Universität zu Köln

Svara, Fabian, Foerster, Dominique, Kubo, Fumi ORCID: 0000-0003-4028-3490, Januszewski, Michal ORCID: 0000-0002-3480-2744, dal Maschio, Marco, Schubert, Philipp J., Kornfeld, Joergen ORCID: 0000-0002-2547-8700, Wanner, Adrian A., Laurell, Eva, Denk, Winfried and Baier, Herwig ORCID: 0000-0002-7268-0469 (2022). Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain. Nat. Methods, 19 (11). S. 1357 - 1385. BERLIN: NATURE PORTFOLIO. ISSN 1548-7105

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Abstract

This Resource presents a serial block-face EM dataset of the whole larval zebrafish brain, including automated segmentation of neurons, detection of synapses and reconstruction of circuitry for visual motion processing. 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 x 14 x 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Svara, Fabian UNSPECIFIED UNSPECIFIED UNSPECIFIED Foerster, Dominique UNSPECIFIED UNSPECIFIED UNSPECIFIED Kubo, Fumi UNSPECIFIED orcid.org/0000-0003-4028-3490 UNSPECIFIED Januszewski, Michal UNSPECIFIED orcid.org/0000-0002-3480-2744 UNSPECIFIED dal Maschio, Marco UNSPECIFIED UNSPECIFIED UNSPECIFIED Schubert, Philipp J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Kornfeld, Joergen UNSPECIFIED orcid.org/0000-0002-2547-8700 UNSPECIFIED Wanner, Adrian A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Laurell, Eva UNSPECIFIED UNSPECIFIED UNSPECIFIED Denk, Winfried UNSPECIFIED UNSPECIFIED UNSPECIFIED Baier, Herwig UNSPECIFIED orcid.org/0000-0002-7268-0469 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-689817
DOI:	10.1038/s41592-022-01621-0
Journal or Publication Title:	Nat. Methods
Volume:	19
Number:	11
Page Range:	S. 1357 - 1385
Date:	2022
Publisher:	NATURE PORTFOLIO
Place of Publication:	BERLIN
ISSN:	1548-7105
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language WIRING SPECIFICITY; ORGANIZATION; PROJECTOME; ANATOMY; NETWORK; SYSTEM; AREA Multiple languages Biochemical Research Methods Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/68981