Adult generated neurons in aging M. musculus i

dentateECcagGFP3

Example cutout

# pip install numpy tifffile cloud-volume
import numpy as np
import tifffile
from cloudvolume import CloudVolume

vol = CloudVolume(
    "s3://open-neurodata/ABagemouse/dentateECcagGFP3/Ch0", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[512:1024, 1024:1536, 0:16]

# save cutout as TIFF
tifffile.imwrite("data.tiff", data=np.transpose(cutout))

Documentation for cloud-volume located here

J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns. A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data. Nature Methods, (11)15:846–847, 2018.