Using Plugins

Occasionally certain modules aren’t installed by default into CellProfiler; sometimes they are created just for specific projects but our team isn’t sure they are useful for the general public, some are broadly useful but are missing documentation, some only work for specific versions of CellProfiler, or some may introduce extra libraries or other dependencies that for whatever reason we’re unable or unwilling to include in the overall program. These modules are called Plugins, and you can find them in their own GitHub repository. They are often experimental and may be less likely to work, but you may find a use for one or more of them!

You may download these modules individually by clicking on a module’s name, hitting the “Raw” button on GitHub, then using your browser’s Save function. You can also download the whole repository of pipelines by cloning the whole repository from GitHub using Git, the GitHub app, or by downloading a ZIP file with all the modules using the “Clone or download” green button on the repository’s landing page.

CellProfiler will check for plugins in its plugins directory, which you can set from the File > Preferences menu. Once you’ve obtained the module(s) you’re interested in, either move them to the plugins directory or set the plugins directory to the folder containing your new module(s). Once you’ve done so, simply restart CellProfiler; if the module loads correctly then you should be able to see it in the list of modules and add it to your pipeline. If it does not load correctly, we encourage you to please check the log (see Help > Configuring Logging ) for more information then check for known issues and/or notify us on the issues page or the CellProfiler forum.

Additionally, if you write your own module based on our recommendations, you can add it to your own plugins directory. If you think it fills an unmet need in the CellProfiler code, feel free to contribute it to the CellProfiler-plugins repository!