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CellProfiler-plugins

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A home for community-contributed and experimental CellProfiler modules.

Beginner-level instructions

Beginner guidance for using plugins in CellProfiler

Beginner instructions for installing runCellpose, runStarDist, and all other plugins with CellProfiler from source:

Use

  1. Clone this repository into a folder (PLUGIN_DIRECTORY) on your local computer:

    cd PLUGIN_DIRECTORY
    git clone https://github.com/CellProfiler/CellProfiler-plugins.git
    

    Alternatively download zip and manually extract to PLUGIN_DIRECTORY.

  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 make sure you have Visual Studio 2017 installed then 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
    

ImageJ requirements

If using the RunImageJScript module, please note:

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Community-contributed and experimental CellProfiler modules.

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