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To meet this challenge, we have created \u201cencoding manifolds\u201d that reveal the overall responses of brain areas to diverse stimuli and organize individual neurons in stimulus-response coordinates according to their selectivity and response dynamics. Here we use encoding manifolds to compare the population-level encoding of primary visual cortex (VISp) with that of five higher visual areas (VISam, VISal, VISpm, VISlm, and VISrl), using data from the Allen Institute Visual Coding\u2013Neuropixels dataset from the mouse. We show that the topology of the encoding manifold for VISp and for higher visual areas is continuous, with smooth coordinates along which stimulus selectivity and response dynamics are organized with layer and cell-type specificity. Surprisingly, the manifolds revealed novel relationships between how natural scenes are encoded relative to static gratings\u2014a relationship conserved across visual areas. Namely, neurons preferring natural scenes preferred either low or high spatial frequency gratings, but not intermediate ones. Analyzing responses by cortical layer reveals a preference for gratings concentrated in layer 6, whereas preferences for natural scenes tended to be higher in layers 2\/3 and 4. The results demonstrate how machine learning approaches can be used to organize and visualize the structure of sensory coding, thereby revealing novel relationships within and across brain areas and sensory stimuli.<\/jats:p>","DOI":"10.1371\/journal.pone.0356243","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T17:35:30Z","timestamp":1789666530000},"page":"e0356243","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Functional organization and natural scene responses across mouse visual cortical areas revealed with encoding manifolds"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1996-2173","authenticated-orcid":true,"given":"Luciano","family":"Dyballa","sequence":"first","affiliation":[{"name":"IE University","place":["Madrid, Spain"],"department":["School of Science and Technology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Greg D.","family":"Field","sequence":"additional","affiliation":[{"name":"University of California","place":["Los Angeles, California, United States of America"],"department":["Jules Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1546-5831","authenticated-orcid":true,"given":"Michael P.","family":"Stryker","sequence":"additional","affiliation":[{"name":"University of California","place":["San Francisco, California, United States of America"],"department":["Department of Physiology"]},{"name":"University of California","place":["San Francisco, California, United States of America"],"department":["Kavli Institute for Fundamental Neuroscience"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2205-6895","authenticated-orcid":true,"given":"Steven W.","family":"Zucker","sequence":"additional","affiliation":[{"name":"Yale University","place":["New Haven, Connecticut, United States of America"],"department":["Department of Computer Science"]},{"name":"Yale University","place":["New Haven, Connecticut, United States of America"],"department":["Department of Biomedical Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,17]]},"reference":[{"issue":"4","key":"pone.0356243.ref001","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2317773121","article-title":"Population encoding of stimulus features along the visual hierarchy","volume":"121","author":"L Dyballa","year":"2024","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0356243.ref002","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.conb.2021.10.010","article-title":"Neural population geometry: An approach for understanding biological and artificial neural networks","volume":"70","author":"S Chung","year":"2021","journal-title":"Curr Opin Neurobiol"},{"issue":"7852","key":"pone.0356243.ref003","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/s41586-020-03171-x","article-title":"Survey of spiking in the mouse visual system reveals functional hierarchy","volume":"592","author":"JH Siegle","year":"2021","journal-title":"Nature"},{"issue":"1","key":"pone.0356243.ref004","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41593-019-0550-9","article-title":"A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex","volume":"23","author":"SEJ de Vries","year":"2020","journal-title":"Nat Neurosci"},{"key":"pone.0356243.ref005","article-title":"Sharing neurophysiology data from the Allen Brain Observatory","volume":"12","author":"SEJ de Vries","year":"2023","journal-title":"Elife"},{"key":"pone.0356243.ref006","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1146\/annurev-neuro-102320-085825","article-title":"How Cortical Circuits Implement Cortical Computations: Mouse Visual Cortex as a Model","volume":"44","author":"CM Niell","year":"2021","journal-title":"Annu Rev Neurosci"},{"key":"pone.0356243.ref007","unstructured":"Allen Institute. 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Blot","year":"2021","journal-title":"Neuron"},{"issue":"6","key":"pone.0356243.ref037","article-title":"Segregated Subnetworks of Intracortical Projection Neurons in Primary Visual Cortex","volume":"100","author":"M-H Kim","year":"2018","journal-title":"Neuron"},{"key":"pone.0356243.ref038","unstructured":"Bertram J, Dyballa L, Keller TA, Kinger S, Zucker SW. Manifolds and Modules: How Function Develops in a Neural Foundation Model. arXiv preprint. 2025; arXiv:2512.07869."},{"issue":"10","key":"pone.0356243.ref039","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1016\/0042-6989(78)90232-8","article-title":"Spatial frequency analysis of the visual environment: anisotropy and the carpentered environment hypothesis","volume":"18","author":"E Switkes","year":"1978","journal-title":"Vision Res"},{"issue":"3","key":"pone.0356243.ref040","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1023\/A:1011139631724","article-title":"Modeling the Shape of the Scene: A Holistic Representation of the Spatial Envelope","volume":"42","author":"A Oliva","year":"2001","journal-title":"International Journal of Computer Vision"},{"issue":"4","key":"pone.0356243.ref041","doi-asserted-by":"crossref","DOI":"10.1167\/10.4.6","article-title":"Animal detection in natural scenes: critical features revisited","volume":"10","author":"FA 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of recurrent processing for figure-ground perception in mice","volume":"7","author":"L Kirchberger","year":"2021","journal-title":"Sci Adv"},{"key":"pone.0356243.ref049","first-page":"2023","article-title":"Visual information is broadcast among cortical areas in discrete channels","volume":"2023","author":"Y Yu","year":"2023","journal-title":"bioRxiv"},{"issue":"13","key":"pone.0356243.ref050","doi-asserted-by":"crossref","first-page":"110606","DOI":"10.1016\/j.celrep.2022.110606","article-title":"Coarse-to-fine processing drives the efficient coding of natural scenes in mouse visual cortex","volume":"38","author":"R Skyberg","year":"2022","journal-title":"Cell Rep"},{"issue":"45","key":"pone.0356243.ref051","doi-asserted-by":"crossref","first-page":"11763","DOI":"10.1523\/JNEUROSCI.3297-06.2006","article-title":"Dynamic spatial processing originates in early visual pathways","volume":"26","author":"EA Allen","year":"2006","journal-title":"J Neurosci"},{"issue":"5","key":"pone.0356243.ref052","doi-asserted-by":"crossref","first-page":"1976","DOI":"10.1523\/JNEUROSCI.22-05-01976.2002","article-title":"Dynamics of spatial frequency tuning in macaque V1","volume":"22","author":"CE Bredfeldt","year":"2002","journal-title":"J Neurosci"},{"issue":"3","key":"pone.0356243.ref053","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1073\/pnas.022638499","article-title":"Spatial frequency and orientation tuning dynamics in area V1","volume":"99","author":"JA Mazer","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"pone.0356243.ref054","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1152\/jn.00022.2012","article-title":"Dynamics of spatial frequency tuning in mouse visual cortex","volume":"107","author":"S Vreysen","year":"2012","journal-title":"J Neurophysiol"},{"issue":"1156","key":"pone.0356243.ref055","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1098\/rspb.1979.0029","article-title":"A computational theory of human stereo vision","volume":"204","author":"D Marr","year":"1979","journal-title":"Proc R Soc Lond B Biol Sci"},{"issue":"4","key":"pone.0356243.ref056","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.pneurobio.2007.09.001","article-title":"Time course of visual perception: coarse-to-fine processing and beyond","volume":"84","author":"J Hegd\u00e9","year":"2008","journal-title":"Prog Neurobiol"},{"key":"pone.0356243.ref057","volume-title":"Allen Brain Observatory \u2013 Neuropixels Visual Coding","author":"Allen Institute","year":"2019"},{"key":"pone.0356243.ref058","doi-asserted-by":"crossref","unstructured":"Martin D, Fowlkes C, Tal D, Malik J. 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