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

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.

Automated summary

This article presents a resource on a serial block-face electron microscopy dataset of the larval zebrafish brain, which includes automated segmentation of neurons, detection of synapses, and reconstruction of visual motion processing circuitry. This resource provides a foundation for synaptic-resolution circuit analyses in the zebrafish nervous system by utilizing high-resolution imaging and efficient tracing tools.