Study of the Size and Shape of Synapses in the Juvenile Rat Somatosensory Cortex with 3D Electron Microscopy

Abstract Changes in the size of the synaptic junction are thought to have significant functional consequences. We used focused ion beam milling and scanning electron microscopy (FIB/SEM) to obtain stacks of serial sections from the six layers of the rat somatosensory cortex. We have segmented in three-dimensions a large number of synapses (n = 6891) to analyze the size and shape of excitatory (asymmetric) and inhibitory (symmetric) synapses, using dedicated software. This study provided three main findings. Firstly, the mean synaptic sizes were smaller for asymmetric than for symmetric synapses in all cortical layers. In all cases, synaptic junction sizes followed a log-normal distribution. Secondly, most cortical synapses had disc-shaped postsynaptic densities (93%). A few were perforated (4.5%), while a smaller proportion (2.5%) showed a tortuous horseshoe-shaped perimeter. Thirdly, the curvature was larger for symmetric than for asymmetric synapses in all layers. However, there was no correlation between synaptic area and curvature. Significance Statement The size of synapses correlates with functional aspects such as the probability of neurotransmitter release or the number of postsynaptic receptors. The data obtained in the present study is based on the analysis of thousands synaptic junctions, that have been imaged and segmented in 3D with semi automated electron microcopy and image analysis methods, providing a robust set of morphologic data. Since currently-available 3D quantitative data are scarce and mainly based on individual cases, the present results in conjunction with other crucial microanatomical data —such as the number and distribution of different types of synapses and the identification of postsynaptic targets in different cortical layers— will help to better understand the structure of microcircuits and to build realistic cortical models.