Visium cell counts: cellpose option

LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

http://research.libd.org/spatialDLPFC/

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Visium cell counts: cellpose option #95

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

This would be similar to #93, however it would involve the histology images instead of the IF ones. If it works, we would ultimately create a CSV file with the key and the cell_count column which could be loaded into the SPE objects using spatialLIBD::cluster_import(). This part would be done by (TBD).

We would then compare the results against VistoSeg #92. This comparison would likely be done by @abspangler13.

abspangler13 commented 2 years ago

[ ] Do I still need to update the segmentations for my spe object.

lcolladotor commented 2 years ago

We decided not to this anymore.