Allen Reference Atlas

Adult Mouse Reference Atlas from the Allen Institute

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Data

sagittal_10um Viz

average, nissl, segmentations

Example cutout
# pip install numpy tifffile cloud-volume
import numpy as np
import tifffile
from cloudvolume import CloudVolume

vol = CloudVolume(
    "s3://open-neurodata/ara_2016/sagittal_10um/nissl_10um", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[512:1024, 0:512, 512:528]

# save cutout as TIFF
tifffile.imwrite("data.tiff", data=np.transpose(cutout))

Documentation for cloud-volume located here

sagittal_25um Viz

average, nissl, segmentations

sagittal 50um Viz

average, nissl, segmentations, mesh

sagittal_100um Viz

average, segmentations

Publications

Allen Institute for Brain Science. Allen Mouse Common Coordinate Framework ALLEN MOUSE COMMON COORDINATE FRAMEWORK AND REFERENCE ATLAS. Technical White Paper, 2017.

A. R. Jones, C. C. Overly, and S. M. Sunkin. The Allen Brain Atlas: 5 years and beyond. Nature Reviews Neuroscience, 2009.

E. Lein, M. Hawrylycz, N. Ao, M. Ayres, A. Bensinger, A. Bernard, A. Boe, M. Boguski, K. Brockway, E. Byrnes, and Others. Genome-wide atlas of gene expression in the adult mouse brain. Nature, 2006.

To access this data, please view the guide.

Data on this page are licensed under Allen Terms of Use.