Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

Nicholas L. Turner; Thomas Macrina; J. Alexander Bae; Runzhe Yang; Alyssa M. Wilson; Casey Schneider-Mizell; Kisuk Lee; Ran Lu; Jingpeng Wu; Agnes L. Bodor; Adam A. Bleckert; Derrick Brittain; Emmanouil Froudarakis; Sven Dorkenwald; Forrest Collman; Nico Kemnitz; Dodam Ih; William M. Silversmith; Jonathan Zung; Aleksandar Zlateski; Ignacio Tartavull; Szi chieh Yu; Sergiy Popovych; Shang Mu; William Wong; Chris S. Jordan; Manuel Castro; Jo Ann Buchanan; Daniel J. Bumbarger; Marc Takeno; Russel Torres; Gayathri Mahalingam; Leila Elabbady; Yang Li; Erick Cobos; Pengcheng Zhou; Shelby Suckow; Lynne Becker; Liam Paninski; Franck Polleux; Jacob Reimer; Andreas S. Tolias; R. Clay Reid; Nuno Maçarico da Costa; H. Sebastian Seung

doi:10.1016/j.cell.2022.01.023

Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

Nicholas L. Turner, Thomas Macrina, J. Alexander Bae, Runzhe Yang, Alyssa M. Wilson, Casey Schneider-Mizell, Kisuk Lee, Ran Lu, Jingpeng Wu, Agnes L. Bodor, Adam A. Bleckert, Derrick Brittain, Emmanouil Froudarakis, Sven Dorkenwald, Forrest Collman, Nico Kemnitz, Dodam Ih, William M. Silversmith, Jonathan Zung, Aleksandar ZlateskiIgnacio Tartavull, Szi chieh Yu, Sergiy Popovych, Shang Mu, William Wong, Chris S. Jordan, Manuel Castro, Jo Ann Buchanan, Daniel J. Bumbarger, Marc Takeno, Russel Torres, Gayathri Mahalingam, Leila Elabbady, Yang Li, Erick Cobos, Pengcheng Zhou, Shelby Suckow, Lynne Becker, Liam Paninski, Franck Polleux, Jacob Reimer, Andreas S. Tolias, R. Clay Reid, Nuno Maçarico da Costa, H. Sebastian Seung

Computer Science

Research output: Contribution to journal › Article › peer-review

39 Scopus citations

Abstract

We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm³ 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.

Original language	English (US)
Pages (from-to)	1082-1100.e24
Journal	Cell
Volume	185
Issue number	6
DOIs	https://doi.org/10.1016/j.cell.2022.01.023
State	Published - Mar 17 2022

All Science Journal Classification (ASJC) codes

Biochemistry, Genetics and Molecular Biology(all)

Keywords

mouse, cortex, 3D reconstruction, electron microscopy, calcium imaging, pyramidal cell, mitochondria, synaptic connectivity, inhibitory cell, visual cortex

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10.1016/j.cell.2022.01.023

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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., ... Seung, H. S. (2022). Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity. Cell, 185(6), 1082-1100.e24. https://doi.org/10.1016/j.cell.2022.01.023

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title = "Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity",

abstract = "We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm3 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.",

keywords = "mouse, cortex, 3D reconstruction, electron microscopy, calcium imaging, pyramidal cell, mitochondria, synaptic connectivity, inhibitory cell, visual cortex",

author = "Turner, {Nicholas L.} and Thomas Macrina and Bae, {J. Alexander} and Runzhe Yang and Wilson, {Alyssa M.} and Casey Schneider-Mizell and Kisuk Lee and Ran Lu and Jingpeng Wu and Bodor, {Agnes L.} and Bleckert, {Adam A.} and Derrick Brittain and Emmanouil Froudarakis and Sven Dorkenwald and Forrest Collman and Nico Kemnitz and Dodam Ih and Silversmith, {William M.} and Jonathan Zung and Aleksandar Zlateski and Ignacio Tartavull and Yu, {Szi chieh} and Sergiy Popovych and Shang Mu and William Wong and Jordan, {Chris S.} and Manuel Castro and Buchanan, {Jo Ann} and Bumbarger, {Daniel J.} and Marc Takeno and Russel Torres and Gayathri Mahalingam and Leila Elabbady and Yang Li and Erick Cobos and Pengcheng Zhou and Shelby Suckow and Lynne Becker and Liam Paninski and Franck Polleux and Jacob Reimer and Tolias, {Andreas S.} and Reid, {R. Clay} and {da Costa}, {Nuno Ma{\c c}arico} and Seung, {H. Sebastian}",

note = "Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",

year = "2022",

month = mar,

day = "17",

doi = "10.1016/j.cell.2022.01.023",

language = "English (US)",

volume = "185",

pages = "1082--1100.e24",

journal = "Cell",

issn = "0092-8674",

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Turner, NL, Macrina, T, Bae, JA, Yang, R, Wilson, AM, Schneider-Mizell, C, Lee, K, Lu, R, Wu, J, Bodor, AL, Bleckert, AA, Brittain, D, Froudarakis, E, Dorkenwald, S, Collman, F, Kemnitz, N, Ih, D, Silversmith, WM, Zung, J, Zlateski, A, Tartavull, I, Yu, SC, Popovych, S, Mu, S, Wong, W, Jordan, CS, Castro, M, Buchanan, JA, Bumbarger, DJ, 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, AS, Reid, RC, da Costa, NM & Seung, HS 2022, 'Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity', Cell, vol. 185, no. 6, pp. 1082-1100.e24. https://doi.org/10.1016/j.cell.2022.01.023

TY - JOUR

T1 - Reconstruction of neocortex

T2 - Organelles, compartments, cells, circuits, and activity

AU - Turner, Nicholas L.

AU - Macrina, Thomas

AU - Bae, J. Alexander

AU - Yang, Runzhe

AU - Wilson, Alyssa M.

AU - Schneider-Mizell, Casey

AU - Lee, Kisuk

AU - Lu, Ran

AU - Wu, Jingpeng

AU - Bodor, Agnes L.

AU - Bleckert, Adam A.

AU - Brittain, Derrick

AU - Froudarakis, Emmanouil

AU - Dorkenwald, Sven

AU - Collman, Forrest

AU - Kemnitz, Nico

AU - Ih, Dodam

AU - Silversmith, William M.

AU - Zung, Jonathan

AU - Zlateski, Aleksandar

AU - Tartavull, Ignacio

AU - Yu, Szi chieh

AU - Popovych, Sergiy

AU - Mu, Shang

AU - Wong, William

AU - Jordan, Chris S.

AU - Castro, Manuel

AU - Buchanan, Jo Ann

AU - Bumbarger, Daniel J.

AU - Takeno, Marc

AU - Torres, Russel

AU - Mahalingam, Gayathri

AU - Elabbady, Leila

AU - Li, Yang

AU - Cobos, Erick

AU - Zhou, Pengcheng

AU - Suckow, Shelby

AU - Becker, Lynne

AU - Paninski, Liam

AU - Polleux, Franck

AU - Reimer, Jacob

AU - Tolias, Andreas S.

AU - Reid, R. Clay

AU - da Costa, Nuno Maçarico

AU - Seung, H. Sebastian

PY - 2022/3/17

Y1 - 2022/3/17

N2 - We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm3 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.

AB - We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm3 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.

KW - mouse, cortex, 3D reconstruction, electron microscopy, calcium imaging, pyramidal cell, mitochondria, synaptic connectivity, inhibitory cell, visual cortex

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UR - http://www.scopus.com/inward/citedby.url?scp=85126290259&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2022.01.023

DO - 10.1016/j.cell.2022.01.023

M3 - Article

C2 - 35216674

AN - SCOPUS:85126290259

SN - 0092-8674

VL - 185

SP - 1082-1100.e24

JO - Cell

JF - Cell

IS - 6

ER -

Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

Abstract

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