connectome/ kə-nek-tohm /A connectome is a wiring diagram of the brain.
n. A connectome is a map of all the neural connections in a brain or nervous system.
Connectomics was named Method of the Year in 2025.Nature Methods recognized electron microscopy-based connectomics for the new questions its wiring diagrams make possible.
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Scale changes the question. MRI maps highways between brain regions. Electron microscopy maps alleyways between individual cells. This guide focuses on the latter.
01 / THE PIPELINE
From tissue to queryable circuit.
Five transformations. Each preserves information—and introduces a new kind of uncertainty.
A preserved brain is stained with heavy metals, cut or milled into ultrathin layers, then scanned with an electron beam. Each image is only a flat field of membranes. Thousands of images make a volume.
4 × 4 × 30 nmtypical Fish1 voxel
02 / HUMAN IN THE LOOP
The machine draws. People decide.
A cell is proofread through repeated branch extension and merger removal: reconnect pieces that belong to one cell, and separate branches that belong to different cells.
FALSE MERGERTwo cells share one segment.Correct it with a split.
FALSE SPLITOne cell occupies separate segments.Correct it with a merge.
PROOFREADING LAB · REPRESENTATIVE 2D + 3D VIEWS0/4 ACTIONS SAVED
FALSE JUNCTION
CANDIDATE CONTINUATION
3 / 3 MAJOR ENDS CHECKED
2D EM · Z 344
BEFOREONE SEGMENT · TWO CELLS
BACKBONE REVIEWED
CLASS · INTRINSICSIDE · LEFTTYPE · REVIEWED
3D SEGMENTATION MESH · BEFORE
TARGET / SIDE A CANDIDATE / SIDE B CUT SEEDS
1Find the false junction2Seed both sides3Preview the cut4Split the body
WHAT THE REVIEWER DOESA foreign branch has been fused to the target cell. Place red and blue seed groups on opposite sides of the false junction, preview the cut, then split the body.WATCH THE REAL WORKFLOW ↗
The EM and public MICrONS mesh render are representative views, not a co-registered case. The interactions reproduce the correction logic shown in FlyWire and NeuTu.
COLLABORATIVE LAYER
One map, many kinds of attention.
Proofreaders correct false merges and false splits, reviewers declare a reconstruction ready under project-specific criteria, and annotators attach evidence-backed labels with provenance. Researchers and citizen scientists share that careful work—and often become experts themselves.
A synapse-resolution reference turns the nervous system from something you observe into something you can address. You no longer sample neurons and hope. You name them.
Every capability below was impractical without a wiring diagram of named cells, and is now routine somewhere in the field. The shift is from describing a circuit to interrogating one: the map is a queryable object, and each answer it returns is a hypothesis you can take back to a live animal and try to break.
TARGET
Record the cell you meant to record
Choose which neuron to patch, image or ablate because its partners are already known. Physiology stops being a lottery over whatever the pipette found.
PREDICT
Simulate, then try to falsify
Run the measured graph forward and ask what it should do. A prediction that survives contact with real activity is evidence; one that fails localises the missing biology.
CLASSIFY
Type a cell by who it talks to
Connectivity separates cell types that no stain distinguishes, and it names the ones nobody has described yet.
TRACE
Walk backwards from behaviour
Start at a muscle and follow the graph upstream to the specific cells that drive it, then test them one at a time.
COMPARE
Ask what is conserved
Two individuals, or two species, and the same circuit in both. Difference becomes measurable rather than anecdotal.
INTERVENE
Design the experiment on the map first
Pick the minimal set of cells whose silencing should change a behaviour, before touching an animal.
What wiring still does not give you. A connectome says where signals may travel, not the rules by which each cell transforms them. Neurotransmitter identity, receptor complement, plasticity and a body that keeps changing all sit outside the graph. The target is not a frozen diagram but a versioned, multimodal model of a living circuit, and every question above gets sharper as those layers arrive.
05 / DATASET OBSERVATORY
The public connectomics field.
A living catalog of major public micro connectomics datasets. Last reviewed August 2026. For a list of macro connectomics datasets, visit this page.
23records shown
40 YEARS OF OPEN MAPS
From one worm to a world of brains.
Released datasets lead into active programs. Scroll sideways to move from the first complete nervous-system connectome to the current global frontier.
PUBLIC DATASET ACTIVE PROGRAMEvery card states its mapping scale.
Scale note. Synapse-resolution connectomes, single-neuron projectomes and multiscale brain atlases answer different questions. The timeline keeps them together to show the field’s trajectory—not to imply that they are technically equivalent.
Scope note. “Complete” means complete to the authors’ declared anatomical and technical scope, not error-free or biologically exhaustive. Connectomes remain versioned scientific objects.
SECTION FEED Z 0712 · one plane at a time
