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Journal Article

A cellular-resolution atlas of the larval zebrafish brain

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Kunst,  Michael
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Laurell,  Eva
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Mokayes,  Nouwar
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Kramer,  Anna
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Kubo,  Fumi
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Fernandes,  António M.
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Förster,  Dominique
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Dal Maschio,  Marco
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Baier,  Herwig
Department: Genes-Circuits-Behavior / Baier, MPI of Neurobiology, Max Planck Society;

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Citation

Kunst, M., Laurell, E., Mokayes, N., Kramer, A., Kubo, F., Fernandes, A. M., et al. (2019). A cellular-resolution atlas of the larval zebrafish brain. Neuron, 103(1), 21-38.e5. doi:10.1016/j.neuron.2019.04.034.


Cite as: https://hdl.handle.net/21.11116/0000-0005-ACBF-3
Abstract
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.