C. elegans connectome explorer

This is a worm with a real brain.

Not a cartoon of one. Every one of its 302 neurons exists here, connected by the same 3,502 chemical synapses and 816 electrical gap junctions mapped from the actual animal under an electron microscope. We placed this virtual nervous system inside a body, gave the body a world with food in it, and let it run.

The worm finds food. It slows down when it arrives. It dwells. If the food runs out, it searches. None of this is scripted. The behavior emerges from the wiring diagram, the same way it does in the one-millimeter animal crawling through soil.

What you’re watching

The top panel is the nervous system: 302 neurons positioned along the worm’s anatomy, colored by their membrane potential. Teal dots are excited, rose dots are inhibited. The glow reflects activity averaged across each ganglion (cluster of neurons).

The bottom panel is the world: a 20mm arena with food patches (amber gradients). The worm is the amber line. When an ablation preset is selected, a cyan control worm (intact nervous system) appears in the same arena so you can directly compare behavior.

Replicating the wet lab

In real neuroscience, researchers destroy specific neurons with a laser and observe what the animal can no longer do. Every preset in the dropdown above replicates one of these classic experiments:

• AWC ablation: the worm can no longer smell volatile attractants. It wanders randomly instead of navigating toward food. In 1993, Bargmann showed this by killing the AWC neurons with a laser in the living animal. The virtual worm shows the same deficit.

• CEP ablation: the worm finds food but doesn’t slow down. CEP neurons detect bacteria mechanically and release dopamine. Without them, the “basal slowing response” disappears (Sawin et al. 2000). Compare the amber worm (no CEP) to the cyan control: same arena, different behavior on the food patch.

• AIY ablation: the worm spirals in tight circles, unable to suppress reversals. AIY is a critical interneuron that tells the motor system “keep going, you’re heading the right way.” Without it, the worm turns constantly (Gray et al. 2005).

• AVA ablation: the worm can only move forward. AVA drives backward locomotion. Kill it and the animal loses the ability to reverse, one of the first things Chalfie demonstrated in 1985.

Each of these results was first observed in a living animal under a microscope. The fact that the same behaviors appear here, from nothing but the wiring diagram and a physics simulation, is the point.

Under the hood

The nervous system runs as a 302×302 matrix multiply at every integration step. Each neuron has a continuous membrane potential (not a binary spike, since C. elegans neurons are non-spiking). Signal propagates through signed chemical synapses and ohmic gap junctions. Four neuromodulators (dopamine, serotonin, octopamine, tyramine) reconfigure the network based on context: food presence, hunger, recent history.

The body is a 20-segment chain driven by motor neurons that convert neural activity into a sinusoidal crawling wave at ~0.5 Hz. A behavioral state machine handles the transitions between forward runs, reversals, omega turns, slowing, and dwelling, with transition rates modulated by the sensory-interneuron pathway.

The connectome is from Cook et al. 2019 (Nature), accessed via wormneuroatlas. Synaptic signs come from the literature (Chalasani 2007, Suzuki 2008), atlas predictions, and a neurotransmitter-based heuristic calibrated for C. elegans (where glutamate is often inhibitory via GluCl channels, unlike in vertebrates).

Hover over the neural panel to identify individual neurons by name, type, neurotransmitter, and behavioral role.