title: Automated synaptic connectivity inference for volume electron microscopy.
abstract: Teravoxel volume electron microscopy data sets from neural tissue can now be acquired in weeks, but data analysis requires years of manual labor. We developed the SyConn framework, which uses deep convolutional neural networks and random forest classifiers to infer a richly annotated synaptic connectivity matrix from manual neurite skeleton reconstructions by automatically identifying mitochondria, synapses and their types, axons, dendrites, spines, myelin, somata and cell types. We tested our approach on serial block-face electron microscopy data sets from zebrafish, mouse and zebra finch, and computed the synaptic wiring of songbird basal ganglia. We found that, for example, basal-ganglia cell types with high firing rates in vivo had higher densities of mitochondria and vesicles and that synapse sizes and quantities scaled systematically, depending on the innervated postsynaptic cell types.
authors.affiliation: Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany.|Max Planck Institute for Medical Research, Heidelberg, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Dorkenwald
authors.affiliation: Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany.|Max Planck Institute for Medical Research, Heidelberg, Germany.
authors.forename: Philipp J
authors.initials: PJ
authors.lastname: Schubert
authors.affiliation: Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany.|Max Planck Institute for Medical Research, Heidelberg, Germany.
authors.forename: Marius F
authors.initials: MF
authors.lastname: Killinger
authors.affiliation: Max Planck Institute for Medical Research, Heidelberg, Germany.
authors.forename: Gregor
authors.initials: G
authors.lastname: Urban
authors.affiliation: Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany.
authors.forename: Shawn
authors.initials: S
authors.lastname: Mikula
authors.affiliation: Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Svara
authors.affiliation: Max Planck Institute of Neurobiology, Planegg-Martinsried, Germany.
authors.forename: Joergen
authors.initials: J
authors.lastname: Kornfeld
mesh_terms: D000818:Animals; D001369:Axons / Q000648:ultrastructure; D003712:Dendrites / Q000648:ultrastructure; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D051379:Mice; D008854:Microscopy, Electron / Q000379:methods*; D016571:Neural Networks, Computer; D016501:Neurites / Q000648:ultrastructure; D012984:Software; D013569:Synapses / Q000502:physiology*; D015027:Zebrafish