Connectome · Grey Matter

A connectome is the complete wiring diagram of a nervous system or a piece of one, every neuron and every synapse between them, and it is made by cutting preserved tissue into thousands of thin sections, imaging each with an electron microscope and tracing every cell through the stack.

Connectome. A connectome is the complete wiring diagram of a nervous system or a piece of one, every neuron and every synapse between them, and it is made by cutting preserved tissue into thousands of thin sections, imaging each with an electron microscope and tracing every cell through the stack.

The first was the nematode C. elegans, published in 1986 by John White, Eileen Southgate, Nichol Thomson and Sydney Brenner, its 302 neurons traced by hand through serial micrographs. Machine segmentation changed the scale. FlyWire, published in 2024, maps the whole brain of one adult female fruit fly: 139,255 neurons and about 50 million chemical synapses, from some 7,000 sections imaged at 4 by 4 nm and 40 nm thick, segmented by neural networks and proofread by hand. MICrONS, published in 2025, covers a cubic millimetre of mouse visual cortex with 200,000 cells and 523 million synapses, and adds what most connectomes lack: before the tissue was cut, the responses of 75,000 of its neurons to visual stimuli were recorded with calcium imaging.

It records anatomy, never traffic. It says which cells touch and through how many synapses, and it leaves out how strong each synapse is at a given moment and, unless predicted from the images, whether it excites or inhibits.

Chemical signals that travel outside synapses are invisible in it. neuromodulation can reconfigure the same wiring into different working circuits, which is a large part of why the worm's behaviour still cannot be read from its diagram after four decades.

Electrical synapses are hard to see. The gap junctions that form them are small and less distinct than chemical synapses in micrographs, so they are the least complete part of most maps.

It describes one individual at one instant. The fly map is a single female fly, and the tissue is fixed, so variation between brains and change with learning must come from other animals and other methods.

A wiring diagram says which neurons can talk to which, and leaves open what they say.

It constrains every model of a circuit and settles none alone.

Questions: Can a light-sheet microscope map the wiring of a whole brain? It maps the long-range wiring and stops short of the synapses. A cleared mouse brain can be imaged whole in minutes at a few micrometres, enough to follow labelled neurons and their projections from one region to another. A synapse is tens of nanometres across, so deciding which cell touches which needs electron microscopy at a few nanometres, the method behind the fly connectome. The two are complementary: light-sheet gives the whole organ at cellular scale quickly, electron microscopy gives every contact in a small volume slowly. What did MICrONS add to a wiring diagram? It recorded what the neurons did before mapping how they were wired. While a mouse watched films, calcium imaging followed the responses of about 75,000 neurons in a cubic millimetre of visual cortex; the same cube was then cut and imaged by electron microscopy, and 523 million synapses were traced among its 200,000 cells. Because each reconstructed neuron could be matched to its recorded responses, the map could be asked who connects to whom by function. One answer was a like-to-like rule: excitatory neurons that respond to similar features are more likely to be connected, within and across layers and areas. Why does knowing every connection of the worm not predict what it does? The wiring of C. elegans has been known since 1986, but a diagram lists possible paths and says little about which ones are in use. Neuromodulators such as serotonin, dopamine and neuropeptides change how excitable neurons are and how strongly synapses transmit, often acting on cells they have no synapse with, so the same wiring can run as different functional circuits depending on hunger, stress or what the animal has just sensed. Studies in crustaceans, worms, flies and the retina have shown such switches repeatedly. A connectome fixes the hardware, and the modulators choose the program running on it.