SyConn2: Dense synaptic connectivity inference for volume electron microscopy

Schubert, Philipp J.; Dorkenwald, Sven; Januszewski, Michał; Klimesch, Jonathan; Svara, Fabian; Mancu, Andrei; Ahmad, Hashir; Fee, Michale S.; Jain, Viren; Kornfeld, Jörgen

doi:10.1038/s41592-022-01624-x

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SyConn2: Dense synaptic connectivity inference for volume electron microscopy

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Schubert, Philipp J.
Department: Electrons-Photons-Neurons / Denk, MPI of Neurobiology, Max Planck Society;
Research Group: Circuits of Birdsong / Kornfeld, MPI of Neurobiology, Max Planck Society;

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Dorkenwald, Sven
Department: Electrons-Photons-Neurons / Denk, MPI of Neurobiology, Max Planck Society;

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Klimesch, Jonathan
Department: Electrons-Photons-Neurons / Denk, MPI of Neurobiology, Max Planck Society;

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Svara, Fabian
Department of Computational Neuroethology, Max Planck Institute for Neurobiology of Behavior – caesar, Max Planck Society;

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Mancu, Andrei
Research Group: Circuits of Birdsong / Kornfeld, MPI of Neurobiology, Max Planck Society;

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Ahmad, Hashir
Research Group: Circuits of Birdsong / Kornfeld, MPI of Neurobiology, Max Planck Society;

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Kornfeld, Jörgen
Research Group: Circuits of Birdsong / Kornfeld, MPI of Neurobiology, Max Planck Society;

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Citation

Schubert, P. J., Dorkenwald, S., Januszewski, M., Klimesch, J., Svara, F., Mancu, A., et al. (2022). SyConn2: Dense synaptic connectivity inference for volume electron microscopy. Nature Methods, 19, 1367-1370. doi:10.1038/s41592-022-01624-x.

Cite as: https://hdl.handle.net/21.11116/0000-000C-0072-3

Abstract

The ability to acquire ever larger datasets of brain tissue using volume
electron microscopy leads to an increasing demand for the automated
extraction of connectomic information. We introduce SyConn2, an
open-source connectome analysis toolkit, which works with both on-site
high-performance compute environments and rentable cloud computing
clusters. SyConn2 was tested on connectomic datasets with more
than 10 million synapses, provides a web-based visualization interface
and makes these data amenable to complex anatomical and neuronal
connectivity queries.