Use cellprofiler as a python package


I am new to Cellprofiler but I would like to integrate the Cellprofiler analysis part to my codes so I am wondering if there is any tutorial for this task? The current tutorial contains only four lines and I am not quite sure how to use it properly.

Many thanks!

You can use python to run a pipeline configured in the GUI in headless mode (version 2.2 only). See this post: CellProfiler install from source and run headless to solve batch processing memory errors

Using CP as a python API is non-trivial and not really possible at the moment. See this post: CellProfiler 4.0.0 timeline and roadmap

Thank you for the help. Good luck with the developing process! Looking forward to it.