Zebrafish larvae show characteristic prey capture behavior in response to small moving objects. The neural mechanism used to recognize objects as prey remains largely unknown. We devised a machine learning behavior classification system to quantify hunting kinematics in semi-restrained animals exposed to a range of virtual stimuli. Two-photon calcium imaging revealed a small visual area, AF7, that was activated specifically by the optimal prey stimulus. This pretectal region is innervated by two types of retinal ganglion cells, which also send collaterals to the optic tectum. Laser ablation of AF7 markedly reduced prey capture behavior. We identified neurons with arbors in AF7 and found that they projected to multiple sensory and premotor areas: the optic tectum, the nucleus of the medial longitudinal fasciculus (nMLF) and the hindbrain. These findings indicate that computations in the retina give rise to a visual stream which transforms sensory information into a directed prey capture response.DOI: http://dx.doi.org/10.7554/eLife.04878.001

The advent of multimodal brain atlases promises to accelerate progress in neuroscience by allowing in silico queries of neuron morphology, connectivity, and gene expression. We used multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) technology to generate expression maps across the larval zebrafish brain for a growing set of marker genes. The data were registered to the Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing covisualization of gene expression, single-neuron tracings, and expertly curated anatomical segmentations. Using post hoc HCR labeling of the immediate early gene cfos , we mapped responses to prey stimuli and food ingestion across the brain of freely swimming larvae. This unbiased approach revealed, in addition to previously described visual and motor areas, a cluster of neurons in the secondary gustatory nucleus, which express the marker calb2a, as well as a specific neuropeptide Y receptor, and project to the hypothalamus. This discovery exemplifies the power of this new atlas resource for zebrafish neurobiology.

The advent of multimodal brain atlases promises to accelerate discoveries in neuroscience by offering in silico queries of cell types, connectivity and gene expression in regions of interest. We employed multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) to generate expression maps for an initial set of 200 marker genes across the larval zebrafish brain. The data were registered to the Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing co-visualization of gene expression patterns, single-neuron tracings, transgenic lines and anatomical segmentations. Additionally, brain activity maps of freely swimming larvae were generated at single-cell resolution using HCR labeling of the immediate-early gene cfos and integrated into the atlas. As a proof of concept, we identified a novel class of cerebellar eurydendroid cells that express calb2a, project to the hypothalamus and are activated in animals that have recently ingested food. Thus, a cellular-resolution gene expression atlas will not only help with rapid identification of marker genes for neuronal populations of interest, but also bridge the molecular and circuit levels by anchoring genetic information to functional activity maps and synaptic connectivity.

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