Harris et al. (2015)

A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.

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Data

spine Viz

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

vol = CloudVolume(
    "s3://open-neurodata/kharris15/spine/em", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[4096:4608, 2560:3072, 48:64]

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

Documentation for cloud-volume located here

apical Viz

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

vol = CloudVolume(
    "s3://open-neurodata/kharris15/apical/em", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[4096:4608, 3584:4096, 112:128]

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

Documentation for cloud-volume located here

oblique Viz

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

vol = CloudVolume(
    "s3://open-neurodata/kharris15/oblique/em", mip=0, use_https=True
)

# load data into numpy array
cutout = vol[2560:3072, 3072:3584, 48:64]

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

Documentation for cloud-volume located here

Tools

A portal into the 3D ultrastructure of the brain.

SynapseWeb

Program for tracing serial sections

Reconstruct

Caching gateway to connect a CATMAID (or other visualization) server to ndstore

CAJAL

Publications

K. M. Harris, J. Spacek, M. E. Bell, P. H. Parker, L. F. Lindsey, A. D. Baden, J. T. Vogelstein, and R. Burns. A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development. Scientific Data, 2015.

To access this data, please view the guide.

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

Please use this DOI when citing this data: 10.7281/T11Z429Q