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In the analysis of image-based biomedical data, such as functional magnetic resonance imaging (fMRI) or magnetic resonance spectroscopy (fMRI), data sets from 40 to 90 MB are not uncommon, and some experimental fMRI paradigms require as much as 200 MB of storage. Software systems for the analysis of such data require a flexible data model, fast computational techniques and a graphical user interface. Object-oriented programming languages, such as Java and C++, facilitate software reuse and maintainability and provide the foundations for the development of complex data analysis applications. A is paper explores the advantages and disadvantages of using these two programming environments when processing large datasets.