omicverse.io.spatial.write_visium_hd_cellseg

omicverse.io.spatial.write_visium_hd_cellseg#

omicverse.io.spatial.write_visium_hd_cellseg(adata, path, sample=None)[source]#

Export cell-level AnnData to SpaceRanger v4-compatible directory structure.

Creates the following output files:

path/
├── filtered_feature_cell_matrix.h5
├── graphclust_annotated_cell_segmentations.geojson
└── spatial/
    ├── tissue_hires_image.png
    ├── tissue_lowres_image.png
    └── scalefactors_json.json
Parameters:

  • adata (AnnData) – Cell-level AnnData from bin_to_cell() or read_visium_hd_seg(). Must have obs["geometry"] (WKT strings) and obsm["spatial"].

  • path (str or Path) – Output directory to write SpaceRanger-like structure.

  • sample (str, optional) – Sample key in adata.uns["spatial"]. If None, uses the first key.

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