A portal into the 3D ultrastructure of the brain.
Harris et al. (2015)
A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.
From the laboratory of Kristen M Harris, PhD, three volumes of hippocampal CA1 neuropil in adult rat were imaged at an XY resolution of ~2 nm on serial sections of ~50-60 nm thickness. All axons, dendrites, glia, and synapses were reconstructed in a cube surrounding a large dendritic spine, a cylinder surrounding an oblique dendritic segment, and a parallelepiped surrounding an apical dendritic segment.
Learn MoreData
spine i
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 i
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 i
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
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