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@gnodar01
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Adds a dockerfile and makefile for creating an image that has both cellpose and omnipose in it.

Have not deployed an image to the cellprofiler profile on dockerhub yet. Have not added the option to include this in runcellpose.py yet. Waiting for results of #4870 before determining if this works well enough.

I Have added the image to my personal repo (for now) here.

@gnodar01 gnodar01 marked this pull request as draft February 14, 2024 20:32
@ErinWeisbart
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It seems like the auto-download of models upon first run is not currently working for omnipose.
Cellpose says that this is now supported by omnipose not cellpose.
I've implemented a workaround mentioned on the forum

@ErinWeisbart
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My workaround doesn't work. I also don't know how to reconcile list of model names from the the OSF repo

'bact_fluor_cp','bact_fluor_omni','bact_phase_omni','cyto2_omni','plant_cp','plant_omni'

with the list of model names in the omnipose docs

'bact_phase_omni','bact_fluor_omni','cyto2_omni','worm_omni','plant_omni','bact_phase_affinity'

So I'm going to revert the model download I added and leave it at no pretrained and list in the RunCellpose module only the models that are currently supported for download and someone can revisit this in the future if we want to expand support of omnipose models.

@ErinWeisbart ErinWeisbart marked this pull request as ready for review August 4, 2025 18:24
@ErinWeisbart ErinWeisbart requested a review from bethac07 August 4, 2025 18:24
@bethac07 bethac07 merged commit f12a6f1 into master Aug 4, 2025
@bethac07 bethac07 deleted the cellpose_with_omnipose branch August 4, 2025 20:42
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4 participants