OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry | 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 Research Article OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry Dean Tessone, Mohamed Kamal, Valerie Hennes, James Hicks, Peter Kuhn This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9558630/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Imaging Mass Cytometry (IMC) enables spatially resolved single-cell proteomics, but fragmented data analysis tools limit reproducibility. We present OpenIMC, an open-source platform consolidating IMC workflows into a cohesive environment. OpenIMC integrates visualization, preprocessing, segmentation, feature extraction, phenotyping, and spatial analysis. Accessible via graphical and command-line interfaces sharing a backend, the platform ensures consistent execution. Built for scalability and reproducibility, OpenIMC automatically records analytical parameters and enables sharing of complete sessions. Case studies analyzing blood-derived cells and tissue slices validate the software platform by recovering known phenotypes and structural organization. OpenIMC lowers technical barriers, supporting rigorous, scalable single-cell and spatial proteomics. Imaging Mass Cytometry Single-cell proteomics Spatial proteomics Image analysis Multiplexed imaging Open-source software Batch correction Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryFigures.docx Cite Share Download PDF Status: Posted 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-9558630","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":633989661,"identity":"26330c0b-c4ff-441b-a9ab-88df80ed57ca","order_by":0,"name":"Dean Tessone","email":"","orcid":"","institution":"University of Southern California","correspondingAuthor":false,"prefix":"","firstName":"Dean","middleName":"","lastName":"Tessone","suffix":""},{"id":633989662,"identity":"301f6ed7-1464-45a5-bea1-7b8e31ddc782","order_by":1,"name":"Mohamed Kamal","email":"","orcid":"","institution":"University of Southern 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