CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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Add RunCellpose plugin #124

Closed DavidStirling closed 3 years ago

DavidStirling commented 3 years ago

This plugin provides a wrapper around Cellpose's deep learning segmentation models. Current features:

Current interface: image

Current figure display (with probability export on):

image

I'm not sure how best to setup tests/integration into the rest of the repo. pip install cellpose gets you running on a CPU, but will add pytorch and other libraries as dependencies. Since full GPU setup is a bit complex it might be worth moving towards setting requirements per-plugin rather than across the whole repository?

bethac07 commented 3 years ago

I can't test the GPU mode on my Mac but CPU mode seems to be working nicely!