Segmentation (no CLI) - Githubissues

czbiohub-sf / shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

BSD 3-Clause "New" or "Revised" License

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Segmentation (no CLI) #106

Closed edyoshikun closed 2 weeks ago

edyoshikun commented 8 months ago

This PR allows one to use Cellpose segmentation with and without slurmkit. I added a yml config that points to the nucleus and membrane models and a function that performs the segmentation on czyx_arrays.

[ ] There is no current CLI call for this, but we can set it up if needed.
[ ] Tests for the functions

ieivanov commented 1 week ago

@edyoshikun will move the segmentation workflow to VisCy after we create ~iphub~