CellProfiler-plugins

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:

• Windows
• Mac_Intel_version

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:

• You will also need to install Maven
• CellProfiler will need to be built from source due to the requirement of additional libraries