Pre-CAT: A web-based, graphical user-interface toolbox for preclinical CEST-MRI data processing and analysis

TL;DR

Pre-CAT is an open-source, web-based GUI toolbox developed in Python to standardize and simplify preclinical CEST-MRI data analysis across various acquisition types and contrast mechanisms.

Contribution

It introduces a modular, user-friendly platform supporting multiple CEST-MRI protocols, promoting collaboration and reducing redundancy in preclinical research.

Findings

Demonstrated analysis pipelines for Z-spectroscopy, CEST-MRF, and quantitative CEST.

Pre-CAT can be used online or locally, completing analysis in about one minute.

Aims to standardize and foster collaboration in preclinical CEST-MRI data analysis.

Abstract

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.