Functional connectomics spanning multiple areas of mouse visual cortex
Understanding the brain requires understanding neurons' functional responses to the circuit architecture shaping them. Here we introduce the MICrONS functional connectomics dataset with dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher visual areas (VISrl, VISal and VISlm) in an awake mouse that is viewing natural and synthetic stimuli. These data are co-registered with an electron microscopy reconstruction containing more than 200,000 cells and 0.5 billion synapses. Proofreading of a subset of neurons yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections that map up to thousands of cell-to-cell connections per neuron. Released as an open-access resource, this dataset includes the tools for data retrieval and analysis<sup>1,2</sup>. Accompanying studies describe its use for comprehensive characterization of cell types<sup>3-6</sup>, a synaptic level connectivity diagram of a cortical column<sup>4</sup>, and uncovering cell-type-specific inhibitory connectivity that can be linked to gene expression data<sup>4,7</sup>. Functionally, we identify new computational principles of how information is integrated across visual space<sup>8</sup>, characterize novel types of neuronal invariances<sup>9</sup> and bring structure and function together to uncover a general principle for connectivity between excitatory neurons within and across areas<sup>10,11</sup>.
Authors
- Ágnes L. Bodor (ORCID: https://orcid.org/0000-0003-2082-9935)
- Ben Silverman
- Victoria A. Rose (ORCID: https://orcid.org/0000-0003-4863-9279)
- Lindsey Kitchell (ORCID: https://orcid.org/0000-0002-5498-5306)
- R. Clay Reid (ORCID: https://orcid.org/0000-0002-8697-6797)
- Rachael Swanstrom (ORCID: https://orcid.org/0009-0002-9703-521X)
- Sergiy Popovych (ORCID: https://orcid.org/0000-0002-6158-9782)
- JoAnn Buchanan (ORCID: https://orcid.org/0000-0002-4212-5560)
- Szi-chieh Yu (ORCID: https://orcid.org/0009-0001-9684-0156)
- Jordan Matelsky (ORCID: https://orcid.org/0000-0002-9470-760X)
- Stelios Papadopoulos (ORCID: https://orcid.org/0000-0001-7991-6377)
- Clare Gamlin (ORCID: https://orcid.org/0000-0002-5975-7003)
- Taliah Muhammad (ORCID: https://orcid.org/0000-0002-3242-5391)
- Ryan Willie
- Cameron Smith (ORCID: https://orcid.org/0000-0002-2079-4667)
- Nuno Maçarico da Costa (ORCID: https://orcid.org/0000-0003-2001-4568)
- Thomas Macrina (ORCID: https://orcid.org/0000-0002-0622-9338)
- Paul G. Fahey (ORCID: https://orcid.org/0000-0001-6844-3551)
- Adrian Wanner (ORCID: https://orcid.org/0000-0002-5864-8577)
- Selden Koolman
- Russel Torres (ORCID: https://orcid.org/0000-0002-2876-4382)
- Sven Dorkenwald (ORCID: https://orcid.org/0000-0003-2352-319X)
- Shanka Subhra Mondal (ORCID: https://orcid.org/0000-0003-1252-0129)
- Runzhe Yang
- Emmanouil Froudarakis (ORCID: https://orcid.org/0000-0002-3249-3845)
- Manuel Castro (ORCID: https://orcid.org/0000-0001-9569-6116)
- Leila Elabbady (ORCID: https://orcid.org/0000-0002-1452-1603)
- Fabian H. Sinz (ORCID: https://orcid.org/0000-0002-1348-9736)
- Emily Joyce (ORCID: https://orcid.org/0000-0001-5794-6321)
- Merlin Moore
- Zheng Huan Tan (ORCID: https://orcid.org/0000-0002-1886-2421)
- Shelby Suckow
- Jay Gager (ORCID: https://orcid.org/0000-0002-8001-2604)
- Erika Neace (ORCID: https://orcid.org/0000-0002-8075-6160)
- Nicholas L. Turner (ORCID: https://orcid.org/0000-0001-5382-3420)
- Caitlyn Bishop
- H. Sebastian Seung (ORCID: https://orcid.org/0000-0002-8591-6733)
- William Silversmith (ORCID: https://orcid.org/0000-0002-5485-5341)
- Elanine Miranda (ORCID: https://orcid.org/0000-0002-1633-9303)
- Chris Xu (ORCID: https://orcid.org/0000-0002-3493-6427)
- Nico Kemnitz (ORCID: https://orcid.org/0000-0002-0260-4532)
- Jingpeng Wu (ORCID: https://orcid.org/0000-0003-1604-8802)
- Edgar Y. Walker (ORCID: https://orcid.org/0000-0003-0057-957X)
- Patricia K. Rivlin (ORCID: https://orcid.org/0000-0002-3435-1955)
- Kyle Willie
- Sam Kinn (ORCID: https://orcid.org/0000-0003-1951-8224)
- Marc Takeno (ORCID: https://orcid.org/0000-0002-8384-7500)
- Daniel J. Bumbarger (ORCID: https://orcid.org/0000-0001-6224-1633)
- Andreas S. Tolias (ORCID: https://orcid.org/0000-0002-4305-6376)
- Shang Mu (ORCID: https://orcid.org/0000-0003-0393-467X)
- James Hebditch
- Xaq Pitkow (ORCID: https://orcid.org/0000-0001-6376-329X)
- Akhilesh Halageri (ORCID: https://orcid.org/0000-0001-7367-4776)
- Brendan Celii (ORCID: https://orcid.org/0009-0008-5489-7438)
- Kai Kuehner
- Daniel Xenes (ORCID: https://orcid.org/0009-0008-4812-0120)
- Bethanny Danskin (ORCID: https://orcid.org/0000-0002-4832-1220)
- Amy Sterling (ORCID: https://orcid.org/0000-0002-4961-3954)
- Oluwaseun Ogedengbe
- Jacob Reimer (ORCID: https://orcid.org/0000-0003-4364-8846)
- William Gray-Roncal (ORCID: https://orcid.org/0000-0002-7362-9665)
- Chi Zhang (ORCID: https://orcid.org/0000-0001-5780-4569)
- Casey M Schneider-Mizell (ORCID: https://orcid.org/0000-0001-9477-3853)
- Brock A. Wester (ORCID: https://orcid.org/0000-0002-1500-2143)
- Rob Young
- Grace Williams
- Tim Fliss
- Eric Mitchell (ORCID: https://orcid.org/0000-0002-7487-1744)
- Gayathri Mahalingam (ORCID: https://orcid.org/0000-0003-3718-5013)
- Forrest Collman (ORCID: https://orcid.org/0000-0002-0280-7022)
- Barak Nehoran (ORCID: https://orcid.org/0000-0001-7371-0829)
- Erick Cobos
- Derrick Brittain (ORCID: https://orcid.org/0000-0003-3890-2862)
- Daniel Kapner
- Saumil S. Patel (ORCID: https://orcid.org/0000-0002-2386-8940)
- Mahaly Baptiste
- Fei Ye (ORCID: https://orcid.org/0000-0001-8617-1051)
- Kai Li (ORCID: https://orcid.org/0000-0002-2095-7024)
- Tianyu Wang (ORCID: https://orcid.org/0000-0002-6087-6376)
- J. Alexander Bae (ORCID: https://orcid.org/0000-0002-4681-6342)
- Christos Papadopoulos (ORCID: https://orcid.org/0009-0008-0669-7968)
- Wenjing Yin (ORCID: https://orcid.org/0000-0003-1932-5561)
- Kisuk Lee (ORCID: https://orcid.org/0000-0001-5707-0155)
- Zhen Jia (ORCID: https://orcid.org/0000-0003-3543-2324)
- Dimitri Yatsenko (ORCID: https://orcid.org/0000-0002-1844-641X)
- William Wong
- Ran Lu
- Sarah Williams
- Victoria Brooks
- Anthony Ramos
- Chris Jordan
- Sarah McReynolds
- Justin Ellis-Joyce
- Maya R. Baptiste
- Guadalupe Jovita Yasmin Perez Vega
- Zachary M. Sauter
Institutions
- Allen Institute for Brain Science (US)
- Baylor College of Medicine (US)
- Neurosciences Institute (US)
- Princeton University (US)
- Cornell University (US)
- Paul Scherrer Institute (CH)
- Johns Hopkins University Applied Physics Laboratory (US)
- Max Planck Institute for Intelligent Systems (DE)
- Allen Institute (US)
- Artificial Intelligence in Medicine (Canada) (CA)
- Max Planck Institute for Biology (DE)
- Massachusetts Institute of Technology (US)
- University of Göttingen (DE)
- Rice University (US)
- Carnegie Mellon University (US)
- Foundation for Research and Technology Hellas (GR)
Publication Details
- Journal
- Nature
- Published
- 2025-04-09
- DOI
- https://doi.org/10.1038/s41586-025-08790-w
- Citations
- 117
- Primary Topic
- Neural dynamics and brain function
- Type
- article
- Field-Weighted Citation Impact
- 161.72