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: http://cellprofiler.org/
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 is available on the CellProfiler web site, http://cellprofiler.org/
For any Flux-specific assistance running CellProfiler, contact email@example.com.