Access to additional info. in xenium spatial data

[DabinJeong]

Hello,

Thank you for creating such an amazing benchmark dataset.
For the Xenium benchmark (Tasks 1, 3, 4, 5, and 8), I’m planning to use cell x,y coordinates for my model, but I couldn’t find the x,y coordinates in the provided h5ad file.
Could you provide an h5ad file that includes the x,y coordinates?

Best regards,
Dabin

[pauldoucet]

Hello @DabinJeong ,

This tutorial (section "Linking transcripts with cells") shows how to access xenium cell segmentation for any HEST sample. The cell coordinates we provide were aligned using a non-rigid Valis transform, which is more precise than the affine transformation offered by 10x Genomics.