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Extend sq.read.visium to standard Visium HD format #969

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KarolineHoller opened this issue Mar 6, 2025 · 1 comment
Open

Extend sq.read.visium to standard Visium HD format #969

KarolineHoller opened this issue Mar 6, 2025 · 1 comment

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@KarolineHoller
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Description

In the current version of read.visium, spatial positions are read in as a csv file. Please extend this function to parquet files, as most recent Visium HD output provides these tables in a different format.

tissue_positions_file = (
path / "spatial/tissue_positions.csv"
if (path / "spatial/tissue_positions.csv").exists()
else path / "spatial/tissue_positions_list.csv"

add: else path / " spatial/tissue_positions.parquet"

@maltekuehl
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Hi, I think most development for reading in newer formats is happening in the spatialdata-io package, you might want to check it out. Perhaps a maintainer can answer whether squidpy plans to eventually deprecate its own io functionality or extend it again.

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