atlannot.merge_original.coarse module

The coarse merging of the annotation atlases.

atlannot.merge_original.coarse.coarse_merge(annotation, annotation2, brain_regions)[source]

Perform the coarse atlas merging.

Parameters:

  • annotation (np.ndarray) – The first atlas to merge, usually CCFv2.

  • annotation2 (np.ndarray) – The second atlas to merge, usually CCFv3.

  • brain_regions (dict) – The brain regions dictionary. Can be obtained from the “msg” key of the brain_regions.json (1.json) file.

Returns:

  • ccfv2_corrected (np.ndarray) – The merged CCFv2 atlas.

  • ccfv3_corrected (np.ndarray) – The merged CCFv3 atlas.