Survey of spiking in the mouse visual system reveals functional hierarchy

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically 1 . 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...

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Published in	Nature (London) Vol. 592; no. 7852; pp. 86 - 92
Main Authors	Siegle, Joshua H., Jia, Xiaoxuan, Durand, Séverine, Gale, Sam, Bennett, Corbett, Graddis, Nile, Heller, Greggory, Ramirez, Tamina K., Choi, Hannah, Luviano, Jennifer A., Groblewski, Peter A., Ahmed, Ruweida, Arkhipov, Anton, Bernard, Amy, Billeh, Yazan N., Brown, Dillan, Buice, Michael A., Cain, Nicolas, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Chvilicek, Maggie, Cox, Timothy C., Dai, Kael, Denman, Daniel J., de Vries, Saskia E. J., Dietzman, Roald, Esposito, Luke, Farrell, Colin, Feng, David, Galbraith, John, Garrett, Marina, Gelfand, Emily C., Hancock, Nicole, Harris, Julie A., Howard, Robert, Hu, Brian, Hytnen, Ross, Iyer, Ramakrishnan, Jessett, Erika, Johnson, Katelyn, Kato, India, Kiggins, Justin, Lambert, Sophie, Lecoq, Jerome, Ledochowitsch, Peter, Lee, Jung Hoon, Leon, Arielle, Li, Yang, Liang, Elizabeth, Long, Fuhui, Mace, Kyla, Melchior, Jose, Millman, Daniel, Mollenkopf, Tyler, Nayan, Chelsea, Ng, Lydia, Ngo, Kiet, Nguyen, Thuyahn, Nicovich, Philip R., North, Kat, Ocker, Gabriel Koch, Ollerenshaw, Doug, Oliver, Michael, Pachitariu, Marius, Perkins, Jed, Reding, Melissa, Reid, David, Robertson, Miranda, Ronellenfitch, Kara, Seid, Sam, Slaughterbeck, Cliff, Stoecklin, Michelle, Sullivan, David, Sutton, Ben, Swapp, Jackie, Thompson, Carol, Turner, Kristen, Wakeman, Wayne, Whitesell, Jennifer D., Williams, Derric, Williford, Ali, Young, Rob, Zeng, Hongkui, Naylor, Sarah, Phillips, John W., Reid, R. Clay, Mihalas, Stefan, Olsen, Shawn R., Koch, Christof
Format	Journal Article
Language	English
Published	London Nature Publishing Group UK 01.04.2021 Nature Publishing Group
Subjects	631/378/2613 631/378/3917 631/378/3920 9/30 Action Potentials - physiology Animals Brain Cerebral cortex Correlation analysis Cross correlation Datasets Datasets as Topic Electrophysiology Frequency dependence Functional morphology Humanities and Social Sciences Latency Locking Male Mice Mice, Inbred C57BL multidisciplinary Neocortex Neural coding Neural networks Observatories Optimization algorithms Photic Stimulation Physiology Pipelines Polls & surveys Quality control Retina Science Science (multidisciplinary) Spiking Thalamus Thalamus - anatomy & histology Thalamus - cytology Thalamus - physiology Visual Cortex - anatomy & histology Visual Cortex - cytology Visual Cortex - physiology Visual signals Visual stimuli Visual system Visual tasks
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ISSN	0028-0836 1476-4687 1476-4687
DOI	10.1038/s41586-020-03171-x

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Summary:	The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically 1 . 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 Observatory 2 —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 Atlas 3 . 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. A large, open dataset containing parallel recordings from six visual cortical and two thalamic areas of the mouse brain is presented, from which the relative timing of activity in response to visual stimuli and behaviour is used to construct a hierarchy scheme that corresponds to anatomical connectivity data.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Author contributions C.K., S.R.O., J.H.S., X.J., S.G., C.B., S.M., D.J.D., S.E.J.d.V., M.A.B. and R.C.R. developed the concepts of the project. C.K., S.R.O., J.H.S., P.A.G., R.C.R., C.F., S.M., H.Z. and S.D. supervised the project. J.H.S., X.J., S.D., G.H., T.K.R., S.G., C.B., S.R.O., J.L., N.G., A.A., A.B., Y.N.B., M.A.B., L.C., N.C., S.C., A.C., T.C.C., S.E.J.d.V., D.J.D., R.D., D.F., E.C.G., R. Howard, B.H., R.I., I.K., J.K., S.L., J.A.L., P.L., J.H.L., A.L., Y.L., F.L., K.M., L.N., T.N., P.R.N., G.K.O., M.O., J.P., M. Reding, D.R., M. Robertson, S.S., C.N., C.S., D.M., T.M., K.T., M.S., D.S., J.S., D.W., A.W., R.A., D.B., M.C., E.L., K.R., K. North, B.S., E.J., K.J., J.M., K. Ngo, M.G., D.O., J.A.H. and J.D.W. undertook investigation and validation, developed the methodology and performed formal analyses. J.H.S., X.J., N.G., K.D., S.G., C.B., S.E.J.d.V., M.P., D.O., J.K., N.C., H.C., D.R., D.W., J.G., M.A.B., P.L. and G.H. developed software. J.H.S., N.G., X.J., K.D., D.F., J.G., R. Hythen, W.W. and R.Y. curated the data. C.T., S.N., L.C., L.E., N.H. and J.W.P. were involved in project administration. J.H.S., X.J., S.G., C.B., S.R.O., H.C., S.D., P.A.G. and D.S. performed data visualization. C.K., S.R.O., J.H.S. and X.J. wrote the original draft of the manuscript, with input and editing from S.M., H.C., C.B. and S.G. All authors reviewed the manuscript.
ISSN:	0028-0836 1476-4687 1476-4687
DOI:	10.1038/s41586-020-03171-x