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Estimate cell nucleis #4

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stefanhahmann opened this issue Dec 6, 2022 · 0 comments
Open

Estimate cell nucleis #4

stefanhahmann opened this issue Dec 6, 2022 · 0 comments

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@stefanhahmann
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stefanhahmann commented Dec 6, 2022 •
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User Story

I would like to be able that cell nucleis are determined automatically by means of segmentation approaches

Acceptance Criteria

  1. Use StarDIST Python implementation (https://github.com/stardist/stardist) to estimate cell nuclei positions and forms
  2. StarDIST may be combined with algorithmic approaches, such as MorphoLibJ/CLIJ
  3. Derive ellipsoids params (center, lengths of axes) of nucleis from StarDIST star-convex polygons
  4. Allow Mastodon/BDV to show StarDIST star-convex polygons
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