Mass spectrometry imaging (MSI) is a powerful label-free molecular imaging technique for biological research, which enables simultaneous localization of multiple classes of biomolecules with high sensitivity and unprecedented molecular specificity. By acquiring a full mass spectrum in each pixel of a virtual grid, MSI generates hundreds of molecular images in a single experiment. Recent advances in MSI technology focus on the enhancement of the spatial resolution, depth of molecular coverage and acquisition throughput, all of which substantially increase the data size. The interpretation of complex MSI data is a major bottleneck on the path to scientific discovery, which motivates the development of computational tools for data mining and visualization .