Bock et al. (2011)
Layer 2/3 - Davi Bock, Ph.D. and Wei-Chung Allen Lee, Ph.D., in the laboratory of Clay Reid, M.D., Ph.D. acquired a beautiful volume of mouse primary visual cortical data, spanning layers 1, 2/3, and upper layer 4. In addition to the electron microscope (EM) data, they used two-photon microscopy to determine the functional properties of about 14 of the cells in the same volume. Images were collected at approximately 4x4x45 cubic nanometers with a total volume of approximately 450x350x50 cubic microns.Learn More
# pip install numpy tifffile cloud-volume import numpy as np import tifffile from cloudvolume import CloudVolume vol = CloudVolume( "s3://open-neurodata/bock11/image", mip=0, use_https=True ) # load data into numpy array cutout = vol[65024:65536, 62464:62976, 3616:3632] # save cutout as TIFF tifffile.imwrite("data.tiff", data=np.transpose(cutout))
Documentation for cloud-volume located here
D. D. Bock, W. C. A. Lee, A. M. Kerlin, M. L. Andermann, G. Hood, A. W. Wetzel, S. Yurgenson, E. R. Soucy, H. S. Kim, and R. C. Reid. Network anatomy and in vivo physiology of visual cortical neurons. Nature, 2011.
nature video. Untangling the brain - by Nature Video. YouTube, 2011.