search

dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics
Other
41 stars 1 forks source link

protein info from CosMX #8

Open cstrlln opened 4 months ago

cstrlln commented 4 months ago

Thank you for the tool!

any suggestions on how to reintegrate the surface protein staining data from CosMX (e.g CD45, panCK) after segmenting with proseg?

dcjones commented 4 months ago

Great question! I don't have a solution for this right now. In principle, you would compute the aggregate marker intensity across the polygons that proseg outputs, but I don't have a workflow for this yet.

A lot of the major platforms support (or soon will support) protein staining, so I imagine I'll develop something, but I haven't done so yet. Leaving this issue open as a reminder in the mean time.