squidpy.read.vizgen

squidpy.read.vizgen(path, *, counts_file, meta_file, transformation_file=None, library_id='library', **kwargs)

Read Vizgen formatted dataset.

In addition to reading the regular Vizgen output, it loads the metadata file and optionally loads the transformation matrix.

See also

• Vizgen data release program.

• squidpy.pl.spatial_scatter() on how to plot spatial data.

Parameters:

• path (str | Path) – Path to the root directory containing Vizgen files.

• counts_file (str) – File containing the counts. Typically ends with _cell_by_gene.csv.

• meta_file (str) – File containing the spatial coordinates and additional cell-level metadata.

• transformation_file (str | None) – Transformation matrix file for converting micron coordinates into pixels in images.

• library_id (str) – Identifier for the Vizgen library. Useful when concatenating multiple anndata.AnnData objects.

Return type:

AnnData

Returns:

Annotated data object with the following keys:

• anndata.AnnData.obsm ['spatial'] - spatial spot coordinates in microns.

• anndata.AnnData.obsm ['blank_genes'] - blank genes from Vizgen platform.

• anndata.AnnData.uns ['spatial']['{library_id}']['scalefactors']['transformation_matrix'] - transformation matrix for converting micron coordinates to pixels. Only present if transformation_file != None.