Using Cellprofiler In Python command line


Hi all,

Wondering if there is a tutorial on how to use CellProfiler in python 3 or 2 from a script in the command line? Would be very interested if there is a way to export my pipeline into a script.



We don’t have an official tutorial, but you may be interested in this repo.


Yay! Thank you.
Can I use this in Python 3?


I don’t think so, as CP is Python 2, but I am not a SWE so my best advice would be to try it because I might be wrong :slight_smile: