scanpy==1.9.3 anndata==0.9.1 umap==0.5.3 numpy==1.22.4 scipy==1.10.1 pandas==2.0.0 scikit-learn==1.2.2
I am attempting to visualise NanoString spatial transcriptomics using sq.pl.spatial_segment() and am passing the usual arguments; adata, color, library_key, and seg_cell_id. However, it is failing to overlay cell images onto the graphs and returning a type-error:
TypeError: ‘collection’ must be an instance of matplotlib.collections.Collection, not a matplotlib.image.AxesImage
My guess is that it seems SquidPy is not passing the images onto the collection object when plotting multiple FOV’s and retaining it in an image container.
Has anyone encountered this error, and is there a fix?
Any help would much be appreciated. Thanks