Problems with Python when Seurat --> AnnData

[nsdelablancac]

Hi all!

I'd like to use some Python packages in my already processed Seurat data. To this aim, I transformed the Seurat object into AnnData as specified here: https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html. However, this transformed object has some compatibility problems in Python:

• Spatial not detected: sc.pl.spatial(adata, img_key="hires", color="seurat_clusters", size=1.5)

• Genes specified differently and not detected sc.pl.highest_expr_genes(adata, n_top=20, )

This is my object:

I'm quite new in Python and Python objects and I'm not able to see the problem cause the transformation Seurat-->AnnData seems to be completed. Could you please help me?

Thank you in advance! Best.