Kasthuri et al. (2015)

Bobby Kasthuri, Ph.D. under the tutelage of Jeff Lichtman, M.D., Ph.D., acquired a data set from mouse cortex with a 3x3x30 cubic nanometer spatial resolution, yielding 660GB of images. This beautiful data was published Friday, July 30th 2015 in Cell.

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Data

kasthuri11 Viz

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

vol = CloudVolume(
    "s3://open-neurodata/kasthuri/kasthuri11/image", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[11264:11776, 13312:13824, 912:928]

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

Documentation for cloud-volume located here

kasthuri14Maine Viz

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

vol = CloudVolume(
    "s3://open-neurodata/kasthuri/kasthuri14Maine/image", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[2560:3072, 3072:3584, 1184:1200]

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

Documentation for cloud-volume located here

kasthuri14s1colEM Viz

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

vol = CloudVolume(
    "s3://open-neurodata/kasthuri/kasthuri14s1colEM/image", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[28672:29184, 15872:16384, 112:128]

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

Documentation for cloud-volume located here

Tools

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

mojo

Reproducible Scalable Science

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VAST Lite: Volume Annotation and Segmentation Tool

vast

Publications

N. Kasthuri, K. J. Hayworth, D. R. Berger, R. L. Schalek, J. A. Conchello, S. Knowles-Barley, D. Lee, A. Vázquez-Reina, V. Kaynig, T. R. Jones, M. Roberts, J. L. Morgan, J. C. Tapia, H. S. Seung, W. G. Roncal, J. T. Vogelstein, R. Burns, D. L. Sussman, C. E. Priebe, H. Pfister, and J. W. Lichtman. Saturated Reconstruction of a Volume of Neocortex. Cell, 2015.

To access this data, please view the guide.

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