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

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 μm3) surrounding a large dendritic spine, a cylinder (~43 μm3) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm3) 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).

Mitochondrial support of persistent presynaptic vesicle mobilization with age-dependent synaptic growth after LTP

“…Postsynaptic density (PSD) areas were measured according to the orientation in which they were sectioned (Harris et al, 2015). Perfectly cross-sectioned synapses had distinct pre- and postsynaptic membranes, clefts, and docked vesicles, and their areas were calculated by summing the product of PSD length and section thickness for each section spanned.…”

Nanoconnectomic upper bound on the variability of synaptic plasticity

“…Prior work suggests that such pairs of spines are more similar in size than those from the same axon on different dendrites ( Sorra and Harris, 1993 ). Here we evaluated this axon-spine coupling in a complete nanoconnectomic three-dimensional reconstruction from serial electron microscopy (3DEM) ( Harris et al, 2015 ) of hippocampal neuropil. We determined the similarity of synapses among pairs of spines and set an upper bound on the variability and the time window over which pre- and postsynaptic histories would need to be averaged to achieve the observed precision.…”

A genetic probe for visualizing glutamatergic synapses and vesicles by 3D electron microscopy

“…While we focus here on describing VTA glutamate neuron projections that have some specific properties, some features are nonetheless consistent with prior descriptions of other glutamatergic synapses. Presynaptic boutons of excitatory synapses have been depicted to contain round, clear vesicles of diverse size, a general phenomenon described in several species and brain regions (Harris et al, 2015;Qu et al, 2009;Tao et al, 2018). The smaller ones range between ~30 to 50 nm, while other synapses contain also bigger vesicles (>60nm) consisting of clear vesicles as well as dense core vesicles (Harris and Weinberg, 2012).…”