Deisseroth et al. (2016)
Twelve CLARITY mouse brains (5 wild type controls and 7 behaviorally challenged) were prepared by Li Ye, and imaged using CLARITY-Optimized Light-sheet Microscopy (COLM) (whole brain COLM imaging and data stitching performed by R. Tomer, in preparation).
# pip install numpy tifffile cloud-volume import numpy as np import tifffile from cloudvolume import CloudVolume vol = CloudVolume( "s3://open-neurodata/kutten/Cocaine174/Grayscale", mip=0, use_https=True ) # load data into numpy array cutout = vol[10752:11264, 13312:13824, 704:720] # save cutout as TIFF tifffile.imwrite("data.tiff", data=np.transpose(cutout))
Documentation for cloud-volume located here
K. S. Kutten, J. T. Vogelstein, N. Charon, L. Ye, K. Deisseroth, and M. I. Miller. Deformably registering and annotating whole CLARITY brains to an atlas via masked LDDMM. Optics, Photonics and Digital Technologies for Imaging Applications IV, 2016.