I started looking at cellprofiler in headless mode. I could run it with command like
‘cellprofiler -r -c -i /input -o /output --pipeline=…’
As I understand, each pipeline involves multiple modules so is it possible to execute each module alone in commandline? For example, can we do something like
‘python -m cellprofiler.identifyprimaryobjects -i /input-image-dir/ -o /output-dir’
if this is not possible, what is the best approach to execute individual module alone?
Thanks very much for any help