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

Scientific Data
Kristen HarrisRandal Burns

Abstract

Resurgent interest in synaptic circuitry and plasticity has emphasized the importance of 3D reconstruction from serial section electron microscopy (3DEM). Three volumes of hippocampal CA1 neuropil from adult rat were imaged at X-Y resolution of ~2 nm on serial sections of ~50-60 nm thickness. These are the first densely reconstructed hippocampal volumes. All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long). The data provide standards for identifying ultrastructural objects in 3DEM, realistic reconstructions for modeling biophysical properties of synaptic transmission, and a test bed for enhancing reconstruction tools. Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites. The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).

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Citations

Dec 1, 2015·ELife·Thomas M BartolTerrence J Sejnowski
Sep 30, 2015·Hippocampus·Deborah J WatsonKristen M Harris
Mar 23, 2018·Journal of Immigrant and Minority Health·Wei-Chen LeeBen G Raimer
Apr 8, 2020·Nanoscale·Shekhar KediaDeepak Nair
May 18, 2019·The Journal of Physiology·Gaurang Mahajan, Suhita Nadkarni
Jan 8, 2020·The Journal of Comparative Neurology·Ernesto HernandezLynne A Oland
Feb 2, 2021·ACS Chemical Neuroscience·Thomas SteinkellnerDaniela Boassa
Feb 25, 2021·Communications Biology·Nishant SinghSuhita Nadkarni
Apr 12, 2021·Journal of Neuroscience Methods·Alexander SongAdam S Charles

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Methods Mentioned

BETA
electron microscopy

Software Mentioned

Matlab
CATMAID
OCP Annotation Toolkit
Open Connectome
SynapseWeb
3DEM
R
TrakEM2
OCPtilecache
VolRover

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