Survey of spiking in the mouse visual system reveals functional hierarchy

Joshua H. Siegle (), Xiaoxuan Jia (), Séverine Durand, Sam Gale, Corbett Bennett, Nile Graddis, Greggory Heller, Tamina K. Ramirez, Hannah Choi, Jennifer A. Luviano, Peter A. Groblewski, Ruweida Ahmed, Anton Arkhipov, Amy Bernard, Yazan N. Billeh, Dillan Brown, Michael A. Buice, Nicolas Cain, Shiella Caldejon, Linzy Casal, Andrew Cho, Maggie Chvilicek, Timothy C. Cox, Kael Dai, Daniel J. Denman, Saskia E. J. Vries, Roald Dietzman, Luke Esposito, Colin Farrell, David Feng, John Galbraith, Marina Garrett, Emily C. Gelfand, Nicole Hancock, Julie A. Harris, Robert Howard, Brian Hu, Ross Hytnen, Ramakrishnan Iyer, Erika Jessett, Katelyn Johnson, India Kato, Justin Kiggins, Sophie Lambert, Jerome Lecoq, Peter Ledochowitsch, Jung Hoon Lee, Arielle Leon, Yang Li, Elizabeth Liang, Fuhui Long, Kyla Mace, Jose Melchior, Daniel Millman, Tyler Mollenkopf, Chelsea Nayan, Lydia Ng, Kiet Ngo, Thuyahn Nguyen, Philip R. Nicovich, Kat North, Gabriel Koch Ocker, Doug Ollerenshaw, Michael Oliver, Marius Pachitariu, Jed Perkins, Melissa Reding, David Reid, Miranda Robertson, Kara Ronellenfitch, Sam Seid, Cliff Slaughterbeck, Michelle Stoecklin, David Sullivan, Ben Sutton, Jackie Swapp, Carol Thompson, Kristen Turner, Wayne Wakeman, Jennifer D. Whitesell, Derric Williams, Ali Williford, Rob Young, Hongkui Zeng, Sarah Naylor, John W. Phillips, R. Clay Reid, Stefan Mihalas, Shawn R. Olsen () and Christof Koch
Additional contact information
Joshua H. Siegle: Allen Institute for Brain Science
Xiaoxuan Jia: Allen Institute for Brain Science
Séverine Durand: Allen Institute for Brain Science
Sam Gale: Allen Institute for Brain Science
Corbett Bennett: Allen Institute for Brain Science
Nile Graddis: Allen Institute for Brain Science
Greggory Heller: Allen Institute for Brain Science
Tamina K. Ramirez: Allen Institute for Brain Science
Hannah Choi: Allen Institute for Brain Science
Jennifer A. Luviano: Allen Institute for Brain Science
Peter A. Groblewski: Allen Institute for Brain Science
Ruweida Ahmed: Allen Institute for Brain Science
Anton Arkhipov: Allen Institute for Brain Science
Amy Bernard: Allen Institute for Brain Science
Yazan N. Billeh: Allen Institute for Brain Science
Dillan Brown: Allen Institute for Brain Science
Michael A. Buice: Allen Institute for Brain Science
Nicolas Cain: Allen Institute for Brain Science
Shiella Caldejon: Allen Institute for Brain Science
Linzy Casal: Allen Institute for Brain Science
Andrew Cho: Allen Institute for Brain Science
Maggie Chvilicek: Allen Institute for Brain Science
Timothy C. Cox: University of Missouri-Kansas City School of Dentistry
Kael Dai: Allen Institute for Brain Science
Daniel J. Denman: Allen Institute for Brain Science
Saskia E. J. Vries: Allen Institute for Brain Science
Roald Dietzman: Allen Institute for Brain Science
Luke Esposito: Allen Institute for Brain Science
Colin Farrell: Allen Institute for Brain Science
David Feng: Allen Institute for Brain Science
John Galbraith: Allen Institute for Brain Science
Marina Garrett: Allen Institute for Brain Science
Emily C. Gelfand: Allen Institute for Brain Science
Nicole Hancock: Allen Institute for Brain Science
Julie A. Harris: Allen Institute for Brain Science
Robert Howard: Allen Institute for Brain Science
Brian Hu: Allen Institute for Brain Science
Ross Hytnen: Allen Institute for Brain Science
Ramakrishnan Iyer: Allen Institute for Brain Science
Erika Jessett: Allen Institute for Brain Science
Katelyn Johnson: Allen Institute for Brain Science
India Kato: Allen Institute for Brain Science
Justin Kiggins: Allen Institute for Brain Science
Sophie Lambert: Allen Institute for Brain Science
Jerome Lecoq: Allen Institute for Brain Science
Peter Ledochowitsch: Allen Institute for Brain Science
Jung Hoon Lee: Allen Institute for Brain Science
Arielle Leon: Allen Institute for Brain Science
Yang Li: Allen Institute for Brain Science
Elizabeth Liang: Allen Institute for Brain Science
Fuhui Long: Allen Institute for Brain Science
Kyla Mace: Allen Institute for Brain Science
Jose Melchior: Allen Institute for Brain Science
Daniel Millman: Allen Institute for Brain Science
Tyler Mollenkopf: Allen Institute for Brain Science
Chelsea Nayan: Allen Institute for Brain Science
Lydia Ng: Allen Institute for Brain Science
Kiet Ngo: Allen Institute for Brain Science
Thuyahn Nguyen: Allen Institute for Brain Science
Philip R. Nicovich: Allen Institute for Brain Science
Kat North: Allen Institute for Brain Science
Gabriel Koch Ocker: Allen Institute for Brain Science
Doug Ollerenshaw: Allen Institute for Brain Science
Michael Oliver: Allen Institute for Brain Science
Marius Pachitariu: Janelia Research Campus
Jed Perkins: Allen Institute for Brain Science
Melissa Reding: Allen Institute for Brain Science
David Reid: Allen Institute for Brain Science
Miranda Robertson: Allen Institute for Brain Science
Kara Ronellenfitch: Allen Institute for Brain Science
Sam Seid: Allen Institute for Brain Science
Cliff Slaughterbeck: Allen Institute for Brain Science
Michelle Stoecklin: Allen Institute for Brain Science
David Sullivan: Allen Institute for Brain Science
Ben Sutton: Allen Institute for Brain Science
Jackie Swapp: Allen Institute for Brain Science
Carol Thompson: Allen Institute for Brain Science
Kristen Turner: Allen Institute for Brain Science
Wayne Wakeman: Allen Institute for Brain Science
Jennifer D. Whitesell: Allen Institute for Brain Science
Derric Williams: Allen Institute for Brain Science
Ali Williford: Allen Institute for Brain Science
Rob Young: Allen Institute for Brain Science
Hongkui Zeng: Allen Institute for Brain Science
Sarah Naylor: Allen Institute for Brain Science
John W. Phillips: Allen Institute for Brain Science
R. Clay Reid: Allen Institute for Brain Science
Stefan Mihalas: Allen Institute for Brain Science
Shawn R. Olsen: Allen Institute for Brain Science
Christof Koch: Allen Institute for Brain Science

Nature, 2021, vol. 592, issue 7852, 86-92

Abstract: Abstract The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically1. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset—part of the Allen Brain Observatory2—that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas3. We find that four classical hierarchical measures—response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale—are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.

Date: 2021
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DOI: 10.1038/s41586-020-03171-x

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