{"paper_id":"9b4d0987-94e2-4a1b-8784-5411dc97fc6f","body_text":"Spike inference from calcium imaging data acquired with GCaMP8 indicators | 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 Analysis Spike inference from calcium imaging data acquired with GCaMP8 indicators Peter Rupprecht, Márton Rózsa, Xusheng Fang, Karel Svoboda, Fritjof Helmchen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6306814/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Neuroscience can only be reproducible when its key methods are quantitative and interpretable. Calcium imaging is such a key method which, however, records neuronal activity only indirectly and is therefore difficult to interpret. These difficulties arise primarily from the kinetics, nonlinearity, and sensitivity of the calcium indicator, but also depend on the methods for calcium signal analysis. Here, we evaluate the ability of the recently developed calcium indicator GCaMP8 to reveal neuronal spiking, and we investigate how existing spike inference methods (CASCADE, OASIS, MLSpike) should be adapted for optimal performance. We demonstrate, both for principal cells and interneurons, that algorithms require fine-tuning to obtain optimal results with GCaMP8 data. Specifically, supervised algorithms adapted for GCaMP8 result in more linear and therefore more accurate recovery of complex spiking events. In addition, analysis of cortical ground truth recordings shows that GCaMP8s and GCaMP8m – but not GCaMP6, GCaMP7f or GCaMP8f – are able to reliably detect isolated action potentials for realistic noise levels. Finally, we demonstrate that, due to their fast rise times, GCaMP8 indicators support shorter closed-loop latencies for real-time detection of neuronal activity. Together, our study provides demonstrations, tools, and guidelines to optimally process and quantitatively interpret calcium signals obtained with GCaMP8. Biological sciences/Physiology/Neurophysiology Biological sciences/Neuroscience Biological sciences/Biological techniques/Sensors and probes/Fluorescent proteins Full Text Additional Declarations There is NO Competing Interest. Cite Share Download PDF Status: Under Review 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-6306814\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":false,\"archivedVersions\":[],\"articleType\":\"Analysis\",\"associatedPublications\":[],\"authors\":[{\"id\":447052743,\"identity\":\"f4df2d89-c10e-49bc-82fd-065b88c4b184\",\"order_by\":0,\"name\":\"Peter 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