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Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity
Open accessAbstract
We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm 3 of electron microscopic images, including pyramidal and non-pyramidal neurons, astrocytes, microglia, oligodendrocytes and precursors, pericytes, vasculature, nuclei, mitochondria, and synapses. Visual responses of a subset of pyramidal cells are included. The data are publicly available, along with tools for programmatic and three-dimensional interactive access. Brief vignettes illustrate the breadth of potential applications relating structure to function in cortical circuits and neuronal cell biology. Mitochondria and synapse organization are characterized as a function of path length from the soma. Pyramidal connectivity motif frequencies are predicted accurately using a configuration model of random graphs. Pyramidal cells receiving more connections from nearby cells exhibit stronger and more reliable visual responses. Sample code shows data access and analysis.
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“A high clustering coefficient and an over-representation of highly connected motifs suggest that the local structure of the brain displays a high degree of non-randomness, consistent with previous studies in C. elegans7,21 and in the mouse cortex11,24,25.”
From Network statistics of the whole-brain connectome of Drosophila (2024) · cites this paper as [11]
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Metadata
- Authors
- Turner, N. L., Macrina, T., Bae, J. A., Yang, R., Wilson, A. M., Schneider-Mizell, C., Lee, K., Lu, R., Wu, J., Bodor, A. L., Bleckert, A. A., Brittain, D., Froudarakis, E., Dorkenwald, S., Collman, F., Kemnitz, N., Ih, D., Silversmith, W. M., Zung, J., Zlateski, A., Tartavull, I., Yu, S.-C., Popovych, S., Mu, S., Wong, W., Jordan, C. S., Castro, M., Buchanan, J., Bumbarger, D. J., Takeno, M., Torres, R., Mahalingam, G., Elabbady, L., Li, Y., Cobos, E., Zhou, P., Suckow, S., Becker, L., Paninski, L., Polleux, F., Reimer, J., Tolias, A. S., Reid, R. C., da Costa, N. M., & Seung, H. S.
- Affiliations
- Princeton University (US)
- Allen Institute for Brain Science (US)
- Baylor College of Medicine (US)
- Massachusetts Institute of Technology (US)
- Columbia University (US)
- Mortimer B. Zuckerman Mind Brain Behavior Institute (US)
- Corresponding author
- Seung, H. Sebastian
- ORCID
- Turner, Nicholas L.
- Macrina, Thomas
- Bae, J. Alexander
- Yang, Runzhe
- Wilson, Alyssa M.
- Schneider-Mizell, Casey
- Lee, Kisuk
- Lu, Ran
- Wu, Jingpeng
- Bleckert, Adam A.
- Brittain, Derrick
- Froudarakis, Emmanouil
- Dorkenwald, Sven
- Collman, Forrest
- Kemnitz, Nico
- Ih, Dodam
- Silversmith, William M.
- Zung, Jonathan
- Zlateski, Aleksandar
- Tartavull, Ignacio
- Yu, Szi-chieh
- Mu, Shang
- Jordan, Chris S.
- Castro, Manuel
- Buchanan, JoAnn
- Bumbarger, Daniel J.
- Takeno, Marc
- Torres, Russel
- Mahalingam, Gayathri
- Elabbady, Leila
- Li, Yang
- Zhou, Pengcheng
- Becker, Lynne
- Paninski, Liam
- Polleux, Franck
- Reimer, Jacob
- Tolias, Andreas S.
- Reid, R. Clay
- da Costa, Nuno Maçarico
- Seung, H. Sebastian
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2022-03
- Volume
- 185
- Issue
- 6
- Pages
- 1082-1100.e24
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC9337909
- OpenAlex
- W4213455879
- Cited by
- 206
- References
- 188
- Citations by year
- 2026: 37 · 2025: 50 · 2024: 49 · 2023: 44 · 2022: 24
- FWCI
- 18.46
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 381 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (5u01mh114824-05)
- National Institute of Mental Health (U01 MH114824, RF1MH117815, RF1MH123400, T32MH065214)
- National Eye Institute (R01EY027036)
- National Institute of Neurological Disorders and Stroke (R01NS104926, U19NS104648, R01NS107483)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
- Keywords
- neocortex, cortical reconstruction, pyramidal neurons, non-pyramidal neurons, astrocytes, microglia, oligodendrocytes, pericytes, cortical vasculature, mitochondria, synaptic organization, visual responses, cortical circuits, electron microscopy
- MeSH terms
- Animals, Microscopy, Electron, Synapses, Organelles, Pyramidal Cells, Neocortex, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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