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Traditional analyses of in vivo 1D MR spectroscopy of brain metabolites have been limited to the inspection of one-dimensional free induction decay (FID) signals from which only a limited number of metabolites are clearly observable. In this article we introduce a novel set of algorithms to process and characterize two-dimensional in vivo MR correlation spectroscopy (2D COSY) signals. 2D COSY data was collected from phantom solutions of topical metabolites found in the brain, namely glutamine, glutamate, and creatine. A statistical peak-detection and object segmentation algorithm is adapted for 2D COSY signals and applied to phantom solutions containing varied concentrations of glutamine and glutamate. Additionally, quantitative features are derived from peak and object structures, and we show that these measures are correlated with known phantom metabolite concentrations. These results are encouraging for future studies focusing on neurological disorders that induce subtle changes in brain metabolite concentrations and for which accurate quantitation is important.