Community-contributed and experimental CellProfiler modules.
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AetherUnbound Merge pull request #74 from AllenInstitute/bugfix/merge-object-backgr…
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Set the size of the background to zero
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cellprofiler_plugins Initial checkin. Jun 9, 2017
tests Add unit tests for max seeds per object Jul 17, 2018
.gitignore merge gitignore from CellProfiler Jul 28, 2017
.travis.yml Fix caching section for Travis CI May 11, 2018
README.md updated install instructions May 8, 2018
activecontourmodel.py Boolean subtraction to logical xor Mar 22, 2018
blobdetection.py add export option for blob centers Jun 18, 2018
classifypixelsunet.py Added license for classifypixelsunet plugin Sep 12, 2018
constrainobjects.py Add the rest of ConstrainObjects functionality May 9, 2018
convertoutlinestoobjects.py Add option to filter objects by size Jan 25, 2018
declump.py Add intensity based declumping Apr 18, 2018
edgedetection.py EdgeDetection module added Aug 30, 2017
environment.yml add python.app Mar 9, 2018
exporttocellh5.py Fix imports for ExportToCellH5 Jan 12, 2018
gammacorrection.py Set module_name for GammaCorrection, HistogramEqualization Jan 12, 2018
histogramequalization.py Set module_name for GammaCorrection, HistogramEqualization Jan 12, 2018
imagegradient.py ImageGradient module added Aug 30, 2017
laplacianofgaussian.py LaplacianOfGauussian module added Aug 30, 2017
measure_population_context.py Update imports for MeasurePopulationContext Jan 12, 2018
measureimagefocus.py update hyperlink Mar 1, 2018
measureradialentropy.py remove cruft and and superfluous import Feb 20, 2018
measuretrackquality.py Initial checkin. Jun 9, 2017
mergeobjects.py Set the size of the background to zero Sep 12, 2018
predict.py added support for 1 channel images (gray value image data) Feb 3, 2018
randomwalkeralgorithm.py Move RandomWalkerAlgorithm from CellProfiler to CellProfiler-plugins (r… Jun 19, 2017
requirements-windows.txt added requirements files for windows machines May 7, 2018
requirements.txt Merge pull request #44 from CellProfiler/unet4nuclei May 4, 2018
runimagej.py reorganize: alphabetize Mar 9, 2018
seedobjects.py Add capacity to specify maximum number of seeds per object Jul 17, 2018
shollanalysis.py sholl analysis Apr 2, 2018
tophattransform.py added TopHatTransform module Aug 30, 2017

README.md

CellProfiler-plugins

Build Status

A home for community-contributed and experimental CellProfiler modules.

Beginner-level instructions

Please see help here: https://github.com/CellProfiler/CellProfiler/blob/master/cellprofiler/data/help/other_plugins.rst

Use

  1. Clone this repository:

    cd PLUGIN_DIRECTORY
    git clone https://github.com/CellProfiler/CellProfiler-plugins.git
    
  2. Install required dependencies:

    cd CellProfiler-plugins
    pip install -r requirements.txt
    

    To install CellProfiler-plugins on a windows machine with support for the deep learning module ClassifyPixels-UNet use

    cd CellProfiler-plugins
    pip install -r requirements-windows.txt
    
  3. Configure CellProfiler plugins directory in the GUI via Preferences > CellProfiler plugins directory (you will need to restart CellProfiler for the change to take effect). When running CellProfiler via the command line, use the --plugins-directory flag to specify the plugins directory, for example:

    cellprofiler --run --run-headless --project PROJECT_FILE --plugins-directory PLUGIN_DIRECTORY/CellProfiler-plugins