3D Pipeline API

Cell Neighbor Detection & Graph Construction (3D)

interscellar.api.wrapper_3d.find_cell_neighbors_3d(ome_zarr_path: str, metadata_csv_path: str, max_distance_um: float = 0.5, voxel_size_um: tuple = (0.56, 0.28, 0.28), centroid_prefilter_radius_um: float = 75.0, cell_id: str = 'CellID', cell_type: str = 'phenotype', centroid_x: str = 'X_centroid', centroid_y: str = 'Y_centroid', centroid_z: str = 'Z_centroid', db_path: str | None = None, output_csv: str | None = None, output_anndata: str | None = None, n_jobs: int = 1, return_connection: bool = False, save_surfaces_pickle: str | None = None, load_surfaces_pickle: str | None = None, save_graph_state_pickle: str | None = None) → Tuple[DataFrame | None, object | None, object | None]

interscellar.api.wrapper_3d.compute_interscellar_volumes_3d(ome_zarr_path: str, neighbor_pairs_csv: str, global_surface_pickle: str | None = None, halo_bboxes_pickle: str | None = None, neighbor_db_path: str | None = None, voxel_size_um: tuple = (0.56, 0.28, 0.28), db_path: str | None = None, output_csv: str | None = None, output_anndata: str | None = None, output_mesh_zarr: str | None = None, output_cell_only_zarr: str | None = None, max_distance_um: float = 3.0, intracellular_threshold_um: float = 1.0, n_jobs: int = 4, return_connection: bool = False, intermediate_results_dir: str = 'intermediate_interscellar_results') → Tuple[DataFrame | None, object | None, object | None]

interscellar.api.wrapper_3d.compute_cell_only_volumes_3d(ome_zarr_path: str, interscellar_volumes_zarr: str, output_zarr_path: str | None = None, neighbor_db_path: str | None = None) → DataFrame