Running pipeline without CP GUI?

cellprofiler

#1

Hi,

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 (https://github.com/CellProfiler/CellProfiler/wiki#Running_CellProfiler_from_the_command_line)
but yet unsure whether it is possible. Please let me know if this is possible.

Thank you for reading
JH


#2

Hi,

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.