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Arkhipov A, da Costa N, de Vries S, Bakken T, Bennett C, Bernard A, Berg J, Buice M, Collman F, Daigle T, Garrett M, Gouwens N, Groblewski PA, Harris J, Hawrylycz M, Hodge R, Jarsky T, Kalmbach B, Lecoq J, Lee B, Lein E, Levi B, Mihalas S, Ng L, Olsen S, Reid C, Siegle JH, Sorensen S, Tasic B, Thompson C, Ting JT, van Velthoven C, Yao S, Yao Z, Koch C, Zeng H. Integrating multimodal data to understand cortical circuit architecture and function. Nat Neurosci 2025; 28:717-730. [PMID: 40128391 DOI: 10.1038/s41593-025-01904-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/21/2025] [Indexed: 03/26/2025]
Abstract
In recent years there has been a tremendous growth in new technologies that allow large-scale investigation of different characteristics of the nervous system at an unprecedented level of detail. There is a growing trend to use combinations of these new techniques to determine direct links between different modalities. In this Perspective, we focus on the mouse visual cortex, as this is one of the model systems in which much progress has been made in the integration of multimodal data to advance understanding. We review several approaches that allow integration of data regarding various properties of cortical cell types, connectivity at the level of brain areas, cell types and individual cells, and functional neural activity in vivo. The increasingly crucial contributions of computation and theory in analyzing and systematically modeling data are also highlighted. Together with open sharing of data, tools and models, integrative approaches are essential tools in modern neuroscience for improving our understanding of the brain architecture, mechanisms and function.
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Affiliation(s)
| | | | | | | | | | | | - Jim Berg
- Allen Institute, Seattle, WA, USA
| | | | | | | | | | | | | | - Julie Harris
- Allen Institute, Seattle, WA, USA
- Cure Alzheimer's Fund, Wellesley Hills, MA, USA
| | | | | | | | | | | | | | - Ed Lein
- Allen Institute, Seattle, WA, USA
| | | | | | - Lydia Ng
- Allen Institute, Seattle, WA, USA
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Parker PRL, Martins DM, Leonard ESP, Casey NM, Sharp SL, Abe ETT, Smear MC, Yates JL, Mitchell JF, Niell CM. A dynamic sequence of visual processing initiated by gaze shifts. Nat Neurosci 2023; 26:2192-2202. [PMID: 37996524 PMCID: PMC11270614 DOI: 10.1038/s41593-023-01481-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/04/2023] [Indexed: 11/25/2023]
Abstract
Animals move their head and eyes as they explore the visual scene. Neural correlates of these movements have been found in rodent primary visual cortex (V1), but their sources and computational roles are unclear. We addressed this by combining head and eye movement measurements with neural recordings in freely moving mice. V1 neurons responded primarily to gaze shifts, where head movements are accompanied by saccadic eye movements, rather than to head movements where compensatory eye movements stabilize gaze. A variety of activity patterns followed gaze shifts and together these formed a temporal sequence that was absent in darkness. Gaze-shift responses resembled those evoked by sequentially flashed stimuli, suggesting a large component corresponds to onset of new visual input. Notably, neurons responded in a sequence that matches their spatial frequency bias, consistent with coarse-to-fine processing. Recordings in freely gazing marmosets revealed a similar sequence following saccades, also aligned to spatial frequency preference. Our results demonstrate that active vision in both mice and marmosets consists of a dynamic temporal sequence of neural activity associated with visual sampling.
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Affiliation(s)
- Philip R L Parker
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA
- Behavioral and Systems Neuroscience, Department of Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Dylan M Martins
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA
| | - Emmalyn S P Leonard
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA
| | - Nathan M Casey
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA
| | - Shelby L Sharp
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA
| | - Elliott T T Abe
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA
| | - Matthew C Smear
- Institute of Neuroscience and Department of Psychology, University of Oregon, Eugene, OR, USA
| | - Jacob L Yates
- Department of Biology and Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD, USA
- Herbert Wertheim School of Optometry and Vision Science, University of California, Berkeley, CA, USA
| | - Jude F Mitchell
- Department of Brain and Cognitive Sciences and Center for Visual Sciences, University of Rochester, Rochester, NY, USA.
| | - Cristopher M Niell
- Institute of Neuroscience and Department of Biology, University of Oregon, Eugene, OR, USA.
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