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This PR is dependent on scverse/spatialdata-plot#446. Furthermore, the gene expression data is in a different coordinate system now, namely
Visium_HD_Mouse_Small_Intestine
. This coordinate system does not have the image elmentVisium_HD_Mouse_Small_Intestine_full_image
anymore. This element is only present inglobal
. This PR therefore uses in that caseVisium_HD_Mouse_Small_Intestine_hires_image
instead.This makes it so that the notebook can run, but some of the resulting plots have changed as a result. @LucaMarconato is the change of where element live intended and thus this PR is ok, or is this actually showing an issue in the visiumhd reader?