Contributing New Plugins#

Within our CellProfiler wiki, you can find an orientation to CellProfiler code.

In the CellProfiler repository, within cellprofiler/modules/plugins you can find two different templates to use for creating your own plugin. provides a template that takes one image as an input and produces a second image for downstream processing. provides a template that measures a property of an image both for the image as a whole and for every object in the image.

In your plugin, we appreciate if you also include:

  • display functionality

  • extensive module documentation

  • references and citation information in your module documentation

Please create a Pull Request to the CellProfiler-plugins repository to submit your plugin for inclusion in the repository.

In your PR, you must:

In your PR, we appreciate if you also include:

  • unit tests for your plugin

  • customized installation in, if your plugin has dependencies

Contributing bug fixes or updating deprecated plugins#

Please create a Pull Request to the CellProfiler-plugins repository to submit a bug fix or plugin un-deprecation. If you would like to update a currently deprecated plugin, we encourage you to read closed Issues in GitHub relevant to the plugin as they may contain helpful information about bugs present at the time of deprecation.

Having your plugin cited#

While we cannot guarantee that users will cite your plugin, we have introduced a Citation generator into CellProfiler (currently available in CellProfiler from source and will be in CellProfiler 5) that scans all modules in a user’s pipeline and generates a citation file for them that includes citation information for any modules (including plugins) that have specific citation information in them.

See Citing Plugins for information on citing CellProfiler Plugins.