2D vs. 3D segementation

[Zach-Sten]

Hello,

I've been using the tool and have had good success with resegmenting cells, getting polygon masks, and exporting to Xenium Explorer! I'm enjoying the tool but would like to know if there's an option to toggle between 2D and 3D transcript coordinates. I believe this is an option in Baysor and am wondering if one of the reasons I see overlapping polygons using generate_boundaries is because of Segger taking into account the z_location information.

Additionally, are there any recommendations or metrics folks have come across of for identifying areas of contamination without using a paired sc-RNAseq reference?