sainsc.io.read_VisiumHD

sainsc.io.read_VisiumHD(path, *, gene_name=False, raw=False, n_threads=None)

Read a VisiumHD sample.

Parameters:

  • path (PathLike or str) – Path to the 2um bin directory of the sample. The filtered or raw h5 file and the spatial/tissue_positions.parquet file are required.

  • gene_name (bool, optional) – If True will use the ‘name’ column otherwise the ‘id’ column is used as gene identifier.

  • raw (bool, optional) – If False the filtered barcode-feature matrix will be used. If True the raw matrix is loaded.

  • n_threads (int | None, optional) – Number of threads used for reading file and processing. If None or 0 this will default to the number of available CPUs.

Return type:

LazyKDE

Raises:

FileNotFoundError – If either the h5-file or the barcode position file are not found at their default path.