ViPRE: an open-source software implementation for end-to-end analysis of mass spectrometry data

H. Elmi; A. Jamzad; M. Sharp; J. R. Rodgers; M. Kaufmann; T. Jamaspishvili; R. Iseman; D. Berman; J. Rudan; G. Fichtinger; P. Mousavi

doi:10.1117/12.2654425

3 April 2023 ViPRE: an open-source software implementation for end-to-end analysis of mass spectrometry data

H. Elmi, A. Jamzad, M. Sharp, J. R. Rodgers, M. Kaufmann, T. Jamaspishvili, R. Iseman, D. Berman, J. Rudan, G. Fichtinger, P. Mousavi

Author Affiliations +

Proceedings Volume 12466, Medical Imaging 2023: Image-Guided Procedures, Robotic Interventions, and Modeling; 1246621 (2023) https://doi.org/10.1117/12.2654425
Event: SPIE Medical Imaging, 2023, San Diego, California, United States

Conference Poster

Abstract

Mass Spectrometry Imaging (MSI) is a powerful tool capable of visualizing molecular patterns to identify disease markers in tissue analysis. However, data analysis is computationally heavy and currently time-consuming as there is no single platform capable of performing the entire preprocessing, visualization, and analysis pipeline end-to-end. Using different software tools and file formats required for such tools also makes the process prone to error. The purpose of this work is to develop a free, open-source software implementation called “Visualization, Preprocessing, and Registration Environment” (ViPRE), capable of end-to-end analysis of MSI data. ViPRE was developed to provide various functionalities required for MSI analysis including data import, data visualization, data registration, Region of Interest (ROI) selection, spectral data alignment and data analysis. The software implementation is offered as an open-source module in 3D Slicer, a medical imaging platform. It is also designed for flexibility and usability throughout the user experience. ViPRE was tested using sample MSI data to evaluate the computational pipeline, with the results showing successful implementation of its functionalities and end-to-end usage. A preliminary usability test was also performed to assess user experience, with findings showing positive results. ViPRE aspires to satisfy the need for a single-stop comprehensive interface for MSI data analysis. The source code and documentation will be made publicly available.

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H. Elmi, A. Jamzad, M. Sharp, J. R. Rodgers, M. Kaufmann, T. Jamaspishvili, R. Iseman, D. Berman, J. Rudan, G. Fichtinger, and P. Mousavi "ViPRE: an open-source software implementation for end-to-end analysis of mass spectrometry data", Proc. SPIE 12466, Medical Imaging 2023: Image-Guided Procedures, Robotic Interventions, and Modeling, 1246621 (3 April 2023); https://doi.org/10.1117/12.2654425

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