# SPDX-FileCopyrightText: 2024 Carlo Castoldi # # SPDX-License-Identifier: CC0-1.0 # This is a configuration file for BraiAn, a extension helps managing multiple QuPath projects ensuring consistency. # Typically, in whole-brain datasets, one brain = one QuPath project and BraiAn makes sure the exact same analysis parameters are # consistently applied across different projects. # It is meant to be placed either in a QuPath project folder, or in its parent directory. # Ideally, the parent directory contains multiple QP projects for which the same parameteres are used in the analysis. # If a value is not defined in the YAML, BraiAn will apply a default value. classForDetections: null # DEFAULT: null (i.e. applies BraiAn on the whole image) # Class of the annotations in which BraiAn's cell detection analysis is desired detectionsCheck: apply: true # DEFAULT: false # If set to true, each detection on a channel (different from 'controlChannel') is ascribable to a cell detection in the 'controlChannel'. # It finds detections in 'controlChannel' that contains the detections' centroid of remaining channels # It is useful only when 'channelDetections' has more than one value controlChannel: "AF568" # DEFAULT: first of channelDetectionsChannel # Image channel whose detections are used to apply the check. Usually it is "DAPI". # If used to compute overlaps between two markers, select a channel whose marker is cytoplasmic rather than nuclear (has larger detections) # Cell detection parameters for each color channel channelDetections: # DEFAULT: empty (i.e. BraiAn does not work on any imagge channel) # - name: "DAPI" # if no parameters are defined for one channel, BraiAn will use QuPath's default values - name: "AF568" # cFos parameters: requestedPixelSizeMicrons: 1 # DEFAULT: 0.5 # Choose pixel size at which detection will be performed - higher values are likely to be faster, but may be less accurate; # set <= 0 to use the full image resolution # Nucleus parameters backgroundRadiusMicrons: 10 # DEFAULT: 8.0 # Radius for background estimation, should be > the largest nucleus radius, or <= 0 to turn off background subtraction backgroundByReconstruction: true # DEFAULT: true # Use opening-by-reconstruction for background estimation (default is 'true'). # "Opening by reconstruction tends to give a 'better' background estimate, because it incorporates more information across # the image tile used for cell detection. # *However*, in some cases (e.g. images with prominent folds, background staining, or other artefacts) # this can cause problems, with the background estimate varying substantially between tiles. # Opening by reconstruction was always used in QuPath before v0.4.0, but now it is optional. medianRadiusMicrons: 0.0 # DEFAULT: 0.0 # Radius of median filter used to reduce image texture (optional) sigmaMicrons: 1.5 # DEFAULT: 1.5 # Sigma value for Gaussian filter used to reduce noise; increasing the value stops nuclei being fragmented, but may reduce the accuracy of boundaries minAreaMicrons: 20.0 # DEFAULT: 10.0 # Detected nuclei with an area < minimum area will be discarded maxAreaMicrons: 1000.0 # DEFAULT: 400.0 # Detected nuclei with an area > maximum area will be discarded # Intensity parameters # threshold: -1 # DEFAULT: 100 # Intensity threshold - detected nuclei must have a mean intensity >= threshold histogramThreshold: # if 'histogramThreshold' parameter is specified, it will ignore 'threshold' and try to automatically compute one based on the image histogram resolutionLevel: 4 # DEFAULT: 4 # resolution level at which the histogram is computed smoothWindowSize: 15 # DEFAULT: 15 # size of the window used by the moving average to smooth the histogram peakProminence: 100 # DEFAULT: 100 # amount of prominence from the surrounding values in the histogram for a local maximum to be considered a 'peak' nPeak: 1 # DEFAULT: 1 # n-th peak to use as threshold (starts from 1) watershedPostProcess: true # DEFAULT: true # Split merged detected nuclei based on shape ('roundness') # Cell parameters cellExpansionMicrons: 5.0 # DEFAULT: 5.0 # Amount by which to expand detected nuclei to approximate the full cell area includeNuclei: true # DEFAULT: false # If cell expansion is used, optionally include/exclude the nuclei within the detected cells # General parameters smoothBoundaries: true # DEFAULT: true # Smooth the detected nucleus/cell boundaries makeMeasurements: true # DEFAULT: true # Add default shape & intensity measurements during detection classifiers: # DEFAULT empty (i.e. no classifier is applied) # A list of classifiers to apply in sequence to the channel's detections # The order of the classifiers is important. If they work on overlapping annotations, the intersection is classified using the latter classifier - name: "AF568_cFos_classifier" # DEFAULT: null # name of the classifier's json file to use on this channel detections # Contrary to what QuPath does by default, BraiAn searches it in the project's directory or in its parent directory annotationsToClassify: # DEFAULT: empty (i.e. the classifier is applied on all detections) # List of the annotation names for which the classifier is applied - name: "AF647" # Arc1 parameters: requestedPixelSizeMicrons: 1 # Nucleus parameters backgroundRadiusMicrons: 20 backgroundByReconstruction: true medianRadiusMicrons: 0.0 sigmaMicrons: 1.5 minAreaMicrons: 40.0 maxAreaMicrons: 1000.0 # Intensity parameters # threshold: -1 histogramThreshold: resolutionLevel: 4 smoothWindowSize: 15 peakProminence: 100 nPeak: 1 watershedPostProcess: true # Cell parameters cellExpansionMicrons: 5.0 includeNuclei: true # General parameters smoothBoundaries: true makeMeasurements: true classifiers: - name: "AF647_Arc1_subcortical_classifier" - name: "AF647_Arc1_isocortex_classifier" annotationsToClassify: - "Isocortex" - "CTXsp" - "OLF" - "CA1"