generating masks from proseg segmentation

[dpschreiner]

as i understand it from this page, running xeniumranger --import-segmentation with baysor-style inputs does not generate masks in cells.zarr.zip.

yet i would like to use proseg segmentation as a mask to calculate intensities from a post-xenium-run fluorescent image which i have aligned using Xenium Explorer.

would you instead recommend either the proseg polygons or voxel outputs?

thanks in advance! great tool!

[dcjones]

Yeah, in principle you should be able to use the polygons that proseg outputs, but it would probably require a little work to get mean intensities using these.

First, proseg's polygons are in microns, so they'd need to be converted to pixels, then you'd need some code to average intensities in these polygons. I'm not sure what tools exist for this. I'll probably be looking at some post-xenium imaging data in the near future, so hopefully I'll have a more concrete solution soon!