Visium observation with NaN metadata

[jychien]

Description

When tissue_positions.csv rather than tissue_positions_list.csv is in the spatial directory for a Visium dataset, the resulting AnnData object has:

• NaN in adata.obs array_row, array_col, and in_tissue
• nan in adata.obsm[‘spatial’] for the first cell barcode in the tissue_positions.csv list.

Minimal reproducible example

Traceback

It looks like this the issue could be that it should be header=0 rather than header=1 in this line:

squidpy/src/squidpy/read/_read.py

Line 87 in 945e127

header=1 if tissue_positions_file.name == "tissue_positions.csv" else None,

Version

squidpy 1.2.3 and later

[LLehner]

Hi @jychien, the squidpy reader functions will be deprecated eventually, since we use spatialdata-io for reading now. I would suggest to use the Visium reader from spatialdata-io which loads the data into a spatialdata object.

sdata = sd.visium("path/to/directory")

The anndata object with coordinates can be found under sdata.tables, so you can continue to use squidpy as usal for analysis.