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Replicate workflow for nuclei segmentation and shape measurements #21

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sunyi000 opened this issue Sep 18, 2024 · 0 comments
Open

Replicate workflow for nuclei segmentation and shape measurements #21

sunyi000 opened this issue Sep 18, 2024 · 0 comments
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tutorials dev This issue involves writing tutorials workflows dev This issue involves workflow development

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@sunyi000
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sunyi000 commented Sep 18, 2024 •
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TO DO:

  • before 'threshold' step, add some preprocessing steps, e.g. smoothing
  • make it work with 3D image
  • try replacing 'threshold' and 'label map' with cellpose
  • post processing after measurements, for example, once we have the tables, find out eccentricity, no. of circles etc.
@beatrizserrano beatrizserrano moved this to Unassigned in BH2024 Sep 18, 2024
@beatrizserrano beatrizserrano added tutorials dev This issue involves writing tutorials workflows dev This issue involves workflow development labels Sep 18, 2024
@kostrykin kostrykin changed the title Workflow for nuclei segmentation and shape measurements Replicate workflow for nuclei segmentation and shape measurements Sep 18, 2024
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tutorials dev This issue involves writing tutorials workflows dev This issue involves workflow development
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