Running pipeline without CP GUI?



I’m trying to run specific pipeline( made at CP 2.2.0) without Cell profiler GUI.
By using matlab or python.
Before running it needs to input image files, and set output image & csv file path.

I’m looking up at (
but yet unsure whether it is possible. Please let me know if this is possible.

Thank you for reading



You can definitely do so from the command line, but there are some differences in how CellProfiler runs (primarily that it will only operate on one core at a time rather than the multicore behavior from the GUI). This wiki page has information on how to call it headless, how to pass a file list or CSV, etc.