To support Space Ranger v3.1.2 for Visium HD

[lijinbio]

Hi there,

The current spatialdata_io.visium_hd() function cannot be used to load the output of Space Ranger 3.1.2, as its output file names differ significantly from the current implementation, which requires dataset_id in the file names. See the description of the output for v3.1.2 at:
https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/output-overview

Could you suggest how to correctly load Space Ranger v3.1.2 output using spatialdata_io.visium_hd()? Any workaround solutions would be greatly appreciated. Thanks!

[LucaMarconato]

Hi @lijinbio, can you try this PR please? #264

[lijinbio]

Hi @LucaMarconato, yes, I will try it out. However, after a quick search, I noticed that dataset_id is also used for several other files, including:

spatialdata-io/src/spatialdata_io/readers/visium_hd.py

Line 236 in 625c77c

shapes_name = dataset_id + "_" + bin_size_str

spatialdata-io/src/spatialdata_io/readers/visium_hd.py

Line 316 in 625c77c

images[dataset_id + "_hires_image"],

spatialdata-io/src/spatialdata_io/readers/visium_hd.py

Line 334 in 625c77c

images[dataset_id + "_lowres_image"],

Do you think the fix in the PR will address these image files as well? Thanks.

[LucaMarconato]

Hi, thanks for reporting, I have made some changes to the linked PR and merged it. Please if you test it, it would be great to learn your feedback.