Donders Institute for Brain, Cognition and Behaviour
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Thesis defense Meike Sievers (Donders Series 608)

25 April 2023

Promotor: prof. dr. M.N. Helmstaedter
Copromotor: prof. dr. G.J. Laurent

Large-scale connectomics in mouse barrel cortex

Volume electron microscopy (3D EM) has enabled dense mapping of the brain’s wiring diagram, the so-called connectome, at single-synapse resolution. The technological challenge in acquiring connectomes arises from the spatial scales which need to be bridged (10-6-10-5 to 10-1-100 mm). In mammalian brains, a cubic millimeter is considered the minimal target volume to capture a sufficient large number of sufficiently complete neurons, which is a prerequisite for comprehensive neuron-to-neuron network analyses. However, the effective imaging rate of conventional single-beam scanning EMs (SEMs) is ultimately limited by the scan speed of the electron beam, and previously reported dataset volumes have been restricted to a few hundred micrometer edge length. In this work experimental and computational methods for high-throughput multi-beam SEM (MultiSEM) combined with automated tape collecting ultramicrotomy (ATUM) are implemented and employed to acquire and analyze a millimeter scale connectomics dataset of the mouse barrel cortex encompassing complete cortical columns.