loading the brain
4,172 traced neurons
4,172 traced neurons, 82,606 inferred connections, every flash is a real cell firing
scanning
scanning. the tectum is empty and both eyes are wide.
The larval zebrafish is the only vertebrate whose entire brain has been recorded cell by cell while the animal was alive and behaving. Ahrens and colleagues did it in 2013 with light sheet microscopy, about 80 percent of the neurons at 0.8 Hz. It was possible because the larva is transparent. That is what this page is: a transparent animal with its brain showing.
The positions of 4,172 neurons, each one traced by hand and registered into a standard brain of 597 by 974 by 359 micrometres, and the anatomical region each cell body falls in. Source: the mapzebrain single neuron atlas, Kunst and colleagues, Neuron 2019.
The connections. The zebrafish connectome is not finished. What exists publicly is the traced atlas plus a whole brain electron microscopy effort still under way. The links drawn here come from arbor contact: when the terminal of one neuron sits within 4 micrometres of the skeleton of another, three times or more, we count it as a connection. That is not a verified synapse and we do not pretend it is.
The sign of each connection, and the model. The data carry no excitatory or inhibitory labels, so we follow the anatomy: cerebellar output is GABAergic and enters as inhibitory, the hindbrain carries many glycinergic interneurons and a fixed deterministic fraction of it is inhibitory, everything else is excitatory. The neurons themselves are leaky integrate and fire. The simulation runs in your browser, so your fish is not firing the same spikes as anyone else's.
Prey capture in the larva is one of the best described vertebrate behaviours there is. Prey enters the visual field, AF7 responds, the optic tectum builds the map, the eyes converge, the body turns, a few approach swims close the distance, and the mouth opens. The escape is the other side: the Mauthner cell fires once and the body snaps into a C, about 5 milliseconds from cell to muscle. Here, buys are prey and sells are the shadow.