spatialdata_io.xenium#
- spatialdata_io.xenium(path, n_jobs=1, cells_as_circles=True, cell_boundaries=True, nucleus_boundaries=True, cell_labels=True, nucleus_labels=True, transcripts=True, morphology_mip=True, morphology_focus=True, aligned_images=True, imread_kwargs=mappingproxy({}), image_models_kwargs=mappingproxy({}), labels_models_kwargs=mappingproxy({}))#
Read a 10X Genomics Xenium dataset into a SpatialData object.
This function reads the following files:
'experiment.xenium': File containing specifications.'nucleus_boundaries.parquet': Polygons of nucleus boundaries.'cell_boundaries.parquet': Polygons of cell boundaries.'transcripts.parquet': File containing transcripts.'cell_feature_matrix.h5': File containing cell feature matrix.'cells.parquet': File containing cell metadata.'morphology_mip.ome.tif': File containing morphology mip.'morphology_focus.ome.tif': File containing morphology focus.
See also
- Parameters:
path (str | Path) – Path to the dataset.
n_jobs (int (default:
1)) – Number of jobs to use for parallel processing.cells_as_circles (bool (default:
True)) – Whether to read cells also as circles. Useful for performant visualization. The radii of the nuclei, not the ones of cells, will be used; using the radii of cells would make the visualization too cluttered (the cell boundaries are computed as a maximum expansion of the nuclei location and therefore the corresponding circles would show considerable overlap).cell_boundaries (bool (default:
True)) – Whether to read cell boundaries (polygons).nucleus_boundaries (bool (default:
True)) – Whether to read nucleus boundaries (polygons).cell_labels (bool (default:
True)) – Whether to read cell labels (raster). The polygonal version of the cell labels are simplified for visualization purposes, and using the raster version is recommended for analysis.nucleus_labels (bool (default:
True)) – Whether to read nucleus labels (raster). The polygonal version of the nucleus labels are simplified for visualization purposes, and using the raster version is recommended for analysis.transcripts (bool (default:
True)) – Whether to read transcripts.morphology_mip (bool (default:
True)) – Whether to read the morphology mip image (available in versions < 2.0.0).morphology_focus (bool (default:
True)) – Whether to read the morphology focus image.aligned_images (bool (default:
True)) – Whether to also parse, when available, additional H&E or IF aligned images.imread_kwargs (Mapping[str, Any] (default:
mappingproxy({}))) – Keyword arguments to pass to the image reader.image_models_kwargs (Mapping[str, Any] (default:
mappingproxy({}))) – Keyword arguments to pass to the image models.labels_models_kwargs (Mapping[str, Any] (default:
mappingproxy({}))) – Keyword arguments to pass to the labels models.
- Return type:
SpatialData
- Returns: