sainsc.io.read_Xenium

sainsc.io.read_Xenium(filepath, *, binsize=0.5, remove_features=XENIUM_CTRLS, n_threads=None)

Read a Xenium transcripts file.

Parameters:

  • filepath (PathLike or str) – Path to the Xenium transcripts file. Both, csv.gz and parquet files, are supported.

  • binsize (float, optional) – Size of each bin in um.

  • remove_features (Collection[str], optional) – List of regex patterns to filter the ‘feature_name’ column, sainsc.io.XENIUM_CTRLS by default. For Xenium v3 parquet files the data is automatically filtered with the ‘is_gene’ column, as well.

  • 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