sequences into Matlab native .mat files from the protocol framework.

icy-median-filter-imagej
type: software
has author: Alexandre Dufour
has documentation: Median-filter-via-imageJ
has function: operation Image processing
has function: operation Image convolution
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-09T11:25:13
modified: 2023-04-29T20:21:37
title: ICY Median filter via ImageJ
comment: This protocol perform a median filter on the active sequence using the ImageJ rank filter plugin. Then, it converts the result back into Icy for display. An example showing passing data between ICY and ImageJ using ImagePlus object.

icy-membrane-filter
type: software
has author: Alexandre Dufour
has author: Sorin Pop
has documentation: Membrane-Filter
has function: operation Edge detection
has function: operation Image enhancement
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: membrane-filter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/6115880
has reference publication: Image filtering using anisotropic structure tensor for cell membrane enhancement in 3D microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/465
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/880
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:44
modified: 2023-04-29T14:14:51
title: Icy Membrane Filter

icy-mereotopology
type: software
has function: operation Feature extraction
has location: MereoTopology
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-16T11:47:32
title: Icy MereoTopology
comment: Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned byte of short format.

icy-microscope-remote
type: software
has function: operation 2409
has location: microscope-remote
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-16T11:41:22
title: Icy Microscope Remote

icy-middlebury-color-coder
type: software
has author: Alexandre Dufour
has author: Timothée Lecomte
has documentation: Middlebury-Color-Coder
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/909
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2020-03-02T20:36:13
title: Icy Middlebury Color Coder
comment: This plugin can display a 2D flow as a color-coded sequence, following the Middlebury color code.

icy-multi-touch-provider
type: software
has author: Alexandre Dufour
has documentation: Multi-Touch-provider
has function: operation 2409
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/672
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:30:19
title: Icy Multi-Touch provider
comment: Multi-touch provider allowing developers to let their plug-in receive rich multi-touch interaction. Currently supports Mac OS X, and generates raw finger events as well as pre-processed 2-finger gestures (pinch, drag, rotation).

icy-nherve-toolbox
type: software
has author: Nicolas Hervé
has implementation: http://biii.eu/taxonomy/term/4340
has location: NHerve-Toolbox
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/501
requires: http://biii.eu/node/615
requires: http://biii.eu/node/8
requires: http://biii.eu/node/819
created: 2013-10-11T13:08:41
modified: 2019-10-18T11:09:48
title: Icy NHerve Toolbox

icy-non-linear-filter
type: software
has author: Dufour Alexandre
has author: Pop Sorin
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: Non-linear-Filter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/11
requires: http://biii.eu/node/465
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/880
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2019-10-18T10:23:08
title: Icy Non-linear Filter

icy-opencl-lab
type: software
has author: Alexandre Dufour
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4340
has location: OpenCL-Lab
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T10:14:51
title: Icy OpenCL Lab

icy-opencv
type: software
has author: Alexandre Dufour
has documentation: OpenCV
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD
has location: OpenCV
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2018-11-07T14:06:15
modified: 2023-04-29T19:37:42
title: Icy-OpenCV
comment: OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org

icy-overlay-tutorial-1
type: software
has author: Fab and Stef
has author: Stephane Dallongeville
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Overlay-tutorial-1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T10:10:42
title: Icy Overlay tutorial 1

icy-overlay-tutorial-2
type: software
has documentation: overlay-tutorial-2
has type: http://biii.eu/taxonomy/term/3570
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:24:59
title: Icy Overlay tutorial 2
comment: A slightly different painter than Overlay tutorial 1, focusing on canvas parameters instead of image parameters.

icy-painting
type: software
has author: Dallongeville Stephane
has author: Provoost Thomas
has author: de Chaumont Fabrice
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4340
has location: Painting
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T11:06:58
title: Icy Painting

icy-particle-tracking-benchmark-generator
type: software
has author: Nicolas Chenouard
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4340
has location: Particle-tracking-benchmark-generator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1590
requires: http://biii.eu/node/741
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:43
modified: 2019-10-18T09:54:36
title: Icy Particle tracking benchmark generator

icy-pde-shock-filter
type: software
has author: Dufour Alexandre
has author: Pop Sorin
has function: operation Image enhancement
has implementation: http://biii.eu/taxonomy/term/4340
has location: PDE-Shock-Filter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/11
requires: http://biii.eu/node/465
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/880
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2019-10-18T10:19:01
title: Icy PDE Shock Filter

icy-projection
type: software
has author: Fabrice de Chaumont
has documentation: Projection
has function: operation Projection
has implementation: http://biii.eu/taxonomy/term/4340
has location: Projection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2019-10-18T11:30:18
title: Icy Projection

icy-protocols
type: software
has author: Alexandre Dufour
has documentation: protocols
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: protocols
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/320
requires: http://biii.eu/node/8
requires: http://biii.eu/node/913
created: 2017-01-26T17:05:15
modified: 2019-10-18T11:59:52
title: Icy Protocols

icy-protocols-sdk
type: software
has author: Alexandre Dufour
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4340
has location: Protocols-SDK
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:46
modified: 2019-10-18T11:21:38
title: Icy Protocols SDK

icy-ptr335-slope-computation
type: software
has author: Dufour Alexandre
has author: Pop Sorin
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: PTR335-Slope-Computation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2019-10-18T09:18:45
title: Icy PTR335 Slope Computation

icy-ring-roi
type: software
has author: de Chaumont Fabrice
has function: operation 3553
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Ring-ROI
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T11:12:35
title: Icy Ring ROI

icy-roi-color-coding
type: software
has author: Alexandre Dufour
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-color-coding
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:04:03
title: Icy ROI color coding

icy-ruler-helper
type: software
has author: Provoost Thomas
has author: de Chaumont Fabrice
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has location: Ruler-Helper
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/526
requires: http://biii.eu/node/565
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2019-10-18T11:50:45
title: Icy Ruler Helper

icy-script-block-v1
type: software
has author: Fabrice de Chaumont
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4340
has location: Script-Block-v1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-17T09:25:12
title: Icy Script Block v1

icy-spot-tracking
type: software
has author: Nicolas Chenouard
has documentation: spot-tracking
has function: operation Particle tracking
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3.0
has location: spot-tracking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/6517432
has reference publication: Multiple Hypothesis Tracking for Cluttered Biological Image Sequences
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/49
requires: http://biii.eu/node/741
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2019-10-18T09:47:28
modified: 2023-04-29T14:54:18
title: Icy Spot Tracking
comment: This plugin ships automated methods for extracting trajectories of multiples objects in a sequence of 2D or 3D images. Up to version 2 it was known as the ‘Probabilistic particle tracker’ plugin.

icy-thresholder
type: software
has author: Dufour Alexandre
has documentation: Thresholder
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: Thresholder
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2023-04-29T14:30:18
title: Icy Thresholder
comment: Extract image features based on one or more intensity thresholds, and output the result as a labeled image or as a region of interest.

icy-udwt-wavelet-residual-remover
type: software
has author: Fabrice de Chaumont
has function: operation Image reconstruction
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: UDWT-Wavelet-Residual-Remover
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/11
requires: http://biii.eu/node/49
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:38:30
title: Icy UDWT Wavelet Residual Remover

icy-video-recorder
type: software
has author: Dallongeville, Stephane
has author: Provoost, Thomas
has author: de Chaumont, Fabrice
has implementation: http://biii.eu/taxonomy/term/4340
has location: Video-Recorder
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2019-10-18T15:26:00
title: Icy Video Recorder

icy-webcam-capture-xuggler
type: software
has author: de Chaumont, Fabrice
has implementation: http://biii.eu/taxonomy/term/4340
has location: Webcam-Capture-(Xuggler
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:46
modified: 2019-10-18T15:22:51
title: Icy Webcam Capture (Xuggler)

icy-widefield-fluorescence-microscope-psf
type: software
has documentation: Widefield-Fluorescence-Microscope-PSF
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Widefield-Fluorescence-Microscope-PSF
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic Widefield microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/593
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:44
modified: 2019-10-18T14:43:36
title: Icy Widefield Fluorescence Microscope PSF

icy-workspace-editor
type: software
has author: Fabrice de Chaumont
has author: Stephane Dallongeville
has author: Thomas Provoost
has documentation: Workspace-Editor
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4340
has location: Workspace-Editor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-18T14:13:12
title: Icy Workspace Editor

icy-xuggler-slider
type: software
has author: Fabrice de Chaumont
has author: Thomas Provoost
has function: operation 3096
has location: Xuggler-Slider
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T16:09:26
title: Icy Xuggler Slider
comment: This plugin is a tutorial for the audio and video editing library Xuggler for developers. The slider will show the right image at the exact frame.

identifydeadworms
type: software
has author: Wählby Carolina
has function: operation Image classification
has implementation: http://biii.eu/taxonomy/term/4340
has location: IdentifyDeadWorms.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: 10.1038/nmeth.1984
has reference publication: An image analysis toolbox for high-throughput C. elegans assays
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-02T15:04:30
title: IdentifyDeadWorms
comment: Identifies dead worms based on a couple of parameters.

identifyobjectsingrid
type: software
has author: Carpenter Anne
has documentation: objectprocessing.html#identifyobjectsingrid
has documentation: Manual version 3.0.0
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-02T16:44:56
title: IdentifyObjectsInGrid
comment: This module identifies objects that are contained within in a grid pattern, allowing you to measure the objects using Measure modules. It requires you to have defined a grid earlier in the pipeline, using the DefineGrid module. For several of the automatic options, you will need to enter the names of previously identified objects. Typically, this module is used to refine locations and/or shapes of objects of interest that you roughly identified in a previous Identify module. Within this module, objects are re-numbered according to the grid definitions rather than their original numbering from the earlier Identify module. If placing the objects within the grid is impossible for some reason (the grid compartments are too close together to fit the proper sized circles, for example) the grid will fail and processing will be canceled unless you choose to re-use a grid from a previous successful image cycle.

identifyobjectsmanually
type: software
has author: Carpenter Anne
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: objectprocessing.html#identifyobjectsmanually
has location: manual version 3.0.0
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T16:40:05
title: IdentifyObjectsManually
comment: This module lets you outline the objects in an image using the mouse.

identifyprimaryobjects
type: software
has author: Carpenter Anne
has documentation: objectprocessing.html#identifyprimaryobjects
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/31
requires: http://biii.eu/node/49
requires: http://biii.eu/node/826
created: 2013-10-11T13:08:44
modified: 2020-03-02T14:40:34
title: IdentifyPrimaryObjects
comment: Identify objects (as nuclei) within an image without needing the assistance of another cellular feature (as cell).

identifysecondaryobjects
type: software
has documentation: objectprocessing.html#identifysecondaryobjects
has documentation: CP-Manual 3.1.9
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-17T08:11:02
title: IdentifySecondaryObjects
comment: IdentifySecondaryObjects identifies objects (e.g., cells) using objects identified by another module (e.g., nuclei) as a starting point.

identifytertiaryobjects
type: software
has author: Carpenter Anne
has documentation: objectprocessing.html#identifytertiaryobjects
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: objectprocessing.html
has location: Manual version 3.0.0
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2023-05-03T09:31:35
title: IdentifyTertiaryObjects
comment: Allows the identification of objects by subtracting secondary objects from primary objects. For example allows to segment the cytoplasm by subtracting nuclei from cells.

idr-py
type: software
created: 2018-08-20T09:20:53
modified: 2018-08-20T09:20:53
title: idr-py

idtracker-tracking-animals
type: software
has author: Arganda, Sara
has author: Hinz, Robert C.
has author: Pérez-Escudero, Alfonso
has author: Vicente-Page, Julian
has author: de Polavieja, Gonzalo G. (orcid.org/0000-0001-5359-3426)
has documentation: Direct link to idtracker user guide pdf
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4341
has license: Free Non-comercial use, Patented PCT/ES2013/070585
has location: download
has location: idTracker Download
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: nmeth.2994
has reference publication: Pérez-Escudero et. al. (2014) "idTracker: tracking individuals in a group by automatic identification of unmarked animals"
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/101
created: 2014-12-09T16:02:30
modified: 2023-05-08T07:00:20
title: idTracker: Tracking animals
comment: idTracker is a videotracking software that keeps the correct identity of each individual during the whole video. It works for many animal species including mice, insects (Drosophila, ants) and fish (zebrafish, medaka, stickleback). idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. Technique details and analyses of several applications are described in Pérez-Escudero et al (2014). Video protocol: https://www.youtube.com/watch?v=oC9tp5TKAyw Example image: Example video of 5 zebrafish

idtrackerai
type: software
has author: Bergomi, Mattia G
has author: Heras, Francisco J. H.
has author: Hinz, Robert C.
has author: Romero-Ferrero, Francisco
has author: de Polavieja, Gonzalo G. (orcid.org/0000-0001-5359-3426)
has documentation: index.html
has documentation: idtracker.ai user guide page
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL V3
has location: latest
has location: idtracker.ai main page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41592-018-0295-5
has reference publication: arXiv.1803.04351
has reference publication: idtracker.ai: Tracking all individuals in large collectives of unmarked animals (arXiv preprint)
has reference publication: idtracker.ai: tracking all individuals in small or large collectives of unmarked animals (Nature Methods)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1157
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1476
created: 2023-05-08T07:01:42
modified: 2023-05-11T11:01:51
title: idtracker.ai
comment: Algorithm and software created to extract animal trajectories from videos of a collection of animals up to 100 individuals. Idtrackerai uses two convolutional networks: one for animal identification and another to detect when animals touch or cross each other.

ij-opencv
type: software
has documentation: IJ-OpenCV
has type: http://biii.eu/taxonomy/term/8
created: 2018-11-07T14:04:35
modified: 2018-11-07T14:05:13
title: IJ-OpenCV

ijblob
type: software
has author: Thorsten Wagner
has documentation: ijblob
has function: operation Feature extraction
has function: operation Shape features
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: ijblob
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-11-27T14:23:33
modified: 2020-03-03T09:29:59
title: ijblob
comment: ## Features >The IJBlob library indentifying connected components in binary images. The algorithm used for connected component labeling is: >Chang, F. (2004). A linear-time component-labeling algorithm using contour tracing technique. Computer Vision and Image Understanding, 93(2), 206220. doi:10.1016/j.cviu.2003.09.002 ##Reference Wagner, T and Lipinski, H 2013. IJBlob: An ImageJ Library for Connected Component Analysis and Shape Analysis. Journal of Open Research Software 1(1):e6, DOI:

ikosa
type: software
has author: KMLVision
has function: operation 2409
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4342
has location: www.ikosa.ai
has location: Webpage, hosted server after Log-in
has topic: topic 3474
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2019-06-07T06:58:29
modified: 2019-10-16T09:13:17
title: Ikosa
comment: online image data management system which supports authenticated image upload, cloud-based storage, project-based management and viewing of standard and whole slide images. One can use different annotation tools to highlight important objects or areas within images. It is the first basic version and new features such as sharing for easy collaboration with your colleagues or first automated analysis applications based on artificial intelligence will be added soon. Ikosa Portal: multi user image data management Ikosa Prisma: Automated Image Analysis based on deep learning (available in summer 2019) Free if limited to 2 users and 1 gigabyte, otherwise montly fees.

ilastik
type: software
has author: ilastik team
has function: operation 3553
has function: operation Cell counting
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Image tracking
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv2
has location: www.ilastik.org
has location: Officlal Ilastik Website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: http://ieeexplore.ieee.org/document/5872394/
has reference publication: s41592-019-0582-9
has reference publication: Conference paper describing the first release of ilastik (version 0.5)
has reference publication: ilastik: interactive machine learning for (bio)image analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Digital histology
has topic: topic R96toeNl9iMp8oqv9augU84
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: gallery.html
has usage example: Some example applications and screenshots
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/73
created: 2013-10-15T18:35:26
modified: 2021-06-30T07:40:29
title: ilastik
comment: ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing. ilastik (the image learning, analysis, and segmentation toolkit) provides non-experts with a menu of pre-built image analysis workflows. ilastik handles data of up to five dimensions (time, 3D space, and spectral dimension). Its workflows provide an interactive experience to give the user immediate feedback on the quality of the results yielded by her chosen parameters and/or labelings. The most commonly used workflow is pixel classification, which requires very little parameter tuning and instead offers a machine learning technique for segmenting an image based on local image features computed for each pixel. Other workflows include: Object classification: Similar to pixel classification, but classifies previously segmented objects by object characteristics in a subsequent step Autocontext: This workflow improves the pixel classification workflow by running it in multiple stages and showing each pixel the results of the previous stage. Carving: Semi-automated segmentation of 3D objects (e.g. neurons) based on user-provided seeds Manual Tracking: Semi-automated cell tracking of 2D+time or 3D+time images based on manual annotations Automated tracking: Fully-automated cell tracking of 2D+time or 3D+time images with some parameter tuning Density Counting: Learned cell population counting based on interactively provided user annotation Strengths: interactive, simple interface (for non-experts), …

ilastik-automatic-tracking
type: software
has documentation: tracking#sec automatic
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4341
has location: download.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/6751475
has reference publication: s41592-019-0582-9
has reference publication: Conservation Tracking
has reference publication: ilastik
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Supervised learning
has type: http://biii.eu/taxonomy/term/8
has usage example: tracking#sec automatic
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/88
created: 2013-10-15T10:45:51
modified: 2023-04-28T13:12:40
title: ilastik - Automatic Tracking
comment: Fully-automated cell tracking of 2D+time or 3D+time images with some parameter tuning

ilastik-carving
type: software
has documentation: carving
has function: operation Image segmentation
has function: operation Interactive segmentation
has function: operation Watershed
has function: operation RBNng13hEB0CJD5VzSKqrfB
has location: download.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 978-3-642-23623-5 82
has reference publication: Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: carving
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/88
created: 2013-10-15T10:45:51
modified: 2023-04-28T13:07:21
title: ilastik - Carving
comment: Semi-automated segmentation of 3D objects (e.g. neurons) based on user-provided seeds.

ilastik-density-counting
type: software
has author: ilastik team
has documentation: counting.html
has function: operation Cell counting
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4341
has location: download.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/6460719
has reference publication: Learning to Count with Regression Forest and Structured Labels
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/88
created: 2013-10-15T10:45:51
modified: 2020-03-02T20:12:32
title: ilastik - Density Counting
comment: This workflow estimates (densely distributed) object counts by the density of objects in the image without performing segmentation or object detection. Current version only works for 2D images of roundish objects with similar sizes on relatively homogeneous background. Users should provide a few labels of background and objects (especially on clustered objects), and the tool predicts the density of objects on the entire image. Counting is then estimated by integrating the density values on the whole image or specified rectangular regions of interests.

ilastik-manual-tracking
type: software
has documentation: tracking#sec manual
has function: operation Image tracking
has location: download.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: tracking#sec manual
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/88
created: 2013-10-15T10:45:51
modified: 2019-11-14T11:58:06
title: ilastik - Manual Tracking
comment: Semi-automated cell tracking of 2D+time or 3D+time images based on manual annotations

image-anonymisation
type: software
has author: Christophe Leterrier
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2014-12-09T10:01:30
modified: 2017-09-12T18:03:48
title: Image anonymisation
comment: This macro copies all images from one folder to another, randomizing names but keeping channels from the same image grouped. This is useful for blind quantification of images.

image-build-tutorial-1
type: software
has location: Image build tutorial 1
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:17
title: Image build tutorial 1

image-calculator-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.imgjep.ImgJEPNodeFactory#Image Calculator
has documentation: nodepit
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:46
modified: 2020-03-03T17:59:06
title: Image Calculator (KNIME)

image-classification-deep-learning-knime
type: software
has author: Thomas Laurent orcid.org/0000-0001-7686-3249
has comparison: qualitative-annotations-fiji-plugins
has comparison: Qualitative annotation plugins
has documentation: Pr6KGHrgSyo
has documentation: YouTube tutorial
has function: operation Image classification
has location: ImageClassification-DeepLearning
has location: KNIME workflows on the KNIME Hub
has reference publication: f1000research.26872.1
has reference publication: Open-access publication
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: zenodo.3997728
has usage example: Example of dataset and associated trained model
openess: http://biii.eu/taxonomy/term/3575
created: 2020-11-12T16:49:25
modified: 2020-11-20T10:09:58
title: Image-classification with deep learning in KNIME
comment: Set of KNIME workflows for the training of a deep learning model for image-classification with custom images and classes. The workflows take ground-truth category annotations as a table generated by the qualitative annotations plugins in Fiji. Workflows for the training of a model AND for the prediction of image-category for new images are provided. There are different workflows if you do: - binary image-classification (images get classified in 1 category out of 2 possible categories) - classification from possibly more than 2 categories (images are classified in 1 category out of N possible categories). The training workflows take care of image pre-processing and allows the visualization of the training and validation losses in real time along the training. For the training, transfer learning from a pre-trained VGG16 base is performed, with freshly initialized fully connected layers. Only the fully connected layers are trained, the VGG16 base is frozen is this workflow, but once the fully connected layers trained the base could also be finetuned. In practice, it often works well with the frozen base.

image-composite-editor
type: software
has author: Microsoft Research Interactive Visual Media Group
has license: Free
has location: image-composite-editor
has platform: http://biii.eu/taxonomy/term/31
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/317
created: 2017-03-09T09:31:27
modified: 2017-09-13T10:16:52
title: Image Composite Editor
comment: ICE (Image Composite Editor) is a fast, fully automatic software by Microsoft that can create large montages from overlapping images. Although it is tailored around the task of stitching together images from a photo camera, it also works on biological images taken from light and electron microscopes. It has limited command line options, which however could facilitate batch processing (https://social.microsoft.com/Forums/en-US/806bf0c5-af8f-4526-9b90-6d28096441d2/faq-frequently-asked-questions-for-image-composite-editor?forum=ice).

image-converter-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.ConvertImgNodeFactory#Image Converter
has function: operation 3434
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2020-03-03T17:29:49
title: Image Converter (KNIME)

image-convolution-ebimage
type: software
has documentation: EBImage.pdf
has function: operation Image enhancement
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:43
modified: 2020-03-03T09:25:44
title: Image Convolution (EBImage)

image-cropper-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.ImgCropperNodeFactory2#Image Cropper
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2020-03-03T12:58:20
title: Image Cropper (KNIME)

image-data-explorer
type: software
has author: Aliaksandr Halavatyi
has author: Christian Tischer orcid.org/0000-0003-4105-1990
has author: Coralie Muller orcid.org/0000-0002-5186-1666
has author: Jean-Karim Heriche orcid.org/0000-0001-6867-9425
has author: Kimberly Meechan orcid.org/0000-0003-4939-4170
has documentation: home
has documentation: Image data explorer wiki
has function: operation_0226
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: image-data-explorer
has location: Repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: journal.pone.0273698
has reference publication: The Image Data Explorer: Interactive exploration of image-derived data
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2019-03-29T07:47:38
modified: 2022-10-12T14:18:48
title: Image Data Explorer
comment: The Image Data Explorer is a Shiny app that allows the interactive visualization of images and ROIs associated with data points shown in a scatter plot. It is useful for exploring the relationships between images/ROIs and associated data represented in tabular format. Additional functionalities include data annotation, dimensionality reduction and classification and feature selection.

image-denoising-using-matlab
type: software
has author: Sébastien Tosi
has documentation: matlab#h.p aNkqTXR9ENfE
has documentation: Online documentation
has function: operation RDyyXyhf1oHK93opXhEnRND
has location: matlab#h.p aNkqTXR9ENfE
has location: MATLAB dode
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-08T14:37:11
modified: 2023-04-28T14:56:57
title: Image denoising using Matlab
comment: If your images are corrupted by a strong dominant Gaussian noise you can try this simple filter. It is based on thresholding in the DCT domain and is usually vastly superior to typical Gaussian filtering in term of detail preservation / noise reduction trade-off. The filter unfortunately introduces some block like artifacts that can be mitigated by averaging out overlaping shifted windows (as implemented in the Matlab version) and performing maximum intensity projection after the filtering: As such the filter is way more adapted to process 3D stacks that you plan to maximum intensity project than to process single z slice images.

image-expression-parser
type: software
has author: Tinevez Jean-Yves
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Image Expression Parser
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2020-03-03T11:06:26
title: Image Expression Parser
comment: This plugin parses arbitrary mathematical expressions and compute results using images as variables.

image-normalizer-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.ImgNormalizerNodeFactory#Image Normalizer
has function: operation Image enhancement
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-03T11:37:11
title: Image Normalizer (KNIME)

image-process-tutorial-1
type: software
has location: Image process tutorial 1
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2017-09-13T10:02:15
title: Image process tutorial 1

image-reader-knime
type: software
has documentation: org.knime.knip.io.nodes.imgreader2.readfromdialog.ImgReader2NodeFactory#Image Reader
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-03T11:45:52
title: Image Reader (KNIME)

image-registration-matlab-image-processing-toolbox
type: software
has documentation: image-registration.html
has documentation: Image Registration
has function: operation 2928
has function: operation Image registration
has function: operation R9EjejimBB0tmnQRmZt0RhA
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has license: commercial
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
has usage example: registering-multimodal-3-d-medical-images.html
has usage example: Register Multimodal 3-D Medical Images
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/89
requires: http://biii.eu/node/90
created: 2019-10-17T11:31:48
modified: 2020-10-19T15:08:20
title: Image registration in Matlab with Image Processing Toolbox
comment: Align two images using intensity correlation, feature matching, or control point mapping Together, Image Processing Toolbox™ and Computer Vision Toolbox™ offer four image registration solutions: interactive registration with a Registration Estimator app, intensity-based automatic image registration, control point registration, and automated feature matching.

image-stabilizer
type: software
has author: Kang Li
has documentation: Image Stabilizer.html
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: Image Stabilizer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2018-06-06T16:59:56
title: Image Stabilizer
comment: This plugin stabilizes jittery image stacks using the Lucas-Kanade algorithm. It supports both grayscale and color images. See also this [tweet](https://twitter.com/christlet/status/1004402506485719040)

image-stitching
type: software
has author: Preibisch Stephan
has documentation: Image Stitching
has function: operation Image processing
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv2
has location: Image Stitching
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: btp184
has reference publication: Globally optimal stitching of tiled 3D microscopic image acquisitions
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1012
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2020-03-03T10:16:08
title: Image Stitching
comment: The plugin performs stitching of images of a tiled scan to reconstruct the image of the whole sample.

image-stitching-0
type: software
has location: Image Stitching
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:40
modified: 2017-09-12T09:03:48
title: Image Stitching

image-writer-knime
type: software
has documentation: org.knime.knip.io.nodes.imgwriter2.ImgWriter2NodeFactory#Image Writer
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2020-03-03T17:40:09
title: Image Writer (KNIME)

imagebrowser
type: software
has author: Hervé, Nicolas
has documentation: ImageBrowser
has function: operation Image visualisation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2019-10-17T11:43:36
title: ImageBrowser
comment: Browse files in directories with thumbnails view

imagehts
type: software
has author: Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber
has license: LGPL-2.1
has location: imageHTS.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/286
requires: http://biii.eu/node/474
created: 2016-12-09T11:19:20
modified: 2017-09-13T10:16:47
title: imageHTS
comment: imageHTS is an R/Bioconductor package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.

imagej
type: software
has author: Wayne Rasband
has documentation: User Guides
has license: Public Domain
has location: imagej.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: nmeth.2089
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3566
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-04-05T12:58:30
modified: 2017-09-13T10:12:46
title: ImageJ
comment: Bio Image Analysis tool from REF

imagej-2x
type: software
has author: Curtis Ruden
has implementation: http://biii.eu/taxonomy/term/4339
has license: Public Domain
has location: imagej.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.2089
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-22T19:14:07
modified: 2020-03-03T20:08:55
title: ImageJ 2.x
comment: BioImage Analysis Tool for all! ImageJ2

imagej-align-rgb-planes
type: software
has author: Gabriel Landini
has documentation: Align RGB planes
has function: operation Rotation
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RDr8xcZEa4L3mZsslmhhee8
has license: GNU General Public license
has location: align rgb.zip
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1008
requires: http://biii.eu/node/38
requires: http://biii.eu/node/923
created: 2013-10-11T13:08:41
modified: 2018-05-03T00:56:19
title: ImageJ Align RGB planes
comment: From the plugin inline help: " Align RGB planes v1.7 by G.Landini Changes the alignment of the RGB planes independently. Red Green and Blue checkboxes switch ON and OFF the planes and undo the alignment since last plane change. Note that when switching planes, the portion of the previously edited plane left outside the image frame is lost. Rotation, Width and Height changes are interpolated (so there is some loss of sharpness) and do not retain the image portions outside the image frame. You can use the Resize2Rotate macro to avoid losing any image data. The Rotate, Width and Height sliders set integer values, but fractional values can also be typed in the entry boxes. Just make sure you press [RETURN] after the number is typed. The Revert button works only with single images, not stacks. Note: When using stacks, 2 buttons [< Prev] and [Next >] are added to the panel. Do not use the slide bar in the stack window, but use those buttons instead."

imagej-analyze-skeleton
type: software
has author: Ignacio Arganda-Carreras orcid.org/0000-0003-0229-5722
has function: operation Pixel classification
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation RBNng13hEB0CJD5VzSKqrfB
has license: GNU General Public License v3.0
has location: AnalyzeSkeleton
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: full
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
has usage example: AnalyzeSkeleton
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/636
created: 2017-09-12T10:23:39
modified: 2023-04-27T12:09:17
title: ImageJ Analyze Skeleton
comment: This plugin tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple points and branches, and measures their average and maximum length. Tags are shown in a new window displaying every tag in a different color. You can find it under [Plugins>Skeleton>Analyze Skeleton (2D/3D)]. See Skeletonize3D for an example of how to produce skeleton images. The voxels are classified into three different categories depending on their 26 neighbors: - End-point voxels: if they have less than 2 neighbors. - Junction voxels: if they have more than 2 neighbors. - Slab voxels: if they have exactly 2 neighbors. End-point voxels are displayed in blue, slab voxels in orange and junction voxels in purple. Notice here that, following this notation, the number of junction voxels can be different from the number of actual junctions since some junction voxels can be neighbors of each other. Output data type: table result, image of the skeleton

imagej-auto-crop
type: software
has documentation: Auto Crop
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has location: Select Bounding Box.java
has location: Source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2018-05-14T21:27:41
title: ImageJ Auto Crop
comment: This plugin can find the smallest bounding box of an image (or a rectangular part defined by a selection) by cropping as much background as possible. Found in Fiji, under Image> Adjust. In the version labeled with (guess background color), the plugin tries to determine the background color by looking at the pixels on the border of the image, while Auto Crop uses the currently selected background color which can be changed by double-clicking on the pipette symbol or using the Image > Color > Color Picker.... Instead of cropping right away, you can set the selection to the rectangle that would be cropped to using Edit > Selection > Select Bounding Box.

imagej-bandpass-filter
type: software
has author: Joachim Walter
has function: operation Edge detection
has function: operation Image enhancement
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: fft-filter.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-15T17:37:38
modified: 2019-10-28T11:42:16
title: ImageJ Bandpass filter
comment: The Fourier transform of an image produces a representation in frequency space: i.e. separated according to spatial frequency (effectively scale). The 2D amplitude map of the different spatial frequencies is symmetrical, and is commonly displayed with low spatial frequencies (large features) in the centre, highest spatial frequencies (small features) at the edges. Fourier filtering involves suppressing or enhancing features in the Fourier domain before carrying out an inverse Fourier transform to obtain a filtered real-space image. ImageJ's _Process > FFT > Bandpass Filter_ implements two common Fourier-filtering functions: 1. filtering for specific sizes of feature in an image by selecting minimum and maximum feature sizes (selecting a radial band of frequencies in Fourier space); 2. filtering out repetitive horizontal or vertical stripes by cutting out a zero-frequency stripe in the orthogonal direction in frequency space. The example image above shows the effect of filtering for 2 feature size ranges: 0-8 pixels, and 8-256 pixels; where the former appears "flattened" or washed-out, and the latter very blurred. The small images displayed to the lower-right of each filtered image correspond to the mask applied to the Fourier transform. Such filtering can be useful prior to global thresholding, for noise suppression, etc.

imagej-built-macro-functions
type: software
has documentation: functions.html
has documentation: List of Built-in Macro Functions (ImageJ website)
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD-2
has location: source
has location: ImageJ source code (go to ij.Macro package then Functions java file)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-25T14:18:27
modified: 2019-02-25T14:38:03
title: ImageJ Built-in Macro Functions
comment: A set of ImageJ Built-in Macro Functions used to perform operations on the ImageJ platform.

imagej-feature-extraction
type: software
has author: Stephan Saalfeld
has function: operation Object detection
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: Feature Extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: B:VISI.0000029664.99615.94
has reference publication: IJCV publication
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2023-05-03T10:10:24
title: ImageJ Feature Extraction
comment: Automatic finding of image features are very convenient for registering two images to align them in proper orientation. Two image plugins are implemented for extracting image features and are placed as menu items at: [Plugins > Feature Extraction > Extract SIFT Correspondences] and [Plugins > Feature Extraction > Extract MOPS Correspondences]. For more details, see the linked page in Fiji wiki. For details about SIFT algorithm, see 2569. For more details about MOPS algorithm, see 2570.

imagej-macro
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2017-09-13T10:02:47
title: ImageJ Macro

imagej-plugin-lineagetracker
type: software
has author: Downey MJ, Jeziorska DM, Ott S, Tamai TK, Koentges G, Vance KW, Bretschneider T.
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: lineagetracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: pnas.1320474111
has reference publication: Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-09-08T09:20:06
modified: 2019-10-21T12:30:13
title: ImageJ Plugin LineageTracker
comment: ## Short Summary Quote from the plugin page: >LineageTracker offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The methods are designed for fluorescent cells and have been used to analyse Schizosaccharomyces pombe, C2C12 mouse stem cells or migrating RPE cells. This tool also allows flexible cell segmentation and extendable in all aspects. The webpage is detailed with usage from ImageJ macro. Rather than being simply a component, the plugin is indeed a framework with set of components. ## Misc info A tip from the plugin author in ImageJ mailing list (08.Sep.2015): > We have an additional script to export only a selected range of frames. I can send you that if you think LineageTracker is something for you. To be on the safe side I would try it with an older version of ImageJ. We have experienced some problems, mostly related to Java. Java 8 seems to fix most of it. ## References 2630: Application example. 2631: Plugin Paper.

imagej-plugin-non-local-means-filtering
type: software
has author: Thorsten Wagner, Pascal Behnel
has documentation: Non Local Means Denoise
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: Non Local Means Denoise
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: ipol.2011.bcm nlm
has reference publication: A Non-Local Algorithm for Image Denoising
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-02-19T14:57:30
modified: 2019-10-21T12:38:51
title: ImageJ Plugin for Non-Local-Means Filtering
comment: A more modern approach for denoising / smoothening before segmentation, works like Gaussian blurring but preserves edges and boundaries. Listed in Fiji update sites. ## Algorithm Algorithm description is in [this page](http://www.ipol.im/pub/art/2011/bcm_nlm/) 2612. ## Example usage Localization of Membrane bound protein in Arabidopsis meristem was analyzed using the non-local-mean filter for refining its position 2613. ## impression It's effect is somewhere between Gaussian blurring and anistropic diffusion.

imagej-plugin-ridge-detection
type: software
has author: Thorsten Wagner
has documentation: Ridge Detection
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: Ridge Detection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://10.1109/34.659930
has reference publication: An unbiased detector of curvilinear structures
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2015-02-19T16:28:30
modified: 2019-10-21T12:33:24
title: ImageJ Plugin Ridge Detection
comment: A convenient tool for detecting lines! After the detection, detected lines are overlaid to the image. The plugin also stores these lines as ROIs, which could then easily be analyzed as vector information. Instead, the list of coordinates of all detected lines are placed in "contour" table. This could be used for redrawing or converting them as arrays. ## Algorithm See 2615.

imagej-threshold
type: software
has documentation: 146-28.html#toc-Subsection-28.2.4
has documentation: ImageJ online user manual
has function: operation Image thresholding
has location: download.html
has location: Download ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2023-04-26T15:34:18
modified: 2023-04-26T15:42:10
title: ImageJ Threshold
comment: This ImageJ function automatically or interactively sets lower and upper threshold values, segmenting grayscale images into features of interest and background.

imagej2
type: software
has author: Arena Ellen T.
has author: DeZonia Barry E.
has author: Eliceiri Kevin W.
has author: Hiner Mark C.
has author: Rueden Curtis T.
has author: Schindelin Johannes
has author: Walter Alison E.
has documentation: ImageJ2#Publications
has function: operation 2945
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD2
has location: Downloads
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: 10.1186/s12859-017-1934-z
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2020-03-03T09:30:02
title: ImageJ2

imagej2-plugin-knime
type: software
has documentation: imagej
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/464
created: 2013-10-11T13:08:44
modified: 2020-03-03T13:01:57
title: ImageJ2 Plugin KNIME

imagejfiji
type: software
created: 2018-10-17T17:50:09
modified: 2018-10-17T17:50:09
title: ImageJ/FIJI

imagejfx
type: software
has author: Cyril MONGIS
has documentation: imagejfx-core#be-aware-before-installing-imagej-fx
has documentation: github
has function: operation 2409
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has location: www.imagejfx.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2017-02-15T09:40:59
modified: 2023-04-29T13:06:04
title: ImageJFX
comment: The ImageJFX Project aims to create a new user interface for the software ImageJ in order to ease scientific image analysis. While keeping the core components of ImageJ, ImageJFX brings scientists closer to their goal by making the interface clearer for beginners and more practical for advanced users.

imagem
type: software
has author: David Legland
has documentation: 45847-imagem
has function: operation 2409
has function: operation 3443
has function: operation Image segmentation
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: ImageM
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1290
requires: http://biii.eu/node/89
created: 2020-03-05T09:56:02
modified: 2020-10-19T14:48:52
title: ImageM
comment: ImageM integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".

imagemagick
type: software
created: 2018-05-31T19:58:47
modified: 2018-05-31T19:58:47
title: ImageMagick

imagemath
type: software
has author: Carpenter Anne
has documentation: imageprocessing.html#imagemath
has documentation: manual version 3.1.9
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:44
modified: 2020-03-02T16:50:01
title: ImageMath
comment: ImageMath performs simple mathematical operations on image intensities, like addition, subtraction, multiplication, division...

imagepro
type: software
has license: commercial
has location: http://www.mediacy.com/index.aspx%3Fpage%3DImage_Pro_Software
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-11-07T20:23:57
modified: 2017-09-12T18:05:39
title: ImagePro
comment: Image-Pro software includes the latest tools for scientific and industrial image analysis and image processing. Capture, process, measure, share, visualize and compare. ImagePro Insight ImagePro Priemier

imagepy
type: software
has DOI: bty313
has documentation: imagepy
has function: operation_0337
has function: operation 2409
has function: operation 2945
has function: operation Image processing
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD
has location: imagepy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: bty313
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-05-25T07:52:09
modified: 2018-10-18T15:35:57
title: ImagePy
comment: This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.

imagesciencejar
type: software
created: 2018-05-24T01:29:54
modified: 2018-05-24T01:29:54
title: ImageScience.jar

imaris
type: software
has author: Bitplane
has function: operation_0337
has function: operation Image registration
has function: operation Image tracking
has function: operation RBNng13hEB0CJD5VzSKqrfB
has license: commercial
has location: www.bitplane.com
has platform: http://biii.eu/taxonomy/term/31
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/87
created: 2013-10-15T18:31:07
modified: 2019-10-17T10:14:36
title: Imaris
comment: Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological objects such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect spherical objects and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space. ImarisCell is a tool to detect nuclei, cell boundaries and vesicles and track these through time. ImarisFilament is a module that lets users trace neurons and detect spines. For any detected object Imaris computes a large set of statistics values such as volume, surface area, maximum intensity of first channel, number of vesicles per cell etc. These values can be exported to Excel and statistics software packages. The measurements can also be analyzed directly within ImarisVantage which is a statistics tool that provides the link back to the 3D objects and the original image data. Strengths: - good visualization - user friendly interface - reads most microscopy file formats - image analysis workflows are very easy to apply - interactive editing of objects to correct errors during automatic detection - large data visualization (hundreds of GB)

imaris-tracking
type: software
has author: Bitplane
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2014-12-08T14:45:34
modified: 2017-09-13T10:14:10
title: Imaris Tracking
comment: ImarisTrack allows 3D tracking of spots and objects, with straightforward manual adjustment of automatic tracking results.

imarisanimation
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:10:23
title: ImarisAnimation

imarisannotate
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:43
modified: 2023-05-02T16:41:58
title: ImarisAnnotate

imarisbatch
type: software
has location: imarisbatch
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:22
title: ImarisBatch

imariscell
type: software
has function: operation 3443
has function: operation Cell segmentation
has function: operation Image visualisation
has location: imaris-for-cell-biologists
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:40
modified: 2019-10-16T11:08:56
title: ImarisCell

imariscoloc
type: software
has location: imariscoloc
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:09:28
title: ImarisColoc

imarisfilamenttracer
type: software
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4341
has location: packages
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/471
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:46
modified: 2020-03-01T11:03:55
title: ImarisFilamentTracer

imarisimageprocessing
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1008
requires: http://biii.eu/node/491
requires: http://biii.eu/node/544
requires: http://biii.eu/node/787
requires: http://biii.eu/node/835
requires: http://biii.eu/node/983
created: 2013-10-15T10:45:49
modified: 2017-09-13T10:11:16
title: ImarisImageProcessing

imarisisosurface
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/826
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:40
modified: 2017-09-13T10:01:45
title: ImarisIsoSurface

imarismeasurementpro
type: software
has location: measurementpro
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:00
title: ImarisMeasurementPro

imarisreader-matlab
type: software
has author: Peter Beemiller
has function: operation 3434
has location: http://open.bitplane.com/tabid/235/Default.aspx%3Fid%3D122
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/87
created: 2013-10-15T10:45:49
modified: 2020-03-02T16:54:55
title: ImarisReader for MATLAB
comment: ImarisReader is a set of classes for reading the data stored in ims files. ImarisReader can read the primary image data, as well as the data for segmented objects: Cells, Filaments, Spots and Surfaces.

imarissectionview
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-15T10:45:49
modified: 2017-09-12T09:41:32
title: ImarisSectionView

imarissliceview
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-15T10:45:49
modified: 2017-09-12T09:41:39
title: ImarisSliceView

imarisspots
type: software
has implementation: http://biii.eu/taxonomy/term/4341
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:43
modified: 2020-03-01T11:39:30
title: ImarisSpots

imaristrack
type: software
has location: imaristrack
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/211
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:47
title: ImarisTrack

imarisvantage
type: software
has location: imarisvantage
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:38
title: ImarisVantage

imarisvolumerendering
type: software
has location: imaris
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/87
created: 2013-10-11T13:08:40
modified: 2017-09-13T10:02:04
title: ImarisVolumeRendering

imarisxt
type: software
has author: Oxford Instruments
has documentation: imarisxt
has documentation: ImageJ and Fiji Support in ImarisXT
has location: imarisxt
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/322
requires: http://biii.eu/node/38
requires: http://biii.eu/node/555
requires: http://biii.eu/node/607
requires: http://biii.eu/node/87
requires: http://biii.eu/node/892
created: 2013-10-11T13:08:47
modified: 2020-03-01T14:51:22
title: ImarisXT

imglib2
type: software
has author: Stephan Saalfeld, Stephan Preibisch, Tobias Pietzsch, Curtis Rueden, Barry DeZonia, Christian Dietz, Martin Horn, Mark Hiner, et al
has documentation: ImgLib2 Documentation
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: imglib2.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: PMC3496339
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-15T18:08:18
modified: 2020-03-01T12:18:52
title: ImgLib2
comment: ImgLib2 is a generic, multi-dimensional data processing library allowing for processing algorithms to be defined in a data-type, dimension, and container independent manner. Due to its interface-based design, it is easy to write adapters to virtually all existing data containers. It is the basis of KNIME, ImageJ2 and a couple of Fiji plugins.

imjoy
type: software
has author: Hjelmare, Martin
has author: Mueller, Florian
has author: Ouyang, Wei
has documentation: repo
has documentation: ImJoy Plugin Repository
has function: operation 2423
has function: operation 2990
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4342
has license: MIT License
has location: https://imjoy.io/%23/
has location: ImJoy webapp website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4668
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2019-02-06T22:37:52
modified: 2023-04-30T15:16:41
title: ImJoy
comment: ImJoy is a plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. ImJoy runs on mobile and desktop environment cross different operating systems, plugins can run in the browser, localhost, remote and cloud servers. With ImJoy, delivering Deep Learning tools to the end users is simple and easy thanks to its flexible plugin system and sharable plugin URL. Developer can easily add rich and interactive web interfaces to existing Python code.

immunomembrane
type: software
has author: Jorma Isola
has author: Vilppu Tuominen
has documentation: immunomembrane
has function: operation Cell segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has location: immunomembrane 1.0i.jar
has location: immunomembrane_1.0i.jar
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.1365-2559.2011.04142.x
has reference publication: Tuominen et al. (2011) ImmunoMembrane: a publicly available web application for digital image analysis of HER2 immunohistochemistry
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T11:36:01
modified: 2018-06-07T00:21:43
title: ImmunoMembrane
comment: Quantification of HER2 immunohistochemistry. ImmunoMembrane is an ImageJ plugin for assessing HER2 immunohistochemistry, described in [bib]2472[/bib]. It is important to read the URL documentation and original paper to understand how to use the plugin appropriately. There is web service available. Users can upload image data to process them and get cell membrane to be segmented: [Web ImmunoMembrane]() Note also that the *pixel size* is not read automatically from the image, but rather the *source image scale* should be entered into the dialog box - and the image rescaled accordingly prior to analysis. This scale value is the *inverse* of the value normally found for *pixel width* and *pixel height* under *Image -> Properties...* (i.e. pixel width & height are given in microns per pixel; the dialog box asks for pixels per micron).

immunoratio
type: software
has author: Jorma Isola
has author: Vilppu Tuominen
has function: operation Image deconvolution
has license: GNU General Public License
has location: index.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: bcr2615
has reference publication: ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/337
requires: http://biii.eu/node/38
created: 2014-12-08T14:26:46
modified: 2018-04-28T21:13:59
title: ImmunoRatio
comment: Analyzing ER, PR, and Ki-67 immunohistochemistry ImmunoRatio is an ImageJ plugin to quantify haematoxylin and DAB-stained tissue sections by measuring the percentage of positively stained nuclear area (labeling index), described in [bib]2452[/bib]. Notes for use: It is important to read the URL instructions and original paper to understand what is being measured. In particular, the primary measurement made is percentage of the total nuclear area, not the percentage of detected nuclei (the latter being the more common method of assessing e.g. Ki67). This may be further modified by the Result correction equation. Ultimately ImmunoRatio relies on thresholding (color deconvolved [bib]2451[/bib]) images to define 'nucleus' vs 'non-nucleus' regions according to staining intensity. Therefore dark artefacts, such as tissue folds, are likely to cause errors. The pixel size is not read automatically from the image, but rather the source image scale should be entered into the dialog box - and the image rescaled accordingly prior to analysis. This scale value is the inverse of the value normally found for pixel width and pixel height under Image -> Properties... (i.e. pixel width & height are given in microns per pixel; the dialog box asks for pixels per micron). Web application: ImmunoRatio Example Image: Sample ImmunoRatio results References [2452] Tuominen VJ, Ruotoistenmäki S, Viitanen A, Jumppanen M, Isola J. 2010. ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67.. Breast Cancer Res. 12(4):R56. [2451] Ruifrok AC, Johnston DA. 2001. Quantification of histochemical staining by color deconvolution.. Anal Quant Cytol Histol. 23(4):291-9.

imod
type: software
has author: David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong
has documentation: #Guides
has documentation: list of all guides and tutorials
has function: operation 2928
has function: operation 3443
has license: GPLv2
has location: imod
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: jsbi.1996.0013
has reference publication: Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD J. Struct. Biol. 116:71-76
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-24T15:53:28
modified: 2023-04-27T15:22:31
title: IMOD
comment: IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. Included are two programs with graphical interface: 3dmod, for displaying and segmenting 2D images and 3D volumes; etomo, for reconstructing tomographic volumes from tilt series of images. Processing can be distributed on multiple cores and executed in batch mode.

import-images-trakem
type: software
created: 2018-01-30T16:32:31
modified: 2018-01-30T16:32:31
title: import images into TrakEM

import-roi-imagej
type: software
has author: Dufour Alexandre orcid.org/0000-0002-9417-7389
has function: operation Image classification
has implementation: http://biii.eu/taxonomy/term/4340
has location: import-roi-from-imagej
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2019-10-16T10:57:08
title: Import ROI from ImageJ
comment: Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a block for Protocols

incucyte-base-analysis-software
type: software
has function: operation 2945
has function: operation Cell segmentation
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has location: incucyte-base-software#id-791490
has location: Ordering Information
has platform: http://biii.eu/taxonomy/term/30
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic Fluorescent microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/3567
has usage example: S0006295216301769
has usage example: A novel real time imaging platform to quantify macrophage phagocytosis
openess: http://biii.eu/taxonomy/term/3577
created: 2023-04-26T16:00:05
modified: 2023-04-26T16:18:40
title: Incucyte Base Analysis Software
comment: The Incucyte® Base Analysis Software provides a guided interface and purpose-built tools, which include the process of acquiring, viewing, analyzing and sharing images of living cells.

infectioncounter
type: software
has author: Joe Grove
has function: operation Cell counting
has location: InfectionCounter
has location: GitHub InfectionCounter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: v8070201
has reference publication: Infection Counter: Automated Quantification of in Vitro Virus Replication by Fluorescence Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/657
created: 2016-10-24T13:46:16
modified: 2018-05-16T20:40:13
title: InfectionCounter
comment: Estimate the frequency of hepatitis C virus infected cells based on the intensity of viral antigen associated immunofluorescence. The core is an ImageJ Macro, so it's easy to modify for one's own needs (Link to the code).

inputexternal-cellprofiler
type: software
has documentation: manuals
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:44
modified: 2020-03-01T11:26:52
title: InputExternal (CellProfiler)

insegt
type: software
has function: operation Interactive segmentation
has function: operation Pixel classification
has function: operation Texture extraction
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4339
has location: texture gui handout.zip
has location: Download the GUI handout zip file
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: https://arxiv.org/abs/1809.02226
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2020-03-05T09:39:48
modified: 2023-04-28T12:58:22
title: InSegt
comment: This tool allows the user to define structures of interest by interactively marking a subset of pixels. Thanks to the real-time feedback, the user can place new markings strategically, depending on the current outcome.

insert-poisson-noise
type: software
has author: Janick Cardinale
has author: Mosaic group
has documentation: PoissonNoise manual.pdf
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-15T10:45:49
modified: 2019-10-17T13:05:12
title: Insert Poisson noise
comment: This plugin can be used to add synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. It can be used to generate benchmark images in order to assess the accuracy and robustness of image processing algorithms as a function of the noise level present in images.

inspectj
type: software
has author: Jafarpour Aliakbar orcid.org/0000-0002-1460-5743
has author: Jaiswal Astha
has author: Lorenz Holger
has documentation: InspectJ
has function: operation 3443
has function: operation RDetoixS3xEu0agR2CebaoB
has function: operation Image validation
has implementation: http://biii.eu/taxonomy/term/4340
has location: InspectJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
has usage example: Tutorials and demos on YouTube
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-12-09T17:11:53
modified: 2018-12-09T17:36:08
title: InspectJ
comment: InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity. InspectJ_v2 is a newer version for advanced users. It applies additional features like histogram equalization and gamma correction for improved image inspections.

integral-image-filters
type: software
has author: Stephan Saalfeld
has function: operation 3443
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: Integral Image Filters
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2020-03-01T11:10:45
title: Integral Image Filters

intelligent-imaging
type: software
has author: Sébastien Tosi
has documentation: intelligent-screening#h.p u1JpCvtEtZ05
has documentation: Online documentation
has function: operation 2409
has location: intelligent-screening
has location: The webpage with download links
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic High content screening
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T14:30:43
modified: 2023-04-28T15:23:47
title: Intelligent Imaging
comment: The linked webpage presents a collection of ImageJ macros for Intelligent Imaging (Feedback to microscope system for the secondary scan). An ImageJ macro able to control some microscopes (Micro-manager or Leica CAM controlled) to acquire high resolution images of only some structures (e.g. isolated cells) or events (e.g. mitosis) within a sample. The scan is sequenced as a primary (low resolution monitoring) scan and a secondary (high resolution, multi-dimensional) scan.

intelligent-matrix-screener-remote-control
type: software
has author: Megias Diego orcid.org/0000-0003-0755-0518
has DOI: 10.1038/srep10502
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: imsrc.bioinfo.cnio.es
has platform: http://biii.eu/taxonomy/term/32
has reference publication: srep10502
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-28T11:14:56
modified: 2018-01-28T11:16:33
title: intelligent Matrix Screener Remote Control
comment: Integrates hardware control of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of identified regions of interest.

intellij-idea
type: software
has documentation: documentation
has documentation: Support
has implementation: http://biii.eu/taxonomy/term/4341
has location: download
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3577
created: 2018-10-18T13:17:55
modified: 2019-03-25T15:56:44
title: IntelliJ IDEA
comment: IDE for JVM Every aspect of IntelliJ IDEA is specifically designed to maximize developer productivity. Together, the powerful static code analysis and ergonomic design make development not only productive but also an enjoyable experience. It can be seen as an alternative to Eclipse for example for java based development. It exists in both a commercial and a free and open source version.

intensity-profile-icy
type: software
has author: abrice de Chaumont
has documentation: Intensity-Profile
has function: operation 3441
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has location: Intensity-Profile
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2023-04-29T15:18:56
title: Intensity Profile (Icy)
comment: Plots an intensity profile of a given ROI. Can plot mean over T or/and Z too.

intensity-projection
type: software
has author: https://orcid.org/0000-0002-9417-7389
has function: operation Image visualisation
has function: operation Projection
has implementation: http://biii.eu/taxonomy/term/4340
has location: intensity-projection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/798
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2020-03-01T11:49:26
title: Intensity Projection

interaction-analysis
type: software
has author: Aleksandra Radenovic
has author: Arun Shivanandan
has author: Grégory Paul
has author: Ivo F Sbalzarini
has author: Jo A Helmuth
has author: MOSAIC group
has documentation: IAPManual.pdf
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-372
has reference publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-349
has reference publication: 1471-2105/11/372
has reference publication: 1471-2105/14/349
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/79
created: 2013-10-15T10:45:49
modified: 2019-10-17T11:50:33
title: Interaction Analysis
comment: This plugin can be used for inferring spatial interactions between patterns of spot-like objects in images or between coordinates read from a file.

interactive-affine
type: software
has author: Stephan Saalfeld
has documentation: Transform Affine.html
has documentation: Javadoc
has function: operation R8ANfLkuHu47r739AkhxrId
has implementation: http://biii.eu/taxonomy/term/4340
has location: Transform Affine.java
has location: Source code (Bundled with Fiji)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:47
modified: 2018-05-30T08:41:48
title: Interactive Affine
comment: quote: >This plugin allows to apply a free affine transformation to a 2D image in an interactive way.

interactive-annotator-knime
type: software
has documentation: org.knime.knip.io.nodes.annotation.create.OverlayAnnotatorNodeFactory#Interactive Annotator
has function: operation 3553
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-02T21:25:52
title: Interactive Annotator (KNIME)

interactive-density-counting-using-ilastik
type: software
has author: ilastik team
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/73
requires: http://biii.eu/node/88
created: 2014-12-08T16:00:27
modified: 2017-09-13T10:14:15
title: Interactive Density Counting using ilastik
comment: This workflow estimates (densely distributed) object counts by the density of objects in the image without performing segmentation or object detection. Current version only works for 2D images of roundish objects with similar sizes on relatively homogeneous background. Users should provide a few labels of background and objects (especially on clustered objects), and the tool predicts the density of objects on the entire image. Counting is then estimated by integrating the density values on the whole image or specified rectangular regions of interests.

interactive-features-visualization-knime
type: software
has author: Thomas Laurent 0000-0001-7686-3249
has comparison: configTFvis.json
has comparison: Similar view in the tensorflow embedding projector
has documentation: A4Eqe1Aju4A
has documentation: Youtube tutorial
has function: operation_0337
has function: operation 2990
has function: operation Clustering
has location: O3Q36l xNLQ85IRg
has location: Download the workflow from the KNIME-Hub
has reference publication: fcell.2020.00583
has reference publication: Open-access publication
has topic: topic High content screening
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2020-09-09T14:29:58
modified: 2020-10-14T07:40:23
title: Interactive features visualization in KNIME
comment: KNIME workflow to visualize a dataset described by multiple quantitative features (ex: a list of samples or cells, each described with multiple morphological features) as a 3D cloud of points (each point corresponding to one sample/cell) as well as a line plot (1 line per sample/cell). For the 3D plot, the workflow uses Principal Component Analysis (PCA) for dimensionality reduction, ie it simplifies the information for each sample from n-features to 3 pseudo-features which are used as x,y,z-coordinates for each sample. The original features should cover similar value range, to make sure the PCA is not biased towards the large values features. One option is to normalize the values (min/max or Z-score). Also make sure that the resulting PCA represents a decent % of the original data variance (at least 70%). Otherwise the PCA plot will not be representative of the original data-distribution. The % is shown in the title of the PCA plot. The workflow is interactive and so selecting in one panel of the figure will highlight in the other panel too. It was originally published for the visualization of phenotypic kidney features in zebrafish, but the workflow is generic by design and can be reused for any quantitative feature set.

interactive-image-viewer-ebimage
type: software
has documentation: EBImage.pdf
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:43
modified: 2020-03-02T21:22:27
title: Interactive Image Viewer (EBImage)
comment: display-shiny

interactive-moving-least-squares-imagej
type: software
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU General Public License
has location: Interactive Moving Least Squares
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T16:44:43
title: Interactive Moving Least Squares (ImageJ)

interactive-perspective
type: software
has author: Stephan Saalfeld
has documentation: Interactive Perspective
has function: operation Warping
has implementation: http://biii.eu/taxonomy/term/4340
has location: Interactive Perspective
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:47
modified: 2020-03-01T13:04:01
title: Interactive Perspective

interactive-rigid-imagej
type: software
has author: Stephan Saalfeld
has documentation: Interactive Rigid
has function: operation Image visualisation
has function: operation R8ANfLkuHu47r739AkhxrId
has implementation: http://biii.eu/taxonomy/term/4340
has location: Interactive Rigid
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T21:29:49
title: Interactive Rigid (ImageJ)

interactive-similarity
type: software
has author: https://orcid.org/0000-0002-4106-1761
has function: operation Geometrical transform
has implementation: http://biii.eu/taxonomy/term/4340
has location: Interactive Similarity
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-01T11:51:54
title: Interactive Similarity

interactive-stack-rotation-imagej
type: software
has author: Stephan Saalfeld
has function: operation Rotation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Interactive Stack Rotation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2020-03-02T21:07:23
title: Interactive Stack Rotation (ImageJ)

interactive-volume-interest-extractor-large-3d-stacks
type: software
has author: Sébastien Tosi
has function: operation 2409
has location: image-j-fiji#h.p ID 1541
has location: ImageJ macro - Interactive Volume of Interest Extractor in Large 3D Stacks
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p ID 1541
has usage example: User guide - Interactive Volume of Interest Extractor in Large 3D Stacks
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T14:34:46
modified: 2023-04-28T14:48:24
title: Interactive Volume of Interest Extractor in Large 3D Stacks
comment: This macro allows to interact with a large, single channel, z-stack (possibly exceeding the main memory of the computer) and to extract a volume of interest by marking several reference points.

interactive-watershed
type: software
has author: Benoit Lombardot
has documentation: Interactive Watershed
has function: operation Cell segmentation
has function: operation Interactive segmentation
has function: operation Spot extraction
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD3
has location: Interactive Watershed
has location: Interactive Watershed on the ImageJ wiki
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-10-18T08:53:18
modified: 2018-10-18T09:07:16
title: Interactive watershed
comment: The interactive Watershed Fiji plugin provides an interactive way to explore local maxima and threshold values while a resulting label map is updated on the fly. After the user has found a reliable parameter configuration, it is possible to apply the same parameters to other images in a headless mode, for example via ImageJ macro scripting.

internet-connectivity-monitor-icy
type: software
has implementation: http://biii.eu/taxonomy/term/4339
has location: Internet-Connectivity-Monitor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:41
modified: 2020-03-01T11:14:39
title: Internet Connectivity Monitor (Icy)

intramodal-registration-software
type: software
has author: Philippe Thévenaz
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4341
has location: registration
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4241
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:43
modified: 2020-03-01T10:59:22
title: Intramodal registration software

invert-icy
type: software
has function: operation Geometrical transform
has implementation: http://biii.eu/taxonomy/term/4340
has location: Invert
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-01T11:30:33
title: Invert (Icy)

inverter-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.InverterNodeFactory2#Inverter
has function: operation 2409
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:41
modified: 2020-03-01T10:50:36
title: Inverter (KNIME)

invertforprinting
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/imageprocessing.html%3Fhighlight%3Dinvert%23module-cellprofiler.modules.invertforprinting
has function: operation 3434
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4339
has location: releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-01T11:59:29
title: InvertForPrinting

ir-tools
type: software
has author: James G. Nagy
has author: Per Christian Hansen
has author: Silvia Gazzola
has function: operation Optimisation or refinement
has implementation: http://biii.eu/taxonomy/term/4339
has license: 3-Clause BSD
has location: IRtools
has location: github page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: s11075-018-0570-7
has reference publication: IR Tools: A MATLAB Package of Iterative Regularization Methods and Large-Scale Test Problems
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2020-03-03T09:48:17
modified: 2020-03-03T09:58:51
title: IR tools
comment: A MATLAB Package of Iterative Regularization Methods and Test Problems for Linear Inverse Problems (for Matlab Version 9.3 or later).

isbi-challenge-tracks-importer
type: software
has author: Chenouard, Nicolas
has author: de Chaumont, Fabrice
has documentation: isbi-challenge-tracks-importer
has function: operation 2945
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2019-10-17T11:27:10
title: ISBI Challenge Tracks Importer
comment: TrackProcessor for the TrackManager plugin that allows importing/exporting tracks. Input and output files are in the .xml format used for the ISBI'2012 Particle Tracking Challenge. Tracks are loaded/exported in/from the TrackManager plugin

isbi-tracking-challenge-batch-scoring
type: software
has author: de Chaumont, Fabrice
has documentation: isbi-tracking-challenge-batch-scoring
has function: operation 2945
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:44
modified: 2019-10-17T11:28:18
title: ISBI Tracking Challenge Batch Scoring
comment: Dedicated to score tracking dataset from the ISBI tracking challenge

ise-meshtools
type: software
has author: Renaud Lebrun
has license: GNU General Public License v2
has location: tutorialsMeshtools
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3593
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2015-01-07T11:15:51
modified: 2017-09-12T18:01:57
title: ISE-MeshTools
comment: ISE-MeshTools is a software designed by Renaud Lebrun, from the university of Montpellier II. ISE-MeshTools is a system for the processing and editing of series of 3D triangular meshes. The system provides a set of tools for editing, positioning, deforming, labelling, measuring and rendering sets of 3D meshes. Features include:  Retrodeformation for un-deforming fossils/deformed specimens  Point and curve primitives for placing the exact type of landmark points youre interested in  Easy to use 3D interface for positioning and manipulating sets of surfaces and landmark primitives  Mesh tagging, labelling and colouring (to allow for the creation of anatomy atlases)  Mesh scalar computation and colouring (based upon curvature/thickness etc...) Lebrun, R., ISE-MeshTools, a 3D interactive fossil reconstruction freeware., 12th Annual Meeting of EAVP, Torino, Italy ; 06/2014

isodata-classifier
type: software
has function: operation Image classification
has location: IsoData Classifier
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2020-03-01T11:33:31
title: IsoData Classifier
comment: This plugin calculates a classification based on the histogram of the image by generalizing the IsoData algorithm to more than two classes. This plugin works on 8-bit and 16-bit grayscale images only.

isotropic-super-resolution-em
type: software
has author: Bogovic John orcid.org/0000-0002-4829-9457
has author: Heinrich Larissa
has author: Saalfeld Stephan orcid.org/0000-0002-4106-1761
has function: operation Image enhancement
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL
has location: em-superresolution-keras
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://arxiv.org/abs/1706.03142
has reference publication: Heinrich et al. "Deep Learning for Isotropic Super-Resolution from Non-Isotropic 3D Electron Microscopy."
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3474
has topic: topic R9zg34pnGmTyzPidJj9vfJt
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1201
requires: http://biii.eu/node/1202
created: 2018-01-30T15:57:04
modified: 2023-04-29T09:24:35
title: Isotropic Super-Resolution for EM
comment: Super-resolve anisotropic EM data along low-res axis with deep learning.

iterative-closest-point-registration
type: software
has author: Jakob Wilm
has author: Hans Martin Kjer
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has reference publication: bscthesis.pdf
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2016-09-15T18:45:05
modified: 2023-04-26T07:49:21
title: iterative closest point registration
comment: The ICP algorithm takes two point clouds as an input and return the rigid transformation (rotation matrix R and translation vector T), that best aligns the point clouds. Example: [R,T] = icp(q,p,10); Aligns the points of p to the points q with 10 iterations of the algorithm. The transformation is then applied using R*p + repmat(T,1,length(p)); The file has implemented both point to point and point to plane as well as a couple of other features such as extrapolation, weighting functions, edge point rejection, etc.

iterative-deconvolve-3d
type: software
has function: operation Image deconvolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: Iterative Deconvolve 3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-01T11:41:51
title: Iterative Deconvolve 3D

itk
type: software
has function: operation 3443
has function: operation Image registration
has function: operation Image segmentation
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4339
has license: Apache 2.0
has location: itk.org
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-15T18:47:12
modified: 2019-10-14T16:47:51
title: ITK
comment: ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. It is widely used and contributed in the medical imaging field. Strengths Highly optimized C++, well commented Consistently updated (new) algorithms many tools and softwares are built upon it connected with VTK Insight Journal (open code and sample data) Extensive list of examples & tutorials Limitations yet detached from the bioimage analysis world hard to use for end users without development skills

itk-snap
type: software
has author: Guido Gerig
has author: Paul A. Yushkevich
has documentation: pmwiki.php
has documentation: Wiki
has function: operation 3553
has function: operation Active contours
has function: operation Image segmentation
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has license: -
has location: www.itksnap.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: j.neuroimage.2006.01.015
has reference publication: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 2006 Ju
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-11-07T20:19:17
modified: 2023-03-15T14:48:39
title: ITK-SNAP
comment: ITK-SNAP is a software application used to segment structures in 3D medical images. It can also be used as a 3D annotation tool for deep learning. It is based on ITK, VTK libraries.

itrack4u
type: software
has author: Fabrice P. Cordelières
has documentation: home
has function: operation RDsrmC9l0bZw9kGJzGMCyY8
has location: itrack4usoftware
has location: iTrack4U website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: journal.pone.0081266
has reference publication: Cordeliéres et. al. (2013) Automated Cell Tracking and Analysis in Phase-Contrast Videos (iTrack4U): Development of Java Software Based on Combined Mean-Shift Processese
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3385
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1308
requires: http://biii.eu/node/38
created: 2017-09-12T10:27:34
modified: 2018-05-20T23:22:00
title: iTrack4U
comment: iTrack4U is a Java-based software using ImageJ and jMathPlot libraries, which aims at automatically tracking cells recorded in phase-contrast microscopy. It includes all tools from image files preprocessing, tracking to data extraction and visualization. Please cite Cordeliéres et. al. (2013) when using this software package!

jacop
type: software
has author: Fabrice P. Cordelières
has author: Susanne Bolte
has documentation: http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Aanalysis%253Ajacop_2.0%253Ajust_another_colocalization_plugin%253Astart
has documentation: Jacop website
has function: operation Image colocalization
has function: operation Colocalisation analysis
has function: operation Pixel-based colocalisation
has location: http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Aanalysis%253Ajacop_2.0%253Ajust_another_colocalization_plugin%253Astart
has location: download Jacop
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-04-05T13:49:50
modified: 2018-11-16T08:47:48
title: JACoP
comment: This ImageJ plug-in is a compilation of co-localization tools. It allows: -Calculating a set of commonly used co-localization indicators: Pearson's coefficient Overlap coefficient k1 & k2 coefficients Manders' coefficient Generating commonly used visualizations: -Cytofluorogram Having access to more recently published methods: -Costes' automatic threshold Li's ICA Costes' randomization Objects based methods (2 methods: distances between centres and centre-particle coincidence)

jama
type: software
has documentation: jama
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1329
created: 2018-05-24T01:29:54
modified: 2018-06-06T13:17:20
title: Jama
comment: JAMA is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts. It is intended to serve as the standard matrix class for Java, and will be proposed as such to the Java Grande Forum and then to Sun. A straightforward public-domain reference implementation has been developed by the MathWorks and NIST as a strawman for such a class. We are releasing this version in order to obtain public comment. There is no guarantee that future versions of JAMA will be compatible with this one.

javadoc-parser
type: software
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: javadoc-parser
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/11
requires: http://biii.eu/node/8
requires: http://biii.eu/node/805
created: 2013-10-11T13:08:40
modified: 2020-03-01T11:07:02
title: JavaDoc Parser

javafx
type: software
created: 2018-12-09T17:09:28
modified: 2018-12-09T17:09:28
title: JavaFX

jdk
type: software
created: 2018-06-06T13:16:15
modified: 2018-06-06T13:16:15
title: JDK

jfilament
type: software
has author: Dimitrios Vavylonis
has author: Matt Smith
has author: Xiaolei Huang
has documentation: basics2d.chy
has function: operation Active contours
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: index.chy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: cm.20481
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
has usage example: basics3d.chy
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-13T10:24:00
modified: 2017-09-13T11:38:46
title: JFilament
comment: JFilament is an ImageJ plugin for segmentation and tracking of 2D and 3D filaments in fluorescenece microscopy images. The main algorithm used in Jfilament is "Stretching Open Active Contours" (SOAC). In order to use this method, the user must define seed points in the image where the SOAC method will begin. JFilament also includes 2D "closed" active contours which can be used for tasks such as segmentation and tracking of cell boundaries.

jicbioimage
type: software
has author: Tjelvar S. G. Olsson
has author: Matthew Hartley
has documentation: jicbioimage.readthedocs.io
has documentation: doc and tutorials
has function: operation 3443
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has location: installation notes.html
has location: Download page
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: peerj.2674
has reference publication: jicbioimage: a tool for automated and reproducible bioimage analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/469
created: 2016-11-15T13:48:19
modified: 2018-08-17T13:27:52
title: jicbioimage
comment: The jicbioimage Python package makes it easy to explore microscopy data in a programmatic fashion (python). Exploring images via coding means that the exploratory work becomes recorded and reproducible. Furthermore, it makes it easier to convert the exploratory work into (semi) automated analysis work flows. Features: Built in functionality for working with microscopy data Automatic generation of audit trails Python integration Works with Python 2.7, 3.3 and 3.4

jipipe-visual-batch-processing-imagej
type: software
has author: Zoltán Cseresnyés
has documentation: overview
has documentation: Online documentation
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD-2-Clause
has location: s41592-022-01744-4#code-availability
has location: Code sites
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41592-022-01744-4
has reference publication: JIPipe: visual batch processing for ImageJ
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: tutorials
has usage example: Tutorials
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1394
requires: http://biii.eu/node/60
created: 2023-04-29T08:51:12
modified: 2023-04-29T09:11:20
title: JIPipe: visual batch processing for ImageJ
comment: JIPipe is a visual programming language to realize code-free workflow building for ImageJ-based image analyses. GUI, graphical user interface. Currently, JIPipe unifies the functionality of over 1,000 ImageJ commands into a standardized interface, represented as nodes in the pipeline flow chart. The window-based data management implemented in ImageJ is replaced with a table-based model designed for batch processing. JIPipe is also available from within the ImageJ update service.

jmathplot
type: software
created: 2018-05-20T23:22:00
modified: 2018-05-20T23:22:00
title: jMathPlot

jslic
type: software
has author: Jiri Borovec
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: CMP-BIA tools
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 262916451 jSLIC superpixels in ImageJ
has reference publication: jSLIC: superpixels in ImageJ
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
has usage example: http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin:segmentation:jslic:start
has usage example: jSLIC: superpixels
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-03-08T10:19:38
modified: 2019-03-08T12:06:47
title: jSLIC
comment: jSLIC superpixels - is a segmentation method for clustering similar regions - superpixels - in the given image which are usually used for other segmentation techniques. The only two parameters are average (initial) size of each superpixel and rigidity parameter in range (0,1)

junction-mapper
type: software
has author: Tomlinson Chris
has documentation: documentation.html
has documentation: User guide and detailed computations of parameters
has function: operation 2945
has function: operation Feature extraction
has function: operation Shape features
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL v3.0
has location: Junction Mapper
has location: Git Hub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: eLife.45413
has reference publication: Junction Mapper is a novel computer vision tool to decipher cell–cell contact phenotypes (Elife 2019) Helena Brezovjakova, Chris Tomlinson, et al
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3568
created: 2023-03-22T17:08:12
modified: 2023-04-27T10:36:26
title: Junction Mapper
comment: Junction Mapper is a semi-automated software (Java Desktop application) for analysing data from images of cells in close proximity to each other in monolayers. The focus of Junction Mapper is to measure the morphology of cell boundaries, define single junctions and quantify the length, area and intensity of the staining of different proteins localised at cell-cell contacts. The output are various unique parameters that assess the contacting interface between cells and up to two junctional markers.

jupyter
type: software
created: 2018-10-18T08:44:52
modified: 2018-10-18T08:44:52
title: Jupyter

jupyter-notebook
type: software
has documentation: latest
has documentation: Online documentatoin
has implementation: http://biii.eu/taxonomy/term/4342
has license: modified BSD license
has location: install
has location: Install it
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-10-18T08:44:52
modified: 2023-05-02T14:18:55
title: Jupyter notebook
comment: The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. Try Jupyter (https://try.jupyter.org) is a site for trying out the Jupyter Notebook, equipped with kernels for several different languages (Julia, R, C++, Scheme, Ruby) without installing anything. Click the link below to go to the page.

jython-execnet-icy
type: software
has author: Alexandre Dufour
has author: Stephane Dallongeville
has author: Timothée Lecomte
has documentation: jython-execnet-for-icy
has location: http://icy.bioimageanalysis.org/download-file/%3Fid%3D15137
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/380
created: 2013-10-11T13:08:43
modified: 2020-03-01T15:06:34
title: Jython execnet for Icy
comment: Enables Python scripts that are run inside Icy to communicate with other Python instances outside Icy. This allows the access to CPython-only libraries such as Numpy. Resources requiring this include: CalloseCounter, BioFlow, EvaFE In Python

jython-extras-icy
type: software
has implementation: http://biii.eu/taxonomy/term/4340
has location: Jython Extras for Icy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/380
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2020-03-01T11:54:14
title: Jython Extras for Icy

jython-icy
type: software
has author: Alexandre Dufour
has author: Stephane Dallongeville
has author: Timothée Lecomte
has documentation: jython-for-icy
has location: http://icy.bioimageanalysis.org/download-file/%3Fid%3D14653
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/355
requires: http://biii.eu/node/380
requires: http://biii.eu/node/805
created: 2013-10-11T13:08:41
modified: 2020-03-01T17:11:01
title: Jython for Icy
comment: Python engine for Icy, based on Jython. Required for: CalloseCounter, BioFlow, EvaFE In Python, Python Plugin Packager, Python Extractor, Jython execnet for Icy

jython-imagej
type: software
created: 2018-10-18T13:20:10
modified: 2018-10-18T13:20:10
title: Jython for ImageJ

kalman-stack-filter-imagej
type: software
has author: Christopher Philip Mauer
has documentation: Kalman Stack Filter
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: Kalman Stack Filter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2020-03-02T21:18:46
title: Kalman Stack Filter (ImageJ)

kappa
type: software
has author: Hadrien Mary
has author: Kevan Lu
has documentation: Kappa User Manual.pdf
has function: operation Shape features
has license: MIT License
has location: kappa
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2017-09-12T12:50:52
modified: 2017-09-21T14:50:43
title: Kappa
comment: Kappa is a Fiji plugin for Curvature Analysis. It allows a user to measure curvature in images in a convenient way. You can trace an initial shape with a B-Spline curve in just a few clicks and then fit that curve to image data with a minimization algorithm. It’s fast and robust.

keras
type: software
created: 2018-01-30T16:00:37
modified: 2018-01-30T16:00:37
title: Keras

kmeans-color-quantization
type: software
has author: Nicolas Hervé
has documentation: kmeans-color-quantization
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: kmeans-color-quantization
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2023-04-29T15:23:39
title: KMeans Color Quantization
comment: Quantize a color image in any given number of colors.

knime
type: software
created: 2017-09-13T08:53:00
modified: 2017-09-13T08:53:00
title: KNIME

knime-align-image
type: software
has author: KNIME
has author: University of Konstanz
has function: operation Image registration
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2019-10-16T16:52:40
title: KNIME align image
comment: The input image is aligned using a simple cross-correlation approach on the smoothed image. This node is contained in KNIME Image Processing extension

knime-anisotropic-diffusion
type: software
has author: KNIME
has author: University of Konstanz
has function: operation RDyyXyhf1oHK93opXhEnRND
has location: image-processing
has reference publication: https://ieeexplore.ieee.org/document/56205
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:43
modified: 2019-10-16T16:53:30
title: KNIME Anisotropic Diffusion
comment: This Node implements the so-called anisotropic diffusion scheme of Perona and Malik, 1990. For details on the anisotropic diffusion principles, see: http://en.wikipedia.org/wiki/Anisotropic_diffusion, and the original paper: Perona and Malik. Scale-Space and Edge Detection Using Anisotropic Diffusion. IEEE Transactions on Pattern Analysis and Machine Intelligence (1990) vol. 12 pp. 629-639 The Options allows to use different Functions to be used for filtering. This node is contained in KNIME Image Processing extension

knime-auto-crop
type: software
has author: KNIME
has author: University of Konstanz
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has implementation: http://biii.eu/taxonomy/term/4340
has location: image-processing
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2019-10-16T16:54:35
title: KNIME Auto Crop
comment: Automatically crops an image by finding the smallest bounding box which still contains all pixels of the specified value. Options include Pixel values, Margin, and more... This KNIME node is included in the KNIME Image Processing Extension

knime-average-filter
type: software
has author: KNIME
has author: University of Konstanz
has documentation: org.knime.knip.base.nodes.filter.AverageFilterNodeFactory#Average Filter
has function: operation Image processing
has function: operation RDyyXyhf1oHK93opXhEnRND
has location: org.knime.knip.feature.feature.group
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2019-10-16T18:03:16
title: KNIME Average Filter
comment: Applies average filtering to images in n-dimensions

knime-connected-component-analysis
type: software
has author: KNIME
has author: University of Konstanz
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:44
modified: 2019-10-18T11:46:50
title: KNIME Connected Component Analysis
comment: Identifies connected components in an image. Connected component labeling (alternatively connected component analysis) is an algorithmic application of graph theory, where subsets of connected components are uniquely labeled. Connected component labeling is used in computer vision to detect connected regions in binary digital images. A graph, containing vertices and connecting edges, is constructed from relevant input data. The vertices contain information required by the comparison heuristic, while the edges indicate connected 'neighbors'. An algorithm traverses the graph, labeling the vertices based on the connectivity and relative values of their neighbors. Connectivity is determined by the medium; image graphs, for example, can be 4-connected or 8-connected. Copied from wikipedia [1] [2] This node is contained in KNIME Image Processing Extension

knime-convex-hull
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/728
created: 2013-10-11T13:08:44
modified: 2018-12-20T18:26:50
title: KNIME Convex Hull

knime-fill-holes
type: software
has documentation: image-processing
has function: operation Closing
has implementation: http://biii.eu/taxonomy/term/4340
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2019-10-16T13:28:29
title: KNIME Fill Holes
comment: Fill holes in a binary image.

knime-image-processing-and-analysis
type: software
has license: GPL
has location: image-processing
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/17
requires: http://biii.eu/node/321
requires: http://biii.eu/node/326
requires: http://biii.eu/node/38
requires: http://biii.eu/node/463
requires: http://biii.eu/node/469
requires: http://biii.eu/node/502
requires: http://biii.eu/node/711
requires: http://biii.eu/node/713
requires: http://biii.eu/node/716
requires: http://biii.eu/node/744
requires: http://biii.eu/node/750
requires: http://biii.eu/node/751
requires: http://biii.eu/node/754
requires: http://biii.eu/node/77
requires: http://biii.eu/node/80
requires: http://biii.eu/node/896
created: 2013-10-11T13:04:34
modified: 2017-09-13T10:01:44
title: KNIME Image Processing and Analysis
comment: KNIME is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. Its an open integration platform and provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. One of these extensions adds the ability for image analysis allowing to process, segment and further analyze images which can easily be used in combination with the other extensions, potentially from other fields.

knime-min-filter
type: software
has documentation: org.knime.knip.base.nodes.filter.nonlinear.MinFilterNodeFactory
has function: operation 3443
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2019-10-16T14:31:34
title: KNIME Min Filter

knime-multilevel-thresholding
type: software
has documentation: org.knime.knip.base.nodes.proc.multilvlthresholding.MultilevelThresholderNodeFactory
has function: operation Image thresholding
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:43
modified: 2019-10-16T14:35:04
title: KNIME Multilevel Thresholding
comment: The method to use for thresholding. Currently only OTSU is available.

knime-variance-filter
type: software
has documentation: org.knime.knip.base.nodes.filter.VarianceFilterNodeFactory#Variance Filter
has function: operation Object detection
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2019-10-18T14:38:39
title: KNIME Variance Filter

knossos-3d-image-visualization-and-annotation-tool
type: software
has author: Max Planck Institute for Medical Research in Heidelberg, Germany
has function: operation 3553
has function: operation Image segmentation
has function: operation Image visualisation
has function: operation Skeletonization
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has location: knossostool.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RByvmgDpAo4FOrMdvTm1gwR
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-01T17:18:55
modified: 2023-04-26T11:23:45
title: KNOSSOS - 3D image visualization and annotation tool
comment: It is a tool to visualize and annotate volume image data of electron microscopy. Users can annotate objects (e.g. neurons) and skeleton structures. It provides the ability to overlaying the image data with user annotations, representing the spatial structure and the connectivity of labeled objects, and displaying a three dimensional model of it. It can be extended by plugins written in python. A similar, web-based implementation is being developed at webknossos.info. Example datasets are also available.

kymograph-generation
type: software
has function: operation 3443
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
requires: http://biii.eu/node/38
created: 2018-02-01T19:07:57
modified: 2018-02-23T11:41:15
title: kymograph generation
comment: Kymograph generation under ImageJ: one simple solution, plot a line (ROI line) on the first frame, where you want to generate the kymograph. Use Image / Stacks / Reslice It will generate a new image were Y dimension is the time, and X the position on the line you have drawn.

kymographtracker-0
type: software
has author: Nicolas Chenouard
has documentation: KymographTracker
has function: operation Image tracking
has location: KymographTracker
has location: CIY KymographTracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: ICIP.2010.5652479
has reference publication: Curvelet analysis of kymograph for tracking bi-directional particles in fluorescence microscopy images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: https://doi.org/10.1101/329300
has usage example: bioRxiv 329300 Bidirectional intraflagellar transport is restricted to only two microtubule doublets in the trypanosome flagellum
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-08T14:04:21
modified: 2019-10-29T17:25:32
title: KymographTracker
comment: Generation of Kymographs using 2D+t images. In the generated kymographs, objects can be tracked and the results are visualized.

kymoquant
type: software
has author: Kota Miura
has documentation: kymoquant
has location: K kymoquant.ijm
has location: K_kymoquant.ijm
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T16:40:17
modified: 2018-05-29T00:40:13
title: Kymoquant
comment: Measurement of kymograph generally deals with slanted streaks in kymograph to measure velocity of movements. This is a pretty much manual procedure that needs hands-on work. Kymoquant analyzes kymograph by treating patterns appearing in kymograph as texture: for a specified area in kymograph, it detects the most likely orientation of streaks and outputs this result as velocity. This workflow was created to ease the situation when it is difficult to find major direction of streaks only with eyes.

label-connected-objects-ebimage
type: software
has author: Grégoire Pau
has author: Mike Smith
has author: Oleg Sklyar
has author: https://orcid.org/0000-0002-0474-2218
has author: https://orcid.org/0000-0003-0285-2787
has documentation: bwlabel.html
has function: operation Cell counting
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/969
created: 2013-10-11T13:08:43
modified: 2020-03-01T11:19:10
title: Label Connected Objects (EBImage)

labelimages-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/fileprocessing.html%3Fhighlight%3Dlabelimages%23module-cellprofiler.modules.labelimages
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: gb-2006-7-10-r100
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:44
modified: 2020-03-03T08:16:35
title: LabelImages (CellProfiler)
comment: Label images according to their position in plates.

labkit
type: software
has author: Arzt Matthias
has author: Jug Florian orcid.org/0000-0002-8499-5812
has author: Pietzsch Tobias
has author: Schmidt Deborah orcid.org/0000-0002-8621-9438
has documentation: Labkit
has function: operation 3553
has function: operation Image segmentation
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: imglib2-labkit
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
has usage example: Labkit
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-12-09T18:30:07
modified: 2023-04-28T13:14:15
title: Labkit
comment: Labkit is an open-source tool to segment truly large image data using sparse training data. It has an intuitive and responsive user interface based on Big Data Viewer, allowing users to conveniently browse and annotate even terabyte sized image volumes. Update site: Labkit

labview
type: software
has author: National Instruments
has license: commercial
has location: labview
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2016-05-30T16:03:53
modified: 2017-09-12T18:01:41
title: Labview
comment: A commercial software traditionally used in Industry and Engineering/Science to enable fast software development and deployment of a very broad range of devices control. Labview enables graphically oriented programming (no text-based coding) and offers many ready-made tools to perform basic tasks on complex data (including image data), maths operation, data handling and representation. For Image processing and analysis, Labview offers the integrated "NI Vision" tool, used in image-based quality control of production lines with a broad selection of Image-based filters/operations. In microscopy, Labview can be used efficiently to perform any kind of instrument control, and in particular "Feedback Microscopy" (also called intelligent microscopy, etc...) where the live analysis of a captured image will update the target of the microscope to make it understand where to image efficiently.

lama-localization-microscopy-analyzer
type: software
has author: Mike Heilemann
has author: Sebastian Malkush
has function: operation Cell segmentation
has function: operation Colocalisation analysis
has license: GPLv3
has location: Lama
has location: GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: srep34486
has reference publication: 10.1038/srep34486
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-07-12T14:13:42
modified: 2023-05-03T13:27:03
title: Lama: The LocAlization Microscopy Analyzer
comment: LocAlization Microscopy Analyzer (LAMA) is a software tool that contains several well-established data post processing algorithms for single-molecule localization microscopy (SMLM) data. LAMA has implemented algorithms for cluster analysis, colocalization analysis, localization precision estimation and image registration. LAMA works with a graphical user interface (GUI), and accepts simple input data formats as supported by various single- molecule localization software tools.

landmark-correspondences
type: software
has author: Stephan Saalfeld
has function: operation Geometrical transform
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: Landmark Correspondences
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:44
modified: 2021-05-19T18:57:38
title: Landmark Correspondences
comment: The plugin Landmark Correspondences calculates a transformation between two corresponding landmark clouds and renders a transformed image. The landmarks are read from point selections over two images. The transformation is estimated by a least squares or Moving Least Squares fit for the available models.

landmark-detection-dmbl-model-prediction
type: software
has author: Vandaele, Rémy
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4340
has location: W LandmarkDetect-ML-DMBL-Pred
has location: Neubias BIAFLOWS workflow of landmark detection with DMBL models (Prediction)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: j.media.2013.02.004
has reference publication: Global localization of 3D anatomical structures by pre-filtered Hough Forests and discrete optimization
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1376
requires: http://biii.eu/node/1413
requires: http://biii.eu/node/1483
created: 2019-03-15T02:19:12
modified: 2020-10-19T15:06:28
title: Landmark detection DMBL model prediction
comment: This workflow predict landmark positions on images by using DMBL landmark detection models.

landmark-detection-dmbl-model-training
type: software
has author: Vandaele, Rémy
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4340
has location: W LandmarkDetect-ML-DMBL-Train
has location: Neubias BIAFLOWS workflow of landmark detection with DMBL models (Training)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: j.media.2013.02.004
has reference publication: Global localization of 3D anatomical structures by pre-filtered Hough Forests and discrete optimization
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RxfmHE99gOkUOOML5krfsJ
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1376
requires: http://biii.eu/node/1413
requires: http://biii.eu/node/1483
created: 2019-03-15T01:35:42
modified: 2019-03-15T02:17:57
title: Landmark detection DMBL model training
comment: This workflow trains DMBL landmark detection models from a dataset of annotated images.

landmark-detection-lc-models-prediction
type: software
has author: Vandaele, Rémy
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4340
has location: W LandmarkDetect-ML-LC-Pred
has location: Neubias BIAFLOWS workflow of landmark detection with LC models (Prediction)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: TPAMI.2014.2382106
has reference publication: Robust and Accurate Shape Model Matching Using Random Forest Regression-Voting
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1376
requires: http://biii.eu/node/1413
created: 2019-03-15T01:19:31
modified: 2019-03-15T02:24:27
title: Landmark detection LC models prediction
comment: This workflow predict landmark positions on images by using LC landmark detection models.

landmark-detection-lc-models-training
type: software
has author: Vandaele, Rémy
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4340
has location: W LandmarkDetect-ML-LC-Train
has location: Neubias BIAFLOWS workflow of landmark detection with LC models (Training)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: TPAMI.2014.2382106
has reference publication: Robust and Accurate Shape Model Matching Using Random Forest Regression-Voting
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1376
requires: http://biii.eu/node/1413
created: 2019-03-15T01:04:59
modified: 2023-04-28T13:11:06
title: Landmark detection LC models training
comment: This workflow trains LC landmark detection models from a dataset of annotated images.

landmark-detection-mset-models-prediction
type: software
has author: Vandaele, Rémy
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4340
has license: Apache 2.0
has location: run.py
has location: Neubias BIAFLOWS workflow of landmark detection with MSET models (Prediction)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41598-017-18993-5
has reference publication: Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1376
created: 2019-03-15T01:00:11
modified: 2019-03-15T01:03:42
title: Landmark detection MSET models prediction
comment: This workflow predict landmark positions on images by using MSET landmark detection models.

landmark-detection-mset-models-training
type: software
has author: Vandaele, Rémy
has comparison: #tabs-dashboard-7908102
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4340
has license: Apache 2.0
has location: W LandmarkDetect-ML-MSET-Train
has location: Neubias BIAFLOWS workflow of landmark detection with MSET models (Training)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41598-017-18993-5
has reference publication: Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1376
requires: http://biii.eu/node/1413
created: 2019-03-15T00:48:02
modified: 2019-03-15T01:04:31
title: Landmark detection MSET models training
comment: This workflow trains MSET landmark detection models from a dataset of annotated images.

laplacian-philippe-thevenaz
type: software
has author: Philippe Thévenaz
has function: operation Image enhancement
has license: see http://bigwww.epfl.ch/thevenaz/differentials/index.html#LegalBlurb
has location: index.html
has location: Image Differentials
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: http://ieeexplore.ieee.org/document/799930/
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-12T15:42:43
modified: 2017-09-12T15:48:07
title: Laplacian by Philippe Thévenaz
comment: Computes image Laplacian Based on the algorithm described in the paper below. Splines: A Perfect Fit for Signal and Image Processing M. Unser IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999. DOI: 10.1109/79.799930 http://ieeexplore.ieee.org/document/799930/

larome
type: software
has author: Romain Guiet
has documentation: ijp-LaRoMe
has documentation: GitHub readme
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD3
has location: ijp-LaRoMe
has location: GitHub source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2021-01-23T03:05:07
modified: 2021-01-23T03:20:33
title: LaRoME
comment: Quote: >LaRoME = Label + Region Of Interest + Measure >Label image (aka Count Masks): An image in which pixels of an object have all the same value. Each object has a unique value. >Measurement image: An image in which pixels of an object have all the same value, corresponding to a measurement (Area, Angle, Mean...)

larva-tracking-knime
type: software
has function: operation Image segmentation
has function: operation RDsrmC9l0bZw9kGJzGMCyY8
has location: 02 Larva Tracking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2020-03-01T11:37:30
title: Larva-Tracking (KNIME)

lbadsa
type: software
has author: Aurélien Stalder
has DOI: j.colsurfa.2010.04.040
has documentation: dropanalysis
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: dropanalysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: S0927775710002761
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-10-16T11:21:01
modified: 2020-10-19T15:10:07
title: LBADSA
comment: LBADSA is based on the fitting of the Young-Laplace equation to the image data to measure drops.

leaf-infection-tools
type: software
has author: Volker Baecker
has documentation: Leaf Infection Tools
has function: operation Image colocalization
has function: operation Colocalisation analysis
has license: CeCILL-C
has location: Leaf Infection Tools
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: 9665.short
has usage example: The Multiplicity of Cellular Infection Changes Depending on the Route of Cell Infection in a Plant Virus
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1141
requires: http://biii.eu/node/1142
requires: http://biii.eu/node/38
created: 2014-12-08T16:58:59
modified: 2018-11-16T08:46:57
title: Leaf Infection Tools
comment: The Leaf Infection Tools allow to measure the area of leaves, of two stainings in different channels and of the overlap region of the two stainings. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Leaf_Infection_Tools Test image: http://biii.eu/node/1143

leaf-segmentation-using-trainable-weka-segmentation-plugin
type: software
has author: Albert Cardona
has author: Ignacio Arganda-Carreras
has author: Johannes Schindelin
has author: Verena Kaynig
has function: operation Image segmentation
has location: #complete-macro-example
has location: Trainable Weka Segmentation Macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-09T14:16:37
modified: 2023-04-28T12:21:05
title: Leaf Segmentation using Trainable Weka Segmentation plugin
comment: An example macro introduced in the documentation page of the ImageJ plugin Trainable Weka Segmentation (in Fiji, it's bundled). A segmentation protocol based on machine learning. Full macro is available in the "Download" Link. This plugin can be trained to learn from the user input and perform later the same task in unknown (test) data. Weka: it makes use of all the powerful tools and classifiers from the latest version of Weka. Segmentation: it provides a labeled result based on the training of a chosen classifier. Trainable Weka Segmentation Complete macro example is at the end of the page.

level-sets
type: software
has author: Curtis Rueden
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Level Sets
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2020-03-01T11:43:42
title: Level Sets

libtiff
type: software
has documentation: document.html
has documentation: libtiff documentation
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4241
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: libtiff.html
has usage example: Using The TIFF Library
openess: http://biii.eu/taxonomy/term/3575
created: 2018-05-31T19:58:47
modified: 2023-04-26T15:08:23
title: Libtiff
comment: LibTIFF - TIFF Library and Utilities. This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data. libtiff is a library, for reading and writing TIFF, a small collection of tools for doing simple manipulations of TIFF images.

lif-extractor
type: software
has author: Christophe Leterrier
has location: LIF Extractor 1.3.txt
has location: LIF Extractor Macro text file
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/469
created: 2014-12-09T09:35:58
modified: 2018-05-07T14:50:37
title: LIF Extractor
comment: This macro extracts .lei and .lif multichannel Z-stacks into multiple .tif stacks, splitting the channels into different stacks. Several options are possible such as background substraction, various filters, or optional reset of spatial scale. Requires Bio-Formats plugin

lif-projector
type: software
has author: Christophe Leterrier
has function: operation Projection
has location: LIF Projector 1.3.txt
has location: LIF Projector
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
requires: http://biii.eu/node/469
created: 2014-12-09T09:44:18
modified: 2018-05-07T14:47:58
title: LIF Projector
comment: This macro is similar to the LIF_Extractor, but it will output Z-projection of each Z-stack. You can choose the type of projection in addition to the other options. Requires Bio-Formats plugin

ligand-receptor-ratio-quantifier-icy
type: software
has author: Fabrice de Chaumont
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: Ligand-Receptor-ratio-quantifier
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-02T16:00:26
title: Ligand-Receptor ratio quantifier (Icy)

limeseg
type: software
has author: Nicolas Chiaruttini
has DOI: https://doi.org/10.1101/267534
has documentation: Video Tutorials
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: LimeSeg
has location: Source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://www.biorxiv.org/content/early/2018/02/18/267534
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-02-21T06:10:01
modified: 2018-05-10T12:37:07
title: LimeSeg
comment: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation **Download instruction:** There is no download but you can easily install this plugin via ImageJ update site. If you reallu need to download the jar file, access the file in the update site repository ([Link]())

linear-kuwahara-imagej
type: software
has function: operation Edge detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: Linear Kuwahara
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2020-03-02T15:36:52
title: Linear Kuwahara (ImageJ)

linear-stack-alignment-sift-imagej
type: software
has author: Stephan Saalfeld
has documentation: Linear Stack Alignment with SIFT
has function: operation 2928
has implementation: http://biii.eu/taxonomy/term/4340
has location: Linear Stack Alignment with SIFT
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T16:24:02
title: Linear Stack Alignment with SIFT (ImageJ)

list-all-threads
type: software
has location: List all threads
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2017-09-13T10:02:09
title: List all threads

list-plugins-tutorial
type: software
has location: List plugins tutorial
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:08:14
title: List plugins tutorial

loaddata-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/fileprocessing.html%3Fhighlight%3Dloaddata%23module-cellprofiler.modules.loaddata
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:40
modified: 2020-03-02T14:01:39
title: LoadData (CellProfiler)

loadimages-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/fileprocessing.html%3Fhighlight%3Dloadimages%23module-cellprofiler.modules.loadimages
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-02T12:22:10
title: LoadImages (CellProfiler)

loadsingleimage-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/fileprocessing.html%3Fhighlight%3Dloadsingleimage%23module-cellprofiler.modules.loadsingleimage
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T15:03:59
title: LoadSingleImage (CellProfiler)

lobster
type: software
has type: http://biii.eu/taxonomy/term/3567
created: 2020-03-04T08:51:27
modified: 2020-10-19T14:50:10
title: LobSTer
comment: LobSTEr : handle terabyte of data without concerns about the memory available . 75 workflows available no programming , matlab based

local-binary-pattern-general-code
type: software
has author: Ojala T, Pietikäinen M & Mäenpää T
has function: operation Image processing
has function: operation Object detection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2017-02-13T14:00:06
modified: 2019-10-18T16:29:37
title: Local BInary Pattern (general code)
comment: Matlab implementation (2014) of Local Binary Pattern. Used for texture image analysis with insensitivity to local average value. Good explanation here: http://www.ee.oulu.fi/research/imag/mvg/files/pdf/ICCV2009_tutorial.pdf

local-extrema-icy
type: software
has author: Alexandre Dufour
has documentation: Local-Extrema
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: Local-Extrema
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:44
modified: 2020-03-02T12:26:29
title: Local Extrema (Icy)

local-normalization-imagej
type: software
has author: Daniel Sage
has documentation: localnormalization
has function: operation Illumination correction
has implementation: http://biii.eu/taxonomy/term/4340
has location: localnormalization
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2020-03-02T15:10:31
title: Local Normalization (ImageJ)

local-phase-quantization-lpq-descriptors
type: software
has author: Center for machine vision and signal analysis (Oulu University)
has function: operation Image processing
has function: operation Object detection
has location: LPQMatlab
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2017-02-13T14:55:26
modified: 2019-10-18T16:18:54
title: Local Phase Quantization (LPQ) descriptors
comment: This is a Matlab implementation of Local Phase Quantization (LPQ) texture descriptors that is robust to image blurring due to the use of phase information. Theoretical background could be found here: http://www.ee.oulu.fi/research/mvmp/mvg/files/pdf/ICISP08.pdf

local-thickness-imagej
type: software
has author: Bob Dougherty
has documentation: LocalThicknessEd.pdf
has function: operation Feature extraction
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4340
has location: Local Thickness
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T15:54:12
title: Local Thickness (ImageJ)

local-thresholding-knime
type: software
has documentation: org.knime.knip.base.nodes.seg.local.LocalThresholderNodeFactory2#Local Thresholding
has location: image-processing
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2019-10-16T15:22:03
title: Local Thresholding (KNIME)
comment: Thresholding method The used thresholding Method: Mean, Median, Sauvola, MidGrey, Bernsen, Niblack. Mean, Niblack and Sauvola are implemented using the fast integral image approach.

local-z-projector
type: software
has author: Tinevez Jean-Yves orcid.org/0000-0002-0998-4718
has author: Valon Léo
has comparison: 2021.01.15.426809v3
has comparison: The main paper contains a comparison of LZP performance against existing software of this category.
has DOI: https://doi.org/10.1101/2021.01.15.426809
has documentation: localzprojector
has documentation: Documentation on GitLab
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD 3
has location: 2021.01.15.426809v3
has location: The preprint.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/8
has usage example: https://zenodo.org/record/4629187
has usage example: Example dataset and usage #4
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/80
requires: http://biii.eu/node/94
created: 2021-05-05T14:00:00
modified: 2021-05-05T14:12:49
title: Local Z Projector
comment: Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, possibly over time, possibly very large. LZP performs projection of a surface of interest on a 2D plane from a 3D image. It is a simple tool that focuses on usability and is designed to be adaptable to many different use cases and image quality. It can work with 3D movies over time with multiple channels. It can work with images much larger than available RAM out of the box. It takes advantage of computers with multiple cores, and can be used in scripts.

localcurvature
type: software
has author: Andrzej Oles
has DOI: btq046
has documentation: EBImage.pdf
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4341
has license: LGPL
has location: EBImage.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: https://academic.oup.com/bioinformatics/article/26/7/979/211835
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1152
created: 2013-10-15T10:45:51
modified: 2019-10-16T10:47:03
title: localCurvature
comment: Computes signed curvature along a line.

localization-microscopy-filtering-using-palmsiever
type: software
has author: Thomas Pengo, Seamus Holden
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/76
created: 2014-12-09T14:37:24
modified: 2017-09-12T18:02:48
title: Localization microscopy filtering using PALMsiever
comment: Sieving (or filtering) is choosing the good localizations and discarding the false ones. This operation is performed by inspecting the distribution of the localizations' fitted parameters and changing the min and max accordingly.

loci-bioformats-plugin
type: software
created: 2018-05-14T22:32:17
modified: 2018-05-14T22:32:17
title: LOCI Bioformats plugin

log-2d-canvas-icy
type: software
has location: icy.bioimageanalysis.org
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2020-03-02T16:09:36
title: Log 2D canvas (Icy)

log-spot-detection-trackmate
type: software
has location: image-processing
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/726
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:05:01
title: LoG Spot Detection (TrackMate)

log3d
type: software
has author: Daniel Sage
has documentation: LoG3D
has function: operation Image processing
has function: operation Spot extraction
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: LoG3D.zip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: TIP.2005.852787
has reference publication: Sage et al. (2005) Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-05-25T16:48:36
modified: 2018-10-18T15:34:09
title: Log3D
comment: >The freely available software module below is a 3D LoG filter. It applies a LoG (Laplacian of Gaussian or Mexican Hat) filter to a 2D image or to 3D volume. Here, we have a fast implementation. It is a perfect tool to enhance spots, like spherical particles, in noisy images. This module is easy to tune, only by selecting the standard deviations in X, Y and Z directions. # IJ Macro command example ``` run("LoG 3D", "sigmax=1 sigmay=1 sigmaz=13 displaykernel=0 volume=1"); ```

lsm-toolbox-imagej
type: software
has author: Jerome Mutterer
has author: Patrick Pirrotte
has documentation: LSM Toolbox
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: LSM Toolbox
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T21:15:35
title: LSM Toolbox (ImageJ)

luigi
type: software
has documentation: stable
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has license: Apache
has location: luigi
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-30T15:28:34
modified: 2018-01-30T15:30:49
title: Luigi
comment: Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in. The purpose of Luigi is to address all the plumbing typically associated with long-running batch processes. You want to chain many tasks, automate them, and failures will happen. These tasks can be anything, but are typically long running things like Hadoop jobs, dumping data to/from databases, running machine learning algorithms, or anything else.

lymphatic-vessel-density-calculation
type: software
has author: Cédric Balsat
has author: Nicolas Signolle
has function: operation Image segmentation
has location: https://www.hindawi.com/journals/isrn/2011/354861/
has location: Whole Slide Quantification of Stromal Lymphatic Vessel Distribution and Peritumoral Lymphatic Vessel Density in Early Invasive Cervical Cancer: A Method Description
has reference publication: http://dx.doi.org/10.5402/2011/354861
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1026
requires: http://biii.eu/node/137
created: 2014-12-09T12:09:05
modified: 2018-04-28T21:25:31
title: Lymphatic Vessel Density calculation
comment: This article Baslat et al. presents a method to compute Lymphatic Vessel Density on an image of the whole slide (a workflow documented as text). Vessels are obtained with a Maximum Entropy Thresholding applied on the excess Red channel (2 times the red values minus blue+green value). Stroma tissue is obtained with a Moment Preserving Thresholding on the blue channel.

maars
type: software
has author: Tong LI, Hadrien Mary
has documentation: doc
has function: operation Cell segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has location: MAARS
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: 1601.long
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
created: 2018-02-07T18:37:35
modified: 2018-05-22T00:36:54
title: MAARS
comment: automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

magic-montage
type: software
has author: Jerome Mutterer
has documentation: http://imagejdocu.tudor.lu/doku.php%3Fid%3Dvideo%253Autilities%253Acreating_montages_with_magic_montage
has documentation: Video Tutorial
has function: operation Montage
has location: http://imagejdocu.tudor.lu/doku.php%3Fid%3Dhowto%253Aworking%253Awork_with_magic_montage
has location: Magic Montage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T11:24:25
modified: 2018-08-17T13:00:31
title: Magic Montage
comment: This tool adds to ImageJ functions to build and organize montages. It comes with the ImageJ installer but can also be downloaded from the ImageJ wiki. A video tutorial is available.

magnifier-icy
type: software
has author: Alexandre Dufour https://orcid.org/0000-0002-9417-7389
has implementation: http://biii.eu/taxonomy/term/4340
has location: Magnifier
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2020-03-02T13:30:19
title: Magnifier (Icy)
comment: Ads a magnifier on top of the default 2D viewer to zoom in and inspect individual pixel values

mahotas
type: software
has author: Luis Pedro Coelho
has documentation: mahotas.readthedocs.io
has function: operation Image classification
has function: operation Image processing
has function: operation Image thresholding
has function: operation Morphological operations
has function: operation Shape features
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has location: install.html
has location: How to install Mahotas
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: jors.ac
has reference publication: Coelho, L.P. 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software 1(1):e3
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1312
created: 2013-10-15T18:27:40
modified: 2020-03-03T11:02:34
title: Mahotas
comment: This library gives the numpy-based infrastructure functions for image processing with a focus on bioimage informatics. It provides image filtering and morphological processing as well as feature computation (both image-level features such as Haralick texture features and SURF local features). These can be used with other Python-based libraries for machine learning to build a complete analysis pipeline. Mahotas is appropriate for users comfortable with programming or builders of end-user tools. ==== Strengths The major strengths are in speed and quality of documentation. Almost all of the functionality is implemented in for multiple dimensions. It can be used with other Python packages which provide additional functionality. Mahotas and all packages on which it relies are open-source.

mahotas-convolution
type: software
has author: Luis Pedro Coelho
has documentation: api.html#mahotas.convolve
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4339
has location: install.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:59:26
title: Mahotas / Convolution
comment: ### mahotas.convolve(f, weights, mode='reflect', cval=0.0, out={new array}) Convolution of `f` and `weights` Convolution is performed in doubles to avoid over/underflow, but the result is then cast to `f.dtype`. This conversion may result in over/underflow when using small integer types or unsigned types (if the output is negative). Converting to a floating point representation avoids this issue: ``` c = convolve(f.astype(float), kernel) ```

mahotas-distance-transform
type: software
has author: Luis Pedro Coelho
has documentation: distance.html
has function: operation Distance transform
has implementation: http://biii.eu/taxonomy/term/4339
has location: distance.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: distance.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:02:34
title: Mahotas / Distance Transform

mahotas-feature-computation
type: software
has author: Luis Pedro Coelho
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: features.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:59:26
title: Mahotas / Feature Computation

mahotas-imread
type: software
has author: Luis Pedro Coelho
has documentation: imread
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: imread
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:59:26
title: Mahotas / Imread

mahotas-labeled-image-manipulation
type: software
has author: Luis Pedro Coelho
has documentation: labeled.html
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4339
has location: labeled.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:27:37
title: Mahotas / Labeled image manipulation
comment: Labeled images are integer images where the values correspond to different regions. I.e., region 1 is all of the pixels which have value 1, region two is the pixels with value 2, and so on. By convention, region 0 is the background and often handled differently.

mahotas-morphological-operators
type: software
has author: Luis Pedro Coelho
has documentation: morphology.html
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4339
has location: morphology.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:19:45
title: Mahotas / Morphological Operators

mahotas-multidimensional-interpolation
type: software
has author: Luis Pedro Coelho
has implementation: http://biii.eu/taxonomy/term/4339
has location: mahotas.readthedocs.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:02:34
title: Mahotas / Multidimensional interpolation

mahotas-surf
type: software
has author: Luis Pedro Coelho
has documentation: surf.html
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: surf.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:00:29
title: Mahotas / SURF

mahotas-thresholding
type: software
has author: Luis Pedro Coelho
has documentation: thresholding.html
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4339
has location: thresholding.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:59:26
title: Mahotas / Thresholding

mahotas-wavelets
type: software
has author: Luis Pedro Coelho
has documentation: wavelets.html
has function: operation Image reconstruction
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4339
has location: wavelets.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/85
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:59:26
title: Mahotas / Wavelets

make-fiji-package
type: software
has author: Johannes Schindelin
has location: Make Fiji Package
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-10-16T14:34:58
title: Make Fiji Package
comment: The Fiji Packager allows you to bundle an existing Fiji installation so you can share all the plugins and update sites with colleagues. It makes a single archive (.zip, .tar.gz, .tar.bz2 are supported at the moment) from the files in Fiji.app/.

makeprojection-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/imageprocessing.html%3Fhighlight%3Dmakeprojection%23module-cellprofiler.modules.makeprojection
has function: operation Image processing
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-02T12:23:34
title: MakeProjection (CellProfiler)

mamut
type: software
has author: Pietzsch Tobias
has author: Tinevez Jean-Yves orcid.org/0000-0002-0998-4718
has function: operation 3441
has function: operation 3553
has function: operation Cell tracking
has function: operation Image tracking
has function: operation Image visualisation
has function: operation Object detection
has function: operation Overlay
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: MaMuT
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://www.biorxiv.org/content/early/2017/02/28/112623
has reference publication: Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Light-sheet microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has training material: http://biii.eu/node/1219
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1171
requires: http://biii.eu/node/330
requires: http://biii.eu/node/79
created: 2018-02-04T14:23:45
modified: 2018-10-18T15:38:19
title: MaMuT
comment: MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

mamut2r
type: software
has author: Louveaux, Marion orcid.org/0000-0002-1794-3748
has author: Rochette, Sébastien orcid.org/0000-0002-1565-9313
has DOI: zenodo.1467431
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL 3
has location: mamut2r
has location: Marion Louveaux mamut2r Github repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has type: http://biii.eu/taxonomy/term/3567
has usage example: mamut2r
openess: http://biii.eu/taxonomy/term/3575
created: 2019-02-06T22:59:02
modified: 2019-02-06T23:12:19
title: mamut2r
comment: The goal of mamut2r is to imports data coming from .xml files generated with the Fiji MaMuT plugin for lineage and tracking of biological objects. {mamut2r} also allows to create lineage plots.

manual-frame-drift-registration
type: software
has author: Kota Miura
has function: operation Image registration
has function: operation R7MFwdgojfmkZ07yWbdcda0
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has location: NicoleFrameShifter.ijm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/446
created: 2013-10-22T19:35:40
modified: 2018-10-18T15:28:46
title: Manual Frame Drift Registration
comment: An ImageJ macro for correcting frame drift occurred during image acquisition. It often happens that you have an image sequence that shows problematic drifting of image frame and at the same time you have some landmarks that could be used for correcting the drift. This ImageJ macro allows you to Manually track the landmark using ImageJ Manual Tracking Plugin. Using the coordinates recorded in the Result window, each frame is shifted back so that the landmark stays in a single place.

manual-tnt-annotation-icy
type: software
has author: Fabrice de Chaumont
has documentation: Manual-TNT-Annotation
has function: operation_0226
has location: Manual-TNT-Annotation
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2023-05-02T11:06:20
title: Manual TNT Annotation (Icy)

manual-tracking-components-imagej
type: software
has author: E. Meijering
has author: Fabrice Cordelieres
has author: TrackMate developers
has documentation: Manual tracking with TrackMate
has function: operation Image tracking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-09T10:35:01
modified: 2018-05-27T15:40:59
title: Manual Tracking Components of ImageJ
comment: The Fiji distribution of ImageJ comes with several manual tracking tools, two of which are particularly useful: * _Plugins->Tracking->Manual Tracking_ * _Plugins->Tracking->Manual tracking with TrackMate_ (TrackMate is an advanced automatic tracking tool, with the option for manual editing of tracks) The _Manual Tracking_ plugin is quick to use, intuitive and produces easy-to-understand output. TrackMate has the advantage that automatic detection and linkage can be combined with manual input. ### Update sites MtrackJ (**[see the component page here](http://biii.eu/mtrackj)) can be installed via Fiji update sites. It has many shortcut keys enabled so for manually tracking many data, it will become quite efficient as you get used to the short-cut key operation. ### Pre-processing Pre-processing steps before manual tracking might include: * denoising and/or deconvolution * flicker and photobleaching correction, e.g. using Fiji's _Image->Adjust->Bleach Correction_ * flat-field correction, and/or bandpass (ImageJ's _Process->FFT->Bandpass filter_) according to the size of the features of interest

manual-tracking-imagej
type: software
has author: Fabrice Cordelieres
has documentation: Manual Tracking plugin.pdf
has documentation: [PDF] detailed instrucitons
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: track.html
has location: Download page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2019-10-17T15:57:08
title: Manual Tracking ImageJ
comment: An ImageJ plugin for manually tracking objects by mouse clicking. This plugin is bundled with Fiji.

manual-tracking-trackmate
type: software
has author: Jean-Yves Tinevez
has documentation: Manual tracking with TrackMate
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: TrackMate -3.5.3
has location: GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.ymeth.2016.09.016
has reference publication: Tinevez et al (2017) TrackMate: An open and extensible platform for single-particle tracking
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-05-27T15:31:18
modified: 2018-05-27T15:36:20
title: Manual tracking with TrackMate
comment: Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji).

mark-objects-ebimage
type: software
has documentation: EBImage.pdf
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:41
modified: 2020-03-02T16:05:41
title: Mark Objects (EBImage)
comment: paintObjects

marker-controlled-watershed-imagej
type: software
has author: David Legland
has author: Ignacio Arganda-Carreras
has documentation: Marker-controlled Watershed
has function: operation Morphological operations
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has location: Marker-controlled Watershed
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Marker-controlled Watershed
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T14:26:56
modified: 2020-03-02T20:01:35
title: Marker-controlled Watershed (ImageJ)
comment: Marker-controlled Watershed is an ImageJ/Fiji plugin to segment grayscale images of any type (8, 16 and 32-bit) in 2D and 3D based on the marker-controlled watershed algorithm (Meyer and Beucher, 1990). This algorithm considers the input image as a topographic surface (where higher pixel values mean higher altitude) and simulates its flooding from specific seed points or markers. A common choice for the markers are the local minima of the gradient of the image, but the method works on any specific marker, either selected manually by the user or determined automatically by another algorithm. Marker-controlled Watershed needs at least two images to run: The Input image: a 2D or 3D grayscale image to flood, usually the gradient of an image. The Marker image: an image of the same dimensions as the input containing the seed points or markers as connected regions of voxels, each of them with a different label. They correspond usually to the local minima of the input image, but they can be set arbitrarily. And it can optionally admit a third image: The Mask image: a binary image of the same dimensions as input and marker which can be used to restrict the areas of application of the algorithm. Set to "None" to run the method on the whole input image. Rest of parameters: Calculate dams: select to enable the calculation of watershed lines. Use diagonal connectivity: select to allow the flooding in diagonal directions.

mask-rcnn
type: software
has author: Matterport, Inc.
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT
has location: Mask RCNN
has location: Mask-RCNN Github repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1201
requires: http://biii.eu/node/1202
requires: http://biii.eu/node/1413
created: 2019-03-15T11:31:40
modified: 2020-10-19T14:28:38
title: Mask-RCNN
comment: This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image. It's based on Feature Pyramid Network (FPN) and a ResNet101 backbone.

maskeditor-icy
type: software
has author: Nicolas Hervé
has documentation: MaskEditor
has function: operation 3096
has function: operation 3553
has location: MaskEditor
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2023-05-02T16:43:06
title: MaskEditor (Icy)

maskimage-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/imageprocessing.html%3Fhighlight%3Dmaskimage%23module-cellprofiler.modules.maskimage
has function: operation 3096
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T16:17:58
title: MaskImage (CellProfiler)

maskobjects-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/objectprocessing.html%3Fhighlight%3Dmaskobjects%23module-cellprofiler.modules.maskobjects
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T15:13:41
title: MaskObjects (CellProfiler)

math-operations-icy
type: software
has author: Alexandre Dufour; https://orcid.org/0000-0002-9417-7389
has author: Yoann Le Montagner
has implementation: http://biii.eu/taxonomy/term/4340
has location: math-operations-2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/582
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:44
modified: 2023-04-29T13:48:06
title: Math operations++ (Icy)
comment: Short Description Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequence3', in a single step. All the operations are executed pointwise. Documentation This plugin is similar to the Math operations plugin: it provides usual pointwise math operations on sequences, such as addition, product, absolute value extraction, rounding to the closest integer, etc. However, it also allows the user to perform complex combinations of theses operations, using a mathematical expression interpretor.

math-operations-icy-0
type: software
has author: Alexandre Dufour; https://orcid.org/0000-0002-9417-7389
has author: Yoann Le Montagner
has documentation: math-operations
has function: operation 2945
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: math-operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
has usage example: math-operations
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:43
modified: 2023-04-29T14:02:40
title: Math operations (Icy)
comment: Short Description Execute some simple math operations on sequences, such as addition, product, absolute value extraction, rounding to the closest integer, etc. All the operations are executed pointwise.

mathematica
type: software
has author: Wolfram
has documentation: mathematica
has function: operation_0337
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4341
has license: Commercial
has location: mathematica
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2019-10-16T12:44:37
modified: 2020-10-19T15:10:18
title: Mathematica
comment: Wolfram Mathematica (usually termed Mathematica) is a modern technical computing system spanning most areas of technical computing — including neural networks, machine learning, image processing, geometry, data science, visualizations, and others. The system is used in many technical, scientific, engineering, mathematical, and computing fields.

matlab
type: software
has author: Mathworks
has license: commercial
has location: image
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/474
requires: http://biii.eu/node/819
created: 2013-10-24T15:34:47
modified: 2017-09-13T10:12:58
title: MATLAB
comment: MATLAB is famous, so this page is only for being the landing page for components and workflows.

matlab-celldetector
type: software
has author: Alison Noble
has author: Andrew Zisserman
has author: Carlos Arteta
has author: Victor Lempitsky
has documentation: README.txt
has function: operation Cell segmentation
has location: CellDetect v1.0.tar.gz
has location: CellDetect_v1.0.tar.gz
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: arteta12.pdf
has reference publication: 978-3-642-33415-3 43
has reference publication: Arteta et al (2012) Learning to Detect Cells Using Non-overlapping Extremal Regions
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has topic: topic Digital histology
has topic: topic Fluorescent microscopy
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/89
created: 2014-12-09T13:13:47
modified: 2018-06-04T12:45:23
title: MATLAB CellDetector
comment: CellDetector can detect cells (or other objects) in microscopy images such as histopathology, fluorescence, phase contrast, bright field, etc. It uses a machine learning-based method where a cell model is learned from simple dot annotations on a few images for training and predict on test sets. The installation requires some efforts but the instruction is well explained. Training parameters should be tuned for different datasets, but the default settings could be a good starting point.

matlab-communicator-icy
type: software
has author: Yoann Le Montagner
has implementation: http://biii.eu/taxonomy/term/4340
has location: Matlab communicator
has platform: http://biii.eu/taxonomy/term/30
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/653
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2019-10-16T15:22:48
title: Matlab communicator (Icy)
comment: This plugin provides low-level tools needed to execute some functions on Icy from a Matlab application. The Matlab X server plugin, which turns Icy into an image/video/sequence viewer for Matlab, is a typical example of what can be done with Matlab communicator. (last activity Feb 2013)

matlab-compiler-runtime
type: software
created: 2017-09-12T15:00:23
modified: 2017-09-12T15:00:23
title: Matlab compiler runtime

matlab-computer-vision-system-toolbox
type: software
has license: commercial
has location: index.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/101
requires: http://biii.eu/node/211
requires: http://biii.eu/node/239
created: 2013-10-15T18:38:05
modified: 2017-09-13T10:12:41
title: Matlab Computer Vision System Toolbox
comment: The Matlab Computer Vision System Toolbox extends the Matlab core functionality with general purpose image processing functions for feature detection & extraction, object detection & tracking and motion estimation. Strengths: - Most functions extend to nD - optimized functions (muti-threaded for some) - Matlab community (Matlab central) - relatively low entry-threshold for functionality - Tutorials & Webinars Limitations: - no embedded visualization of nD Microscopy data

matlab-curve-fitting-toolbox
type: software
created: 2018-05-16T17:02:57
modified: 2018-05-16T17:02:57
title: MATLAB Curve Fitting Toolbox

matlab-exporter-icy
type: software
has author: Yoann Le Montagner
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Matlab exporter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/367
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2020-03-02T12:43:34
title: Matlab exporter (Icy)

matlab-function-caller
type: software
has documentation: Matlab-function-caller
has function: operation 3434
has implementation: http://biii.eu/taxonomy/term/4340
has location: Matlab-function-caller
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/367
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:41
modified: 2020-03-02T15:33:43
title: Matlab function caller

matlab-image-processing-toolbox
type: software
has license: commercial
has location: index.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/101
created: 2013-10-15T18:36:52
modified: 2017-09-13T10:12:40
title: Matlab Image Processing Toolbox
comment: The Matlab image processing toolbox extends the Matlab core functionality with general purpose image processing capabilities. This ranges from image access (read / write), common filters (convolution, morphology, order based, Wiener, feature extraction, image enhancement, ...), image transformation (rotation, affine transformation, ...) to segmentation algorithms (thresholding, watershed, region growing). There is also an extensive list of functions to deal with binary or label mask and perform for instance connected particle analysis or morphological operations. Strengths: - Most functions extend to nD - optimized functions (muti-threaded for some) - Matlab community (Matlab central) - relatively low entry-threshold for functionality - Tutorials & Webinars Limitations: - no embedded visualization of nD Microscopy data

matlab-image-segmentation-tutorial
type: software
has author: Image Analyst@MATLAB Central
has documentation: 25157-image-segmentation-tutorial
has function: operation Image segmentation
has location: 25157-image-segmentation-tutorial
has location: Image Segmentation Tutorial: Functions
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/89
created: 2014-12-09T16:29:58
modified: 2018-05-29T22:44:33
title: MATLAB Image Segmentation Tutorial
comment: Quote > Perfect for the beginner, this demo illustrates simple object detection (segmentation, feature extraction), measurement, and filtering. Requires the Image Processing Toolbox (IPT) because it demonstrates some functions supplied by that toolbox, plus it uses the "coins" demo image supplied with that toolbox. If you have the IPT (you can check by typing ver on the command line), you should be able to run this demo code simply by copying and pasting this code into a new editor window, and then clicking the green "run" triangle on the toolbar. >First finds all the objects, then filters results to pick out objects of certain sizes. The basic concepts of thresholding, labeling, and regionprops are demonstrated with a simple example. >It's a good tutorial for those users new to MATLAB's image processing capabilities to learn on, before they go on to more sophisticated algorithms.

matlab-importer-icy
type: software
has author: Yoann Le Montagner
has function: operation 3434
has location: matlab-importer
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/420
requires: http://biii.eu/node/829
created: 2013-10-11T13:08:46
modified: 2019-10-16T15:28:35
title: Matlab importer (Icy)
comment: Import Matlab *.mat files as sequences in Icy.

matlab-io-icy
type: software
has documentation: Matlab-IO
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Matlab-IO
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/403
requires: http://biii.eu/node/420
requires: http://biii.eu/node/680
requires: http://biii.eu/node/789
requires: http://biii.eu/node/8
requires: http://biii.eu/node/829
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:09:22
title: Matlab IO (Icy)

matlab-optimization-toolbox
type: software
created: 2018-04-28T16:49:27
modified: 2018-04-28T16:49:27
title: MATLAB Optimization toolbox

matlab-qu
type: software
has author: Aaron Christian Ponti
has documentation: http://www.scs2.net/next/index.php%3Fid%3D120
has function: operation_0337
has function: operation 3443
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: http://www.scs2.net/next/index.php%3Fid%3D120
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:21:12
title: MATLAB/ Qu

matlab-signal-processing-toolbox
type: software
created: 2018-05-29T22:36:39
modified: 2018-05-29T22:36:39
title: MATLAB Signal Processing Toolbox

matlab-statistics-toolbox
type: software
created: 2018-04-28T16:49:27
modified: 2018-04-28T16:49:27
title: MATLAB Statistics toolbox

matlab-wavelet-toolbox
type: software
has documentation: wavelet.html
has function: operation Image processing
has function: operation Object detection
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/101
created: 2019-10-18T16:35:24
modified: 2020-03-02T14:45:29
title: MATLAB Wavelet toolbox

matlab-x-server
type: software
has author: Yoann Le Montagner
has documentation: Matlab-X-server
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Matlab-X-server
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/789
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2020-03-02T16:13:52
title: Matlab X server
comment: Use Icy as an image viewer from Matlab.

matlabpyrtools
type: software
has author: Eero P. Simoncelli
has function: operation Image processing
has function: operation Object detection
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has location: matlabPyrTools
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1592
created: 2017-02-13T12:30:11
modified: 2019-10-18T16:43:29
title: matlabPyrTools
comment: This package contains some MatLab tools for multi-scale image processing. Briefly, the tools include: - Recursive multi-scale image decompositions (pyramids), including Laplacian pyramids, QMFs, Wavelets, and steerable pyramids. These operate on 1D or 2D signals of arbitrary dimension. Data structures are compatible with the MatLab wavelet toolbox. - Fast 2D convolution routines, with subsampling and boundary-handling. - Fast point-operations, histograms, histogram-matching. - Fast synthetic image generation: sine gratings, zone plates, fractals, etc. - Display routines for images and pyramids. These include several auto-scaling options, rounding to integer zoom factors to avoid resampling artifacts, and useful labeling (dimensions and gray-range).

matplotlib
type: software
has documentation: index.html
has documentation: Online documentation
has function: operation_0337
has function: operation 2409
has function: operation 3441
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: index.html
has usage example: Tutorials
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-05-27T17:47:50
modified: 2023-04-26T14:57:55
title: matplotlib
comment: Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.

maven
type: software
has documentation: ref
has documentation: Reference documentation
has implementation: http://biii.eu/taxonomy/term/4339
has location: download.cgi
has location: Downloading Apache Maven
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-12-09T17:09:28
modified: 2023-05-02T12:59:46
title: Maven
comment: Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

max-filter-knime
type: software
has documentation: org.knime.knip.base.nodes.filter.nonlinear.MaxFilterNodeFactory#Max Filter
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2020-03-02T15:27:47
title: Max Filter (KNIME)

max-homogeneity-knime
type: software
has documentation: org.knime.knip.base.nodes.filter.maxhomogenity.MaxHomogenityNodeFactory#Max Homogeneity
has function: operation Homogeneity
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-02T14:39:20
title: Max Homogeneity (KNIME)

maximum-3d-vib-protocol
type: software
has author: Schindelin, Johannes
has author: Schmid, Benjamin
has documentation: minimum-3d-filter-vib-protocol
has documentation: Minimum/Maximum/Median page at ImageJ.net website
has function: operation Morphological operations
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL v3.0
has location: VIB
has location: VIB Protocol repository at Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/903
created: 2019-02-26T15:06:14
modified: 2019-02-26T15:10:01
title: Maximum (3D) VIB Protocol
comment: This component convolves the image with maximum filter. Each voxel is set to the maximum value of its neighborhood. The neighborhood is defined by a kernel, which has a diameter of 3 voxels.

maximum-entropy-threshold-imagej
type: software
has author: Jerek Sacha
has documentation: Maximum Entropy Threshold
has function: operation Image segmentation
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: fiji.sc
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:47
modified: 2020-03-02T20:44:50
title: Maximum Entropy Threshold (ImageJ)
comment: This plugin threshold an image using the Maximum Entropy algorithm, which aims at maximizing the inter-class entropy. Entropy is defined as -sum(p.*log2(p)), where p contains the histogram bin counts. This thresholding is very useful to segment images with few bright objects on large dark background. In ImageJ/FIJI you can acces this tool in Image->Adjust->Threshold and choose in the list In Aphelion, you can access this tool in Seglmentation->Threshold-> AphImgEntropyThreshold

maximum-finder-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.maxfinder.MaximumFinderNodeFactory#Maximum Finder
has function: operation Image segmentation
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:43
modified: 2020-03-02T14:41:11
title: Maximum Finder (KNIME)

mcib3d-library
type: software
has author: Thomas Boudier
has function: operation_0226
has function: operation 2409
has function: operation 3443
has function: operation Image enhancement
has function: operation Image segmentation
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4340
has location: mcib3d-library
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/411
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2023-05-03T15:46:09
title: mcib3d library
comment: Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite.

mcluigi
type: software
has author: Pape Constantin
has function: operation 2990
has function: operation Image segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has location: mc luigi
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nmeth.4151
has reference publication: Beier et al. "Multicut brings automated neurite segmentation closer to human performance"
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1198
requires: http://biii.eu/node/73
created: 2018-01-30T15:32:42
modified: 2018-01-30T15:39:33
title: McLuigi
comment: Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty

mean-shift
type: software
has location: mean-shift.html
has type: http://biii.eu/taxonomy/term/8
has usage example: TMI2005.pdf
created: 2018-05-20T16:21:09
modified: 2018-05-20T16:28:23
title: Mean shift
comment: Mean shift is a filter which acts as edge preserving filter similarly to non local mean or anisotropic diffusion. Mean shift can be used for denoising, segmentation or clustering. Two parameters are to be tuned, a spatial size of a patch and a gray level or color distance on which the algorithm is applied.

measure-distance-organelles-nucleus-3d
type: software
has author: Christoph Möhl
has function: operation Distance transform
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/87
created: 2014-12-08T14:44:46
modified: 2018-06-09T00:08:52
title: Measure distance of organelles from nucleus in 3D
comment: A simple workflow is described in the following for measuring subcellular localizations of organelle by the distance from the nucleus. For example, you can quantify how far some type of vesicles or protein aggregates are apart from the nucleus border. This workflow is for analyzing 3D data. ## Data requirements: - 3D data, 2 channels - Channel 1: nucleus stain = Channel 2: stain for marker you want to quantify the distance to nucleus for ## Workflow: 1. Nucleus detection: Imaris - Add a new SURFACE object, name it "nuclei" - Follow the object detection wizard to segment nucleus objects 2. Marker object detection: Imaris - Add a new SURFACE object - Follow the object detection wizard to segment nucleus objects 3. Creating of distance map channel: Imaris - In the image processing menu, go to SurfacesFunctions>>Distance Transformation 4. MATLAB: - select nucleus objects and "distance outside objects" - A new image channel should be created now by the Matlab script 5. Distance measurement - The generated distance map channel represents the distance from the nucleus border in pixel values. Thus, the distance of an organelle from the nucleus is equivalent to its mean gray value of the distance map channel. For distance measurement, just export the mean gray value of the distance channel for each object. ** Please note:** In the described workflow, the distance is always calculated to the closest nucleus border. This could be also the nucleus of a neighboring cell, which generates some error. A more complex approach to avoid this error would incorporate a cell segmentation step to assign certain organelle objects to certain cells. Therefore, a cell region marker is needed.

measure-image-intensity-deprecated
type: software
has function: operation 2945
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: measurement.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:44
modified: 2019-10-16T15:12:51
title: Measure Image Intensity (deprecated)
comment: This module has been deprecated; in Cell Profiler 3.0, it is a function in module "Measurement"

measure-rosette-area-tool
type: software
has author: Volker Baecker
has documentation: Measure Rosette Area Tool
has function: operation Image thresholding
has license: CeCILL-C
has location: Measure Rosette Area Tool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: https://www.ncbi.nlm.nih.gov/pubmed/20631317%3Fdopt%3DAbstract
has usage example: Arabidopsis plants acclimate to water deficit at low cost through changes of carbon usage: an integrated perspective using growth, metabolite, enzyme, and gene expression analysis.
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T14:16:47
modified: 2017-09-13T16:17:48
title: Measure Rosette Area Tool
comment: The Measure Rosette Area Tool allows to measure the area of the rosettes of arabidopsis plants. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Measure_Rosette_Area_Tool Example data: http://biii.eu/node/1146, http://biii.eu/node/1145

measurecorrelation-cellprofiler
type: software
has documentation: index.html
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-02T15:24:03
title: MeasureCorrelation (CellProfiler)
comment: not available anymore in version 3.0 and up?

measuregranularity-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html%3Fhighlight%3Dmeasuregranularity%23module-cellprofiler.modules.measuregranularity
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2020-03-02T21:49:18
title: MeasureGranularity (CellProfiler)

measureimageareaoccupied-cellprofiler
type: software
has documentation: index.html
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T16:21:08
title: MeasureImageAreaOccupied (CellProfiler)

measureimageintensity
type: software
has location: MeasureImageIntensity.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2017-09-13T10:02:45
title: MeasureImageIntensity

measureimagequality-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html%3Fhighlight%3Dmeasureimagequality%23module-cellprofiler.modules.measureimagequality
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T12:33:00
title: MeasureImageQuality (CellProfiler)

measureneurons-cellprofiler
type: software
has function: operation Feature extraction
has function: operation Neuron image analysis
has implementation: http://biii.eu/taxonomy/term/4339
has location: MeasureNeurons.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T13:07:23
title: MeasureNeurons (CellProfiler)
comment: not available anymore in version 3.0 and up? The forum discussion below might be of interest. Sample cppproj files are available in the discussion. [Measure Neurons - Total Neuron Length Measurement](http://forum.cellprofiler.org/t/creating-a-pipeline-to-measure-neurons/4750)

measureobjectintensity-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html%3Fhighlight%3Deasureobjectintensity%23module-cellprofiler.modules.measureobjectintensity
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T12:57:10
title: MeasureObjectIntensity (CellProfiler)

measureobjectintensitydistribution
type: software
has location: measurement.html#measureobjectintensitydistribution
has location: Measure Object Intensity Distribution
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: http://journals.sagepub.com/doi/full/10.1177/1087057116652064
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2018-06-01T00:07:08
title: MeasureObjectIntensityDistribution
comment: quote: > MeasureObjectIntensityDistribution measures the spatial distribution of intensities within each object. Old Name: MeasureObjectRadialDistribution

measureobjectneighbors-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html%3Fhighlight%3Dmeasureobjectneighbors%23module-cellprofiler.modules.measureobjectneighbors
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-02T14:57:53
title: MeasureObjectNeighbors (CellProfiler)

measureobjectsizeshape-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html%3Fhighlight%3Dmeasureobjectsizeshape%23module-cellprofiler.modules.measureobjectsizeshape
has function: operation Feature extraction
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:47
modified: 2020-03-02T16:28:40
title: MeasureObjectSizeShape (CellProfiler)

measuretexture
type: software
has location: measuretexture.py
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-16T11:50:31
title: MeasureTexture
comment: It measures the degree and nature of textures within images and objects to quantify their roughness and smoothness.

measuring-confluence-adherent-cell-cultures
type: software
has author: Steven Busschotsa, Sharon OTooleb, John J. OLearya, Britta Stordal
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2014-12-08T16:07:07
modified: 2017-09-12T18:04:19
title: Measuring confluence in adherent cell cultures
comment: This publication describes a very simple protocol to acquire images of adherent cell cultures over time and how to process these images in ImageJ to measure the area fraction (confluence).

membranequant
type: software
has function: operation Image segmentation
has location: membranequant module
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-11T13:08:44
modified: 2018-10-19T14:27:41
title: MembraneQuant
comment: MembraneQuant performs automatic evaluation on IHC membrane stainings (HER2, EGFR etc). Using color deconvolution, MembraneQuant detects cell membrane and measures staining intensity on the chromogen channel. This way it is possible to calibrate the software to the actual stain protocol in the pathology lab. The algorithm categorizes the detected membrane to weak positive, medium positive and strong positive classes. This software has an IVD certification for HER2 quantification.

merge-images
type: software
has documentation: EBImage.pdf
has function: operation Image processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
requires: http://biii.eu/node/973
created: 2013-10-11T13:08:44
modified: 2019-10-16T11:10:54
title: Merge Images

mergeoutputfiles
type: software
has function: operation 2409
has location: mergeoutputfiles.py
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:40
modified: 2019-10-16T10:08:48
title: MergeOutputFiles

merger
type: software
has documentation: org.knime.knip.base.nodes.misc.merger.MergerNodeFactory#Merger
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:43
modified: 2019-10-16T12:41:09
title: Merger
comment: Merges images from different columns to one image object as follows: the input images are regarded as one single line of pixels (depending on the iteration order of each underlying image factory).

metamorph
type: software
has license: commercial
has location: metamorph.html
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-11-07T20:16:04
modified: 2017-09-12T18:05:44
title: Metamorph
comment: Metamorph provides all tools needed to perform analysis of acquired images with user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.

metroloj
type: software
has author: Cordelières Fabrice P
has author: Matthews Cédric
has documentation: http://web.archive.org/web/20201127013301/https://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin:analysis:metroloj:start
has documentation: The MetroloJ plugin
has function: operation Image validation
has implementation: http://biii.eu/taxonomy/term/4340
has location: http://web.archive.org/web/20201127013301/https://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin:analysis:metroloj:start
has location: A static image of the website (a old version downloadable)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: ImageJ-MetroloJ.pdf
has reference publication: MetroloJ: an ImageJ plugin to help monitor microscopes’ health.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-01-30T09:17:11
modified: 2023-05-03T10:02:40
title: MetroloJ
comment: This plugin allows measuring relevant parameters which helps testing, following and comparing microscopes performances. This is achieved by extracting four indicators out of standardized images, acquired from standardized samples: the estimation of the detector sensitivity, the evaluation of the field illumination homogeneity, the system resolution, and finally the characterization of its spectral registration.

mevislab
type: software
has author: Fraunhofer MEVIS
has documentation: documentation
has documentation: user tutorial and documentation for development and scripting
has function: operation_0337
has function: operation Image registration
has function: operation Image segmentation
has function: operation Morphological operations
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4341
has location: www.mevislab.de
has location: MeVisLab homepage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has programming language: http://biii.eu/taxonomy/term/4817
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3444
has topic: topic 3452
has topic: topic RxfmHE99gOkUOOML5krfsJ
has type: http://biii.eu/taxonomy/term/3567
has usage example: publications
has usage example: publications that use MeVisLab
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3576
openess: http://biii.eu/taxonomy/term/3577
created: 2019-01-29T20:12:17
modified: 2019-01-30T10:02:45
title: MeVisLab

mevislab-xmarkershortestpath-module-dijsktra-shortest-path
type: software
has author: Ola Friman
has documentation: XMarkerShortestPath.html
has documentation: XMarkerShortestPath documentation
has function: operation 2945
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1421
created: 2019-01-29T21:15:02
modified: 2019-02-04T17:00:22
title: MeVisLab XMarkerShortestPath module (Dijsktra shortest path)

mia
type: software
has author: Stephen Cross
has DOI: zenodo.1201320
has DOI: MIA on Zenodo
has documentation: modules.html
has documentation: List of modules
has function: operation 3443
has function: operation Cell counting
has function: operation Image registration
has function: operation Image segmentation
has function: operation Image tracking
has function: operation Image visualisation
has function: operation Morphological operations
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU General Public License v3.0
has location: modularimageanalysis
has location: MIA installation instructions
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: zenodo.1201320
has reference publication: MIA on Zenodo
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
has usage example: mia examples
has usage example: Example workflows
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1057
requires: http://biii.eu/node/79
created: 2022-05-31T07:32:53
modified: 2022-06-01T14:52:36
title: MIA
comment: ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets. MIA is designed for “out-of-the-box” compatibility with spatially-calibrated 5D images, yielding measurements in both pixel and physical units. Functionality can be extended both internally, via integration with SciJava’s scripting interface, and externally, with Java modules that extend the MIA framework. Both have full access to all objects and images in the analysis workspace. Workflows are, by default, compatible with batch processing multiple files within a single folder. Thanks to Bio-Formats, MIA has native support for multi-series image formats such as Leica .lif and Nikon .nd2. Workflows can be automated from initial image loading through processing, object detection, measurement extraction, visualisation, and data exporting. MIA includes near 200 modules integrated with key ImageJ plugins such as Bio-Formats, TrackMate and Weka Trainable Segmentation. Module(s) can be turned on/off dynamically in response to factors such as availability of images and objects, user inputs and measurement-based filters. Switches can also be added to “processing view” for easy workflow control. MIA is developed in the Wolfson Bioimaging Facility at the University of Bristol.

miatool
type: software
has license: Unknown
has location: miatool
has platform: http://biii.eu/taxonomy/term/31
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/286
created: 2016-10-09T17:01:48
modified: 2017-09-13T10:16:37
title: MIATool
comment: The Microscopy Image Analysis Tool (MIATool) is a software application designed for the viewing and processing of N-dimensional array of images. At its core is an image viewer which allows the traversal of an N-dimensional array of images. Besides the standard display as pixels of varying intensity values, options are available to view the images as mesh or contour plots. The current version of MIATool supports four different image editing tools which can be used to process the images displayed in the viewer. The intensity adjustment tool provides different ways to modify the pixel intensity values, and the crop tool allows trimming of the images to retain only the portion that is of interest. The two remaining tools - the segmentation tool and the label tool - can be used for manual image segmentation and image labeling.

mice-profiler-label-analyser
type: software
has documentation: mice-profiler-label-analyser
has function: operation 2945
has function: operation Trajectory analysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth.1924
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-16T10:36:12
title: Mice Profiler Label Analyser
comment: Mice Profiler uses geometrical primitives to model and track two mice without requiring any specific tagging. The program monitors a comprehensive repertoire of behavioral states and their temporal evolution, allowing the identification of key elements that trigger social contact. Mice Profiler Label Analyser performs temporal analysis of data from Mice Profiler.

mice-profiler-tracker
type: software
has function: operation Image tracking
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: mice-profiler-tracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth.1924.html
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: 9sgoB-StV-k
has usage example: Video tutorial
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2023-04-29T15:40:32
title: Mice Profiler Tracker
comment: Mice Profiler tracks multiple mice from a top view video.

mice-profiler-video-label-maker
type: software
has location: Mice Profiler Video Label Maker
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:05:37
title: Mice Profiler Video Label Maker

micro-manager
type: software
has license: -
has location: MMwiki
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-11-07T20:16:58
modified: 2017-09-13T10:13:11
title: Micro-Manager
comment: -

micro-manager-icy
type: software
has author: Thomas Provoost, Stephane Dallongeville
has documentation: micro-manager-for-icy
has implementation: http://biii.eu/taxonomy/term/4340
has location: micro-manager-for-icy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2020-03-02T13:51:37
title: Micro-Manager for Icy

microbej
type: software
has author: Adrien Ducret, Yves Brun, Ellen Quardokus
has documentation: documentation
has function: operation 2945
has function: operation Image thresholding
has function: operation Image tracking
has function: operation Morphological operations
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: www.microbej.com
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-10-04T11:53:07
modified: 2023-04-26T11:14:18
title: MicrobeJ
comment: This is an ImageJ plugin to analyze bacterial cells. It provides a user-friendly interface and a powerful suite of detection, analysis and data presentation tools. It works with individual phase or fluorescence images as well as stacks, hyperstacks, and folders of any of these types. Even large image sets are analyzed rapidly generating raw tabular data that can either be saved or copied as is, or have additional statistical analysis performed and graphically represented directly from within MicrobeJ, making it an all-in-one image analysis solution.

micromanager-icy
type: software
has documentation: micro-manager-for-icy
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2019-10-16T10:17:46
title: Micromanager for Icy

micromanagerlibs-deprecated
type: software
has author: Thomas Provoost, Stephane Dallongeville
has documentation: micromanagerlibs-deprecated
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2020-03-02T13:51:08
title: MicroManagerLibs (deprecated)
comment: Used to be the micro manager libraries but now that is an empty plugin (provided for backward compatibility).

microscope-advanced-acquisition-deprecated
type: software
has documentation: microscope-advanced-acquisition-deprecated
has location: microscope-advanced-acquisition-deprecated
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2023-04-29T14:42:01
title: Microscope Advanced Acquisition (deprecated)

microscope-autopilot
type: software
has author: Eugene Myers
has author: Loic A. Royer
has author: Michael Coleman
has author: Philipp J. Keller
has author: Raghav K. Chhetri
has author: William C. Lemon
has author: Yinan Wan
has documentation: microscopeautopilot.github.io
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4339
has license: Non-Profit Open Software License 3.0 (NPOSL-3.0)
has location: autopilot
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nbt.3708
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-10-18T09:59:10
modified: 2018-10-18T13:16:52
title: Microscope autopilot
comment: AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

microscope-calibrator-manager
type: software
has function: operation Validation
has location: microscope-calibrator-manager
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-16T09:59:07
title: Microscope Calibrator Manager

microscope-calibrator-pixel-size
type: software
has documentation: microscope-calibrator-pixel-size
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/581
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-16T13:39:00
title: Microscope Calibrator Pixel Size
comment: Calibrator for Pixel Size in Calibrator manager.

microscope-image-correlation-spectroscopy-mics
type: software
has author: Chen Chen
has author: Paul-Gilloteaux Perrine
has author: Waharte François
has function: operation Feature extraction
has function: operation RBUpi1JSczmHQSf8Q8fDzG5
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU General public License
has location: http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin:analysis:microscope_image_correlation_spectroscopy:start%26s%5B%5D%3Dspectroscopy
has location: Download page (broken)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s12013-007-9000-5
has topic: topic Image correlation spectroscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-15T11:39:08
modified: 2023-04-27T14:48:39
title: Microscope Image Correlation Spectroscopy MICS
comment: Fluorescence spectroscopy by image correlation is a technique that allows analysing and characterizing the different molecular dynamics from a sequence of fluorescence images. Many image correlation techniques have been developed for different applications but in particular to study the mechanisms of cell adhesion during migration. These techniques can be used with most imaging modalities: e.g. fluorescence widefield, confocal microscopy, TIRFM. They allow to obtain information such as the density in molecules, diffusion coefficients, the presence of several populations, or the direction and speed of a movement corresponding to active transport when spatial and temporal correlations are taken into account (STICS: Spatio-Temporal Image Correlation Spectroscopy). This plugin is based on ICS_tools plugin by Fitz Elliott, available here. Some bugs have been removed, ROI does not need to be squared, fitting is weighted in order to give more weight to the smaller lags (temporal or spatial) Exemple of use on sample data [fluorescent beads](http://biii.info/node/2577 "Beads") - Select an ROI, start by ICS to get the right PSF size - Then run TICS and select diffusion, or diffusion plus flow model. Remove the first line (autocorrelation) which corresponds to the noise autocorrelation before fitting.

microscope-live-3d-deprecated
type: software
has documentation: microscope-live-3d-deprecated
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2019-10-16T13:03:06
title: Microscope Live 3D (deprecated)

microscope-live-deprecated
type: software
has documentation: microscope-live-deprecated
has location: microscope-live-deprecated
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/116
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2023-04-29T14:27:21
title: Microscope Live (deprecated)

microscope-snapper-icy-deprecated
type: software
has author: Stephane Dallongeville
has author: Thomas Provoost
has documentation: microscope-snapper-deprecated
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: microscope-snapper-deprecated
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/499
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2023-04-29T15:07:20
title: Microscope Snapper (Icy) (deprecated)

microscopy-blocks-icy
type: software
has documentation: microscopy-blocks-deprecated
has implementation: http://biii.eu/taxonomy/term/4340
has location: microscopy-blocks-deprecated
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2023-04-29T14:16:51
title: Microscopy Blocks (Icy)
comment: Deprecated ! Use the new Micro-Manager blocks plugin.

microscopy-image-browser-mib
type: software
has author: Ilya Belevich
has function: operation_0337
has function: operation Image enhancement
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has location: mib.helsinki.fi
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: journal.pbio.1002340
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3385
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-09-12T13:24:24
modified: 2023-05-12T15:52:11
title: Microscopy Image Browser (MIB)
comment: Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. MIB is a freely available, user-friendly software for effective image processing of multidimensional datasets that improves and facilitates the full utilization of acquired data and enables quantitative analysis of morphological features. Its open-source environment enables fine tuning and possibility of adding new plug-ins to customize the program for specific needs of any research project.

microtubule-end-tracking-drosophila-oocyte
type: software
has author: Graeme Ball
has function: operation Image tracking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: jcb.201103160
has reference publication: Parton et al (2011) A PAR-1-dependent orientation gradient of dynamic microtubules directs posterior cargo transport in the Drosophila oocyte
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1326
requires: http://biii.eu/node/1327
requires: http://biii.eu/node/330
requires: http://biii.eu/node/79
requires: http://biii.eu/node/893
created: 2014-12-08T13:26:38
modified: 2023-05-03T08:51:56
title: Microtubule end tracking in Drosophila Oocyte
comment: Microtubule end tracking in live cell fluorescent images of Drosophila oocyte involves overcoming the following challenges, which can be tackled by a series of preprocessing steps and tracking described in Parton et al (2011) illumination flicker & photobleaching: suppress by normalising intensities, e.g. using Image->Adjust->Bleach Correction in Fiji/ImageJ uneven illumination: Fourier bandpass filtering (e.g. Process->FFT->Bandpass Filter) preserves features within a selected size range high background / poor contrast: foreground filter, e.g. Temporal Median filter tracking: e.g. TrackMate in Fiji/ImageJ (segmentation using DoG detector)

microtubule-length-analysis
type: software
has author: Perrine Paul-Gilloteaux
has documentation: cid.curie.fr
has function: operation Image segmentation
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1140
requires: http://biii.eu/node/261
requires: http://biii.eu/node/79
created: 2014-12-08T14:32:27
modified: 2023-05-03T08:39:51
title: Microtubule Length Analysis
comment: Task Quantify the length of microtubules (MT) and the MT average density per cell. Workflow descriptions Simple two step workflow, allowing visual & manual correction of microtubule between the 2 steps. Batch measurement of microtubule lengths for multiple images is achieved by segmenting the MTs and then their skeletonizations. The number of pixels in the microtubule is proportional to their length, so the length can be estimated. Script Workflow is written as an ImageJ macro (Fiji) with following steps: 1. The enhancement of tubular structure by computing eigenvalues of the hessian matrix on a Gaussian filtered version of the image ( sigma 1 pixel), as implemented in the tubeness plugin. 2. The tubules were then thresholded , and structures containing less than 3 pixels were discarded. 3. If needed, a visual check and correction of segmented microtubule is then performed. 4. After correction, segmented MTs were then reduced to a 1-pixel thick line using the skeletonize plugin of Fiji. The length of the skeletonized microtubules was then directly proportional to their length. 5. Data were grouped by condition and converted back to micrometers units under Matlab for the statistical tests. Pitfalls Commented but not that general without editing some fields in the macros. Sample Data Sample data and workflow (see above URL) can be accessed by - login: biii - password Biii! Misc 3D version also available here. Use of components Skeletonize and Tubeness Filter

microtubules-tool-3d
type: software
has author: Volker Baecker
has documentation: Microtubules Tool (3D)
has function: operation Image thresholding
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has license: CeCILL-C
has location: Microtubules Tool (3D)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/261
requires: http://biii.eu/node/38
requires: http://biii.eu/node/670
requires: http://biii.eu/node/764
requires: http://biii.eu/node/79
created: 2013-10-30T19:05:39
modified: 2023-05-03T08:48:10
title: Microtubules Tool (3D)
comment: The tool measures the total length of the microtubules in a 3D image. See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Microtubules_Tool_(3… You can find a test image here.

microtubuletracker-fiji
type: software
has author: Varun Kapoor
has documentation: MicrotubuleTracker
has function: operation Image tracking
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: MicrotubuleTracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic R7WRbf9Y8ySw9QWPwAjzcUa
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
has usage example: MicrotubuleTracker
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-01-28T11:39:13
modified: 2023-05-03T08:36:00
title: MicrotubuleTracker in FIJI
comment: MTrack is a tool, which detects, tracks, and measures the behavior of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such an in vitro reconstitution approach, stabilized, non-dynamic microtubule seeds serve as nucleation points for dynamically growing microtubules. MTrack is a bi-modular tool. The first module detects and tracks the growing microtubule ends and creates trajectories. The second module uses these trajectories to fit models of dynamic behavior (polymerization and depolymerization velocities, catastrophe and rescue frequencies). It also computes statistics such as length and lifetime distributions when analyzing more than one movie (batch mode).

mij
type: software
has author: Daniel Sage
has documentation: mij
has function: operation 3434
has implementation: http://biii.eu/taxonomy/term/4340
has location: mij
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T21:37:39
title: MIJ
comment: A Java package for running ImageJ and Fiji within Matlab.

mina-mitochondrial-network-analysis
type: software
has documentation: mina
has documentation: MiNA - Mitochondrial Network Analysis
has function: operation 3443
has function: operation Image thresholding
has function: operation Morphological operations
has function: operation Skeletonization
has implementation: http://biii.eu/taxonomy/term/4340
has location: mina#installation
has location: Installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
has usage example: mina#processing-pipeline-and-usage
has usage example: Processing Pipeline and Usage
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2023-04-27T11:44:24
modified: 2023-04-27T12:05:48
title: MiNA - Mitochondrial Network Analysis
comment: MiNA is a simplified workflow for analyzing mitochondrial morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops, 3D Viewer, Skeletonize (2D/3D), Analyze Skeleton, and Ridge Detection. In short, the tool estimates mitochondrial footprint (or volume) from a binarized copy of the image as well as the lengths of mitochondrial structures using a topological skeleton. The values are reported in a table and overlays (or a 3D rendering) are generated to assess the accuracy of the analysis.

miniature-faking
type: software
has function: operation Image processing
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Miniature Faking
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-16T10:19:01
title: Miniature Faking

minimum-cost-z-surface-projection
type: software
has author: Benoit Lombardot
has documentation: Minimum Cost Z surface Projection
has function: operation Projection
has implementation: http://biii.eu/taxonomy/term/4340
has location: Minimum Cost Z surface Projection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-10-18T09:29:35
modified: 2018-10-18T13:16:04
title: Minimum cost Z surface projection
comment: This plugin detects a minimum cost z-surface in a 3D volume. A z surface is a topographic map indicating the altitude z as a function of the position (x,y) in the image. The cost of the surface depends on pixel intensity the surface is going through. This plugin find the z-surface with the lowest intensity in an image.

mipav
type: software
has documentation: MIPAV Help
has function: operation 3443
has function: operation Image colocalization
has function: operation Image registration
has function: operation Image segmentation
has function: operation Image smoothing
has function: operation Image thresholding
has function: operation Image visualisation
has function: operation Object detection
has function: operation Pixel classification
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4339
has location: mipav.cit.nih.gov
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic 3444
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RxfmHE99gOkUOOML5krfsJ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-30T15:40:55
modified: 2018-11-16T08:46:57
title: MIPAV
comment: The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.

mips-psfs
type: software
has author: Jens Rietdorf
has author: Laurent Gelman
has function: operation 3443
has function: operation Image visualisation
has license: Freely available upon request to the author
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: routine-assessment-fluorescence-microscope-performance
has reference publication: Published in Imaging and Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2019-02-03T09:43:56
modified: 2023-04-27T14:53:36
title: MIPs for PSFs
comment: The macro generates orthogonal projections from bead images along the lateral and axial dimensions which are displayed using a customized look-up-table to color code intensities. A Gaussian curve is fit to the intensity profile of a fluorescent bead image and full-with-at-half-maximum (FWHM) values are extracted, and listed next to theoretical values for comparison.

mitobo
type: software
has documentation: MiToBoManual.pdf
has documentation: MiToBo-Guide (pdf)
has function: operation_0337
has function: operation 2945
has function: operation Cell segmentation
has function: operation Feature extraction
has function: operation Object detection
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has location: Main Page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
requires: http://biii.eu/node/79
created: 2018-12-10T23:11:59
modified: 2023-04-30T15:33:32
title: MiToBo
comment: "The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0. MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes."

mixture-modeling-thresholding
type: software
has author: Christopher Mei, Maxime Dauphin
has documentation: Mixture Modeling Thresholding
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/671
created: 2013-10-11T13:08:46
modified: 2019-10-16T14:47:16
title: Mixture Modeling Thresholding
comment: This plugin automatically threshold an image using the Mixture Modeling algorithm. It is an histogram-based technique that assumes that the histogram distribution is represented by two Gaussian curves.

mobie-fiji-viewer
type: software
has author: Pape Constantin
has author: Tisher Christian
has documentation: mobie-viewer-fiji
has documentation: Git Hub
has function: operation_0337
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: MoBIE
has location: From Fiji add the MoBie site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41592-023-01776-4
has reference publication: Pape, C., Meechan, K., Moreva, E. et al. MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data. Nat Methods (2023).
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3385
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
has usage example: 2020.02.26.961037v1.abstract
has usage example: Whole-body integration of gene expression and single-cell morphology
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1171
requires: http://biii.eu/node/79
created: 2020-09-09T11:25:07
modified: 2023-03-06T15:32:34
title: MoBIE Fiji Viewer
comment: MoBIE (Multimodal Big Image Data Exploration) is a framework for sharing and interactive browsing of multimodal big image data. The MoBIE Fiji viewer is based on BigDataViewer and enables browsing of MoBIE datasets. It is also called Platybrowser, and uses the n5 format.

mobie-utils-python
type: software
has author: Tisher Christian
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: mobie-utils-python
has location: github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2020-09-09T11:37:42
modified: 2020-09-09T11:43:46
title: MoBIE-Utils-Python
comment: The library contains several helper functions to generate MoBIE project folders and add data to it. Itis a python library to generate data in the MoBIE data storage layout. For further information, look to http://biii.eu/mobie-fiji-viewer

moment-thresholding-imagej
type: software
has author: W. Tsai
has documentation: Auto Threshold#Moments
has function: operation Image segmentation
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 0734-189X(85)90133-1
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2014-12-09T10:08:27
modified: 2020-03-02T20:47:53
title: Moment thresholding (ImageJ)
comment: This method allows to compute a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose Moments in the list. In Aphelion, the tool is in Segmentation->Threshold->AphImgMomentThreshold The original paper is 2449

monogenicj
type: software
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has implementation: http://biii.eu/taxonomy/term/4340
has location: monogenicj
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: unser0907.html
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T11:00:16
title: MonogenicJ
comment: MonogenicJ performs multiresolution monogenic analyses of 2D images. It extracts wavelet-domain features that characterize the local orientation, the phase and the dominant frequency of an image patch at various levels of resolution.

montage-2d
type: software
has author: Alexandre Dufour
has documentation: Montage-2D
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-16T14:03:57
title: Montage 2D
comment: Displays 3D data as 2D montages of all slices.

mophological-image-operations
type: software
has documentation: org.knime.knip.base.nodes.proc.binary.morphops.MorphImgOpsNodeFactory
has function: operation Morphological operations
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2019-10-16T14:29:39
title: Mophological Image Operations
comment: Perform morphological operations (like erode and dilate or open and close) on images.

morph
type: software
has documentation: imageprocessing.html#morph
has function: operation Morphological operations
has location: Morph.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-16T15:17:40
title: Morph
comment: This module performs a series of morphological operations on a binary image or grayscale image, resulting in an image of the same type.

morphographx
type: software
has author: Pierre Barbier de Reuille, http://orcid.org/0000-0002-9970-765X
has author: Richard S Smith, http://orcid.org/0000-0001-9220-0787
has DOI: eLife.05864
has documentation: software
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4341
has location: MorphoGraphX
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: eLife.05864
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-09-12T09:22:27
modified: 2020-03-03T19:54:40
title: MorphoGraphX
comment: MorphoGraphX is a free Linux application for the visualization and analysis of 3D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 3D live-imaged confocal data sets. The main research interests adressed by MorphoGraphX are: Shape extraction Growth analysis Signal quantification Protein localization

morpholeaf
type: software
has author: Eric Biot (eric biot AT versailles inra fr)
has function: operation Image registration
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: morpholeaf.versailles.inra.fr
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/153
created: 2016-10-05T21:40:54
modified: 2018-10-18T15:31:08
title: Morpholeaf
comment: The MorphoLeaf application allows you to extract the contour of multiple leaf images and identify their biologically-relevant landmarks. These landmarks are then used to quantify morphological parameters of individual leaves and to reconstruct average leaf shapes. MorphoLeaf is developed by the Modeling and Digital Imaging and the Transcription Factors and Architecture teams of the Institut Jean-Pierre Bourgin, INRA Versailles, France, and the Biophyscis and Development group at RDP, Lyon.

morpholibj
type: software
has author: Arganda-Carreras, Ignacio
has author: Legland, David
has documentation: MorphoLibJ-manual-v1.3.3.pdf
has documentation: MorphoLibJ user manual (v1.3.3)
has function: operation Cell counting
has function: operation Cell segmentation
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Morphological operations
has function: operation Shape features
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has location: MorphoLibJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: btw413
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-10-01T16:31:47
modified: 2023-04-25T17:17:43
title: MorphoLibJ
comment: MorphoLibJ is a library of plugin for ImageJ with functionalities for image processing such as filtering, reconstructing, segmenting, etc... Tools are based on Mathematical morphology with more rigorous mathematical approach than in the standard tools of ImageJ in particular for surface (or perimeter) measurements which are usually based on voxel counting. http://imagej.net/MorphoLibJ#Measurements Among the features: Morphological operations : Dilation, Erosion, Opening, Closing , Top hat (white and black), Morphological gradient (aka Beucher Gradient), Morphological Laplacian, Morphological reconstruction, Maxima/Minima , Extended Maxima/Minima -Watershed (classic or controlled) -Image overlay -Image labelling -Geodesic diameter -Region Adjacency Graph -Granulometry curves, morphological image analysis.

morpholibj-using-morphological-reconstructions-isolate-objects
type: software
has author: Fabrice Cordelières
has function: operation Image segmentation
has function: operation Morphological operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/1057
requires: http://biii.eu/node/38
created: 2016-10-01T15:44:34
modified: 2023-05-03T14:19:07
title: MorphoLibJ: using morphological reconstructions to isolate objects
comment: When trying to isolate objects, one strategy might be to use regular morphological operations (opening/closing) to remove small objects that are not of interest. In case small objects are made of a large number of pixels, this operation might impair the remaining objects' contours. An alternative strategy might be to use morphological reconstruction. In short, seed is placed on the image, on objects, then conditional dilation is performed from those seeds. Here is how to proceed, using MorphoLibJ: Open an image Use the multi-point selection tool and place seeds on objects of interest Create a new image of same size, black background Transfer the selection to the new image (Edit/Selection/Restore selection) Draw (make sure you're using white foreground) the multiple point selection Launch the Morphological reconstruction plugin: Plugins > MorphoLibJ > Morphological reconstruction

morphological-operations
type: software
has location: EBImage.pdf
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/332
requires: http://biii.eu/node/86
requires: http://biii.eu/node/971
requires: http://biii.eu/node/975
requires: http://biii.eu/node/979
requires: http://biii.eu/node/998
created: 2013-10-11T13:08:40
modified: 2017-09-13T10:01:58
title: Morphological Operations

morphological-segmentation-imagej
type: software
has author: David Legland
has author: Ignacio Arganda-Carreras
has documentation: Morphological Segmentation
has function: operation Morphological operations
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has location: Morphological Segmentation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Morphological Segmentation
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T14:20:42
modified: 2020-03-02T20:05:40
title: Morphological Segmentation (ImageJ)
comment: Morphological Segmentation is an ImageJ/Fiji plugin that combines morphological operations, such as extended minima and morphological gradient, with watershed flooding algorithms to segment grayscale images of any type (8, 16 and 32-bit) in 2D and 3D. Morphological Segmentation runs on any open grayscale image, single 2D image or (3D) stack. If no image is open when calling the plugin, an Open dialog will pop up. The user can pan, zoom in and out, or scroll between slices (if the input image is a stack) in the main canvas as if it were any other ImageJ window. On the left side of the canvas there are three panels of parameters, one for the input image, one with the watershed parameters and one for the output options. All buttons, checkboxes and input panels contain a short explanation of their functionality that is displayed when the cursor lingers over them. Image pre-processing: some pre-processing is included in the plugin to facilitate the segmentation task. However, other pre-preprocessing may be required depending on the input image. It is up to the user to decide what filtering may be most appropriate upstream.

morphomaths
type: software
has function: operation Morphological operations
has location: MorphoMaths
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/8
requires: http://biii.eu/node/826
requires: http://biii.eu/node/971
requires: http://biii.eu/node/998
created: 2013-10-11T13:08:43
modified: 2019-10-16T11:25:59
title: MorphoMaths
comment: Icy Morphomath operators: erosion, dilation, opening, closing, top-hat, gradient, distance map, skeleton and watershed.

morphonet
type: software
has author: Faure Emmanuel orcid.org/0000-0003-2787-0885
has DOI: s41467-019-10668-1
has DOI: DOI 10.1038/s41467-019-10668-1
has documentation: HelpGeneral.html
has documentation: MorphoNet General Help Pages
has function: operation_0226
has function: operation_0337
has function: operation 3553
has function: operation Image visualisation
has function: operation RDggamr21qZlMqkQmyOdC7l
has function: operation Surface rendering
has implementation: http://biii.eu/taxonomy/term/4342
has license: CeCILL
has location: morphonet.org
has location: MorphoNet Main website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41467-019-10668-1
has reference publication: Nature Communications 2019 : MorphoNet: an interactive online morphological browser to explore complex multi-scale data
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
has usage example: MorphoNet Tutorials.html
has usage example: MorphoNet Tutorials
openess: http://biii.eu/taxonomy/term/3575
created: 2020-03-02T11:09:11
modified: 2020-03-02T13:35:24
title: MorphoNet
comment: MorphoNet is a novel concept of web-based morphodynamic browser to visualise and interact with complex datasets, with applications in research and teaching. MorphoNet offers a comprehensive palette of interactions to explore the structure, dynamics and variability of biological shapes and its connection to genetic expressions. By handling a broad range of natural or simulated morphological data, it fills a gap which has until now limited the quantitative understanding of morphodynamics and its genetic underpinnings by contributing to the creation of ever-growing morphological atlases.

morphonet-python-api
type: software
has author: Faure Emmanuel orcid.org/0000-0003-2787-0885
has function: operation_0226
has function: operation_0337
has function: operation Validation
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4342
has license: CeCILL
has location: HelpAPI.html
has location: MorphoNet Python API Main Page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41467-019-10668-1
has reference publication: Nature Communications 2019
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
has usage example: MorphoNet Tutorial1.1.html
has usage example: How to upload a dataset on MorphoNet
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1626
created: 2020-03-03T09:25:27
modified: 2020-10-19T14:51:06
title: MorphoNet Python API
comment: The Morphonet Python API provide an easy interface to interact directly with the MorphoNet server. Very useful to upload, download your dataset and superimpose on it any quantitative and quantitative informations.

mosaicexplorerj
type: software
has author: Sebastien Tosi
has documentation: MosaicExplorerJ
has documentation: Online documentation
has function: operation 2409
has function: operation Image stitching
has location: MosaicExplorerJ
has location: github site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: https://f1000research.com/articles/9-1308
has reference publication: F1000Research article
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: MosaicExplorerJ
has usage example: Video Tutorials
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2023-04-27T11:36:41
modified: 2023-04-28T15:41:51
title: MosaicExplorerJ
comment: It stitches 3D tiles from terabyte-size microscopy datasets. Stitching does not require any prior information on the actual positions of the tiles, sample fiducials, or conversion of raw TIFF images, and the stitched images can be explored instantly. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-side lightsheet illumination and dual-side camera detection.

mosaicia
type: software
has author: A. Shivanandan, A. Radenovic, and I. F. Sbalzarini
has function: operation Image segmentation
has function: operation Interactive segmentation
has function: operation Particle tracking
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: MosaicIA
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/79
created: 2016-07-12T14:03:02
modified: 2019-10-21T09:06:24
title: MosaicIA
comment: MosaicIA is a tool to analyze the spatial distribution of objects in images. It estimates from an observed particle or object distribution what hypothetical interaction between the objects is most likely to have created this distribution.

mosaicj
type: software
has author: Philippe Thévenaz
has documentation: mosaicj
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4340
has location: mosaicj
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: thevenaz0701.html
has reference publication: User-Friendly Semiautomated Assembly of Accurate Image Mosaics in Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/915
created: 2013-10-11T13:08:46
modified: 2019-10-16T12:51:47
title: MosaicJ
comment: This plugin facilitates the assembly of a mosaic of overlapping individual images, or tiles. It provides a semi-automated solution where the initial rough positioning of the tiles must be performed by the user, and where the final delicate adjustments are performed by the plugin. The MosaicJ plugin requires that a second plugin, named TurboReg, is installed.

mosaicsuite
type: software
has author: Baumgartner, Benedikt
has author: Berger, Phillip
has author: Bugarski, Milica
has author: Cardinale, Janick
has author: Helmuth, Jo
has author: Incardona, Pietro
has author: Koumoutsakos, Petros
has author: Mansouri, Maysam
has author: Niemann, Axel
has author: Paul, Gregory
has author: Radenovic, Aleksandra
has author: Rizk, Aurelien
has author: Sbalzarini, Ivo F. (orcid.org/0000-0003-4414-4340)
has author: Shivanandan, Arun
has author: Ziegler, Urs
has documentation: index.html
has documentation: MosaicSuite Documentation
has function: operation_0337
has function: operation Illumination correction
has function: operation Image segmentation
has function: operation Particle tracking
has function: operation Spot extraction
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation Colocalisation analysis
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: MosaicSuite.git
has location: gitlab
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/3567
has usage example: Rizk2014.pdf
has usage example: Squassh segmentation
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
requires: http://biii.eu/node/94
created: 2016-10-06T13:27:43
modified: 2023-05-08T01:12:00
title: MosaicSuite
comment: Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included: 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time. Optimal filament segmentation of 2D images. Curvature filters for image filtering, denoising, and restoration. Image naturalization for image enhancement based on gradient statistics of natural-scence images. Tool for automatically send and distribute jobs on clusters and get back the results. Multi-region image segmentation of 2D and 3D images without needing to know the number of regions beforehand. Squassh for globally optimal segmentation of piecewise constant regions in 2D and 3D images and for object-based co-localization analysis. Tool for inferring spatial interactions between patterns of objects in images or between coordinates read from a file. Tool for robust, histogram-based background subtraction well suited to correct for inhomogeneous illumination artifacts. A tool to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images. A tool to measure the 3D Point-Spread Function of a confocal microscope from an image stack. Addition of synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. Convolution of an image with a Bessel function in order to simulate imaging with a microscope. A utility to detect bright spots in images and estimate their center. A utility to create manual segmentations to be used as ground truth to test and benchmark automatic segmentation algorithms. A tool for replacing one color in an image with another color.

most-raytracer
type: software
has author: Jingpeng Wu
has function: operation Image enhancement
has function: operation Image segmentation
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has license: Apache 2.0
has location: neurontracing MOST
has location: MOST Github repository in Vaa3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: j.neuroimage.2013.10.036
has reference publication: 3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has topic: topic 3452
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2017-09-14T16:21:57
modified: 2017-09-14T16:58:10
title: MOST-Raytracer
comment: This project was designed for vectorize and analyze the blood vessels in the mouse brain. This plugin requires the definition of seed point detection settings by the user (Semi-automated).

motility-analysis-mean-square-displacement
type: software
has author: Herbert, Sébastien, ORCID:
has author: Tinevez, Jean-Yves, ORCID: 0000-0002-0998-4718
has programming language: http://biii.eu/taxonomy/term/4223
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3577
created: 2019-02-05T10:05:35
modified: 2019-02-05T10:36:21
title: Motility analysis with mean-square displacement
comment: Tracking tools, such as TrackMate, produce tracks and their role stops there. However, tracks are just an intermediate data structure in the workflow. Their subsequent analysis produces the numbers upon which scientific conclusions are made. The track analysis is most often specific to the scientific question to be addressed, and therefore tracking tools remain generic and seldom include specialized analysis modules. Another toolset is required for track analysis; this workflow focuses on using MATLAB.

mountainsmap
type: software
has author: Digital Surf
has license: Commercial
has location: mntkey.html
has platform: http://biii.eu/taxonomy/term/31
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/132
requires: http://biii.eu/node/286
requires: http://biii.eu/node/726
created: 2014-12-09T16:29:52
modified: 2017-09-13T10:15:46
title: MountainsMap
comment: MountainsMap is a surface imaging and metrology software published by the company Digital Surf. Its main application is micro-topography, the science of studying surface texture and form in 3D at the microscopic scale. The software is used mainly with stylus-based or optical profilometers, optical microscopes and scanning probe microscopes. MountainsMap is mainly offered as embedded or optional OEM analysis software by most profilometer and microscope manufacturers, usually under their respective brands; it is sold for instance as: MountainsMap - X on Nikon's microscopes Leica Map on Leica's microscopes ConfoMap on Carl Zeiss' microscopes

moving-least-squares
type: software
has location: Moving Least Squares
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:09:14
title: Moving Least Squares

mri-simulation-and-reconstruction
type: software
has author: Matthieu Guerquin-Kern
has documentation: mri-reconstruction
has function: operation Image reconstruction
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4339
has location: mri-reconstruction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: guerquinkern1201.html
has reference publication: Realistic Analytical Phantoms for Parallel Magnetic Resonance Imaging
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3444
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:44
modified: 2020-03-02T21:44:59
title: MRI Simulation and Reconstruction

msdanalyzer
type: software
has author: Jean-Yves Tinevez
has documentation: msdanalyzer
has documentation: Tutorial explaining the principles of MSD analysis and how to use the tool.
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD
has location: msdanalyzer
has location: GitHub repository for the code.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: http://jcb.rupress.org/content/204/2/231
has reference publication: Publication for which the tool was built.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Statistics
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1300
created: 2018-10-17T14:40:37
modified: 2018-10-18T15:24:57
title: @msdanalyzer
comment: Mean square displacement (MSD) analysis is a technique commonly used in colloidal studies and biophysics to determine what is the mode of displacement of particles followed over time. In particular, it can help determine whether the particle is: freely diffusing; transported; bound and limited in its movement. On top of this, it can also derive an estimate of the parameters of the movement, such as the diffusion coefficient. @msdanalyzer is a MATLAB per-value class that helps performing this kind of analysis. The user provides several trajectories he measured, and the class can derive meaningful quantities for the determination of the movement modality, assuming that all particles follow the same movement model and sample the same environment.

msrc-registration-toolbox
type: software
has author: Heath Patterson orcid.org/0000-0002-0064-1583
has function: operation Image registration
has function: operation R9EjejimBB0tmnQRmZt0RhA
has implementation: http://biii.eu/taxonomy/term/4341
has license: Apache 2.0
has location: regToolboxMSRC
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: acs.analchem.8b02884
has reference publication: acs.analchem.8b02885
has reference publication: Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy
has reference publication: Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2019-03-20T12:16:56
modified: 2021-05-19T18:53:45
title: MSRC Registration Toolbox
comment: This python toolbox performs registration between 2-D microscopy images from the same tissue section or serial sections in several ways to achieve imaging mass spectrometry (IMS) experimental goals. This code supports the following works and enables others to perform the workflows outlined in the following works, please cite them if you use this toolbox: Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy, 10.1021/acs.analchem.8b02884 Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy, 10.1021/acs.analchem.8b02885

mtrack2-imagej
type: software
has author: Johannes Schindelin
has author: Nico Stuurman
has documentation: MTrack2
has function: operation RDsrmC9l0bZw9kGJzGMCyY8
has implementation: http://biii.eu/taxonomy/term/4340
has location: MTrack2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T15:46:03
title: MTrack2 (ImageJ)

mtrackj
type: software
has author: Erik Meijering
has documentation: mtrackj
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has license: Custom (see documentation page)
has location: mtrackj
has location: Installation instruction (update sites)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: B978-0-12-391857-4.00009-4
has reference publication: Meijering et al (2012) Methods for Cell and Particle Tracking
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1309
requires: http://biii.eu/node/38
created: 2014-12-21T01:52:50
modified: 2018-05-27T15:15:29
title: MTrackJ
comment: Manual Tracking GUI. Many shortcut keys, and after being experienced, manual tracking can efficiently done. Post-editing capability to delete segments, merge and splitting tracks is quite useful.

multi-kymograph
type: software
has author: Arne Seitz
has author: Jens Rietdorf
has documentation: kymograph description.pdf
has documentation: kymograph_description.pdf
has function: operation Image tracking
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: kymograph.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T12:07:37
modified: 2023-05-03T09:09:10
title: Multi Kymograph
comment: This macro and plugins suite for ImageJ (and Fiji) serves to measure the velocity of moving structures and visualize them, from image time series (2D over time). The module can be installed in ImageJ as a Macro Menu and each function/component can be called separately. The full workflow consists in calling some, or all, the functions sequentially in order to get from the image preparation (e.g. filtering and visualization of tracks) to the production of the kymographs (time vs. distance plot) and their analysis (retrieving the velocities). Here is the full workflow sequence: Load image sequence Crop and time-filter the image sequence ("Walking average" plugin) Generate tracks by z-projection ("Stack difference" plugin) Select tracks and restore them in the original stack. execute plugin "multiple kymograph" Analyse: select edges of moving tracks graphically and quantify movement in a table. input: 8-bit, 16-bit stacks, 2D in time. Calibrated is better for meaningful velocity measurements. ouput: the kymograph image, the velocity measurements tables. Requires ImageJ version: 1.33.n minimum. Example of applications: velocity of moving objects/ structures with sharp edges, incl. the velocity of microtubules (and their plus ends), the velocity of vesicles or particles along a 2D path the velocity of migration of the edge of a cell or a multicellular group retraction velocity of contractile bundles (e.g. actin fibers) or multicellular tissues after mechanical disruption (e.g. laser surgery)

multi-otsu-threshold
type: software
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: Multi Otsu Threshold
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Multi Otsu Threshold
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/508
requires: http://biii.eu/node/671
created: 2013-10-11T13:08:44
modified: 2019-10-16T11:30:14
title: Multi Otsu Threshold
comment: This ImageJ plugin segments the image in classes by thresholding. It uses the same algorithm found in Otsu Thresholding, but was adapted to output more than 2 classes out of the process.

multi-template-matching
type: software
has author: Gehrig Jochen
has author: Thomas Laurent orcid.org/0000-0001-7686-3249
has documentation: Youtube tutorials
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RDetoixS3xEu0agR2CebaoB
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Multi-Template-Matching
has location: GitHub repos
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has reference publication: s12859-020-3363-7
has reference publication: Multi-Template Matching
has reference publication: Multi-Template-Matching
has reference publication: Article in BMC Bioinformatics
has reference publication: KNIME workflow
has reference publication: Python package on PyPI
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic High content screening
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2019-04-29T09:45:55
modified: 2020-10-19T15:09:23
title: Multi-Template matching
comment: Multi-template matching can be used to localize multiple objects using one or a set of template images. Contrary to previous implementations that allow to use only one template, here a set of templates can be used or the initial template(s) can be transformed by rotation/flipping. Multiple objects detection without redundant detections is possible thanks to a Non-Maxima Supression relying on the degree of overlap between detections. The solution is available as a Fiji plugin (Multi-Template Matching AND IJ-OpenCV update sites), as a Python package (Multi-Template-Matching on PyPI) and as a KNIME workflow (via KNIME Hub).

multi-touch-gestures
type: software
has documentation: multi-touch-gestures
has function: operation 2409
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/360
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-16T12:55:36
title: Multi-touch gestures
comment: Drag, rotate & zoom in your image using two-finger gestures (in 2D and 3D).

multiple-image-processor
type: software
has author: Nathaniel Gonzalez Santiago
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv2
has location: Multiple Image Processor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:43
modified: 2019-10-15T15:34:21
title: Multiple Image Processor

multistackreg
type: software
has author: Brad Busse
has function: operation 2928
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: downloads.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3382
has topic: topic 3385
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
requires: http://biii.eu/node/915
created: 2016-10-04T11:17:22
modified: 2023-04-26T11:35:52
title: MultiStackReg
comment: This ImageJ plugin aligns the slices of a stack just like the stackreg plugin on which it is built. It allows to save the transformations and to apply them to another stack. It furthermore allows to register two stacks.

multithreaded-image-processing
type: software
has function: operation 2409
has location: Multithreaded Image Processing in Clojure
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T13:19:07
title: Multithreaded Image Processing
comment: An example Clojure script illustrating how to run concurrent threads that perform independent tasks, and how to combine their results afterwards.

multithreaded-image-processing-javascript
type: software
has author: Albert Cardona
has function: operation 2409
has location: Multithreaded Image Processing in Javascript
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:09:11
title: Multithreaded Image Processing in Javascript

multithresholder-imagej
type: software
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: MultiThresholder
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2020-03-02T16:42:07
title: MultiThresholder (ImageJ)

multiview-reconstruction
type: software
has author: Preibisch Stephan orcid.org/0000-0002-0276-494X
has author: Saalfeld Stephan orcid.org/0000-0002-4106-1761
has author: Schinelin Johannes
has author: Tomancak Pavel orcid.org/0000-0002-2222-9370
has documentation: Multiview-Reconstruction#Detailed Tutorials
has function: operation_0337
has function: operation Image deconvolution
has function: operation Image registration
has function: operation R8ANfLkuHu47r739AkhxrId
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RBPObKBKIMwjdLygBOlvojW
has function: operation RBh3vNecu5XlIPh3kbMM4Cq
has function: operation RDr8xcZEa4L3mZsslmhhee8
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL-2.0
has location: Multiview-Reconstruction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4358
has reference publication: nmeth.2929
has reference publication: nmeth0610-418
has reference publication: doi:10.1038/nmeth.2929
has reference publication: doi:10.1038/nmeth0610-418
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3567
has usage example: Multiview-Reconstruction#Video Tutorials .26 Scientific Talks
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1171
requires: http://biii.eu/node/38
requires: http://biii.eu/node/80
created: 2018-01-28T11:29:49
modified: 2018-01-30T11:34:23
title: Multiview Reconstruction
comment: The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images. The software is designed for lightsheet fluorescence microscopy (LSFM), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks.

muscleqnt-muscle-fiber-counting
type: software
has author: Steven D. Flygare
has function: operation Cell counting
has function: operation Cell segmentation
has function: operation Shape features
has location: muscleQNT
has location: github: stevendflygare/muscleQNT
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: ncomms8087
has reference publication: Muscle stem cells contribute to myofibres in sedentary adult mice
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1287
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/85
created: 2017-02-13T12:29:10
modified: 2023-04-27T11:18:28
title: muscleQNT: Muscle fiber counting
comment: A workflow in Python to measure muscule fibers corresponding to the method used in Keefe, A.C. et al. Muscle stem cells contribute to myofibres in sedentary adult mice. Nat. Commun. 6:7087 doi: 10.1038/ncomms8087 (2015). Example image: muscleQNT/15536_2032_0.tif ...

mycosis-lung-quantifier
type: software
has location: Mycosis Lung Quantifier
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:08:24
title: Mycosis Lung Quantifier

myotracker
type: software
has author: Jose Fernandez
has implementation: http://biii.eu/taxonomy/term/4340
has location: journal.pone.0091791.s002
has location: Jar and documentation package
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: journal.pone.0091791
has reference publication: Fernández et al. (2014) Automated Detection and Measurement of Isolated Retinal Arterioles by a Combination of Edge Enhancement and Cost Analysis.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-09T15:44:10
modified: 2018-05-30T23:01:19
title: Myotracker
comment: ImageJ plugin to analyze changes in vessel diameters, described in Fernández er al (2014). More specifically the paper describes the measurement of isolated retinal arterioles (ca 50 micrometer diameter) but can be used for diameter measurements of similar vessel structures.

mytardis
type: software
has documentation: latest
has documentation: Online documentation
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: Apache v2
has location: www.mytardis.org
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-13T14:29:47
modified: 2023-05-03T14:37:58
title: MyTardis
comment: MyTardis is free and open-source data management software. It facilitates annotation, sharing and archiving of data and metadata collected from different modalities. It focuses on integration with scientific instruments, instrument facilities and research storage and computing infrastructure; to address the challenges of data storage, data access, collaboration and data publication. It is currently being used to capture data from areas such as optical microscopy, electron microscopy, medical imaging, protein crystallography, neutron and X-ray scattering, flow cytometry, genomics and proteomics. Key features: Easy instrument integration. Discipline specific: MX, Imaging, Microscopy, Genomics ... Wide range of data formats & supported instruments. Secure cloud data storage & access. Simple data sharing. Researcher controlled data publishing. APIs for programmatic access to data and metadata.

name-landmarks-and-register
type: software
has location: Name Landmarks and Register
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:23
title: Name Landmarks and Register

nanoj
type: software
has function: operation 3443
has function: operation Image processing
has function: operation Image registration
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has location: NanoJ-Core
has location: NanoJ GitHUB
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic Super-resolution microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-06T09:24:40
modified: 2023-05-03T09:13:48
title: NanoJ
comment: Set of Tools for super resolution microscopy

napari-image-viewer
type: software
has author: Juan Nunez-Iglesias
has author: Kira Evans
has author: Nicholas Sofroniew
has author: Talley Lambert
has documentation: napari.org
has documentation: Documentation
has function: operation_0337
has function: operation Image visualisation
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD-3
has location: napari
has location: GitHub repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2019-11-08T09:06:22
modified: 2021-10-14T17:34:43
title: Napari image viewer
comment: Summary napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (e.g. numpy, scipy). It includes critical viewer features out-of-the-box, such as support for large multi-dimensional data, and layering and annotation. By integrating closely with the Python ecosystem, napari can be easily coupled to leading machine learning and image analysis tools (e.g. scikit-image, scikit-learn, TensorFlow, PyTorch), enabling more user-friendly automated analysis. Installation The installation procedure for Silicon Mac (M1 Processor, arm64 ) requires some tricks. As of Oct 2021, this procedure by Peter Sobolewski works but: For installing pyqt5, use a slightly different command `brew install PyQt@5` to install PyQt5.

napari-pyclesperanto-assistant
type: software
has author: Robert Haase, Talley Lambert
has documentation: napari pyclesperanto assistant
has function: operation 3443
has location: napari-pyclesperanto-assistant
has location: Napari Hub
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
has usage example: Demo video
openess: http://biii.eu/taxonomy/term/3575
created: 2021-07-10T10:52:30
modified: 2021-07-10T11:03:37
title: napari-pyclesperanto-assistant
comment: The napari-pyclesperanto-assistant is a yet experimental napari plugin for building GPU-accelerated image processing workflows targeting life-sciences and bio-image analysis. It is part of the clEsperanto project. It uses pyclesperanto and pyopencl as backend for processing images.

nblast
type: software
has author: Costa Marta orcid.org/0000-0001-5948-3092
has author: Jefferis Gregory orcid.org/0000-0002-0587-9355
has documentation: nat.nblast
has function: operation 2945
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has location: nat.nblast
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: https://www.sciencedirect.com/science/article/pii/S0896627316302653%3Fvia%253Dihub
has reference publication: Costa et al. "NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases"
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1192
created: 2018-01-30T08:59:39
modified: 2018-10-18T15:39:39
title: NBLAST
comment: This R package implements the NBLAST neuron similarity algorithm described in a preprint available at http://dx.doi.org/10.1101/006346. In addition to basic pairwise comparison, the package implements search of databases of neurons. There is also suport for all x all comparison for a group of neurons. This can produce a distance matrix suitable for hierarchical clustering, which is also implemented in the package.

nctutw
type: software
has author: Chiang, Ann-Shyn
has author: Ching, Yu-Tai
has author: Chuang, Chao-Chun
has author: Lee, Ping-Chang
has function: operation Closing
has function: operation Neuron image analysis
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: bigneuron ytc nctuTW
has location: nctuTW Plugin Github repository in Vaa3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: journal.pcbi.1002658
has reference publication: High-throughput computer method for 3d neuronal structure reconstruction from the image stack of the Drosophila brain and its applications
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2017-09-13T17:23:11
modified: 2023-05-08T01:31:47
title: nctuTW
comment: nctuTW is a "high-throughput computer method of reconstructing the neuronal structure of the fruit fly brain. The design philosophy of the proposed method differs from those of previous methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal structure is then constructed from the 2D skeletons. Biologists tend to use confocal microscopes for optimal images in a slice for human visualization; and images in two consecutive slices contain overlapped information. Consequently, a spherical object becomes oval in the image stack; that is, neurons in the image stack do not reflect the true shape of the neuron. This is the main reason we chose not to work directly on the 3D volume. The proposed method comprises two steps. The first is the image processing step, which involves computing a set of voxels that is a superset of the 3D centerlines of the neuron. The shortest path graph algorithm then computes the centerlines. The proposed method was applied to process more than 16 000 neurons. By using a large amount of reconstructions, this study also demonstrated a result derived from the reconstructed data using the clustering technique." (Extracted from reference publication) Illustrative image shows gold standard (top) and method results (bottom).

nd-safir
type: software
has author: Boulanger Jérôme
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4341
has location: nd-safir
has location: Download binaries
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: boulanger tmi2010.pdf
has reference publication: J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero Patch-based non-local functional for denoising fluorescence microscopy image sequence
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic Widefield microscopy
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/8
has usage example: pnas.1004037107
has usage example: Fast live simultaneous multiwavelength four-dimensional optical microscopy
openess: http://biii.eu/taxonomy/term/3576
openess: http://biii.eu/taxonomy/term/3577
created: 2020-05-03T15:34:53
modified: 2020-10-19T14:47:30
title: nd-safir
comment: ND-SAFIR is a software for denoising n-dimentionnal images especially dedicated to microscopy image sequence analysis. It is able to deal with 2D, 3D, 2D+time, 3D+time images have one or more color channel. It is adapted to Gaussian and Poisson-Gaussian noise which are usually encountered in photonic imaging. Several papers describe the detail of the method used in ndsafir to recover noise free images (see references). It is available either in Metamorph (commercial version), either as command line tool. Source are available on demand.

ndpi-export-regions-tool
type: software
has author: Bäcker Volker orcid.org/0000-0002-9129-6403
has documentation: NDPI Export Regions Tool
has documentation: NDPI_Export_Regions_Tool Documentation
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT
has location: NDPI Export Regions Tool
has location: NDPI_Export_Regions_Tool Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2021-07-05T13:45:21
modified: 2021-07-05T14:15:50
title: NDPI Export Regions Tool
comment: The tool exports rectangular regions, defined with the NDP.view 2 software (hammatsu) from the highest resolution version of the ndpi-images and saves them as tif-files. Click the button and select the input folder. The input folder must contain pairs of ndpi and ndpa files. The regions will be exported to a subfolder of the input folder names zones.

ndpiextractroi
type: software
has author: Paul-Gilloteaux Perrine
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: NDPI extractROI
has location: github
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/127
created: 2020-12-07T18:49:01
modified: 2020-12-07T18:55:42
title: ndpi_extractroi
comment: This small plugin demonstrates the use of OpenSlide in java: it will extract an imageJ roi drawn from the thumbnail of the whole slide image, or the full image at the desired resolution from an hammatsu NDPI file. Note that z stack are not supported by openslide (neitheir ndpiS).

ndpitools
type: software
has author: Deroulers Christophe
has documentation: ndpitools
has documentation: online documentation
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: NDPITools .jar
has location: jar download link
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2020-12-07T18:56:54
modified: 2020-12-07T19:03:56
title: NDPItools
comment: Using a Hamamatsu slide scanner such as the NanoZoomer, you may end up with NDPI files that can't always be directly open in standard image analysis software such as ImageJ. NDPITools is a collection of software that can convert NDPI files to standard TIFF files, possibly cutting them into smaller JPEG or TIFF pieces that will better fit into your computer's memory. It comes with a bundle of plugins for ImageJ which enable the use of the software directly inside ImageJ with point-and-click.

nemo-dots-assembly-single-particle-tracking-and-analysis
type: software
has author: Herbert, Sébastien, ORCID:
has author: Tinevez, Jean-Yves, ORCID: 0000-0002-0998-4718
has reference publication: http://jcb.rupress.org/content/204/2/231
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3577
created: 2019-02-04T22:57:15
modified: 2020-10-20T09:40:20
title: The NEMO dots assembly: Single-particle tracking and analysis
comment: This workflow presents single-particle tracking in Fiji using Track-Mate, and track motility analysis in MATLAB using @msdanalyzer.

nessys
type: software
has author: Blin Guillaume orcid.org/0000-0002-9295-237X
has documentation: nessys
has function: operation 3096
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv3
has location: nessys
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-12-10T15:43:15
modified: 2018-12-11T00:58:36
title: Nessys
comment: Nessys: Nuclear Envelope Segmentation System Nessys is a software written in Java for the automated identification of cell nuclei in biological images (3D + time). It is designed to perform well in complex samples, i.e when cells are particularly crowded and heterogeneous such as in embryos or in 3D cell cultures. Nessys is also fast and will work on large images which do not fit in memory. Nessys also offers an interactive user interface for the curation and validation of segmentation results. Think of this as a 3D painter / editor. This editor can also be used to generate manually segmented images to use as ground truth for testing the accuracy of the automated segmentation method. Finally Nessys, contains a utility for assessing the accuracy of the automated segmentation method. It works by comparing the result of the automated method to a manually generated ground truth. This utility will provide two types of output: a table with a number of metrics about the accuracy and an image representing a map of the mismatch between the result of the automated method and the ground truth.

net-network-extraction-tool
type: software
has author: http://orcid.org/0000-0002-4274-4580
has documentation: network extraction
has function: operation Image thresholding
has function: operation Shape features
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: network extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s13029-017-0064-3
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-09-12T17:21:22
modified: 2023-05-03T09:37:28
title: NET - Network Extraction Tool
comment: The ultimate goal of the NET framework is to make images of networks processable by computers. Therefore we want to have a pixel based image as input, as output we want a representation of the network visible in the image that retains as much information about the original network as possible. NET achives this by first segmenting the image and then vectorizing the network and then extracting information. The information we extract is First and foremost the graph of the network. We find the crossings (nodes) and connections between crossings (edges) and therefore extract information about the neighborhood relations, the topology of the network. We also extract the coordinates of all nodes which enables us to embed them into space. We therefore extract information about the geometry of the network. Last but not least we track the radii of the edges in the extraction process. Therefore every edge has a radius which can be identified with its conductivity. In the following we will first provide detailed instructions on how to install NET on several platforms. Then we describe the functionality and options of each of the four scripts that make up the NET framework.

neural-circuit-tracer
type: software
has author: Chothani, Paarth
has author: Mehta, Vivek
has author: Stepanyants, Armen
has documentation: tools
has documentation: Neural Circuit Tracer Tool main page
has function: operation Image enhancement
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4341
has location: tools
has location: Neurogeometry Group Northeastern University main page
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3594
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: s12021-011-9121-2
has reference publication: Automated Tracing of Neurites from Light Microscopy Stacks of Images
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RBKlmE9DGTZwEwxw0juThGg
has type: http://biii.eu/taxonomy/term/3567
has usage example: tools
has usage example: Neural Circuit Tracer Tool main page (example videos)
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/1117
created: 2017-09-12T14:15:57
modified: 2018-04-11T10:01:47
title: Neural Circuit Tracer
comment: Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. "The Neural Circuit Tracer is open source software built using Java (Sun Microsystems) and Matlab (MathWorks, Inc., Natick MA). It is based on the core of ImageJ (http://rsbweb.nih.gov/ij) and the graphic user interface has been developed by using Java Swings. The software combines anumber of functionalities of ImageJ with several newly developed functions for automated and manual tracing of neurites. The Neural Circuit Tracer is designed in a way that will allow the users to add any plug-ins developed for ImageJ. More importantly, functions written in MatLab and converted into Java with Matlab JA toolbox can also be added to the Neural Circuit Tracer."

neuritetracer
type: software
has author: Pool Madeleine
has author: Thiemann Joachim
has documentation: NeuriteTracer Manual.pdf
has documentation: NeuriteTracer Manual
has function: operation Image processing
has function: operation Image smoothing
has function: operation Morphological operations
has function: operation Neuron image analysis
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4341
has license: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
has location: NeuriteTracer.html
has location: NeuriteTracer pug-in page - McGill University Fournier Lab
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: j.jneumeth.2007.08.029
has reference publication: NeuriteTracer: A novel ImageJ plugin for automated quantification of neurite outgrowth
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-01-28T11:18:13
modified: 2023-04-27T10:58:56
title: NeuriteTracer
comment: "The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length."[...]" NeuriteTracer is a fast simple-to-use ImageJ plugin for the analysis of outgrowth in two-dimensional fluorescence microscopy images of neuronal cultures. The plugin performed well on images from three different types of neurons with distinct morphologies." This plugin requires parameter setting: Threshold levels and scale (see more details on the related publication)

neuroanatomy-toolbox
type: software
has author: Jefferis Gregory orcid.org/0000-0002-0587-9355
has DOI: zenodo.10171
has documentation: nat-package.html
has function: operation_0337
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4339
has location: nat
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Microscopy
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: nat.examples
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-30T08:37:54
modified: 2018-10-18T15:35:57
title: NeuroAnatomy Toolbox
comment: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. nat is the core package of a wider suite of neuroanatomy tools introduced at http://jefferislab.github.io.

neuroconductor
type: software
has author: Adi Gherman
has author: Brandon Whitcher
has author: Brian Avants
has author: Brian Caffo
has author: Ciprian Crainiceanu
has author: Jean-Philippe Fortin
has author: Muschelli John
has documentation: neuroc-help
has documentation: Several tutorials available
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has location: releases
has location: code hosting
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: kxx068
has reference publication: Neuroconductor: an R platform for medical imaging analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1284
created: 2018-04-18T09:28:56
modified: 2018-04-18T09:45:01
title: Neuroconductor
comment: Neuroconductor is an open-source platform for rapid testing and dissemination of reproducible computational imaging software, specialized in brain medical imaging (MRI, fMRI, DTI, etc...) but that could be used on a wider range of images. The goals of the project are to: provide a centralized repository of R software dedicated to image analysis; disseminate quickly software updates; educate a large, diverse community of scientists using detailed tutorials and short courses; ensure quality via automatic and manual quality controls; and promote reproducibility of image data analysis. Based on the programming language R, Neuroconductor starts with 68 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing.

neuroglancer
type: software
has author: google
has documentation: README.md
has documentation: Documentation Readme.md
has function: operation_0337
has function: operation 2409
has function: operation Image visualisation
has location: neuroglancer
has location: GitHub (Install with NVM) see building section.
has topic: topic_0611
has topic: topic Light-sheet microscopy
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
has usage example: FAFB.surf.vtk.gz","vertexAttributeSources":[],"shader":"void main() {\n emitRGBA(vec4(1.0, 0.0, 0.0, 0.5));\n}\n","visible":false}},"navigation":{"pose":{"position":{"voxelSize":[4,4,40],"voxelCoordinates":[123943.625,73323.8828125,5234]}},"zoomFactor":1210.991144617663},"perspectiveOrientation":[-0.28037887811660767,-0.19049881398677826,-0.13574382662773132,-0.9309519529342651],"perspectiveZoom":213
has usage example: Other example
openess: http://biii.eu/taxonomy/term/3575
created: 2019-08-07T17:49:42
modified: 2023-04-27T11:00:38
title: Neuroglancer
comment: Web based viewer developped for google for very big data: Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). The segmentation has to be done before loading the dataset, it is not done Inside the viewer. This is not an official Google product. It has among other the nice feature of beeing able to generate url for sharing a specific view. Note that the only supported browser for now are Chrome >= 51 Firefox >= 46

neurogps-tree
type: software
has author: Quan Tingwei
has implementation: http://biii.eu/taxonomy/term/4340
has license: slightly revised MIT License. Note the eigen library of NeuroGPSTree use MPL2 licenses when such situations are specified and documented
has location: bigneuron zhouhang hust NeuroGPSTree
has location: HUST NeuroGPS-Tree
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nmeth.3662#s1
has reference publication: NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2018-01-28T11:56:59
modified: 2018-01-28T18:29:16
title: NeuroGPS-Tree
comment: NeuroGPS-Tree is a workflow developed to reconstruct a neuronal population from a dense, large-scale data set. NeuroGPS-Tree is suitable for processing image stacks acquired by different image modalities.

neurolucida
type: software
has function: operation Cell segmentation
has function: operation Feature extraction
has function: operation Neuron image analysis
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: neurolucida
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RC91JqkkQnsmvg8zuG6Td7q
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2017-02-13T12:27:00
modified: 2020-03-05T10:28:30
title: Neurolucida
comment: Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma, and 4) the complexity and extension of neurons. See 10.3389/fnins.2012.00049

neuromorph
type: software
has author: Anne Jorstad
has author: Biago Nigro
has author: Corrado Cali
has author: Daniya Boges
has author: Graham Knott
has author: Tom Boissonnet
has documentation: wiki
has function: operation 2945
has function: operation 3553
has function: operation Image visualisation
has function: operation Volume rendering
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU General Public License as published by the Free Software Foundation
has location: NeuroMorph
has location: Git hub to download the software
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 10.1007/s12021-014-9242-5
has reference publication: full
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3452
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1386
created: 2018-11-07T13:20:26
modified: 2019-02-03T14:45:58
title: NeuroMorph
comment: NeuroMorph is a toolset designed to import, analyze, and visualize mesh models in Blender. It has been developed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, but much of its functionality can be applied to any 3D mesh. These mesh objects can be generated by any 3D image segmentation software, such as ilastik or Fiji.

neuron-tracing-3d-imagej
type: software
has author: Chessel, Anatole
has author: Tosí, Sébastien
has comparison: #tabs-benchmark-1915382
has comparison: BIAFLOWS Neuron Tracing 3D project
has function: operation Edge detection
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has location: macro.ijm
has location: Neubias BIAFLOWS workflow of Neuron Tracing 3D with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-26T14:39:23
modified: 2019-02-26T15:53:31
title: Neuron Tracing 3D (ImageJ)

neuron-tracing-3d-rivuletpy
type: software
has author: Pavie, Benjamin
has author: Scholz, Leandro
has author: Tosí, Sebastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM:NEURON-TRACING-3D
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: W FilamentTracing3D Rivuletpy
has location: Neubias BIAFLOWS workflow of Neuron Tracking with Rivuletpy (Rivulet 2)
has reference publication: TMI.2018.2833420
has reference publication: Automated 3-D Neuron Tracing With Precise Branch Erasing and Confidence Controlled Back Tracking
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2020-01-23T16:07:51
modified: 2023-05-01T16:22:45
title: Neuron Tracing 3D (Rivuletpy)
comment: Rivuletpy dockerised workflow for BIAFLOWS.

neuron-tracing-vaa3d-app2
type: software
has author: Pavie, Benjamin
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NEURON-TRACING-3D
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: W NeuronTracing vaa3d app2
has location: Neubias BIAFLOWS workflow of Neuron Tracking with Vaa3d APP2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: btt170
has reference publication: APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
requires: http://biii.eu/node/64
created: 2020-01-23T15:35:57
modified: 2023-05-01T16:24:33
title: Neuron Tracing Vaa3D (App2)
comment: Vaa3d All-Path-Pruning 2.0 (APP2) dockerised workflow for BIAFLOWS.

neuron-tracing-vaa3d-bjut-fm-spanning-tree
type: software
has author: Pavie, Benjamin
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NEURON-TRACING-3D
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: v0.4
has location: Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d BJUT Fast Marching Spanning Tree
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2020-01-27T05:25:33
modified: 2023-05-01T16:26:18
title: Neuron Tracing Vaa3D (BJUT FM Spanning Tree)
comment: Vaa3d BJUT Fast Marching Spanning Tree algorithm dockerised workflow for BIAFLOWS

neuron-tracing-vaa3d-most
type: software
has author: Pavie, Benjamin
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NEURON-TRACING-3D
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: W Neuron3dTree vaa3d most
has location: Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d MOST
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: j.neuroimage.2013.10.036
has reference publication: 3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1166
requires: http://biii.eu/node/62
created: 2020-01-23T16:18:19
modified: 2023-05-01T16:27:59
title: Neuron Tracing Vaa3D (MOST)
comment: 3D Neuron Tracing with a Dockerized version of Vaa3D MOST Raytracer.

neuron-tracing-vaa3d-mst
type: software
has author: Pavie, Benjamin
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NEURON-TRACING-3D
has location: W NeuronTracing vaa3d mst
has location: Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d MST
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2020-01-23T16:13:49
modified: 2023-05-01T16:25:33
title: Neuron Tracing Vaa3D (MST)
comment: 3D Neuron Tracing using Dockerized version of Vaa3D Minimum Spanning Tree (MST).

neuronj
type: software
has author: Erik Meijering
has documentation: manual
has documentation: NeuronJ Manual Page
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://imagescience.org/meijering/publications/1016/
has reference publication: Design and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence Microscopy Images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-18T09:40:21
title: NeuronJ

neuronmetrics
type: software
has author: Rakhi Gibbons
has documentation: http://djhurij4nde4r.cloudfront.net/attachments/files/000/000/390/original/neuronmetricsusermanual07_0320.pdf%3F1454523958
has function: operation Neuron image analysis
has function: operation Shape features
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has location: ua07-056 neuronmetrics-software-for-semi-automated-processing-of-cultured-neuron-images
has platform: http://biii.eu/taxonomy/term/30
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: S000689930603215X
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2017-09-12T16:21:39
modified: 2018-01-29T08:49:30
title: NeuronMetrics
comment: The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating neural “branch number” (a measure of the axonal complexity) from two-dimensional images. In addition, the tool features a novel method for modeling neural structure in large “gaps” that result from image artifacts.

neuronstudio
type: software
has author: Alfredo Rodriguez Sr. Software Engineer
has author: Doug Ehlenberger Software Engineer
has author: Patrick R. Hof Co-Investigator
has author: Susan L. Wearne Principal Investigator
has documentation: index.html
has documentation: NeuronStudio Online Help Manual
has function: operation Neuron image analysis
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has license: This software is provided "as is" and without warranties or representations, either express or implied, as to performance, merchantability, or fitness for any particular purpose and the user assumes all risks when using it. You may not decompile, disassem
has location: tools-ns.html
has location: Currently, the original web page for download seems to be gone ( relocated ?)
has platform: http://biii.eu/taxonomy/term/31
has reference publication: j.neuroscience.2005.05.053
has reference publication: New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
created: 2013-10-31T12:18:26
modified: 2023-04-27T11:03:05
title: NeuronStudio
comment: Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009. NeuronStudio is being developed at the Computational Neurobiology and Imaging Center (CNIC), a research laboratory at the Neuroscience Department of the Mount Sinai School of Medicine in New York. NeuronStudio can be used with default parameters or user-defined parameters (Fully or semi-automated).

neurphologyj
type: software
has author: Eric Hwang
has documentation: Manual.pdf
has location: neurphologyJ.html
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: NeurphologyJ interactive .txt
has reference publication: https://doi.org/10.1186/1471-2105-12-230
has reference publication: Code
has reference publication: NeurphologyJ: An automatic neuronal morphology quantification method and its application in pharmacological discovery
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2016-10-24T13:46:16
modified: 2018-04-27T00:14:58
title: NeurphologyJ
comment: ImageJ macro for the morphometry of neurites. > NeurphologyJ; it is capable of automatically quantifying neuronal morphology such as soma number and size, neurite length, neurite ending points and attachment points. NeurphologyJ is implemented as a plugin to ImageJ, an open-source Java-based image-processing and analysis platform.

neutube-or-neutu
type: software
has author: Feng, Linqing
has author: Kim, Jinhyun
has author: Zhao, Ting
has documentation: manual
has documentation: neuTube Manual web page
has function: operation 3096
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has license: This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
has location: www.neutracing.com
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has programming language: http://biii.eu/taxonomy/term/4241
has reference publication: ENEURO.0049-14.2014
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/601
created: 2016-10-01T15:31:03
modified: 2023-04-27T11:30:09
title: neuTube (or NeuTu)
comment: neuTube is a collection of neuron reconstruction tools from fluorescence microscope images. It has an interactive system with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can automatically recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages. neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.

nherve-imageanalysis-toolbox
type: software
has author: Nicolas Hervé
has documentation: nherve-imageanalysis-toolbox
has function: operation 3443
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/467
requires: http://biii.eu/node/537
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-16T16:03:09
title: NHerve ImageAnalysis Toolbox
comment: A toolbox to chain image analysis processes.

nherve-matrix
type: software
has documentation: NHerve-Matrix
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2019-10-16T16:05:34
title: NHerve Matrix

niftynet
type: software
has author: Li W., Wang G., Fidon L., Ourselin S., Cardoso M.J., Vercauteren T.
has DOI: 978-3-319-59050-9 28
has documentation: dev
has function: operation Image segmentation
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has license: Apache License, Version 2.0.
has location: www.niftynet.io
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://arxiv.org/abs/1711.01666
has reference publication: 10.1007/978-3-319-59050-9 28
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic 3444
has topic: topic 3474
has training material: http://biii.eu/node/1275
has type: http://biii.eu/taxonomy/term/3567
has usage example: model zoo.md
has usage example: list of example pre-trained networks with doc
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1201
created: 2018-03-20T16:53:11
modified: 2023-04-28T12:45:31
title: NiftyNet
comment: NiftyNet is a TensorFlow-based open-source convolutional neural networks (CNNs) platform for research in medical image analysis and image-guided therapy. NiftyNet’s modular structure is designed for sharing networks and pre-trained models. Using this modular structure you can: Get started with established pre-trained networks using built-in tools; Adapt existing networks to your imaging data; Quickly build new solutions to your own image analysis problems.

noise-generator
type: software
has author: Le Montagner Yoann
has documentation: noise-generator
has documentation: doc link
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: noise-generator
has location: Install using ICY. Code is in the JAR
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-16T11:04:16
title: Noise generator
comment: Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pepper, etc.) to a sequence. ICY plugin.

noise-suppression-using-simple-spatial-filters
type: software
has author: Graeme Ball
has function: operation Image processing
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2014-12-08T16:03:40
modified: 2018-11-26T08:32:22
title: Noise Suppression using Simple Spatial Filters
comment: Simple spatial filters can be used to suppress noise in raw image data (i.e. by averaging intensities). The best choice of filter depends on the nature of the noise, but Gaussian filtering works well for Poisson noise (i.e. commonly observed photon-counting shot noise); whereas a median filter is ideal for salt-and-pepper noise. A larger filter radius leads to stronger noise suppression but more blurring. The URL above describes the simple 2D spatial filters available in ImageJ, but similar filters are available in most software. For 3D data, 3D versions of these filters work best (since there are more pixels to average within the same radius).

nuclearquant
type: software
has function: operation Cell segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has location: nuclearquant module
has location: module page with restricted access
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/1110
created: 2013-10-11T13:08:43
modified: 2023-04-26T14:11:36
title: NuclearQuant
comment: NuclearQuant is a QuantCenter module. It is designed for cell nuclei detection and quantification of IHC stained samples. NuclearQuant measures several morphological features besides stain intensity. The cell nuclei classification and the final score are calculated by the intensity score and the proportion score.

nuclei-segmentation-2d-imagej
type: software
has author: Bäcker, Volker
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS Nuclei Segmentation project
has function: operation Image segmentation
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has location: macro.ijm
has location: Neubias BIAFLOWS workflow of nuclei segmentation with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-05T12:49:19
modified: 2023-05-09T18:39:08
title: Nuclei Segmentation 2D (ImageJ)
comment: The macro will segment nuclei and separate clustered nuclei using a binary watershed. As a result an index-mask image is written for each input image.

nuclei-segmentation-2d-watershed-nucseg3dthr-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS NUCLEI-SEGMENTATION-3D
has location: W NucSeg3DThr-ImageJ
has location: Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ImageJ
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2020-01-23T14:21:28
modified: 2023-04-27T18:10:48
title: Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ)
comment: The macro will segment nuclei and separate clustered nuclei in a 3D image using a 2D Gaussian blur, followed by Thresholding, 2D hole filling and a 2D watershed. As a result an index-mask image is written for each input image.

http://biii.eu/nuclei-segmentation-3d-nucleisegmentation3d-ilastik
type: software
has author: Paavolainen, Lassi
has comparison: analysis
has comparison: BIAFLOWS NUCLEI-SEGMENTATION-3D
has function: operation Pixel classification
has location: W NucleiSegmentation3D-ilastik
has location: Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ilastik
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41592-019-0582-9
has reference publication: ilastik: interactive machine learning for (bio)image analysis
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/88
created: 2020-01-23T14:47:13
modified: 2023-04-28T11:26:55
title: Nuclei Segmentation 3D (NucleiSegmentation3D-ilastik)
comment: Execute Nuclei Segmentation in 3D images using pixel classification with ilastik.

http://biii.eu/nuclei-segmentation-3d-watershed-nucleisegmentation3d-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS NUCLEI-SEGMENTATION-3D
has function: operation Image segmentation
has function: operation Image smoothing
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4340
has location: IJNuclei3DSegmentation.ijm
has location: Neubias BIAFLOWS workflow of nuclei segmentation 3D with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-05T14:38:45
modified: 2023-04-27T18:06:47
title: Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ)
comment: The macro will segment nuclei and separate clustered nuclei in a 3D image using a distance transform watershed. As a result an index-mask image is written for each input image.

nuclei-segmentation-cellpose
type: software
has comparison: analysis
has comparison: BIAFLOWS Nuclei Segmentation project
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4342
has location: W NucleiSegmentation-Cellpose
has location: Neubias BIAFLOWS Benchmarking workflow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2023-04-27T16:33:51
modified: 2023-05-02T09:53:23
title: Nuclei Segmentation (Cellpose)
comment: This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It performs 2D nuclei segmentation using pre-trained nuclei segmentation models of Cellpose. And it was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

nuclei-segmentation-cellprofiler
type: software
has author: Paavolainen, Lassi
has comparison: analysis
has comparison: BIAFLOWS Nuclei Segmentation project
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: CP detect nuclei.cppipe
has location: Neubias BIAFLOWS workflow of nuclei segmentation with CellProfiler pipeline
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2019-02-27T13:58:26
modified: 2023-01-23T16:05:12
title: Nuclei Segmentation (CellProfiler)
comment: This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

nuclei-segmentation-deepcell
type: software
has author: Paavolainen, Lassi
has comparison: analysis
has comparison: BIAFLOWS Nuclei Segmentation project
has location: Dockerfile
has location: Neubias BIAFLOWS workflow of Nuclei Segmentation with DeepCell
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: journal.pcbi.1005177
has reference publication: Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1317
requires: http://biii.eu/node/1322
requires: http://biii.eu/node/1376
created: 2020-01-23T13:15:18
modified: 2023-04-28T12:06:37
title: Nuclei Segmentation (DeepCell)
comment: Nuclei Segmentation using Deep Learning for single cell analysis (DeepCell).

nuclei-segmentation-ilastik
type: software
has author: Paavolainen, Lassi
has comparison: analysis
has comparison: Neubias BIAFLOWS nuclei segmentation project
has function: operation Pixel classification
has implementation: http://biii.eu/taxonomy/term/4340
has location: W NucleiSegmentation-ilastik
has location: Neubias BIAFLOWS workflow of Nuclei Segmentation with Ilastik and Python
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41592-019-0582-9
has reference publication: Ilastik: Interactive learning and segmentation toolkit
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/88
created: 2019-03-15T14:26:04
modified: 2023-04-25T17:39:19
title: Nuclei Segmentation (ilastik)
comment: NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

nuclei-segmentation-mask-rcnn
type: software
has author: Paavolainen, Lassi
has comparison: analysis
has comparison: Neubias BIAFLOWS Nuclei Segmentation Project
has documentation: Mask RCNN
has documentation: Mask R-Matterport - CNN for object detection and instance segmentation on Keras and TensorFlow
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: W NucleiSegmentation-MaskRCNN
has location: Neubias BIAFLOWS workflow of Nuclei Segmentation with Mask-RCNN
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2019-03-15T11:20:26
modified: 2023-01-23T16:10:11
title: Nuclei Segmentation (Mask-RCNN)
comment: NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses Matterport Mask-RCNN. Keras implementation. The model was trained with Kaggle 2018 Data Science Bowl images.

nuclei-segmentation-python
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS Nuclei Segmentation project
has function: operation Adaptative thresholding
has function: operation Image smoothing
has function: operation Watershed
has function: operation RBNng13hEB0CJD5VzSKqrfB
has location: script.py
has location: Neubias BIAFLOWS workflow of nuclei segmentation with Python
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1288
created: 2019-02-26T11:44:29
modified: 2023-05-02T09:59:30
title: Nuclei Segmentation (Python)
comment: This workflow processes images of cells with discernible nuclei and outputs a binary mask containing where nuclei are detected.

nuclei-segmentation-stardist
type: software
has comparison: analysis
has comparison: BIAFLOWS Nuclei Segmentation project
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4342
has location: W NucleiSegmentation-Stardist
has location: Neubias BIAFLOWS Benchmarking workflow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2023-04-27T16:39:53
modified: 2023-05-02T09:56:34
title: Nuclei Segmentation (Stardist)
comment: This workflow applies a Stardist pre-trained model (versatile_fluo or versatile_HE) depending on the input images ie. uses both models for a dataset including both fluorescence (grayscale or RGB where all channels are equal) and H&E stained (RGB where channels are not equal) images. This version uses tensorflow CPU version (See Dockerfile) to ensure compatibility with a larger number of computers. A GPU version should be possible by adapting the Dockerfile with tensorflow-gpu and/or nvidia-docker images.

nuclei-segmentation-u-net
type: software
has author: Paavolainen, Lassi
has comparison: analysis
has comparison: Neubias BIAFLOWS Nuclei Segmentation Project
has location: W NucleiSegmentation-UNet
has location: Neubias BIAFLOWS workflow of Nuclei Segmentation with U-Net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: cyto.a.23863
has reference publication: Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/1288
created: 2020-01-23T14:03:27
modified: 2023-01-23T16:11:35
title: Nuclei Segmentation (U-Net)
comment: U-Net segmentation as presented in Reference Publication. The model predicts three classes: background, edge and foreground. The model was trained with Kaggle Data Science Bowl (DSB) 2018 training set.

nuclei-tracking-imagej
type: software
has author: Bäcker, Volker
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: NucleiTracking.ijm
has location: Neubias BIAFLOWS workflow of nuclei tracking with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-26T15:30:06
modified: 2023-05-01T16:50:19
title: Nuclei Tracking (ImageJ)

nuclei-tracking-trackmate
type: software
has author: Paavolainen, Lassi
has DOI: analysis
has DOI: BIAFLOWS-PROBLEM: NUCLEI-TRACKING-NODIVISION
has function: operation Particle tracking
has location: W NucleiTrackingTrackmate-IJ
has location: Neubias BIAFLOWS workflow of Particle Tracking with TrackMate
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: j.ymeth.2016.09.016
has reference publication: TrackMate: An open and extensible platform for single-particle tracking
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1612
requires: http://biii.eu/node/330
created: 2020-01-23T15:01:46
modified: 2023-05-01T16:46:32
title: Nuclei Tracking (TrackMate)
comment: Track non-dividing particles in 2D time-lapse image.

nucleus-counter-imagej
type: software
has location: Nucleus Counter
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/38
requires: http://biii.eu/node/826
created: 2013-10-11T13:08:41
modified: 2020-03-03T09:02:03
title: Nucleus Counter (ImageJ)
comment: Bundled with MBF pacakge.

nucleusj
type: software
has author: Poulet, Alex
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: releases
has location: Github Releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: btu774
has reference publication: Poulet, Axel, Ignacio Arganda-Carreras, David Legland, Aline V. Probst, Philippe Andrey, and Christophe Tatout. “NucleusJ: An ImageJ Plugin for Quantifying 3D Images of Interphase Nuclei.” Bioinformatics 31, no. 7 (April 1, 2015): 1144–46.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: 978-1-4939-7318-7 33
has usage example: Desset et al. “Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ.” Methods in Molecular Biology (Clifton, N.J.) 1675 (2018): 615–32.
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1057
requires: http://biii.eu/node/79
created: 2019-12-12T23:40:22
modified: 2023-04-29T09:41:27
title: NucleusJ
comment: Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

numpy
type: software
has documentation: stable
has documentation: NumPy documentation
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: install
has location: Install NumPy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-04-26T23:54:02
modified: 2023-04-26T14:26:35
title: NumPy
comment: NumPy (Numerical Python) is an open source Python library that’s used in almost every field of science and engineering. It’s the universal standard for working with numerical data in Python, and it’s at the core of the scientific Python and PyData ecosystems. The NumPy library contains multidimensional array and matrix data structures. It provides ndarray, a homogeneous n-dimensional array object, with methods to efficiently operate on it. NumPy can be used to perform a wide variety of mathematical operations on arrays. NumPy users include everyone from beginning coders to experienced researchers doing state-of-the-art scientific and industrial research and development. The NumPy API is used extensively in Pandas, SciPy, Matplotlib, scikit-learn, scikit-image and most other data science and scientific Python packages. Learn more about NumPy here!

nvidia-cuda-9
type: software
created: 2019-02-19T15:43:55
modified: 2019-02-19T15:43:55
title: NVidia CUDA 9

nyquist-sampling-calculator
type: software
has author: Praveen Pankajakshan, Timothée Lecomte
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: Nyquist-Sampling-Calculator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://www.osapublishing.org/viewmedia.cfm%3Fr%3D1%26rwjcode%3Djosaa%26uri%3Djosaa-11-5-1619%26html%3Dtrue
has reference publication: The spatial frequency cut-off in three-dimensional imaging
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:55:58
title: Nyquist Sampling Calculator
comment: This plugin calculates the Nyquist sampling, in the radial and axial direction for your Microscope.

object-classification-using-ilastik
type: software
has author: ilastik team
has documentation: objects.html
has function: operation Image segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/73
requires: http://biii.eu/node/88
created: 2014-12-08T16:41:35
modified: 2018-05-16T00:00:15
title: Object Classification using ilastik
comment: This workflow classifies objects based on object-level features (e.g. intensity based, morphology based, etc) and user annotations. It needs segmentation images besides the raw image data. Segmentation images can be obtained from ilastik pixel classification, or binary segmentation images from other tools. Within the object classification, one can prefilter objects through thresholds (on pixel probability image) or object sizes (on segmentation image). Outputs are predicted classification label images. Selected features can also be exported. Advanced users also have possibilities to add customized (object) features for classification in a simple plugin fashion through python scripts.

object-tracking-and-metadata-management
type: software
has author: Cellprofiler team
has documentation: #Tracking
has function: operation Cell tracking
has location: ExampleTrackObjects.zip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2014-12-08T14:39:45
modified: 2018-05-16T00:11:31
title: Object Tracking and Metadata Management
comment: The goal of this workflow is to track cells captured in a time-lapse movie of a syncytial blastoderm stage Drosophila embryo and quantify their movement. >This example shows an example of object tracking. This pipeline analyzes a time-lapse experiment to identify the cells and track them from frame to frame, which is challenging since the cells are also moving. In addition, this pipeline also extracts metadata from the filename and uses groups the images by metadata in order to independently process several sequences of images and output the measurements of each. **Sample images** A portion of a time lapse movie of a syncytial blastoderm stage Drosophila embryo with a GFP-histone gene which renders chromatin fluorescent in live embryos. The movie shows nuclear divisions 10 through 13. Victoria Foe made this movie on a Bio-Rad Radiance 2000 laser scanning confocal microscope using a 40X 1.3NA oil objective. The frames are 7 seconds apart and plays at 30 frames per second GFP-histone transformed files provided by Rob Saint V.Foe and G.Odell, . 26 July 2001

object-tracking-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION
has function: operation Image tracking
has location: W ObjectTracking-ImageJ
has location: Neubias BIAFLOWS workflow of Object Tracking with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2020-01-23T15:10:05
modified: 2023-05-01T16:40:58
title: Object Tracking (ImageJ)
comment: Object tracking. For each time-frame, an image mask is obtained from median filtering (user defined radius), thresholding (user defined level) and hole filling. Convex objects are split apart by distance map watershed from regional intensity maxima (user defined noise tolerance), eroded (user defined radius) and analyzed as 3D particles (assuming some overlap between objects from a frame to the next frame). Finally, division events are analyzed and accounted for to relabel objects.

object-tracking-mu-lux-cz
type: software
has author: Lux, Filip
has author: Matula, Petr
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION
has documentation: MU-Lux-CZ.pdf
has documentation: DEscription of the algorithm from Cell Tracking Challenge Page
has function: operation Image tracking
has location: cell tracker.py
has location: Neubias BIAFLOWS workflow of Object Tracking with MU-Lux
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: ISBI.2019.8759594
has reference publication: DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
requires: http://biii.eu/node/1201
requires: http://biii.eu/node/1202
requires: http://biii.eu/node/128
created: 2020-01-23T15:23:14
modified: 2023-05-01T16:43:29
title: Object Tracking (MU-Lux-CZ)
comment: Cell tracking using MU-Lux-CZ algorithm. Dockerized Workflow for BIAFLOWS implemented by Martin Maska (Masaryk University).

object-tracking-octave
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION
has function: operation Image tracking
has location: W ObjectTracking-Octave
has location: Neubias BIAFLOWS workflow of Object Tracking with Octave
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: btz945
has reference publication: LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/113
created: 2020-01-23T15:15:33
modified: 2023-05-01T16:44:56
title: Object Tracking (Octave)
comment: Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version).

oligomacro-toolset
type: software
has author: Fabrice Cordelières
has documentation: README.md
has documentation: Instructions
has function: operation 3441
has function: operation 3443
has function: operation Cell segmentation
has function: operation Cell tracking
has location: IJ Toolset-OligoMacro
has location: IJ-Toolset_OligoMacro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: glia.23342
has reference publication: Azevedo MM, Domingues HS, Cordelières FP, Sampaio P, Seixas AI, Relvas JB. Jmy regulates oligodendrocyte differentiation via modulation of actin cytoskeleton dynamics. Glia. 2018;00:1–19.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Widefield microscopy
has topic: topic R7WRbf9Y8ySw9QWPwAjzcUa
has topic: topic R9P5gEAm1wic4R2PcZ7ZpPA
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/3568
has usage example: glia.23342
has usage example: Jmy regulates oligodendrocyte differentiation via modulation of actin cytoskeleton dynamics
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/597
requires: http://biii.eu/node/915
created: 2019-10-27T18:07:26
modified: 2023-05-03T10:14:40
title: OligoMacro Toolset
comment: OligoMacro Toolset, is an ImageJ macro-toolset aimed at isolating oligodendrocytes from wide-field images, tracking isolated cells, characterizing processes morphology along time, outputting numerical data and plotting them. It takes benefit of ImageJ built-in functions to process images and extract data, and relies on the R software in order to generate graphs.

omero
type: software
has author: OME Consortium
has documentation: partner
has documentation: OMERO extensions (partner projects)
has function: operation 2409
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: GPL v2
has location: www.openmicroscopy.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/77
created: 2013-10-15T18:00:59
modified: 2018-10-18T15:38:19
title: OMERO
comment: OMERO is a free, open source image management software. It is client-server based system which supports 5D images, including big images and high-content screening data. Data are stored on a server using relational database. They are accessed using 3 main clients, a desktop client, a web client and a command line tool. There are bindings from OMERO to other image analysis packages, like FLIMfit, OMERO.searcher. The data in OMERO are organized in groups. A user can be a member of one or more groups. This groups can be collaborative or private, there are 4 levels of permissions to access/edit/annotate/delete the data of other users. The package is supported not only by community forums, but also by a dedicated team which helps users to solve their problems and deals with the bugs submitted via error submission system. ###Strengths Open source, scalable software, Supports diverse sets of imaging applications and domains (EM,LM, HCS, DigPath) Cross-platform, Java-based application, API support for Java, Python, C++, Django, On-line Forums, Automatic QA and upload of software errors Multi-dimensional images, Web access, Free Demo-server accounts ### Limitations Enterprise-scale software, so complex install, requires expertise, Actively developing API, Python scripts and functions still developing

omero-flimfit
type: software
has documentation: docs.flimfit.org
has location: downloads
has location: OMERO FLIMfit download page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2019-01-11T14:55:55
title: OMERO FLIMfit
comment: FLIMfit is an OMERO client-side MATLAB application for fitting and visualising time-resolved FLIM data. It supports key data formats including: - Becker and Hickl .sdt - LaVision BioTech .msr - PicoQuant .bin - OME-TIFF files; Several options for curve fitting are available. Results can be saved back in OMERO, which also facilitates working collaboratively on the data analysis.

omeroeditor
type: software
has documentation: omero.editor
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4341
has location: site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2019-10-18T15:52:25
title: OMERO.editor

omerofigure
type: software
has author: Will Moore
has documentation: omero-figure
has documentation: GitHUb
has license: AGPL
has location: #install
has location: Installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/77
created: 2014-12-09T10:50:51
modified: 2018-05-27T14:40:35
title: OMERO.figure
comment: OMERO.figure is an OMERO web application that makes generating figures from images in an OMERO image database very quick and easy. The images in the figure link back to the original data, greatly simplifying the process of adjusting the view and keeping track of original data. PDF documents are generated, which can be opened using e.g. Adobe Illustrator or Inkscape in order to produce the final finished figure.

omeroinsight-client
type: software
has author: OME Developers
has documentation: getting-started-5.html
has documentation: Getting Started
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2018-05-26T13:15:01
title: OMERO.insight client
comment: OMERO is an image database application consisting of a server and several clients, the most important of which are the web client and _Insight_ java application. Metadata are extracted from images that have been imported (either using the Insight client, or directly from the filesystem), and this is accessible for search. A standardised hierarchy of `Project > Dataset > Image` in which image thumbnails can be viewed, combined with group membership, tagging, and attachment of results and other files gives a powerful framework for organising scientific image data. Images can also be analysed server-side or client-side within the base OMERO application or one of its many extensions. OMERO has APIs for extension in multiple languages: java, python, C++ and MATLAB; and such extensions have easy access to the image data and metadata in the database

omeroinsight-ij-client
type: software
has location: imagej.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2017-09-13T10:11:32
title: OMERO.insight-ij client

omeromatlab
type: software
has location: Matlab.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2017-09-13T10:11:33
title: OMERO.matlab

omerosearcher
type: software
has location: searcher
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2017-09-13T10:11:35
title: OMERO.searcher

omeroserver
type: software
has documentation: omero.server
has location: server-overview.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-15T10:45:49
modified: 2020-03-03T11:08:20
title: OMERO.server

omeroweb-client
type: software
has documentation: clients-overview.html
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4342
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/77
created: 2013-10-15T10:45:49
modified: 2020-03-03T10:45:51
title: OMERO.web client

omerowebtagging
type: software
has documentation: web-tagging.html
has documentation: pdf
has function: operation_0226
has implementation: http://biii.eu/taxonomy/term/4340
has license: GNU AFFERO GENERAL PUBLIC LICENSE
has location: omero.webtagging
has location: Installation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/957
created: 2013-10-15T10:45:49
modified: 2023-05-02T16:36:45
title: OMERO.webtagging
comment: OMERO.webtagging is the umbrella name for tools developed to enhance use of text annotations (tags) in OMERO. There are two tools at present, autotag and tagsearch.

open-microscopy-environment-ome
type: software
has function: operation_0337
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: www.openmicroscopy.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/469
requires: http://biii.eu/node/77
created: 2013-10-11T13:08:41
modified: 2019-11-14T14:54:47
title: Open Microscopy Environment (OME)

open-virtual-stack-fiji
type: software
has implementation: http://biii.eu/taxonomy/term/4340
has type: http://biii.eu/taxonomy/term/8
has usage example: 1209
created: 2018-01-30T16:32:31
modified: 2018-01-30T16:37:22
title: Open Virtual stack in Fiji

opencl
type: software
has documentation: opencl
has implementation: http://biii.eu/taxonomy/term/4339
has location: opencl
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has programming language: http://biii.eu/taxonomy/term/4241
has reference publication: opencl-2.2.html
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
created: 2018-01-28T15:54:59
modified: 2018-01-28T16:05:06
title: OpenCL
comment: OpenCL (Open Computing Language) is a framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-programmable gate arrays (FPGAs) and other processors or hardware accelerators. OpenCL specifies programming languages (based on C99 and C++11) for programming these devices and application programming interfaces (APIs) to control the platform and execute programs on the compute devices. OpenCL provides a standard interface for parallel computing using task- and data-based parallelism. OpenCL is an open standard maintained by the non-profit technology consortium Khronos Group. Conformant implementations are available from Altera, AMD, Apple, ARM, Creative, IBM, Imagination, Intel, Nvidia, Qualcomm, Samsung, Vivante, Xilinx, and ZiiLABS.[7][8] Source: https://en.wikipedia.org/wiki/OpenCL

opencomet
type: software
has author: Benjamin Gyori
has author: Gireedhar Venkatachalam
has documentation: documentation.html#video tutorial
has documentation: Video Tutorial
has location: www.cometbio.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.redox.2013.12.020
has reference publication: OpenComet: An automated tool for comet assay image analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-03-09T13:42:05
modified: 2023-05-03T14:40:51
title: OpenComet
comment: This workflow will batch process a directory of images: - comets should be horizontally oriented, tails to the right. Additional preprocessing is required if the gel does not match with this orientation (Rotate images, Using ImageJ/Transform Image or TransformJ plugin for example). Then using the plugin: Uneven background correction Automatic detection of comet shapes with outliers detection Automatic detection of the heads of comets (brightest region or profile analysis) Statistical values of tails, heads and Olive moments. Manual correction is available. Does live analysis with Micro-Manager

opencv
type: software
has license: BSD
has location: opencv.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/211
created: 2013-11-07T19:53:48
modified: 2017-09-13T10:13:06
title: OpenCV
comment: OpenCV is released under a BSD license and hence its free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 6 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.

opencv-biologically-inspired-vision-models-and-derivative-tools
type: software
has documentation: bioinspired retina.html
has documentation: Bioinspired Module Retina Introduction
has function: operation Edge detection
has function: operation Image enhancement
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: group bioinspired.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T08:43:48
modified: 2020-03-03T10:06:18
title: OpenCV / Biologically Inspired Vision Models and Derivative Tools
comment: The module provides biological visual systems models (human visual system and others). It also provides derivated objects that take advantage of those bio-inspired models.

opencv-camera-calibration-and-3d-reconstration
type: software
has documentation: tutorial table of content calib3d.html
has documentation: Camera calibration and 3D reconstruction (calib3d module)
has function: operation Image reconstruction
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T09:31:39
modified: 2019-11-13T12:03:08
title: OpenCV / Camera Calibration and 3D reconstration

opencv-computational-photography
type: software
has documentation: tutorial table of content photo.html
has documentation: Computational photography (photo module)
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: opencv.org
has location: OpenCV website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T09:37:20
modified: 2019-11-13T12:23:39
title: OpenCV / Computational Photography

opencv-cuda
type: software
has documentation: cuda intro.html
has documentation: CUDA Module Introduction
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T09:27:54
modified: 2023-05-03T14:42:30
title: OpenCV / CUDA
comment: The OpenCV CUDA module is a set of classes and functions to utilize CUDA computational capabilities. It is implemented using NVIDIA* CUDA* Runtime API and supports only NVIDIA GPUs. The OpenCV CUDA module includes utility functions, low-level vision primitives, and high-level algorithms. The utility functions and low-level primitives provide a powerful infrastructure for developing fast vision algorithms taking advantage of CUDA whereas the high-level functionality includes some state-of-the-art algorithms (such as stereo correspondence, face and people detectors, and others) ready to be used by the application developers. The CUDA module is designed as a host-level API. This means that if you have pre-compiled OpenCV CUDA binaries, you are not required to have the CUDA Toolkit installed or write any extra code to make use of the CUDA.

opencv-feature2d-module
type: software
has documentation: tutorial table of content features2d.html
has documentation: 2D Features framework (feature2d module)
has function: operation 3443
has function: operation Feature extraction
has function: operation Image tracking
has function: operation Object detection
has function: operation R9EjejimBB0tmnQRmZt0RhA
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: opencv.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T08:30:27
modified: 2019-10-18T15:35:42
title: OpenCV feature2d module

opencv-flann-clustering-and-search-multi-dimensional-spaces
type: software
has documentation: flann.html
has function: operation 2990
has function: operation Clustering
has license: BSD
has location: opencv.org
has location: OpenCV website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T09:49:24
modified: 2019-11-14T10:18:44
title: OpenCV / flann. Clustering and Search in Multi-Dimensional Spaces

opencv-high-level-gui
type: software
has documentation: tutorial table of content highgui.html
has documentation: High Level GUI and Media (highgui module)
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: group highgui.html
has location: OpenCV HighGUI module
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T10:05:39
modified: 2019-11-14T11:17:54
title: OpenCV / High-level GUI
comment: While OpenCV was designed for use in full-scale applications and can be used within functionally rich UI frameworks (such as Qt*, WinForms*, or Cocoa*) or without any UI at all, sometimes there it is required to try functionality quickly and visualize the results. This is what the HighGUI module has been designed for. It provides easy interface to: Create and manipulate windows that can display images and "remember" their content (no need to handle repaint events from OS). Add trackbars to the windows, handle simple mouse events as well as keyboard commands.

opencv-image-processing
type: software
has documentation: tutorial py table of contents imgproc.html
has documentation: Image Processing in OpenCV
has function: operation Geometrical transform
has function: operation Image processing
has function: operation Image smoothing
has function: operation Image thresholding
has function: operation Morphological operations
has function: operation Object detection
has function: operation Watershed
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: group imgproc.html
has location: OpenCV Image Processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T10:25:18
modified: 2019-11-14T11:50:50
title: OpenCV / Image Processing

opencv-image-stiching
type: software
has documentation: tutorial table of content stitching.html
has documentation: Images stitching (stitching module)
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: group stitching.html
has location: Images stitching
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T13:24:05
modified: 2019-11-14T12:59:32
title: OpenCV / Image Stiching

opencv-machine-learning
type: software
has documentation: ml intro.html
has documentation: Machine Learning Overview
has function: operation 2990
has function: operation 3443
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD
has location: group ml.html
has location: Machine Learning
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
created: 2017-09-14T13:32:46
modified: 2019-11-14T13:16:54
title: OpenCV / Machine Learning

openimadis
type: software
has author: France BioImaging
has author: Institut Curie Pict
has author: Strand
has documentation: wiki
has function: operation 2409
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4342
has location: openimadis
has location: Download page
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
has usage example: openimadis-micropicell.sante.univ-nantes.fr
has usage example: Micropicell
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1299
created: 2018-08-17T13:41:03
modified: 2018-10-18T15:38:19
title: Openimadis
comment: OpenImadis stands for Open Image Discovery: A platform for Image Life Cycle Management. It was previously called CID iManage (for Curie Image Database). No image data conversions, no duplication. - Uploads data to a secure server in the original format - Unique id for data Supports sharing and collaboration with access control - Allows users to upload, view, update or download data based on their access privileges Supports multiple ways of attaching meta-information - Annotations, comments and file attachments -Analysis results as query-able visual objects Supports Archiving (data moving to another long-term storage but still searchable) Facilitates custom visualization and analysis - Access data from preferred analysis and visualization tools - Access relevant bits of data to build efficient web and mobile application Facilitate easy access to analysis and visualization applications hosted on other servers - Run analysis on dedicated compute clusters - Access applications hosted and published by other users Highly Scalable - Supports on-the-fly addition of server nodes to scale concurrent usage

openmole
type: software
has license: AGPLv3 free software license
has location: www.openmole.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-11-07T19:51:19
modified: 2017-09-12T18:05:52
title: OpenMOLE
comment: OpenMOLE (Open MOdeL Experiment) is a workflow engine designed to leverage the computing power of distributed execution environments for naturally parallel processes. A process is told naturally parallel if the same computation runs many times for a set of different inputs, such as model experiment or data processing It is free software distributed under the AGPLv3 free software license.

openslide
type: software
has author: Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, M. Satyanarayanan
has documentation: wiki
has documentation: Documentation WIKI
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has license: GNU Lesser GPL, v2.1
has location: openslide.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4241
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T09:33:03
modified: 2020-12-07T09:25:06
title: OpenSlide
comment: >OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Python and Java bindings are also available. The Python binding includes a Deep Zoom generator and a simple web-based viewer. The Java binding includes a simple image viewer.

optical-flow
type: software
has author: Timothée Lecomte
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/239
requires: http://biii.eu/node/8
created: 2014-12-09T09:48:34
modified: 2018-05-14T23:06:06
title: Optical Flow
comment: This protocol computes the optical flow of a 2D+T sequence. The results are displayed with flow arrows painted on top of the original sequence, and also with two additional sequences for the norm of the flow and a color-coded presentation of the flow following the Middlebury convention.

optical-flow-horn-schunck-icy
type: software
has author: Alexandre Dufour
has author: Timothée Lecomte
has documentation: Optical-Flow---Horn-Schunck
has function: operation Optical flow analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Optical-Flow---Horn-Schunck
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/369
requires: http://biii.eu/node/376
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/909
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:46
modified: 2020-03-02T20:34:37
title: Optical Flow - Horn-Schunck (Icy)

orbit
type: software
has author: Manuel Stritt
has documentation: OrbitHandbook.pdf
has documentation: Handbook
has function: operation Cell segmentation
has function: operation Interactive segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv3 license
has location: download
has location: Download Orbit
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: publications
has reference publication: List of publications
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-02-23T11:01:16
modified: 2023-04-28T13:00:13
title: Orbit
comment: Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans. It can connect to image servers, e.g. Omero. Analysis can be done on your local computer or via scaleout functionality in a distrubuted computing environment like a Spark cluster. Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in. In addition a versatile API allows you to enhance Orbit and to run your own scripts.

organise-image-data-using-omero
type: software
has author: OME Developers
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/77
created: 2014-12-09T11:17:44
modified: 2018-08-16T15:42:25
title: Organise Image Data using OMERO
comment: OMERO is an image database application consisting of a server and several clients, the most important of which are the web client and _Insight_ java application. Metadata are extracted from images that have been imported (either using the Insight client, or directly from the filesystem), and this is accessible for search. A standardised hierarchy of _Project > Dataset > Image_ in which image thumbnails can be viewed, combined with group membership, tagging, and attachment of results and other files gives a powerful framework for organising scientific image data. Images can also be analysed server-side or client-side within the base OMERO application or one of its many extensions. OMERO has APIs for extension in multiple languages: java, python, C++ and MATLAB; and such extensions have easy access to the image data and metadata in the database.

organoid
type: software
has author: Jonathan M. Matthews
has DOI: journal.pcbi.1010584
has DOI: OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics
has function: operation Cell segmentation
has function: operation Feature extraction
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4339
has location: OrganoID
has location: GitHub
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/3567
has usage example: OrganoID#usage
has usage example: Usage
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2023-05-02T14:25:28
modified: 2023-05-02T15:46:05
title: OrganoID
comment: OrganoID is an image analysis platform that automatically recognizes, labels, and tracks single organoids, pixel-by-pixel, in brightfield and phase-contrast microscopy experiments. The platform was trained on images of pancreatic cancer organoids and validated on separate images of pancreatic, lung, colon, and adenoid cystic carcinoma organoids.

organoseg
type: software
has author: Kevin A. Janes
has comparison: s41598-017-18815-8
has comparison: Compare OrganoSeg against CellProfiler1, MorphoLibJ1, and ImageJ
has function: operation Cell segmentation
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has location: s41598-017-18815-8#Sec16
has location: Download OrganoSeg in Supplementary File S1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: s41598-017-18815-8
has reference publication: OrganoSeg publication at Scientific Reports
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has topic: topic RNFOzq5E0ZVBh5Euhn06rn
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/89
created: 2023-05-02T15:22:02
modified: 2023-05-02T16:10:03
title: OrganoSeg
comment: OrganoSeg is an open-source software that integrates segmentation, filtering, and analysis for breast-cancer spheroid and colon and colorectal-cancer organoid morphologies.

orientationj
type: software
has author: Daniel Sage
has documentation: theoretical-background.pdf
has documentation: theory
has function: operation_0337
has function: operation 3443
has function: operation Edge detection
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: orientation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 10.1007/s10237-011-0325-z
has reference publication: 10.1007/978-3-319-28549-8 3
has reference publication: https://www.ahajournals.org/doi/full/10.1161/STROKEAHA.108.528091%3Furl_ver%3DZ39.88-2003%26rfr_id%3Dori%253Arid%253Acrossref.org%26rfr_dat%3Dcr_pub%253Dpubmed
has reference publication: 10.1007/978-3-319-28549-8_3
has reference publication: 10.1161/STROKEAHA.108.528091
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
has usage example: #soft
has usage example: Test images
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-17T15:43:29
title: OrientationJ
comment: The aim of this plugin is to characterise the orientation and isotropy properties of a region of interest (ROI) in an image, based on the evaluation of the gradient structure tensor in a local neighborhood.

oriented-contours
type: software
has author: Pau Gregoire
has documentation: EBImage.pdf
has documentation: pdf
has function: operation Feature extraction
has location: ocontour.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: ocontour.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:46
modified: 2019-10-18T09:15:05
title: Oriented Contours

orion
type: software
has author: Alberto Santamaría-Pang
has author: Bradley E. Losavio
has author: Costa M. Colbert
has author: Ioannis A. Kakadiaris
has author: Peter Saggau
has author: Yong Liang
has function: operation Image deconvolution
has function: operation Image enhancement
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: orion
has location: CBL-ORION Github repository page
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: jn.90627.2008
has reference publication: Live Neuron Morphology Automatically Reconstructed From Multiphoton and Confocal Imaging Data
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RBKlmE9DGTZwEwxw0juThGg
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-09-12T16:37:59
modified: 2023-05-03T13:20:18
title: ORION
comment: ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction. A project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. The goal of this project is to develop a computational and experimental framework to allow real-time mapping of functional imaging data (e.g., spatio-temporal patterns of dendritic voltages or intracellularions) to neuronal structure, during the very limited duration of an acute experiment.

orthanc
type: software
has author: Jodogne Sébastien
has function: operation 2409
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: Jodogne, S. The Orthanc Ecosystem for Medical Imaging. J Digit Imaging 31, 341–352 (2018).
has location: download.php
has location: Access to download and source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: s10278-018-0082-y
has reference publication: Jodogne, S. The Orthanc Ecosystem for Medical Imaging. J Digit Imaging 31, 341–352 (2018).
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3444
has topic: topic RBHw300pzIYcttGsAmIZvk5
has topic: topic RDos3h5yRfjhLUcOImDOFgB
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/8
has usage example: https://www.orthanc-server.com/static.php%3Fpage%3Dreferences
has usage example: Users of Orthanc
openess: http://biii.eu/taxonomy/term/3575
created: 2023-03-14T11:20:10
modified: 2023-03-14T11:32:58
title: Orthanc
comment: Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images. Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol. Orthanc can turn any computer running Windows, Linux or OS X into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies. What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc. Orthanc also features a plugin mechanism to add new modules that extends the core capabilities of its REST API. A Web viewer, a PostgreSQL database back-end, a MySQL database back-end, and a reference implementation of DICOMweb are currently freely available as plugins.

orthogonal-views-imagej
type: software
has documentation: 146-28.html#toc-Subsubsection-28.6.10
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-11-08T18:03:38
modified: 2020-03-03T09:20:56
title: Orthogonal Views (ImageJ)
comment: A menu item in ImageJ that allows you to inspect a 3D stack with orthogonal views (XY, XZ, YZ planes). Slicing plane could be interactively moved by dragging crosses. Pedro Almada wrote a plugin to save the current orthogonal views as montage. ## ImageJ Macro Usages [Save orthogonal views | OrthoSaver](http://uic.igc.gulbenkian.pt/macros/OrthoSaver.ijm) >ImageJ's orthogonal viewer for 3D stacks doesn't let you easily save the current orthogonal view. This macro, once installed, lets users create a montage with the currently open orthogonal views and selection guides. To use it, open an image z-stack and open the orthogonal viewer. With the mouse, choose which are the sections of interest to you and without moving the mouse, press F2. You'll get a montage of the currently selected orthogonal view.

otsu-thresholding
type: software
has location: Otsu Thresholding
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
requires: http://biii.eu/node/671
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:05:37
title: Otsu Thresholding

oufti
type: software
has author: Graeme Ball
has documentation: tutorial.htm
has function: operation Cell segmentation
has function: operation Cell tracking
has function: operation Spot extraction
has license: GNUv3
has location: download.html
has location: Oufti (compiled version, Matlab independent)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: j.1365-2958.2011.07579.x
has reference publication: Paintdakhi et al (2015) Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis
has reference publication: Sliusarenko et al (2011) High‐throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio‐temporal dynamics
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-08T16:55:58
modified: 2018-05-25T22:52:55
title: Oufti
comment: Oufti (previously named MicrobeTracker) is a MATLAB application / suite of tools for analysing fluorescent spots inside microbes. MicrobeTracker can identify cell outlines and fluorescent foci, and generate plots and statistics based on positions and intensity (kymographs, histograms etc.) The MATLAB code is easy to modify and extend to add additional plots and statistics: see e.g. [Lesterlin et al. (2014)](http://www.ncbi.nlm.nih.gov/pubmed/24362571). The Outfi Forum is [quite active](https://groups.google.com/forum/#!forum/ouftiinfo).

overlayoutlines
type: software
has author: Carpenter Ann
has documentation: imageprocessing.html#overlayoutlines
has documentation: CellProfiler manual
has function: operation_0226
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: overlayoutlines.py
has location: GIT HUB, but comes with CellProfiler main installation
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-10-16T10:43:52
title: OverlayOutlines
comment: OverlayOutlines is a module from CellProfiler to place outlines of objects over a desired image.

ovuscule
type: software
has author: Philippe Thévenaz
has documentation: ovuscule
has documentation: user manual
has function: operation Active contours
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has location: ovuscule
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: thevenaz1101.html
has reference publication: The Ovuscule
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-18T10:00:30
title: Ovuscule

paintera
type: software
has author: Bogovic John orcid.org/0000-0002-4829-9457
has author: Günther Ulrik orcid.org/0000-0002-1179-8228
has author: Hanslovsky Philipp orcid.org/0000-0002-9416-6516
has author: Leite Vanessa
has author: Nunez-Iglesias Juan http://orcid.org/0000-0002-7239-5828
has author: Pietzsch Tobias
has author: Saalfeld Stephan orcid.org/0000-0002-4106-1761
has documentation: paintera
has function: operation Image reconstruction
has function: operation Image visualisation
has function: operation Neuron image analysis
has function: operation Volume rendering
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has function: operation Slice rendering
has function: operation Surface rendering
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v2.0
has location: paintera
has location: Paintera on GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic R96toeNl9iMp8oqv9augU84
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1393
requires: http://biii.eu/node/1394
created: 2018-12-08T16:38:48
modified: 2018-12-09T17:28:32
title: Paintera
comment: Paintera is a general visualization tool for 3D volumetric data and proof-reading in segmentation/reconstruction with a primary focus on neuron reconstruction from electron micrographs in connectomics. It features/supports: Views of orthogonal 2D cross-sections of the data at arbitrary angles and zoom levels Mipmaps for efficient display of arbitrarily large data at arbitrary scale levels Label data Painting Manual agglomeration 3D visualization as polygon meshes Meshes for each mipmap level Mesh generation on-the-fly via marching cubes to incorporate painted labels and agglomerations in 3D visualization. Marching Cubes is parallelized over small blocks. Only relevant blocks are considered (huge speed-up for sparse label data). Paintera is implemented in Java and makes extensive use of the UI framework JavaFX

palmsiever
type: software
has author: Thomas Pengo, Seamus Holden
has function: operation_0337
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL
has location: palm-siever
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: btu720
has reference publication: PALMsiever Bioinformatics 2015
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Super-resolution microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-15T17:54:43
modified: 2023-05-03T14:10:42
title: PALMsiever
comment: PALMsiever is a MATLAB-based application that allows the filtering (sieving) and analysis of localization-microscopy data. It provides the ability to render the data using different visualization algorithms and perform simple measurements on the point-localization data. It is extensible using simple MATLAB scripts and a number of plugins is already provided with the software itself, including a clustering algorithm and 3D rendering. Strengths: intuitive, easy navigation through the point-localization data Limitations: no multi-color

pandore
type: software
has author: Clouard et. al.
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: Original
has location: Pandore
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2015-01-16T01:16:25
modified: 2023-04-29T12:51:43
title: Pandore
comment: Pandore is a standardized library of image processing operators. The current version contains image processing operators that operate on grayscale, color and multispectral, 1D, 2D and 3D images. Link: Operator Index

panoramic-viewer
type: software
has author: 3DHISTECH
has function: operation_0226
has function: operation_0337
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4341
has location: pannoramic viewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-10-11T13:08:44
modified: 2019-11-14T11:43:57
title: Panoramic Viewer
comment: When opening the Pannoramic Viewer you see all of your virtual slides in thumbnail view. Selecting one (or up to 10 at a time) the slide gets under the virtual objective of the virtual microscope. Here you can move and change the magnification of the slide quickly and easily using the mouse. Emphasizing 'quickly' is important considering the fact that the size of an average virtual slide can easily be more than 1 GB. Main characteristics: Seamless zooming and moving of the virtual slide Bookmarking (annotating) on the spot, i.e. defining the specific part of the sample by drawing; finding and reading of previously made bookmarks Easy and precise measurements Real-time changing of brightness, contrast and color bias Fluorescent slide handling, separate channel view & pseudo-colorization Slide uploading and downloading for teleconsultation Synchronized viewing (moving and zooming) of multiple slides for comparison purposes Publication quality image capture of displayed areas (.JPG, .BMP, .TIFF) TIFF, MIRAX slide and Meta-XML export for Carl Zeiss AxioVision™ compatibility Scanmap export for rescanning existing digital slides Easily expandable functionality via the software modules

parallel-iterative-deconvolution
type: software
has author: Piotr Wendykier
has documentation: Parallel Iterative Deconvolution
has function: operation Image deconvolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: Parallel Iterative Deconvolution
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/114
requires: http://biii.eu/node/38
requires: http://biii.eu/node/389
created: 2013-10-11T13:08:44
modified: 2019-10-16T16:10:59
title: Parallel Iterative Deconvolution
comment: An ImageJ plugin for iterative deblurring.

parallel-spectral-deconvolution
type: software
has author: Piotr Wendykier
has documentation: Parallel Spectral Deconvolution
has function: operation Image deconvolution
has implementation: http://biii.eu/taxonomy/term/4340
has location: Parallel Spectral Deconvolution
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: parallelspectraldeconvolution
has reference publication: book
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Parallel Spectral Deconvolution
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-18T10:06:55
title: Parallel Spectral Deconvolution

paraview
type: software
has author: Kitware
has documentation: tutorials
has documentation: Tutorials
has function: operation_0337
has function: operation Image visualisation
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4341
has location: download
has location: Download Paraview
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: Ahrens, James, Geveci, Berk, Law, Charles, ParaView: An End-User Tool for Large Data Visualization, Visualization Handbook, Elsevier, 2005, ISBN-13: 978-0123875822
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1075
created: 2018-11-23T07:50:24
modified: 2018-11-23T08:04:16
title: Paraview
comment: ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.

particle-tracker
type: software
has author: MOSAIC Group
has documentation: Particle Tracker
has function: operation Particle tracking
has function: operation Spot extraction
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Particle Tracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/16043363
has reference publication: Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-18T09:05:50
title: Particle Tracker

particle-tracker-2d3d
type: software
has author: Guy Levy
has author: Ivo Sbalzarini
has author: Janicke Cardinale
has author: Mosaic group
has documentation: ParticleTracker manual addendum.pdf
has documentation: Addendum for 3D analysis
has function: operation Image tracking
has function: operation Particle tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: ImageJ.git
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://www.sciencedirect.com/science/article/pii/S1047847705001267%3Fvia%253Dihub
has reference publication: 10.1016/j.jsb.2005.06.002
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
has usage example: tutorial.html
has usage example: Sample data and tutorial
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/79
created: 2013-10-15T10:45:51
modified: 2019-10-17T11:08:52
title: Particle Tracker 2D/3D
comment: Easy-to-use, computationally efficient, two- and three-dimensional, feature point-tracking tool for the automated detection and analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no apriori mathematical modelling of the motion, it is self-initialising, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. The plugin is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. It allows the user to visualize and analyze the detected particles and found trajectories in various ways: Preview and save detected particles for separate analysis Global non progressive view on all trajectories Focused progressive view on individually selected trajectory Focused progressive view on trajectories in an area of interest It also allows the user to find trajectories from uploaded particles position and information text files and then to plot particles parameters vs. time - along a trajectory

particle-tracking-imagej
type: software
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: NUCLEI-TRACKING-NODIVISION
has function: operation Particle tracking
has location: W LogPartTrack IJ
has location: Neubias BIAFLOWS workflow of Particle Tracking with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1038
requires: http://biii.eu/node/38
created: 2020-01-23T14:55:45
modified: 2023-05-01T16:47:35
title: Particle Tracking (ImageJ)
comment: Particle tracking in 2D time-lapse based on linking closest regional intensity minima (user defined noise tolerance) detected from Laplacian of Gaussian filtered images (user defined radius). A maximum linking distance is set (user defined).

particle-tracking-omero
type: software
has author: Danuser lab
has documentation: u-track-2.1.2.pdf
has documentation: [PDF] u-track Documentation Release 2.1.2
has function: operation Image tracking
has location: https://downloads.openmicroscopy.org/u-track/2.1.2/
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: nmeth.1237
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/77
requires: http://biii.eu/node/954
created: 2014-12-09T11:55:45
modified: 2018-05-27T14:53:03
title: Particle tracking with OMERO
comment: u-Track is a client-side OMERO MATLAB application implementing the sophisticated multiple-particle tracking algorithm of Jaqaman et al. . It works on data previously imported into an OMERO server, and produces results in the form of MATLAB data structures as well as providing functionality to visualise these results.

particles-animation
type: software
has author: Dallongeville Stephane
has implementation: http://biii.eu/taxonomy/term/4340
has location: Particles-animation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-18T09:10:21
title: Particles animation
comment: A fun simulator. It's not very useful for biology but it's a good demo!

partseg
type: software
has author: Bokota Grzegorz orcid.org/0000-0002-5470-1676
has documentation: PartSeg
has function: operation Cell segmentation
has function: operation Feature extraction
has function: operation Image segmentation
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL v3
has location: PartSeg
has location: Tool webpage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: tutorial diferrent neurons
has usage example: Usage PartSeg as library
openess: http://biii.eu/taxonomy/term/3575
created: 2019-01-11T14:22:59
modified: 2019-01-16T18:12:30
title: PartSeg
comment: There are many methods in bio-imaging that can be parametrized. This gives more flexibility to the user as long as tools provide easy support for tuning parameters. On the other hand, the datasets of interest constantly grow which creates the need to process them in bulk. Again, this requires proper tool support, if biologist is going to be able to organize such bulk processing in an ad-hoc manner without the help of a programmer. Finally, new image analysis algorithms are being constantly created and updated. Yet, lots of work is necessary to extend a prototype implementation into product for the users. Therefore, there is a growing need for software with a graphical user interface (GUI) that makes the process of image analysis easier to perform and at the same time allows for high throughput analysis of raw data using batch processing and novel algorithms. Main program in this area are written in Java, but Python grow in bioinformatics and will be nice to allow easy wrap algorithm written in this language. Here we present PartSeg, a comprehensive software package implementing several image processing algorithms that can be used for analysis of microscopic 3D images. Its user interface has been crafted to speed up workflow of processing datasets in bulk and to allow for easy modification of algorithm’s parameters. In PartSeg we also include the first public implementation of Multi-scale Opening algorithm descibed in [1]. PartSeg allows for segmentation in 3D based on finding connected components. The segmentation results can be corrected manually to adjust for high noise in the data. Then, it is possible to calculate some standard statistics like volume, mass, diameter and their user-defined combinations for the results of the segmentation. Finally, it is possible to superimpose segmented structures using weighted PCA method. Conclusions: PartSeg is a comprehensive and flexible software dedicated to help biologists in processing, segmentation, visualization and the…

patternquant
type: software
has location: patternquant module
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2013-10-11T13:08:43
modified: 2017-09-12T10:22:52
title: PatternQuant

pausecellprofiler-cellprofiler
type: software
has documentation: cp2 manual 9978.pdf
has documentation: CellProfiler 2.0 manual pdf
has function: operation Validation
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/30
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-03T17:25:18
title: PauseCellProfiler (CellProfiler)
comment: not available on version 2.1 and up.

performing-automatic-registration-clem
type: software
has author: Perrine Paul Gilloteaux orcid.org/0000-0003-3903-4841
has function: operation 2928
has function: operation Image registration
has function: operation Spot extraction
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RLtOI0poPsYRHzgXbAcr2E
has location: AutomaticRegistration
has location: Protocol can be downloaded from Icy toolbar
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2017-05-05T14:47:35
modified: 2020-03-01T10:31:57
title: performing automatic registration for CLEM
comment: This is an example workflow of how to perform automatic registration by - first detecting spots in both images using wavelet segmentation (with different scale according to the image scale) - second using Ec-Clem autofinder to register both images Click on a block to know more about a tool. Non referenced tools are non clickable.

performing-fluorescence-recovery-after-photobleaching-frap-experiment
type: software
has author: Bechara Kachar
has author: Chan-Ying Zheng
has author: Ronald S. Petralia
has author: Ya-Xian Wang
has DOI: http://doi.org/10.3791/2568
has location: fluorescence-recovery-after-photobleaching-frap-fluorescence-tagged
has location: Jove video tutorial
has reference publication: http://doi.org/10.3791/2568
has reference publication: Fluorescence Recovery After Photobleaching (FRAP) of Fluorescence Tagged Proteins in Dendritic Spines of Cultured Hippocampal Neurons
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1293
requires: http://biii.eu/node/38
created: 2014-12-09T11:32:56
modified: 2018-05-07T16:46:16
title: Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment
comment: The article describes how a FRAP experiment can be conducted and subsequently analyzed. This includes steps in ImageJ and subsequent normalization of the intensity data. This is a qualitative analysis, and curve fitting is done using Excel. Requires "Template matching and Slice alignment plugin"

phantast-fiji
type: software
has author: Nicolas Jaccard
has documentation: PHANTAST-FIJI
has documentation: Github Repo
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has license: https://github.com/nicjac/PHANTAST-FIJI/blob/master/LICENSE
has location: releases
has location: GitHub PHANTAST Releases
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: bit.25115
has reference publication: Jaccard et. al. (2013) Automated Method for the Rapid and Precise Estimation of Adherent Cell Culture Characteristics from Phase Contrast Microscopy Images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RtBCcu7zJiS0phrbR2HzAI
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-05-19T09:28:05
modified: 2018-05-19T09:33:37
title: PHANTAST for FIJI
comment: The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

phenoripper
type: software
has author: Altschuler Steven J
has author: Pavie Benjamin / orcid.org/0000-0002-0249-3844
has author: Rajaram Satwik / orcid.org/0000-0001-8242-4402
has author: Wu Lani F / orcid.org/0000-0002-0052-7537
has documentation: phenoripper
has documentation: PhenoRipper github site
has function: operation 2409
has function: operation 2945
has function: operation 3443
has function: operation Cell counting
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License
has location: phenoripper
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth.2097.html
has reference publication: PhenoRipper, Nature Methods 9, 635–637 (2012)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3385
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T16:43:40
modified: 2023-04-28T15:00:38
title: PhenoRipper
comment: An easy to use, image analysis software package that enables rapid exploration and interpretation of microscopy data.

phindr3d
type: software
has author: Andrews, David W.; orcid.org/0000-0002-9266-7157
has author: Hariharan, Santosh; orcid.org/0000-0002-0941-0044
has author: Lourenco, Corey; orcid.org/0000-0001-9075-7661
has author: Mergenthaler, Philipp; orcid.org/0000-0002-9753-6711
has author: Pemberton, James M.; orcid.org/0000-0001-8386-1081
has author: Penn, Linda Z.; orcid.org/0000-0001-8133-5459
has documentation: Phindr3D
has function: operation_0337
has function: operation 2945
has function: operation 2990
has function: operation 3443
has function: operation Image classification
has function: operation Image processing
has function: operation Neuron image analysis
has function: operation Object detection
has function: operation RDetoixS3xEu0agR2CebaoB
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License Version 3
has location: Phindr3D
has location: Phindr3D on GitHub
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: journal.pcbi.1008630
has reference publication: Phindr3D original publication
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic High content screening
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2021-05-26T19:54:42
modified: 2021-05-26T20:30:53
title: Phindr3D
comment: Phindr3D is a comprehensive shallow-learning framework for automated quantitative phenotyping of three-dimensional (3D) high content screening image data using unsupervised data-driven voxel-based feature learning, which enables computationally facile classification, clustering and data visualization. Please see our GitHub page and the original publication for details.

pil
type: software
created: 2018-04-26T23:54:02
modified: 2018-04-26T23:54:02
title: PIL

pillow
type: software
has author: Alex Clark
has documentation: Pillow
has function: operation 3443
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: Pillow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2013-10-11T13:08:43
modified: 2020-03-03T09:09:20
title: pillow
comment: A fork of PIL python package, with small collection of image import/export and image processing modules. See [Reference Documentation](http://pillow.readthedocs.org/en/latest/reference/index.html) for more details. Though this package mostly works in any platform, some of them are limited to Windows. This package is a part of [pythonxy](https://code.google.com/p/pythonxy/).

piv-analyser
type: software
has documentation: PIV analyser
has function: operation Optical flow analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: PIV analyser
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/239
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:35:17
title: PIV analyser
comment: This plugin calculates the optic flow for each pair of images made with the given stack.

pixbleach
type: software
has location: pixbleach
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:39
title: PixBleach

pixel-classification-glas-challenge-unet
type: software
has author: Mormont, Romain
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: GLAND-SEGMENTATION-TEST
has function: operation Image smoothing
has function: operation Pixel classification
has implementation: http://biii.eu/taxonomy/term/4340
has location: v1.3.0
has location: Neubias BIAFLOWS workflow of pixel classification with UNet
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/1476
requires: http://biii.eu/node/1478
created: 2019-03-14T23:38:32
modified: 2023-05-01T16:37:20
title: Pixel classification for GlaS challenge with UNet
comment: This workflow segments glands from H&E stained histopathological images from the Gland Segmentation Challenge (GlaS2015) using deep learning (UNet). UNet implementation largely inspired from PyTorch-UNet by Milesial.

pixel-classification-using-ilastik
type: software
has author: ilastik team
has documentation: pixelclassification.html
has function: operation Image segmentation
has function: operation Object detection
has function: operation Pixel classification
has location: pixelClassification 2dcells.zip
has location: pixelClassification_2dcells.zip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/73
requires: http://biii.eu/node/88
created: 2014-12-08T17:43:57
modified: 2018-10-18T15:31:08
title: Pixel Classification using ilastik
comment: This workflow classifies, or segments, the pixels of an image given user annotations. It is especially suited if the objects of interests are visually (brightness, color, texture) distinct from their surrounding. Users can iteratively select pixel features and provide pixel annotations through a live visualization of selected feature values and current prediction responses. Upon users' satisfaction, the workflow then predicts the remaining unprocessed image(s) regions or new images (as batch processing). Users can export (as images of various formats): selected features, annotations, predicted classification probability, simple segmentation, etc. This workflow is often served as one of the first step options for other workflows offered by ilastik, such as object classification, automatic tracking.

pixfret-0
type: software
has author: Laurent Gelman
has location: pixfret-tool
has location: omictools.com/pixfret-tool
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: jemt.20215
has reference publication: PixFRET, an ImageJ plug‐in for FRET calculation that can accommodate variations in spectral bleed‐throughs
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2014-12-09T14:22:03
modified: 2018-05-16T20:55:47
title: PixFRET
comment: The ImageJ pligin, called PixFRET, allows a simple and rapid determination of channel bleed-through parameters and the display of normalized FRET images. see 2521 Input data type: Stacks with 2 channels (controls for bleed-through calculation) or 3 channels (FRET calculation) Output data type: One Image with FRET values and One image with normalized FRET values

piximi
type: software
has function: operation Image classification
has implementation: http://biii.eu/taxonomy/term/4342
has location: piximi
has location: Github
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
has usage example: piximi.app
has usage example: Web server
openess: http://biii.eu/taxonomy/term/3575
created: 2020-03-04T08:35:18
modified: 2020-03-04T08:47:16
title: Piximi
comment: Web based application for deep learning cell classifier . Aim to replace cellprofiler analyst and advanced cell classifier . Under construction.

plugin-design-guidelines
type: software
has documentation: PlugIn Design Guidelines
has function: operation 2409
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4342
has location: PlugIn Design Guidelines
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: PlugIn Design Guidelines
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3570
has usage example: PlugIn Design Guidelines
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:16:58
title: PlugIn Design Guidelines

plustiptracker
type: software
has author: Alexandre Matova
has author: Gaudenz Danuser
has author: Kathryn T. Applegate
has author: Khuloud Jaqaman
has author: Maria H. Bagonis
has author: Sebastien Besson
has documentation: #utrack anc
has function: operation Image tracking
has license: GPLv3
has location: download
has location: u-track 2.2
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: j.jsb.2011.07.009
has reference publication: plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1289
requires: http://biii.eu/node/1290
requires: http://biii.eu/node/1300
requires: http://biii.eu/node/89
created: 2014-12-08T11:53:11
modified: 2023-05-03T08:42:10
title: plusTipTracker
comment: The workflow contains a Matlab package (plusTipTracker) for segmentation and tracking of microtubule tips, based on fluorescence time-lapse movies from microtubule tip markers such as EB-GFP. The tracking model accounts for the specific movement characteristics of microtubules Moreover, scripts for secondary analysis of detected microtubule paths are provided. plusTipTracker is part of u-track 2.0 package. The workflow is described in the reference.

point-cloud-analyst-poca
type: software
has author: Levet Florian orcid.org/0000-0002-4009-6225
has author: Sibarita Jean-Baptiste orcid.org/0000-0002-9920-7700
has DOI: s41592-023-01811-4
has documentation: poca-smlm.github.io
has documentation: Documentation
has function: operation_0337
has function: operation 2945
has function: operation Cell segmentation
has function: operation Image colocalization
has function: operation Interactive segmentation
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL v3
has location: PoCA
has location: Github repository of PoCA with code source and compiled versions for Windows
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: s41592-023-01811-4
has reference publication: Original publication link in Nature Methods
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Super-resolution microscopy
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
has usage example: releases
has usage example: Few datasets are available with the compiled version of PoCA
openess: http://biii.eu/taxonomy/term/3575
created: 2023-03-17T08:27:59
modified: 2023-05-11T11:03:54
title: Point Cloud Analyst (PoCA)
comment: SMLM is a mature but still growing field, which still lacks efficient and user-friendly analysis and visualization software platform adapted for both users and developers. We here introduce PoCA, a powerful open-source software platform dedicated to the visualization and analysis of 2D and 3D point-cloud data. PoCA allows manipulating large datasets, and integrates a plugin architecture, a native batch analysis engine and a Python code interpreter, facilitating both the analysis of data and the integration of new methods.

point-picker-imagej
type: software
has author: Philippe Thévenaz
has documentation: pointpicker
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: pointpicker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/321
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2020-03-02T08:52:06
title: Point Picker (ImageJ)

populationprofiler
type: software
has author: Matuszewski, D. J.
has author: Puigvert, J. C.
has author: Sintorn, I.-M.
has author: Wählby, C.
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD-3-clause
has location: PopulationProfiler.html
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-15T10:52:25
modified: 2020-03-03T20:14:35
title: PopulationProfiler
comment: PopulationProfiler  is light-weight cross-platform open-source tool for data analysis in image-based screening experiments. The main idea is to reduce per-cell measurements to per-well distributions, each represented by a histogram. These can be optionally further reduced to sub-type counts based on gating (setting bin ranges) of known control distributions and local adjustments to histogram shape. Such analysis is necessary in a wide variety of applications, e.g. DNA damage assessment using foci intensity distributions, assessment of cell type specific markers, and cell cycle analysis.

priismive
type: software
has author: IVE development team
has license: Custom
has location: IVE
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2014-12-15T13:24:32
modified: 2017-09-12T18:02:11
title: PRIISM/IVE
comment: Priism is an image processing, analysis and visualisation application for multidimensional light and electron microscopy data. It uses the Image Visualization Environment (IVE) library, which is a closed-source C library with documented C and FORTRAN APIs. Priism/IVE was developed at UCSF, and can be obtained free of charge by sending an email request to the developers. Many of the same processing and analysis functions available in other image processing applications can be found here (cropping, resizing, spatial filters, Fourier transforms, segmentation etc.), and it includes a comprehensive html-based offline manual. The "SoftWoRx" package of GE Healthcare (formerly Applied Precision) was based on Priism/IVE.

processing
type: software
has location: processing.org
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2019-10-16T11:41:54
title: Processing
comment: Processing is a flexible software sketchbook and a language for learning how to code within the context of the visual arts. Since 2001, Processing has promoted software literacy within the visual arts and visual literacy within technology.

projector-knime
type: software
has function: operation Image visualisation
has function: operation Projection
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:43
modified: 2020-03-01T16:25:21
title: Projector (KNIME)

protein-array-analyzer-imagej
type: software
has author: Carpentier Gilles
has documentation: dotblot.html
has documentation: Documentation
has function: operation 3443
has function: operation Illumination correction
has implementation: http://biii.eu/taxonomy/term/4340
has location: Protein Array Analyzer.txt
has location: Macro link (toolset)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-05-17T13:49:31
modified: 2020-10-19T15:09:37
title: Protein Array Analyzer for ImageJ
comment: Protein array is used to analyze protein expressions by screening simultaneously several protein-molecule interactions such as protein-protein and protein-DNA interactions. In most cases, the detection of interactions leads to an image containing numerous lines of spots that will be analyzed by comparing tables of intensity values. To describe the observed different patterns of expression, users generally show histograms with the original associated images [1]. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns. The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer, [2], [3] a graphically interfaced tool that greatly simplifying analysis of dot arrays.

protein-micro-array-analysis
type: software
has author: Sébastien Tosi
has function: operation Image segmentation
has location: image-j-fiji#h.p EUvDaIbbaMUY
has location: ImageJ Macro: Protein MicroArray Analysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
has usage example: image-j-fiji#h.p EUvDaIbbaMUY
has usage example: User guide - Protein MicroArray Analysis
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-08T14:04:17
modified: 2023-04-28T14:12:32
title: Protein Micro-array Analysis
comment: This macro performs measurements of average and standard deviation intensity inside wells of a protein microarray (the number of wells is limited to 250, the image should be cropped for larger arrays). The macro requires the "ImageJ plugins toolkit". To ensure compatibility with Fiji you should download the version 1.6.1. The installation instructions can be found here, it only consists in un-compressing the .jar file from the previous archive to Fiji plugins folder. sample image: link

protractor-icy
type: software
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4340
has location: Protractor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/565
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2020-03-01T16:19:48
title: Protractor (Icy)

protractor-roi-cutter-icy
type: software
has function: operation 3096
has function: operation Rhb4iyLUQWY4HnhPpuqNNI
has implementation: http://biii.eu/taxonomy/term/4340
has location: Protractor-ROI-Cutter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/565
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2020-03-01T16:15:03
title: Protractor ROI Cutter (Icy)

psf-generator
type: software
has author: Aguet, François
has author: Kirshner, Hagai
has author: Sage, Daniel
has author: Unser, Michael
has documentation: psfgenerator
has function: operation Image visualisation
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has location: psfgenerator
has location: PSF Generator at Bioimedical Imaging Group @ EPFL
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.1365-2818.2012.03675.x
has reference publication: https://infoscience.epfl.ch/record/163617
has reference publication: 3‐D PSF fitting for fluorescence microscopy: implementation and localization application
has reference publication: Comparison of Deconvolution Software in 3D Microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3567
has usage example: psfgenerator
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2019-10-18T09:35:22
title: PSF Generator
comment: PSF Generator is a software package that allows one to generate and visualize various 3D models of a microscope PSF. The current version has more than fifteen different models. 3D diffractive models: scalar-based diffraction model Born & Wolf, scalar-based diffraction model with 3 layers Gibson & Lanni, and vectorial-based model Richards & Wolf, and Variable Refractive Index Gibson & Lanni model. Defocussing a 2D lateral function with 1D axial function: the available lateral functions are: "Gaussian", "Lorentz", "Cardinale-Sine", "Cosine", "Circular-Pupil", "Astigmatism", "Oriented-Gaussian", "Double-Helix". Optical Transfer Function generated in the Fourier domain: Koehler simulation, defocus simulation.

psf-lab
type: software
has author: Jörg C. Woehl
has author: Michael J. Nasse
has author: the One Molecule Group
has documentation: PSF Lab Getting Started.pdf
has documentation: Getting started manual
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4341
has location: software
has location: PSFLab
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has reference publication: https://www.osapublishing.org/josaa/abstract.cfm%3Furi%3Djosaa-27-2-295
has reference publication: 10.1364/JOSAA.27.000295
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: PSF Lab data example.mat
has usage example: Example
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/389
created: 2016-10-10T13:39:34
modified: 2019-10-16T16:47:44
title: PSF Lab
comment: PSF Lab is a software program that calculates the illumination point spread function of a confocal microscope under various imaging conditions. It is available in 32-bit and 64-bit for Windows and in 64-bit for Mac.

psf-tool-2d
type: software
has documentation: PSFtool.pdf
has documentation: tutorial pdf
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-15T10:45:51
modified: 2019-11-14T10:31:44
title: PSF Tool 2D

psfj
type: software
has author: Knop Mickael
has author: Mongis Cyril
has author: Theer Patrick
has documentation: psfj
has documentation: GitHub repo
has function: operation Optimisation or refinement
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL 3.0
has location: psfj
has location: HomePage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.3102
has reference publication: Article (Nature Method)
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2019-12-19T13:20:34
modified: 2020-10-19T15:07:32
title: PSFj
comment: PSFj is a software tool that automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations. PSFj provides reporting functions to document the momentary performance of a system and it allows for the export of the obtained data, e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a stand-alone application.

pta2
type: software
has author: Yoshiyuki Arai
has function: operation Particle tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: PTA2
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-12-12T23:35:27
modified: 2023-05-03T11:47:51
title: PTA2
comment: "PTA2 is an ImageJ1.x plugins that enable automatic particle tracking" This plugin is developed specifically for single-molecule imaging, so it's good at tracking spots with noisy background.

puredenoise
type: software
has author: Florian Luisier
has documentation: denoise
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: denoise
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: denoise
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-21T08:55:52
title: PureDenoise
comment: Outline The incessant development of improved microscopy imaging techniques, as well as the advent of highly selective fluorescent dyes has made possible the precise identification of tagged molecules in almost any biological specimen. Of particular interest are the visualization and the study of living cells, which induce tight constraints on the imaging process. To avoid the alteration of the sample and to achieve a high temporal resolution, low fluorophore concentrations, low-power illumination and short exposure time need to be used in practice. Such restrictions have a tremendous impact on the image quality. This is why we have recently introduced a new method, coined PURE-LET [1,2,3], for efficient, fast, and automatic denoising of multidimensional fluorescence microscopy images.

pybpdl
type: software
has author: Jiri Borovec
has function: operation 3443
has function: operation Image registration
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD-3
has location: pyBPDL
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 978-3-319-54427-4 40
has reference publication: Binary Pattern Dictionary Learning for Gene Expression Representation in Drosophila Imaginal Discs.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2019-03-08T10:47:14
modified: 2019-03-09T08:22:09
title: pyBPDL
comment: The Binary Pattern Dictionary Learning (BPDL) package is suitable for image analysis on a set/sequence of images to determine an atlas of a compact region. In particular, the application can be maping gene activation accross many samples, brain activations in a time domain, etc.

pydensecrf
type: software
has author: Beyer, Lucas
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has location: pydensecrf
has location: pydensecrf GitHub repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nips
has reference publication: Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2019-03-15T00:16:06
modified: 2019-03-15T00:24:51
title: pydensecrf
comment: This is a (Cython-based) Python wrapper for Philipp Krähenbühl's Fully-Connected CRFs (version 2).

pyimagej
type: software
has author: Curtis T. Rueden
has documentation: latest
has documentation: PyImageJ’s documentation
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: pyimagej
has location: GitHub repo of pyimagej: Python wrapper for ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41592-022-01655-4
has reference publication: PyImageJ: A library for integrating ImageJ and Python
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: use cases.html
has usage example: Use cases
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2020-01-23T15:05:23
modified: 2023-04-29T08:42:33
title: pyimagej
comment: pyimagej provides a set of wrapper functions for integration between ImageJ and Python. It also provides a high-level entry point for invoking ImageJ server APIs.

pyimsegm
type: software
has author: Jiri Borovec
has documentation: pyImSegm
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD-3
has location: pyImSegm
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: 978-3-319-67389-9 3
has reference publication: 1.JEI.26.6.061610
has reference publication: 1.JEI.26.6.061611
has reference publication: Detection and Localization of Drosophila Egg Chambers in Microscopy Images.
has reference publication: Region growing using superpixels with learned shape prior.
has reference publication: Supervised and unsupervised segmentation using superpixels, model estimation, and Graph Cut.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2019-03-08T10:11:52
modified: 2019-03-08T12:06:05
title: pyImSegm
comment: Collection of several basic standard image segmentation methods focusing on medical imaging. In particular, the key block/applications are (un)supervised image segmentation using superpixels, object centre detection and region growing with a shape prior. Besides the open-source code, there is also a few sample images.

pyme
type: software
has author: David Baddeley
has documentation: python-microscopy
has documentation: Source code repo
has function: operation_0337
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has implementation: http://biii.eu/taxonomy/term/4339
has location: InstallationWithAnaconda.html
has location: Installation via Anaconda
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1323
created: 2019-04-14T13:58:16
modified: 2023-04-25T17:46:49
title: PYME
comment: >The PYthon Microscopy Environment is an open-source package providing image acquisition and data analysis functionality for a number of microscopy applications, but with a particular emphasis on single molecule localisation microscopy (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX. It comes with 3 main modules: - PYMEAcquire - Instrument control and simulation - dh5view - Image Data Analysis and Viewing - VisGUI - Visualising Localization Data Sets

pystackreg
type: software
has author: Gregor Lichtner
has documentation: latest
has function: operation 2928
has function: operation Image registration
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has location: pystackreg
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: pystackreg
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/597
requires: http://biii.eu/node/915
created: 2018-07-10T15:17:09
modified: 2018-08-07T11:41:25
title: pystackreg
comment: Python/C++ port of the ImageJ extension TurboReg/StackReg written by Philippe Thevenaz/EPFL. A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.

pytfm
type: software
has author: Andreas Bauer
has documentation: index.html
has documentation: Welcome to pyTFM’s documentation!
has function: operation RBUpi1JSczmHQSf8Q8fDzG5
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL3
has location: releases
has location: GitHub source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: journal.pcbi.1008364
has reference publication: Bauer, Andreas et al. “pyTFM: A tool for traction force and monolayer stress microscopy.” PLoS computational biology vol. 17,6 e1008364. 21 Jun. 2021, doi:10.1371/journal.pcbi.1008364
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: tutorials.html
has usage example: Tutorials
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2021-09-29T07:24:18
modified: 2021-10-18T06:40:37
title: pyTFM
comment: Quote: pyTFM is a python package that allows you to analyze force generation and stresses in cells, cell colonies, and confluent cell layers growing on a 2-dimensional surface. This package implements the procedures of Traction Force Microscopy and Monolayer Stress Microscopy. In addition to the standard measures for stress and force generation, it also includes the line tension, a measure for the force transfer exclusively across cell-cell boundaries. pyTFM includes an addon for the image annotation tool clickpoints allowing you to quickly analyze and vizualize large datasets.

python
type: software
has documentation: https://docs.python.org/3/
has documentation: Python 3 documentation
has function: operation_0337
has function: operation 2409
has function: operation 2945
has function: operation 3441
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: Examples
has usage example: Beginner's guide
openess: http://biii.eu/taxonomy/term/3575
created: 2018-05-25T01:04:59
modified: 2023-04-26T14:50:57
title: Python
comment: Python is a programming language.

python-27
type: software
has documentation: https://docs.python.org/2.7/
has documentation: Online documentatoin
has function: operation_0337
has function: operation 2409
has function: operation 2945
has function: operation 3441
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: https://www.python.org/download/releases/2.7/
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-06-04T13:13:43
modified: 2023-04-26T14:51:38
title: Python 2.7
comment: Python is a programming language. Python 2.7.0 was released on July 3rd, 2010. Python 2.7 is scheduled to be the last major version in the 2.x series before it moves into an extended maintenance period. This release contains many of the features that were first released in Python 3.1. A bugfix release, 2.7.16, is currently available. Its use is recommended.

python-36
type: software
created: 2019-01-02T17:15:39
modified: 2019-01-02T17:15:39
title: Python 3.6

python-bioformats
type: software
has author: Lee Kamentsky, Vebjorn Ljosa
has license: GPL
has location: python-bioformats
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2014-03-06T21:16:29
modified: 2017-09-12T18:05:26
title: python-bioformats
comment: Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. Python-bioformats uses the python-javabridge to start a Java virtual machine from Python and interact with it. Python-bioformats was developed for and is used by the cell image analysis software CellProfiler (cellprofiler.org). PyPI record: https://pypi.python.org/pypi/python-bioformats Documentation: http://pythonhosted.org/python-bioformats/ GitHub repository: https://github.com/CellProfiler/python-bioformats Report bugs here: https://github.com/CellProfiler/python-bioformats/issues python-bioformats is licensed under the GPL license to be compatible with the copy of Bio-Formats that is distributed with the package, but is compatible with a BSD license if loci_tools.jar is replaced with SCIFIO jars. See the accompanying file LICENSE for details.

python-javabridge
type: software
has author: Vebjorn Ljosa, Lee Kamentsky, Johannes Schindelen
has license: BSD
has location: python-javabridge
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2014-03-06T21:04:25
modified: 2017-09-12T18:05:27
title: python-javabridge
comment: The javabridge Python package makes it easy to start a Java virtual machine (JVM) from Python and interact with it. Python code can interact with the JVM using a low-level API or a more convenient high-level API. PyPI record: https://pypi.python.org/pypi/javabridge Documentation: http://pythonhosted.org/javabridge/ GitHub repository: https://github.com/CellProfiler/python-javabridge Report bugs here: https://github.com/CellProfiler/python-javabridge/issues python-javabridge is licensed under the BSD license. See the accompanying file LICENSE for details.

pythonxy
type: software
has author: pierre.raybaut, grizzly.nyo
has function: operation_0337
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL v3
has location: python-xy.github.io
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2013-10-25T15:08:14
modified: 2019-10-18T14:21:07
title: pythonxy
comment: **Python(x,y)** is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Many python libraries related to numerical calculation are packaged, so you do not need to search and install them individually. Included libraries are listed **[here](https://code.google.com/p/pythonxy/wiki/StandardPlugins).**

pytorch
type: software
has implementation: http://biii.eu/taxonomy/term/4339
has location: pytorch.org
has location: PyTorch website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has programming language: http://biii.eu/taxonomy/term/4358
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
has usage example: 978-3-030-00889-5 22
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2019-03-14T23:47:49
modified: 2019-10-14T16:53:45
title: PyTorch
comment: PyTorch is an open-source machine learning library for Python, based on Torch, used for applications such as natural language processing.

pyxit-landmark-detection
type: software
has author: Raphaël Marée
has author: Rémy Vandaele
has function: operation RDggamr21qZlMqkQmyOdC7l
has implementation: http://biii.eu/taxonomy/term/4341
has license: Apache2
has location: landmark model builder
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://orbi.uliege.be/handle/2268/99199
has reference publication: Automatic localization of interest points in zebrafish images with tree-based methods
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Supervised learning
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/141
created: 2017-02-13T12:29:06
modified: 2019-10-18T16:32:12
title: Pyxit Landmark detection
comment: It is a trainable interest point (anatomical landmarks) detection algorithm. It requires images and interest point coordinates. It can run independantly (using csv files to describe coordinates) or it can be executed using Cytomine. Typical application: Morphometric studies (e.g. in zebrafish/drosphila development) Used in: Evaluation and Comparison of Anatomical Landmark Detection Methods for Cephalometric X-Ray Images: A Grand Challenge http://dx.doi.org/10.1109/TMI.2015.2412951 Automatic localization of interest points in zebrafish images with tree-based methods

pyxit-object-classification-model-builder
type: software
has author: Gilles Louppe
has author: Raphaël Marée
has function: operation RDetoixS3xEu0agR2CebaoB
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has license: Apache License 2.0
has location: pyxit
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: S0167865516000179
has reference publication: Towards Generic Image Classification using Tree-based Learning: an Extensive Empirical Study
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-13T12:11:25
modified: 2023-05-02T16:27:10
title: Pyxit object classification model builder
comment: This module is for learning classification models from ground-truth data (supervised learning). It downloads from Cytomine-Core annotation images and coordinate of annotated objects from project(s) and build a annotation classification model which is saved locally. It is used by Cytomine DataMining applications: classification_validation, classification_model_builder, classification_prediction, segmentation_model_builder and segmentation_prediction. But it can be run without Cytomine on local data (using dir_ls and dir_ts arguments).

pyxit-object-classification-prediction
type: software
has author: Gilles Louppe
has author: Raphaël Marée
has function: operation RDetoixS3xEu0agR2CebaoB
has location: classification prediction
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: S0167865516000179
has reference publication: Towards Generic Image Classification using Tree-based Learning: an Extensive Empirical Study
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/141
created: 2017-02-13T12:14:17
modified: 2019-10-18T16:55:36
title: Pyxit object classification prediction
comment: This module is for applying classification models on objects. It downloads from Cytomine-Core annotation images and coordinate of annotated objects from project(s) and build a annotation classification model which is saved locally. It downloads from Cytomine-Core annotations images from an image (e.g. detected by an object finder), apply a classification model (previously saved locally), and uploads to Cytomine-Core annotation terms (in a userjob layer).

pyxit-segmentation-model-builder
type: software
has author: Gilles Louppe
has author: Raphaël Marée
has function: operation Image segmentation
has function: operation RDetoixS3xEu0agR2CebaoB
has location: segmentation model builder
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: ISBI.2014.6868017
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/141
created: 2017-02-13T12:19:22
modified: 2019-10-18T16:52:00
title: Pyxit segmentation model builder
comment: This is a learnable segmentation algorithm based on ground-truth images and segmentation mask. It learns a multiple output pixel classification algorithm. It downloads from Cytomine-Core annotation images+alphamasks from project(s), build a segmentation (pixel classifier) model which is saved locally. Typical application: tumor detection in tissues in histology slides. It is based on "Fast Multi-Class Image Annotation with Random Subwindows and Multiple Output Randomized Trees" http://orbi.ulg.ac.be/handle/2268/12205 and was used in "A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning" http://orbi.ulg.ac.be/handle/2268/162084?locale=en

pyxit-segmentation-model-prediction
type: software
has author: Raphaël Marée, Gilles Louppe, Loic Rollus, Olivier Caubo, Benjamin Stévens
has function: operation Image classification
has function: operation Image segmentation
has location: segmentation prediction
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://orbi.ulg.ac.be/handle/2268/12205
has reference publication: Fast Multi-Class Image Annotation with Random Subwindows and Multiple Output Randomized Trees
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
has usage example: http://orbi.ulg.ac.be/handle/2268/162084%3Flocale%3Den
has usage example: A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/141
created: 2017-02-13T12:24:11
modified: 2019-10-18T16:49:11
title: Pyxit segmentation model prediction
comment: This is the "prediction step" of the Pyxit segmentation model builder. It is a learnable segmentation algorithm based on ground-truth images and segmentation mask. It learns a multiple output pixel classification algorithm. It downloads from Cytomine-Core annotation images+alphamasks from project(s), build a segmentation (pixel classifier) model which is saved locally. Typical application: tumor detection in tissues in histology slides.

qcanet
type: software
has author: Funahashi Lab.
has documentation: QCANet
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has license: MIT
has location: QCANet
has location: GitHub repo
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://doi.org/10.1101/324186
has reference publication: bioarxiv
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1317
requires: http://biii.eu/node/1323
requires: http://biii.eu/node/1324
created: 2018-06-04T13:07:29
modified: 2018-06-04T13:13:43
title: QCAnet
comment: Quantitative Criterion Acquisition Network (QCA Net) performs instance segmentation of 3D fluorescence microscopic images. QCA Net consists of Nuclear Segmentation Network (NSN) that learned nuclear segmentation task and Nuclear Detection Network (NDN) that learned nuclear identification task. QCA Net performs instance segmentation of the time-series 3D fluorescence microscopic images at each time point, and the quantitative criteria for mouse development are extracted from the acquired time-series segmentation image. The detailed information on this program is described in our manuscript posted on bioRxiv.

quality-metric-3d-spim-stacks
type: software
has author: David ROUSSEAU
has location: 2-plot GL-std Macro.ijm
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-05-20T18:59:48
modified: 2019-01-24T13:36:26
title: Quality metric of 3D SPIM stacks
comment: An ImageJ/Fiji macro which measures quality through two stacks of images assumed to be acquired from two opposite angle of views using gray-level standard deviation.

quantcenter
type: software
has function: operation_0337
has function: operation 2945
has function: operation Cell segmentation
has function: operation Image classification
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RDetoixS3xEu0agR2CebaoB
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: quantcenter
has location: QuantCenter page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Digital histology
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RBNoPZIOvBhdWGe8mFNpoWQ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2017-02-13T17:34:26
modified: 2023-04-26T14:16:10
title: QuantCenter
comment: QuantCenter is the framework for 3DHISTECH image analysis applications. with the goal of helping the pathologists to diagnose in an easier way. QuantCenter, is optimized for whole slide quantification. It has a linkable algorithm concept that tries to provide an easy-to-use and logical workflow. The user has different quantification modules that he or she could link one after other to fine-tune or to speed up the analysis.

quantification-outer-ring-diameters-centriole-or-pcm-proteins-cycling-hela-cells-interphase
type: software
has author: Open Microscopy Environment
has function: operation 2945
has function: operation Feature extraction
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4342
has location: https://idr-analysis.openmicroscopy.org/itr-public/user/c82f051a-478d-427f-aa17-31b69cb7e07d/notebooks/notebooks/idr0021.ipynb%3Fredirects%3D1
has location: Description of the workflow in ITR
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has programming language: http://biii.eu/taxonomy/term/4525
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has topic: topic High content screening
has topic: topic RC91JqkkQnsmvg8zuG6Td7q
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1070
requires: http://biii.eu/node/1284
requires: http://biii.eu/node/38
requires: http://biii.eu/node/920
requires: http://biii.eu/node/953
created: 2018-08-16T10:32:37
modified: 2018-10-18T15:35:57
title: Quantification of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase
comment: This workflow can be ran with data from 3D-SIM showing the centrosomes in order to compare the distribution of diameters of rings (or toroids) of different proteins from the centrioles or the peri centriolar material. It aims to reproduce the results of the Nature Cell Biology Paper Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material from the same data set but with a different analysis method. It is slightly different from the methods described in the paper itself, where the method was to work on a maximum intensity projection of a 3D-SIM stack, and then to fit circle to the centrioles to estimate the diameters of the toroids. In this workflow, the images are read from the IDR , then process by thresholding (Maximum entropy auto thresholding with Image J), and processed by Analyze Particles with different measurement sets, including the bouding box. Then the analysis of diameters and the statistical test are performed using R. All the code and data sets are available, and in the case of this paper have shown a layered organisation of the proteins.

quantifish
type: software
has author: Stirling David orcid.org/0000-0001-6802-4103
has DOI: zenodo.1298428
has DOI: Zenodo
has documentation: README.md
has documentation: Manual
has function: operation Cell counting
has function: operation Image registration
has function: operation Image thresholding
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v3.0
has location: QuantiFish
has location: GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41598-020-59932-1
has reference publication: Analysis tools to quantify dissemination of pathology in zebrafish larvae
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3382
has topic: topic 3385
has topic: topic Fluorescent microscopy
has topic: topic R8XUtD89JCyeUaaVebe9Mkw
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2021-01-06T18:42:37
modified: 2021-01-06T18:51:54
title: QuantiFish
comment: QuantiFish is a quantification program intended for measuring fluorescence in images of zebrafish, although use with images of other specimens is possible. This package is geared towards analysis of fluorescent infection models. The software is designed to automate processing of images of single fish, and outputs results as a .csv file. Alongside measures of total fluorescence above a threshold, this package also introduces several measures for dissemination and distribution of fluorescence throughout the specimen.

quantifying-staining-tissue-sections
type: software
has author: Peter Bankhead
has documentation: Colour Deconvolution
has documentation: Fiji colour deconvolution page (same plugin)
has function: operation R7qn3VpJyCAPGqdW6ia3h2d
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://pubmed.ncbi.nlm.nih.gov/11531144/
has reference publication: Ruifork and Johnston (2001), Quantification of histochemical staining by color deconvolution
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/337
requires: http://biii.eu/node/38
created: 2014-12-08T14:10:02
modified: 2023-04-29T20:32:11
title: Quantifying staining in tissue sections
comment: [no download link, this description itself explains the steps to quantify staining in tissue sections] The Color Deconvolution plugin for ImageJ can be used to digitally separate up to three stains from brightfield images, after which standard ImageJ commands can be used. The algorithm is described in Ruifork and Johnston (2001). **However**, it is **very** important to take into consideration the caveats on the linked URL. In particular, note that: - Stain colors depend on numerous factors, such as the precise stains and scanner; therefore, the 'default' stain vectors (used to define the colors) are unlikely to be optimal and may be very inaccurate. See the URL instructions for how to create new stain vectors. - Pixel values should be interpreted with extreme caution; in particular, note the warning regarding 'brown' staining that *attempting to quantify DAB intensity using this plugin is not a good idea*. Note, the pixel values provided by this plugin are 8-bit and **not** equivalent to 'optical densities' frequently presented in the literature. Color deconvolution is particularly helpful in separating stains so that stained regions can be detected (e.g. by setting a threshold), and then the number or areas of stained structures may be quantified. Two potential approaches would be: 1. If one measurement should be made for the entire image: - *Image > Adjust > Threshold...* - *Edit > Selection > Create Selection* - *Analyze > Measure* 2. If distinct structures should be measured: - *Image > Adjust > Threshold...* - *Analyze > Analyze Particles...*

quantile-filter-knime
type: software
has documentation: org.knime.knip.base.nodes.filter.nonlinear.QuantileFilterNodeFactory#Quantile Filter
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-02T09:56:00
title: Quantile Filter (KNIME)

quantitative-analysis-focal-adhesion-dynamics
type: software
has author: Christoph Möhl
has documentation: olympus-website-bioimage-data-analysis
has function: operation Particle tracking
has location: https://www.dropbox.com/s/hpgnnl9vo3kyddi/2016_BIASBOOK_Materials.zip%3Fdl%3D0
has location: ZIpped codes and sample images
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: jcs.090746
has reference publication: Quantitative mapping of averaged focal adhesion dynamics in migrating cells by shape normalization
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-08T13:29:00
modified: 2018-05-16T21:31:40
title: Quantitative analysis of focal adhesion dynamics
comment: The quantification is explained in detail in chapter 8 "Cell Polarity - Focal Adhesion and Actin Dynamics in Migrating Cells" in "Bioimage Data Analysis Book" [downloadable from here](https://www.imaging-git.com/olympus-website-bioimage-data-analysis). For codes and sample images, download the zipped archive (linked under "Download").

quantitative-analysis-focal-adhesions
type: software
has author: Berrin Ozdil
has author: Devrim Pesen-Okvur
has author: Utku Horzum
has documentation: S2215016114200203
has function: operation Image segmentation
has function: operation Image thresholding
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: j.mex.2014.06.004
has reference publication: Horzum et al. (2014) Step-by-step quantitative analysis of focal adhesions
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1314
requires: http://biii.eu/node/38
requires: http://biii.eu/node/759
created: 2014-12-08T13:18:21
modified: 2018-05-25T16:48:36
title: Quantitative analysis of focal adhesions
comment: Simple workflow description for ImageJ, step-by-step description for delineating focal adhesions, count and characterize their positions. Measurement of dynamics is not involved.

quickfit-3
type: software
has author: Jan Wolfgang Krieger
has author: Jörg Langowski
has documentation: quickfit
has documentation: documentation
has function: operation 3441
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL 3.0
has location: QuickFit3
has location: GIT HUB
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescence correlative spectroscopy
has topic: topic Image correlation spectroscopy
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
has usage example: nprot.2015.100
has usage example: Imaging fluorescence (cross-) correlation spectroscopy in live cells and organisms
openess: http://biii.eu/taxonomy/term/3575
created: 2019-11-22T04:51:24
modified: 2020-10-19T15:10:24
title: QuickFit 3
comment: QuickFit 3 is a data evaluation software for FCS Fluorescence Correlation Spectroscopy and imagingFCS (imFCS) measurements, developed in the group B040 (Prof. Jörg Langowski) at the German Cancer Research Center (DKFZ). Actually QuickFit 3 itself is a project manager and all functionality is added as plugins. A set of tested plugins for FCS, imagingFCS and some microscopy-related image processing tasks is supplied together with the software.

quickpalm
type: software
has author: Ricardo Henriques, et al
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/116
requires: http://biii.eu/node/38
created: 2014-12-09T10:31:35
modified: 2017-09-12T18:03:45
title: quickPALM
comment: QuickPALM is a set of programs to aid in the acquisition and image analysis of data in photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM). QuickPALM features the associated QuickPALM ImageJ plugin, which enables PALM/STORM 2D/3D/4D particle detection and image reconstruction in ImageJ.

quimp
type: software
has author: Piotr Baniukiewicz (ORCID: 0000-0002-4687-9407)
has author: Till Bretschneider (ORCID: 0000-0002-5317-603X)
has documentation: quimpdoc
has function: operation Cell segmentation
has function: operation Cell tracking
has function: operation Image tracking
has function: operation Interactive segmentation
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4340
has license: University License
has location: quimp
has location: QuimP
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/60
created: 2017-09-11T10:49:04
modified: 2023-05-02T10:39:49
title: QuimP
comment: Summary QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane. QuimP's unique selling point is the possibility to aggregate data from many cells in form of spatio-temporal maps of dynamic events, independently of cell size and shape. QuimP has been successfully applied to address a wide range of problems related to cell movement in many different cell types. Introduction In transmembrane signalling the cell membrane plays a fundamental role in localising intracellular signalling components to specific sites of action, for example to reorganise the actomyosin cortex during cell polarisation and locomotion. The localisation of different components can be directly or indirectly visualised using fluorescence microscopy, for high-throughput screening commonly in 2D. A quantitative understanding demands segmentation and tracking of whole cells and fluorescence signals associated with the moving cell boundary, for example those associated with actin polymerisation at the cell front of locomoting cells. As regards segmentation, a wide range of methods can be used (threshold based, region growing, active contours or level sets) to obtain closed cell contours, which then are used to sample fluorescence adjacent to the cell edge in a straightforward manner. The most critical step however is cell edge tracking, which links points on contours at time t to corresponding points at t+1. Optical flow methods have been employed, but usually fail to meet the requirement that total fluorescence must not change. QuimP uses a method (ECMM, electrostatic contour migration method (Tyson et al., 2010) which has been shown to outperform traditional level set methods. ECMM minimises the sum of path lengths connecting all pairs of points, equivalent to minimising the energy required for cell deformation. The original segmentation based on an active contour method and outline tracking algorithms have been described in (Dorm…

qupath
type: software
has author: Bankhead Peter orcid.org/0000-0003-4851-8813
has DOI: https://doi.org/10.1101/099796
has DOI: 10.1101/099796
has documentation: wiki
has documentation: QuPath wiki
has function: operation_0226
has function: operation 3553
has function: operation Cell segmentation
has function: operation Interactive segmentation
has function: operation Pixel classification
has license: GPL3
has location: qupath.github.io
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: http://biorxiv.org/content/early/2017/01/12/099796
has reference publication: QuPath preprint
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Digital histology
has topic: topic Supervised learning
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2017-02-13T14:23:19
modified: 2023-04-28T12:16:13
title: QuPath
comment: QuPath is open source software for Quantitative Pathology. QuPath has been developed as a research tool at Queen's University Belfast.

http://biii.eu/r
type: software
created: 2017-09-14T08:15:16
modified: 2017-09-14T08:15:16
title: R

r-project-statistical-computing
type: software
created: 2018-04-18T09:45:01
modified: 2018-04-18T09:45:01
title: R Project for Statistical Computing

radial-reslice
type: software
created: 2018-02-01T19:07:57
modified: 2018-02-01T19:07:57
title: radial reslice

rapidstorm
type: software
has author: André Lampe
has author: Sarah Aufmkolk
has author: Steve Wolter
has author: Sven Proppert
has author: Teresa Klein
has documentation: rapidSTORM
has documentation: https://www.biozentrum.uni-wuerzburg.de/super-resolution/archiv/rapidstorm/
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL & LGPL
has location: rapidSTORM
has location: rapidSTORM.github.io
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nmeth.2224
has reference publication: Wolter et al (2012) rapidSTORM: accurate, fast open-source software for localization microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Super-resolution microscopy
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T14:27:50
modified: 2023-05-02T10:24:03
title: RapidSTORM
comment: The rapidSTORM project is an open source evaluation tool that provides fast and highly configurable data processing for single-molecule localization microscopy such as dSTORM. It provides both two-dimensional and three-dimensional, multi-color data analysis as well as a wide range of filtering and image generation capabilities. The general operation of rapidSTORM is described in Wolter et al (2012).

rapidstorm-usage-tutorial
type: software
has author: RapidSTORM authors
has documentation: index.html
has documentation: Basic use tutorial
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/130
created: 2014-12-09T14:15:51
modified: 2023-05-02T10:29:39
title: RapidSTORM usage tutorial
comment: [as of 20180524, the website is temporary not functioning do to web defacement - please check again later] This tutorial will exemplify basic rapidSTORM usage by showing how to convert an Andor SIF acquisition to a super-resoluted image with rapidSTORM.

rats-robust-automatic-threshold-selection
type: software
has author: Ben Tupper
has documentation: RATS: Robust Automatic Threshold Selection
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: RATS: Robust Automatic Threshold Selection
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: Digital+Image+Analysis+of+Microbes:+Imaging,+Morphometry,+Fluorometry+and+Motility+Techniques+and+Applications-p-9780471974406
has reference publication: Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-18T12:09:09
title: RATS: Robust Automatic Threshold Selection

readimage-ebimage
type: software
has documentation: EBImage.pdf
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2020-03-03T09:14:33
title: readImage (EBImage)

real-time-multi-view-deconvolution
type: software
has author: Huisken Jan
has author: Schmid Benjamin
has function: operation Image deconvolution
has function: operation RBPObKBKIMwjdLygBOlvojW
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4241
has programming language: http://biii.eu/taxonomy/term/4358
has reference publication: https://academic.oup.com/bioinformatics/article/31/20/3398/196164
has reference publication: doi:10.1093/bioinformatics/btv387
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-30T11:59:14
modified: 2018-01-30T12:03:07
title: Real-time multi-view deconvolution
comment: In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution simultaneously fuses and deconvolves the images in 3D, but processing takes a multiple of the acquisition time and constitutes the bottleneck in the imaging pipeline. Here, we show that MV deconvolution in 3D can finally be achieved in real-time by processing cross-sectional planes individually on the massively parallel architecture of a graphics processing unit (GPU). Our approximation is valid in the typical case where the rotation axis lies in the imaging plane.

realistic-analytical-phantoms-parallel-mri
type: software
has author: Matthieu Guerquin-Kern
has documentation: mriphantom
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4339
has location: mriphantom
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: guerquinkern1201.html
has reference publication: Realistic Analytical Phantoms for Parallel Magnetic Resonance Imaging
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3444
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:43
modified: 2020-03-01T15:35:00
title: Realistic Analytical Phantoms for Parallel MRI

reconstruct
type: software
has author: John C. Fiala
has documentation: software-0
has documentation: Reconstruct Software Main page (link to user manual)
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has license: GPLv2
has location: software-0
has location: Reconstruct Software Download
has platform: http://biii.eu/taxonomy/term/31
has reference publication: journal.pone.0005655
has reference publication: Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RBZsLMTdyuEDtVe2fge61l0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
created: 2017-09-13T11:40:49
modified: 2017-09-13T12:29:47
title: Reconstruct
comment: By combining multiple image alignment and tracing into one program, Reconstruct (TM) allows images to be processed more efficiently. Tracing can be done directly on the transformed images and alignments can be asily modified. Reconstruct (TM) was developed from years of experience working with high magnification serial section images of brain tissue. (Extracted from User Manual) "The original platform of the Reconstruct program allows a user to trace objects in serial sections by manually drawing the outline of each object on each section, which is time-consuming. We modified Reconstruct to enable semi-automatic tracing of axons using a region-growing algorithm called wildfire."

reconstruct-reader
type: software
has author: Larry Lindsey
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Reconstruct Reader
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/663
created: 2013-10-11T13:08:43
modified: 2019-10-18T11:25:32
title: Reconstruct Reader

rectangular-finite-elements
type: software
has author: Dufour, Alexandre
has author: Lecomte, Timothée
has implementation: http://biii.eu/taxonomy/term/4340
has location: Rectangular-Finite-Elements
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/836
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:13:42
title: Rectangular Finite Elements

region-competition
type: software
has author: Grégory Paul
has author: Ivo F Sbalzarini
has author: Janick Cardinale
has author: Mosaic group
has documentation: Installation
has function: operation Cell segmentation
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: imageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: Cardinale2012.pdf
has topic: topic 3382
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/79
created: 2013-10-15T10:45:51
modified: 2019-10-17T11:28:52
title: Region Competition
comment: Image segmentation based on the MOSAIC Discrete region competition algorithm.

register-virtual-stack-slices-fiji
type: software
has author: Albert Cardona
has author: Ignacio Arganda-Carreras
has author: Stephan Saalfeld
has documentation: Register Virtual Stack Slices
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:41
modified: 2020-03-02T20:24:25
title: Register Virtual Stack Slices (Fiji)
comment: This plugin takes a sequence of image slices stored in a folder, and delivers a list of registered image slices (with enlarged canvas). One of the images in the sequence can be selected by the user as reference and it will remain intact. The plugin can perform 6 types of image registration techniques: * Translation * Rigid (translation + rotation) * Similarity (translation + rotation + isotropic scaling) * Affine * Elastic (via bUnwarpJ with cubic B-splines) * Moving least squares All models are aided by automatically extracted SIFT features. [Source code](https://github.com/trakem2/register_virtual_stack_slices) ### Installation This plugin is bundled with the Fijij package.

register-virtual-stack-slices-imagej
type: software
has author: Albert Cardona, Ignacio Arganda-Carreras and Stephan Saalfeld
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: Register Virtual Stack Slices
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T14:28:18
modified: 2020-03-02T20:23:25
title: Register Virtual Stack Slices (ImageJ)
comment: A Jython script using the plugin : Register Virtual Stack Slices It takes a sequence of image slices stored in a folder, and delivers a list of registered image slices (with enlarged canvas). One of the images in the sequence can be selected by the user as reference and it will remain intact. The plugin can perform 6 types of image registration techniques: - Translation - Rigid (translation + rotation) - Similarity (translation + rotation + isotropic scaling) - Affine - Elastic (via bUnwarpJ with cubic B-splines) - Moving least squares All models are aided by automatically extracted SIFT features.

registrationshop
type: software
has author: Smit Noeska
has function: operation_0337
has function: operation Image registration
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4341
has location: Registrationshop
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1075
requires: http://biii.eu/node/1278
created: 2019-01-21T14:12:17
modified: 2019-01-21T15:08:09
title: Registrationshop
comment: It is an interactive front-end visualization for registration software based on Elasix (VTK/ITK)

relate
type: software
has documentation: relate
has documentation: Link to product page
has function: operation_0337
has function: operation 3441
has function: operation 3443
has function: operation Image deconvolution
has function: operation Image registration
has function: operation Image segmentation
has function: operation Overlay
has function: operation Particle tracking
has function: operation RDyyXyhf1oHK93opXhEnRND
has function: operation Slice rendering
has function: operation Surface rendering
has implementation: http://biii.eu/taxonomy/term/4341
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3385
has topic: topic Statistics
has topic: topic R7LElbFkBgKS401YKsVtNck
has topic: topic R7Vn7GbwtqVvGWNAMGdcNW1
has topic: topic R8Ss4wIFt90wZ1yjFLfXyPM
has topic: topic R9zg34pnGmTyzPidJj9vfJt
has topic: topic RBNfUSYBOKUapWrsyPMMTkw
has topic: topic RBZsLMTdyuEDtVe2fge61l0
has topic: topic RBfI2XgIsxcfKonPPluKAhK
has topic: topic RByvmgDpAo4FOrMdvTm1gwR
has topic: topic RXLeVr0cHSXzTSRyO5zwZD
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
has usage example: relate#3
has usage example: Relate image gallery
openess: http://biii.eu/taxonomy/term/3577
created: 2023-03-29T08:32:25
modified: 2023-03-31T08:27:57
title: Relate
comment: Relate is a correlative software package optimised to work with EM, EDS, EBSD, & AFM data and images. It provides the tools you need to correlate data from different microscopes, visualise multi-layered data in 2D and 3D, and conduct correlative analyses. Combining data from different imaging modalities (e.g. AFM, EDS & EBSD) Interactive display of multi-layer correlated data Analytical tools for metadata interrogation Documented workflows and processes Correlate Import data from AZtec using the H5oina file format Import AFM data Correlate both sets of data using intuitive image overlays and image matching tools Produce combined multimodal datasets Visualise 2D display of multi-layered data 3D visualisation of topography combined with AFM material properties, EM images, and EDS & EBSD map overlays Customisation of colour palettes, data overlays, image rendering options, and document display Export images and animations Analyse Generate profile (cross section) views of multimodal data Measure and quantify data across multiple layers Analyse areas via data thresholding using amount of x-ray counts, phase maps, height, or other material properties. Select an extensive range of measurement parameters Export analytical data to text or CSV files

relateobjects
type: software
has documentation: relateobjects.py
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2019-10-29T17:04:07
title: RelateObjects

remove-objects-ebimage
type: software
has author: Oleg Sklyar
has documentation: EBImage.pdf
has function: operation 3096
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:44
modified: 2020-03-02T09:16:32
title: Remove Objects (EBImage)

renameorrenumberfiles
type: software
has documentation: cp2 manual 9978.pdf
has documentation: CellProfiler 2.0 manual pdf
has function: operation 2409
has location: RenameOrRenumberFiles.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:44
modified: 2020-03-01T15:45:00
title: RenameOrRenumberFiles

render
type: software
has author: Saalfed lab
has documentation: render-ws-java-client.md
has documentation: List of services
has function: operation_0337
has function: operation 2409
has function: operation 2928
has function: operation Feature extraction
has function: operation Image stitching
has function: operation Image visualisation
has function: operation Montage
has function: operation R9EjejimBB0tmnQRmZt0RhA
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPL-2.0
has location: render
has location: Github Page
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/4668
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic_0611
has topic: topic RBZsLMTdyuEDtVe2fge61l0
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/80
created: 2022-03-16T05:51:46
modified: 2022-03-16T06:15:45
title: Render
comment: A collection of Java tools and HTTP services (APIs) for rendering transformed image tiles that includes: a JSON data model for render, tile, and transform specifications, a Java stand-alone render application / library, a set of render web services that provide RESTful APIs to persisted collections of tile and transform specifications, and a set of Java clients for processing/rendering data that utilize the render web services to retrieve and/or store persisted specifications. Docker packaging for building the libraries and deploying the render web services The basic concept is to render images (tiles) based on transformation files, without having to store the big generated image from an alignment of tiles (mosaicking).

replace-red-magenta
type: software
has author: Johannes Schindelin
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has location: Replace Red with Magenta
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-11-11T23:13:54
modified: 2019-11-11T23:13:54
title: Replace Red with Magenta
comment: This plugin converts all occurrences of red in a red/green image with magenta, effectively replacing it with a magenta/green merge. Note: the plugin completely ignores the blue channel, and replaces it with a copy of the red channel.

report-bug
type: software
has author: Johannes Schindelin
has author: Mark Longair
has function: operation 2945
has location: Report a Bug
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-18T11:38:45
title: Report a Bug

resampler-knime
type: software
has documentation: de.openms.knime.nodes.Resampler.ResamplerNodeFactory
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2020-03-01T17:02:00
title: Resampler (KNIME)

rescaleintensity
type: software
has author: Cell Profiler team
has function: operation R7MFwdgojfmkZ07yWbdcda0
has location: RescaleIntensity.html
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:46
modified: 2019-11-11T23:21:31
title: RescaleIntensity
comment: **RescaleIntensity** changes the intensity range of an image to your desired specifications. This module lets you rescale the intensity of the input images by any ofseveral methods. You should use caution when interpreting intensity and texture measurements derived from images that have been rescaled because certain options for this module do not preserve the relative intensities from image to image.

resize-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/imageprocessing.html%3Fhighlight%3Dresize%23module-cellprofiler.modules.resize
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2020-03-02T08:23:17
title: Resize in CellProfiler

resize-ebimage
type: software
has documentation: EBImage.pdf
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-15T10:45:51
modified: 2020-03-02T08:10:58
title: Resize in EBImage

resize-using-high-quality-interpolation
type: software
has author: Arrate Muñoz
has author: Daniel Sage
has author: David Leroux
has author: Michael Unser
has documentation: resize
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: resize
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: munoz0101.html
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2020-03-03T20:05:59
title: Resize using high-quality interpolation

resolving-process-clathrin-mediated-endocytosis-using-correlative-light-electron-microscopy-clem
type: software
has author: Paul-Gilloteaux, Perrine ORCID: 0000-0002-4822-165X
has author: Schorb, Martin ORCID: 0000-0003-4910-1868
has reference publication: science.aaa9555
has reference publication: Ori Avinoam, Martin Schorb, Carsten J. Beese, John A. G. Briggs, and Marko Kaksonen. Endocytic sites mature by continuous bending and remodeling of the clathrin coat. Science (New York, N.Y.), 348(6241):1369– 1372, June 2015. ISSN 1095-9203
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3577
created: 2019-02-05T10:50:19
modified: 2019-02-05T11:26:43
title: Resolving the process of Clathrin mediated endocytosis using Correlative Light & Electron Microscopy (CLEM)
comment: Multimodal image registration based on manual selection of matching pairs of landmarks. This image registration workflow is based on MATLAB’s image processing toolbox using the identification of sites of clathrin-mediated endocytosis by correlative light electron microscopy (CLEM) as an example.

restoretools
type: software
has documentation: index.html
has function: operation Image deconvolution
has function: operation Image reconstruction
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4339
has location: index.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-15T10:45:51
modified: 2020-03-03T09:57:45
title: restoreTools
comment: Most of RestoreTools is now bundled with IR tools.

retinex
type: software
has author: Francisco Jiménez Hernández
has documentation: Color constancy
has function: operation R7MFwdgojfmkZ07yWbdcda0
has location: Retinex
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T11:33:09
title: Retinex
comment: Retinex filtering is based on Land's theory of image perception, proposed to explain the perceived colour constancy of objects under varying illumination conditions. Several approaches exist to implement the retinex principles, among these the multiscale retinex with colour restoration algorithm (MSRCR) combines colour constancy with local contrast enhancement so images are rendered similarly to how human vision is believed to operate.

rgb-gray-merge-imagej
type: software
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: RGB-Gray Merge
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-01T17:17:29
title: RGB-Gray Merge (ImageJ)

rgb-measure-plus
type: software
has author: Dimiter Prodanov
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: RGB Measure Plus
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-18T11:40:48
title: RGB Measure Plus

rgb-montage
type: software
has author: unknown
has function: operation Image visualisation
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: RGB to Montage
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-18T11:33:05
title: RGB to Montage

rgb-profiler
type: software
has author: Christophe Laummonerie
has author: Jerome Mutterer
has function: operation 3441
has implementation: http://biii.eu/taxonomy/term/4340
has location: RGB Profiler
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-18T11:27:55
title: RGB Profiler

rhino-library
type: software
has author: Stephane Dallongeville
has author: Thomas Provoost
has author: Timothée Lecomte
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4340
has location: Rhino-Library
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/805
created: 2013-10-11T13:08:41
modified: 2020-03-02T08:30:34
title: Rhino Library

rivulet
type: software
has author: Feng, Dagan
has author: Liu, Sidong
has author: Liu, Siqi
has author: Peng, Hanchuan (http://orcid.org/0000-0002-3478-3942)
has author: Zhang, Donghao
has comparison: s12021-016-9302-0
has comparison: Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking
has documentation: wiki
has documentation: Rivulet Matlab GUI Wiki
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has license: Apache 2.0
has location: RivuletStudio
has location: Rivulet Studio Github Repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: s12021-016-9302-0
has reference publication: Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/8
has usage example: s12021-016-9302-0
has usage example: Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2017-09-12T01:50:05
modified: 2023-04-28T13:16:51
title: Rivulet
comment: "we propose a novel automatic 3D neuron reconstruction algorithm, named Rivulet, which is based on the multi-stencils fast-marching and iterative back-tracking. The proposed Rivulet algorithm is capable of tracing discontinuous areas without being interrupted by densely distributed noises." This plugin can be used with default parameters or with user-defined parameters. Example image obtained from Rivulet Wiki website (https://github.com/RivuletStudio/Rivulet-Neuron-Tracing-Toolbox/wiki)

rivulet-2-rivuletpy
type: software
has author: Cai, Weidong
has author: Liu, Siqi
has author: Peng, Hanchuan
has author: Song, Yang
has author: Zhang, Donghao
has function: operation Distance transform
has function: operation Image thresholding
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD 3-Clause "New" or "Revised" License
has location: rivuletpy
has location: Rivulet project Github repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1322
requires: http://biii.eu/node/1347
requires: http://biii.eu/node/1348
created: 2018-09-09T14:45:18
modified: 2020-01-23T16:07:31
title: Rivulet 2 (Rivuletpy)

rodcellj
type: software
has author: Daniel Sage
has author: Daniel Schmitter
has function: operation Cell segmentation
has function: operation Cell tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: rodcellj
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: schmitter1301.html
has reference publication: A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-18T11:46:06
title: RodCellJ

roi-1-click-tools-imagejfiji
type: software
has author: Thomas Laurent orcid.org/0000-0001-7686-3249
has DOI: micropub.biology.000215
has DOI: DOI
has documentation: ZPS78T -gUs
has documentation: YouTube tutorial
has function: operation_0226
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD-2
has location: Fiji-RoiClickTools
has location: GitHub repo
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: micropub-biology-000215
has reference publication: Article in microPublication Biology
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2020-03-30T09:00:17
modified: 2020-10-19T14:48:24
title: ROI 1-click tools for ImageJ/Fiji
comment: This macro toolset offers additional click tools for the rapid annotations of ROI in ImageJ/Fiji. The ROI 1-click tools can be setup with a predefined shape, and custom actions to perform upon click (Add to ROI Manager, Run Measure, Go to next slice, run a macro command...) To install in Fiji, just activate the ROI 1-click tools

roi-image-process-tutorial-1
type: software
has location: ROI image process tutorial 1
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/463
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:05:53
title: ROI image process tutorial 1

roi-image-process-tutorial-2
type: software
has function: operation 3441
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-image-process-tutorial-2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/463
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2023-04-29T15:44:30
title: ROI image process tutorial 2
comment: This tutorial explain how to create an intensity profile over an ROI.

roi-intensity-evolution-icy
type: software
has documentation: ROI-Intensity-Evolution
has function: operation_0337
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-Intensity-Evolution
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2020-03-01T17:12:43
title: ROI Intensity Evolution (Icy)

roi-measure-icy
type: software
has author: Dufour, Alexandre
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-Measures
has location: ROI-Measures from Alexandre Dufour's Github repositoty
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2019-02-26T11:29:59
modified: 2019-10-18T11:54:31
title: ROI Measure for Icy
comment: ROI measurement plug-in for Icy.

roi-pool-icy
type: software
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI Pool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/712
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-02T09:20:10
title: ROI Pool (Icy)

roi-statistics
type: software
has author: Dufour Alexandre
has function: operation Cell counting
has function: operation Feature extraction
has function: operation Shape features
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI Statistics
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2018-08-07T13:43:36
title: ROI Statistics
comment: This tool compute measures on the ROIs of the chosen sequence, updates the measures live when ROIs are changed and allows to copy/paste the measures to 3rd-party sheet edition softwares. Measures include geometric (bounding box) and intensity information. It can complement the default ICY built inROI table, where measurements such as volume meausirements, intensity measurements, ... are built in and can be exported as excel as well.

roi-tagger-icy
type: software
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-Tagger
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/361
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2020-03-01T17:08:09
title: ROI Tagger (Icy)

roi-tooltip-icy
type: software
has author: Stephane Dallongeville
has documentation: ROI-ToolTip
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-ToolTip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2023-04-29T14:11:21
title: ROI ToolTip (Icy)
comment: Displays a live tool tip on the current focused ROI in an image. The tooltip displays the following informations about the ROI: – position and size. – number of interior points and contour points. – perimeter, area, surface area, volume. – min, max, mean intensity. This plugin is a daemon plugin, that means plugin is automatically loaded when Icy starts.

roi-tutorial-1
type: software
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: ROI-tutorial-1
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2020-03-01T16:30:10
title: ROI tutorial 1
comment: tutorial.

rolling-ball-background-subtraction
type: software
has author: Janice Keller
has author: Michael Castle
has function: operation Image enhancement
has location: Rolling Ball Background Subtraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-10-29T17:07:29
title: Rolling Ball Background Subtraction

romero-gateway
type: software
has author: Open Microscopy Environment
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: rOMERO-gateway
has location: git source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: fit-model-growth-yeast-cells
has usage example: a notebook using it
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/956
created: 2018-08-20T08:53:21
modified: 2018-08-20T08:58:30
title: rOMERO-gateway
comment: R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava

root-tools
type: software
has author: Volker Baecker
has documentation: Root Tools
has documentation: documentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: root tools.txt
has location: Root Tools Macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T16:54:51
modified: 2018-05-03T12:56:22
title: Root tools
comment: The root tools help to efficiently measure the following characteristics of plant roots: the angle of the opening of the whole root the depth to which it goes down the number of roots at multiple depths (for example 30cm, 35cm, ...) the diameters of the roots at multiple depths (for example 30cm, 35cm, ...)

runimagej
type: software
has location: RunImageJ.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-16T11:11:16
title: RunImageJ
comment: Via the RunImageJ module, CellProfiler can load images, run an ImageJ macro or plugin on them, and retrieve the results for downstream analysis via the RunImageJ module.

same-slice-multiple-images
type: software
has documentation: Same Slice in Multiple Images
has function: operation 2409
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has location: Same Slice in Multiple Images
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Same Slice in Multiple Images
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-17T08:27:27
title: Same Slice in Multiple Images
comment: This is an example that find all the image.bin.gz files from channel 01 under a directory and makes an image stack of all the slices numbered 23. It needs to be customized to be useful to you.

save-animated-gif-imagej
type: software
has author: Ryan Raz
has function: operation 2409
has location: Save as animated gif
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2020-03-02T11:00:56
title: Save as animated gif (ImageJ)

saveimages-cellprofiler
type: software
has documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/fileprocessing.html%3Fhighlight%3Dsaveimage%23module-cellprofiler.modules.saveimages
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has location: www.cellprofiler.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:40
modified: 2020-03-02T12:03:11
title: SaveImages (CellProfiler)

scale-bar
type: software
has documentation: Scale-Bar
has function: operation_0226
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/564
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:43
modified: 2023-04-29T20:12:18
title: Scale Bar
comment: Displays a scale bar overlay on the sequence. Warning: this plugin needs correct sequence metadata to be effective. Otherwise it will display wrong values.

scenery
type: software
has author: Günther Ulrik
has DOI: zenodo.1111824
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4339
has location: scenery
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: examples
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1185
created: 2018-01-28T11:33:53
modified: 2018-01-28T12:20:48
title: scenery
comment: scenery is a scenegraphing and rendering library. It allows you to quickly create high-quality 3D visualisations based on mesh data. scenery contains both a OpenGL 4.1 and Vulkan renderer. The rendering pipelines of both renderers are configurable using YAML files, so it's easy to switch between e.g. Forward Shading and Deferred Shading, as well as stereo rendering. Rendering pipelines can be switched on-the-fly. Both renderers support rendering to head-mounted VR goggles like the HTC Vive or Oculus Rift via OpenVR/SteamVR.

schnitzcells
type: software
has documentation: http://easerver.caltech.edu/wordpress/schnitzcells/%3Fpage_id%3D84
has documentation: User Manual
has license: GPL (registration required)
has location: schnitzcells
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nprot.2011.432
has reference publication: Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nature Protocols 7, 80–88 (2012)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3567
has usage example: http://easerver.caltech.edu/wordpress/schnitzcells/%3Fpage_id%3D93
has usage example: Video Tutorials
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-15T18:43:23
modified: 2017-09-13T10:12:42
title: Schnitzcells
comment: Schnitzcells is a MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells. The software package is developed most specifically for bacteria and has been instrumental in analyzing E.coli and B. subtilis movies. The software contains functions that segment cells (based on either fluorescence or phase images),tracks cells in a frame-to-frame manner,build lineage trees and quantitatively extracts fluorescence. Strength: tools for manually editing segmentation and lineage, well documented, free matlab source code, sample data Limitations: no support, changes need to be done directly in the matlab code

scientifig
type: software
has author: Aigouy Benoit
has function: operation Montage
has implementation: http://biii.eu/taxonomy/term/4340
has implementation: http://biii.eu/taxonomy/term/4341
has location: software
has location: webpage
has reference publication: nmeth.2692
has reference publication: ScientiFig: a tool to build publication-ready scientific figures. Aigouy B, Mirouse V. Nat Methods.
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2018-08-17T13:01:50
modified: 2018-08-17T13:09:47
title: ScientiFig
comment: ScientiFig is a free tool to help you create, format or reformat scientific figures. It comes either as a stand alonesoftware, either as a Fiji/IJ plugin.

scijava
type: software
has documentation: www.scijava.org
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4342
has location: www.scijava.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/649
created: 2013-10-11T13:08:44
modified: 2020-03-02T11:59:32
title: SciJava

scikit-image
type: software
has author: Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu and the scikit-image contributors.
has documentation: dev
has documentation: Scikit-image Documentation (Manual, installation guides, introductory examples)
has function: operation 2945
has function: operation Image processing
has location: scikit-image.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T10:33:32
modified: 2018-12-17T01:00:14
title: scikit-image
comment: Image processing library for Python >The scikit-image SciKit (toolkit for SciPy) extends scipy.ndimage to provide a versatile set of image processing routines. It is written in the Python language. This SciKit is developed by the SciPy community. All contributions are most welcome!

scikit-learn-sklearn
type: software
has DOI: 1034765#.W8mhARO2ns0
has DOI: https://zenodo.org/record/1034765#.W8mhARO2ns0
has documentation: documentation.html
has documentation: Documentation of scikit-learn 0.20.0
has function: operation 2423
has function: operation 2945
has function: operation RDetoixS3xEu0agR2CebaoB
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD license
has location: install.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: pedregosa11a.html
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has training material: http://biii.eu/node/1384
has type: http://biii.eu/taxonomy/term/3567
has usage example: index.html
has usage example: Link to examples
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1317
created: 2018-10-18T10:29:30
modified: 2018-10-19T09:34:17
title: scikit-learn (sklearn)
comment: Scikit-learn (sklearn) is a python library used for machine learning. sklearn contains simple and efficient tools for data mining and data analysis. Modules and functions include those for classification, regression, clustering, dimensionality reduction, model selection and data preprocessing. Many people have contributed to sklearn (list of authors)

scipion
type: software
has author: J.M. de la Rosa Trevín orcid.org/0000-0002-3320-1269
has function: operation 2928
has function: operation Image reconstruction
has function: operation R1NVO6hpWWcs99UiEFiOfK
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: home
has location: download link
has platform: http://biii.eu/taxonomy/term/30
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/51
created: 2017-08-21T10:27:31
modified: 2017-10-13T14:58:51
title: Scipion
comment: Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

scipy
type: software
has documentation: scipy
has documentation: SciPy documentation
has function: operation 2409
has function: operation Image processing
has function: operation Parameter optimisation
has implementation: http://biii.eu/taxonomy/term/4339
has location: install
has location: Install SciPy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: index.html#user-guide
has usage example: User guide
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-04-26T23:54:02
modified: 2023-04-26T14:37:27
title: SciPy
comment: SciPy is a collection of mathematical algorithms and convenience functions built on the NumPy extension of Python. It adds significant power to the interactive Python session by providing the user with high-level commands and classes for manipulating and visualizing data. With SciPy, an interactive Python session becomes a data-processing and system-prototyping environment. Find more about SciPy here!

sciview
type: software
has author: Günther Ulrik orcid.org/0000-0002-1179-8228
has author: Haase Robert
has author: Harrington Kyle orcid.org/0000-0002-7237-1973
has author: Pietzsch Tobias
has author: Royer Loic orcid.org/0000-0002-9991-9724
has author: Saalfeld Stephan orcid.org/0000-0002-4106-1761
has documentation: SciView
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD 2-Clause "Simplified" License
has location: SciView
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-12-09T18:08:09
modified: 2019-10-15T08:40:11
title: SciView
comment: SciView is an ImageJ/FIJI plugin for 3D visualization of images and meshes. It uses the Scenery and ClearVolume infrastructure. SciView integrates ImageJ2 functionality, including ImageJ Ops and ImageJ Mesh, to provide the ability to interact with image and mesh data in 3D and interface with the popular Fiji software ecosystem. An update site is available: http://sites.imagej.net/SciView/

screen-shot-icy
type: software
has documentation: Screen-shot
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Screen-shot
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
created: 2013-10-11T13:08:43
modified: 2020-03-02T11:09:30
title: Screen shot (Icy)

script-editor
type: software
has documentation: Script-Editor
has function: operation 3096
has implementation: http://biii.eu/taxonomy/term/4340
has location: Script-Editor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/320
requires: http://biii.eu/node/371
requires: http://biii.eu/node/589
requires: http://biii.eu/node/8
requires: http://biii.eu/node/842
created: 2013-10-11T13:08:46
modified: 2023-04-26T07:50:30
title: Script Editor

seeded-watershed
type: software
has documentation: org.knime.knip.base.nodes.seg.WatershedNodeFactory#Seeded Watershed
has function: operation Watershed
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/87344
has reference publication: Watersheds in digital spaces: An efficient algorithm based on immersion simulations
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:46
modified: 2019-10-17T09:18:22
title: Seeded Watershed

seg3d
type: software
has documentation: seg3d.html
has function: operation 3553
has function: operation Image segmentation
has function: operation Image visualisation
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD
has location: seg3d.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/601
created: 2013-10-11T13:08:44
modified: 2020-03-02T10:01:01
title: Seg3D

segment-cropper-knime
type: software
has documentation: org.knime.knip.base.nodes.seg.cropper.SegmentCropperNodeFactory#Segment Cropper
has function: operation Image classification
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:41
modified: 2020-03-02T11:27:57
title: Segment Cropper (KNIME)

segmentation-and-quantification-subcellular-structures-fluorescence-microscopy-images-using-squassh
type: software
has author: Berger P
has author: Bugarski M
has author: Incardona P
has author: Mansouri M
has author: Niemann A
has author: Paul G
has author: Rizk A
has author: Sbalzarini IF
has author: Ziegler U
has documentation: Squassh.pdf
has documentation: Fiji-Squassh colocalization plugin notes by Chong Zhang
has function: operation Image colocalization
has function: operation Image segmentation
has function: operation Colocalisation analysis
has location: nprot.2014.037
has location: The paper.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nprot.2014.037
has reference publication: Rizk2014.pdf
has reference publication: Rizk et al. (2014) Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
has reference publication: The reference above in PDF @ MOSAIC website
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/965
created: 2014-12-09T14:35:31
modified: 2018-11-16T08:46:57
title: Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
comment: A workflow template to analyze subcellular structures in fluorescence 2D/3D microscopy images based on a Fiji plugin **Squassh** is described in Rizek et al (2014). The workflow employs detecting, segmenting, and quantifying subcellular structures. For segmentation, it accounts for the microscope optics and for uneven image background. Further analyses include both colocalization and shape analyses. However, it does not work directly for time-lapse data. A brief summary note can be found here.

segmentation-and-tracking-mammary-epithelial-organoids-brightfield-microscopy
type: software
has author: Lucia Hradecká
has function: operation Cell segmentation
has function: operation Cell tracking
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4339
has location: organoids.html
has location: CBIA site on RELIABLE SEGMENTATION AND TRACKING OF ORGANOIDS
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3594
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: https://ieeexplore.ieee.org/document/9905630
has reference publication: IEEE Transactions on Medical Imaging publication
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2023-05-02T19:13:40
modified: 2023-05-02T21:20:33
title: Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy
comment: This workflow describes a deep-learning based pipeline for reliable single-organoid segmentation and tracking in 2D+t high-resolution brightfield microscopy of mouse mammary epithelial organoids. The pipeline involves a four-layer U-Net to infer semantic segmentation predictions, adaptive morphological filtering to establish candidate organoid instances, and a shape-similarity-constrained, instance-segmentation-correcting tracking step to associate the corresponding organoid instances in time. It is particularly focused on automatically detecting an organoid located approximately in the center of the first frame and track all its subsequent instances in the remaining frames, emphasizing on accurate organoid boundary delineation. Furthermore, segmentation network was trained using plausible pix2pixHD-generated bioimage data. Syntheric image simulator code and data are also available here.

segmentation-clustered-cells-matlab
type: software
has author: Steve Eddins
has documentation: cell-segmentation
has function: operation Cell segmentation
has function: operation Morphological operations
has function: operation Watershed
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2014-12-09T14:35:36
modified: 2018-05-30T00:53:31
title: Segmentation of Clustered Cells in MATLAB
comment: A clear tutorial on how to write a MATLAB script to segment clustered cells. The full script is downloadable near the bottom of the article.

segmentation-editor
type: software
has author: Johannes Schindelin, Francois Kusztos, Benjamin Schmid
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Segmentation Editor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T16:28:01
title: Segmentation Editor

semi-automated-quantification-three-stages-phagocytosi-using-imagej
type: software
has function: operation Cell segmentation
has function: operation Interactive segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has license: free
has location: Phagocytosis-Analysis
has location: ImageJ macros
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: 978-1-4939-6581-6 13
has reference publication: https://www.future-science.com/doi/10.2144/000114075
has reference publication: High-throughput quantification of early stages of phagocytosis
has reference publication: Image-Based Analysis of Phagocytosis: Measuring Engulfment and Internalization
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/3568
has usage example: BTN5503-Hamilton Su 229872a.doc
has usage example: User manual
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2023-04-25T15:09:13
modified: 2023-04-26T15:58:00
title: Semi-automated quantification of three stages of phagocytosi using ImageJ
comment: The authors present an ImageJ-based, semi-automated phagocytosis workflow to rapidly quantitate three distinct stages during the early engulfment of opsonized beads.

sendemail-cellprofiler
type: software
has documentation: SendEmail.html
has implementation: http://biii.eu/taxonomy/term/4339
has location: SendEmail.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2020-03-02T10:58:59
title: SendEmail (CellProfiler)
comment: not available anymore in version 3.0 and up?

separate-image-channel-folder
type: software
has author: Stephane Dallongeville
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-09T10:33:19
modified: 2020-03-02T13:51:08
title: Separate image channel in folder
comment: This protocol takes a folder containing images as input and extract each channel in a separate sub folder.

sequence-blocks-icy
type: software
has author: Stephane Dallongeville
has author: Thomas Provoost
has documentation: Sequence-Blocks
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has location: Sequence-Blocks
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2020-03-02T11:18:57
title: Sequence Blocks (Icy)

sequence-comparator
type: software
has author: Yoann Le Montagner
has documentation: Sequence-comparator
has function: operation 2945
has implementation: http://biii.eu/taxonomy/term/4340
has location: Sequence-comparator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/705
requires: http://biii.eu/node/8
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:43
modified: 2020-03-02T11:14:09
title: Sequence comparator

series-labeler
type: software
has function: operation_0226
has implementation: http://biii.eu/taxonomy/term/4340
has location: Series Labeler
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T16:37:05
title: Series Labeler

sgp-dec-scaled-gradient-projection-method-2d-and-3d-images-deconvolution
type: software
has author: Bertero M
has author: Boccacci P
has author: Cavicchioli R
has author: Vicidomini G
has author: Zanella R
has author: Zanghirati G
has author: Zanni L
has documentation: SGPdec doc.pdf
has function: operation Image deconvolution
has location: sgp deblurring boundary.zip
has location: sgp_deblurring_boundary.zip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: srep02523
has reference publication: Zanella et al (2013) Towards real-time image deconvolution: application to confocal and STED microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RC91JqkkQnsmvg8zuG6Td7q
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/89
created: 2014-12-09T14:03:10
modified: 2018-06-02T22:40:11
title: SGP-dec, A Scaled Gradient Projection method for 2D and 3D images deconvolution
comment: A deconvolution component applicable to confocal and STED microscopy. The MATLAB function fo this package implements the SGP method for n-dimensional object deblurring with the option of boundary effects removal. Although this is a preliminary version, results seem to be good from their paper (Zanella et al 2013).

shape-index-map
type: software
has author: Johannes Schindelin
has documentation: Shape Index Map
has function: operation Feature extraction
has function: operation Shape features
has location: fiji.sc
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T18:00:30
title: Shape Index Map

shepp-logan-phantom
type: software
has author: Philippe Thévenaz
has documentation: Shepp-Logan Phantom
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has implementation: http://biii.eu/taxonomy/term/4340
has location: shepplogan
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/6499235
has reference publication: The Fourier Reconstruction of a Head Section
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic R96toeNl9iMp8oqv9augU84
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-16T16:58:30
title: Shepp-Logan Phantom

shifted-linear-interpolation
type: software
has author: Philippe Thévenaz
has function: operation Geometrical transform
has implementation: http://biii.eu/taxonomy/term/4341
has location: shiftedlin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4241
has reference publication: https://ieeexplore.ieee.org/stamp/stamp.jsp%3Farnumber%3D1288196
has reference publication: Linear Interpolation Revitalized
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: #Examples
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:44
modified: 2019-10-16T18:32:01
title: Shifted-Linear Interpolation

shiny-r-package
type: software
has function: operation 3441
has implementation: http://biii.eu/taxonomy/term/4339
has location: shiny.rstudio.com
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has topic: topic Statistics
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-28T11:42:08
modified: 2018-01-28T11:48:57
title: Shiny - R package
comment: Shiny is an R package that makes it easy to build interactive web apps straight from R.

shinyhtm
type: software
has author: Botelho Hugo orcid.org/0000-0002-4208-1086
has author: Tischer Christian
has documentation: shinyHTM
has function: operation_0337
has function: operation 3441
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: shinyHTM
has location: shinyHTM on GitHub
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic High content screening
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-12-08T16:20:42
modified: 2018-12-08T16:34:02
title: shinyHTM
comment: shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data. Within shinyHTM the user is guided through a linear workflow which follows the following best practices: Inspect the numerical data through plotting Measurements are linked to raw images Perform quality control to exclude images with aberrations or where image analysis failed Perform a reproducible data analysis Normalize data and report statistical significance Image visualization relies on Fiji/ImageJ, along with its wealth of analytical tools. shinyHTM can be used to analyze image features obtained with CellProfiler, ImageJ or any other bioimage analysis software. The output of analysis is a publication-ready scoring of the data. shinyHTM is based on the R shiny package.

sholl-analysis-imagej
type: software
has documentation: Sholl Analysis
has documentation: Scholl Analysis Plugin Doc page
has function: operation Object detection
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has location: Sholl Analysis
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth.3125
has reference publication: Ferreira, T. A., Blackman, A. V., Oyrer, J., Jayabal, S., Chung, A. J., Watt, A. J., … van Meyel, D. J. (2014). Neuronal morphometry directly from bitmap images. Nature Methods, 11(10), 982–984.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2023-05-03T19:48:06
title: Sholl Analysis (ImageJ)
comment: The Sholl technique is used to describe neuronal arbors. This plugin can perform Sholl directly on 2D and 3D grayscale images of isolated neurons. Its internal algorithm to collect data is based upon how Sholl analysis is done by hand — it creates a series of concentric shells (circles or spheres) around the focus of a neuronal arbor, and counts how many times connected voxels defining the arbor intersect the sampling shells. The major advantages of this plugin over other implementations are: When analyzing images directly, it does not require previous tracing of the arbor (although it can also analyze traced arbors) It combines curve fitting with several methods to automatically retrieve quantitative descriptors from sampled data, which allows direct statistical comparisons between arbors It allows continuous and repeated sampling around user-defined foci It allows batch processing

sigma-filter
type: software
has documentation: Sigma Filter
has function: operation Image enhancement
has function: operation Image smoothing
has function: operation R7MFwdgojfmkZ07yWbdcda0
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: Sigma Filter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-17T09:03:07
title: Sigma Filter

simcheck
type: software
has author: Ball, Graeme orcid.org/0000-0002-6526-2306
has author: Schermelleh, Lothar orcid.org/0000-0002-1612-9699
has DOI: srep15915
has DOI: 10.1038/srep15915
has documentation: SIMcheck.html
has documentation: SimCheck documentation
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: SIMCheck.php
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: srep15915
has reference publication: 10.1038/srep15915
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RC91JqkkQnsmvg8zuG6Td7q
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-02-13T12:24:29
modified: 2019-02-05T11:18:48
title: SIMcheck
comment: SIMcheck is an ImageJ plugin suite for assessing the quality and reliability of Structured Illumination Microscopy (SIM) data. The quality of the raw data, the quality of the reconstruction and the calibration of the microscope can be tested.

simple-mser-based-segmentation-tool-spot-detection-234d
type: software
has author: Varun Kapoor
has documentation: MSER parameters
has documentation: Explanation of how to tune MSER parameters
has implementation: http://biii.eu/taxonomy/term/4340
has location: 1Ge1p8x2ZNRy3GxS0QlrYis9i7u7suZOV
has location: Source: https://github.com/kapoorlab/Fiji-MSER, https://github.com/kapoorlab/MasterPanels
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
has usage example: https://twitter.com/EntraCod/status/1353070156868587520
openess: http://biii.eu/taxonomy/term/3575
created: 2021-01-24T23:14:17
modified: 2021-01-25T00:16:21
title: A simple MSER based segmentation tool for spot detection in 2/3/4D.
comment: MSER based on implementation in imglib2 provided as an interactive GUI tool for spot detection in 2/3/4D images.

simple-neurite-tracer
type: software
has author: Ferreira Tiago
has author: Longair Mark
has function: operation_0337
has function: operation Image segmentation
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Simple Neurite Tracer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: btr390
has reference publication: Longair MH, Baker DA, Armstrong JD. Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 2011
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: tracing-neurons-using-fiji-imagej
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:46
modified: 2023-05-03T08:58:16
title: Simple Neurite Tracer
comment: Plugin designed to allow easy semi-automatic tracing of neurons or other filament-like structures (e.g., microtubules, blood vessels) through either 2D images or 3D image stacks. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software. This plugin is included in Fiji by default.

simple-operations-icy
type: software
has author: Alexandre Dufour
has author: Sorin Pop
has documentation: Simple-Operations
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has location: Simple-Operations
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/11
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:44
modified: 2020-03-02T10:43:56
title: Simple Operations (Icy)

simple-tracing-df-tracing
type: software
has author: Gonzalez-Bellido, Paloma T.
has author: Peng, Hanchuan (http://orcid.org/0000-0002-3478-3942)
has author: Yang, Jinzhu
has function: operation Adaptative thresholding
has function: operation Distance transform
has function: operation Image enhancement
has function: operation Image segmentation
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has location: neurontracing simpletracing
has location: Simple Tracing Github repository in Vaa3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://doi.org/10.1186/1471-2105-14-93
has reference publication: A distance-field based automatic neuron tracing method
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2017-09-14T15:42:08
modified: 2023-05-03T14:39:12
title: Simple Tracing DF-Tracing
comment: We have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically. Two distance-transform based “force” fields are used: one for “pressure”, which is the distance transform field of foreground pixels (voxels) to the background, and another for “thrust”, which is the distance transform field of the foreground pixels to an automatically determined seed point. The coupling of these two force fields can“push” a “rolling ball” quickly along the skeleton of a neuron, reconstructing the 3D cell morphology.

simple-tracker
type: software
has author: Jean-Yves Tinevez
has function: operation Cell tracking
has function: operation Particle tracking
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD
has location: 34040-simple-tracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
has usage example: TestSimpleTracker.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2018-10-17T15:17:12
modified: 2018-10-17T15:31:47
title: Simple-Tracker
comment: SIMPLETRACKER a simple particle tracking algorithm that can deal with gaps. Tracking , or particle linking, consist in re-building the trajectories of one or several particles as they move along time. Their position is reported at each frame, but their identity is yet unknown: we do not know what particle in one frame corresponding to a particle in the previous frame. Tracking algorithms aim at providing a solution for this problem. simpletracker.m is - as the name says - a simple implementation of a tracking algorithm, that can deal with gaps. A gap happens when one particle that was detected in one frame is not detected in the subsequent one. If not dealt with, this generates a track break, or a gap, in the frame where the particle disappear, and a false new track in the frame where it re-appear.

simpleelastix
type: software
has author: Kasper Marstal
has documentation: simpleelastix.readthedocs.io
has function: operation Image registration
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has license: Apache
has location: simpleelastix.github.io
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
created: 2017-02-13T14:59:17
modified: 2021-05-19T18:51:28
title: simpleElastix
comment: quote: > Elastix cite{Klein2010} is an open source, command-line program for intensity-based registration of medical images that allows the user to quickly configure, test, and compare different registration methods. SimpleElastix is an extension of SimpleITK cite{Lowekamp2013} that allows you to configure and run Elastix entirely in Python, Java, R, Octave, Ruby, Lua, Tcl and C# on Linux, Mac and Windows. The goal is to bring robust registration algorithms to a wider audience and make it easier to use elastix, e.g. for Java-based enterprise applications or rapid Python prototyping. Python example ```python import SimpleITK as sitk resultImage = sitk.Elastix(sitk.ReadImage("fixedImage.nii"), sitk.ReadImage("movingImage.nii")) ```

simpleitk
type: software
has function: operation 2409
has function: operation 3443
has function: operation Image registration
has function: operation Image segmentation
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4339
has location: gettingStarted.html
has location: SimpleITK getting started
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/4236
has programming language: http://biii.eu/taxonomy/term/4728
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: TUTORIAL
has usage example: Online tutorial
openess: http://biii.eu/taxonomy/term/3575
created: 2018-09-09T20:49:25
modified: 2023-05-02T12:52:07
title: simpleITK
comment: SimpleITK provides a simplified interface to ITK in a variety of languages. A user can either download pre-built binaries, if they are available for the desired platform and language, or SimpleITK can be built from the source code. Currently, Python binaries are available on Microsoft Windows, GNU Linux and Mac OS X. C# and Java binaries are available for Windows. We are also working towards supporting R packaging.

simtoolbox
type: software
has author: Fliegel Karel
has author: Hagen Guy M.
has author: Krizek Pavel
has author: Lukes Tomás
has author: Ovesný Martin
has function: operation Image processing
has function: operation Image reconstruction
has function: operation R8V95OnTjs7fCvVXWjaXrh6
has license: GPL
has location: simtoolbox
has reference publication: btv576
has reference publication: 10.1364/OE.22.029805
has topic: topic RC91JqkkQnsmvg8zuG6Td7q
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-01T18:10:22
modified: 2018-11-26T08:30:04
title: SIMToolbox
comment: SIMToolbox: a MATLAB toolbox for structured illumination microscopy SIMToolbox is an open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy. Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination. 2665

simucell
type: software
has license: free ?
has location: simucell
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-11-07T20:26:20
modified: 2017-09-13T10:13:12
title: SimuCell
comment: An open-source framework to synthetically generate fluorescent microscopic images of cellular population.

simulate-color-blindness
type: software
has author: Johannes Schindelin
has documentation: Simulate Color Blindness
has documentation: Documentation
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Daltonize .java
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:44
modified: 2019-10-17T08:57:16
title: Simulate Color Blindness
comment: This plugin simulates color blindness. It is based on http://quarkphysics.ca/phys1/light/u-light.htm

siox-simple-interactive-object-extraction
type: software
has author: Ignacio Arganda-Carreras
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: SIOX: Simple Interactive Object Extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-18T11:36:42
title: SIOX: Simple Interactive Object Extraction

skeletonize
type: software
has author: Wayne Rasband
has documentation: 146-29.html#sub:Skeletonize
has function: operation Feature extraction
has function: operation Morphological operations
has implementation: http://biii.eu/taxonomy/term/4340
has location: imagej.net
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-05-25T20:27:39
modified: 2023-04-27T10:51:32
title: Skeletonize
comment: ImageJ native "Skeletonize" implementation. - works only with 8-bit binary image. A faster implementation is available as a plugin Skeletonize3D written by Ignacio Arganda-Carreras. Pros of this plugin is summarized here.

skeletonize3d
type: software
has author: Ignacio Arganda-Carreras
has function: operation Morphological operations
has function: operation Skeletonization
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Skeletonize3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2023-04-27T10:52:09
title: Skeletonize3D
comment: For post-processing analysis, use Analyze Skeleton plugin written by the same author.

skin-tools
type: software
has author: Volker Baecker
has documentation: Skin Tools
has location: Skin Tools
has location: Skin Tools website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: 273769192 ImageJ Macro Tool Sets for Biological Image Analysis
has reference publication: 2012. ImageJ Macro Tool Sets for Biological Image Analysis. ImageJ User and Developer Conference 2012.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-14T07:22:56
modified: 2018-06-06T02:02:51
title: Skin Tools
comment: The skin tools measure the thickness of the epidermis and the interdigitation index. The input images are masks that represent the epidermis and that have been created from images of stained histological sections. The mask must touch the left and right border of the image. The dermal-epidermal border must be on the lower site of the image. The interdigitation index can be measured for one or more segments per image. As a measure of the thickness of the epidermis the lengths of a number of random line segments are measured. The line segments start at the lower border, are perpendicular to the lower border and end at the opposite border of the mask. See installation Instructions on the website.

sldc-segment-locate-dispatch-classify
type: software
has author: Raphaël Marée
has author: Romain Mormont
has documentation: wiki
has function: operation Cell segmentation
has function: operation Object detection
has location: sldc
has location: GitHub: waliens/sldc
has programming language: http://biii.eu/taxonomy/term/3592
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/128
requires: http://biii.eu/node/141
requires: http://biii.eu/node/286
created: 2017-02-13T11:59:09
modified: 2023-04-28T13:08:44
title: SLDC (Segment Locate Dispatch Classify)
comment: SLDC is an open-source Python workflow. SLDC stands for Segment Locate Dispatch Classify. This framework aims at facilitating the development of algorithms for detecting objects in multi-gigapixel images. Particularly, it provides algorithm developers with a structure to define problem-dependent components of their processing workflow (i.e. segmentation and classification) in a concise way. Every other concern such as parallelization and large image handling are encapsulated by the framework. It also features a powerful and customizable logging system and some components to apply several workflows one after another on a same image. SLDC can work on local images or interact with Cytomine Example image: Toy image data

sleap
type: software
has author: Castro, Marielisa D.
has author: D`uva, John
has author: Deutsch, David S.
has author: Falkner, Annegret L.
has author: Kislin, Mikhail
has author: Kocher, Sarah D.
has author: Li, Junyu
has author: Matsliah, Arie
has author: McKenzie-Smith, Grace C.
has author: Mitelut, Catalin C.
has author: Murthy, Mala
has author: Normand, Edna
has author: Papadoyanis, Eleni S.
has author: Pereira, Talmo D. (orcid.org/0000-0001-9075-8365)
has author: Ravindranath, Shruthi
has author: Sanes, Dan H.
has author: Shaevitz, Joshua W.
has author: Tabris, Nathaniel
has author: Turner, David M.
has author: Wang, Samuel S.-H.
has author: Wang, Z. Yan
has documentation: index.html
has documentation: SLEAP guides page
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4339
has license: The Clear BSD License
has location: releases
has location: SLEAP releases page on Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: s41592-022-01495-2
has reference publication: SLEAP: A deep learning system for multi-animal pose tracking (Nature Methods publication)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1201
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1312
created: 2023-05-08T07:35:19
modified: 2023-05-11T11:00:33
title: SLEAP
comment: Open source deep learning based framework for multi-animal pose tracking. It can track animal and any number of animals and has a labeling/training GUI for learning and proofreading.

slice-labeler-imagej
type: software
has author: Pedro Ramos-Cabrer
has documentation: Slice Labeler
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: Slice Labeler
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2020-03-02T11:35:13
title: Slice Labeler (ImageJ)

slice-traveler
type: software
has documentation: Slice-Traveler
has function: operation 2409
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-17T08:35:06
title: Slice Traveler

slidetoolkit
type: software
has author: Bastiaan G. L. Nelissen
has author: Frans L. Moll
has author: Gerard Pasterkamp
has author: Joost A. van Herwaarden
has author: Paul J. van Diest
has documentation: guides
has documentation: Instruction doc in the Github repo, installation procedures as well
has function: operation Image segmentation
has function: operation Image stitching
has license: MIT
has location: slideToolkit
has location: github: repo
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4680
has programming language: http://biii.eu/taxonomy/term/4681
has reference publication: journal.pone.0110289
has reference publication: Nelissen et al. (2014) SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/127
requires: http://biii.eu/node/1319
requires: http://biii.eu/node/1320
requires: http://biii.eu/node/1321
requires: http://biii.eu/node/1322
requires: http://biii.eu/node/31
created: 2014-12-09T09:59:34
modified: 2023-05-03T13:09:39
title: slideToolkit
comment: SlideToolkit is a collection of command-line tools to assist with the automated histology analysis of whole-slide images. The publication linked in the "reference" details the actual workflow. This includes tools to organize the data, perform tiling and subsequent batch processing of the generated tiles in a cell profiler pipeline. All the tools are designed to run on a single PC or on a HPC system. The scripts in the toolkit are on github under MIT licence.

sloth
type: software
has author: Monika Kauer
has documentation: https://pypi.org/project/SLOTH/0.0.7/
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4339
has license: GPLv3
has location: Installing.html
has location: Installation instruction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: S0091-679X(10)95013-9
has reference publication: A protocol in Methods in Cell Biology (not by the SLOTH author)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1286
requires: http://biii.eu/node/1288
requires: http://biii.eu/node/1312
requires: http://biii.eu/node/1317
created: 2014-12-09T16:50:19
modified: 2023-05-03T08:53:29
title: SLOTH
comment: A collection for tracking microtubule dynamics, written in Python.

sme
type: software
has author: Genovisio Auguste orcid.org/0000-0003-1877-5595
has author: Rexhepaj Elton
has author: Shihavuddin Asm orcid.org/0000-0002-4137-9374
has function: operation Projection
has implementation: http://biii.eu/taxonomy/term/4340
has location: SME
has location: SME code and plugin on github.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: ncomms15554
has reference publication: Smooth 2D manifold extraction from 3D image stack.
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2019-10-15T10:50:23
modified: 2019-10-15T11:36:20
title: SME
comment: Smooth 2D Manifold Extraction (SME). Three-dimensional fluorescence microscopy followed by image processing is routinely used to study biological objects at various scales such as cells and tissue. However, maximum intensity projection, the most broadly used rendering tool, extracts a discontinuous layer of voxels, obliviously creating important artifacts and possibly misleading interpretation. Here we propose smooth manifold extraction, an algorithm that produces a continuous focused 2D extraction from a 3D volume, hence preserving local spatial relationships. We demonstrate the usefulness of our approach by applying it to various biological applications using confocal and wide-field microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation of 3D image stacks with maximum accuracy.

snakemake
type: software
has author: Johannes Köster
has author: Sven Rahmann
has documentation: index.html
has implementation: http://biii.eu/taxonomy/term/4339
has location: snakemake.git
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: https://academic.oup.com/bioinformatics/article/28/19/2520/290322
has type: http://biii.eu/taxonomy/term/8
has usage example: spim registration
openess: http://biii.eu/taxonomy/term/3575
created: 2019-03-25T16:08:14
modified: 2019-03-25T16:29:23
title: Snakemake
comment: A Python based workflow management software that allows to create workflows that seamlessly scale from a single workstation to a high performance computing cluster or cloud environments.

snakuscule
type: software
has documentation: snakuscule
has function: operation Active contours
has implementation: http://biii.eu/taxonomy/term/4340
has location: snakuscule
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: thevenaz0801.html
has reference publication: Snakuscules
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-17T08:41:20
title: Snakuscule

soax
type: software
has author: Dimitrios Vavylonis
has author: Ting Xu
has author: Xiaolei Huang
has DOI: srep09081
has documentation: soax manual.pdf
has documentation: SOAX User Manual
has function: operation 3443
has function: operation Active contours
has function: operation Skeletonization
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4341
has location: soax
has location: Dowload Soax software
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/517
created: 2017-05-15T09:02:48
modified: 2023-05-03T08:52:45
title: SOAX
comment: SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. SOAX provides 3D visualization for exploring image data and visually checking results against the image. Quantitative analysis functions based on extracted networks are also implemented in SOAX, including spatial distribution, orientation, and curvature of filamentous structures. SOAX also provides interactive manual editing to further improve the extraction results, which can be saved in a file for archiving or further analysis. Useful for microtubules or actin filaments. Observation: Depending on the operating system, the installation may or may not require Boost C++, ITK and VTK libraries. Windows has a standalone executable application without the need of those.

sobel-filter-knime
type: software
has documentation: org.knime.knip.base.nodes.filter.SobelNodeFactory#Sobel Filter
has function: operation Edge detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-02T10:50:59
title: Sobel Filter (KNIME)

soda-suite
type: software
has author: Dallongeville Stéphane
has author: Danglot Lydia orcid.org/0000-0001-6190-6605
has author: Dufour Alexandre
has author: Faklaris Orestis
has author: Grassart Alexandre
has author: Lagache Thibault orcid.org/0000-0002-7033-4677
has author: Olivo-Marin Jean-Christophe orcid.org/0000-0001-6796-0696
has author: Sauvonnet Nathalie
has function: operation Colocalisation analysis
has function: operation Pixel-based colocalisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: SODA-suite
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: s41467-018-03053-x
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Super-resolution microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2019-01-15T16:24:45
modified: 2023-04-29T13:51:57
title: SODA suite
comment: Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

softworx-50
type: software
has license: commercial
has location: softworx.asp
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2013-11-07T20:27:27
modified: 2017-09-12T18:05:37
title: softWoRx 5.0
comment: softWoRx® 5.0 is the latest in DeltaVision image acquisition software. Find samples, acquire images and process data quickly and efficiently with the intuitive user interface. softWoRx 5.0 includes visualization and measurement tools and exports data in a wide variety of formats making it a versatile tool for more than just image acquisition.

spark-stitcher
type: software
has author: Pisarev Igor
has function: operation Illumination correction
has function: operation Image registration
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4339
has location: stitching-spark
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3385
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-01-30T16:31:36
modified: 2018-01-30T16:34:42
title: Spark Stitcher
comment: Reconstruct big images from overlapping tiled images on a Spark cluster. The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching

sparkmaster
type: software
has author: Aleksey V. Zima
has author: Donald M. Bers
has author: Eckard Picht
has author: Lothar A. Blatter
has documentation: sparkmasterhome
has implementation: http://biii.eu/taxonomy/term/4340
has location: sparkmasterhome
has location: google site: sparkmaster plugin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: S0006-3495(99)77229-2
has reference publication: ajpcell.00586.2006
has reference publication: Cheng et. al. (1999)
has reference publication: Picht et. al. (2007)
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T16:53:54
modified: 2018-05-20T21:07:28
title: SparkMaster
comment: Analyzing Ca2+ sparks ImageJ plugin to detect and measure Ca2+ sparks in linescan images, described in Picht et. al. (2007). The algorithm is based on that described by Cheng et al. (1999). Care should be taken to ensure that detections belong to 'true' events, as without any additional background subtraction steps the algorithm is not appropriate for images in which the baseline fluorescence varies substantially.

spatial-statistics-2d3d-imagej-plugin
type: software
has author: Philippe Andrey
has author: Thomas Boudier
has documentation: http://web.archive.org/web/20180416235955/http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Aanalysis%253Aspatial_statistics_2d_3d%253Astart
has documentation: Online documentatoin (Archived old website image)
has function: operation Feature extraction
has function: operation RDetoixS3xEu0agR2CebaoB
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4340
has location: http://web.archive.org/web/20180416235955/http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Aanalysis%253Aspatial_statistics_2d_3d%253Astart
has location: Download (Archived old website image)
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2023-05-03T15:54:18
title: Spatial statistics 2D/3D ImageJ plugin
comment: The plugin analyses a point pattern (positions of objects of interest) distributed within a reference structure. This analysis allows in particular to assess deviation from spatial randomness, and to reveal trends for clustering (attraction) or regularity (repulsion). No edge correction is performed, as it is assumed that no point is expected outside the reference structure. This plugin comes together with 3D ImageJ suites plugin.

spatial-transforms-ebimage
type: software
has documentation: EBImage.pdf
has function: operation Geometrical transform
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:46
modified: 2020-03-02T10:36:31
title: Spatial Transforms (EBImage)

spheres-and-tubes-3d
type: software
has documentation: Spheres and Tubes in 3D
has function: operation R9FvNkpDIaqZQhLVlPsHisj
has location: fiji.sc
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/601
created: 2013-10-11T13:08:43
modified: 2019-10-16T16:52:29
title: Spheres and Tubes in 3D
comment: An example ImageJ plugin illustrating how to create and display 3D tubes and 3D spheres in the 3D Viewer.

spheroid-simulator
type: software
has author: S. PREIBISCH
has documentation: nmeth.2929.html
has reference publication: multiview-simulation
has type: http://biii.eu/taxonomy/term/8
created: 2018-05-20T18:04:41
modified: 2018-05-20T18:09:49
title: Spheroid simulator
comment: It simulates a three-dimensional ground-truth that resembles aspects of a biological object like a spheroid. For each simulated view the signal is attenuated, convolved with an effective PSF, and anisotropically sampled using a Poisson process.

sphire
type: software
has author: Schulte Meike
has location: sphire.mpg.de
has location: Website
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2020-03-24T09:55:11
modified: 2020-03-24T09:57:44
title: SPHIRE
comment: SPHIRE is a new software suite designed for easy access to cryo electron microscopy with the clear goal of quality assessment and result reproducibility by statistical resampling. While being well suited for cryo-EM novices, experienced users will find comfort in the accessibility of almost every possible variable in advanced option tabs and the transparent, easily customizable Python-based framework for non-standard processing pipelines. In a visually appealing and easy-to-use graphical user interface (GUI) the user will find an array of programs which will guide through the complete process of high-resolution cryo-EM. This begins with movie frame alignments (movie), CTF estimation of raw electron micrographs (cter) and picking/stack creation (window) and continues with reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).

spim-bead-registration
type: software
has author: Johannes Schindelin
has author: Pavel Tomancak
has author: Stephan Preibisch
has author: Stephan Saalfeld
has function: operation R9EjejimBB0tmnQRmZt0RhA
has location: SPIM Bead Registration (deprecated)
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2023-04-27T14:50:50
title: SPIM Bead Registration

spim-de-striper
type: software
has author: Sébastien Tosi
has function: operation Image processing
has function: operation R7MFwdgojfmkZ07yWbdcda0
has location: image-j-fiji#h.p hxgk--RmqPll
has location: deStriper macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p hxgk--RmqPll
has usage example: User guide - SPIM de-striper
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2014-12-08T14:20:47
modified: 2023-04-28T14:22:51
title: SPIM de-striper
comment: This macro implements a filter that is meant to attenuate close to parallel intensity stripes in an image, such as often happening in light sheet microscopy. The results are usually decent even when the stripes show a large angular spread due to light sheet refraction at the sample surface. The filter can process a 3D stack but the processing is performed slice by slice. Example image is available in the documentation link.

spim-registration-method-imagej
type: software
has documentation: SPIM Registration Method
has function: operation R9EjejimBB0tmnQRmZt0RhA
has implementation: http://biii.eu/taxonomy/term/4340
has location: SPIM Registration Method
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: nmeth0610-418.html
has reference publication: Software for bead-based registration of selective plane illumination microscopy data
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Light-sheet microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2023-04-27T15:10:35
title: SPIM Registration Method (ImageJ)
comment: This plugin combines the idea of using fiduciary markers, local descriptors and geometric hashing and applies global optimization. It can register an arbitrary number of partially overlapping point clouds. It is robust with respect to the amount of incorporated beads, bead distribution, amount of overlap, and can reliably detect non-affine disturbances (e.g. abrupt agarose movement) that might occur during imaging. For details about the SPIM registration, fusion & deconvolution please have a look at the Multiview Reconstruction Plugin. It is much more powerful, flexible and completely integrated with the BigDataViewer.

spimagine
type: software
has author: Martin Weigert
has documentation: spimagine#usage
has documentation: Documentation on usage
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4341
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: spimagine
has reference publication: GITHUB
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1186
created: 2019-01-24T14:02:45
modified: 2019-01-24T16:15:22
title: Spimagine
comment: Spimagine is a python package to interactively visualize and process time lapsed volumetric data as generated with modern light sheet microscopes (hence the Spim part). The package provides a generic 3D+t data viewer and makes use of GPU acceleration via OpenCL. If provides further an image processor interface for the GPU accelerated denoising and deconvolution methods of gputools. It is only for display (no analysis). The only drawback: it does not handle multichannel time lapse 3D data (only one channel at a time).

spine-classification-based-kernel-density-estimation
type: software
has author: M U Ghani
has function: operation 2990
has function: operation Neuron image analysis
has license: MIT
has location: license.txt
has location: GitHub repo
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: j.jneumeth.2016.12.006
has reference publication: Dendritic spine classification using shape and appearance features based on two-photon microscopy
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/89
created: 2017-02-13T15:13:46
modified: 2018-08-16T15:46:15
title: Spine classification based on kernel density estimation
comment: We propose to use a kernel density estimation (KDE) based approach for classification. This non-parametric approach intrinsically provides the likelihood of membership for each class in a principled manner. The implementation was used in Ghani2016. Any papers using this code should cite Ghani2016 accordingly. The software has been tested under Matlab R2013b. Sample Data: Annotated two-photon images of dendritic spines

splash-screen-maker-icy
type: software
has author: Fabrice de Chaumont
has documentation: Splash-Screen-Maker
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Splash-Screen-Maker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2020-03-02T11:39:02
title: Splash Screen Maker (Icy)

spline-deformation-generator
type: software
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Spline Deformation Generator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-16T18:25:41
title: Spline Deformation Generator

spline-interpolation
type: software
has author: Philippe Thévenaz
has documentation: interpolation
has function: operation Image processing
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4339
has location: interpolation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4241
has reference publication: thevenaz0002.html
has reference publication: Interpolation Revisited
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: interpolation
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:41
modified: 2020-03-02T10:19:56
title: Spline Interpolation

spline-pyramids-software
type: software
has author: Daniel Sage
has author: Michael Unser
has author: Patrick Brigger
has documentation: pyramids
has function: operation Image processing
has implementation: http://biii.eu/taxonomy/term/4339
has location: pyramids
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4241
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T13:08:43
modified: 2020-03-02T11:23:23
title: Spline Pyramids Software

splitter-knime
type: software
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
created: 2013-10-11T13:08:44
modified: 2020-03-02T10:05:12
title: Splitter (KNIME)

splitting-clustered-cells
type: software
has author: Steve Eddins
has function: operation Watershed
has location: watershed-transform-question-from-tech-support
has location: Watershed transform question from tech support
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/826
created: 2014-12-09T14:16:07
modified: 2018-05-15T12:22:47
title: Splitting clustered cells
comment: A clear tutorial for splitting connected particles (cells) in a binary mask.

spot-detection-3d-hessian-imagej
type: software
has author: Tosi, Sebastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: SPOT-DETECTION-3D
has location: W SpotDetection3D-Hessian-IJ
has location: Neubias BIAFLOWS workflow of Spot Detection 3D Hessian with ImagJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1038
requires: http://biii.eu/node/1455
requires: http://biii.eu/node/1605
requires: http://biii.eu/node/38
created: 2020-01-23T12:53:44
modified: 2023-05-01T17:00:28
title: Spot Detection 3D Hessian (ImageJ)
comment: 3D spot detection using the Determinant of Hessian (DoH) and the detection of 3D minima.

spot-detection-3d-icy
type: software
has author: Baecker, Volker
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: SPOT-DETECTION-3D
has function: operation Spot extraction
has location: W SpotDetection3D-Icy
has location: Neubias BIAFLOWS workflow of Spot Detection 3D with Icy protocol
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
created: 2020-01-23T12:36:28
modified: 2023-05-01T16:59:49
title: Spot Detection 3D (Icy)
comment: Spot detection in 3D images by Wavelet Adaptive Threshold in Icy.

spot-detection-3d-imagej
type: software
has author: Bäcker, Volker
has author: Tosí, Sébastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: SPOT-DETECTION-3D
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: IJSpotDetection3D.ijm
has location: Neubias BIAFLOWS workflow of Spot Detection 3D with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1038
requires: http://biii.eu/node/1070
requires: http://biii.eu/node/38
created: 2019-02-25T14:46:28
modified: 2023-05-01T16:58:55
title: Spot Detection 3D (ImageJ)
comment: This workflow detects spots from a 3D image by using straightforward set of ImageJ components. It receives the Laplacian Radius and the Threshold value s input.

spot-detection-and-codistribution-analysis
type: software
has author: Perrine Paul-Gilloteaux orcid.org/0000-0003-3903-4841
has function: operation Image colocalization
has function: operation Spot extraction
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation Colocalisation analysis
has location: JCS supplementary sofwtare
has platform: http://biii.eu/taxonomy/term/30
has reference publication: jcb.201306162
has reference publication: Monteiro et al. (2013) Endosomal WASH and exocyst complexes control exocytosis of MT1-MMP at invadopodia
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
requires: http://biii.eu/node/38
created: 2014-12-08T12:07:28
modified: 2023-04-29T11:52:33
title: spot detection and codistribution analysis
comment: WASH, Exo84, and cortactin spot detection and codistribution analysis To detect endosomes, an automatic Otsu threshold is applied to the Gaussian-filtered MT1-MMPpositive endosome image (= 1.5 pixels for the sample image). Statistics about each endosome are then saved, for example random positioning of spots can be compared to actual positioning. For each endosome, WASH and Exo84 (or WASH and cortactin) spots are searched for in a neighboring of x pixels in their respective channel. Their number and position are saved per endosome (**see the macro in Text file S2 downloadable from here**). From the position of WASH and Exo84 (or WASH and cortactin) spots around each endosomes, each WASH spot is paired with its closest Exo84 (or cortactin) spot neighbor, optimized over all spots around this endosome. This allowed measuring of the distribution of distance between WASH-Exo84 (or WASH-cortactin) spots (**for the co-distribution analysis, see matlab scripts in Zip file S3 downloadable).

spot-detection-dmap-imagej
type: software
has author: Tosi, Sebastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: SPOT-DETECTION-2D
has function: operation Distance transform
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: IJSpotDetection.ijm
has location: Neubias BIAFLOWS workflow of Spot Detection Dmap with ImageJ
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1038
requires: http://biii.eu/node/1455
requires: http://biii.eu/node/38
created: 2020-01-23T12:24:09
modified: 2023-05-01T16:56:17
title: Spot Detection Dmap (ImageJ)
comment: This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius), thresholding (user defined threshold) and finding local intensity maxima in mask distance map (Dmap).

spot-detection-icy
type: software
has author: Marée, Raphaël
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: SPOT-DETECTION-2D
has function: operation Spot extraction
has location: protocol.protocol
has location: Neubias BIAFLOWS workflow of Spot Detection with Icy protocol
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
created: 2019-02-26T10:57:51
modified: 2023-05-01T16:57:02
title: Spot Detection (Icy)
comment: This workflow uses ICY wavelet based spot detector to detect spots in 2D images.

spot-detection-imagej
type: software
has author: Bäcker, Volker
has author: Tosí, Sébastien
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: IJSpotDetection.ijm
has location: Neubias BIAFLOWS workflow of Spot Detection with ImageJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1038
requires: http://biii.eu/node/1042
requires: http://biii.eu/node/1455
requires: http://biii.eu/node/38
created: 2019-02-25T14:00:16
modified: 2020-01-16T15:59:28
title: Spot detection (ImageJ)
comment: This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius) and detecting regional intensity minima (user defined noise tolerance).

spot-detection-knime
type: software
has documentation: org.knime.knip.base.nodes.proc.spotdetection.WaveletSpotDetectionNodeFactory#Spot Detection
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4339
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1130
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:44
modified: 2020-03-02T10:32:59
title: Spot Detection (KNIME)

spot-detection-utilities
type: software
has documentation: spot-detection-utilities
has function: operation Particle tracking
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL3
has location: spot-detection-utilities
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2023-04-29T14:24:34
title: Spot detection utilities
comment: A set of classes and functions which can be used by plugins performing spot detection and spot tracking.

spot-detector-icy
type: software
has author: Fabrice de Chaumont http://orcid.org/0000-0001-7613-7204
has documentation: Spot-Detector
has documentation: documentation
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation Spot extraction
has location: Spot-Detector
has location: Plugin can be downloaded from Icy toolbar
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3385
has topic: topic RDdX0TswBVhmWiS1dI3pghN
has type: http://biii.eu/taxonomy/term/8
has usage example: http://biii.eu/node/50
has usage example: example of workflow using it
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2017-05-05T14:24:45
modified: 2020-03-03T13:37:55
title: Spot Detector (Icy)
comment: Spot detector detects and counts spots, based on wavelet transform. - Detects spots in noisy images 2D/3D. - Depending on objective, spots can be nuclei, nucleus or cell - Versatile input: sequence or batch of file. - Detects spot in specific band/channel. - Multi band labeling: automaticaly creates ROIs from one band and count in the same or an other band. - Filters detection by size. - Sort detection by ROIs - Output data in XLS Excel files: number of detection by ROIs, and each detection location and size. - Outputs withness image with ROIs and detection painted on it. - Outputs binary detection image. - Displays detections - Displays tags

spotdetectionij
type: software
has author: Tosi Sebastien
has comparison: analysis
has comparison: BIAFLOWS-PROBLEM: SPOT-DETECTION-2D
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: IJSpotDetection.ijm
has location: git source code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1038
requires: http://biii.eu/node/1042
requires: http://biii.eu/node/38
created: 2018-10-18T16:50:14
modified: 2023-05-01T16:57:39
title: SpotDetectionIJ
comment: This is a classical workflow for spot detection or blob like structures (vesicules, melanosomes,...) Step 1 Laplacian of Gaussian to enhance spots . Paraeters= radius, about the average spot radius Step 2 Detect minima (using Find Maxima with light background option to get minima). Parameter : Tolerance to Noise: to be tested, hard to predict. About the height of the enhanced feautures peaks

spotdistance
type: software
has author: Daniel Sage
has documentation: spotdistance
has function: operation 2945
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: spotdistance
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-29T17:52:17
title: SpotDistance
comment: An ImageJ plugin for evaluate intra-nuclear 3D cross-distances between fluorescent spots in multi-channel images ![image](http://bigwww.epfl.ch/sage/soft/spotdistance/meta/splash.png)

spotfinderm
type: software
has author: Sliusarenko O, Heinritz J, Emonet T, and Jacobs-Wagner C
has documentation: helpSpotFinderM.htm
has function: operation Cell tracking
has function: operation Spot extraction
has location: helpSpotFinderM.htm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
created: 2014-12-15T23:48:24
modified: 2019-10-28T11:12:43
title: SpotFinderM
comment: Quote: *A GUI-based program which manually detects spots and places them into previously detected meshes. Currently the program runs from MATLAB only. *

spotfinderz
type: software
has documentation: helpSpotFinder.htm
has function: operation Image tracking
has location: helpSpotFinder.htm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: helpSpotFinder.htm
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2014-12-15T23:45:40
modified: 2019-10-21T12:54:08
title: SpotFinderZ
comment: Quote: *SpotFinderZ (from now on simply SpotFinder) detects round, usually diffraction-limited spots inside bacterial cells outlined with MicrobeTracker and places them into the meshes structure produced by MicrobeTracker. The program is written in MATLAB and saves the data in the MicrobeTracker format by appending additional fields.*

spots-colocalization-comdet
type: software
has author: Eugene Katrukha
has documentation: Spots colocalization (ComDet)
has documentation: @ImageJ.net
has function: operation Spot extraction
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Ekatrukha
has location: Fiji Update Site
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
has usage example: How-to-use-plugin-(Text-Tutorial)
has usage example: How to use plugin (Text Tutorial)
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1310
requires: http://biii.eu/node/38
created: 2018-12-17T00:42:30
modified: 2018-12-17T00:49:34
title: Spots colocalization (ComDet)
comment: Quote " finding and/or analyzing colocalization of bright intensity spots (cells, particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc). " Uses Gaussian-Mexican hat convolution for preprocessing.

spotsizer
type: software
has implementation: http://biii.eu/taxonomy/term/4341
has location: CIcsiro:15330v003
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/27712582
has reference publication: Spotsizer: High through-put quantitative analysis of microbial growth
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
created: 2017-02-15T12:05:01
modified: 2020-03-03T16:46:47
title: Spotsizer
comment: Spotsizer is a software tool that automates analysis of large volumes of photographic images of growing microbes.

spottracker
type: software
has documentation: spottracker
has function: operation Particle tracking
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: spottracker
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: sage0501.html
has reference publication: Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Fluorescence lifetime imaging
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2020-03-02T10:13:26
title: SpotTracker

squassh
type: software
has author: MOSAIC Group
has documentation: SplitBregmanSeg.pdf
has function: operation Cell segmentation
has function: operation Image colocalization
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Squassh
has location: Install via update site.
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: Paul2013a.pdf
has reference publication: Rizk2014.pdf
has reference publication: Algorithm
has reference publication: Workflow
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1063
requires: http://biii.eu/node/79
created: 2013-10-15T10:45:51
modified: 2019-10-17T11:16:17
title: Squassh
comment: Squassh is a tool for 2D and 3D segmentation and quantification of subcellular shapes in fluorescence microscopy images. It provides globally optimal detection and segmentation of objects with constant internal intensity distribution, followed by object-based colocalization analysis. The segmentation computed by Region Competition can optionally correct for the PSF of the microscope, hence providing optimally deconvolved segmentations. Part of the mosaic suite

squirrel
type: software
has author: Culley, Siân orcid.org/0000-0003-2112-0143
has author: Henriques, Ricardo orcid.org/0000-0002-2043-5234
has DOI: nmeth.4605
has documentation: NanoJ-SQUIRREL - Manual.pdf
has documentation: Manual hosted on github
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL v3.0
has location: NanoJ-Core
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.4605
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Statistics
has topic: topic Super-resolution microscopy
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
has usage example: downloads
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1443
requires: http://biii.eu/node/38
created: 2018-12-09T17:41:11
modified: 2023-05-02T11:03:21
title: SQUIRREL
comment: NanoJ-SQUIRREL (Super-resolution Quantitative Image Rating and Reporting of Error Locations) is a software package designed for assessing and mapping errors and artefacts within super-resolution images. This is achieved through quantitative comparison with a reference image of the same structure (typically a widefield, TIRF or confocal image). SQUIRREL produces quantitative maps of image quality and resolution as well as global image quality metrics.

sr-tesseler
type: software
has author: Florian Levet, Jean-Baptiste Sibarita
has DOI: nmeth.3579
has function: operation 2945
has function: operation Cell segmentation
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv3
has location: releases
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nmeth.3579
has reference publication: SR-Tesseler Nature Methods 2015
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Super-resolution microscopy
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-07-12T13:54:11
modified: 2023-05-03T13:34:00
title: SR-Tesseler
comment: Localization-based super-resolution techniques open the door to unprecedented analysis of molecular organization. This task often involves complex image processing adapted to the specific topology and quality of the image to be analyzed. SR-Tesseler is an open-source segmentation software using Voronoï tessellation constructed from the coordinates of localized molecules. It allows precise, robust and automatic quantification of protein organization at different scales, from the cellular level down to clusters of a few fluorescent markers. SR-Tesseler is insensitive to cell shape, molecular organization, background and noise, allowing comparing efficiently different biological conditions in a non-biased manner, and perform quantifications on various proteins and cell types. SR-Tesseler software comes with a very simple and intuitive graphical user interface, providing direct visual feedback of the results and is freely available under GPLv3 license.

ssim-toolbox-icy
type: software
has author: Yoann Le Montagner
has documentation: SSIM-toolbox
has function: operation 3443
has function: operation Image validation
has implementation: http://biii.eu/taxonomy/term/4340
has location: SSIM-toolbox
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/document/1284395
has reference publication: Image quality assessment: from error visibility to structural similarity
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/880
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:44
modified: 2023-04-29T15:15:02
title: SSIM toolbox (Icy)
comment: The SSIM is an index measuring the structural similarity between two images. It is valued between -1 and 1. When two images are nearly identical, their SSIM is close to 1.

stabitissue
type: software
has author: Iván Gómez Conde, David Olivieri, Carlos Tadokoro
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPLv3
has location: stabitissue
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: journal.ppat.1003154
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2016-10-10T15:26:12
modified: 2019-10-21T08:39:40
title: StabiTissue
comment: - 2D Stabilization in each slice of the stacks in time. - 3D Stabilization intravital imaging of all the stacks (including the dimension Z) - create the videos and the stabilized images in a new folder 2701

stack-manipulation
type: software
has documentation: Stack Manipulation
has function: operation 2409
has function: operation 3096
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Stack Manipulation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T09:22:06
title: Stack Manipulation

stack-objects
type: software
has author: Sklyar Oleg
has documentation: stackObjects.html
has function: operation Feature extraction
has function: operation RBNng13hEB0CJD5VzSKqrfB
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has location: EBImage.pdf
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: stackObjects.html
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-11T13:08:41
modified: 2019-10-17T11:56:38
title: Stack Objects

stack-rotation
type: software
has documentation: Stack-Rotation
has function: operation Rotation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Stack-Rotation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/11
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:41
modified: 2019-10-17T11:40:43
title: Stack Rotation

stack-rotation-angle
type: software
has function: operation Rotation
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: Stack-Rotation-by-Angle
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/11
requires: http://biii.eu/node/438
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:43
modified: 2019-10-17T09:42:35
title: Stack Rotation by Angle

stackreg
type: software
has author: Philippe Thévenaz
has documentation: stackreg
has documentation: Documentation
has function: operation 2928
has function: operation Image registration
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has implementation: http://biii.eu/taxonomy/term/4340
has location: StackReg .java
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: thevenaz9801.html
has reference publication: 10.1109/83.650848
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic_0611
has topic: topic 3385
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/38
requires: http://biii.eu/node/915
created: 2013-10-11T13:08:43
modified: 2022-03-16T06:54:35
title: StackReg
comment: This plugin registers (= aligns, matches) a stack of image slices.

staingan
type: software
has author: Shadi Albarqouni
has function: operation R7MFwdgojfmkZ07yWbdcda0
has location: StainGAN
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: 1804.01601v1.pdf
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has topic: topic Widefield microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2018-09-27T08:48:01
modified: 2018-09-27T08:48:01
title: StainGAN
comment: A deep-learning solution for stain color normalization in digital histology images

stardist-imagej
type: software
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation Model-based segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: stardist
has location: Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 978-3-030-00934-2 30
has reference publication: Cell Detection with Star-Convex Polygons
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3385
has topic: topic 3474
has topic: topic Fluorescent microscopy
has topic: topic Light-sheet microscopy
has topic: topic RBKlmE9DGTZwEwxw0juThGg
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2020-03-03T15:07:18
modified: 2023-04-26T17:33:17
title: StarDist - ImageJ
comment: This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

statcoloc
type: software
has function: operation Colocalisation analysis
has function: operation Pixel-based colocalisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: StatColoc
has location: An image of the link a few years ago
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2023-05-02T12:06:24
title: StatColoc

statistical-region-merging
type: software
has documentation: Statistical Region Merging
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has function: operation Model-based segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Statistical Region Merging
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T13:33:44
title: Statistical Region Merging

steerablej
type: software
has author: François Aguet
has documentation: steerable
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: download.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://ieeexplore.ieee.org/document/1307008/
has reference publication: Design of Steerable Filters for Feature Detection Using Canny-Like Criteria
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-17T09:47:12
title: SteerableJ
comment: Fast edge and ridge detection, irrespective of their orientation.

stereo-viewer
type: software
has author: Delgado-Gonzalo Ricard
has documentation: Stereo-Viewer
has function: operation 2409
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Stereo-Viewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:44
modified: 2019-10-17T14:34:19
title: Stereo Viewer

stitching-2d3d
type: software
has author: Preibisch Stephan
has documentation: 3D
has function: operation Image stitching
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4340
has location: 3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 1463.pdf
has reference publication: Globally optimal stitching of tiled 3D microscopic image acquisitions
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-10-17T11:45:32
title: Stitching 2D/3D

stochastic-denoising
type: software
has author: Funke Jan
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: Stochastic Denoising
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: EstradaFleetJepsonBMVC2009.pdf
has reference publication: Stochastic Image Denoising
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:43
modified: 2019-10-17T14:18:30
title: Stochastic Denoising

strahler-analysis
type: software
has author: Tiago Ferreira
has DOI: 49399#.XadNXC2ZORs
has DOI: 10.5281/zenodo.49399
has documentation: Strahler Analysis
has documentation: documentation
has function: operation Skeletonization
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: Neuroanatomy
has location: hIPNAT_.jar
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1072
requires: http://biii.eu/node/38
requires: http://biii.eu/node/670
created: 2013-10-11T13:08:46
modified: 2023-04-27T11:07:58
title: Strahler Analysis
comment: This plugin performs Strahler analysis on topographic skeletons (2D/3D). Strahler numbering is a numerical procedure that summarizes the branching complexity of mathematical trees.

straighten
type: software
has function: operation Warping
has location: Straighten...
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: Straighten...
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T09:36:00
title: Straighten

straightenworms
type: software
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has location: straightenworms.py
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/296
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2019-10-17T11:32:26
title: StraightenWorms

substract-roi
type: software
has author: de Chaumont Fabrice
has function: operation 2409
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has location: Substract-ROI
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T08:54:44
title: Substract ROI

sumproduct
type: software
has author: Kavalerov, Ilya
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has location: sumproduct
has location: sumproduct GitHub repository
has platform: http://biii.eu/taxonomy/term/30
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: http://web4.cs.ucl.ac.uk/staff/D.Barber/pmwiki/pmwiki.php%3Fn%3DBrml.HomePage
has reference publication: Bayesian Reasoning and Machine Learning
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2019-03-15T01:54:49
modified: 2019-03-15T02:09:13
title: sumproduct
comment: An implementation of Belief Propagation for factor graphs, also known as the sum-product algorithm

super-resolution-radial-fluctuations-srrf
type: software
has author: Dylan M. Owen
has author: George Ashdown
has author: Nils Gustafsson
has author: Pedro Matos Pereira
has author: Ricardo Henriques
has author: Siân Culley
has DOI: ncomms12471
has documentation: 41467 2016 BFncomms12471 MOESM1138 ESM.zip
has documentation: User guide zip file
has function: operation Image deconvolution
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: 41467 2016 BFncomms12471 MOESM1138 ESM.zip
has location: The SRRF algorithm source code and plugin for ImageJ and Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: ncomms12471
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Super-resolution microscopy
has topic: topic Widefield microscopy
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-02-22T10:41:42
modified: 2023-05-03T09:13:20
title: Super-Resolution Radial Fluctuations (SRRF)
comment: SRRF is a high-performance analytical approach for Live-cell Super-Resolution Microscopy, provided as a fast GPU-enabled ImageJ plugin. SRRF is capable of extracting high-fidelity super-resolution information from TIRF, widefield and confocals using conventional fluorophores such as GFP. SRRF is capable of live-cell imaging over timescales ranging from minutes to hours.

sure-let-wavelet-denoising
type: software
has author: Florian Luisier, Thierry Blu
has documentation: suredenoising
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4341
has location: suredenoising
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: luisier0701.html
has reference publication: A New SURE Approach to Image Denoising: Interscale Orthonormal Wavelet Thresholding
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:41
modified: 2019-10-16T16:47:35
title: SURE-LET Wavelet Denoising
comment: This package implements the interscale orthonormal wavelet thresholding algorithm based on the SURE-LET principle. A multichannel extension is also available. Java Applets are available too.

suresim
type: software
has author: Frank Herrmannsdörfer
has author: Mike Heilemann
has author: Thomas Kuner
has author: Varun Venkataramani
has license: GNU GPLv3
has location: http://www.ana.uni-heidelberg.de/%3Fid%3D198
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: nmeth.3775
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-05T16:23:56
modified: 2018-10-19T10:43:45
title: SuReSim
comment: SuReSim (Super Resolution Simulation) is an open-source simulation software for Single Molecule Localization Microscopy (SMLM). The workflow of the SuReSim algorithm starts from a ground truth structure and lets the user choose to either directly simulate 3D localizations or to create simulated *.tiff-stacks that the user can analyze with any given SMLM reconstruction software. A 3D structure of any geometry, either taken from electron microscopy, designed de-novo from assumptions or known structural facts, is fluorophore-labeled in silico. A defined set of parameters is used to calculate and visualize the 3D localizations of the corresponding labels. The software package is accompanied with a library of model structures that can be imported and simulated. Users manual with tutorial provided.

survos
type: software
has author: Basham, Mark orcid.org/0000-0002-8438-1415
has author: Luengo, Imanol
has documentation: docs
has documentation: SuRVoS docs
has function: operation 2423
has function: operation 3553
has function: operation Image segmentation
has function: operation Interactive segmentation
has function: operation Pixel classification
has implementation: http://biii.eu/taxonomy/term/4341
has license: Apache version 2.0
has location: SuRVoS
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has reference publication: j.jsb.2017.02.007
has reference publication: SuRVoS: Super-Region Volume Segmentation workbench
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic 3474
has topic: topic R9O3HmIAjoN5IqXXXRukzzr
has topic: topic R9zg34pnGmTyzPidJj9vfJt
has topic: topic RBZsLMTdyuEDtVe2fge61l0
has topic: topic RByvmgDpAo4FOrMdvTm1gwR
has topic: topic RDCjx86atJP685sX1zrE2ia
has type: http://biii.eu/taxonomy/term/8
has usage example: https://doi.org/10.3791/56162
has usage example: Volume Segmentation and Analysis of Biological Materials Using SuRVoS (Super-region Volume Segmentation) Workbench
openess: http://biii.eu/taxonomy/term/3575
created: 2018-01-28T11:13:35
modified: 2018-10-18T15:38:19
title: SuRVoS
comment: SuRVoS: Super-Region Volume Segmentation workbench A volume is first partitioned into Super-Regions (superpixels or supervoxels) and then interactively segmented by the user providing training annotations. SuRVoS can then learn from and extend the annotations to the whole volume.

swimming-pool-emitter
type: software
has author: Dallongeville Stephane
has author: Fab and Stef
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Swimming-Pool-Emitter
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-17T14:38:15
title: Swimming Pool Emitter

swimming-pool-listener
type: software
has author: Dallongeville Stephane
has author: Fab and Stef
has documentation: Swimming-Pool-Listener
has function: operation RBNng13hEB0CJD5VzSKqrfB
has implementation: http://biii.eu/taxonomy/term/4340
has location: Swimming-Pool-Listener
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-17T10:29:56
title: Swimming Pool Listener

symmetric-exponential-b-spline
type: software
has author: Kirshner Hagai
has documentation: sym-exp-spline
has implementation: http://biii.eu/taxonomy/term/4339
has location: sym-exp-spline
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: kirshner1104.html
has reference publication: https://ieeexplore.ieee.org/document/5071184%3Farnumber%3D5071184
has reference publication: A Sampling Theory Approach for Continuous ARMA Identification
has reference publication: On the Role of Exponential Splines in Image Interpolation
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:43
modified: 2019-10-17T11:23:04
title: Symmetric Exponential B-spline

synactj
type: software
has author: Schmied Christopher
has comparison: full#supplementary-material
has comparison: https://www.frontiersin.org/articles/10.3389/fcomp.2021.777837/full#supplementary-material
has documentation: SynActJ
has function: operation Neuron image analysis
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT License
has location: SynActJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: fcomp.2021.777837
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/3568
has usage example: zenodo.5644945
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2023-03-21T13:26:40
modified: 2023-03-22T08:39:26
title: SynActJ
comment: SynActJ (Synaptic Activity in ImageJ) is an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using an R Shiny workflow.

sync-windows
type: software
has author: Hiner Mark
has author: Kelly Patrick
has author: Schindelin Johannes
has author: Walter Joachim
has documentation: Sync Windows
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Sync Windows
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2019-10-17T10:20:39
title: Sync Windows

synpanal
type: software
has author: Eric Danielson, Sang H. Lee
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL
has location: synpanal
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: journal.pone.0115298
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-11T15:42:39
modified: 2020-03-05T12:06:53
title: SynPAnal
comment: This software is designed for the rapid semi-automatic detection and quantification of synaptic protein puncta from 2D immunofluorescence images generated by confocal laser scanning microscopy.

syntax-highlighting
type: software
has location: Syntax Highlighting
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2017-09-13T10:09:46
title: Syntax Highlighting

tango-tools-analysis-nuclear-genome-organization
type: software
has author: Jean Ollion, Julien Cochennec, Christophe Escudé, François Loll, Thomas Boudier
has DOI: btt276
has documentation: https://tango.mnhn.fr/tiki-index.php%3Fpage%3DGetting%2520Started
has documentation: Tutorial
has function: operation_0337
has function: operation 3443
has function: operation Image processing
has location: https://tango.mnhn.fr/tiki-index.php%3Fpage%3DDownloads
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: btt276
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2015-02-18T13:10:05
modified: 2023-04-26T13:23:46
title: TANGO Tools for Analysis of Nuclear Genome Organization
comment: ## About TANGO software is an open-source software for Analysis of Nuclear Genome Organization. It is composed of an ImageJ plugin for batch processing and analysis, and a R package for statistical analysis. Reference: 2528 ## Some key features - Image import uses bioimage formats. - Construction of workflow in GUI by choosing filters / segmentation strategy for - Prefiltering - Segmentation - Postfiltering - Isolated nuclei could individually be inspected, deleted from list and subjected for detailed analysis. - Uses MCIB3D library as backend. - Basic usage is to segment nucleus, crop them to single nucleus objects, segment substructures within objects and measure their properties. - Optionally R can be connected to do detailed analysis of results. - Uses MongoDB to manage huge data set.

tem-exosomeanalyzer
type: software
has author: Martin Maska
has author: Pavel Matula
has documentation: exosomeanalyzer.html
has documentation: Home page
has function: operation Image segmentation
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4341
has location: TEM ExosomeAnalyzer.zip
has location: Direct link to download
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/3593
has topic: topic_0611
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
created: 2019-01-21T15:28:38
modified: 2019-01-21T15:43:53
title: TEM ExosomeAnalyzer
comment: TEM ExosomeAnalyzer is a program for automatic and semi-automatic detection of extracellular vesicles (EVs), such as exosomes, or similar objects in 2D images from transmission electron microscopy (TEM). The program detects the EVs, finds their boundaries, and reports information about their size and shape. The software has been developed in terms of project MUNI/M/1050/2013 and supported by Grant Agency of Masaryk University. The EVs are detected based on the shape and edge contrast criteria. The exact shapes of the EVs are then segmented using a watershed-based approach. With proper parameter settings, even images with EVs both lighter and darked than the background, or containing artifacts or precipitated stain can be processed. If the fully-automatic processing fails to produce the correct results, the program can be used semi-automatically, letting the user adjust the detection seeds during the intermediate steps, or even draw the whole segmentation manually.

template-matching-and-slice-alignment-imagej-plugins
type: software
has author: Qingzong TSENG
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: template-matching-ij-plugin
has location: Plugin website
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/108
requires: http://biii.eu/node/38
created: 2018-05-07T17:01:19
modified: 2018-05-09T02:08:58
title: Template Matching and Slice Alignment--- ImageJ Plugins
comment: This ImageJ plugin contains two functions. The first one is the cvMatch_Template. It implements the template matching function from the OpenCV library. The second function Align_slices in stack utilized the previous matching function to do slice registration(alignment) based on a selected landmark. For more details, refer to the page of each component. cvMatch_Template Align Slices in Stack

temporal-color-code
type: software
has author: Miura Kota
has author: Schindelin Johannes
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Temporal-Color Code
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T10:25:37
title: Temporal-Color Code

temporal-medial-filter
type: software
has author: Graeme Ball
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: IJ Temporal
has location: Part of the collection Temporal Plugin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1328
created: 2018-06-05T01:22:18
modified: 2018-06-05T01:27:06
title: Temporal Medial Filter
comment: This component can be used to find moving foreground features, which can be a powerful way to suppress false background detections in subsequent tracking steps. set time window, and standard deviations above background for foreground time window should be more than 2x larger than time taken for a feature to traverse a pixel (NB. total window is 2x half-width +1) moving foreground identified by intensity increase relative to background average (i.e. median) for a pixel over a given time window "soft" segmentation, yielding foreground probability related to excess intensity (in standard deviations) over background level crude Anscombe transform applied to data to stabilize the variance

tensorflow
type: software
has documentation: tutorials
has documentation: Get started
has function: operation Image classification
has function: operation Image enhancement
has function: operation Image segmentation
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4339
has location: install
has location: Multiplatform links to python packages
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2018-01-30T16:00:37
modified: 2023-04-28T11:57:41
title: Tensorflow
comment: "An open source machine learning framework for everyone " TensorFlow™ is an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning and the flexible numerical computation core is used across many other scientific domains.

terastitcher
type: software
has author: Bria Alessandro
has author: Iannello Giulio
has author: Onofri Leonardo
has documentation: User's-guide
has function: operation 2928
has function: operation Image registration
has function: operation Image stitching
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has implementation: http://biii.eu/taxonomy/term/4341
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-316
has reference publication: doi:10.1186/1471-2105-13-316
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3577
created: 2018-01-30T08:40:05
modified: 2018-01-30T08:49:39
title: TeraStitcher
comment: TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently visualized (e.g. Vaa3D-TeraFly) and processed.

test-java3d
type: software
has author: Schmid Benjamin
has documentation: Test Java3D
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Test Java3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:40
modified: 2019-10-17T14:31:07
title: Test Java3D

texture-analyzer-imagej
type: software
has author: Julio E. Cabrera
has documentation: texture.html
has function: operation Object detection
has function: operation Texture extraction
has implementation: http://biii.eu/taxonomy/term/4340
has location: texture.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: TexturalFeatures.pdf
has reference publication: Texture parameters for image classification
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T13:13:44
modified: 2020-03-02T20:58:20
title: Texture Analyzer (ImageJ)
comment: This plugin will return on a full 256-grey level image (limitation in this version) or on a ROI several texture features such as described in Haralick publication. Can be run in batch mode.

texture-segmentation
type: software
has author: Hervé Nicolas
has documentation: TextureSegmentation
has documentation: full documentation
has function: operation Image segmentation
has implementation: http://biii.eu/taxonomy/term/4340
has location: Texture-Segmentation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://ieeexplore.ieee.org/abstract/document/5872508
has reference publication: Statistical color texture descriptors for histological images analysis
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/467
requires: http://biii.eu/node/481
requires: http://biii.eu/node/537
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-17T14:13:05
title: Texture Segmentation

thot
type: software
has author: Briane Vincent
has author: Kervrann Charles
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: http://serpico.rennes.inria.fr/doku.php%3Fid%3Dsoftware:thot:index
has location: Link to package
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has topic: topic Statistics
has topic: topic R8oQpUEjKZjNQCTB4x3JQuJ
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2018-01-31T09:22:24
modified: 2018-10-18T15:24:57
title: THOT
comment: Classification of trajectoire: need tracking results as input and will then classify the trajectories as brownian motion, confined brownian or directed.

threeb-3b-microscopy-analysis-software
type: software
has author: Randall Division of Cell and Molecular Biophysics at the Kings College London
has documentation: 3b
has documentation: Project Website
has function: operation Image deconvolution
has function: operation R8EfungVXA0oQM2Ac7YY5eu
has implementation: http://biii.eu/taxonomy/term/4340
has location: ThreeB.zip
has location: Stable version
has platform: http://biii.eu/taxonomy/term/31
has reference publication: nmeth.2342.html
has reference publication: Nature Methods publication
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Super-resolution microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2018-09-21T11:42:45
modified: 2023-05-02T10:07:06
title: ThreeB 3B Microscopy Analysis Software
comment: Bayesian analysis of blinking and bleaching, or 3B microscopy, is a method which analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution.

thresholded-pixel-density
type: software
has author: de Chaumont Fabrice
has documentation: Thresholded-pixel-density
has function: operation Feature extraction
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: Thresholded-pixel-density
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:40
modified: 2023-04-29T14:06:44
title: Thresholded pixel density
comment: For each ROI, computes the number of pixel over a threshold. This plugin also provides the density and outputs results as an excel file.

thresholder-imagej
type: software
has documentation: Thresholding
has documentation: Fiji Documentation (Links to ImageJ documentation)
has function: operation Image segmentation
has function: operation Image thresholding
has implementation: http://biii.eu/taxonomy/term/4340
has location: source
has location: Threshold.java source code, go to ij.plugin package and Thresholder java file
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2019-02-25T12:04:49
modified: 2019-02-25T13:53:19
title: Thresholder (ImageJ)

thunderstorm
type: software
has author: G. M. Hagen
has author: J. Borkovec
has author: M. Ovesný
has author: P. Krízek
has author: Z. vindrych
has function: operation_0337
has function: operation 3443
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: thunderstorm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Super-resolution microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-10-04T12:15:29
modified: 2020-03-05T15:36:53
title: ThunderSTORM
comment: ThunderSTORM is an open-source, interactive, and modular plug-in for ImageJ designed for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. Our philosophy in developing ThunderSTORM has been to offer an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data.

time-stamper
type: software
has author: White Daniel James
has documentation: Time Stamper
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: Time Stamper
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T14:22:39
title: Time Stamper

timestamp-overlay
type: software
has author: Dufour Alexandre
has author: de Chaumont Fabrice
has documentation: TimeStamp-Overlay
has function: operation 3553
has implementation: http://biii.eu/taxonomy/term/4340
has location: TimeStamp-Overlay
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:46
modified: 2019-10-17T10:15:48
title: TimeStamp Overlay

timp
type: software
has author: Sergey Laptenok
has documentation: v018i08
has license: GPLv3
has location: v018i08
has location: Code is provided as supplementary to the paper
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has reference publication: v018i08
has reference publication: 2007. Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP. Journal of Statistical Software. 18:1–20.
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1152
created: 2017-09-14T08:15:16
modified: 2018-05-29T00:56:59
title: TIMP
comment: A complete package for fluorescence lifetime analysis implemented as an R package with sample data.

tissue-analysis-histological-sections
type: software
has author: Sébastien Tosi
has function: operation Pixel classification
has location: image-j-fiji#h.p fu3UP-9ubsE6
has location: TrainableWekaMacro macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic 3474
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/3568
has usage example: image-j-fiji#h.p fu3UP-9ubsE6
has usage example: User guide - Trainable WEKA Segmentation batch processing
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/324
requires: http://biii.eu/node/79
created: 2014-12-08T14:16:23
modified: 2023-04-28T14:08:23
title: Tissue analysis from histological sections
comment: This macro batch processes all the 2D images (tif and jpg files) located in a user defined folder by calling Fiji Weka trainable segmentation to classify each pixel, and reports the areas of each class in a human readable results table. The classifier to be applied to each image should be previously trained on a representative image by an expert and exported to file (Save classifier) into the image folder to be processed.

tissue-cell-segmentation
type: software
has author: Sébastien Tosi
has function: operation Image segmentation
has function: operation Watershed
has location: image-j-fiji#h.p Omc27ZTInjJP
has location: Tissue Cell Geometry Stats macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p Omc27ZTInjJP
has usage example: User guide - Automated Multicellular Tissue Analysis
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T12:06:19
modified: 2023-04-28T14:04:24
title: Tissue Cell Segmentation
comment: This macro is meant to segment the cells of a multicellular tissue. It is written for images showing highly contrasted and uniformly stained cell membranes. The geometry of the cells and their organization is automatically extracted and exported to an ImageJ results table. This includes: Cell area, major, minor fitted ellipse radii + major axis orientation and number of neighbors of the cells. Manual correction of the automatic segmentation is supported (merge split cells, split merged cells). Sample image data is available in the documentation page.

topoj
type: software
has author: Hovis David
has documentation: TopoJ
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has location: TopoJ
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T11:38:15
title: TopoJ

tracing-data-using-palmsiever
type: software
has author: Thomas Pengo
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/76
created: 2014-12-09T14:46:25
modified: 2017-09-12T18:02:42
title: Tracing data using PALMsiever
comment: Tracer allows the user to create a trace along a structure in an image. It uses the underlying molecule positions, not the rendered image.

track-cell-intensity
type: software
has author: Alexandre Dufour
has documentation: Track cell intensity
has documentation: Track_cell_intensity
has function: operation Active contours
has function: operation Cell tracking
has location: http://icy.bioimageanalysis.org/repository/getProtocolFile%3FprotocolId%3D16%26version%3D2
has location: ICY protocol
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3595
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
created: 2014-12-09T10:01:23
modified: 2018-05-14T23:25:12
title: Track cell intensity
comment: Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

track-manager
type: software
has author: Fabrice de Chaumont
has documentation: track-manager
has documentation: Documentation
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: http://icy.bioimageanalysis.org/download-file/%3Fid%3D65846
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/651
requires: http://biii.eu/node/654
requires: http://biii.eu/node/741
requires: http://biii.eu/node/814
requires: http://biii.eu/node/815
requires: http://biii.eu/node/82
requires: http://biii.eu/node/837
requires: http://biii.eu/node/855
requires: http://biii.eu/node/861
requires: http://biii.eu/node/864
requires: http://biii.eu/node/871
requires: http://biii.eu/node/977
created: 2013-10-11T13:08:46
modified: 2019-10-17T08:22:59
title: Track Manager
comment: The track manager enables the use of DSP-like trackProcessors. This can affect the display of tracks, selection in time or by ROIs, and also compute some views like the overlaid and animated local flow graph, polar graph.

track-processor-color
type: software
has author: Fabrice de Chaumont
has documentation: track-processor-color
has documentation: Documentation
has function: operation_0337
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: http://icy.bioimageanalysis.org/download-file/%3Fid%3D14216
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/82
requires: http://biii.eu/node/861
requires: http://biii.eu/node/977
created: 2013-10-11T13:08:46
modified: 2019-10-17T08:24:59
title: Track Processor Color
comment: Track Processor to color tracks in the Track Manager

track-processor-display-track-number
type: software
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-Display-Track-Number
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
requires: http://biii.eu/node/977
created: 2013-10-11T13:08:46
modified: 2019-10-17T09:38:52
title: Track Processor Display Track Number

track-processor-export-track-excel
type: software
has documentation: Track-Processor-export-track-to-Excel
has function: operation 2409
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-export-track-to-Excel
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
requires: http://biii.eu/node/977
created: 2013-10-11T13:08:46
modified: 2019-10-17T12:33:39
title: Track Processor export track to Excel

track-processor-flow
type: software
has author: Fabrice de Chaumont
has documentation: Track-Processor-Flow
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-Flow
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:46
modified: 2019-10-17T10:00:55
title: Track Processor Flow

track-processor-instant-speed
type: software
has author: Fabrice de Chaumont
has documentation: track-processor-instant-speed
has documentation: Documentation
has function: operation Image tracking
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has license: GpLv3
has location: http://icy.bioimageanalysis.org/download-file/%3Fid%3D65814
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic 3385
has topic: topic RL4rPCXlIu9uzNrGcbcSNp
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/736
requires: http://biii.eu/node/741
requires: http://biii.eu/node/861
requires: http://biii.eu/node/977
created: 2013-10-11T13:08:46
modified: 2019-10-17T08:21:20
title: Track Processor Instant Speed
comment: This display the Instant Speed of tracks for the Icy Track Manager.

track-processor-intensity-profile
type: software
has author: Nicolas Chenouard
has documentation: track-processor-intensity-profile
has documentation: Documentation
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: http://icy.bioimageanalysis.org/download-file/%3Fid%3D15033
has location: Download
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/741
requires: http://biii.eu/node/82
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:46
modified: 2019-10-16T17:40:55
title: Track Processor Intensity Profile
comment: A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.

track-processor-msd
type: software
has author: de Chaumont Fabrice
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-MSD
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:46
modified: 2019-10-17T13:51:52
title: Track Processor MSD

track-processor-roi-gate
type: software
has author: de Chaumont Fabrice
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-ROI-Gate
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:44
modified: 2019-10-18T08:58:11
title: Track Processor ROI Gate

track-processor-speed-profiler
type: software
has location: Track Processor Speed Profiler
has location: http://icy.bioimageanalysis.org/plugin/Track-Processor-Speed-Profiler ?
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:44
modified: 2019-10-17T15:13:16
title: Track Processor Speed Profiler

track-processor-time-clip
type: software
has author: de Chaumont Fabrice
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-Time-Clip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:44
modified: 2019-10-17T14:07:05
title: Track Processor Time Clip

track-processor-track-length
type: software
has documentation: Track-Processor-Track-Length
has function: operation Trajectory analysis
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-Track-Length
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:44
modified: 2019-10-17T10:10:56
title: Track Processor Track Length

track-processor-z-clip
type: software
has author: Dufour Alexandre
has author: Pop Sorin
has documentation: Track-Processor-Z-Clip
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-Z-Clip
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:44
modified: 2019-10-17T12:13:27
title: Track Processor Z Clip

track-processor-zero-origin
type: software
has documentation: Track-Processor-Zero-Origin
has implementation: http://biii.eu/taxonomy/term/4340
has location: Track-Processor-Zero-Origin
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:46
modified: 2023-04-29T15:26:03
title: Track Processor Zero Origin
comment: Translate the tracks so that first detection is at 0,0,0 location.

tracking-focal-adhesions-2d-time-lapse-movies
type: software
has author: A.S. SECHI
has author: I. GAMPER
has author: T. AACH
has author: T. WÜRFLINGER
has function: operation Image segmentation
has function: operation Image tracking
has reference publication: j.1365-2818.2010.03404.x
has reference publication: WÜRFLINGER et. al. (2011) Automated segmentation and tracking for large‐scale analysis of focal adhesion dynamics
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2014-12-08T14:19:05
modified: 2023-05-03T14:30:37
title: Tracking of focal adhesions in 2D time lapse movies
comment: Tracking of focal adhesions includes a number of challenges: Detection of focal adhesion regions in areas of highly variable background Separation of "clumped" adhesions in different objects. Dynamics: Focal adhesions dynamically, grow, shrink, change their shape, they can fuse with neighboring adhesions or one adhesion can be split into multiple children. Würflinger et al (2011) describe how to detect focal adhesion objects and how to track them over time. Interestingly, tracking results are fed back to segmentation to improve separation of clumped adhesions. The authors implemented the workflow in Matlab, but do not provide a ready-to-use script.

tracking-performance-measures
type: software
has documentation: Tracking-Performance-Measures
has function: operation 2945
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: Tracking-Performance-Measures
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: http://www.ncbi.nlm.nih.gov/pubmed/24441936
has reference publication: Objective Comparison of Particle Tracking Methods
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/741
requires: http://biii.eu/node/8
requires: http://biii.eu/node/861
created: 2013-10-11T13:08:46
modified: 2023-04-29T15:03:41
title: Tracking Performance Measures

tracking20
type: software
has author: Paul-Gilloteaux Perrine
has documentation: Trackingv2.0.zip
has documentation: Step by step help Pdf insite the .zip
has function: operation Image tracking
has function: operation Particle tracking
has implementation: http://biii.eu/taxonomy/term/4340
has location: Trackingv2.0.zip
has location: Download link
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: 306
has usage example: Worflow using this plugin
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1310
requires: http://biii.eu/node/38
created: 2018-05-24T01:29:54
modified: 2019-08-30T16:27:00
title: Tracking2.0
comment: This method was originally designed to track objects (not necessarily spots) already identified in 2D frames and has been applied previously to particle tracking and analysis in high-speed atomic force microscopy image series.

trackmate
type: software
has author: Jean-Yves Tinevez
has documentation: TrackMate-manual.pdf
has documentation: Manual
has function: operation Particle tracking
has function: operation Spot extraction
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: TrackMate
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: j.ymeth.2016.09.016
has reference publication: Tinevez et. al. (2017) TrackMate: An open and extensible platform for single-particle tracking
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:40
modified: 2019-10-17T08:27:18
title: TrackMate
comment: TrackMate provides the tools to perform single particle tracking (SPT). SPT is an image analysis challenge where the goal is to segment and follow over time some labeled, spot-like structures. Each spot is segmented in multiple frames and its trajectory is reconstructed by assigning it an identity over these frames, in the shape of a track. These tracks can then be either visualized or yield further analysis results such as velocity, total displacement, diffusion characteristics, division events, etc...

trackobjects
type: software
has documentation: TrackObjects.html
has documentation: TrackObjects module
has function: operation Image tracking
has location: trackobjects.py
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:41
modified: 2019-10-17T13:47:27
title: TrackObjects

trainable-weka-segmentation
type: software
has author: Johannes Schindelin
has author: Albert Cardona
has author: Ignacio Arganda-Carreras
has author: Verena Kaynig
has documentation: Trainable Weka Segmentation
has function: operation 3553
has function: operation Image segmentation
has function: operation Pixel classification
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: Trainable Segmentation
has location: Releases in the Github repo
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: 10.1093/bioinformatics/btx180
has reference publication: Arganda-Carreras et al (2017) Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:40
modified: 2023-04-28T12:12:44
title: Trainable Weka Segmentation
comment: The Trainable Weka Segmentation is a Fiji plugin that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations. Weka (Waikato Environment for Knowledge Analysis) can itself be called from the plugin. It contains a collection of visualization tools and algorithms for data analysis and predictive modeling, together with graphical user interfaces for easy access to this functionality. As described on their wikipedia site, the advantages of Weka include: - freely availability under the GNU General Public License - portability, since it is fully implemented in the Java programming language and thus runs on almost any modern computing platform - a comprehensive collection of data preprocessing and modeling techniques - ease of use due to its graphical user interfaces - Weka supports several standard data mining tasks, more specifically, data preprocessing, clustering, classification, regression, visualization, and feature selection. The main goal of this plugin is to work as a bridge between the Machine Learning and the Image Processing fields. It provides the framework to use and, more important, compare any available classifier to perform image segmentation based on pixel classification.

trakem2
type: software
has author: Albert Cardona
has author: Curtis Rueden
has author: Stephan Saalfeld
has documentation: TrakEM2
has documentation: Documentation
has function: operation 2928
has function: operation 3553
has function: operation Feature extraction
has function: operation Image registration
has function: operation Image stitching
has function: operation Image visualisation
has function: operation R3BGvVm77d5vFMF6f28ZiW
has function: operation R8ANfLkuHu47r739AkhxrId
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: trakem2.html
has location: TrakEM2
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: journal.pone.0038011
has reference publication: 10.1371/journal.pone.0038011
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/601
created: 2013-10-11T13:08:44
modified: 2022-03-16T06:26:03
title: TrakEM2
comment: TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets.

trakem2-lens-distortion-correction
type: software
has author: Saalfeld Stephan orcid.org/0000-0002-4106-1761
has function: operation Geometrical transform
has function: operation Warping
has function: operation R3BGvVm77d5vFMF6f28ZiW
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: confocal-lens
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/8
has usage example: https://www.youtube.com/watch%3Fv%3DlPt-WQuniUs
has usage example: Multi-color lens distortion and shift correction
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/663
requires: http://biii.eu/node/79
created: 2018-01-28T11:38:33
modified: 2018-05-22T00:35:10
title: Trakem2 lens distortion correction
comment: Calculates and corrects for lens-distortion models including chromatic abberation from confocal stacks.

transform-virtual-stack-slices
type: software
has author: Albert Cardona
has author: Ignacio Arganda-Carreras
has author: Stephan Saalfeld
has documentation: Transform Virtual Stack Slices
has function: operation Geometrical transform
has function: operation R9Vc5BV3ZMcLHEL6WEceXbY
has implementation: http://biii.eu/taxonomy/term/4340
has location: Transform Virtual Stack Slices
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-18T14:02:41
title: Transform Virtual Stack Slices

transformj
type: software
has author: Erik Meijering
has function: operation Geometrical transform
has function: operation R8ANfLkuHu47r739AkhxrId
has implementation: http://biii.eu/taxonomy/term/4340
has location: transformj
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2015-01-03T04:46:05
modified: 2019-10-29T17:20:54
title: TransformJ
comment: A Java Package for Geometrical Image Transformation, works up to 5D. - Affine - Crop - Embed - Matrix - Mirror - Rotate - Scale - Translate - Turn

tremap
type: software
has author: Liu,, Xiaoxiao
has author: Long, Brian
has author: Peng, Hanchuan (http://orcid.org/0000-0002-3478-3942)
has author: Zhou, Zhi
has comparison: s12021-015-9278-1
has comparison: TReMAP: Automatic 3D Neuron Reconstruction Based on Tracing, Reverse Mapping and Assembling of 2D Projections
has function: operation Image thresholding
has function: operation Neuron image analysis
has function: operation R9Qf06vxvFj2UbAk7pW3IMG
has implementation: http://biii.eu/taxonomy/term/4340
has license: MIT License
has location: bigneuron zz neurontracing TReMAP
has location: TReMAP Plugin Github repository in Vaa3D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: s12021-015-9278-1
has reference publication: TReMAP: Automatic 3D Neuron Reconstruction Based on Tracing, Reverse Mapping and Assembling of 2D Projections
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has type: http://biii.eu/taxonomy/term/8
has usage example: s12021-015-9278-1
has usage example: TReMAP: Automatic 3D Neuron Reconstruction Based on Tracing, Reverse Mapping and Assembling of 2D Projections
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/62
created: 2017-09-12T00:57:12
modified: 2018-04-11T10:38:22
title: TReMAP
comment: "we present a new fully automated 3D reconstruction algorithm, called TReMAP, short for Tracing, Reverse Mapping and Assembling of 2D Projections. Instead of tracing a 3D image directly in the 3D space as seen in majority of the tracing methods, we first trace the 2D projection trees in 2Dplanes, followed by reverse-mapping the resulting 2D tracing results back into the 3D space as 3D curves; then we use a minimal spanning tree (MST) method to assemble all the 3D curves to generate the final 3D reconstruction. Because we simplify a 3D reconstruction problem into 2D, the computational costs are reduced dramatically." Suitable for high throughput neuron image analysis (image sizes >10GB). This plugin can be used with default parameters or user-defined parameters.

ttk-topology-toolkit
type: software
has function: operation_0337
has function: operation 2945
has function: operation Clustering
has implementation: http://biii.eu/taxonomy/term/4341
has license: BSD
has location: downloads.html
has location: download ttk
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: ttk.pdf
has reference publication: The Topology Toolkit J. Tierny, G. Favelier, J. Levine, C. Gueunet, M. Michaux. IEEE Transactions on Visualization and Computer Graphics.
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Statistics
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1389
created: 2018-11-23T08:10:32
modified: 2018-11-23T08:15:51
title: TTK the Topology Toolkit
comment: The Topology ToolKit (TTK) is an open-source library and software collection for topological data analysis in scientific visualization. TTK can handle scalar data defined either on regular grids or triangulations, either in 2D or in 3D. It provides a substantial collection of generic, efficient and robust implementations of key algorithms in topological data analysis. It includes: · For scalar data: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, topological simplification; · For bivariate scalar data: fibers, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces; · For uncertain scalar data: mandatory critical points; · For time-varying scalar data: critical point tracking; · For high-dimensional / point cloud data: dimension reduction; · and more! TTK makes topological data analysis accessible to end users thanks to easy-to-use plugins for the visualization front end ParaView. Thanks to ParaView, TTK supports a variety of input data formats. TTK is written in C++ but comes with a variety of bindings (VTK/C++, Python) and standalone command-line programs. It is modular and easy to extend. We have specifically developed it such that you can easily write your own data analysis tools as TTK modules.

tube-un-winder
type: software
has author: Sébastien Tosi
has function: operation Projection
has location: image-j-fiji#h.p aUjb4MQ qAni
has location: TubeUnwinder macro
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p aUjb4MQ qAni
has usage example: User guide - Tube unfolder
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2014-12-08T14:26:31
modified: 2023-04-28T14:05:49
title: Tube un-winder
comment: This macro can be used to un-wide a tubular structure and flatten its surface (like peeling of and flattening the skin of a banana). The macro can only process a single channel 3D stack but it is easy to process multiple channels by exporting and importing ROI manager selections. Technically the macro computes the radial average intensity projection inside a ring centred on the radial symmetry axis of the object. The final image is a radial mapping of the intensity (radial angle along X, axial length along Y). The example image is available in the documentation link.

tubeness
type: software
has author: Johannes Schindelin
has author: Mark Longair
has author: Stephan Preibisch orcid.org/0000-0002-0276-494X
has documentation: tubeness
has function: operation Object detection
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: tubeness
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: https://www.ncbi.nlm.nih.gov/pubmed/10646760
has reference publication: Sato Y, Nakajima S, Shiraga N, Atsumi H, Yoshida S, Koller T, Gerig G, Kikinis R. 1998. Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images.. Med Image Anal. 2(2):143-68.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-13T13:27:04
modified: 2019-10-21T09:10:09
title: Tubeness
comment: This plugin filters a 3D image stack (or 2D image) to produce a score for how "tube-like" each point in the image is. This is useful as a preprocessing step for tracing neurons or blood vessels, for example. For 3D image stacks, the plugin uses the eigenvalues of the Hessian matrix to calculate this measure of "tubeness", using a metrics mentioned in Sato et al 1997 ¹: if the larger two eigenvalues (λ₂ and λ₃) are both negative then value is √(λ₂λ₃), otherwise the value is 0. For 2D images, if the large eigenvalue is negative, we return its absolute value and otherwise return 0. This plugin is now bundled as part of Fiji.

turboreg
type: software
has author: Philippe Thévenaz
has documentation: turboreg
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4340
has location: turboreg
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: thevenaz9801.html
has reference publication: 10.1109/83.650848
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-17T09:28:33
title: TurboReg
comment: The purpose of this plugin is to register—in other words, to align or to match—two images, one of them being called the source image and the other the target image.

turtleseg-3d-image-segmentation-software
type: software
has function: operation Interactive segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has license: commercial
has location: www.turtleseg.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
created: 2016-10-25T12:56:48
modified: 2019-11-13T11:58:11
title: TurtleSeg: 3D Image Segmentation Software
comment: TurtleSeg is an interactive 3D image segmentation tool. TurtleSeg has an automated system, Spotlight, for automatically directing the user towards the next steps. Typically, a user loads a 3D image and then manually contour a sparse number of slices, the full 3D segmentation can then be built automatically.

u-track
type: software
has author: Danuser's Lab
has author: LCCB
has documentation: Readme u-track.pdf
has documentation: Documentation
has function: operation_0337
has function: operation Cell tracking
has function: operation Particle tracking
has function: operation RLtOI0poPsYRHzgXbAcr2E
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has license: GPL
has location: u-track
has location: github
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Microscopy
has topic: topic Fluorescence lifetime imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/469
requires: http://biii.eu/node/89
created: 2013-10-21T11:52:50
modified: 2023-05-03T08:43:09
title: u-track
comment: u-track is a multiple-particle tracking Matlab software that is designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events. Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution. Data can be read using bio-format and interfaced with OMero data base. It comes as a standalone software, but can be used as a library, which is according to the authors the most widely used version of it. Version 2.2 adds parallel processing functionality for multi-movie datasets when using the GUI. Version 2.1 enables the analysis of movies stored on an OMERO server Version 2.0 includes two new tracking applications: microtubule plus-end tracking (previously distributed as plusTipTracker) and nuclei tracking A third optional processing step has been added to the analysis workflow, track analysis, with two methods: motion analysis and microtubule plus-end classification For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008). Besides basic particle tracking, the software supports the features described in Applegate et al. J. Struct. Biol. 176(2):168-84. 2011 for tracking microtubule plus end markers; and in Ng et al. J. Cell Biol. 199(3):545-63. 2012 for tracking fluorescently-labeled cell nuclei.

uneven-illumination-correction
type: software
has author: Tutorial under ImageJ: Gabriel Landini
has function: operation Illumination correction
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
requires: http://biii.eu/node/38
created: 2014-12-08T17:11:30
modified: 2018-01-31T15:37:07
title: Uneven illumination correction
comment: Illumination correction is often important for both accurate segmentation and for intensity measurements. This example shows how the CorrectIlluminationCalculate and CorrectIlluminationApply modules are used to compensate for the non-uniformities in illumination often present in microscopy images.

unifying-parametric-framework-2d-steerable-wavelet-transforms
type: software
has author: Nicolas Chenouard
has author: Zsuzsanna Püspöki
has function: operation Image processing
has function: operation RBYLqCqN4rP7Jy5m5mxpTeM
has location: circular-wavelets
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: puespoeki1502.html
has reference publication: Template-Free Wavelet-Based Detection of Local Symmetries
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:46
modified: 2019-11-15T12:56:07
title: A Unifying Parametric Framework for 2D Steerable Wavelet Transforms
comment: A complete parametric framework and set of MATLAB tools for computing steerable wavelet frames in 2-D.

untangleworms
type: software
has location: UntangleWorms.html
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/31
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:32
title: UntangleWorms
comment: C.elegans will often lie next to each other or cross, forming a tangle of worms in an image. This module will segment them, based on a model, to untangle the individual worms so that they can be treated as if they did not overlap.

untile-ebimage
type: software
has documentation: EBImage.pdf
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4339
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4236
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1128
created: 2013-10-15T10:45:51
modified: 2020-03-03T10:11:27
title: untile (EBImage)

unwarpj
type: software
has author: Carlos Óscar Sánchez Sorzano
has author: Michael Unser
has author: Philippe Thévenaz
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has location: UnwarpJ
has reference publication: sorzano0501.pdf
has reference publication: Elastic Registration of Biological Images Using Vector-Spline Regularization
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:46
modified: 2019-10-18T13:13:38
title: UnwarpJ

update-fiji
type: software
has author: Curtis Rueden
has author: Johannes Schindelin
has documentation: Updater
has implementation: http://biii.eu/taxonomy/term/4340
has license: BSD-2
has location: Update Fiji
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
requires: http://biii.eu/node/94
created: 2013-10-11T13:08:41
modified: 2019-10-17T16:22:00
title: Update Fiji
comment: The purpose of the ImageJ Updater is to keep you up-to-date with all components of ImageJ (or Fiji), i.e. the macros, scripts, plugins and the core components (libraries) needed by the plugins. As of 2011, the ImageJ Updater can handle 3rd-party update sites, i.e. anybody can set up their own update site which users can follow.

upload-sample-image
type: software
has author: Johannes Schindelin
has location: Upload Sample Image
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:41
modified: 2023-05-03T14:15:04
title: Upload Sample Image
comment: It is used to upload a file (not just images) meant for the ImageJ developers. You might need to do this e.g. when the file is too large for email attachments, or when you want to accompany a bug report with a large image. To prevent abuse of this facility, access to the uploaded images is restricted to trusted admins.

using-imagej-analyze-size-shape-and-directionality-networks-coupled-astrocytes
type: software
has author: Steven Condamine, Dorly Verdier, Arlette Kolta.
has documentation: PMC6235419
has function: operation Feature extraction
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: PMC6235419
has reference publication: Analyzing the Size, Shape, and Directionality of Networks of Coupled Astrocytes
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/79
created: 2019-06-21T11:46:00
modified: 2023-04-29T21:24:16
title: Using ImageJ to Analyze the Size, Shape, and Directionality of Networks of Coupled Astrocytes
comment: The research goal of this paper was to provide unbiased counts of labeled astrocytes and to estimate the area they cover, further to develop tools for defining the orientation of coupling within astrocyte networks under different stimuli. In order to count the astrocytes and estimate the area they cover the following steps were used in this software. Pre-processing: z-project (using max intensity); split channels; subtract background; remove outliers. Segmentation: adjust threshold and convert to a binary file; Watershed. Cell counting: Analyze particles Measure Astrocytic network area: select a ROI using the polygon tool; set measurements (area); ROI manager -> add the traced polygon; measure.

using-script-editor
type: software
has author: Johannes Schindelin
has author: Sumit Dubey
has documentation: Using the Script Editor
has function: operation 3096
has location: Using the Script Editor
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-18T14:40:53
title: Using the Script Editor

v3dlib
type: software
has license: -
has location: viewing-3d-images-with-v3dlib.html
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2013-11-07T20:29:12
modified: 2017-09-12T18:05:35
title: v3dlib
comment: v3dlib library is a cross-platform C++ library written in wxWidgets for displaying 3D images. The most important part of the library is a window that can display 3D images of various types (RGB, RGB16, GRAY8, GRAY16, and float). The window can easily be extended of a new functionality and is used in many applications (e.g., viewer3d, Acquiarium, batchcrop, and others).

vaa3d
type: software
has author: Fuhui Long
has author: Hanchuan Peng (http://orcid.org/0000-0002-3478-3942)
has author: Zongcai Ruan
has documentation: Vaa3D Wiki
has function: operation_0226
has function: operation_0337
has function: operation 2409
has function: operation Cell segmentation
has function: operation Image registration
has implementation: http://biii.eu/taxonomy/term/4341
has license: MIT License
has location: Vaa3D-Wiki
has location: Vaa3D Wiki
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: nbt.1612.html
has reference publication: V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Statistics
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/321
requires: http://biii.eu/node/601
requires: http://biii.eu/node/62
requires: http://biii.eu/node/92
created: 2017-09-12T00:02:42
modified: 2023-05-03T14:52:33
title: Vaa3D
comment: Vaa3D is a handy, fast, and versatile 3D/4D/5D Image Visualization and Analysis System for Bioimages and Surface Objects. It also provides many unique functions that you may not find in other software. It is Open Source, and supports a very simple and powerful plugin interface and thus can be extended and enhanced easily. Vaa3D is cross-platform (Mac, Linux, and Windows). This software suite is powerful for visualizing large- or massive-scale (giga-voxels and even tera-voxels) 3D image stacks and various surface data. Vaa3D is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes Vaa3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, Vaa3D streamlines the workflow of visualization-assisted analysis. Vaa3D can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales... it comes with a number of plugins and toolboxes. Importantly, you can now write your own plugins to take advantage of the Vaa3D platform, possibly within minutes!

variational-algorithms-remove-stationary-noise
type: software
has author: Fehrenbach Jérôme
has author: Lorenzo Corinne
has author: Weiss Pierre
has documentation: Documentation VSNR V2 Fiji.pdf
has function: operation RDyyXyhf1oHK93opXhEnRND
has implementation: http://biii.eu/taxonomy/term/4340
has location: PageCodes.html
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: TIP.2012.2206037
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: ImagesTest.zip
openess: http://biii.eu/taxonomy/term/3575
created: 2014-12-09T14:54:02
modified: 2023-05-02T17:09:43
title: Variational algorithms to remove stationary noise
comment: Variational algorithms to remove stationary noise. Application to microscopy imaging. This plugin allows to denoise images degraded with stationary noise. Stationary noise can be seen as a generalization of the standard white noise. Typical applications of this plugin are: - Standard white noise denoising using a total variation and fidelity term minimization. Even though total variation denoising is not the state of the art (regarding SNR improvement), it may be very valuable for further tasks such as image seg- mentation). - Destriping (the problem that motivated us to develop these ideas). - Deconvolution (even though most users won't be able to use this feature). - Cartoon + texture decomposition which might be useful to compress images, analyse textures or simplify segmentation like tasks.

vascusynth
type: software
has author: Hamarneh, Ghassan
has author: Jassi, Preet
has documentation: j0ws9u
has documentation: VascuSynth: Vascular Tree Synthesis Software
has function: operation RDFFD5jBfUw74a3vJeBAGB1
has implementation: http://biii.eu/taxonomy/term/4341
has location: vascusynth.cs.sfu.ca
has location: VascuSynth website
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: j.compmedimag.2010.06.002
has reference publication: VascuSynth: Simulating Vascular Trees for Generating Volumetric Image data with Ground Truth Segmentation and Tree Analysis
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1468
requires: http://biii.eu/node/92
created: 2019-02-28T08:44:33
modified: 2023-04-26T13:27:25
title: VascuSynth
comment: VascuSynth is an ITK-based synthetic image generator. It synthesizes volumetric images of vascular trees and generates a .gxl file of the ground-truth tree structure. VascuSynth receives a number of .txt configuration files and is capable of generating both ground truth ('ideal') images and images with added noise. The user is capable of choosing from a set simple noise additions and artefacts.

vast-lite
type: software
has author: Berger Daniel R.
has DOI: fncir.2018.00088
has documentation: VAST Lite V1 3 0 RC1 Manual.pdf
has documentation: User guide
has function: operation_0226
has function: operation 3553
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4341
has location: vast
has location: VAST Lite Download Page
has platform: http://biii.eu/taxonomy/term/31
has reference publication: full
has reference publication: Paper
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic Microscopy
has topic: topic R9zg34pnGmTyzPidJj9vfJt
has topic: topic RByvmgDpAo4FOrMdvTm1gwR
has type: http://biii.eu/taxonomy/term/3567
has usage example: Series of video tutorials
openess: http://biii.eu/taxonomy/term/3576
created: 2020-03-01T14:56:22
modified: 2023-04-26T10:33:25
title: VAST Lite
comment: VAST (Volume Annotation and Segmentation Tool) is a utility application for manual annotation of large EM stacks. General labeling tool, used for a large variety of 3D data sets; electron-microscopic, multi-channel light-microscopic, and Micro-CT data sets as well as videos, and annotating arbitrary structures, regions and locations, depending on the user’s needs.

vib-protocol
type: software
has author: Benjamin Schmid
has author: Johannes Schindelin
has author: Mark Longair
has function: operation 2928
has license: GPLv3
has location: VIB Protocol
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/923
created: 2013-10-11T13:08:46
modified: 2019-10-18T12:33:04
title: VIB Protocol

vibe-z
type: software
has author: Olaf Ronneberger
has function: operation Image registration
has function: operation RCPVGO34XrwrJasQ5yWBg9k
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: vibez.informatik.uni-freiburg.de
has reference publication: nmeth.2076
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has topic: topic Rn8MnorStmqIkNlAVZWBc0
has topic: topic Multimodal imaging
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2016-10-17T10:11:19
modified: 2021-05-19T18:55:45
title: ViBE-Z
comment: The Virtual Brain Explorer (ViBE-Z) is a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. It automatically detects 14 predefined anatomical landmarks for aligning data. It also offers a database and atlas. The ViBE-Z database, atlas and software are provided via a web interface. A data preparation step is needed in order to provide the right input data and format.

video-importer
type: software
has location: video-importer-deprecated
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/364
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:41
modified: 2019-10-18T13:10:07
title: Video Importer

view5d
type: software
has author: Jean-Yves Tinevez
has author: Rainer Heintzmann
has function: operation Image visualisation
has implementation: http://biii.eu/taxonomy/term/4340
has location: View5D
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2013-10-11T13:08:44
modified: 2019-10-18T14:10:27
title: View5D

vigra
type: software
has author: Ullrich Koethe and many contributors
has documentation: Tutorial.html
has function: operation 2990
has function: operation Geometrical transform
has function: operation Morphological operations
has function: operation Texture extraction
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4339
has license: MIT
has location: vigra
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2013-10-11T14:51:29
modified: 2019-03-11T00:52:03
title: VIGRA
comment: VIGRA is a free C++ and Python library that provides fundamental image processing and analysis algorithms. Its generic architecture allows it to be used in many different application contexts and ecosystems. It is designed as an intelligent library (using the C++ template mechanism) which allows users to write code at a fairly high level of abstraction and optimizes away the abstraction overhead upon compilation. It can therefore work efficiently on very large data and forms the basis of [ilastik](https://www.ilastik.org/) and [CellCognition](https://cellcognition-project.org/). **Strengths**: open source, high quality algorithms, unlimited array dimension, arbitrary pixel types and number of channels, high speed, well tested, very flexible, easy-to-use Python bindings, support for many common file formats (including HDF5) **Limitations**: no GUI, C++ not suitable for everyone, BioFormats not supported, parallelization requires external control **Images and Multi-dimensional Arrays**: templated image data structures for arbitrary pixel types, fixed-size vectors multi-dimensional arrays for arbitrary high dimensions pre-instantiated images with many different scalar and vector valued pixel types (byte, short, int, float, double, complex, RGB, RGBA etc.) 2-dimensional image iterators, multi-dimensional iterators for arbitrary high dimensions, adapters for various image and array subsets **input/output of many image file formats**: Windows BMP, GIF, JPEG, PNG, PNM, Sun Raster, TIFF (including 32bit integer, float, and double pixel types and multi-page TIFF), Khoros VIFF, HDR (high dynamic range), Andor SIF, OpenEXR input/output of images with transparency (alpha channel) into suitable file formats. comprehensive support for HDF5 (input/output of arrays in arbitrary dimensions) **continuous reconstruction of discrete images using splines**: Just create a SplineImageView of the desired order and access interpolated values and derivative at any real-valued coordinate. **I…

visiopharm
type: software
has author: Visiopharm
has license: Commercial
has location: www.visiopharm.com
has platform: http://biii.eu/taxonomy/term/31
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/286
created: 2014-12-09T16:47:25
modified: 2017-09-13T10:15:53
title: Visiopharm
comment: The software is designed for pathologists. Image analysis protocols are built from graphical user interfaces; there is no need for programming experience or an extensive training program. Cloud and deployed solutions are available. Visiopharm can be employed to develop workflows (apps) for the user. Modular structure with multiple packages: VisiomorphDP TissuemorphDP Arrayimager Tissuealign Visiomorph Tissuemorph Microimager Fluoimager

viv
type: software
has author: Börner, Katy (orcid.org/0000-0002-3321-6137)
has author: Gehlenborg, Nils (orcid.org/0000-0003-0327-8297)
has author: Gold, Ilan (orcid.org/0000-0002-5823-1026)
has author: Herr II, Bruce W. (orcid.org/0000-0002-6703-7647)
has author: Keller, Mark (orcid.org/0000-0003-3003-874X)
has author: Manz, Trevor (orcid.org/0000-0001-7694-5164)
has author: McCallum, Chuck (orcid.org/0000-0003-4039-9768)
has author: Patterson, Nathan (orcid.org/0000-0002-0064-1583)
has author: Spraggins, Jeffrey (orcid.org/0000-0001-9198-5498)
has documentation: viv.gehlenborglab.org
has documentation: Documentation for Viv
has function: operation_0337
has function: operation Image visualisation
has function: operation Overlay
has function: operation Slice rendering
has implementation: http://biii.eu/taxonomy/term/4339
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: MIT
has location: viv
has location: GitHub repository for Viv
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4668
has reference publication: wd2gu
has reference publication: OSF Preprint for Viv
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3382
has topic: topic Microscopy
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/8
has usage example: avivator.gehlenborglab.org
has usage example: Avivator
openess: http://biii.eu/taxonomy/term/3575
created: 2021-02-04T23:31:19
modified: 2021-02-04T23:58:57
title: Viv
comment: Viv is a JavaScript library providing utilities for rendering primary imaging data. Viv supports WebGL-based multi-channel rendering of both pyramidal and non-pyramidal images. The rendering components of Viv are provided as Deck.gl layers, facilitating image composition with existing layers and updating rendering properties within a reactive paradigm.

vmtk-vascular-modeling-toolkit
type: software
has author: David Steinman
has author: Luca Antiga
has documentation: tutorials
has documentation: tutorial
has function: operation_0337
has function: operation Image segmentation
has function: operation Neuron image analysis
has function: operation Volume rendering
has implementation: http://biii.eu/taxonomy/term/4339
has license: BSD-like license
has location: www.vmtk.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3444
has topic: topic Light-sheet microscopy
has type: http://biii.eu/taxonomy/term/3567
has usage example: https://www.ncbi.nlm.nih.gov/pubmed/28350253
has usage example: used to segment blood vessels network in mouse brains on lightsheet data with clearing
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1075
requires: http://biii.eu/node/92
created: 2018-01-28T18:22:05
modified: 2018-08-07T12:05:11
title: VMTK: Vascular Modeling Toolkit
comment: vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. vmtk is composed of C++ classes (VTK and ITK -based algorithms) Python classes (high-level functionality - each class is a script) PypeS - Python pipeable scripts, a framework which enables vmtk scripts to interact with each other

volocity
type: software
has license: commercial
has location: volocity.xhtml
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/601
created: 2013-11-07T19:32:18
modified: 2017-09-13T10:13:05
title: Volocity
comment: -

volocity-3d-object-segmentation-and-tracking
type: software
has documentation: http://cellularimaging.perkinelmer.com/support/dr_simon_vipoir/detail.php%3Fid%3D43
has documentation: Tracking in Volocity4
has function: operation Image tracking
has function: operation Object detection
has location: TrackinginVolocity.pdf
has platform: http://biii.eu/taxonomy/term/30
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/105
created: 2014-12-08T14:06:15
modified: 2018-05-23T23:31:13
title: Volocity - 3D Object Segmentation and Tracking
comment: In the commercial image analysis software "Volocity", automated measurement protocols can be constructed by dragging, dropping and configuring a sequence of individual "tasks". By combining the "Find Objects" task with a subsequent "Track" task, 3D objects can be identified and followed over time. The initial "Find Objects" segmentation can be refined, e.g. using "Separate Touching Objects"; and tracking results in the form of "Measurement Items" can be viewed in tabular form, as a graph, etc.

volocity-quantification
type: software
has function: operation 2945
has function: operation Morphological operations
has function: operation Colocalisation analysis
has implementation: http://biii.eu/taxonomy/term/4341
has location: downloads
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/105
created: 2013-10-11T13:08:43
modified: 2019-10-18T14:35:15
title: Volocity Quantification

volocity-restoration
type: software
has documentation: restoration
has function: operation Image deconvolution
has function: operation Image enhancement
has location: restoration
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/105
created: 2013-10-11T13:08:44
modified: 2019-11-14T10:08:25
title: Volocity Restoration

volocity-visualization
type: software
has function: operation Image visualisation
has location: visualization
has topic: topic 3382
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/105
requires: http://biii.eu/node/601
created: 2013-10-11T13:08:43
modified: 2019-10-16T15:35:36
title: Volocity Visualization
comment: Volocity Visualization is designed to provide rapid, interactive, high resolution volume rendering of multi-channel 3D and 4D data sets. This Volocity product puts you in control of the way that you view your 3D data, offering a choice of rendering methods so that you can achieve the best results. A range of file formats can be imported from wide field and confocal microscopes, and snapshots and movies can be created quickly and easily to share and publish.

volume-calculator
type: software
has author: Peter C. Marks
has function: operation 3443
has function: operation Feature extraction
has function: operation Shape features
has function: operation Skeletonization
has implementation: http://biii.eu/taxonomy/term/4340
has location: Volume Calculator
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/261
requires: http://biii.eu/node/38
requires: http://biii.eu/node/670
created: 2013-10-11T13:08:46
modified: 2019-10-18T12:49:47
title: Volume Calculator

volume-viewer
type: software
has author: Kai Uwe Barthel
has documentation: volume-viewer.html
has function: operation_0337
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPLv3
has location: Volume Viewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3382
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2013-10-11T13:08:46
modified: 2019-10-17T16:27:14
title: Volume Viewer
comment: 3D reslicing and threshold-enabled 3D visualization.

volviewer
type: software
has author: Jerome Avondo
has license: Creative Commons Public license
has location: VolViewer
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3593
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/601
created: 2015-02-12T15:21:19
modified: 2017-09-13T10:16:04
title: VolViewer
comment: # Summary VolViewer is used for viewing volume images from, for example, confocal microscopy or optical projection tomography # Features * Real-time volume rendering using an optimized 3D texture slicing algorithm. * Interactive transfer functions to independently adjust opacity and intensity for up to three data channels. * Real-time per channel thresholding, brightness and contrast operators. * On-the-fly gradient computation for local illumination. * Iso-surface computation with surface smoothing. * Section viewing in any orientation / position. * Real-time volume clipping. * 3D measurements, filters & segmentation. * Key frame interpolation for movie export. * Stereo rendering using either quad buffer or anaglyph mode. * Scripting interface to other systems, e.g. Matlab, OMERO, etc. # Project Status * Not supported anymore # Source code * [Source code](https://github.com/ut666/VolViewer "GitHub repository")

voronoi-imagej
type: software
has author: Michael Schmid
has author: Wayne Rasband
has documentation: 146-29.html#sub:Voronoi
has implementation: http://biii.eu/taxonomy/term/4340
has location: EDM.java
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2016-10-24T13:46:16
modified: 2023-04-29T09:43:46
title: Voronoi ImageJ
comment: A resident function in ImageJ, located in the menu as [Process > Binary > Voronoi]. Quote from the ImageJ reference page: Splits the image by lines of points having equal distance to the borders of the two nearest particles. Thus, the Voronoi cell of each particle includes all points that are nearer to this particle than any other particle. When particles are single points, this process is a Voronoi tessellation (also known as Dirichlet tessellation). The output type (Overwrite, 8-bit, 16-bit or 32-bit) of this command can be set in the [Process > Binary > Options...] dialog box. In the output, the value inside the Voronoi cells is zero; the pixel values of the dividing lines between the cells are equal to the distance between the two nearest particles. This is similar to a medial axis transform of the background, but there are no lines in inner holes of particles.

voronoi-segmentation-knime
type: software
has documentation: org.knime.knip.base.nodes.seg.voronoi.VoronoiSegNodeFactory#Voronoi Segmentation
has function: operation Image segmentation
has function: operation RBNng13hEB0CJD5VzSKqrfB
has location: image-processing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Digital histology
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1130
requires: http://biii.eu/node/71
created: 2013-10-11T13:08:43
modified: 2019-10-18T13:03:40
title: Voronoi Segmentation (KNIME)

voxelytics-align
type: software
has author: ScalableMinds
has documentation: voxelytics-connect
has documentation: Some documentation
has function: operation 2928
has function: operation Image reconstruction
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4342
has location: <nolink>
has location: Access as a serice
has platform: http://biii.eu/taxonomy/term/30
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has topic: topic RByvmgDpAo4FOrMdvTm1gwR
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/1660
created: 2022-03-16T06:43:35
modified: 2022-03-16T06:52:59
title: Voxelytics-Align
comment: Voxelytic-Align is a commercial software provided as a service on cloud targetted to electron microscopy reconstruction (alignement, artifact correction...)

vsi-file-extractor-imagej
type: software
has author: Arne Seitz
has author: Olivier Burri
has author: Romain Guiet
has documentation: ijab-biop vsireader
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: ijab-biop vsireader
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/79
created: 2014-12-08T15:45:37
modified: 2020-03-02T19:56:37
title: VSI File Extractor (ImageJ)
comment: This tool allows for extraction of image series from Olympus Slide Scanners. These VSI files usually contain several images that are too big to load into memory (>50k x 50k pixels). It was written and tested on Fiji and is available from a Fiji Update Site: http://fiji.sc/List_of_update_sites

vtk-overlay-tutorial
type: software
has location: VTK overlay tutorial
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/8
created: 2013-10-11T13:08:43
modified: 2017-09-13T10:06:21
title: VTK overlay tutorial

watershed-algorithm
type: software
has location: Watershed Algorithm (ImageJ plugin)
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/1016
requires: http://biii.eu/node/17
requires: http://biii.eu/node/38
requires: http://biii.eu/node/826
created: 2013-10-11T13:08:44
modified: 2017-09-13T10:07:36
title: Watershed Algorithm

watershed-imagej-ij-152i
type: software
has author: Schmid, Michael
has function: operation Watershed
has location: EDM.java.html
has location: Package ij.plugin.filter class EDM
has reference publication: 1049-9660(92)90008-Q
has reference publication: F. Leymarie, M. D. Levine, in: CVGIP Image Understanding, vol. 55 (1992), pp 84-94
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
created: 2019-02-05T13:22:12
modified: 2019-10-28T11:45:04
title: Watershed (ImageJ ij-1.52i)
comment: Performs watershed algotirhm with ij-1.52i.jar. legacy:ij.plugin.filter.EDM("watershed").

wavelet-spot-detector-block
type: software
has author: de Chaumont, Fabrice
has implementation: http://biii.eu/taxonomy/term/4340
has license: gPLv3
has location: Wavelet Spot Detector Block
has location: Wavelet Spot Detector Block page on Icy
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/49
requires: http://biii.eu/node/82
created: 2013-10-11T13:08:46
modified: 2019-10-17T08:46:04
title: Wavelet Spot Detector Block
comment: Wavelet Spot Detector for Blocks, to integrate in Icy protocols.

wavetracer
type: software
has author: Adel Kechkar, Deepak Nair, Mike Heilemann, Daniel Choquet, Jean-Baptiste Sibarita
has function: operation Image reconstruction
has implementation: http://biii.eu/taxonomy/term/4340
has platform: http://biii.eu/taxonomy/term/31
has reference publication: journal.pone.0062918
has reference publication: 10.1371/journal.pone.0062918
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/115
created: 2016-10-09T16:37:07
modified: 2019-10-18T17:10:50
title: WaveTracer
comment: WaveTracer is a plugin for Metamorph. It represents a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. It relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation.

webknossos-3d-image-annotation-visualization-and-sharing
type: software
has author: Max Planck Institute for Brain Research
has author: scalable minds
has documentation: webknossos
has documentation: Twitter (for software updates)
has function: operation 2409
has function: operation 3553
has function: operation Image segmentation
has function: operation Image visualisation
has function: operation Interactive segmentation
has function: operation Neuron image analysis
has function: operation Overlay
has function: operation Skeletonization
has function: operation Volume rendering
has function: operation Slice rendering
has implementation: http://biii.eu/taxonomy/term/4342
has license: AGPL3
has location: webknossos.org
has location: webKnossos
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4668
has reference publication: nmeth.4331
has reference publication: Boergens, Berning et al., Nature Methods 2017
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3444
has topic: topic 3452
has topic: topic Fluorescent microscopy
has topic: topic RwTXNChEQ9hv7IpvHjQGin
has type: http://biii.eu/taxonomy/term/3567
has usage example: view
has usage example: Demo Dataset (Full female adult fly brain, Zheng et al. 2017)
openess: http://biii.eu/taxonomy/term/3575
created: 2021-02-25T15:00:29
modified: 2021-03-08T13:00:08
title: webKnossos: 3D image annotation, visualization and sharing
comment: webKnossos is an open-source data sharing and annotation platform for tera-scale 2D and 3D image datasets. The core features of webKnossos are: fast 3D data streaming share links to specific locations in the data uniquely fast skeleton annotation (flight mode) and efficient volume annotation mesh rendering collaboration and sharing tools webKnossos facilitates image analysis workflows on multi-terabyte datasets, including visualization of raw and multi-modal microscopy data, distributed training data generation and proof-reading of automatic segmentation. As a scientific resource, webknossos.org serves as a database for published image datasets including their annotations.

white-balance
type: software
has author: Laurent Gelman
has location: https://gist.github.com/lgelman/edf042e8712afa9350ba
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T14:43:09
modified: 2018-05-20T23:37:58
title: White Balance
comment: The Macro processes a composite picture in ImageJ/Fiji and outputs a color-balanced merged RGB image. To calculate the white balance, a rectangle at coordinates (x=100, y=100) and of size (w=100 pixels, h=100 pixels) is used. These values can be changed to make sure that a background region is taken for the calculation in the line: makeRectangle(100,100,100,100). The user could be prompted to draw the region by removing the signs // in the line: // waitForUser("Please draw a region in the background");

wis-neuromath
type: software
has author: Ofra Golani, Meirav Galun, Ida Rishal, Michael Fainzilber
has documentation: neuromath userguide.pdf
has documentation: [PDF] Neuronal Morphology Analysis Tool User Guide
has function: operation Image segmentation
has license: free for non-profit use
has location: made-weizmann
has location: Download (need password from the author)
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: dneu.22061
has reference publication: Rishal et. al. (2012)
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/101
created: 2013-10-11T13:31:24
modified: 2018-05-09T19:39:49
title: WIS-NeuroMath
comment: WIS-NeuroMath - is a software tool for automated analysis and quantification of fluorescent microscopy images of Nerve cells, in both in vivo and in vitro preparations. It allows for accurate detection of neurites in challenging images. Following neurite detection, different types of processing can be carried: Cell Morphology of cultured neurons, Neurite Length Analysis and Ganglion Explant Analysis. Usefull also for angiogenesis analysis.

wis-phagotracker
type: software
has author: Ofra Golani, Meirav Galun, Suha Naffar Abu-Amara , Benjamin Geiger
has documentation: phagotrackeruserguide.pdf
has documentation: [PDF] WIS-PhagoTracker
has function: operation Image segmentation
has function: operation Image tracking
has implementation: http://biii.eu/taxonomy/term/4341
has license: free for non-profit use
has location: made-weizmann
has location: Download needs password from the author.
has platform: http://biii.eu/taxonomy/term/31
has programming language: http://biii.eu/taxonomy/term/4223
has reference publication: journal.pone.0001457
has reference publication: Naffar-Abu-Amara et. al. (2008) Identification of Novel Pro-Migratory, Cancer-Associated Genes Using Quantitative, Microscopy-Based Screening
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3576
requires: http://biii.eu/node/101
created: 2013-10-11T15:17:13
modified: 2023-04-26T13:29:46
title: WIS-PhagoTracker
comment: WIS-PhagoTracker is a software application for quantitative analysis of high throughput cell migration assay. The cell migration assay is based on a modified Phagokinetic tracks procedure, in which motile cells "leave their tracks" on a specialized surface. These tracks are visualized using a screening microscope. WIS-PhagoTracker enables morphometric analysis of such tracks. It uses multiscale segmentation algorithm for fine detection of tracks and cells boundaries. Following the segmentation step, it quantifies various morphometric parameters for each track, such as track area, perimeter, major and minor axis and solidity. All these measures are calculated for each track in each well of a well plate and saved for further statistical analysis WIS-PhagoTracker supports all the analysis phases starting from preprocessing, finding tracks of selected wells or a whole plate, through viewing the results and manually rejecting tracks to statistical analysis of the results. It also supports batch processing of several plates, and analysis of single image files. A user interface enables the user to modify the relevant parameters of the process, according to specific image's requirements. Results are exported into Excel readable files.

wnd-charm
type: software
has author: Ilya Goldberg orcid.org/0000-0001-8514-6110
has function: operation 2945
has function: operation 3443
has function: operation Object detection
has function: operation Shape features
has license: LGPL-2.1
has location: wnd-charm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has reference publication: https://doi.org/10.1186/1751-0473-3-13
has reference publication: Wndchrm – an open source utility for biological image analysis
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3566
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/51
created: 2017-09-12T07:18:27
modified: 2018-10-18T15:35:57
title: wnd-charm
comment: WND-CHARM is a multi-purpose image classifier that can be applied to a wide variety of image classification tasks without modifications or fine-tuning, and yet provides classification accuracy comparable to state-of-the-art task-specific image classifiers. WND-CHARM can extract up to ~3,000 generic image descriptors (features) including polynomial decompositions, high contrast features, pixel statistics, and textures. These features are derived from the raw image, transforms of the image, and compound transforms of the image (transforms of transforms). The features are filtered and weighted depending on their effectiveness in discriminating between a set of predefined image classes (the training set). These features are then used to classify test images based on their similarity to the training classes. This classifier was tested on a wide variety of imaging problems including biological and medical image classification using several imaging modalities, face recognition, and other pattern recognition tasks. WND-CHARM is an acronym that stands for "Weighted Neighbor Distance using Compound Hierarchy of Algorithms Representing Morphology."

workbooks-icy
type: software
has author: Alexandre Dufour
has documentation: Workbooks
has function: operation 2409
has implementation: http://biii.eu/taxonomy/term/4340
has location: Workbooks
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/8
requires: http://biii.eu/node/852
requires: http://biii.eu/node/913
created: 2013-10-11T13:08:44
modified: 2020-03-03T08:15:47
title: Workbooks (Icy)

worm-toolbox-highthroughput-screening-c-elegans
type: software
has author: Anne E Carpenter
has author: Annie L Conery
has author: Carolina Wählby
has author: Eyleen J O'Rourke
has author: Frederick M Ausubel
has author: Gary Ruvkun
has author: Javier E Irazoqui
has author: Katherine L Sokolnicki
has author: Lee Kamentsky
has author: Orane Visvikis
has author: Polina Golland
has author: Tammy Riklin-Raviv
has author: Vebjorn Ljosa
has author: Zihan H Liu
has documentation: wormtoolbox
has location: wormtoolbox
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 10.1038/nmeth.1984
has reference publication: Wählby et al. (2012) An image analysis toolbox for high-throughput C. elegans assays
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2014-12-09T16:20:18
modified: 2018-05-30T17:19:15
title: Worm Toolbox: High.throughput screening of C. elegans
comment: This toolbox is a unique collection of workflow templates for high-throughput screening. 4 different workflow templates are presented in the documentation linked below. >..A toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and imaging systems. This WormToolbox is available through the open-source CellProfiler project and enables objective scoring of whole-worm high-throughput image-based assays of C. elegans for the study of diverse biological pathways that are relevant to human disease.

wormguides-atlas
type: software
has author: The WormGUIDES app is developed and maintained by the laboratories of Dr. Zhirong Bao and Dr. William Mohler. Major contributors of the desktop app include Doris Tang (New York University), Braden Katzman (Columbia University) and Dr. Anthony Santella of the Bao Laboratory. For questions or comments contact support@wormguides.org.
has function: operation_0226
has function: operation_0337
has function: operation 2945
has function: operation Feature extraction
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: unknown
has location: wormguides-atlas
has location: WormGUIDES Atlas
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
created: 2017-04-12T10:08:49
modified: 2023-04-30T16:33:33
title: WormGUIDES Atlas
comment: WormGUIDES Atlas is an interactive 4D portrayal of neural development in C. elegans. It will ultimately contain nuclear positions for every cell in the embryo, identified and tracked from the 2 cell stage until hatching. Single-cell and subcellular information, including neural outgrowth dynamics for each cell as well as cell function, gene expression, the adult neural connectome and related literature will be collated for each cell from public sources and also integrated with the atlas model. WormGUIDES Atlas integrates tools for exploratory data analyses and insight sharing. Navigation is linked between 3D and lineage tree views. In both contexts, community single cell information can be accessed with a click, creating live web queries that summarize knowledge about a cell. In many cases this information can be used to control cell color, creating customized interactive visualizations. A user's insights can be annotated directly into the embryo model with a note-taking interface that attaches each annotation to a cell or other point in space and time. These multi-dimensionally located notes can then be ordered into a (chrono)logical story sequence that explains developmental events as they unfold in the embryo. Annotations can be saved and shared with collaborators or the community.

wormscan
type: software
has author: Mark D. Mathew
has author: Neal D. Mathew
has author: Paul R. Ebert
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: journal.pone.0033483
has reference publication: WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2019-06-07T12:43:40
modified: 2019-10-15T08:59:46
title: WormScan
comment: We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis.

wound-healing-assay-analysis-cellprofiler
type: software
has author: CellProfiler team
has function: operation Image segmentation
has function: operation Wound-healing analysis
has location: #Wound
has location: Wound Healing@CellProfiler
has programming language: http://biii.eu/taxonomy/term/4428
has supported image dimension: http://biii.eu/taxonomy/term/3561
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/31
created: 2014-12-08T17:06:40
modified: 2023-03-10T22:18:32
title: Wound healing assay: analysis in CellProfiler
comment: In this example, cells are grown as a tissue monolayer. Rather than identifying individual cells, this pipeline quantifies the area occupied by the tissue sample. Download package also contains example images.

wound-healing-assay-analysis-imagej
type: software
has author: Fabrice P Cordelières
has author: Lionel Larue
has author: Stuart J Gallagher
has author: William J Ashby
has documentation: http://web.archive.org/web/20160821164358/http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Aanalysis%253Ascratch_wound_assay_automatic_analysis_macro%253Astart
has documentation: Documentation (Archived website image)
has function: operation Image segmentation
has function: operation Wound-healing analysis
has location: http://web.archive.org/web/20160821164358/http://imagejdocu.tudor.lu/doku.php%3Fid%3Dplugin%253Aanalysis%253Ascratch_wound_assay_automatic_analysis_macro%253Astart
has location: automated analysis of scratch wound assays
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T12:01:55
modified: 2023-05-03T15:21:37
title: Wound healing assay: analysis in ImageJ
comment: This macro was designed to measure the size of the scratch wound in a wound scratch assay. It uses an edge-detection and thresholding technique. It will batch process all images in a directory. Images captured by time-lapse should be compiled into stacks using a tool similar to "Metamorph nd & ROI files importer (nd stack builder)" by Fabrice P. Cordelières. Images to be analyzed should be placed in one directory (Source Directory). A second directory should be created to save results files and images (Destination Directory). Setting correct Lower and Upper thresholds is important to obtain a good result. Two macros are available, one using edge detection, the second one using background subtraction.

wound-healing-tool
type: software
has author: Volker Baecker
has documentation: Wound Healing Tool
has license: CeCILL-C
has location: Wound Healing Tool
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has reference publication: 273769192 ImageJ Macro Tool Sets for Biological Image Analysis
has reference publication: 2012. ImageJ Macro Tool Sets for Biological Image Analysis. ImageJ User and Developer Conference 2012.
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
has usage example: optimization-wound-scratch-assay-to-detect-changes-murine-mesenchymal
has usage example: Optimization of the Wound Scratch Assay to Detect Changes in Murine Mesenchymal Stromal Cell Migration After Damage by Soluble Cigarette Smoke Extract.
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2017-09-14T07:49:52
modified: 2017-09-14T14:07:43
title: Wound Healing Tool
comment: The wound healing tool measures the area of a wound in a time series of images of cellular tissue. The tool will measure the area of the wound, i.e. the area that does not contain tissue, in each image. The segmentation is based on the fact that the image is more homogeneous in the region of the wound as in the region of the tissue. Via the options, one of two methods to detect the empty area, can be selected. The first uses edge detection, the second a variance filter. Holes in the detected tissue are filled using morphological operations.

wspm
type: software
has implementation: http://biii.eu/taxonomy/term/4339
has location: wspm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4223
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3578
requires: http://biii.eu/node/101
created: 2013-10-11T13:08:41
modified: 2019-10-18T12:41:44
title: WSPM
comment: Wavelet-based statistical parametric mapping, a toolbox for SPM that incorporates powerful wavelet processing and spatial domain statistical testing for the analysis of fMRI data.

xuvtools
type: software
has author: Aaron Ponti
has author: Mario Emmenlauer
has author: Olaf Ronneberger
has documentation: http://www.xuvtools.org/doku.php%3Fid%3Ddocs:documentation
has function: operation Image reconstruction
has function: operation Image stitching
has implementation: http://biii.eu/taxonomy/term/4341
has license: GNU General Public License v2
has location: www.xuvtools.org
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3593
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic R9Cmje2ZUXyDW6aQAvFhwSM
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/3567
openess: http://biii.eu/taxonomy/term/3575
created: 2016-10-24T13:46:16
modified: 2020-03-05T10:48:22
title: XuvTools
comment: XuvTools (pronounced ex-you-vee-tools) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). XuvTools is free and open source software (see Licensing), so you can start using it immediately. Go to Downloads and give it a try. The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (stitching) and a higher dynamic range (HDR recombination), or better resolution (multi view reconstruction), and to make these tools publicly available.

yapic
type: software
has function: operation Pixel classification
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic 3474
has topic: topic Supervised learning
has type: http://biii.eu/taxonomy/term/8
created: 2020-03-04T09:08:23
modified: 2020-10-19T14:49:46
title: Yapic
comment: Yet another pixel classifier Yapic is a deep learning tool to : train your own filter to enhance the structure of your choice train multiple filter at once it is based on the u-net convolutional filter . To train it : annotation can come from example from Ilastik software , tif labelled files can be transferred to yapic. Training takes about hours to days , prediction takes seconds once trained . It can be ran from command line . note that only 10 to 20 images with sparse labeling are required for efficient training

yeastspotter
type: software
has author: Alan Moses
has author: Alex Lu
has documentation: yeastspotter.csb.utoronto.ca
has function: operation Cell segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has license: MIT
has location: yeast segmentation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3592
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/1312
created: 2019-03-22T17:07:48
modified: 2020-10-19T15:08:56
title: YeastSpotter
comment: >Code to segment yeast cells using a pre-trained mask-rcnn model. We've tested this with yeast cells imaged in fluorescent images and brightfield images, and gotten good results with both modalities. This code implements an user-friendly script that hides all of the messy implementation details and parameters. Simply put all of your images to be segmented into the same directory, and then plug and go.

z-spacing-correction-fiji
type: software
has author: Hanslovsky Philipp
has function: operation Warping
has function: operation R7MFwdgojfmkZ07yWbdcda0
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL
has location: z-spacing
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has reference publication: https://arxiv.org/abs/1411.6970
has reference publication: Hanslovsky et al. "Post-acquisition image based compensation for thickness variation in microscopy section series"
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic_0611
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/79
created: 2018-01-30T16:04:02
modified: 2018-01-30T16:08:10
title: Z-spacing correction for Fiji
comment: Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.

zebrafish-embryo-tool
type: software
has author: Volker Baecker
has documentation: Zebrafish Embryo Tools
has function: operation 2928
has location: Zebrafish Embryo Tools.ijm
has location: Zebrafish_Embryo_Tools.ijm
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has reference publication: journal.pone.0031281
has reference publication: Ghotra et al (2012) Automated Whole Animal Bio-Imaging Assay for Human Cancer Dissemination
has supported image dimension: http://biii.eu/taxonomy/term/3561
has topic: topic Fluorescent microscopy
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-09T16:27:17
modified: 2018-05-29T22:56:18
title: Zebrafish Embryo Tool
comment: Normalize the orientation of the images of the Zebrafish embryos. In the documentation webpage, the aim of the workflow is to normalize the orientation of the images of the Zebrafish embryos, find the point of injection of tumor cells and measure the distribution of Cy3 stained tumor foci. ImageJ macro implementation of the Workflow described in Ghotra et al (2012). Note that currently only the angle and orientation normalization is implemented in this version. Sample images are linked in the documentation webpage.

zen-and-apeer-machine-learning-platform
type: software
has author: Carl Zeiss Microscopy GmbH
has documentation: czmodel
has documentation: Open Source PyPi Package CZMODEL
has function: operation Cell segmentation
has function: operation Image segmentation
has function: operation Pixel classification
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has function: operation Model-based segmentation
has implementation: http://biii.eu/taxonomy/term/4341
has implementation: http://biii.eu/taxonomy/term/4342
has location: zen-intellesis-free-trial-version.html
has location: ZEN Intellesis Trainable Segmentation
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has programming language: http://biii.eu/taxonomy/term/3592
has programming language: http://biii.eu/taxonomy/term/3593
has programming language: http://biii.eu/taxonomy/term/4728
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic_0611
has topic: topic 3385
has topic: topic 3474
has topic: topic Digital histology
has topic: topic Fluorescent microscopy
has topic: topic High content screening
has topic: topic Supervised learning
has type: http://biii.eu/taxonomy/term/3567
has type: http://biii.eu/taxonomy/term/3568
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
openess: http://biii.eu/taxonomy/term/3577
requires: http://biii.eu/node/1345
requires: http://biii.eu/node/1670
created: 2018-08-22T12:48:23
modified: 2023-03-10T22:08:25
title: ZEN and APEER Machine Learning Platform
comment: ZEN and APEER – Open Ecosystem for integrated Machine-Learning Workflows Open ecosystem for integrated machine-learning workflows to train and use machine-learning models for image processing and image analysis inside the ZEN software or on the APEER cloud-based platform Highlights ZEN Simple User Interface for Labeling and Training Engineered Features Sets and Deep Feature Extraction + RF Forrest for Segmentation Object Classification workflows Probability Thresholds and Conditional Random Fields Import your own trained models with support for TensorFlow2 and ONNX Integration into ZEN Measurement Framework Support for Multi-dimensional Datasets and Tile Images open and standardized format to store trained models ZEN Intellesis Segmentation ZEN Intellesis - Pretrained Networks Intellesis Object Classification Highlights APEER Web-based tool to label datasets to train Deep Neural Networks Fully automated hyper-parameter tuning Export of trained models APEER Annotation Tool

zen-blue
type: software
created: 2018-08-22T12:55:40
modified: 2018-08-22T12:55:40
title: ZEN Blue

zerocostdl4mic
type: software
has DOI: s41467-021-22518-0
has documentation: ZeroCostDL4Mic
has documentation: github
has implementation: http://biii.eu/taxonomy/term/4342
has reference publication: s41467-021-22518-0
has reference publication: Democratising deep learning for microscopy with ZeroCostDL4Mic
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has topic: topic 3474
has type: http://biii.eu/taxonomy/term/3567
has usage example: Video Tutorials
openess: http://biii.eu/taxonomy/term/3575
created: 2023-05-12T16:15:59
modified: 2023-05-12T16:22:53
title: ZeroCostDL4Mic
comment: ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy ZeroCostDL4Mic is a collection of self-explanatory Jupyter Notebooks for Google Colab that features an easy-to-use graphical user interface. They are meant to quickly get you started on learning to use deep-learning for microscopy.

zt-hyperstack-stitcher
type: software
has author: Sébastien Tosi
has documentation: image-j-fiji#h.p ID 1316
has documentation: Documentation
has function: operation 2409
has function: operation 2928
has function: operation Image stitching
has location: image-j-fiji#h.p ID 1316
has location: ImageJ macro - (Z,T) Hyperstack Stitcher
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has topic: topic Microscopy
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p ID 1316
has usage example: User guide - (Z,T) Hyperstack Stitcher
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T14:28:48
modified: 2023-04-28T14:32:28
title: (Z,T) Hyperstack Stitcher
comment: This macro builds a stitched image from a muti-position 3D + time hyperstack. The XY positions of the montage should be coded as channels in the input hyperstack. Channel ordering can be configured in the dialog box to adapt to Column/Row and Meander/Comb configurations: The images should appear in this order when browsing the hyperstack with the channel slider. Fine stitching is supported (requires sufficient overlap between the views). The XY displacements of each field of view for stitching are computed for a single reference (Z,T) slice (user configurable) and applied to all slices (Z and T).

ztc-stitcher
type: software
has author: Sébastien Tosi
has documentation: image-j-fiji#h.p ID 1413
has documentation: Documentation
has function: operation Image stitching
has location: image-j-fiji#h.p ID 1413
has location: ImageJ macro - (Z,T,C) Stitcher
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic Microscopy
has type: http://biii.eu/taxonomy/term/8
has usage example: image-j-fiji#h.p ID 1413
has usage example: User guide - (Z,T,C) Stitcher
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
created: 2014-12-08T14:32:02
modified: 2023-04-28T14:40:19
title: (Z,T,C) Stitcher
comment: This macro can stitch a (Z,T,C) data set with virtually no limit on the number of Z slices and time frames. The input to the macro is a folder with the raw tiff images (one image per file) as typically exported by motorized microscopes. These files must all be stores in the same folder and the file naming should ideally comply to OME-TIFF. The macro is however quite flexible: Only --X, --Y and --Z fields with user defined number of digits are compulsory. --T, --C and --L fields with user defined number of digits are necessary for multiple time frames / channels data sets. A compatible data set is provided as a .zip archive. Before processing it unzip it to a given location. The stitching is performed in a reference Z slice (and in a specific reference time frame and channel). The same displacements are applied to all the Z slices, time frames and channels. Before starting the batch processing a montage with the original images of the selected Z slice / time frame / channel is displayed together with the stitched image in this stack. If you are not satisfied with the result you can select another reference. The stitching is then performed time frame by time frame and slice by slice and the stitched images are exported to a single user defined output folder. The macro can also process a data set with multiple channels, the stitching is then computed once on a reference channel and then applied to the other channels.

measure-cell-volume-over-time
type: software
has author: Christoph Moehl
has author: Imaris Tutorials
has DOI: zenodo.13167
has DOI: registration_and_bleaching_correction: initial resease
has documentation: This Page
has function: operation Cell tracking
has location: zenodo.13167
has programming language: http://biii.eu/taxonomy/term/3594
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has type: http://biii.eu/taxonomy/term/3568
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/87
created: 2014-12-09T15:15:17
modified: 2023-05-03T13:41:09
title: Measure cell volume over time
comment: The workflow measures the growth of cells in 3D, combining an ImageJ macro for preprocessing and successive tracking using Imaris. The sample dataset (available in the github repository) contains 2-Photon images of neurons. The neurons were imaged in 3D at two time frames.To allow measuring significant differences in cell volume, the time gap between the frames is large (ca. 30 min) and the animal was removed in the waiting phase. For this reason, there is a considerable shift in sample position between the frames that has to be corrected before cell detection and tracking. The workflow consists of following steps: 1. Import of single tiff slices [imageJ macro] 2. Organizing the data in a 4D time series with 2 time frames [imageJ macro] 3. Correction of shift between the time frames by rigid registration [imagJ macro] 4. Bleaching correction [imageJ macro] 5. Export of preprocessed image data in ics/ids format [imageJ macro] 6. Import of ics/ids data to Imaris [Imaris] 7. Cell object detection as "Imaris Surface Object" [Imaris] 8. Tracking cell objects over time [Imaris] 9. Split Tracks (use Imaris XT extension "Split Tracks") to generate single cell objects [Imaris] 10. Export the statistics: Select the complete folder, go to the statistics tab and use Full Export [Imaris] The preprocessing macro can be referenced here. The sample images were acquired by Cordula Ulbrich (Petzold Group at German Center of Neurodegenerative Disesases (DZNE), Bonn, Germany). Input data type: tiff Output data type: data table

minimum-3d-filter-vib-protocol
type: software
has author: Schindelin, Johannes
has author: Schmid, Benjamin
has documentation: Median
has documentation: Minimum/Maximum/Median page at ImageJ.net website
has function: operation Image convolution
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL v3.0
has location: VIB
has location: VIB Protocol repository at Github
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/3591
has supported image dimension: http://biii.eu/taxonomy/term/3562
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/903
created: 2019-02-25T16:12:56
modified: 2019-02-26T15:06:54
title: Minimum (3D) Filter VIB Protocol
comment: This component convolves the image with minimum filter. Each voxel is set to the minimum value of its neighborhood. The neighborhood is defined by a kernel, which has a diameter of 3 voxels.

qualitative-annotations-fiji-plugins
type: software
has author: Gehrig Jochen orcid.org/0000-0002-1193-1324
has author: Schaefer Franz
has author: Thomas Laurent orcid.org/0000-0001-7686-3249
has DOI: f1000research.26872.1
has DOI: Article DOI
has documentation: Youtube tutorials
has function: operation_0226
has function: operation 3553
has function: operation Image classification
has function: operation RyCFuPLOeGxpcGjYbWcWWD
has implementation: http://biii.eu/taxonomy/term/4340
has license: GPL-v3
has location: Fiji-QualiAnnotations
has location: GitHub repository
has platform: http://biii.eu/taxonomy/term/29
has platform: http://biii.eu/taxonomy/term/31
has platform: http://biii.eu/taxonomy/term/32
has programming language: http://biii.eu/taxonomy/term/4525
has reference publication: f1000research.26872.1
has reference publication: Article
has supported image dimension: http://biii.eu/taxonomy/term/3561
has supported image dimension: http://biii.eu/taxonomy/term/3562
has supported image dimension: http://biii.eu/taxonomy/term/3563
has supported image dimension: http://biii.eu/taxonomy/term/3565
has topic: topic RBDp7HwdUBEjpS6PRjYfV2V
has type: http://biii.eu/taxonomy/term/8
openess: http://biii.eu/taxonomy/term/3575
requires: http://biii.eu/node/38
requires: http://biii.eu/node/79
created: 2020-11-12T10:22:06
modified: 2021-03-05T10:51:46
title: Qualitative annotations Fiji plugins
comment: Set of Fiji plugins facilitating the systematic manual annotation of images or image-regions. From a list of user-defined keywords, these plugins generate an easy-to-use graphical interface with buttons or checkboxes for the assignment of single or multiple pre-defined categories to full images or individual regions of interest. In addition to qualitative annotations, any quantitative measurement from the standard Fiji options can also be automatically reported. Besides the interactive user interface, keyboard shortcuts are available to speed-up the annotation process for larger datasets. The plugins can be installed by activating the Qualitative annotations update site in Fiji.