Question about assignment of transcripts in overlapping regions

[Jwong684]

Hi Kharchenko lab,

I've been trying to implement Baysor on my CosMx data. I wanted some clarification about what Baysor does to overlapping regions.

From my understanding of your paper, it essentially tries to correlate transcripts within the overlapping regions with neighbouring cells and assigns these transcripts to the cell that had the best correlation with the region. I.e. if there are a mix of transcript A and transcript B in an overlapping region, and cell A has a good distribution of transcript A, and cell B of transcript B, then all transcript A's in the overlapping region will be assigned to cell A and transcript B's with cell B.

Is that a good assumption to make? I noticed that the number of cells I get after segmentation seemingly doubles from the default segmentation by CellPose.