BigBrain is free, publicly available, and provides the opportunity for considerable neuroanatomical insights as it allows for extraction of features at high resolution for modeling and simulation.
Enabling an unprecedented look into the human brain, BigBrain spans micro- and macro-scopic scales. While previously available reference brains have been restricted to a single scale, such as whole-brain magnetic resonance imaging in humans or electron microscopy of small sections from small animals, BigBrain is an ultrahigh-resolution three-dimensional model of a full human brain at 20 micrometer resolution, coming closer to touching both camps than any previous dataset.Learn More
# pip install numpy tifffile cloud-volume import numpy as np import tifffile from cloudvolume import CloudVolume vol = CloudVolume( "s3://open-neurodata/bigbrain/release2015/image", mip=0, use_https=True ) # load data into numpy array cutout = vol[3072:3584, 3072:3584, 2848:2864] # save cutout as TIFF tifffile.imwrite("data.tiff", data=np.transpose(cutout))
Documentation for cloud-volume located here
K. Amunts, C. Lepage, L. Borgeat, H. Mohlberg, T. Dickscheid, M. Rousseau, S. Bludau, P. Bazin, L. B. Lewis, A. Oros-Peusquens, N. J. Shah, T. Lippert, K. Zilles, and A. C. Evans. BigBrain: an ultrahigh-resolution 3D human brain model. Science (New York, NY), 2013.