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CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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Cellpose plugin using a subprocess docker #198

Closed callum-jpg closed 1 year ago

bethac07 commented 1 year ago

Testing in process! The docker is ~6 GB, so for me it's taking several minutes to download; we probably want to add a warning to folks.

callum-jpg commented 1 year ago

Changing the subprocess command to result = subprocess.run(cmd, shell=True) will allow you to see the verbose terminal output of cellpose as it runs

callum-jpg commented 1 year ago

So, I'll add this docker functionality to the pre-existing RunCellpose plugin and present the user with an option to run cellpose inside a docker or within a local python environment.

@bethac07 Since this works with built CellProfiler, how should the python option be handled? I suppose it will still be there, but should we throw some sort of error saying that only the docker approach works for the built app?