write_multiscale_ome_zarr#

brainglobe_atlasapi.atlas_generation.stacks.write_multiscale_ome_zarr(images: List[ndarray[tuple[Any, ...], dtype[_ScalarT]]], output_path: Path, transformations: List[List[dict]], axes: List[dict] = [{'name': 'z', 'orientation': {'type': 'anatomical', 'value': 'anterior-to-posterior'}, 'type': 'space', 'unit': 'millimeter'}, {'name': 'y', 'orientation': {'type': 'anatomical', 'value': 'superior-to-inferior'}, 'type': 'space', 'unit': 'millimeter'}, {'name': 'x', 'orientation': {'type': 'anatomical', 'value': 'right-to-left'}, 'type': 'space', 'unit': 'millimeter'}])[source]#

Write a multiscale image pyramid to an OME-Zarr file.

Parameters:

  • images (list of np.ndarray) – A list of image stacks representing different levels of the pyramid.

  • output_path (Path) – The path where the OME-Zarr file will be saved.

  • transformations (list of lists of dicts) – A list of transformations to be saved alongside the images.

  • axes (list of dicts, optional) – A list of axis descriptors to be included in the OME-Zarr metadata. If not provided, defaults to BG_OME_ZARR_AXES.