The localization of a protein to a particular subcellular structure or organelle is an important step in the study of that protein. It is common for investigators to use one of a number of protein tagging techniques (e.g., epitope tagging, fusion with green fluorescent protein, generation of antibodies), along with fluorescence microscopy, to visualize and record the localization pattern of a protein. The major reason for doing this is that the localization of a protein may provide insight into its function (e.g., the observation that the product of a gene implicated in vacuole biogenesis is located in the nucleus suggests that it is a transcription factor) or lend support to a hypothesis regarding its function (the observation that a protein suspected to play a role in nuclear pore function localizes to the nucleus supports the hypothesis). The current state of the art in protein localization relies on individual investigators to make reasoned conclusions regarding the patterns obtained via the microscope. While this approach has worked adequately, improvements need to be made to accommodate the rapidly increasing number of proteins that are discovered and characterized every year.