Save or create to .h5 from a h5ad

Hey Guys!

I’m triying to read some visium data into scanpy. The count matrix was shared in a .csv. I want to convert that into a .h5 file to be able to use sc.read_visium() and load th object along with the image/tissue coordinates. Anyone has done this before?

Best regards,

Hi ,

thanks for the interest in scanpy! We recently released squidpy: a scanpy extension for spatial trnscirptomics data. We made a guide on how to read any spatial data in a shape that is suitable to scanpy/squidpy: Import spatial data in AnnData and Squidpy — squidpy master documentation

essentially, you can just read in the csv and add it to the right anndata slots to be able to use it as visium. Let me know if that helps!

Best,
Giovanni