omicverse.io.read_visium_hd_seg

omicverse.io.read_visium_hd_seg(path, sample=None, cell_segmentations_path='graphclust_annotated_cell_segmentations.geojson', count_h5_path='filtered_feature_cell_matrix.h5', 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 cell-segmentation output and attach geometries + spatial metadata.

Parameters:

  • path (str or Path) – Path to the cell-segmentation output directory.

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

  • cell_segmentations_path (str) – Relative path to segmentation GeoJSON.

  • count_h5_path (str) – Relative path to filtered feature-cell matrix (H5).

  • 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:

Cell-level AnnData with obsm['spatial'], segmentation geometry, and spatial image metadata.

Return type:

anndata.AnnData