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gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells
https://gustaveroussy.github.io/sopa/
BSD 3-Clause "New" or "Revised" License
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[Feature] Save both nucleus + cytoplasm boundaries #18

Closed quentinblampey closed 6 months ago

quentinblampey commented 8 months ago

After segmentation, each cell should correspond to both a nucleus polygon and a cytoplasm polygon

Afterwards, we could know whether transcripts are in the nucleus or the cytoplasm

quentinblampey commented 6 months ago

For now, Sopa is based on either Cellpose or Baysor, which returns one boundary per cell. Therefore, there is no distinction between nucleus and cytoplasm.

If a good segmentation is being developed that returns both boundaries, I will be happy to add it to Sopa. But, meanwhile, I'm closing this issue, feel free to re-open.