save_annotation_masks#

brainglobe_atlasapi.atlas_generation.stacks.save_annotation_masks(stack: List[ndarray[tuple[Any, ...], dtype[_ScalarT]]], output_dir: Path, transformations: List[List[Dict]]) → None[source]#

Save the 4D annotation masks array.

Parameters:

  • stack (List[np.ndarray]) – List of 4D (N, Z, Y, X) arrays, one per scale level.

  • output_dir (Path) – Directory in which to create annotations.ome.zarr.

  • transformations (List[List[Dict]]) – OME-Zarr coordinate transformations, one list per scale level. Each scale must be 4-element: [1, z_mm, y_mm, x_mm].