structure_from_ccf_coords.py

import os

import numpy as np

from allensdk.core.reference_space_cache import ReferenceSpaceCache


resolution = 100  # in microns, options are (10, 25, 50, 100).


cache = ReferenceSpaceCache(
    manifest=os.path.join("allen_ccf", "manifest.json"),  # downloaded files are stored relative to here
    resolution=resolution,
    reference_space_key="annotation/ccf_2017"  # use the latest version of the CCF
)

# The annotation volume maps voxels to structures
annotation, _ = cache.get_annotation_volume()

# the structure tree hold detailed information about annotated structures 
structure_tree = cache.get_structure_tree()

# Some coordinate, in microns
coordinate = np.array([
    5231.15,  # anterior -> posterior
    1500.0,  # dorsal -> ventral
    5200.79  # left -> right
])

voxel = np.round(coordinate / resolution).astype(int)
structure_id = annotation[voxel[0], voxel[1], voxel[2]]

# Each voxel in the annotation volume is annotated as specifically as possible
structure = structure_tree.get_structures_by_id([structure_id])[0]
print(structure)

print("============")

# Structures are organized hierarchically by containment.
ancestors = structure_tree.get_structures_by_id(structure["structure_id_path"])
for ancestor in ancestors[::-1]:
    print(ancestor["name"])