Pre-CAT: A web-based, graphical user-interface toolbox for preclinical CEST-MRI data processing and analysis
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| Autores principales: | , , , , , , , , |
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| Formato: | Preprint |
| Publicado: |
2026
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| author | Weigand-Whittier, Jonah Rubin, Samuel Ayala, Cindy Velasquez, Mark Vladimirov, Nikita Avraham, Hadas Perlman, Or Abraham, M. Roselle Vandsburger, Moriel H. |
| author_facet | Weigand-Whittier, Jonah Rubin, Samuel Ayala, Cindy Velasquez, Mark Vladimirov, Nikita Avraham, Hadas Perlman, Or Abraham, M. Roselle Vandsburger, Moriel H. |
| contents | Purpose: As interest in CEST-MRI grows, particularly in the preclinical setting, the necessity for standardized and easy-to-use acquisition and data analysis pipelines has become apparent. While vendors have increasingly introduced support for CEST acquisitions on both clinical and preclinical hardware, image post-processing and analysis pipelines remain siloed based on privately developed code. We aim to develop an easy-to-use, open-source graphical user interface toolbox for preclinical CEST-MRI data analysis (Preclinical CEST-MRI Analysis Tool; Pre-CAT), supporting multiple acquisition types, organ systems, and CEST contrast mechanisms. Methods: Pre-CAT was developed in Python and utilizes the Numpy, Scipy, and Matplotlib libraries for data analysis and plotting. Inbuilt data processing steps include image loading, reconstruction, post-processing, and segmentation. Pre-CAT also supports data analysis for QUESP, CEST-MRF, and field mapping experiments using consensus protocols and methods. Pre-CAT's web interface and GUI were developed using Streamlit, an open-source Python framework. Pre-CAT is hosted and accessible online and can be downloaded for local installation to complete the data analysis pipeline in roughly one minute using modern hardware. Results: Pre-CAT analysis pipelines for Z-spectroscopy, CEST-MRF, and quantitative CEST (QUESP/QUEST) are demonstrated. Conclusion: With the introduction of Pre-CAT, we aim to standardize the preclinical CEST-MRI data analysis pipeline, fostering collaboration across research sites and reducing methodological redundancy. Pre-CAT is open-source and relatively modular, encouraging the addition of new methods and protocols. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2605_00511 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Pre-CAT: A web-based, graphical user-interface toolbox for preclinical CEST-MRI data processing and analysis Weigand-Whittier, Jonah Rubin, Samuel Ayala, Cindy Velasquez, Mark Vladimirov, Nikita Avraham, Hadas Perlman, Or Abraham, M. Roselle Vandsburger, Moriel H. Medical Physics Purpose: As interest in CEST-MRI grows, particularly in the preclinical setting, the necessity for standardized and easy-to-use acquisition and data analysis pipelines has become apparent. While vendors have increasingly introduced support for CEST acquisitions on both clinical and preclinical hardware, image post-processing and analysis pipelines remain siloed based on privately developed code. We aim to develop an easy-to-use, open-source graphical user interface toolbox for preclinical CEST-MRI data analysis (Preclinical CEST-MRI Analysis Tool; Pre-CAT), supporting multiple acquisition types, organ systems, and CEST contrast mechanisms. Methods: Pre-CAT was developed in Python and utilizes the Numpy, Scipy, and Matplotlib libraries for data analysis and plotting. Inbuilt data processing steps include image loading, reconstruction, post-processing, and segmentation. Pre-CAT also supports data analysis for QUESP, CEST-MRF, and field mapping experiments using consensus protocols and methods. Pre-CAT's web interface and GUI were developed using Streamlit, an open-source Python framework. Pre-CAT is hosted and accessible online and can be downloaded for local installation to complete the data analysis pipeline in roughly one minute using modern hardware. Results: Pre-CAT analysis pipelines for Z-spectroscopy, CEST-MRF, and quantitative CEST (QUESP/QUEST) are demonstrated. Conclusion: With the introduction of Pre-CAT, we aim to standardize the preclinical CEST-MRI data analysis pipeline, fostering collaboration across research sites and reducing methodological redundancy. Pre-CAT is open-source and relatively modular, encouraging the addition of new methods and protocols. |
| title | Pre-CAT: A web-based, graphical user-interface toolbox for preclinical CEST-MRI data processing and analysis |
| topic | Medical Physics |
| url | https://arxiv.org/abs/2605.00511 |