2-D colocalisation in cells using CellProfiler
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
A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images
2D-3D distributed parallel region competition segmentation
This is the source code and data page of a distributed parallel algorithm 2683 for segmentation of large fluorescence microscopy images.
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
2D and 3D mitochondrial shape analysis and network properties
The original paper describes a method to analyze mitochondrial morphology in 2D and 3D.
Chenouard et al.(2014) Objective comparison of particle tracking methods
2D and 3D tracking based on global cost function optimization
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
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
R.A. Tyson, D.B.A. Epstein, K.I. Anderson and T. Bretschneider
Tyson et al (2010) High Resolution Tracking of Cell Membrane Dynamics in Moving Cells: an Electrifying Approach
2D cell tracking and analysis of morphological dynamics
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.
Waithe dominic orcid.org/0000-0003-2685-4226
2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals.
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).
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)
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 (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.
3-D Active Meshes: Fast Discrete Deformable Models for Cell Tracking in 3-D Time-Lapse Microscopy
3D affine transformation based on paired points
Using a text file containing 3D point coordinates as reference pairs, 3D image stack is transformed.
Du CJ, Hawkins PT, Stephens LR, Bretschneider T
Du et al (2013) 3D time series analysis of cell shape using Laplacian approaches
3D cell tracking and quantification of shape changes
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)
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.
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.
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 of synaptic vesicle distribution in serial section TEM (ssTEM)
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
mcib3d Github repository linking to Fill Holes method
Runs fill holes operation on 3D images.
3D Generalized Riesz-Wavelet Toolbox for Matlab
This Matlab code is the 3D extension of the Generalized Riesz-Wavelet Toolbox for Matlab.
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.
Youtube Lecture and Hands-On, NEUBIAS Academy
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
This Javascript works in ImageJ to measure 3D intensity profile along cylindrical space with variable radius.
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
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.
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.
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
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
André Dias, Marco Werner, Kevin R. Ward, Jean-Baptiste Fleuryd and Vladimir A. Baulin
High-throughput 3D visualization of nanoparticles attached to the surface of red blood cells
3D Segmentation & visualization of nanoparticles attached to the surface of red blood cells
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.
Structural coronary artery remodelling in the rabbit fetus as a result of intrauterine growth restriction
3D vessel segmentation of synchrotron phase contrast tomography
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 provides hardware-accelerated 3D visualization of image stacks as volumes, surfaces and orthoslices.
Benjamin Schmid 3Dscript Github repository
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.
download instruction in the documentation page
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 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: Free software for the acquisition and analysis of 3D images of cells in fluorescence microscopy
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.
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.
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 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.
Bevan L. Cheeseman http://orcid.org/0000-0002-9248-5118
Ivo F. Sbalzarini http://orcid.org/0000-0003-4414-4340
Krzysztof Gonciarz http://orcid.org/0000-0001-9054-8341
Ulrik Günther http://orcid.org/0000-0002-1179-8228
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.
Adipocyte quantification ImageJ by Baecker
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)
Osman et. al. (2013) A novel automated image analysis method for accurate adipocyte quantification
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.
Galarraga et. al. (2012), Adiposoft: automated software for the analysis of white adipose tissue cellularity in histological sections
>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 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.
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 routine `errorReport()`. The latter is not included in this distribution; its purpose is to display an error message given by a C-string. Else, the code is self-contained (provided a standard ANSI-C environment is available). It consists of only two files: affine.h and affine.c.
AIR Tools II: Algebraic Iterative Reconstruction Methods, Improved Implementation
AIR Tools is a MATLAB software package for tomographic reconstruction (and other imaging problems) consisting of a number of algebraic iterative reconstruction methods.
Manually selecting line ROIs and align two images.
Template Matching and Slice Alignment--- ImageJ Plugins
Tseng et. al. (2011) A new micropatterning method of soft substrates reveals that different tumorigenic signals can promote or reduce cell contraction levels
**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
Matheus P. Viana https://orcid.org/0000-0001-9288-2108
The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
2-clause BSD license plus clause a third clause that prohibits redistribution for commercial purposes without further permission.
​The Allen Cell Structure Segmenter: Project Page
The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images (biorxiv)
​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 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. "
Zuse Institute Berlin (ZIB) and Thermo Fisher Scientific
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.
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 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.
Documetation of the Analyze Complex Roots Tool
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
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.
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.
This is a scripting example to process stack of images using AnalyzeSkeleton.
Analyze-Spheroid-Cell-Invasion-In-3D-Matrix Documentation
Download Analyze-Spheroid-Cell-Invasion-In-3D-Matrix
CRISPR deletion of MIEN1 in breast cancer cells
Analyze Spheroid Cell Invasion In 3D Matrix
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 with ImageJ
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 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.
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
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.
Manual angle measurements. No javadoc accessible, but can be downloaded from the webpage.
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.
Vector-valued image regularization with PDEs: a common framework for different applications
>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: an ImageJ plugin to ease hand annotation of cellular compartments
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.
Avants et al. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain.
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
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.
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...
Automatic 3D neuron tracing using all-path pruning
"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: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
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.
Acquiarium: Free Software for Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. ISBI 2009
Tutorial: How to count DNA double strand breaks
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.
ImageJ macro tool sets for biological image analysis
Simple system using natural mineral water for high-throughput phenotyping of Arabidopsis thaliana seedlings in liquid culture
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 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
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.
Why join groups? Lessons from parasite-manipulated Artemia.
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 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 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.
Léo Guignard. Quantitative analysis of animal morphogenesis: from high-throughput laser imaging to 4D virtual embryo in ascidians. Theses, Université Montpellier, December 2015.
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
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.
SLT-LoG: A Vesicle Segmentation Method with Automatic Scale Selection and Local Thresholding Applied to TIRF Microscopy
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 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.
Bundled with Fiji. "Do all" is the great feature...
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)
ASAP allows to automatically detect, classify and quantify structures acquired by super resolution microscopy.
Maxime Deforet, Maria Carla Parrini, Laurence Petitjean, Marco Biondini, Axel Buguin, Jacques Camonis, Pascal Silberzan
Automated velocity mapping of migrating cell populations (AVeMap)
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 for parallel Multiview Reconstruction
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.
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.
Erick Martins Ratamero orcid.org/0000-0002-7545-3675
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).
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.
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)
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.
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.
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License
A BaSiC tool for background and shading correction of optical microscopy images, Nat. Comm.
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.
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
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)
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.
Huang, L-K & Wang, M-J J (1995), "Image thresholding by minimizing the measure of fuzziness", Pattern Recognition 28(1): 41-51
Choose the best auto thresholding technique for your data.
Stable Deep Neural Network Architectures for Mitochondria Segmentation on Electron Microscopy Volumes
BiaPy: Bioimage analysis pipelines in Python
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.
Preibisch Stephan orcid.org/0000-0002-0276-494X
Saalfeld Stephan orcid.org/0000-0002-4106-1761
Pietzsch et al. (2015), "BigDataViewer: visualization and processing for large image data sets", Nature Methods 12(6): 481-483,
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.
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.
Bogovic et al Robust registration of calcium images by learned contrast synthesis
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.
The OME Consortium, http://www.openmicroscopy.org/site/about/who-ome
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/)
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.
Lamichhane Santosh orcid.org/0000-0002-9292-3595
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 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.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 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.
Benchmarking of image registration methods for differently stained histological slides.
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 (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 ImageJ plugin for compensating the photobleaching of time-lapse sequences
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).
The purpose of the workflow is .... First you need
Blend two images (Fiji scripting example)
This is a Fiji scripting demo using Clojure.
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.
Gist: MarieLaureB / Morphological_Segmentation
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.
ImageJ Macro: Blood vessel segmentation and network analysis
User guide - Blood vessel segmentation and network analysis
Blood vessel segmentation and network analysis
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 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.
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
Layer for 3D View that displays a Bounding Box around the object.
Evaluation of real-time LBP computing in multiple architectures
BSIF (Binarized Statistical Image Features)
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
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.
2D Image registration method based on elastic deformations represented by B-splines.
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.
Calculate Statistics calculates measures of assay quality (V and Z' factors) and dose response data (EC50) for all measured features made from images.
Center for Biomedical Image Computing and Analytics (CBICA)
SBIA Contribution and Software License Agreement
Cancer Imaging Phenomics Toolkit (CaPTk)
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.
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.
Hartenstein Volker / orcid.org/0000-0001-9676-7393
Saalfeld Stephan / orcid.org/0000-0002-4106-1761
**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.
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.
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 the percentage of stained objects
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
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.
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.
Dimopoulos et al. (2014) Accurate cell segmentation in microscopy images using membrane patterns.
Mayer et al (2013) Using CellX to quantify intracellular events.
Cell segmentation and quantification with CellX
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 in phase contrast images
This Matlab code demonstrates an edge-based active contour model as an application of the Distance Regularized Level Set Evolution (DRLSE) formulation.
Held Michael, Thomas Walter, Sommer Christoph, Rudolf Hoefler
## 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
Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021).
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 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
**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: interactive data exploration, analysis and classification of large biological image sets
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 assay/DNA damage assay
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.
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.
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
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.
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.
in CP 2.1, it was "ApplyThreshold". Renamed to "Threshold" from 3.0.
Plot the centroid tracks and area evolution of the cells of a tissue with membrane labelling.
CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation
An automated MATLAB tool for segmentation of surface stained cells
CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis
A standalone cell tracking software for single cell migration. Tracking of cells in tissue was also done in Drosophila germband.
CellTracker software is a platform for tracking nuclear and cytoplasmic fluorescence intensities from live cell microscopy time series data. Requires visual C++
User Manual is included in the compressed file
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.
Bodor, Gómez-Rodriguez, Moreno & Jansen (2012) Analysis of Protein Turnover by Quantitative SNAP‐Based Pulse‐Chase Imaging
Centromere Recognition and Quantification
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 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.
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.
Tutorial explaining how to display a JFreeChart graph in Icy.
This tutorial explain how to use a deviation renderer JFreeChart chart in Icy.
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.
This Jython script illustrates how to make an image interactive. It let you play chess within Fiji!
Image correction software for chromatic shifts in fluorescence microscopy
A software solution for recording circadian oscillator features in time-lapse live cell microscopy.
"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 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
classification of hemp fibers based on morphological features
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
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.
This originally came from this module. Currently it is available as the ilastik CellProfiler plugin (see this image.sc post for details).
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.
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.
Mapping of brain activity by automated volume analysis of immediate early genes.
Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature.
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 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 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.
Library used by Micro-Manager for fast acquisition.
Sophie V. Pageon, Philip R. Nicovich, Mahdie Mollazade, Thibault Tabarin, Katharina Gaus
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.
Rohlfing et al. Nonrigid image registration in shared-memory multiprocessor environments with application to brains, breasts, and bees.
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).
Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for high-fidelity color printing).
" 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. "
DEPRECATED Use coloc 2!
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.
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
Macenko et al. (2009) A method for normalizing histology slides for quantitative analysis.
Ruifrok and Johnston (2001) Quantification of histochemical staining by color deconvolution.
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).
Image segmentation by representative colors selection. Two versions are available : thresholding positive and negative colors selection and SVM learning
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.
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
Converts an image with multiple color channels to one or more grayscale images.
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
Columbus Image Data Storage and Analysis System
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.
This plugin permit to measure the signal spread of a molecule with respect to the cell area.
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.
Assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation.
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.
Exports connected components data in XLS. Exports All, by T or by ROI
Draws a contour plot on top of a sequence.
> ImageJ/FIJI plugin generating contour lines with equal spacing on top of an image (using overlay).
Converts objects you have identified into an image.
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.
Sample Drift Correction Following 4D Confocal Time-lapse Imaging
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)
CorrectIlluminationCalculate calculates an illumination function that is used to correct uneven illumination/lighting/shading or to reduce uneven background in images.
Schmidt Matthias orcid.org/0000-0002-0161-8326
Ulf-Dietrich Braumann orcid.org/0000-0002-0987-4498
Correlia: an ImageJ plug-in to co-register and visualise multimodal correlative micrographs FLORENS ROHDE, ULF-DIETRICH BRAUMANN, MATTHIAS SCHMIDT. Journal of Microscopy 2020
Correlative Imaging of the Rhizosphere: A Multimethod Workflow for Targeted Mapping of Chemical Gradients
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.
[kaye11](http://stackoverflow.com/users/2307398/kaye11), Curtis Ruden
Stackoverflow: ImageJ counting clumped cells
A workflow combining ImageJ macro and manually using Trainable Weka Segmentation plugin for counting clumped cells.
Algorithm of Find Maxima (ImageJ mailing list)
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.
This plugin explores the algorithms for reconstructing scientific images as a combination of other scientific images drawing from a large database of scientific imagery.
Produces files that allow individual batches of images to be processed separately on a cluster of computers.
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.
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.
Henrik Failmezger, Yinyin Yuan, Oscar Rueda, Florian Markowetz
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.
Select a portion of a sequence in all 5 dimensions.
Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy
CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji
Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.
CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Knime
Deep learning based restoration, with guidelines for training. See also the Fiji plugin.
Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson
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.
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.
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.
Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel
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.
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).
results are compared against two unsupervised methods used in cell segmentation (L2S and CellStar ), and two supervised techniques ANCIS and MultiCell-Net (MCN)
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.
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 for image-based cell profiling
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
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 (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.
This plugins allows debleaching of time sequences of fluorescence images.
Released in 2007, there is a newer "remastered" version "DeconvolutionLab2" (2017)
DeconvolutionLab2 at Bioimedical Imaging Group @ EPFL
DeconvolutionLab2: An open-source software for deconvolution microscopy
Synthetic microtubules - Small 3D data and 3D Theoretical PSF of a realistic specimen
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.
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. Plos computational Biology 2016
DeepCell 2.0: Automated cloud deployment of deep learning models for large-scale cellular image analysis
Fully Convolutional Watershed Distance Transform for 2D Data
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 )
Philip Kollmannsberger orcid.org/0000-0002-8049-61861
Sebastian Britz orcid.org/0000-0002-7566-005X2
Sebastian M. Markert orcid.org/0000-0001-9069-156X2
Version used for the reference publication
DeepCLEM: automated registration for correlative light and electron microscopy using deep learning
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.
Gómez-de-Mariscal, E. et al. DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nat Methods 18, 1192–1195 (2021)
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)
An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks
Produces a grid of desired specifications either manually, or automatically based on previously identified objects.
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
>Plugin to perform Delaunay Triangulation, or draw the Voronoi Diagram for a given point ROI. This plugin comes with Fiji.
A Jython scripting example (but is included as a menu item in Fiji) for screen capturing with certain time delay.
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.
A collection of components for super resolution image data: - Detect Molecules - Reconstruct Image - Results table - Drift correction - Chromatic correction
Six 2D differential operations are implemented in this ImageJ plugin. - Gradient Magnitude - Gradient Direction - Laplacian - Largest Hessian - Smallest Hessian - Hessian Orientation
>This plugin generates theoretical PSFs, assuming they arise only from diffraction.
Some functions for PDE filtering.
free for non-profit use, licensed for profit use
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.
Jean-Yves Tinevez orcid.org/0000-0002-0998-4718
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
Produces an image with measured data on top of identified objects.
DisplayDensityPlot plots measurements as a two-dimensional density plot.
Plots a histogram of the desired measurement.
DisplayPlatemap displays a desired measurement in a plate map view.
DisplayScatterPlot plots the values for two measurements.
DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis
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
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 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/)
MathWorks File Exchange: DNA MicroArray Image Processing Case Study
DNA MicroArray Image Processing Case Study
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.
This ParaViewWeb Docker container is used by the Galaxy Project. Paraview is an VTK based visualization server, for 3D.
Request a non commercial license, download link sent by representatives
List of publications (including image processing publications)
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.
Github for the palm-siever plugin for drift correction
Two workflows are proposed here: one based on fiducials, the other one on cross-correlation.
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 is a collection of two methods (DropSnake and LBADSA) for high-accuracy measure of contact angles for drop measurement.
DropSnake is based on B-spline snakes (active contours) to shape and measure a drop.
> a dynamic version of the Reslice command. Bundled with Fiji.
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)).
Exponential splines and minimal-support bases for curve representation
Snakes with an Ellipse-Reproducing Property
Spline-based framework for interactive segmentation in biomedical imaging
>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.
A Mathematica package available for the symbolic computation of exponential spline related quantities: B-splines, Gram sequence, Green function, and localization filter.
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—an R package for image processing with applications to cellular phenotypes
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
Color space conversions between image modes.
A function to perform morphological operation on binary and grayscale images.
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.
Fill holes in objects Included into EBImage Image processing and analysis toolbox for R
Filters an image using the fast 2D FFT convolution product.
flop mirrors x around the image vertical axis (horizontal reflection).
Process an image using Perreault’s modern constant-time median filtering algorithm.
Computes the oriented contour of objects.
Function to perform an erosion followed by a dilation morphological operation on binary and grayscale images.
rgbImage combines Grayscale images into a Color one.
deletes objects from an image by setting their pixel intensity values to 0.
Transposes an image by swapping its spatial dimensions.
Perrine Paul-Gilloteaux orcid.org/0000-0003-3903-4841
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.
Automatic registration in 2D or 3D based on detection or binary mask. Takes images with detections already done on it.
Edge detection by Deriche's method.
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.
Christoher Schmied https://orcid.org/0000-0003-2058-1124
Helena Klara Jambor https://orcid.org/0000-0003-3397-1842
Effective image visualization for publications – a workflow using open access tools and concepts
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.
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
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 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.
View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset
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 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.
EnhanceEdges enhances or identifies edges in an image, which can improve object identification or other downstream image processing.
EnhanceOrSuppressFeatures enhances or suppresses certain image features (such as speckles, ring shapes, and neurites), which can improve subsequent identification of objects.
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.
Evaluate 3D data with a bead calibration sample
as of 20180529, links are not working due to web defacement.
(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.
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.
Details how to listen and use events provided by the main interface.
Shows how to listen active sequence / viewer events.
Ma, H., Jiang, W., Xu, J. et al. Enhanced super-resolution microscopy by extreme value based emitter recovery. Sci Rep 11, 20417 (2021)
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.
ExpandOrShrinkObjects expands or shrinks objects by a defined distance.
Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy Images
Model-based 2.5-D deconvolution for extended depth-of-field in brightfield microscopy
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.
"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.
"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.
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.
This plugin allows to open images embedded in PDFs.
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
The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive user interaction based on your algorithm’s parameters.
The EzPlug library is meant to help developers write plug-ins fast and efficiently. This tutorial shows EzPlug's features.
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
Abraham, A.V, Ram, S., Chao, J, Ward, E. S, Ober, R. J.
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.
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
Praveen Pankajakshan, Timothée Lecomte, Stephane Dallongeville
Fast Fourier Transform (FFT) for 2D/3D images.
A Fast Multilevel Algorithm for Wavelet-Regularized Image Restoration
A Fast Thresholded Landweber Algorithm for Wavelet-Regularized Multidimensional Deconvolution
Fast Multilevel Thresholded-Landweber Deconvolution Algorithm
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
Online documentatoin (Archived old website image)
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)) )
Asm Shihavuddin orcid.org/0000-0002-4137-9374
FastSME: Faster and Smoother Manifold Extraction From 3D Stack.
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.
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.
Representation of Local Geometry in the Visual System
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
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.
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, an ImageJ plug-in to quantify fibrillar structures in raw microscopy images
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.
Mutterer J., Zinck E., J. Microscopy, 2013
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.
GPL v2 (and others: http://fiji.sc/Fiji:About)
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.
Jefferis Gregory orcid.org/0000-0002-0587-9355
Working version of a simple GUI frontend for CMTK image registration tools in Fiji
Fiji Archipelago is a tool designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other computers.
Neubias BIAFLOWS workflow of Filament Tracing 3D with ImageJ
Neubias BIAFLOWS workflow of Filament Tracing with LocThresh ImageJ
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,
Neubias BIAFLOWS workflow of Filament Tracing with ImageJ
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.
Filopodyan: An open-source pipeline for the analysis of filopodia in JCB 2017
Fiji plugin for detecting, tracking and quantifying filopodia
Provides a selection of spatial, separable and customizable filters in 1D and 2D, with OpenCL implementation if supported.
FilterObjects eliminates objects based on their measurements (e.g., area, shape, texture, intensity).
Find cells using nuclear and membrane fluorescence
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, Draw and Measure Wells in a Multi-Well Plate Picture
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.
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).
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 distance calculation with all those maxima considered equal. For a video detailing how this algorithm works please see: https://youtu.be/f9vXOMKOlaY Or for examples of it being used in practise, please see: https://youtu.be/9wvPsEzRWzI
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: automatic counting of transcripts in 3D FISH images
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 in Human Spermatozoids macro
User guide - FISH Signals detection in Human Spermatozoids
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.
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.
Download last windows version from GitHub
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.
Fit a model for the growth of yeast cells
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)
CellProfiler 3.0: Next-generation image processing for biology
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).
Grab random images from Flickr : in recent uploads in interestingness stream from tags search
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)
FlipAndRotate flips (mirror image) and/or rotates an image
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.
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.
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 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 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.
Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.
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.
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.
FMRIB's Linear Image Registration Tool FLIRT
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
Non linear registration intensity based for MRI brain exams. To be applied after FLIRT
FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets.
Arp2/3 Is Critical for Lamellipodia and Response to Extracellular Matrix Cues but Is Dispensable for Chemotaxis
High-Resolution Quantification of Focal Adhesion Spatiotemporal Dynamics in Living Cells
The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics
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.
Link to manual (please select for latest release).
FoCuS-point download page (please select for latest release).
FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting.
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.
Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data
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.
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)
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
Creative Commons Attribution - ShareAlike 4.0 International license
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.
>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/).
A. Karperien, Charles Sturt University, Australia/Canada, Earth 2007-2012
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 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.
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 and Wavelets," SIAM Review, vol. 42, no. 1, pp. 43-67, March 2000
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
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.
Publication about imaging workflows in Galaxy
Image analysis tools to be used within Galaxy
Galaxy instance with tools for Image analyses shipped in a Docker container.
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.
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.
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.
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
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
Kenneth S. Campbell and Mihail I. Mitov, University of Kentucky
N/A (available at no cost to academic users)
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
This is a set of Matlab routines for computing generalized Daubechies wavelet filters.
Generalized Riesz-Wavelet Toolbox for Matlab
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.
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.
Creative Commons Attribution-ShareAlike 4.0 International License
>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/)**
Gratton Enrico orcid.org/0000-0002-6450-7391
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 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."* *
G. Srinivasa, M. C. Fickus, Y. Guo, A. D. Linstedt and J. Kova?evi?
Active mask segmentation of fluorescence microscope images
Golgi Segmentation by Active Mask framework
Segmentation of Golgi. Sample Images can be found here.
see http://bigwww.epfl.ch/thevenaz/differentials/index.html#LegalBlurb
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/
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.
The grayscale watershed segmentation is useful to segment particles in contact when the model of shape is unknown a priori.
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
CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology
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.
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.
H2 database packaged as an Icy plugin See http://www.h2database.com
Comparison with other methods (from the same authors)
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 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".
MiToBo - A microscope image analysis toolbox
A Toolbox for Image Processing and Analysis, Journal of Open Research Software, 2016, 4:e17
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() ```
Explanation of the Helmholtz Analysis ImageJ Plugin
Measurement of muscle disease by quantitative second-harmonic generation imaging
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).
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/
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.
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.
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.
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".
[Fabrice Duprat](https://www.ipmc.cnrs.fr/~duprat/ipmcgb.htm#debut)
Macro for calculating empty surfaces on histological slices (ex: tubules in a kidney).
An ImageJ macro for calculating empty surfaces on histological slices (ex: tubules in a kidney).
Atlan, Michael https://scholar.google.fr/citations?user=e_K90MoAAAAJ&hl=en
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 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).
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
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.
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
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: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi
Example, data sets available from the paper
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 is a simple commodity class that eases communication between Bitplane Imaris and MATLAB or python using the Imaris XT interface.
Implementation of some image correlation spectroscopy tools
de Chaumont, Fabrice orcid.org/0000-0001-7613-7204
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 headless Intuitive user interface Online management of plugins Connect Icy to Matlab Interactive widgets Build your graphical interface with EzPlug Use the power of your graphic card with OpenCL Loaded with 20 up-to date libs Weaknesses No tutorial for plugins writing..yet See here: http://icy.bioimageanalysis.org/index.php?display=devDoc http://icy.bioimageanalysis.org/index.php?display=detailTag&tagId=29 and here: http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy and also here: http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy Image size limited to 2GigaByte per single 2D channel (means that an image of 40.000x40.000 can be handle by Icy. Still big !) Still you can have a stack of 100000x40Kx40kxUnlimited number of channel if you have RAM. Will be improved
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.
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"
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.
a book by Weickert about anisotropic diffusion, theoretical basis of this filter
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.
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.
For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.
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.
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.
Add a layer on an image to display the detections
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.
Fills holes below a given threshold. 3D data is currently processed slice per slice.
Fills the holes in all the ROI of the active sequence (also works in Protocols).
Automated Quantification of Cell Endocytosis Using Active Contours and Wavelet
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.
This plugin provides import and export Icy sequences into Matlab native .mat files from the protocol framework.
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.
Image filtering using anisotropic structure tensor for cell membrane enhancement in 3D microscopy
Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned byte of short format.
This plugin can display a 2D flow as a color-coded sequence, following the Middlebury color code.
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).
OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org
A slightly different painter than Overlay tutorial 1, focusing on canvas parameters instead of image parameters.
Icy Particle tracking benchmark generator
Multiple Hypothesis Tracking for Cluttered Biological Image Sequences
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.
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 Widefield Fluorescence Microscope PSF
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.
An image analysis toolbox for high-throughput C. elegans assays
Identifies dead worms based on a couple of parameters.
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.
This module lets you outline the objects in an image using the mouse.
Identify objects (as nuclei) within an image without needing the assistance of another cellular feature (as cell).
IdentifySecondaryObjects identifies objects (e.g., cells) using objects identified by another module (e.g., nuclei) as a starting point.
Allows the identification of objects by subtracting secondary objects from primary objects. For example allows to segment the cytoplasm by subtracting nuclei from cells.
de Polavieja, Gonzalo G. (orcid.org/0000-0001-5359-3426)
Free Non-comercial use, Patented PCT/ES2013/070585
Pérez-Escudero et. al. (2014) "idTracker: tracking individuals in a group by automatic identification of unmarked animals"
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
idtracker.ai: Tracking all individuals in large collectives of unmarked animals (arXiv preprint)
idtracker.ai: tracking all individuals in small or large collectives of unmarked animals (Nature Methods)
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.
## 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:
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.
Conference paper describing the first release of ilastik (version 0.5)
ilastik: interactive machine learning for (bio)image analysis
Some example applications and screenshots
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), few parameters, larger-than-RAM data, multi-dimensional data (time, 3D space, channel), headless operation, batch mode, parallelized computation, open source Weaknesses: Pre-built workflows (not reconfigurable), no plugin system, visualization sometimes buggy, must import 3D data to HDF5, tracking requires an external CPLEX installation Supported Formats: hdf5, tiff, jpeg, png, bmp, pnm, gif, hdr, exr, sif
Fully-automated cell tracking of 2D+time or 3D+time images with some parameter tuning
Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images
Semi-automated segmentation of 3D objects (e.g. neurons) based on user-provided seeds.
Learning to Count with Regression Forest and Structured Labels
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.
Semi-automated cell tracking of 2D+time or 3D+time images based on manual annotations
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.
Thomas Laurent orcid.org/0000-0001-7686-3249
Example of dataset and associated trained model
Image-classification with deep learning in KNIME
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.
Microsoft Research Interactive Visual Media Group
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).
Christian Tischer orcid.org/0000-0003-4105-1990
Coralie Muller orcid.org/0000-0002-5186-1666
Jean-Karim Heriche orcid.org/0000-0001-6867-9425
Kimberly Meechan orcid.org/0000-0003-4939-4170
The Image Data Explorer: Interactive exploration of image-derived data
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.
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.
This plugin parses arbitrary mathematical expressions and compute results using images as variables.
Image registration in Matlab with Image Processing Toolbox
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.
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)
Globally optimal stitching of tiled 3D microscopic image acquisitions
The plugin performs stitching of images of a tiled scan to reconstruct the image of the whole sample.
Browse files in directories with thumbnails view
Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber
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.
BioImage Analysis Tool for all! ImageJ2
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."
Ignacio Arganda-Carreras orcid.org/0000-0003-0229-5722
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
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.
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.
List of Built-in Macro Functions (ImageJ website)
ImageJ source code (go to ij.Macro package then Functions java file)
A set of ImageJ Built-in Macro Functions used to perform operations on the ImageJ platform.
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.
Downey MJ, Jeziorska DM, Ott S, Tamai TK, Koentges G, Vance KW, Bretschneider T.
Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution
## 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.
A Non-Local Algorithm for Image Denoising
ImageJ Plugin for Non-Local-Means Filtering
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.
An unbiased detector of curvilinear structures
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.
This ImageJ function automatically or interactively sets lower and upper threshold values, segmenting grayscale images into features of interest and background.
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 integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".
ImageMath performs simple mathematical operations on image intensities, like addition, subtraction, multiplication, division...
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
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.
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)
ImarisTrack allows 3D tracking of spots and objects, with straightforward manual adjustment of automatic tracking results.
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.
Stephan Saalfeld, Stephan Preibisch, Tobias Pietzsch, Curtis Rueden, Barry DeZonia, Christian Dietz, Martin Horn, Mark Hiner, et al
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 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.
Tuominen et al. (2011) ImmunoMembrane: a publicly available web application for digital image analysis of HER2 immunohistochemistry
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: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67
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.
David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong
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
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.
Dufour Alexandre orcid.org/0000-0002-9417-7389
Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a block for Protocols
A novel real time imaging platform to quantify macrophage phagocytosis
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.
Infection Counter: Automated Quantification of in Vitro Virus Replication by Fluorescence Microscopy
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).
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.
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.
Jafarpour Aliakbar orcid.org/0000-0002-1460-5743
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.
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
Integrates hardware control of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of identified regions of interest.
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.
Plots an intensity profile of a given ROI. Can plot mean over T or/and Z too.
This plugin can be used for inferring spatial interactions between patterns of spot-like objects in images or between coordinates read from a file.
quote: >This plugin allows to apply a free affine transformation to a 2D image in an interactive way.
Interactive Density Counting using ilastik
Similar view in the tensorflow embedding projector
Download the workflow from the KNIME-Hub
Interactive features visualization in KNIME
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 Moving Least Squares (ImageJ)
ImageJ macro - Interactive Volume of Interest Extractor in Large 3D Stacks
User guide - Interactive Volume of Interest Extractor in Large 3D Stacks
Interactive Volume of Interest Extractor in Large 3D Stacks
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 on the ImageJ wiki
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.
IR Tools: A MATLAB Package of Iterative Regularization Methods and Large-Scale Test Problems
A MATLAB Package of Iterative Regularization Methods and Test Problems for Linear Inverse Problems (for Matlab Version 9.3 or later).
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
Dedicated to score tracking dataset from the ISBI tracking challenge
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
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.
Heinrich et al. "Deep Learning for Isotropic Super-Resolution from Non-Isotropic 3D Electron Microscopy."
Super-resolve anisotropic EM data along low-res axis with deep learning.
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.
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
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
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.
Cordeliéres et. al. (2013) Automated Cell Tracking and Analysis in Phase-Contrast Videos (iTrack4U): Development of Java Software Based on Combined Mean-Shift Processese
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!
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 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.
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: a tool for automated and reproducible bioimage analysis
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 for ImageJ
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.
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)
User guide and detailed computations of parameters
Junction Mapper is a novel computer vision tool to decipher cell–cell contact phenotypes (Elife 2019) Helena Brezovjakova, Chris Tomlinson, et al
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.
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.
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
Python engine for Icy, based on Jython. Required for: CalloseCounter, BioFlow, EvaFE In Python, Python Plugin Packager, Python Extractor, Jython execnet for Icy
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.
Quantize a color image in any given number of colors.
The input image is aligned using a simple cross-correlation approach on the smoothed image. This node is contained in KNIME Image Processing extension
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
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
Applies average filtering to images in n-dimensions
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 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.
The method to use for thresholding. Currently only OTSU is available.
Max Planck Institute for Medical Research in Heidelberg, Germany
KNOSSOS - 3D image visualization and annotation tool
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 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.
Curvelet analysis of kymograph for tracking bi-directional particles in fluorescence microscopy images
bioRxiv 329300 Bidirectional intraflagellar transport is restricted to only two microtubule doublets in the trypanosome flagellum
Generation of Kymographs using 2D+t images. In the generated kymographs, objects can be tracked and the results are visualized.
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 images according to their position in plates.
Schmidt Deborah orcid.org/0000-0002-8621-9438
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
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: The LocAlization Microscopy Analyzer
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.
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.
Neubias BIAFLOWS workflow of landmark detection with DMBL models (Prediction)
Global localization of 3D anatomical structures by pre-filtered Hough Forests and discrete optimization
Landmark detection DMBL model prediction
This workflow predict landmark positions on images by using DMBL landmark detection models.
Neubias BIAFLOWS workflow of landmark detection with DMBL models (Training)
This workflow trains DMBL landmark detection models from a dataset of annotated images.
Neubias BIAFLOWS workflow of landmark detection with LC models (Prediction)
Robust and Accurate Shape Model Matching Using Random Forest Regression-Voting
This workflow predict landmark positions on images by using LC landmark detection models.
Neubias BIAFLOWS workflow of landmark detection with LC models (Training)
This workflow trains LC landmark detection models from a dataset of annotated images.
Neubias BIAFLOWS workflow of landmark detection with MSET models (Prediction)
Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach
Landmark detection MSET models prediction
This workflow predict landmark positions on images by using MSET landmark detection models.
Neubias BIAFLOWS workflow of landmark detection with MSET models (Training)
This workflow trains MSET landmark detection models from a dataset of annotated images.
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/
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...)
LBADSA is based on the fitting of the Young-Laplace equation to the image data to measure drops.
The Multiplicity of Cellular Infection Changes Depending on the Route of Cell Infection in a Plant Virus
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
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.
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.
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
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
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 Stack Alignment with SIFT (ImageJ)
LobSTEr : handle terabyte of data without concerns about the memory available . 75 workflows available no programming , matlab based
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
Center for machine vision and signal analysis (Oulu University)
Local Phase Quantization (LPQ) descriptors
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
Thresholding method The used thresholding Method: Mean, Median, Sauvola, MidGrey, Bernsen, Niblack. Mean, Niblack and Sauvola are implemented using the fast integral image approach.
Tinevez Jean-Yves orcid.org/0000-0002-0998-4718
The main paper contains a comparison of LZP performance against existing software of this category.
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.
Computes signed curvature along a line.
Localization microscopy filtering using PALMsiever
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.
Sage et al. (2005) Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics
>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"); ```
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.
Whole Slide Quantification of Stromal Lymphatic Vessel Distribution and Peritumoral Lymphatic Vessel Density in Early Invasive Cervical Cancer: A Method Description
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.
automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)
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.
Alexandre Dufour https://orcid.org/0000-0002-9417-7389
Ads a magnifier on top of the default 2D viewer to zoom in and inspect individual pixel values
Coelho, L.P. 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software 1(1):e3
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.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) ```
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 / Multidimensional interpolation
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/.
Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking
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.
Louveaux, Marion orcid.org/0000-0002-1794-3748
Rochette, Sébastien orcid.org/0000-0002-1565-9313
Marion Louveaux mamut2r Github repository
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.
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.
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
An ImageJ plugin for manually tracking objects by mouse clicking. This plugin is bundled with Fiji.
Tinevez et al (2017) TrackMate: An open and extensible platform for single-particle tracking
Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji).
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.
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.
Alexandre Dufour; https://orcid.org/0000-0002-9417-7389
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.
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.
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 is famous, so this page is only for being the landing page for components and workflows.
Arteta et al (2012) Learning to Detect Cells Using Non-overlapping Extremal Regions
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.
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)
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
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
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.
Import Matlab *.mat files as sequences in Icy.
Use Icy as an image viewer from Matlab.
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 is a comprehensive library for creating static, animated, and interactive visualizations in Python.
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.
Minimum/Maximum/Median page at ImageJ.net website
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.
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
Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite.
Beier et al. "Multicut brings automated neurite segmentation closer to human performance"
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 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 of organelles from nucleus in 3D
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.
This module has been deprecated; in Cell Profiler 3.0, it is a function in module "Measurement"
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.
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
not available anymore in version 3.0 and up?
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)
quote: > MeasureObjectIntensityDistribution measures the spatial distribution of intensities within each object. Old Name: MeasureObjectRadialDistribution
It measures the degree and nature of textures within images and objects to quantify their roughness and smoothness.
Steven Busschotsa, Sharon OTooleb, John J. OLearya, Britta Stordal
Measuring confluence in adherent cell cultures
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 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.
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 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.
A static image of the website (a old version downloadable)
MetroloJ: an ImageJ plugin to help monitor microscopes’ health.
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.
user tutorial and documentation for development and scripting
MeVisLab XMarkerShortestPath module (Dijsktra shortest path)
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.
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 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 tracks multiple mice from a top view video.
Adrien Ducret, Yves Brun, Ellen Quardokus
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.
Used to be the micro manager libraries but now that is an empty plugin (provided for backward compatibility).
Microscope Advanced Acquisition (deprecated)
Non-Profit Open Software License 3.0 (NPOSL-3.0)
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.
Calibrator for Pixel Size in Calibrator manager.
Microscope Image Correlation Spectroscopy MICS
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.
Deprecated ! Use the new Micro-Manager blocks plugin.
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.
Parton et al (2011) A PAR-1-dependent orientation gradient of dynamic microtubules directs posterior cargo transport in the Drosophila oocyte
Microtubule end tracking in Drosophila Oocyte
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)
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
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.
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).
A Java package for running ImageJ and Fiji within Matlab.
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.
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.
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.
Freely available upon request to the author
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.
"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."
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.
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).
Whole-body integration of gene expression and single-cell morphology
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.
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
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 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.
Displays 3D data as 2D montages of all slices.
Perform morphological operations (like erode and dilate or open and close) on images.
This module performs a series of morphological operations on a binary image or grayscale image, resulting in an image of the same type.
Pierre Barbier de Reuille, http://orcid.org/0000-0002-9970-765X
Richard S Smith, http://orcid.org/0000-0001-9220-0787
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
Eric Biot (eric biot AT versailles inra fr)
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 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 to isolate objects
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 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.
Icy Morphomath operators: erosion, dilation, opening, closing, top-hat, gradient, distance map, skeleton and watershed.
Faure Emmanuel orcid.org/0000-0003-2787-0885
Nature Communications 2019 : MorphoNet: an interactive online morphological browser to explore complex multi-scale data
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.
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.
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.
A. Shivanandan, A. Radenovic, and I. F. Sbalzarini
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.
User-Friendly Semiautomated Assembly of Accurate Image Mosaics in Microscopy
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.
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.
3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution
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 with mean-square displacement
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 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
Realistic Analytical Phantoms for Parallel Magnetic Resonance Imaging
Tutorial explaining the principles of MSD analysis and how to use the tool.
Publication for which the tool was built.
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.
Heath Patterson orcid.org/0000-0002-0064-1583
Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy
Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy
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
Meijering et al (2012) Methods for Cell and Particle Tracking
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.
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)
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 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).
Drag, rotate & zoom in your image using two-finger gestures (in 2D and 3D).
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.
An example Clojure script illustrating how to run concurrent threads that perform independent tasks, and how to combine their results afterwards.
Multithreaded Image Processing in Javascript
Tomancak Pavel orcid.org/0000-0002-2222-9370
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.
Muscle stem cells contribute to myofibres in sedentary adult mice
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 ...
Fernández et al. (2014) Automated Detection and Measurement of Isolated Retinal Arterioles by a Combination of Edge Enhancement and Cost Analysis.
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 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.
Set of Tools for super resolution microscopy
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.
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.
Costa et al. "NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases"
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 Plugin Github repository in Vaa3D
High-throughput computer method for 3d neuronal structure reconstruction from the image stack of the Drosophila brain and its applications
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).
J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero Patch-based non-local functional for denoising fluorescence microscopy image sequence
Fast live simultaneous multiwavelength four-dimensional optical microscopy
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.
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.
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).
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.
The NEMO dots assembly: Single-particle tracking and analysis
This workflow presents single-particle tracking in Fiji using Track-Mate, and track motility analysis in MATLAB using @msdanalyzer.
Blin Guillaume orcid.org/0000-0002-9295-237X
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.
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.
Neurogeometry Group Northeastern University main page
Automated Tracing of Neurites from Light Microscopy Stacks of Images
Neural Circuit Tracer Tool main page (example videos)
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."
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
NeuriteTracer pug-in page - McGill University Fournier Lab
NeuriteTracer: A novel ImageJ plugin for automated quantification of neurite outgrowth
"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)
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: an R platform for medical imaging analysis
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.
GitHub (Install with NVM) see building section.
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
slightly revised MIT License. Note the eigen library of NeuroGPSTree use MPL2 licenses when such situations are specified and documented
NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites
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 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
GNU General Public License as published by the Free Software Foundation
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.
Neubias BIAFLOWS workflow of Neuron Tracing 3D with ImageJ
Neubias BIAFLOWS workflow of Neuron Tracking with Rivuletpy (Rivulet 2)
Automated 3-D Neuron Tracing With Precise Branch Erasing and Confidence Controlled Back Tracking
Rivuletpy dockerised workflow for BIAFLOWS.
Neubias BIAFLOWS workflow of Neuron Tracking with Vaa3d APP2
Vaa3d All-Path-Pruning 2.0 (APP2) dockerised workflow for BIAFLOWS.
Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d BJUT Fast Marching Spanning Tree
Neuron Tracing Vaa3D (BJUT FM Spanning Tree)
Vaa3d BJUT Fast Marching Spanning Tree algorithm dockerised workflow for BIAFLOWS
Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d MOST
3D Neuron Tracing with a Dockerized version of Vaa3D MOST Raytracer.
Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d MST
3D Neuron Tracing using Dockerized version of Vaa3D Minimum Spanning Tree (MST).
Design and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence Microscopy Images
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.
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
Currently, the original web page for download seems to be gone ( relocated ?)
New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales
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: An automatic neuronal morphology quantification method and its application in pharmacological discovery
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.
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.
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.
A toolbox to chain image analysis processes.
Li W., Wang G., Fidon L., Ourselin S., Cardoso M.J., Vercauteren T.
list of example pre-trained networks with doc
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.
Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pepper, etc.) to a sequence. ICY plugin.
Noise Suppression using Simple Spatial Filters
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 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.
Neubias BIAFLOWS workflow of nuclei segmentation with ImageJ
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.
Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ImageJ
Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ)
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.
Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ilastik
Nuclei Segmentation 3D (NucleiSegmentation3D-ilastik)
Execute Nuclei Segmentation in 3D images using pixel classification with ilastik.
Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ)
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.
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.
Neubias BIAFLOWS workflow of nuclei segmentation with CellProfiler pipeline
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.
Neubias BIAFLOWS workflow of Nuclei Segmentation with DeepCell
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
Nuclei Segmentation using Deep Learning for single cell analysis (DeepCell).
Neubias BIAFLOWS nuclei segmentation project
Neubias BIAFLOWS workflow of Nuclei Segmentation with Ilastik and Python
Ilastik: Interactive learning and segmentation toolkit
NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.
Mask R-Matterport - CNN for object detection and instance segmentation on Keras and TensorFlow
Neubias BIAFLOWS workflow of Nuclei Segmentation with Mask-RCNN
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.
Neubias BIAFLOWS workflow of nuclei segmentation with Python
This workflow processes images of cells with discernible nuclei and outputs a binary mask containing where nuclei are detected.
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.
Neubias BIAFLOWS workflow of Nuclei Segmentation with U-Net
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
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.
BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION
Neubias BIAFLOWS workflow of nuclei tracking with ImageJ
BIAFLOWS-PROBLEM: NUCLEI-TRACKING-NODIVISION
Neubias BIAFLOWS workflow of Particle Tracking with TrackMate
TrackMate: An open and extensible platform for single-particle tracking
Track non-dividing particles in 2D time-lapse image.
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.
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.
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 (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!
The spatial frequency cut-off in three-dimensional imaging
This plugin calculates the Nyquist sampling, in the radial and axial direction for your Microscope.
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.
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
Neubias BIAFLOWS workflow of Object Tracking with ImageJ
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.
DEscription of the algorithm from Cell Tracking Challenge Page
Neubias BIAFLOWS workflow of Object Tracking with MU-Lux
DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed
Cell tracking using MU-Lux-CZ algorithm. Dockerized Workflow for BIAFLOWS implemented by Martin Maska (Masaryk University).
Neubias BIAFLOWS workflow of Object Tracking with Octave
LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data
Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version).
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.
Jmy regulates oligodendrocyte differentiation via modulation of actin cytoskeleton dynamics
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 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
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.
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.
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
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.
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: An automated tool for comet assay image analysis
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 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
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.
Camera calibration and 3D reconstruction (calib3d module)
OpenCV / Camera Calibration and 3D reconstration
Computational photography (photo module)
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.
2D Features framework (feature2d module)
OpenCV / flann. Clustering and Search in Multi-Dimensional Spaces
High Level GUI and Media (highgui module)
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.
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 (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.
Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, M. Satyanarayanan
>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.
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.
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.
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: A versatile deep learning platform for tracking and analysis of single-organoid dynamics
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.
Compare OrganoSeg against CellProfiler1, MorphoLibJ1, and ImageJ
Download OrganoSeg in Supplementary File S1
OrganoSeg publication at Scientific Reports
OrganoSeg is an open-source software that integrates segmentation, filtering, and analysis for breast-cancer spheroid and colon and colorectal-cancer organoid morphologies.
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.
Live Neuron Morphology Automatically Reconstructed From Multiphoton and Confocal Imaging Data
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.
Jodogne, S. The Orthanc Ecosystem for Medical Imaging. J Digit Imaging 31, 341–352 (2018).
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.
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.
Oufti (compiled version, Matlab independent)
Paintdakhi et al (2015) Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis
Sliusarenko et al (2011) High‐throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio‐temporal dynamics
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).
GIT HUB, but comes with CellProfiler main installation
OverlayOutlines is a module from CellProfiler to place outlines of objects over a desired image.
Hanslovsky Philipp orcid.org/0000-0002-9416-6516
Nunez-Iglesias Juan http://orcid.org/0000-0002-7239-5828
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 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 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
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
An ImageJ plugin for iterative deblurring.
Ahrens, James, Geveci, Berk, Law, Charles, ParaView: An End-User Tool for Large Data Visualization, Visualization Handbook, Elsevier, 2005, ISBN-13: 978-0123875822
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.
Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology
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
Neubias BIAFLOWS workflow of Particle Tracking with ImageJ
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).
[PDF] u-track Documentation Release 2.1.2
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.
A fun simulator. It's not very useful for biology but it's a good demo!
Bokota Grzegorz orcid.org/0000-0002-5470-1676
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 analysis of the large microscopic 3D image data. PartSeg provides well established algorithms in an easy-touse, intuitive, user-friendly toolbox without sacrificing their power and flexibility. Examples include Chromosome territory analysis.
not available on version 2.1 and up.
Perrine Paul Gilloteaux orcid.org/0000-0003-3903-4841
Protocol can be downloaded from Icy toolbar
performing automatic registration for CLEM
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.
Fluorescence Recovery After Photobleaching (FRAP) of Fluorescence Tagged Proteins in Dendritic Spines of Cultured Hippocampal Neurons
Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment
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"
Jaccard et. al. (2013) Automated Method for the Rapid and Precise Estimation of Adherent Cell Culture Characteristics from Phase Contrast Microscopy Images
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, Nature Methods 9, 635–637 (2012)
An easy to use, image analysis software package that enables rapid exploration and interpretation of microscopy data.
Hariharan, Santosh; orcid.org/0000-0002-0941-0044
Mergenthaler, Philipp; orcid.org/0000-0002-9753-6711
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.
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/).
This plugin calculates the optic flow for each pair of images made with the given stack.
BIAFLOWS-PROBLEM: GLAND-SEGMENTATION-TEST
Neubias BIAFLOWS workflow of pixel classification with UNet
Pixel classification for GlaS challenge with UNet
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.
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, an ImageJ plug‐in for FRET calculation that can accommodate variations in spectral bleed‐throughs
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
Web based application for deep learning cell classifier . Aim to replace cellprofiler analyst and advanced cell classifier . Under construction.
plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics
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.
Sibarita Jean-Baptiste orcid.org/0000-0002-9920-7700
Github repository of PoCA with code source and compiled versions for Windows
Original publication link in Nature Methods
Few datasets are available with the compiled version of PoCA
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.
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.
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 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.
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.
ImageJ Macro: Protein MicroArray Analysis
User guide - Protein MicroArray Analysis
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
PSF Generator at Bioimedical Imaging Group @ EPFL
3‐D PSF fitting for fluorescence microscopy: implementation and localization application
Comparison of Deconvolution Software in 3D Microscopy
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 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.
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 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.
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.
Binary Pattern Dictionary Learning for Gene Expression Representation in Drosophila Imaginal Discs.
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.
Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials
This is a (Cython-based) Python wrapper for Philipp Krähenbühl's Fully-Connected CRFs (version 2).
GitHub repo of pyimagej: Python wrapper for ImageJ
PyImageJ: A library for integrating ImageJ and Python
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.
Detection and Localization of Drosophila Egg Chambers in Microscopy Images.
Region growing using superpixels with learned shape prior.
Supervised and unsupervised segmentation using superpixels, model estimation, and Graph Cut.
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.
>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
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.
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
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 is a programming language.
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-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.
Vebjorn Ljosa, Lee Kamentsky, Johannes Schindelen
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.
**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 is an open-source machine learning library for Python, based on Torch, used for applications such as natural language processing.
Automatic localization of interest points in zebrafish images with tree-based methods
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
Towards Generic Image Classification using Tree-based Learning: an Extensive Empirical Study
Pyxit object classification model builder
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).
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).
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
Raphaël Marée, Gilles Louppe, Loic Rollus, Olivier Caubo, Benjamin Stévens
Fast Multi-Class Image Annotation with Random Subwindows and Multiple Output Randomized Trees
A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning
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.
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.
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 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 of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase
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.
Stirling David orcid.org/0000-0001-6802-4103
Analysis tools to quantify dissemination of pathology in zebrafish larvae
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.
Fiji colour deconvolution page (same plugin)
Ruifork and Johnston (2001), Quantification of histochemical staining by color deconvolution
[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...*
Quantitative mapping of averaged focal adhesion dynamics in migrating cells by shape normalization
Quantitative analysis of focal adhesion dynamics
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").
Horzum et al. (2014) Step-by-step quantitative analysis of focal adhesions
Quantitative analysis of focal adhesions
Simple workflow description for ImageJ, step-by-step description for delineating focal adhesions, count and characterize their positions. Measurement of dynamics is not involved.
Imaging fluorescence (cross-) correlation spectroscopy in live cells and organisms
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 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.
Piotr Baniukiewicz (ORCID: 0000-0002-4687-9407)
Till Bretschneider (ORCID: 0000-0002-5317-603X)
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 (Dormann et al., 2002; Tyson et al., 2010; Tyson et al., 2014).
Bankhead Peter orcid.org/0000-0003-4851-8813
QuPath is open source software for Quantitative Pathology. QuPath has been developed as a research tool at Queen's University Belfast.
Wolter et al (2012) rapidSTORM: accurate, fast open-source software for localization microscopy
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).
[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.
Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications
RATS: Robust Automatic Threshold Selection
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 for Parallel MRI
Reconstruct Software Main page (link to user manual)
Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images
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."
Image segmentation based on the MOSAIC Discrete region competition algorithm.
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.
Albert Cardona, Ignacio Arganda-Carreras and Stephan Saalfeld
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.
It is an interactive front-end visualization for registration software based on Elasix (VTK/ITK)
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
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).
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.
**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.
Paul-Gilloteaux, Perrine ORCID: 0000-0002-4822-165X
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
Resolving the process of Clathrin mediated endocytosis using Correlative Light & Electron Microscopy (CLEM)
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.
Most of RestoreTools is now bundled with IR tools.
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.
Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking
"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)
Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking
A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis
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
This tutorial explain how to create an intensity profile over an ROI.
ROI-Measures from Alexandre Dufour's Github repositoty
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.
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.
R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava
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, ...)
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.
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.
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 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.
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nature Protocols 7, 80–88 (2012)
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: a tool to build publication-ready scientific figures. Aigouy B, Mirouse V. Nat Methods.
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.
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.
Scikit-image Documentation (Manual, installation guides, introductory examples)
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) 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)
J.M. de la Rosa Trevín orcid.org/0000-0002-3320-1269
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 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!
Harrington Kyle orcid.org/0000-0002-7237-1973
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/
Watersheds in digital spaces: An efficient algorithm based on immersion simulations
Fiji-Squassh colocalization plugin notes by Chong Zhang
Rizk et al. (2014) Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
The reference above in PDF @ MOSAIC website
Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
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.
CBIA site on RELIABLE SEGMENTATION AND TRACKING OF ORGANOIDS
IEEE Transactions on Medical Imaging publication
Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy
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 of Clustered Cells in MATLAB
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.
Johannes Schindelin, Francois Kusztos, Benjamin Schmid
High-throughput quantification of early stages of phagocytosis
Image-Based Analysis of Phagocytosis: Measuring Engulfment and Internalization
Semi-automated quantification of three stages of phagocytosi using ImageJ
The authors present an ImageJ-based, semi-automated phagocytosis workflow to rapidly quantitate three distinct stages during the early engulfment of opsonized beads.
This protocol takes a folder containing images as input and extract each channel in a separate sub folder.
Zanella et al (2013) Towards real-time image deconvolution: application to confocal and STED microscopy
SGP-dec, A Scaled Gradient Projection method for 2D and 3D images deconvolution
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).
The Fourier Reconstruction of a Head Section
Shiny is an R package that makes it easy to build interactive web apps straight from R.
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.
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.
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
Schermelleh, Lothar orcid.org/0000-0002-1612-9699
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.
Explanation of how to tune MSER parameters
Source: https://github.com/kapoorlab/Fiji-MSER, https://github.com/kapoorlab/MasterPanels
A simple MSER based segmentation tool for spot detection in 2/3/4D.
MSER based on implementation in imglib2 provided as an interactive GUI tool for spot detection in 2/3/4D images.
Longair MH, Baker DA, Armstrong JD. Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 2011
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 Tracing Github repository in Vaa3D
A distance-field based automatic neuron tracing method
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.
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.
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 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: 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
An open-source framework to synthetically generate fluorescent microscopic images of cellular population.
This plugin simulates color blindness. It is based on http://quarkphysics.ca/phys1/light/u-light.htm
SIOX: Simple Interactive Object Extraction
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.
For post-processing analysis, use Analyze Skeleton plugin written by the same author.
2012. ImageJ Macro Tool Sets for Biological Image Analysis. ImageJ User and Developer Conference 2012.
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 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: A deep learning system for multi-animal pose tracking (Nature Methods publication)
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.
Instruction doc in the Github repo, installation procedures as well
Nelissen et al. (2014) SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images
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.
A protocol in Methods in Cell Biology (not by the SLOTH author)
A collection for tracking microtubule dynamics, written in Python.
Genovisio Auguste orcid.org/0000-0003-1877-5595
Shihavuddin Asm orcid.org/0000-0002-4137-9374
Smooth 2D manifold extraction from 3D image stack.
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.
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.
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.
Lagache Thibault orcid.org/0000-0002-7033-4677
Olivo-Marin Jean-Christophe orcid.org/0000-0001-6796-0696
Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions
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.
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
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.
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.
An example ImageJ plugin illustrating how to create and display 3D tubes and 3D spheres in the 3D Viewer.
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 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).
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.
Software for bead-based registration of selective plane illumination microscopy data
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 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).
Dendritic spine classification using shape and appearance features based on two-photon microscopy
Spine classification based on kernel density estimation
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
Watershed transform question from tech support
A clear tutorial for splitting connected particles (cells) in a binary mask.
Neubias BIAFLOWS workflow of Spot Detection 3D Hessian with ImagJ
3D spot detection using the Determinant of Hessian (DoH) and the detection of 3D minima.
Neubias BIAFLOWS workflow of Spot Detection 3D with Icy protocol
Spot detection in 3D images by Wavelet Adaptive Threshold in Icy.
Neubias BIAFLOWS workflow of Spot Detection 3D with ImageJ
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.
Monteiro et al. (2013) Endosomal WASH and exocyst complexes control exocytosis of MT1-MMP at invadopodia
spot detection and codistribution analysis
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).
Neubias BIAFLOWS workflow of Spot Detection Dmap with ImageJ
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).
Neubias BIAFLOWS workflow of Spot Detection with Icy protocol
This workflow uses ICY wavelet based spot detector to detect spots in 2D images.
Neubias BIAFLOWS workflow of Spot Detection with ImageJ
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).
A set of classes and functions which can be used by plugins performing spot detection and spot tracking.
Fabrice de Chaumont http://orcid.org/0000-0001-7613-7204
Plugin can be downloaded from Icy toolbar
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
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
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)
Sliusarenko O, Heinritz J, Emonet T, and Jacobs-Wagner C
Quote: *A GUI-based program which manually detects spots and places them into previously detected meshes. Currently the program runs from MATLAB only. *
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.*
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: High through-put quantitative analysis of microbial growth
Spotsizer is a software tool that automates analysis of large volumes of photographic images of growing microbes.
Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics
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
Henriques, Ricardo orcid.org/0000-0002-2043-5234
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.
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.
Image quality assessment: from error visibility to structural similarity
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.
Iván Gómez Conde, David Olivieri, Carlos Tadokoro
- 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
This plugin registers (= aligns, matches) a stack of image slices.
A deep-learning solution for stain color normalization in digital histology images
Cell Detection with Star-Convex Polygons
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.
Design of Steerable Filters for Feature Detection Using Canny-Like Criteria
Fast edge and ridge detection, irrespective of their orientation.
This plugin performs Strahler analysis on topographic skeletons (2D/3D). Strahler numbering is a numerical procedure that summarizes the branching complexity of mathematical trees.
An implementation of Belief Propagation for factor graphs, also known as the sum-product algorithm
The SRRF algorithm source code and plugin for ImageJ and Fiji
Super-Resolution Radial Fluctuations (SRRF)
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.
A New SURE Approach to Image Denoising: Interscale Orthonormal Wavelet Thresholding
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 (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: Super-Region Volume Segmentation workbench
Volume Segmentation and Analysis of Biological Materials Using SuRVoS (Super-region Volume Segmentation) Workbench
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.
A Sampling Theory Approach for Continuous ARMA Identification
On the Role of Exponential Splines in Image Interpolation
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.
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.
Jean Ollion, Julien Cochennec, Christophe Escudé, François Loll, Thomas Boudier
TANGO Tools for Analysis of Nuclear Genome Organization
## 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 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.
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
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
"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 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.
Texture parameters for image classification
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.
Statistical color texture descriptors for histological images analysis
Classification of trajectoire: need tracking results as input and will then classify the trajectories as brownian motion, confined brownian or directed.
Randall Division of Cell and Molecular Biophysics at the Kings College London
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.
For each ROI, computes the number of pixel over a threshold. This plugin also provides the density and outputs results as an excel file.
Fiji Documentation (Links to ImageJ documentation)
Threshold.java source code, go to ij.plugin package and Thresholder java file
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.
Code is provided as supplementary to the paper
2007. Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP. Journal of Statistical Software. 18:1–20.
A complete package for fluorescence lifetime analysis implemented as an R package with sample data.
User guide - Trainable WEKA Segmentation batch processing
Tissue analysis from histological sections
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.
User guide - Automated Multicellular Tissue Analysis
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.
Tracer allows the user to create a trace along a structure in an image. It uses the underlying molecule positions, not the rendered image.
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.
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 to color tracks in the Track Manager
This display the Instant Speed of tracks for the Icy Track Manager.
A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.
http://icy.bioimageanalysis.org/plugin/Track-Processor-Speed-Profiler ?
Translate the tracks so that first detection is at 0,0,0 location.
WÜRFLINGER et. al. (2011) Automated segmentation and tracking for large‐scale analysis of focal adhesion dynamics
Tracking of focal adhesions in 2D time lapse movies
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.
Objective Comparison of Particle Tracking Methods
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.
Tinevez et. al. (2017) TrackMate: An open and extensible platform for single-particle tracking
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...
Arganda-Carreras et al (2017) Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
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 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.
Multi-color lens distortion and shift correction
Calculates and corrects for lens-distortion models including chromatic abberation from confocal stacks.
A Java Package for Geometrical Image Transformation, works up to 5D. - Affine - Crop - Embed - Matrix - Mirror - Rotate - Scale - Translate - Turn
TReMAP: Automatic 3D Neuron Reconstruction Based on Tracing, Reverse Mapping and Assembling of 2D Projections
TReMAP Plugin Github repository in Vaa3D
"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.
The Topology Toolkit J. Tierny, G. Favelier, J. Levine, C. Gueunet, M. Michaux. IEEE Transactions on Visualization and Computer Graphics.
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.
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.
Stephan Preibisch orcid.org/0000-0002-0276-494X
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.
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.
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
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 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.
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.
Template-Free Wavelet-Based Detection of Local Symmetries
A Unifying Parametric Framework for 2D Steerable Wavelet Transforms
A complete parametric framework and set of MATLAB tools for computing steerable wavelet frames in 2-D.
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.
Elastic Registration of Biological Images Using Vector-Spline Regularization
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.
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.
Steven Condamine, Dorly Verdier, Arlette Kolta.
Analyzing the Size, Shape, and Directionality of Networks of Coupled Astrocytes
Using ImageJ to Analyze the Size, Shape, and Directionality of Networks of Coupled Astrocytes
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.
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).
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
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 to remove stationary noise
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: Vascular Tree Synthesis Software
VascuSynth: Simulating Vascular Trees for Generating Volumetric Image data with Ground Truth Segmentation and Tree Analysis
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 (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.
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.
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. **Image Processing**: STL-style image processing algorithms with functors (e.g. arithmetic and algebraic operations, gamma correction, contrast adaptation, thresholding), arbitrary regions of interest using mask images image resizing using resampling, linear interpolation, spline interpolation etc. **geometric transformations**: rotation, mirroring, arbitrary affine transformations automated functor creation using expression templates **color space conversions:** RGB, sRGB, R'G'B', XYZ, L*a*b*, L*u*v*, Y'PbPr, Y'CbCr, Y'IQ, and Y'UV real and complex Fourier transforms in arbitrary dimensions, cosine and sine transform (via fftw) noise normalization according to Förstner computation of the camera magnitude transfer function (MTF) via the slanted edge technique (ISO standard 12233) **Filters:** 2-dimensional and separable convolution, Gaussian filters and their derivatives, Laplacian of Gaussian, sharpening etc. separable convolution and FFT-based convolution for arbitrary dimensional data resampling convolution (input and output image have different size) recursive filters (1st and 2nd order), exponential filters non-linear diffusion (adaptive filters), hourglass filter total-variation filtering and denoising (standard, higer-order, and adaptive methods) **tensor image processing:** structure tensor, boundary tensor, gradient energy tensor, linear and non-linear tensor smoothing, eigenvalue calculation etc. (2D and 3D) distance transform (Manhattan, Euclidean, Checker Board norms, 2D and 3D) morphological filters and median (2D and 3D) Loy/Zelinsky symmetry transform Gabor filters **Segmentation:** edge detectors: Canny, zero crossings, Shen-Castan, boundary tensor corner detectors: corner response function, Beaudet, Rohr and Förstner corner detectors tensor based corner and junction operators **region growing:** seeded region growing, watershed algorithm **Image Analysis:** connected components labeling (2D and 3D) detection of local minima/maxima (including plateaus, 2D and 3D) tensor-basesd image analysis (2D and 3D) powerful incremental computation of region and object statistics **3-dimensional Image Processing and Analysis:** point-wise transformations, projections and expansions in arbitrary high dimensions all functors (e.g. regions statistics) readily apply to higher dimensional data as well separable convolution and FFT-based convolution filters, resizing, morphology, and Euclidean distance transform for arbitrary dimensional arrays (not just 3D) connected components labeling, seeded region growing, watershed algorithm for volume data **Machine Learning:** random forest classifier with various tree building strategies variable importance, feature selection (based on random forest) unsupervised decomposition: PCA (principle component analysis) and pLSA (probabilistic latent semantic analysis) **Mathematical Tools:** special functions (error function, splines of arbitrary order, integer square root, chi square distribution, elliptic integrals) random number generation rational and fixed point numbers quaternions polynomials and polynomial root finding matrix classes, linear algebra, solution of linear systems, eigen system computation, singular value decomposition **optimization:** linear least squares, ridge regression, L1-constrained least squares (LASSO, non-negative LASSO, least angle regression), quadratic programming **Inter-language support:** Python bindings in both directions (use Python arrays in C++, call VIGRA functions from Python) Matlab bindings of some functions
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
Spraggins, Jeffrey (orcid.org/0000-0001-9198-5498)
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.
used to segment blood vessels network in mouse brains on lightsheet data with clearing
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 - 3D Object Segmentation and Tracking
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 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.
3D reslicing and threshold-enabled 3D visualization.
# 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")
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.
Voxelytic-Align is a commercial software provided as a service on cloud targetted to electron microscopy reconstruction (alignement, artifact correction...)
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
F. Leymarie, M. D. Levine, in: CVGIP Image Understanding, vol. 55 (1992), pp 84-94
Performs watershed algotirhm with ij-1.52i.jar. legacy:ij.plugin.filter.EDM("watershed").
Wavelet Spot Detector for Blocks, to integrate in Icy protocols.
Adel Kechkar, Deepak Nair, Mike Heilemann, Daniel Choquet, Jean-Baptiste Sibarita
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.
Boergens, Berning et al., Nature Methods 2017
Demo Dataset (Full female adult fly brain, Zheng et al. 2017)
webKnossos: 3D image annotation, visualization and sharing
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.
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");
Ofra Golani, Meirav Galun, Ida Rishal, Michael Fainzilber
[PDF] Neuronal Morphology Analysis Tool User Guide
Download (need password from the author)
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.
Ofra Golani, Meirav Galun, Suha Naffar Abu-Amara , Benjamin Geiger
Download needs password from the author.
Naffar-Abu-Amara et. al. (2008) Identification of Novel Pro-Migratory, Cancer-Associated Genes Using Quantitative, Microscopy-Based Screening
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.
Wndchrm – an open source utility for biological image analysis
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."
Wählby et al. (2012) An image analysis toolbox for high-throughput C. elegans assays
Worm Toolbox: High.throughput screening of C. elegans
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.
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.
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: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans
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 in CellProfiler
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.
automated analysis of scratch wound assays
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.
Optimization of the Wound Scratch Assay to Detect Changes in Murine Mesenchymal Stromal Cell Migration After Damage by Soluble Cigarette Smoke Extract.
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.
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 (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.
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
>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.
Hanslovsky et al. "Post-acquisition image based compensation for thickness variation in microscopy section series"
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.
Ghotra et al (2012) Automated Whole Animal Bio-Imaging Assay for Human Cancer Dissemination
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 – 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
Democratising deep learning for microscopy with ZeroCostDL4Mic
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.
ImageJ macro - (Z,T) Hyperstack Stitcher
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).
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.
registration_and_bleaching_correction: initial resease
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
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.
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.