What is a connectome? The brain's wiring diagram, and every brain mapped so far

Connectome: a complete map of the neurons in a brain and the connections between them.

Connectomics: the science of mapping and studying connectomes.

Neuron: a nerve cell that passes electrical and chemical signals to other cells.

Synapse: a connection between two neurons, where one passes a signal to the next.

Axon: the long fiber a neuron uses to send signals to other cells.

Electron microscopy (EM): imaging with a beam of electrons instead of light, sharp enough to see individual synapses.

Proofreading: checking and correcting a computer's tracing of neurons through brain images, historically the slowest and most expensive part of mapping.

Neuroplasticity: the brain's ability to change its connections over time, which is how we learn and form memories.

Whole brain emulation: running an accurate model of a specific brain on a computer, also called mind uploading.

A connectome is the brain's wiring diagram. It records which neurons exist, where they are, and which other neurons each one connects to. At its most detailed, it shows every single synapse, the tiny junctions where one neuron passes a signal to another. Think of a city map that shows not just every road but every driveway, every door and which doors open onto which streets.

The word is used at different scales. A neural connectome maps individual neurons and their connections, and it has been made only for small animals and small pieces of mammal brain. A macroscale, or functional, connectome maps the main highways between brain regions, using MRI scans of living people, at a resolution of millimeters. A chemical connectome adds which neurons release, and respond to, each of the many chemicals that change how brain circuits behave, and as of 2025 only the C. elegans worm has one (Wikipedia: Connectome).

The terms connectome and connectomics were introduced independently in 2005 by the neuroscientists Olaf Sporns, at Indiana University, and Patric Hagmann, at Lausanne University Hospital in Switzerland. Both modeled the word on genome, inspired by the Human Genome Project's effort to read the whole of human DNA. If the genome is the full set of genetic instructions, the connectome is the full set of neural connections.

The word reached a wide audience through the neuroscientist Sebastian Seung, who gave a 2010 TED talk titled I am my connectome, arguing that who we are is written in our neural connections. He followed it in 2012 with a book, Connectome: How the Brain's Wiring Makes Us Who We Are (Wikipedia: Connectome). Seung later helped lead FlyWire, the project that mapped the complete adult fruit fly brain.

The standard method has four steps. First, the brain or piece of brain is preserved and stained so that cell membranes show up clearly. Second, it is cut into thousands of slices, each far thinner than a human hair, or shaved away layer by layer. Third, each slice is imaged with an electron microscope, sharp enough to see individual synapses. Fourth, computers stitch the images into a three-dimensional volume and trace each neuron from slice to slice, and people check the tracing for mistakes.

That last step, proofreading, has been the bottleneck. A computer that loses track of one neuron for one slice can merge two cells or split one cell in two, and those errors spread through the whole map. For the adult fruit fly, proofreading involved hundreds of scientists and volunteers over several years. AI has made the tracing far more accurate, and new methods aim to cut the checking down further.

Several of those methods replace electron microscopes with light. One approach, pioneered in Jeff Lichtman's lab at Harvard and called Brainbow, labels individual neurons with more than 100 distinct colors so they can be told apart. Another, proposed by Anthony Zador at Cold Spring Harbor Laboratory, tags each neuron with a unique DNA barcode and reads the connections by sequencing. E11 Bio's PRISM method combines protein barcodes, tissue that is physically expanded so ordinary light microscopes can see fine detail, and AI that checks its own work. E11 Bio says PRISM could make mapping up to 100 times cheaper (Asimov Press).

Less time with every project, which is the most important trend in the field. The first connectome, the 302 neurons of the C. elegans worm, took more than a decade of tracing electron microscope images by hand before it was published in 1986. The adult fruit fly, with nearly 140,000 neurons, took the FlyWire consortium several years, with hundreds of scientists and volunteers checking the computer's tracing. The MICrONS cubic millimeter of mouse brain took more than 150 researchers about seven years (Allen Institute).

Read that table from top to bottom and the speed-up is obvious. Each new map is far bigger than the last, often by hundreds of times, and it takes about the same number of years or fewer. The reasons are faster microscopes, cheaper storage and, above all, AI that can trace neurons through thousands of images with fewer and fewer mistakes. If that trend holds, a whole mammal brain is a matter of years, not generations.

The history of connectomics is a story of slow beginnings and a sudden acceleration. It took decades to get from one worm to one insect, and only a few years to go from a small insect brain to pieces of mammal and human brain.

Two of those maps stand out. The adult fruit fly is the largest complete brain ever mapped, and it is the first complex brain whose wiring diagram has been turned into a working model: a computer simulation built from the map predicted which neurons would fire when the fly tasted sugar and how that would drive feeding, and experiments on real flies confirmed it (Nature). The MICrONS mouse map matters because the scientists recorded the activity of the neurons while the mouse watched videos, then mapped the same neurons' wiring, linking what the circuit does to how it is built.

Enormous. A human brain has about 86 billion neurons (PNAS) and on the order of 100 trillion synaptic connections. For comparison, the human genome has about 3 billion base pairs, so a connectome holds tens of thousands of times more connections than a genome holds letters. The single cubic millimeter of human cortex that Harvard and Google mapped, a piece about the size of half a grain of rice taken from a patient during epilepsy surgery, produced 1,400 terabytes of data.

The scientists behind that map estimated that a whole mouse brain would produce about 1,000 times as much data (ScienceDaily), and a human brain is more than a thousand times larger than a mouse brain. That puts a full human connectome, imaged the same way, far beyond any dataset ever stored. But the history of genome sequencing is a useful guide: the first human genome took about 13 years and billions of dollars, and today one can be read in a day for a few hundred dollars. Connectomics is now where genomics was before the big drop in cost.

There is a harder limit too. Today, a neuron-level connectome can only be made from preserved tissue, which means after death for any large animal. Non-invasive imaging can see individual neurons working only in small, nearly transparent animals, such as larval zebrafish. No technology can yet read every synapse in a living human brain.

Most neuroscientists think memories are stored, at least in large part, in the pattern and strength of connections between neurons. When you learn something, some synapses get stronger, some get weaker, and new ones form. This is neuroplasticity, and it means your connectome is not fixed: it changes every day, and it is different from anyone else's, even an identical twin's.

That is the thinking behind Seung's claim that you are your connectome. If it is right, then a sufficiently detailed map of your connections would contain your memories, your skills and your personality, which is exactly why connectomics is the foundation of mind uploading. Our guide to mind uploading in 2026 explains how a map would become a working mind.

The wiring diagram is probably not the whole story. The strength of each synapse, the chemicals that change how circuits behave and the support cells around neurons all matter, which is why scientists also talk about chemical connectomes and recordings of activity. But the fly results are striking: a model built mainly from wiring predicted real behavior. That suggests the connectome holds much more of what makes a brain itself than skeptics expected.

The Human Connectome Project is a large effort, funded by the US National Institutes of Health and led mainly by a consortium of Washington University in St. Louis and the University of Minnesota, to map the connections between regions of the healthy human brain using MRI scans of living volunteers. It works at the macroscale, measuring the main pathways between brain areas in millimeters, not individual neurons.

That makes it very different from the fly and mouse maps. It cannot show a single synapse, but it can be done on living people, in large numbers, and repeated over time. Its data have helped scientists understand how brain networks differ between people and change with age and disease. Doctors have even begun using connectome maps to plan brain surgery and brain stimulation, an approach first called connectomic surgery in 2012.

The next great milestone is a complete neuron-level map of a mouse brain, with about 70 million neurons. It would be the first whole mammal connectome, and mice share much of their brain organization with people. The US government has been building toward it for a decade: the intelligence research agency IARPA launched the MICrONS project in 2016 to map one cubic millimeter of mouse cortex, and the NIH launched a $150 million program, BRAIN CONNECTS, in 2023 to build tools for mapping whole brains.

E11 Bio is aiming to map a whole mouse brain within about five years, for about $100 million, using its cheaper PRISM method (Asimov Press). And Eon Systems, the startup that reported running a whole fly brain model in a simulated body in March 2026, says the mouse brain is its next target (The Decoder). If a whole mouse brain is mapped and run as a working model, the case that a human brain can be copied will be very hard to dismiss.

Connectomes matter for medicine first. Many brain disorders are thought to involve circuits that are wired or working differently, and maps of those circuits help scientists understand conditions from epilepsy to depression and plan treatments. They matter for artificial intelligence, too: the brain is still the only general intelligence we know of, and its wiring is a guide to how intelligence can be built efficiently.

And they matter for the oldest human question of all: what happens to us. In October 2026, Microsoft AI CEO Mustafa Suleyman said that Google co-founder Larry Page once told him he expected to be exploring the galaxies by the end of the century as something beyond human, and Elon Musk replied that Page might be right. Our guides to digital immortality and the von Neumann probe explain the plan. Every version of it depends on connectomics: you cannot copy a mind you cannot map.

Even a perfect map of your brain would be a map, not a memoir. It would not say which memories mattered most to you, why you made the choices you made, or what you would want your grandchildren to know. Those are things only you can say, in your own words, and today the only way to make sure they last is to record them.

That is what a Persona is: an AI likeness of you built from your own memories and your own cloned voice, which your family can talk to and hear after you die. You build your Persona by talking, answering questions and telling stories, by voice or by typing, and your Persona learns from every conversation. Building is free: you get 25 memories with no card and no time limit, and your free build never expires. Paid plans start at US$14.99 a month.

Executor Lock™, our patent-pending technology, passes control of your Persona to the executor you name after you die, and no third party can ever edit, retrain or impersonate your Persona. Idy® has 78 patents pending, with international protection sought under the Patent Cooperation Treaty, covering consent, verified death, the handover to a named executor, the permanent memory snapshot behind Executor Lock™, and keeping a Persona the same person when AI models change.

This page is part of our series on the people and the science behind the race to outlive the body.

• Digital Immortality: Larry Page and the Race to Upload Minds: the story that started it, and how close we are to copying a mind.

• What Is a Von Neumann Probe? Larry Page's Galaxy Plan: the self-copying spacecraft at the center of Page's plan.

• Why Larry Page Called Elon Musk a Speciesist: the argument Musk says led to OpenAI.

• What Larry Page Believes About AI and Living Forever: his record, in his own words and in other people's accounts.

• Mind Uploading in 2026: How Close Are We?: how close science is to copying a human brain.

• The Billionaires Trying to Live Forever: who is spending what on longevity and digital immortality.

• How to Live Forever: Every Way People Are Trying: every approach, from medicine to mind uploading.

• Cryonics in 2026: Cost, How It Works, Who Signed Up: what it costs, how it works and who has signed up.

Definitions and history come from Wikipedia on the connectome. The brain maps come from OpenWorm, Live Science, the NIH, Nature, ScienceDaily and the Allen Institute, and the neuron count from PNAS. E11 Bio comes from Asimov Press and Eon Systems from The Decoder. We checked every source on October 30, 2026.

The scientists, universities, companies and projects named on this page have no connection to Afterlife.ai™, and nothing on this page suggests that any of them uses or endorses our service.