Closed quentinblampey closed 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.
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