Cellular-resolution atlas of the larval zebrafish brain

3D animation of more than 2000 neurons registered to a standard brain

How many discrete cell types exist in the vertebrate brain and how are they connected? In order to solve this problem, we are classifying neurons in a high-throughput fashion. The larval zebrafish brain is small but displays the basic architecture that is conserved across vertebrates. Neuroanatomical studies have identified all the previously described nuclei and neuropil areas, which divide the larval brain into 128 mutually exclusive, collectively exhaustive (MECE) territories. We are using genetic tricks to stochastically label individual neurons with membrane-targeted fluorophores. Labeled neurons are then imaged by confocal microscopy at high resolution and reconstructed for quantitative morphological analysis. In order to compare neurons between individual fish, we have registered over 4,000 of them to a high-resolution, age-matched standard brain. We also continue to add marker patterns to the standard brain. As of 2021, the set of markers includes hundrets of transgenic lines, genes and antibodies. With support from a local supercomputing center, this atlas has become a web-accessible resource for the entire community.


A Cellular-Resolution Atlas of the Larval Zebrafish Brain
Michael Kunst, Eva Laurell, Nouwar Mokayes, Dominique Förster, Marco Dal Maschio, Herwig Baier
Neuron, May 2019

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