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navinlabcode / CellTrek

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Assigning all single cells #21

Open cadyyuheng opened 2 years ago

cadyyuheng commented 2 years ago

Dear CellTrek Team

I wonder whether there is a way to force assign all single cells to a spatial location? I tried to change dist_thresh=0.55 to dist_thresh=2, but still didn't get all my single cells with at least one position assigned. May I ask 2hat would be a setting so that all cells could be assigned? Thank you!

WandeRum commented 2 years ago

Hi! Thank you for asking. We intentionally keep relative sparse mapping to control the false positives considering 1) ST has RNA diffusion problems to some degree; 2) not all cells are in the slides (or in other words, the cell distribution of ST might be different from SC). But if you really want a very high number of cell mapping, you can try to increase these parameters dist_thresh, spot_n, and intp_pnt. We did test that when you try to map as many cells as possible, you tend to have higher false positive mapping.