EM Core

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EM Core - Abstract While the neural circuits that underlie behavior are of interest to all of the investigators on this grant (and a substantial part of the entire neuroscience community), there have been very few technical approaches that actually provide this kind of information across all levels at which circuits function, including the level of synaptic connections. This electron microscopy core is explicitly designed to provide the “wiring diagrams” of neural circuits in an efficient way. Much of our effort over the past 5 years has been to transform serial electron microscopy of large volumes (such as the fish nervous system) from a heroic to a more mundane enterprise. This transformation required innovations in hardware and software to abbreviate all the time-consuming steps in the connectomic pipeline. In particular we: 1) automated ultra-thin sectioning (using a tape-based approach), 2) automated image acquisition (using a custom multibeam serial electron microscope), 3) automated stitching and registration of the image data on high performance computing clusters, 4) automated segmentation of neurons and synapses on a GPU cluster, and 5) semi-automated proofreading and rendering of the neural circuits with custom software. Because of these developments, we can routinely collect tens of thousands of sections losslessly at 30 nm thickness and acquire images of them at lateral resolutions of 4 x 4 nanometers. This voxel size (480 nm3​ ​) provides enough detail for human or machine vision methods to trace out the finest aspects of neural connectivity. Obtaining this information about neural circuits is relevant inasmuch as it provides insight into circuit function. Hence the tremendous benefit of doing electron microscopy on functionally imaged samples - a main goal of this proposal. Acquiring these circuits is also relevant if neuronal connectivity can be associated with cells of particular types, hence the significant benefit of doing analysis of cell types that have been defined in the fish atlas associated with this proposal. Finally, these circuit diagrams provide ground truth for testing and refining computational theories of brain function, another important prong of this proposal. Because of the speed of the EM Core approaches, we have the ability to acquire datasets of many different fish that each have been used in particular experimental or live-cell imaging contexts. The overarching goal being to provide synaptic level structural information for all research questions where such detailed data can enhance our comprehension of the way fish behavior is instantiated in its nervous system.