Pose-Free 3D Quantitative Phase Imaging of Flowing Cellular Populations

Pose-Free 3D Quantitative Phase Imaging of Flowing Cellular Populations | 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 Pose-Free 3D Quantitative Phase Imaging of Flowing Cellular Populations Feng Pan, Enze Ye, Wei Lin, Shaochi Ren, Yakun Liu, Xiaoping Li, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7646051/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 High-throughput 3D quantitative phase imaging (QPI) in flow cytometry enables label-free, volumetric characterization of individual cells by reconstructing their refractive index (RI) distributions from multiple viewing angles during flow through microfluidic channels. However, current imaging methods assume that cells undergo uniform, single-axis rotation, which require their poses to be known at each frame. This assumption restricts applicability to near-spherical cells and prevents accurate imaging of irregularly shaped cells with complex rotations. As a result, only a subset of the cellular population can be analyzed, limiting the ability of flow-based assays to perform robust statistical analysis. We introduce OmniFHT, a pose-free 3D RI reconstruction framework that leverages the Fourier diffraction theorem and implicit neural representations (INRs) for high-throughput flow cytometry tomographic imaging. By jointly optimizing each cell’s unknown rotational trajectory and volumetric structure under weak scattering assumptions, OmniFHT supports arbitrary cell geometries and multi-axis rotations. Its continuous representation also allows accurate reconstruction from sparsely sampled projections and restricted angular coverage, producing high-fidelity results with as few as 10 views or only 120° of angular range. OmniFHT enables, for the first time, in situ, high-throughput tomographic imaging of entire flowing cell populations, providing a scalable and unbiased solution for label-free morphometric analysis in flow cytometry platforms. Physical sciences/Optics and photonics/Optical techniques/Microscopy/Interference microscopy Physical sciences/Optics and photonics/Optical techniques/Imaging and sensing Full Text Additional Declarations There is no conflict of interest Supplementary Files SupplementaryOmniFHT.pdf Supplemental Methods 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-7646051","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":528620284,"identity":"a95df8f6-5737-4798-b6d5-57e725a54f86","order_by":0,"name":"Feng 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