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    MICrONS Project

    Also known as Machine Intelligence from Cortical Networks, MICrONS dataset

    The MICrONS Project produced a functional wiring diagram of one cubic millimetre of mouse visual cortex, combining activity recordings from about 75,000 neurons with an electron-microscopy reconstruction of more than 200,000 cells.[1][2] Published in Nature in April 2025 and released as open data, it was described by the Allen Institute as the largest wiring diagram and functional map of the brain to date.[3][4]

    Editor reviewedStrict sourcingUpdated Neuroscience and brain-computer interfacesLife sciences
    Key facts

    What it is

    MICrONS combined two kinds of measurement in the same piece of brain. First, researchers used calcium imaging to record the activity of about 75,000 neurons in the primary and higher visual areas of an awake mouse as it viewed natural and synthetic visual stimuli. Then they reconstructed the same tissue with electron microscopy: more than 200,000 cells and about half a billion synapses.[1]

    The name stands for Machine Intelligence from Cortical Networks. The program was coordinated by IARPA, the US intelligence community’s research agency, whose former program manager described it as a moonshot investment.[5] The volume is one cubic millimetre. It contains 523 million synapses and about four kilometres of axons, and the data total 1.6 petabytes.[2]

    How it was made

    The work ran in three stages. Scientists at Baylor College of Medicine and Stanford recorded activity while the mouse watched movies. Allen Institute researchers then cut the same tissue into more than 25,000 slices for electron microscopy, and a Princeton team used AI and machine learning to reconstruct the cells and connections in 3D.[6] The reconstruction relied on automated segmentation followed by human proofreading. Proofread neurons include complete dendritic trees and axons that map up to thousands of connections per neuron.[7] The general method, imaging tissue with electron microscopes and tracing connections, is explained in our brain-mapping explainer.[8]

    More than 150 scientists worked on the project over seven years. Institutions included the Allen Institute, Princeton and Baylor College of Medicine, with funding from IARPA and the NIH BRAIN Initiative.[9]

    What it showed

    The findings appeared as ten studies in Nature-family journals.[6] Accompanying papers used the data to classify cell types, build a synapse-level diagram of a cortical column and describe how inhibitory neurons connect selectively to particular cell types.[10] One analysis found a general “like-to-like” rule: neurons that respond to similar things are more likely to be connected, within and across cortical layers and areas, including feedback connections.[11]

    The dataset also became a test bed for AI. A 2025 study trained a foundation model on visual-cortex activity from several mice. It predicted responses to new kinds of stimuli, adapted to new mice with little extra training, and predicted cell types and connections in the MICrONS data.[12] For the broader use of AI in science, see the AI for science crash course. Because structure and function come from the same cells, researchers can ask how a neuron’s connections relate to what it responds to.[1]

    Open data

    MICrONS was released as an open-access resource, with tools for retrieval and analysis.[3] It sits alongside other large connectomes, such as the 2024 whole fly brain and a 2024 reconstruction of a cubic millimetre of human cortex.[13][14]

    Why it matters for neuroscience

    Most connectomes describe wiring only. MICrONS is unusual because the same neurons were first recorded while working, across primary visual cortex and three higher visual areas, and then reconstructed.[15][1] That lets researchers test ideas about how connectivity shapes what neurons respond to, which is hard to do with recordings from tools like Neuropixels alone.[16][10]

    The scale also shows how far mammalian connectomics still has to go. A whole fly brain contains 139,255 neurons, while MICrONS reconstructed more than 200,000 cells in just one cubic millimetre of mouse cortex.[13][1]

    Questions readers ask

    What did MICrONS map?

    One cubic millimetre of mouse visual cortex, recording the activity of about 75,000 neurons while the mouse viewed visual stimuli, then reconstructing more than 200,000 cells and about half a billion synapses with electron microscopy.[1][2]

    Can anyone use the data?

    Yes. The dataset was released as an open-access resource with tools for retrieving and analysing it.[3]

    Who paid for it?

    The US intelligence research agency IARPA and the NIH BRAIN Initiative.[9]

    Sources

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

    1. [1]

      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

    2. [2]

      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

    3. [3]

      The MICrONS dataset was released as an open-access resource together with tools for data retrieval and analysis. confirmedas of 2025-04-09

    4. [4]

      The Allen Institute described the MICrONS result as the largest wiring diagram and functional map of the brain to date. confirmedas of 2025-04-09

    5. [5]

      MICrONS stands for Machine Intelligence from Cortical Networks and was coordinated by IARPA, whose former program manager called it a moonshot investment. confirmedas of 2025-04-09

    6. [6]

      For MICrONS, Baylor and Stanford scientists recorded activity while a mouse watched movies, Allen Institute researchers cut the same tissue into more than 25,000 slices for electron microscopy, and a Princeton team used AI to reconstruct the cells in 3D; the findings appeared as ten studies in Nature-family journals. confirmedas of 2025-04-09

    7. [7]

      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

    8. [8]

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

    9. [9]

      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

    10. [10]

      Studies accompanying the MICrONS dataset used it to characterize cell types, build a synapse-level connectivity diagram of a cortical column and uncover cell-type-specific inhibitory connectivity. confirmedas of 2025-04-09

    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]

      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

    13. [13]

      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

    14. [14]

      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

    15. [15]

      MICrONS calcium imaging covered primary visual cortex and three higher visual areas in an awake mouse viewing natural and synthetic stimuli. confirmedas of 2025-04-09

    16. [16]

      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

    Revision history (2)
    1. Page created.
    2. Refresh: added what the name means, how the three teams built the dataset, the like-to-like wiring rule and the brain foundation model trained on it.

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

    Cite this page

    "MICrONS Project." ContentLora, updated Oct 10, 2026. https://contentlora.com/wiki/microns-project

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