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

Area of Science:

• Medical Imaging
• Biomedical Engineering
• Radiology

Background:

• Chemical Exchange Saturation Transfer (CEST) Magnetic Resonance Imaging (MRI) is gaining interest in preclinical research.
• Current CEST-MRI data analysis pipelines are often proprietary and lack standardization, hindering collaboration and reproducibility.
• There is a need for accessible, standardized tools for preclinical CEST-MRI data processing and analysis.

Purpose of the Study:

• To develop an easy-to-use, open-source graphical user interface (GUI) toolbox for preclinical CEST-MRI data analysis, named Preclinical CEST-MRI Analysis Tool (Pre-CAT).
• To support multiple acquisition types, organ systems, and CEST contrast mechanisms within a unified platform.
• To standardize the preclinical CEST-MRI data analysis pipeline.

Main Methods:

• Pre-CAT was developed using Python, incorporating libraries such as Numpy, Scipy, and Matplotlib for data analysis and visualization.
• The toolbox includes built-in functionalities for image loading, reconstruction, post-processing, and segmentation.
• A web interface and GUI were created using Streamlit, enabling online accessibility and local installation for rapid data analysis.

Main Results:

• Demonstrated analysis pipelines for various CEST techniques, including Z-spectroscopy, CEST-MRF, and quantitative CEST (QUESP/QUEST).
• The Pre-CAT toolbox facilitates efficient data analysis, with local installations completing pipelines in approximately one minute on modern hardware.
• The tool supports consensus protocols and methods for QUESP, CEST-MRF, and field mapping experiments.

Conclusions:

• Pre-CAT aims to standardize preclinical CEST-MRI data analysis, promoting inter-research site collaboration and reducing methodological redundancy.
• The open-source and modular nature of Pre-CAT encourages community contributions for incorporating new methods and protocols.
• This toolbox provides a valuable resource for advancing preclinical CEST-MRI research through accessible and standardized analysis.