A Cellular-Resolution Atlas of the Larval Zebrafish Brain

Neuron. 2019 Jul 3;103(1):21-38.e5. doi: 10.1016/j.neuron.2019.04.034. Epub 2019 May 27.


Understanding brain-wide neuronal dynamics requires a detailed map of the underlying circuit architecture. We built an interactive cellular-resolution atlas of the zebrafish brain at 6 days post-fertilization (dpf) based on the reconstructions of over 2,000 individually GFP-labeled neurons. We clustered our dataset in "morphotypes," establishing a unique database of quantitatively described neuronal morphologies together with their spatial coordinates in vivo. Over 100 transgene expression patterns were imaged separately and co-registered with the single-neuron atlas. By annotating 72 non-overlapping brain regions, we generated from our dataset an inter-areal wiring diagram of the larval brain, which serves as ground truth for synapse-scale, electron microscopic reconstructions. Interrogating our atlas by "virtual tract tracing" has already revealed previously unknown wiring principles in the tectum and the cerebellum. In conclusion, we present here an evolving computational resource and visualization tool, which will be essential to map function to structure in a vertebrate brain. VIDEO ABSTRACT.

Keywords: brain networks; cerebellum; connectomics; digital atlas; neuroanatomy; single-cell tracing; tectum; tissue clearing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlases as Topic*
  • Brain / anatomy & histology*
  • Brain / cytology*
  • Brain / ultrastructure
  • Brain Mapping
  • Cerebellum / anatomy & histology
  • Connectome
  • Gene Expression
  • Green Fluorescent Proteins
  • Larva / anatomy & histology
  • Larva / cytology
  • Neurons / ultrastructure
  • Transgenes
  • Visual Pathways / anatomy & histology
  • Zebrafish / anatomy & histology*


  • Green Fluorescent Proteins