Hello,

How can I map some annotation performed on quPath (H&E annotation e.g. tumor / stroma / fat / necrosis) on spatial seurat object.

The annotation was performed on the full resolution H&E and the visium spaceranger preprocess was performed on the cytassist image (same slide as the full resolution). Annotation exported from quPath are in geojson format but easily readable in R.

I tried to play with the scale factors that spaceranger computed in order to translate the coordinates found in seurat@images$slice@coordinates and the ones from quPath but without success.

Any idea how to do the translation ?

scalefactors doc from spaceranger page : https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs

Thank you