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Nature. 2017 May 18;545(7654):345-349. doi: 10.1038/nature22356. Epub 2017 May 10.

Whole-brain serial-section electron microscopy in larval zebrafish.

Author information

1
Graduate Program in Neuroscience, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA.
2
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.
3
Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA.
4
Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA.
5
Image and Data Analysis Core, Harvard Medical School, Boston, Massachusetts, USA.
6
School of Electrical and Computer Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.
7
Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
8
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
9
Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.
10
Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
11
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
12
Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA.
13
FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.

Abstract

High-resolution serial-section electron microscopy (ssEM) makes it possible to investigate the dense meshwork of axons, dendrites, and synapses that form neuronal circuits. However, the imaging scale required to comprehensively reconstruct these structures is more than ten orders of magnitude smaller than the spatial extents occupied by networks of interconnected neurons, some of which span nearly the entire brain. Difficulties in generating and handling data for large volumes at nanoscale resolution have thus restricted vertebrate studies to fragments of circuits. These efforts were recently transformed by advances in computing, sample handling, and imaging techniques, but high-resolution examination of entire brains remains a challenge. Here, we present ssEM data for the complete brain of a larval zebrafish (Danio rerio) at 5.5 days post-fertilization. Our approach utilizes multiple rounds of targeted imaging at different scales to reduce acquisition time and data management requirements. The resulting dataset can be analysed to reconstruct neuronal processes, permitting us to survey all myelinated axons (the projectome). These reconstructions enable precise investigations of neuronal morphology, which reveal remarkable bilateral symmetry in myelinated reticulospinal and lateral line afferent axons. We further set the stage for whole-brain structure-function comparisons by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy data from the same specimen. All obtained images and reconstructions are provided as an open-access resource.

PMID:
28489821
PMCID:
PMC5594570
DOI:
10.1038/nature22356
[Indexed for MEDLINE]
Free PMC Article

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