omicverse.space.bin2cell

omicverse.space.bin2cell(adata, labels_key='labels_joint', spatial_keys=['spatial'], diameter_scale_factor=None, add_geometry=False, geometry_key='geometry', geometry_spatial_key='spatial', geometry_force_polygon=False, rename_obs_to_cellid=True, show_progress=True)[source]

Aggregate binned Visium signals into cell-level profiles.

Parameters:

  • adata (AnnData) – Spatial bin-level AnnData.

  • labels_key (str, default='labels_joint') – Label key assigning bins to cells.

  • spatial_keys (list, default=['spatial']) – Spatial coordinate keys to aggregate.

  • diameter_scale_factor (float, optional) – Optional scaling factor for estimated cell diameters.

  • add_geometry (bool, default=False) – Whether to generate polygon geometry from labeled bins and store WKT strings in obs[geometry_key] of the returned cell-level AnnData.

  • geometry_key (str, default='geometry') – Observation column name used to store generated geometry WKT.

  • geometry_spatial_key (str, default='spatial') – Coordinate key in adata.obsm used to reconstruct polygons.

  • geometry_force_polygon (bool, default=False) – If True, convert MultiPolygon geometries to their largest polygon component so each cell gets a single polygon contour.

  • rename_obs_to_cellid (bool, default=True) – If True, rename output obs_names to cellid_XXXXXXXXX-1 using obs['object_id'] and also write obs['cellid'].

  • show_progress (bool, default=True) – Whether to display progress bars during aggregation and (if enabled) geometry reconstruction.

Returns:

Cell-level AnnData generated from labeled bins.

Return type:

AnnData