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[BUG] Neuron segmentation not working #22

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pr4deepr opened this issue Feb 11, 2025 · 0 comments

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pr4deepr commented Feb 11, 2025

Issue summarized here:
https://forum.image.sc/t/stardist-plugin-error-after-fiji-update-only-custom-models/108026

Basically, due to tensorflow configuration issues StarDist is not working. There are temporary workarounds, but this means deepImageJ may not work.

Temporary solution: Use deepImageJ instead for neuron segmentation

export StarDist models to run in deepimagej and use deepimagej for neuron detection workflow.
Only caveat is that nms postprocessing needs to be done separately.

Could use this opportunity to deposit the models on bioimageio via zenodo..

pr4deepr changed the title ~~[BUG] StarDist not working~~ [BUG] Neuron segmentation not working

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