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BayraktarLab / cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
https://cell2location.readthedocs.io/en/latest/
Apache License 2.0
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celltype SC-ST mapping #266

Closed JingGuo1997 closed 1 year ago

JingGuo1997 commented 1 year ago

Hello developers of cell2location,

When I used cell type mapping from single cell data to space, I found that too many spots were predicted as one celltype, but in fact, the number of such cell types in tissues is very small. Can I change parameters and adjust the cell type annotation to match biology？

We look forward to your reply

vitkl commented 1 year ago

Hi @JingGuo1997

I don't understand what you mean. The model predicts the abundance of cell types: one "spot" can contain one or multiple cell types in varying amounts.