The analysis of protein expression in tissue by immunohistochemistry (IHC) presents three significant challenges. They are (1) the time-consuming nature of pathologist-based scoring of slides; (2) the need for objective quantification and localization of protein expression; and (3) the need for a highly reproducible measurement to limit intra- and inter-observer variability. While there are a variety of commercially available platforms for automated chromagen-based and fluorescence-based image acquisition of tissue microarrays, this chapter is focused on the analysis of fluorescent images by AQUA(R) analysis (Automated QUantitative Analysis) and the solutions offered by such a method for research and diagnostics. AQUA analysis is a method for molecularly defining regions of interest or "compartments" within a tissue section. The methodology can be utilized with tissue microarrays to provide rapid, quantitative, localized, and reproducible protein expression data that can then be used to identify statistically relevant correlations in populations. Ultimately this allows for a multiplexed, objective and standardized quantitative approach for biomarker research and diagnostic assay development for protein expression in tissue.