dotools_py.io.read_visium

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dotools_py.io.read_visium#

dotools_py.io.read_visium(path, counts_file='filtered_feature_bc_matrix.h5', library_id=None, load_images=True, source_image_path=None, **kwargs)[source]#

Read SpaceRanger output into AnnData Object.

Adapted from Squidpy.

Parameters:
path str | PathLike[str] | Path

Path to the folder containing the Visium files.

counts_file str (default: 'filtered_feature_bc_matrix.h5')

Name of the file to use as the count file.

library_id str | None (default: None)

Identifier for the Visium library.

load_images bool (default: True)

Whether to load the image or not and save it in adata.uns['spatial']

source_image_path str | PathLike[str] | Path | None (default: None)

Path to the source image.

kwargs

Additional arguments pass when reading the H5 file.

Return type:

AnnData

Returns:

Returns an AnnData Object.

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