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[BUG] Weird 3D artifact when segmenting cells #1069

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lguerard opened this issue Dec 3, 2024 · 0 comments
Open

[BUG] Weird 3D artifact when segmenting cells #1069

lguerard opened this issue Dec 3, 2024 · 0 comments
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bug Something isn't working

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@lguerard
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lguerard commented Dec 3, 2024 •
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Describe the bug
When running Cellpose 3D for cells, I'm getting weird artifacts which looks stripy and quite fuzzy. Also, I'm getting quite a lot of very small one voxel objects. Any ideas how to get rid of that ?

To Reproduce
I have linked the images and settings on the image.sc forum.

Data is available here.

Settings
I’m using :

  • Cellpose 3.0.10
  • model = cyto3
  • cellproba_threshold = -6.0
  • flow_threshold = 0.1

Note
I'm using Cellpose 3.0.10 instead of 3.1.0 as I'm getting cellpose tensors used as indices must be long error otherwise...

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@lguerard lguerard added the bug Something isn't working label Dec 3, 2024
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@lguerard