Is squidpy.read.visium compatible with Visium HD data?

scverse / squidpy

Spatial Single Cell Analysis in Python

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

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Is squidpy.read.visium compatible with Visium HD data? #843

Closed sunyumail93 closed 3 months ago

sunyumail93 commented 3 months ago

Description

I got the following error when using squidpy.read.visium to read Visium HD Space Ranger output dir: FileNotFoundError: [Errno 2] No such file or directory: /outs/binned_outputs/square_016um/spatial/tissue_positions_list.csv I wondered if squidpy is compatible with Visium HD output?

Minimal reproducible example

adata=sq.read.visium("/outs")

Version

squidpy==1.5.0

giovp commented 3 months ago

hi @sunyumail93 indeed it is incompatible, for a visiumHD reader, https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium_hd.html#spatialdata_io.visium_hd