How to add H/E image and alignment file to a pre-existing anndata object?

[thisismuskaangupta]

Dear Team

Thanks for developing this useful tool.
Say I've done processing in Seurat. To use stLearn, I'd have to convert my Seurat object to an anndata object, conveniently done using scCustomize (https://samuel-marsh.github.io/scCustomize/articles/Object_Conversion.html#convert-seurat-or-liger-objects-to-anndata-objects). However, this anndata object would not contain the image.

I saw your stlearn.add.image function to add an image, but it doesn't have a parameter for an alignment file. How could I add an H/E, with alignment, to an anndata object (as this is instructed in the pseudotime with Xenium vignette)?

Thanks
Muskaan

[duypham2108]

Can you try this one for converting from Seurat to anndata? It will also convert the image.
https://github.com/cellgeni/py8rds
https://github.com/cellgeni/py8rds/blob/c1598542db269beb8db1f8055f88fb4841fa822d/tutorials/tutorial.ipynb
Check for the Spatial Seurat section

[thisismuskaangupta]

Thanks for the suggestion. Unfortunately my Seurat object only contains the morphology image, so I'll have to add in the H&E one way or another.