Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution

Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Resource Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution Anan Li, Meng-Ting Zhao, Jiandong Zhou, Tao Jiang, Miao Ren, Chuhao Dou, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5909054/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 19 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract The mammalian brain comprises a vast number of neurons, exhibiting remarkable diversity in both molecular composition and spatial distribution. However, a comprehensive understanding of how these neurons are organized within the brain remains elusive, largely due to the lack of systematic studies providing three-dimensional coverage of molecularly defined neurons across the entire brain. In this study, we utilized transgenic mice and fMOST imaging to map the spatial distribution of glutamatergic, GABAergic, and modulatory neurons at the single-cell level throughout the whole brain. Our approach enabled precise registration of individual cells to a stereotaxic atlas, facilitating the construction of whole-brain cell atlases for commonly used Cre recombinase driver lines. Analysis revealed diverse cellular composition patterns across the brain, aligning with the stereotaxic atlas in some regions while uncovering novel subdivisions in others. Notably, cortical and subcortical nuclei as small as approximately one millimeter in size exhibited intricate three-dimensional organization, suggesting the presence of finer functional zones. Biological sciences/Neuroscience/Genetics of the nervous system Biological sciences/Neuroscience/Cellular neuroscience Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryFigures20250106.pdf Supplementary Figures MovieS1excitatory.mp4 Supplementary Movie 1 MovieS2inhibitory.mp4 Supplementary Movie 2 MovieS3modulatory.mp4 Supplementary Movie 3 Cite Share Download PDF Status: Published Journal Publication published 19 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5909054","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Resource","associatedPublications":[],"authors":[{"id":418760258,"identity":"74832579-c21c-4fd6-93b4-1292570044db","order_by":0,"name":"Anan 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