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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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Tutorial for Visium applicable to Visium HD? #893

Closed spatts14 closed 1 month ago

spatts14 commented 2 months ago

Hi all,

Thanks so much for your work!

I wanted to enquire if the tutorial for visium will still be suitable for visium HD data? Im curious as now the spot sizes are smaller and there is a grid-like system rather than the gaps between previous spots.

Thanks! ...

LLehner commented 1 month ago

Hi @spatts14,

regarding the grid-like system some things will probably need to be adjusted. But all the tutorials will soon get a rework and also incorporate spatialdata, then there will also be a Visium HD tutorial!

LLehner commented 1 month ago

@spatts14 In the meantime i would suggest using the Visium HD reader from spatialdata-io (see API here) and check out the spatialdata Visium HD tutorial here. You can continue working with squidpy, using the spatialdata object.

spatts14 commented 1 month ago

Thanks @LLehner so much! I will check them out. Looking forward to the new tutorials.