Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Open
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

Comments

@KarolineHoller
Copy link

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
Copy link

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants