squidpy.read.vizgen

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

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

Parameters
  • path (Union[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 (Optional[str]) – 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.