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    How brain mapping and connectomics work

    Connectomics maps the connections between neurons by imaging brain tissue with electron microscopes and reconstructing every cell and synapse.[1] Since 2024 the field has finished a whole adult fly brain, a cubic millimetre of mouse visual cortex with about half a billion synapses and, in September 2026, the full male fly central nervous system.[2][3][4]

    Editor reviewedStrict sourcingUpdated Neuroscience and brain-computer interfacesLife sciences

    Why map the brain

    A brain is a network of cells called neurons, joined at contact points called synapses. A connectome is a complete map of that network: which neuron connects to which.[1] Maps like this let scientists trace how a signal from the eye travels through the brain to a muscle, instead of guessing.[2]

    Structure constrains function. Whole-brain connectomes let researchers trace synaptic pathways from sensory inputs to motor outputs and derive region-to-region projection maps.[2] Pairing structure with recorded activity, as MICrONS did, lets them test how connectivity relates to a neuron’s functional responses.[5]

    How a connectome is made

    Scientists slice preserved brain tissue extremely thin, photograph each slice with an electron microscope, and stack the images into a 3D volume.[1] Computers then trace each neuron through the stack, and people check and correct the tracing, a step called proofreading.[6] The data are enormous: one cubic millimetre of mouse brain produced 1.6 petabytes.[3]

    The pipeline is electron-microscopy imaging at synaptic resolution, automated segmentation, synapse detection, and human proofreading.[1][6] The FlyWire resource adds cell-type annotations and machine predictions of neurotransmitter identity.[2] Volumes are petabyte-scale: 1.4 petabytes for a cubic millimetre of human cortex and 1.6 petabytes for MICrONS.[7][3] Google’s connectomics group contributed to the male fly connectome.[8]

    Landmark maps, 2024 to 2026

    MapOrganism and regionScale
    H01 (2024)1 mm³ of human temporal cortex~57,000 cells, ~150 million synapses[7]
    FlyWire (2024)Whole adult female fruit fly brain139,255 neurons, ~50 million synapses[2]
    MICrONS (2025)1 mm³ of mouse visual cortex>200,000 cells, ~0.5 billion synapses[5]
    Male CNS (2026)Whole male fruit fly brain and nerve cordFirst finished full-CNS connectome[4]

    The human sample was removed during surgery to reach an epileptic focus. Its analysis found that glial cells outnumber neurons two to one.[7] FlyWire covers both hemispheres of the fly brain and the optic lobes.[2] MICrONS paired activity recordings from about 75,000 neurons with the wiring of the same tissue.[5] The male fly connectome found 262 sex-specific and 114 sexually dimorphic cell types.[4][9]

    Mapping activity, not just wiring

    Connectomes show structure. Recording technologies show activity. Neuropixels probes can record hundreds of individual neurons at once across several brain regions in moving animals.[10] MICrONS combined both kinds of data in the same piece of tissue.[5] That pairing let researchers test a wiring rule: neurons that respond to similar things are more likely to be connected, across layers and areas.[11] Activity recording has also scaled up. In 2025 the International Brain Laboratory released a map of 621,733 neurons recorded with Neuropixels probes in 139 mice.[12]

    A third kind of map catalogues cell types by their genes. The BRAIN Initiative Cell Census Network’s 2021 atlas of the motor cortex found a cell-type taxonomy shared by mice, marmosets and humans.[13] AI now links these layers: a foundation model trained on mouse visual-cortex activity could predict cell types and connections in the MICrONS wiring data.[14]

    Who funds it

    Large maps are team efforts. MICrONS took more than 150 scientists seven years, with funding from the US intelligence research agency IARPA and the NIH BRAIN Initiative.[15] BRAIN Initiative funding fell from $680 million in 2023 to about $320 million in 2025, then rose to $429 million for 2026.[16][17][18]

    Questions readers ask

    What is a connectome?

    A wiring diagram of a nervous system, built by imaging tissue with electron microscopes and tracing the connections between neurons.[1]

    What is the largest complete brain map?

    The whole-brain fly connectomes. The 2024 female fly brain map has 139,255 neurons, and the male fly central nervous system connectome, including the nerve cord, was published in September 2026.[2][4]

    Has anyone mapped part of a human brain?

    Yes, a small part. A 2024 study reconstructed one cubic millimetre of human temporal cortex, removed during epilepsy surgery, containing about 57,000 cells and 150 million synapses.[7]

    Sources

    Each numbered claim is a statement we checked against the sources listed with it. Status shows how well established it is.

    1. [1]

      Connections between neurons can be mapped by acquiring and analysing electron microscope images of brain tissue. confirmedas of 2024-10-02

    2. [2]

      The FlyWire consortium published in October 2024 a wiring diagram of a whole adult female fruit fly brain with 139,255 neurons and about 50 million chemical synapses, reconstructed from electron microscopy images and covering both hemispheres and the optic lobes. confirmedas of 2024-10-02

    3. [3]

      The MICrONS map covers one cubic millimetre of mouse visual cortex, with 523 million synapses, about four kilometres of axons and 1.6 petabytes of data. confirmedas of 2025-04-09

    4. [4]

      In September 2026 a Janelia-led team published in Cell the first finished connectome of an entire male fruit fly central nervous system, including the brain and nerve cord. confirmedas of 2026-09-03

    5. [5]

      The MICrONS dataset, published in April 2025, pairs calcium imaging of about 75,000 neurons in an awake mouse's visual cortex with an electron microscopy reconstruction of more than 200,000 cells and about half a billion synapses. confirmedas of 2025-04-09

    6. [6]

      Proofreading part of the MICrONS reconstruction produced neurons with complete dendritic trees and axonal projections mapping up to thousands of connections per neuron. confirmedas of 2025-04-09

    7. [7]

      A 2024 study reconstructed a cubic millimetre of human temporal cortex, removed during epilepsy surgery, at nanoscale resolution; it holds about 57,000 cells and 150 million synapses in 1.4 petabytes of data, and analysis showed glia outnumber neurons two to one. confirmedas of 2024-05-10

    8. [8]

      The male fly connectome was produced by Janelia's FlyEM team with the Cambridge Drosophila Connectomics Group and Google's connectomics group. confirmedas of 2026-09-03

    9. [9]

      The male fly connectome team identified 262 sex-specific and 114 sexually dimorphic cell types, making up 4.8 percent of the central brain. confirmedas of 2026-09-03

    10. [10]

      Using two Neuropixels probes, researchers recorded more than 700 well-isolated single neurons simultaneously from five brain structures in an awake mouse. confirmedas of 2017-11-08

    11. [11]

      A 2025 analysis of the MICrONS data found that neurons with similar response properties are preferentially connected within and across cortical layers and areas, including feedback connections. confirmedas of 2025-04-09

    12. [12]

      In 2025 the International Brain Laboratory published a public brain-wide map of 621,733 neurons recorded with 699 Neuropixels probes in 139 mice across 12 laboratories, covering 279 brain areas. confirmedas of 2025-09-03

    13. [13]

      In 2021 the BRAIN Initiative Cell Census Network published, as its first major product, a multimodal cell census and atlas of the mammalian primary motor cortex, including a consensus taxonomy of cell types conserved from mouse to marmoset and human. confirmedas of 2021-10-06

    14. [14]

      A 2025 study trained an AI foundation model on visual-cortex activity from several mice; it predicted responses to new kinds of stimuli, adapted to new mice with little training, and predicted cell types and connectivity in the MICrONS dataset. confirmedas of 2025-04-09

    15. [15]

      More than 150 scientists worked on the MICrONS Project over seven years, with support from IARPA and the NIH BRAIN Initiative; institutions included the Allen Institute, Princeton and Baylor College of Medicine. confirmedas of 2025-04-09

    16. [16]

      BRAIN Initiative funding peaked at $680 million in fiscal 2023 and fell about 40 percent in 2024, largely because of a scheduled drop in 21st Century Cures Act money. confirmedas of 2024-04-18

    17. [17]

      Congress's 2025 budget set aside about $320 million for the BRAIN Initiative, about 20 percent less than in 2024, as Cures Act money fell to $91 million. confirmedas of 2025-04-01

    18. [18]

      For fiscal 2026 the BRAIN Initiative was funded at $429 million, a rise of about one third driven largely by a scheduled increase in 21st Century Cures Act funds to $195 million, under an appropriations act signed on February 3, 2026. confirmedas of 2026-02-03

    Revision history (2)
    1. Page created.
    2. Refresh: added the like-to-like wiring rule, the brain-wide activity map, cell-type atlases and AI models that link activity and wiring.

    Created Oct 10, 2026. Last reviewed by an editor on Oct 10, 2026. Next scheduled review: Jan 10, 2027.

    Cite this page

    "How brain mapping and connectomics work." ContentLora, updated Oct 10, 2026. https://contentlora.com/explain/how-brain-mapping-works

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