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bioRxiv · 10.1101/2025.09.16.676515

OfUSA: OpenfUS Analyzer, a versatile open-source framework for the analysis and visualization of functional ultrasound imaging data across animal models

Huang, Y.-A.·Lambert, T.·Verbeyst, D.·Fitzgerald, N. E.·Grillet, M.·Brunner, C.·Montaldo, G.·Vanduffel, W.·URBAN, A.
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Abstract

Functional ultrasound (fUS) imaging is rapidly gaining interest for its unprecedented ability to study large-scale brain dynamics, yet its adoption and broader dissemination have been hindered by the lack of standardized tools and methodologies to analyze and interpret its rich datasets. We present OpenfUS Analyzer (OfUSA), a companion software suite designed to help researchers quickly engage with fUS data and perform the full range of analyses needed to generate publication-ready results and figures without relying on additional software. OfUSA offers a versatile and modular architecture including preprocessing, recording quality assessment, signal dynamics exploration, statistical analysis and visualization. These functions are separated yet easily combined into analytic pipelines through a programming-free graphical interface. The framework can be applied across species and experimental contexts, either by registering data to anatomical atlases, as shown here for the mouse brain, or by analyzing data without atlas constraints, as illustrated in a primate dataset. This flexibility, together with its comprehensive functionality, makes OfUSA a practical solution for standardized and reproducible analysis of fUS data in both preclinical and translational research. Using OfUSA, we demonstrate the capacity to detect stimulus-evoked responses with high sensitivity, identify their spatial localization within brain networks, and quantify both their extent and temporal dynamics. These results highlight the softwares ability to capture robust activation patterns and provide detailed insights into brain function, thereby accelerating the use of fUS as a powerful tool for systems neuroscience. HighlightsWe present OpenfUS Analyzer (OfUSA), a novel software platform for the complete analysis of functional ultrasound (fUS) datasets. OfUSA combines a user-friendly graphical interface with a standardized, flexible workflow and powerful visualization tools, making it an ideal solution for fUS researchers at all experience levels. The softwares utility is first demonstrated through the analysis of rodent fUS data using a standardized atlas, while its versatility is further emphasized by the successful analysis of a primate fUS dataset without a template, thereby illustrating its adaptability to non-standard experimental conditions.

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Huang, Y.-A., Lambert, T., Verbeyst, D., Fitzgerald, N. E., Grillet, M., Brunner, C., Montaldo, G., Vanduffel, W., URBAN, A.. 2025-09-17. OfUSA: OpenfUS Analyzer, a versatile open-source framework for the analysis and visualization of functional ultrasound imaging data across animal models. https://doi.org/10.1101/2025.09.16.676515

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