Java-based framework for processing and displaying short-echo-time magnetic resonance spectroscopy signals

Magnetic resonance spectroscopy (MRS) can be used to determine in a non-invasive way the concentrations of certain chemical substances, also called metabolites. The spectra of MRS signals contain peaks that correspond to the metabolites of interest. Short-echo-time signals are characterized by heavily overlapping metabolite peaks and require sophisticated processing methods. To be useful in a clinical environment tools are needed that can process those signals in an accurate and fast way. Therefore, we developed novel processing methods and we designed a freely available and open-source framework (http://www.esat.kuleuven.ac.be/sista/members/biomed) in which the processing methods can be integrated. The framework has a set of abstract classes, called hot spots, and its goal is to provide a general structure and determine the control flow of the program. It provides building blocks or components in order to help developers with integrating their methods in the framework via a plug-in system. The framework is designed with the unified modeling language (UML) and implemented in Java. When a developer implements the framework he gets an application that acts like a simple and user-friendly graphical user interface (GUI) for processing MRS data. This article describes in detail the structure and implementation of the framework and the integration of our processing methods in it.