apply image rotation when plotting tissue / cellxgene

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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apply image rotation when plotting tissue / cellxgene #518

Closed mkunst23 closed 2 years ago

mkunst23 commented 2 years ago

Imege rotation

Hi,

when plotting cell position on top of images (sc.pl.spatial) would it be possible to apply a predefined rotation to it? This could either be an argument in the function call or something that can be pulled from the adata.uns' ...

giovp commented 2 years ago

hi @mkunst23 thanks for the interest in Squidpy. I think this is very doable and we are working on something related. For now, you'd have to apply the transform before and save it in adata.uns["spatial"][<library_id>]["images"]... as usual. Let me know if that help, I'll keep this open as reminder

giovp commented 2 years ago

closing due to inactivity

wangjiawen2013 commented 1 year ago

We can rotate the image using 10x genomics loupe browser, but cannot using squidpy. Does Napari support rotation of squidpy h5ad objects ?