Hi, I was going through the resolvi reproducibilty scripts, and for xenium, it seems like fov as batch was used. I was wondering how you were able to get that information in your anndata object, as the table from spatial object from import segmentation does not have fov attached to the obs.
Thank you and warm regards
Jairaj Mathur
Hi, I’m not sure what “as the table from spatial object from import segmentation” refers to. I’m pretty sure that I didn’t do anything fancy to get the FOV information and believe it was just part of the download from 10X. Did they change the underlying files maybe? In terms of results it does not really matter here and running it without FOV should yield very comparable results.
To clarify, when the spatialdata object is created from sdata_io.xenium, the table (anndata object) within that spatialdata object doesnt seem to have the FOV information associated with each cell. I was wondering how did you insert the fov column into the anndata object, which you eventually passed to resolvi.