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

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.