Dyer et al. (2016)

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dyer16 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/dyer/dyer16/image", mip=0, use_https=True

# load data into numpy array
cutout = vol[1024:1536, 1024:1536, 992:1008]

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

Documentation for cloud-volume located here


A Python 2 / 3 module that enables big-data neuroscience, as well as direct interfacing with NeuroData workflows and servers.


Mojo is an interactive proofreading tool for annotation of 3D EM data.


Tomographic reconstruction in Python



E. L. Dyer, W. G. Roncal, H. L. Fernandes, D. Gürsoy, V. De Andrade, R. Vescovi, K. Fezzaa, X. Xiao, J. T. Vogelstein, C. Jacobsen, K. P. Körding, and N. Kasthuri. Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography. eNeuro, 2017.

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