Proteomics is the comprehensive study of all aspects of protein behavior. The subfield of location proteomics is concerned with the systematic analysis of the subcellular location of proteins. In order to perform high-resolution, high-throughput analysis of all protein location patterns, automation is needed both for acquisition and analysis. Automated methods for analyzing subcellular location patterns in fluorescence microscope images have been developed and shown to work well for static 2D and 3D images of single cells. This chapter reviews this work and describes current efforts to extend these approaches, including classification of temporal patterns and building of generative models to represent location patterns.