Prior cell segmentation

dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

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Prior cell segmentation #7

Closed Bo-UT closed 6 months ago

Bo-UT commented 6 months ago

Hi,

Nice tools! I have a quick question, how to input cellpose (nulcear) segmentation as the prior to proseg? Thanks

dcjones commented 6 months ago

There's not currently an option to import directly from cellpose, but if you set up a transcripts csv file that includes a cell assignment, proseg is pretty flexible about input formats.

The two main arguments you need to set

--cell-id-column: name of the csv column that gives the cell assignment (cells can be encoded arbitrarily)
--cell-id-unassigned: value in that column denotes an unassigned transcript.

Bo-UT commented 6 months ago

Thanks a lot! Our data are Xenium, and proseg --xenium worked very well.