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 i Metadata

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

Cocaine175 Viz

Cocaine178 Viz

Fear187 Viz

Fear197 Viz

Fear199 Viz

Control181 Viz

Control182 Viz

Control189 Viz

Control239 Viz

Control258 Viz

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.