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Functional connectomics spanning multiple areas of mouse visual cortex

MICrONS Consortium, View ORCID ProfileJ. Alexander Bae, Mahaly Baptiste, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Brendan Celii, Erick Cobos, Forrest Collman, View ORCID ProfileNuno Maçarico da Costa, View ORCID ProfileSven Dorkenwald, Leila Elabbady, View ORCID ProfilePaul G. Fahey, Tim Fliss, Emmanouil Froudakis, Jay Gager, Clare Gamlin, Akhilesh Halageri, James Hebditch, Zhen Jia, Chris Jordan, Daniel Kapner, View ORCID ProfileNico Kemnitz, Sam Kinn, Selden Koolman, Kai Kuehner, Kisuk Lee, Kai Li, Ran Lu, View ORCID ProfileThomas Macrina, Gayathri Mahalingam, Sarah McReynolds, Elanine Miranda, Eric Mitchell, Shanka Subhra Mondal, Merlin Moore, Shang Mu, Taliah Muhammad, Barak Nehoran, Oluwaseun Ogedengbe, Christos Papadopoulos, View ORCID ProfileStelios Papadopoulos, Saumil Patel, Xaq Pitkow, Sergiy Popovych, Anthony Ramos, R. Clay Reid, Jacob Reimer, View ORCID ProfileCasey M. Schneider-Mizell, View ORCID ProfileH. Sebastian Seung, Ben Silverman, View ORCID ProfileWilliam Silversmith, Amy Sterling, Fabian H. Sinz, View ORCID ProfileCameron L. Smith, Shelby Suckow, Zheng H. Tan, Andreas S. Tolias, Russel Torres, View ORCID ProfileNicholas L. Turner, Edgar Y. Walker, Tianyu Wang, Grace Williams, Sarah Williams, Kyle Willie, Ryan Willie, William Wong, View ORCID ProfileJingpeng Wu, Chris Xu, View ORCID ProfileRunzhe Yang, Dimitri Yatsenko, Fei Ye, Wenjing Yin, Szi-chieh Yu
doi: https://doi.org/10.1101/2021.07.28.454025
1Princeton Neuroscience Institute, Princeton University
4Allen Institute for Brain Sciences
5Department of Neuroscience, Baylor College of Medicine
J. Alexander Bae
1Princeton Neuroscience Institute, Princeton University
3Electrical and Computer Engineering Department, Princeton University
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Mahaly Baptiste
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Agnes L. Bodor
4Allen Institute for Brain Sciences
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Derrick Brittain
4Allen Institute for Brain Sciences
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JoAnn Buchanan
4Allen Institute for Brain Sciences
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Daniel J. Bumbarger
4Allen Institute for Brain Sciences
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Manuel A. Castro
1Princeton Neuroscience Institute, Princeton University
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Brendan Celii
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
7Department of Electrical and Computer Engineering, Rice University
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Erick Cobos
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Forrest Collman
4Allen Institute for Brain Sciences
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  • For correspondence: nunod@alleninstitute.org
Nuno Maçarico da Costa
4Allen Institute for Brain Sciences
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Sven Dorkenwald
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Leila Elabbady
4Allen Institute for Brain Sciences
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Paul G. Fahey
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Tim Fliss
4Allen Institute for Brain Sciences
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Emmanouil Froudakis
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
12Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
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Jay Gager
1Princeton Neuroscience Institute, Princeton University
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Clare Gamlin
4Allen Institute for Brain Sciences
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Akhilesh Halageri
1Princeton Neuroscience Institute, Princeton University
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James Hebditch
1Princeton Neuroscience Institute, Princeton University
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Zhen Jia
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Chris Jordan
1Princeton Neuroscience Institute, Princeton University
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Daniel Kapner
4Allen Institute for Brain Sciences
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Nico Kemnitz
1Princeton Neuroscience Institute, Princeton University
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Sam Kinn
4Allen Institute for Brain Sciences
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Selden Koolman
1Princeton Neuroscience Institute, Princeton University
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Kai Kuehner
1Princeton Neuroscience Institute, Princeton University
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Kisuk Lee
1Princeton Neuroscience Institute, Princeton University
8Brain & Cognitive Sciences Department, Massachusetts Institute of Technology
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Kai Li
2Computer Science Department, Princeton University
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Ran Lu
1Princeton Neuroscience Institute, Princeton University
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Thomas Macrina
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Gayathri Mahalingam
4Allen Institute for Brain Sciences
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Sarah McReynolds
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Elanine Miranda
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Eric Mitchell
1Princeton Neuroscience Institute, Princeton University
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Shanka Subhra Mondal
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Merlin Moore
1Princeton Neuroscience Institute, Princeton University
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Shang Mu
1Princeton Neuroscience Institute, Princeton University
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Taliah Muhammad
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Barak Nehoran
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Oluwaseun Ogedengbe
1Princeton Neuroscience Institute, Princeton University
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Christos Papadopoulos
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Stelios Papadopoulos
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Saumil Patel
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Xaq Pitkow
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
7Department of Electrical and Computer Engineering, Rice University
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Sergiy Popovych
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Anthony Ramos
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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R. Clay Reid
4Allen Institute for Brain Sciences
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  • For correspondence: nunod@alleninstitute.org
Jacob Reimer
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Casey M. Schneider-Mizell
4Allen Institute for Brain Sciences
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H. Sebastian Seung
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Ben Silverman
1Princeton Neuroscience Institute, Princeton University
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William Silversmith
1Princeton Neuroscience Institute, Princeton University
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Amy Sterling
1Princeton Neuroscience Institute, Princeton University
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Fabian H. Sinz
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
9Institute for Bioinformatics and Medical Informatics, University Tübingen
10Institute for Computer Science, University Göttingen
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Cameron L. Smith
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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  • ORCID record for Cameron L. Smith
Shelby Suckow
4Allen Institute for Brain Sciences
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Zheng H. Tan
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Andreas S. Tolias
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
7Department of Electrical and Computer Engineering, Rice University
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Russel Torres
4Allen Institute for Brain Sciences
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Nicholas L. Turner
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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  • ORCID record for Nicholas L. Turner
Edgar Y. Walker
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
9Institute for Bioinformatics and Medical Informatics, University Tübingen
11International Max Planck Research School for Intelligent Systems, University Tübingen
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Tianyu Wang
13School of Applied and Engineering Physics, Cornell University
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Grace Williams
4Allen Institute for Brain Sciences
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Sarah Williams
1Princeton Neuroscience Institute, Princeton University
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Kyle Willie
1Princeton Neuroscience Institute, Princeton University
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Ryan Willie
1Princeton Neuroscience Institute, Princeton University
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William Wong
1Princeton Neuroscience Institute, Princeton University
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Jingpeng Wu
1Princeton Neuroscience Institute, Princeton University
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Chris Xu
13School of Applied and Engineering Physics, Cornell University
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Runzhe Yang
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Dimitri Yatsenko
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Fei Ye
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Wenjing Yin
4Allen Institute for Brain Sciences
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Szi-chieh Yu
1Princeton Neuroscience Institute, Princeton University
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ABSTRACT

The value of an integrated approach for understanding the neocortex by combining functional characterization of single neuron activity with the underlying circuit architecture has been understood since the dawn of modern neuroscience. However, in practice, anatomical connectivity and physiology have been studied mostly separately. Following in the footsteps of previous studies that have combined physiology and anatomy in the same tissue, here we present a unique functional connectomics dataset that contains calcium imaging of an estimated 75,000 neurons from primary visual cortex (VISp) and three higher visual areas (VISrl, VISal and VISlm), that were recorded while a mouse viewed natural movies and parametric stimuli. The functional data were co-registered with electron microscopy (EM) data of the same volume which were automatically segmented, reconstructing more than 200,000 cells (neuronal and non-neuronal) and 524 million synapses. Subsequent proofreading of some neurons in this volume yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections. The largest proofread excitatory axon reached a length of 19 mm and formed 1893 synapses, while the largest inhibitory axon formed 10081 synapses. Here we release this dataset as an open access resource to the scientific community including a set of analysis tools that allows easy data access, both programmatically and through a web user interface.

Competing Interest Statement

TM and HSS disclose financial interests in Zetta AI LLC. JR and AST disclose financial interests in Vathes LLC.

Footnotes

  • https://www.microns-explorer.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Functional connectomics spanning multiple areas of mouse visual cortex
MICrONS Consortium, J. Alexander Bae, Mahaly Baptiste, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Brendan Celii, Erick Cobos, Forrest Collman, Nuno Maçarico da Costa, Sven Dorkenwald, Leila Elabbady, Paul G. Fahey, Tim Fliss, Emmanouil Froudakis, Jay Gager, Clare Gamlin, Akhilesh Halageri, James Hebditch, Zhen Jia, Chris Jordan, Daniel Kapner, Nico Kemnitz, Sam Kinn, Selden Koolman, Kai Kuehner, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Sarah McReynolds, Elanine Miranda, Eric Mitchell, Shanka Subhra Mondal, Merlin Moore, Shang Mu, Taliah Muhammad, Barak Nehoran, Oluwaseun Ogedengbe, Christos Papadopoulos, Stelios Papadopoulos, Saumil Patel, Xaq Pitkow, Sergiy Popovych, Anthony Ramos, R. Clay Reid, Jacob Reimer, Casey M. Schneider-Mizell, H. Sebastian Seung, Ben Silverman, William Silversmith, Amy Sterling, Fabian H. Sinz, Cameron L. Smith, Shelby Suckow, Zheng H. Tan, Andreas S. Tolias, Russel Torres, Nicholas L. Turner, Edgar Y. Walker, Tianyu Wang, Grace Williams, Sarah Williams, Kyle Willie, Ryan Willie, William Wong, Jingpeng Wu, Chris Xu, Runzhe Yang, Dimitri Yatsenko, Fei Ye, Wenjing Yin, Szi-chieh Yu
bioRxiv 2021.07.28.454025; doi: https://doi.org/10.1101/2021.07.28.454025
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Functional connectomics spanning multiple areas of mouse visual cortex
MICrONS Consortium, J. Alexander Bae, Mahaly Baptiste, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Brendan Celii, Erick Cobos, Forrest Collman, Nuno Maçarico da Costa, Sven Dorkenwald, Leila Elabbady, Paul G. Fahey, Tim Fliss, Emmanouil Froudakis, Jay Gager, Clare Gamlin, Akhilesh Halageri, James Hebditch, Zhen Jia, Chris Jordan, Daniel Kapner, Nico Kemnitz, Sam Kinn, Selden Koolman, Kai Kuehner, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Sarah McReynolds, Elanine Miranda, Eric Mitchell, Shanka Subhra Mondal, Merlin Moore, Shang Mu, Taliah Muhammad, Barak Nehoran, Oluwaseun Ogedengbe, Christos Papadopoulos, Stelios Papadopoulos, Saumil Patel, Xaq Pitkow, Sergiy Popovych, Anthony Ramos, R. Clay Reid, Jacob Reimer, Casey M. Schneider-Mizell, H. Sebastian Seung, Ben Silverman, William Silversmith, Amy Sterling, Fabian H. Sinz, Cameron L. Smith, Shelby Suckow, Zheng H. Tan, Andreas S. Tolias, Russel Torres, Nicholas L. Turner, Edgar Y. Walker, Tianyu Wang, Grace Williams, Sarah Williams, Kyle Willie, Ryan Willie, William Wong, Jingpeng Wu, Chris Xu, Runzhe Yang, Dimitri Yatsenko, Fei Ye, Wenjing Yin, Szi-chieh Yu
bioRxiv 2021.07.28.454025; doi: https://doi.org/10.1101/2021.07.28.454025

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