MSI.EAGLE: An Open-Source GUI for Streamlined Mass Spectrometry Imaging Analysis

Boehmler, D. J.; Woolfork, A.; Tan, A. W.; Kain, P.; Sengupta, A.; Patel, O. B.; Akhtar, F.; McClung, G.; Ackerman, D.; Gade, T. P.; Fitzgerald, G. A.; Weljie, A. M.

doi:10.1101/2025.09.03.673811

bioRxiv · 10.1101/2025.09.03.673811

MSI.EAGLE: An Open-Source GUI for Streamlined Mass Spectrometry Imaging Analysis

Boehmler, D. J.·Woolfork, A.·Tan, A. W.·Kain, P.·Sengupta, A.·Patel, O. B.·Akhtar, F.·McClung, G.·Ackerman, D.·Gade, T. P.·Fitzgerald, G. A.·Weljie, A. M.

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Abstract

Mass Spectrometry Imaging (MSI) is an emergent tool for analyzing spatial molecular distributions, yet data complexity often hinders effective analysis. MSI.EAGLE, an open-source R-Shiny application, makes analysis accessible for non-specialists by integrating advanced tools in a user-friendly interface. The workflow leverages tools from the Cardinal MSI package, with enhanced phenotyping, segmentation, statistical analysis and visualization. The application addresses a gap in spatial biology research by empowering a broader scientific community.

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Boehmler, D. J., Woolfork, A., Tan, A. W., Kain, P., Sengupta, A., Patel, O. B., Akhtar, F., McClung, G., Ackerman, D., Gade, T. P., Fitzgerald, G. A., Weljie, A. M.. 2025-09-09. MSI.EAGLE: An Open-Source GUI for Streamlined Mass Spectrometry Imaging Analysis. https://doi.org/10.1101/2025.09.03.673811

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