Overlay custom segmentation using cell segmentation resolver

[EST09]

Hi,

Thank you for SOPA, it looks really helpful. I'd love to use the cell segmentation resolver. However, I'm struggling a little with how best to implement.

I have custom segmentation for a particular cell type in H&E. I've added this as a shape to my spatialdata object in the same coordinate system as cell boundaries (the default Xenium segmentation). I'd love to overlay this custom segmentation onto the default Xenium cell segmentation (cell boundaries) so that any cells/transcripts in the default under the custom segmentation get merged into the custom segmentation but the other cells from the default are kept.

Is there a way to do this in SOPA at all please?

Best wishes, Emily