The PM-2000 platform instrument with AQUA analysis quantitates protein expression within subcellular compartments in tissue sections automatically, with a high level of precision. The multi-tissue platform combines fluorescence-based image analysis with automated microscopy and high-throughput tissue microarray technologies to deliver quantitation, accuracy, reproducibility, and productivity. The goal is to measure absolute numbers of protein molecules within a discrete subcellular location. The system is available for licensing to noncommercial researchers and as a service to industry researchers.