hest.readers.VisiumHDReader

class hest.readers.VisiumHDReader

10x Genomics Visium-HD reader

Methods table

auto_read(path, **read_kwargs)

Automatically detect the file names and determine a reading strategy based on the detected files.

read(img_path, square_16um_path, square_2um_path)

Read a VisiumHD sample such that 16um bins are pooled into 128um pseudo-Visium bins

Methods

VisiumHDReader.auto_read(path: str, **read_kwargs) → HESTData

Automatically detect the file names and determine a reading strategy based on the detected files. For more control on the reading process, consider using read() instead

Parameters:

path (st) – path to the directory containing all the necessary files

Returns:

STObject that was read

Return type:

HESTData

VisiumHDReader.read(img_path: str, square_16um_path: str, square_2um_path: str, metrics_path: str = None, dst_bin_size_um: int = 128, chunk_len=50000) → VisiumHDHESTData

Read a VisiumHD sample such that 16um bins are pooled into 128um pseudo-Visium bins

Parameters:

  • img_path (str) – path to the WSI

  • square_16um_path (str) – path to a square_016um/ Visium HD folder.

  • square_2um_path (str) – Deprecated path to a square_002um/ Visium HD folder.

  • metrics_path (str, optional) – path to a metrics_summary.csv Visium HD file.

  • dst_bin_size_um (int, optional) – 16um spots will be pooled to spots of this size (must be a multiple of the spot size: 16)

  • chunk_len (str, optional) – chunk length while pooling transcripts, a higher number will consume more RAM but might be faster.

Returns:

Visium HD sample

Return type:

VisiumHDHESTData