CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Vendor website:


CellProfiler is available as a module on Flux. To use it, you must first load the module:

$ module load cellprofiler

This will make the cellprofiler program accessible. The options and flags can be displayed like so:

$ cellprofiler -h
Usage: cellprofiler [options] [<output-file>])
where <output-file> is the optional filename for the output file of
measurements when running headless.
The flags -p, -r and -c are required for a headless run.

Additional information

Additional information is available on the CellProfiler web site,

For any Flux-specific assistance running CellProfiler, contact