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A novel method of correlated imaging, combining confocal Raman microscopy (CRM) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) was developed in order to investigate the structural and chemical diversity inherent in three-dimensional (3D) cell cultures. These 3D spheroidal cell cultures are high throughput in vitro model systems that recapitulate some of the chemical and physiological gradients characteristic of tissues. As a result, they are ideal for testing new imaging approaches due to the native diversity of cellular phenotypes found within a single culture. Individually, confocal Raman microscopy (CRM) and mass spectrometry imaging (MSI) produce different kinds of chemical information. CRM imaging reveals differences in cellular integrity and protein secretion across a typical near-equatorial transverse slice, while MSI shows localization of small molecules to discrete regions of the spheroid section. Correlating information obtained from these disparate imaging methods begins with an external fiducial mask, added to the spheroidal samples to orient image acquisition on the two orthogonal platforms. Rather than combine the images directly, principal component analysis is used to reveal the most chemically-informative elements, which are then combined using digital image correlation. Using this approach, relationships between the principal components of each method are visualized so that they may be compared on commensurate spatial length scales.