Add segmentation and segmentation-free methods

theislab / txsim

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Add segmentation and segmentation-free methods #44

Open LouisK92 opened 2 years ago

LouisK92 commented 2 years ago

[x] watershed,
[x] pciseq
[x] nuclear expansion
[x] Cellpose
[x] Baysor,
[x] Stardist,
[ ] ComSeg
[ ] StereoCell
[ ] SCS (github),
[ ] Ilastik,
[x] binning,
[ ] JSTA
[ ] SSAM,
[ ] spage2vec,
[ ] proseg,
[ ] BIDCell,
[ ] TACCO - also ct annotation(?)

assignment

[ ] "custom assignment" (currently we provide custom segmentations, but we also want to support to use prior info on the assignment step)

LouisK92 commented 2 years ago

Binning means to group the reads detected based on a fixed grid or bins. It's useful some times when no nuclear segmentation is available and in this case it can be like the negative control, the case of worse segmentation