sainsc.io.read_StereoSeq_bins

sainsc.io.read_StereoSeq_bins(filepath, bin_size=50, *, spatialdata=False, resolution=None, gene_name=False, exon_count=False, sep='\t', n_threads=None, **kwargs)

Read a Stereo-seq GEM file into bins.

Parameters:

  • filepath (PathLike or str) – Path to the Stereo-seq file.

  • bin_size (int, optional) – Defines the size of bins along both dimensions e.g 50 will results in bins of size 50x50.

  • spatialdata (bool, optional) – If True will load the data as a SpatialData object else as an AnnData object.

  • resolution (float, optional) – Center-to-center distance of Stere-seq beads in nm, if None it will try to detect it from the chip definition in the file header if one exists.

  • gene_name (bool) – If True will use the ‘geneName’ column otherwise the ‘geneID’ column is used as gene identifier.

  • exon_count (bool) – If True will use the ‘ExonCount’ column otherwise the ‘MIDCount’ column is used as counts.

  • sep (str, optional) – Separator used in polars.read_csv().

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

  • kwargs – Other keyword arguments will be passed to polars.read_csv().

Returns:

AnnData or SpatialData object of the bins with coordinates stored in anndata.AnnData.obsm with the key ‘spatial’.

Return type:

AnnData | SpatialData

Raises:

ModuleNotFoundError – If spatialdata is set to True but the package is not installed.