A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.
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).
Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA.
Kristen M
0000-0002-1943-4744
KM
Harris
Department of Pathology, Charles University at Prague, Faculty of Medicine , 500 35 Hradec Kralove, Czech Republic.
Josef
J
Spacek
Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA.
Maria Elizabeth
ME
Bell
Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA.
Patrick H
PH
Parker
Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA.
Laurence F
LF
Lindsey
Department of Computer Science, Institute for Data Intensive Science and Engineering, Johns Hopkins University, 160 Malone Hall, 3400 N. Charles St. , Baltimore, Maryland 21218, USA.
Alexander D
AD
Baden
Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Clark Hall Room 317C, 3400 N. Charles St. , Baltimore, Maryland 21218, USA.
Joshua T
JT
Vogelstein
Department of Computer Science, Institute for Data Intensive Science and Engineering, Johns Hopkins University, 160 Malone Hall, 3400 N. Charles St. , Baltimore, Maryland 21218, USA.
Randal
R
Burns
D000818:Animals; D006624:Hippocampus / Q000033:anatomy & histology*; D007091:Image Processing, Computer-Assisted; D008854:Microscopy, Electron; D019581:Neuropil; D051381:Rats; D012984:Software