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).

Data

Cocaine174 Viz

Example cutout
# 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

Publications

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.

To access this data, please view the guide.

Data on this site are licensed under ODC-By v1.0 license.