Deepcell segmentation without cytoplasm channel

[jamesMo84]

I note that Deepcell provides both a segmentation (nuclear channel only) and mesmer (nuclear and cytoplasm) model (https://www.deepcell.org/predict) Our datasets do not have a single general cytoplasm marker that will capture all cell type cytoplasm required by mesmer model, eg tumour cells vs immune vs stromal cells Can both nuclear_channel=DAPI, cytoplasm_channel=DAPI in mesmer model? or can SegmentMIF(model='segmentation' be supported? thanks!

[jacob-rosenthal]

Hi @jamesMo84 , yes agreed that this would be a very useful feature. I think all it would take is wrapping deepcell.applications.cytoplasm_segmentation.CytoplasmSegmentation and/or deepcell.applications.nuclear_segmentation.NuclearSegmentation inside PathML transforms.

I don't have bandwidth right now to implement, but happy to help answer questions, review code, etc. if you want to give it a shot. Improving integration with deepcell more generally is on the roadmap (#210) as well.