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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Fig. 1: Integration of transcriptomics, morphology and intrinsic electrophysiological properties via the Patch-seq technology.
Fig. 2: Integrating cell types and local connectivity.
Fig. 3: Distinct functional properties of transgenically defined cell types.
Fig. 4: Integration of connectivity and in vivo function.
Fig. 5: Integration of physiology with brain-wide connectivity.
Fig. 6: Integration of data in models.
Data availability
No primary data were generated for this paper.
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These authors contributed equally: Anton Arkhipov, Nuno da Costa, Saskia de Vries.
Authors and Affiliations
Allen Institute, Seattle, WA, USA
Anton Arkhipov, Nuno da Costa, Saskia de Vries, Trygve Bakken, Corbett Bennett, Jim Berg, Michael Buice, Forrest Collman, Tanya Daigle, Marina Garrett, Nathan Gouwens, Peter A. Groblewski, Julie Harris, Michael Hawrylycz, Rebecca Hodge, Tim Jarsky, Brian Kalmbach, Jerome Lecoq, Brian Lee, Ed Lein, Boaz Levi, Stefan Mihalas, Lydia Ng, Shawn Olsen, Clay Reid, Joshua H. Siegle, Staci Sorensen, Bosiljka Tasic, Carol Thompson, Jonathan T. Ting, Cindy van Velthoven, Shenqin Yao, Zizhen Yao, Christof Koch & Hongkui Zeng
The Kavli Foundation, Los Angeles, CA, USA
Amy Bernard
Cure Alzheimer’s Fund, Wellesley Hills, MA, USA
Julie Harris
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Anton Arkhipov
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All authors contributed to the writing of this Perspective.
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Correspondence to Anton Arkhipov, Nuno da Costa or Saskia de Vries.
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Competing interests
H.Z. is on the scientific advisory board of MapLight Therapeutics, Inc. C.K. holds an executive position and has a financial interest in Intrinsic Powers, a company whose purpose is to develop a device that can be used in the clinic to assess the presence and absence of consciousness in patients. This does not pose any conflict of interest with regard to the work undertaken for this publication. All other authors declare no competing interests.
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Arkhipov, A., da Costa, N., de Vries, S. et al. Integrating multimodal data to understand cortical circuit architecture and function. Nat Neurosci (2025). https://doi.org/10.1038/s41593-025-01904-7
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Received:19 December 2023
Accepted:21 January 2025
Published:24 March 2025
DOI:https://doi.org/10.1038/s41593-025-01904-7
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