search

scverse / spatialdata

An open and interoperable data framework for spatial omics data
https://spatialdata.scverse.org/
BSD 3-Clause "New" or "Revised" License
237 stars 47 forks source link

Extract Image features from VisiumHD and Squidpy #548

Open sokratiag opened 7 months ago

sokratiag commented 7 months ago

Hi,

I am wondering if it is possible to extract image features from a visium HD dataset using spatialdata and squidpy? Is this supported?

Thanks, Sokratia

giovp commented 7 months ago

hi @sokratiag , thanks for the question, unfortunately not yet but we plan to have a draft for it soon, following #407

sokratiag commented 6 months ago

Hi @giovp i wonder whether you are planning to have the draft you mention soon? I noticed that there is a function to_legacy_anndata that converts spatialdata object to anndata so then in principle you can use the converted anndata to extract image features using squidpy, however i am not sure if this is a good practise due to the image downscaling. Do you have any recommendations?

Thanks!