spatialdata_io.visium#
- spatialdata_io.visium(path, dataset_id=None, counts_file='filtered_feature_bc_matrix.h5', fullres_image_file=None, tissue_positions_file=None, scalefactors_file=None, imread_kwargs=mappingproxy({}), image_models_kwargs=mappingproxy({}), **kwargs)#
Read 10x Genomics Visium formatted dataset.
This function reads the following files:
(<dataset_id>_)`'filtered_feature_bc_matrix.h5'`
: Counts and metadata file.'spatial/tissue_hires_image.png'
: High resolution image.'spatial/tissue_lowres_image.png'
: Low resolution image.'scalefactors_json.json'
: Scalefactors file.'tissue_positions_list.csv'
(SpaceRanger 1) or'tissue_positions.csv'
(SpaceRanger 2):Spots positions file.
fullres_image_file
: large microscopy image used as input for space ranger.
See also
- Parameters:
path (str | Path) – Path to the directory containing the data.
dataset_id (str | None (default:
None
)) – Dataset identifier to name the constructedSpatialData
elements. The reader will try to infer it from the counts_file filen name (which defaults to'filtered_feature_bc_matrix.h5'
) file name. If the file name does not contain the dataset id, it needs to be provided.counts_file (str (default:
'filtered_feature_bc_matrix.h5'
)) – Name of the counts file, defaults to'filtered_feature_bc_matrix.h5'
; a common alternative is'raw_feature_bc_matrix.h5'
. Also, use when the file names are not following the standard SpaceRanger conventions.fullres_image_file (str | Path | None (default:
None
)) – Path to the full-resolution image.tissue_positions_file (str | Path | None (default:
None
)) – Path to the tissue positions file.scalefactors_file (str | Path | None (default:
None
)) – Path to the scalefactors file.imread_kwargs (Mapping[str, Any] (default:
mappingproxy({})
)) – Keyword arguments passed todask_image.imread.imread()
.image_models_kwargs (Mapping[str, Any] (default:
mappingproxy({})
)) – Keyword arguments passed tospatialdata.models.Image2DModel
.
- Return type:
SpatialData
- Returns: