Boms for StereoSeq

[MargotCh]

Hi,
I was wondering if Boms would work on a StereoSeq dataset? If yes, would you be able to give an example of how to transform the StereoSeq outputs to work with Boms?

Thank you!

[ocimakamboj]

Hi!

Yes, BOMS is designed to work with imaging-based spatial transcriptomics data where you have spatial coordinates for each detected transcript along with its gene identity — so it should work with StereoSeq data as well.

Could you please share a bit more about your dataset format? Specifically: What file format are you using? Does it contain x, y coordinates and gene names for each spot? Are the coordinates in pixels or physical units?
Once I know this, I can help provide an example of how to adapt it for BOMS.