Atomic Localization Fluorescent Microscopy

Atomic Localization Fluorescent Microscopy | 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 Physical Sciences - Article Atomic Localization Fluorescent Microscopy Dirk Englund, Yuqin Duan, Qiushi Gu, Yong Hu, Kevin Chen, Matthew Trusheim This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5744812/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 21 Oct, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Super-resolution microscopy has revolutionized the imaging of complex physical and biological systems by surpassing the Abbe diffraction limit. Recent advancements, particular in single-molecular localization microscopy (SMLM), have pushed localization below nanometer precision [1–5], by applying prior knowledge of correlated fluorescence emission from single emitters [6]. However, averaging down from 1 nm to 1 Ångström requires a hundred-fold increase in collected photon signal [6–8]; this quadratic resource scaling represents a limitation bottleneck in SMLM due to photo-bleaching, extremely long integration times, and other practical constraints [9]. Here, we introduce a super-resolution method that breaks with the this scaling by applying another prior: the structure of the underlying atomic lattice. Specifically, applying this discrete grid imaging technique (DIGIT) in experiments on color centers in a diamond sample, we observe that the localization uncertainty reduces exponentially soon after localization falls below the host crystal’s atomic lattice constant. We demonstrate DIGIT under wide-field illumination for large-scale localization and spectroscopy of quantum emitters. By quantitatively linking the atomistic model of optical transitions in a sample with wide-field imaging readout, DIGIT presents a new tool for applications ranging from the identification of solid-state quantum memories in crystals to, potentially, the direct observation of optical transitions in the electronic structure of molecules. Physical sciences/Optics and photonics/Optical techniques/Imaging and sensing Physical sciences/Optics and photonics/Optical physics Physical sciences/Nanoscience and technology/Techniques and instrumentation/Imaging techniques Full Text Additional Declarations There is NO Competing Interest. Supplementary Files protocol.pdf Extended Data Figure 4 setupextended.pdf Extended Data Figure 1 thetau.pdf Extended Data Figure 3 digitalphysicaltwin3.pdf Extended Data Figure 2 AtomicSupplementary.pdf Supplementary material for Atomic Localization Fluorescent Microscopy imagesequencemovie.avi Supplementary Video 1 Cite Share Download PDF Status: Published Journal Publication published 21 Oct, 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. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-5744812","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Physical Sciences - Article","associatedPublications":[],"authors":[{"id":400513611,"identity":"f12cd1f0-08ed-4149-a971-789ee91abd88","order_by":0,"name":"Dirk Englund","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAuElEQVRIiWNgGAWjYHACxgMMDMxyDMwgNhuRekBajBmYmUnUktjAQKwWfun2C4d5d1inr23nP8DwoewwYS2Sc84UHOY9k5677TAzA+OMc0RoMbiRk3CYt+0wWAszkEFYiz1US7oZSMtfYrQYSKQfAGlJAGthJEaLxI0choNz29INgQ4zONhzLp2wFv4Z6Q8fvG2zljc7f/Dhgx9l1oS1MDDwGMCZB4hRDwTsD4hUOApGwSgYBSMWAABi9Dw2HhH7mQAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-1043-3489","institution":"Massachusetts Institute of Technology","correspondingAuthor":true,"prefix":"","firstName":"Dirk","middleName":"","lastName":"Englund","suffix":""},{"id":400513612,"identity":"029c520d-07e1-4a72-a8a9-af6a68c7b90c","order_by":1,"name":"Yuqin Duan","email":"","orcid":"","institution":"MIT","correspondingAuthor":false,"prefix":"","firstName":"Yuqin","middleName":"","lastName":"Duan","suffix":""},{"id":400513613,"identity":"c4c2f108-4781-46a0-9ec6-a0fee7708141","order_by":2,"name":"Qiushi Gu","email":"","orcid":"","institution":"MIT","correspondingAuthor":false,"prefix":"","firstName":"Qiushi","middleName":"","lastName":"Gu","suffix":""},{"id":400513614,"identity":"5996671a-9dfd-4e51-a9b4-97d8154bbb0e","order_by":3,"name":"Yong Hu","email":"","orcid":"https://orcid.org/0000-0003-3360-7856","institution":"Massachusetts Institute of Technology","correspondingAuthor":false,"prefix":"","firstName":"Yong","middleName":"","lastName":"Hu","suffix":""},{"id":400513615,"identity":"a26ea6a3-9de6-4c57-adbb-36d798e8652c","order_by":4,"name":"Kevin Chen","email":"","orcid":"","institution":"Massachusetts Institute of Technology","correspondingAuthor":false,"prefix":"","firstName":"Kevin","middleName":"","lastName":"Chen","suffix":""},{"id":400513616,"identity":"e95bcc0f-2d41-42d7-a0e4-234fa86b85b6","order_by":5,"name":"Matthew Trusheim","email":"","orcid":"","institution":"Massachusetts Institute of Technology","correspondingAuthor":false,"prefix":"","firstName":"Matthew","middleName":"","lastName":"Trusheim","suffix":""}],"badges":[],"createdAt":"2025-01-01 06:25:09","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5744812/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5744812/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-025-64083-w","type":"published","date":"2025-10-21T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":94062221,"identity":"c9d7e503-f395-4d24-8653-ab0bd5c01bb8","added_by":"auto","created_at":"2025-10-22 07:07:58","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2427224,"visible":true,"origin":"","legend":"Article File","description":"","filename":"AtomicLocalizationFluorescentMicroscopy.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1_covered_83e8a0d2-2f21-4246-afef-ae78567977a4.pdf"},{"id":86826228,"identity":"040b5a9f-7a49-4dc0-a415-d958f696399a","added_by":"auto","created_at":"2025-07-16 04:31:50","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":38443,"visible":true,"origin":"","legend":"Extended Data Figure 4","description":"","filename":"protocol.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1/ce6cf86ad91aadb1cd2ad730.pdf"},{"id":86826230,"identity":"d45d76b0-0f44-4ec4-9cb1-22635430a661","added_by":"auto","created_at":"2025-07-16 04:31:50","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":956742,"visible":true,"origin":"","legend":"Extended Data Figure 1","description":"","filename":"setupextended.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1/df7eca49fc13a9829d503ee4.pdf"},{"id":86826229,"identity":"06d290ea-7c63-4bcc-a492-13c8cbae61db","added_by":"auto","created_at":"2025-07-16 04:31:50","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":801978,"visible":true,"origin":"","legend":"Extended Data Figure 3","description":"","filename":"thetau.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1/b0e00a3c15634aefb665ede2.pdf"},{"id":86826231,"identity":"eb8ebb20-c624-40b7-8589-2ce50f0be087","added_by":"auto","created_at":"2025-07-16 04:31:50","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":3667276,"visible":true,"origin":"","legend":"Extended Data Figure 2","description":"","filename":"digitalphysicaltwin3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1/b4f7f3d160bc800c92ac37f1.pdf"},{"id":86826232,"identity":"64b211a4-69c9-4694-ac51-db7c1ba276f8","added_by":"auto","created_at":"2025-07-16 04:31:51","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":28252999,"visible":true,"origin":"","legend":"Supplementary material for Atomic Localization Fluorescent Microscopy","description":"","filename":"AtomicSupplementary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1/29f1ea8f546045c1efe9f19a.pdf"},{"id":86826234,"identity":"e1956e98-8aa1-4322-9e06-7afd3da78759","added_by":"auto","created_at":"2025-07-16 04:31:57","extension":"avi","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":326258264,"visible":true,"origin":"","legend":"Supplementary Video 1","description":"","filename":"imagesequencemovie.avi","url":"https://assets-eu.researchsquare.com/files/rs-5744812/v1/383e1123133dd554319a9597.avi"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Atomic Localization Fluorescent Microscopy","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5744812/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5744812/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Super-resolution microscopy has revolutionized the imaging of complex physical and biological systems by surpassing the Abbe diffraction limit. Recent advancements, particular in single-molecular localization microscopy (SMLM), have pushed localization below nanometer precision [1–5], by applying prior knowledge of correlated fluorescence emission from single emitters [6]. However, averaging down from 1 nm to 1 Ångström requires a hundred-fold increase in collected photon signal [6–8]; this quadratic resource scaling represents a limitation bottleneck in SMLM due to photo-bleaching, extremely long integration times, and other practical constraints [9]. Here, we introduce a super-resolution method that breaks with the this scaling by applying another prior: the structure of the underlying atomic lattice. Specifically, applying this discrete grid imaging technique (DIGIT) in experiments on color centers in a diamond sample, we observe that the localization uncertainty reduces exponentially soon after localization falls below the host crystal’s atomic lattice constant. We demonstrate DIGIT under wide-field illumination for large-scale localization and spectroscopy of quantum emitters. By quantitatively linking the atomistic model of optical transitions in a sample with wide-field imaging readout, DIGIT presents a new tool for applications ranging from the identification of solid-state quantum memories in crystals to, potentially, the direct observation of optical transitions in the electronic structure of molecules.","manuscriptTitle":"Atomic Localization Fluorescent Microscopy","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-16 04:31:46","doi":"10.21203/rs.3.rs-5744812/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"e96341b4-d023-4d4f-b300-0284167479df","owner":[],"postedDate":"July 16th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":42688624,"name":"Physical sciences/Optics and photonics/Optical techniques/Imaging and sensing"},{"id":42688625,"name":"Physical sciences/Optics and photonics/Optical physics"},{"id":42688626,"name":"Physical sciences/Nanoscience and technology/Techniques and instrumentation/Imaging techniques"}],"tags":[],"updatedAt":"2025-10-22T07:07:49+00:00","versionOfRecord":{"articleIdentity":"rs-5744812","link":"https://doi.org/10.1038/s41467-025-64083-w","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2025-10-21 04:00:00","publishedOnDateReadable":"October 21st, 2025"},"versionCreatedAt":"2025-07-16 04:31:46","video":"","vorDoi":"10.1038/s41467-025-64083-w","vorDoiUrl":"https://doi.org/10.1038/s41467-025-64083-w","workflowStages":[]},"version":"v1","identity":"rs-5744812","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5744812","identity":"rs-5744812","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}