AnnData as input to setup.srt()

[EST09]

Hi,

Thank you for this package. It looks great and I'm really looking forward to using it!

I'm struggling a little with setting up my srt object with an anndata input. I load the anndata from a h5ad file

and then try

dot.srt <- setup.srt(srt_data=ex_anndata$X, srt_coords=ex_anndata$obsm["spatial"])
My ex_anndata$X seems to be a matrix

and my coordinates from ex_anndata$obsm["spatial"] are the same length as my matrix

Please could I check if there's something I'm missing?

I can load from a standard xenium output using the Seurat LoadXenium() function but I've changed the segmentation and saved to a xenium experiment format with sopa, and then Seurat is having trouble with the cell_feature_matrix.zarr.zip files which is why I've gone the h5ad anndata route.

Thank you,

Best wishes,
Emily

[EST09]

sorry I'd supplied srt_data it as spot x gene - transposed it now. Thank you!