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kevinjohncutler / omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation
https://omnipose.readthedocs.io
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CellProfiler plugin issue #84

Closed tsmith1711 closed 5 months ago

tsmith1711 commented 6 months ago

We recently set up cellProfiler with the omnipose plugin on our cluster. When I reach the RunOmnipose part of my pipeline, I receive an error message (attached). We are running cellprofiler using a singularity container. I was able to run the RunOmnipose module locally on my mac in CellProfiler. Please let me know if you need any other specifics!

Screenshot 2024-03-29 at 3 26 21 PM
tsmith1711 commented 6 months ago

Figured it out! I just needed to modify the download_cellpose_models.py file in the following plugin directory: CellProfiler-plugins/dockerfiles/RunCellpose/download_cellpose_models.py

kevinjohncutler commented 5 months ago

@tsmith1711 That is right. Sorry about that, the cellpose team deleted those models to save space. They now download from here.

kevinjohncutler commented 5 months ago

Carsen and I figured out a way to redirect the old download requests, so this issue should be solved for all prior versions including the one used for the cellprofiler plugin.