omicverse.io.read_visium_hd_bin

omicverse.io.read_visium_hd_bin(path, sample=None, binsize=16, count_h5_path='filtered_feature_bc_matrix.h5', count_mtx_dir='filtered_feature_bc_matrix', tissue_positions_path='spatial/tissue_positions.parquet', hires_image_path='spatial/tissue_hires_image.png', lowres_image_path='spatial/tissue_lowres_image.png', scalefactors_path='spatial/scalefactors_json.json')[source]

Read Visium HD bin-level output and attach spatial metadata.

Parameters:

  • path (str or Path) – Path to the SpaceRanger output directory.

  • sample (str, optional) – Sample key stored in adata.uns['spatial']. If None, inferred from path.

  • binsize (int, default 16) – Bin size metadata (for example 2/8/16).

  • count_h5_path (str) – Relative path to bin-level 10x H5 matrix.

  • count_mtx_dir (str) – Relative path to bin-level MTX directory (fallback when H5 unavailable).

  • tissue_positions_path (str) – Relative path to tissue positions table (parquet/csv).

  • hires_image_path (str) – Relative path to hires tissue image.

  • lowres_image_path (str) – Relative path to lowres tissue image.

  • scalefactors_path (str) – Relative path to scalefactors JSON.

Returns:

Bin-level AnnData with obsm['spatial'] and uns['spatial'][sample] metadata.

Return type:

anndata.AnnData