Whole-brain serial-section electron microscopy in larval zebrafish

A complete larval zebrafish brain is examined and its myelinated axons reconstructed using serial-section electron microscopy, revealing remarkable symmetry and providing a valuable resource. Mapping the zebrafish brain Reconstructing neuronal circuits through serial-section electron microscopy (ssEM) requires a sub-nanoscale resolution that is more than 10 orders of magnitude smaller than whole vertebrate brains. This has limited connectomics efforts to elucidate restricted circuits. Florian Engert and colleagues report the ssEM reconstruction of a complete larval zebrafish brain, which reveals remarkable bilateral symmetry in the myelinated axon 'projectome'. The work further illustrates how such datasets can guide co-registering of structural and functional imaging data from a same specimen. High-resolution serial-section electron microscopy (ssEM) makes it possible to investigate the dense meshwork of axons, dendrites, and synapses that form neuronal circuits 1 . 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 2 , 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 1 , 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.