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Cited by 124Advanced Electron Microscopy Techniques and ApplicationsCell Image Analysis TechniquesZebrafish Biomedical Research Applications

Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain

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Svara, Fabian, Förster, Dominique, Kubo, Fumi, Januszewski, Michał, dal Maschio, Marco, Schubert, Philipp J., Kornfeld, Jörgen, Wanner, Adrian A. +3 more·2022·Nature Methods
DOI 10.1038/s41592-022-01621-0PMC PMC9636024
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Abstract

Dense reconstruction of synaptic connectivity requires high-resolution electron microscopy images of entire brains and tools to efficiently trace neuronal wires across the volume. To generate such a resource, we sectioned and imaged a larval zebrafish brain by serial block-face electron microscopy at a voxel size of 14 × 14 × 25 nm 3. We segmented the resulting dataset with the flood-filling network algorithm, automated the detection of chemical synapses and validated the results by comparisons to transmission electron microscopic images and light-microscopic reconstructions. Neurons and their connections are stored in the form of a queryable and expandable digital address book. We reconstructed a network of 208 neurons involved in visual motion processing, most of them located in the pretectum, which had been functionally characterized in the same specimen by two-photon calcium imaging. Moreover, we mapped all 407 presynaptic and postsynaptic partners of two superficial interneurons in the tectum. The resource developed here serves as a foundation for synaptic-resolution circuit analyses in the zebrafish nervous system.

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References 62 · Cited by 124

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Authors
Svara, F., Förster, D., Kubo, F., Januszewski, M., dal Maschio, M., Schubert, P. J., Kornfeld, J., Wanner, A. A., Laurell, E., Denk, W., & Baier, H.
Affiliations
  • Max Planck Institute for Neurobiology of Behavior – caesar (DE)
  • University of Cologne (DE)
  • National Institute of Genetics (JP)
  • Google (Switzerland) (CH)
  • Max Planck Institute for Biological Intelligence (DE)
  • Princeton University (US)
Corresponding author
Baier, Herwig
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2022-10-24
Volume
19
Issue
11
Pages
1357-1366
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/s41592-022-01621-0
PMC
PMC9636024
OpenAlex
W4307231400
Cited by
124
References
62
Citations by year
2026: 22 · 2025: 41 · 2024: 31 · 2023: 25 · 2022: 4 · 2020: 1
FWCI
12.58
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Methods (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
  • DORA PSI (Paul Scherrer Institute) (submittedVersion, other-oa)
  • Padua Research Archive (University of Padova) (submittedVersion, cc-by)
Funders
  • Max-Planck-Gesellschaft
  • Deutsche Forschungsgemeinschaft (SFB 870/TP16, SPP2041)
  • European Molecular Biology Organization
  • Boehringer Ingelheim Fonds
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
Keywords
serial block-face electron microscopy, visual motion processing, pretectum
MeSH terms
Animals, Brain, Larva, Microscopy, Electron, Synapses, Zebrafish

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