Espina: A Software Tool for the Study of 3D Synaptic Organization

Automated electron microscopy methods produce a large number of serial sections that can be stacked to reconstruct a three-dimensional (3D) sample of brain tissue. The visualization, navigation, and analysis of these stacks of serial sections require dedicated software. Here we describe Espina, a software tool which helps to perform the segmentation and analysis of subcellular elements in a reconstructed 3D volume of the brain. Espina can navigate the stack in 3D, allowing the visualization of images through the original plane of section and through the other two orthogonal planes. Synaptic junctions can be identified and segmented in 3D. The software provides the spatial position of synapses, as well as their size and other geometrical features. The shape of synapses can also be analyzed, and the postsynaptic targets (dendritic spines or dendritic shafts) can be identified and tagged. Axons and dendrites can be traced, together with their connections, so the linear density of synapses established by individual fibers can be calculated. Finally, the relationship of synapses with other cellular and subcellular elements such as astrocytes, mitochondria, or multivesicular bodies can be analyzed.