pyXenium.io.read_xenium#

read_xenium(base_path, *, as_='anndata', prefer='auto', include_transcripts=True, stream_transcripts=False, include_boundaries=True, include_images=False, clusters_relpath=DEFAULT_CLUSTER_RELPATH, cluster_column_name='cluster', cells_csv='cells.csv.gz', cells_parquet=None, cells_path=None, cell_groups_path=None, feature_matrix_path=None, cell_id_col=None, cluster_col=None, x_col=None, y_col=None, mex_dirname='cell_feature_matrix', mex_matrix_name='matrix.mtx.gz', mex_features_name='features.tsv.gz', mex_barcodes_name='barcodes.tsv.gz')#
Parameters:

  • base_path (str)

  • as_ (str)

  • prefer (str)

  • include_transcripts (bool)

  • stream_transcripts (bool)

  • include_boundaries (bool)

  • include_images (bool)

  • clusters_relpath (str | None)

  • cluster_column_name (str)

  • cells_csv (str)

  • cells_parquet (str | None)

  • cells_path (str | Path | None)

  • cell_groups_path (str | Path | None)

  • feature_matrix_path (str | Path | None)

  • cell_id_col (str | None)

  • cluster_col (str | None)

  • x_col (str | None)

  • y_col (str | None)

  • mex_dirname (str)

  • mex_matrix_name (str)

  • mex_features_name (str)

  • mex_barcodes_name (str)

Return type:

AnnData | XeniumSlide

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