BEACON - Automated Aberration Correction for Scanning Transmission Electron Microscopy using Bayesian Optimization

BEACON - Automated Aberration Correction for Scanning Transmission Electron Microscopy using Bayesian Optimization | 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 Article BEACON - Automated Aberration Correction for Scanning Transmission Electron Microscopy using Bayesian Optimization Alexander James Pattison, Stephanie Ribet, Marcus Noack, Georgios Varnavides, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5291255/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 24 Aug, 2025 Read the published version in npj Computational Materials → Version 1 posted 13 You are reading this latest preprint version Abstract Aberration correction is an important aspect of modern high-resolution scanning transmission electron microscopy. Most methods of aligning aberration correctors require specialized sample regions and are unsuitable for fine-tuning aberrations without interrupting on-going experiments. Here, we present an automated method of correcting first- and second-order aberrations called BEACON which uses Bayesian optimization of the normalized image variance to efficiently determine the optimal corrector settings. We demonstrate its use on gold nanoparticles and a hafnium dioxide thin film showing its versatility in nano- and atomic-scale experiments. BEACON can correct all first- and second-order aberrations simultaneously to achieve an initial alignment and first- and second-order aberrations independently for fine alignment. Ptychographic reconstructions are used to demonstrate an improvement in probe shape and a reduction in the target aberration. Physical sciences/Nanoscience and technology/Techniques and instrumentation Physical sciences/Nanoscience and technology/Techniques and instrumentation/Microscopy/Transmission electron microscopy aberration correction Bayesian optimization scanning transmission electron microscopy automation machine learning ptychography Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 24 Aug, 2025 Read the published version in npj Computational Materials → Version 1 posted Editorial decision: Revision requested 24 Jun, 2025 Reviews received at journal 08 Jun, 2025 Reviews received at journal 02 Jun, 2025 Reviewers agreed at journal 28 May, 2025 Reviewers agreed at journal 21 May, 2025 Reviewers agreed at journal 16 May, 2025 Reviews received at journal 16 May, 2025 Reviewers agreed at journal 26 Apr, 2025 Reviewers agreed at journal 25 Apr, 2025 Reviewers invited by journal 24 Apr, 2025 Editor assigned by journal 02 Nov, 2024 Submission checks completed at journal 28 Oct, 2024 First submitted to journal 18 Oct, 2024 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-5291255","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":373372499,"identity":"38206f18-f839-45f7-8d31-faade53e36bb","order_by":0,"name":"Alexander James Pattison","email":"","orcid":"","institution":"Lawrence Berkeley National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Alexander","middleName":"James","lastName":"Pattison","suffix":""},{"id":373372500,"identity":"a9a76988-4072-4290-80dc-e1f1a358181d","order_by":1,"name":"Stephanie Ribet","email":"","orcid":"","institution":"Lawrence Berkeley National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Stephanie","middleName":"","lastName":"Ribet","suffix":""},{"id":373372501,"identity":"4cd10b0d-d0a9-4f28-946d-aa08ba914ef5","order_by":2,"name":"Marcus Noack","email":"","orcid":"","institution":"Lawrence Berkeley National Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Marcus","middleName":"","lastName":"Noack","suffix":""},{"id":373372502,"identity":"61e8a011-0eb6-4cbe-bad2-c320f5b08983","order_by":3,"name":"Georgios Varnavides","email":"","orcid":"","institution":"University of California, Berkeley","correspondingAuthor":false,"prefix":"","firstName":"Georgios","middleName":"","lastName":"Varnavides","suffix":""},{"id":373372503,"identity":"d73e4cc0-3be4-48c3-be6e-b2a723b9276d","order_by":4,"name":"Kunwoo Park","email":"","orcid":"","institution":"Seoul National University","correspondingAuthor":false,"prefix":"","firstName":"Kunwoo","middleName":"","lastName":"Park","suffix":""},{"id":373372504,"identity":"cb6464f2-dfd5-4a69-8b1c-cf1db11b6f86","order_by":5,"name":"Earl Kirkland","email":"","orcid":"","institution":"Cornell University","correspondingAuthor":false,"prefix":"","firstName":"Earl","middleName":"","lastName":"Kirkland","suffix":""},{"id":373372505,"identity":"ca3652df-a2ca-4107-9d37-3be73a8264a8","order_by":6,"name":"Jungwon Park","email":"","orcid":"","institution":"Seoul National University","correspondingAuthor":false,"prefix":"","firstName":"Jungwon","middleName":"","lastName":"Park","suffix":""},{"id":373372506,"identity":"9c5b136c-bb9e-4b67-acbf-7cc2d72c7c33","order_by":7,"name":"Colin Ophus","email":"","orcid":"","institution":"Stanford University","correspondingAuthor":false,"prefix":"","firstName":"Colin","middleName":"","lastName":"Ophus","suffix":""},{"id":373372508,"identity":"751718fa-1fe6-4487-afa1-e8f26257466d","order_by":8,"name":"Peter Ercius","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAsUlEQVRIiWNgGAWjYLCCBAYGOT4J5gbStBizSTCSogUIEtuI1mLO3vvww8O2uvQ26cYGxi8Vhwlrsew5biyR2HY4t03mYAOzzBkitBjcSGMDuupAbptEYgOzZFsaEVruPwNpqUtnI17LDTaQFuYEkBbGj202xPgljVki4dxhQ5BfDjOcIUKLOfsxxo8/yurk+aWbDz78USFBhMOQOYd5CGtA08L4gxgto2AUjIJRMOIAAKLqNhd7k2xvAAAAAElFTkSuQmCC","orcid":"","institution":"Lawrence Berkeley National Laboratory","correspondingAuthor":true,"prefix":"","firstName":"Peter","middleName":"","lastName":"Ercius","suffix":""}],"badges":[],"createdAt":"2024-10-18 18:38:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5291255/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5291255/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41524-025-01766-4","type":"published","date":"2025-08-24T16:29:07+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":89847232,"identity":"7cf9fc4d-7ccb-46fd-a02f-aa470770fbd3","added_by":"auto","created_at":"2025-08-25 16:42:21","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":26115920,"visible":true,"origin":"","legend":"","description":"","filename":"BEACON.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5291255/v1_covered_e849f85e-b922-412b-a22b-122ff82013e9.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"BEACON - 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