The unraveling of the complex dynamic networks that underlie cellular (and, by extension, tissue, organ, and organism) function requires sophisticated mathematical models and, in order to test those models, rich data sets. In addition, even in clonal populations of cells, there is a wide range of variability in cellular function at any given time, even in simple parameters such as the concentration of critical signaling components such as receptors or transcription factors. It remains a matter of conjecture as to whether this is noise, to which the system is inherently robust, or whether the cellular control network can exist in multiple discrete internal states, with indistinguishable input/output characteristics. Fluorescent protein-based methods have two features useful for addressing these issues. First, they can be used to retrieve data from individual cells. Second, in combination with confocal fluorescence microscopy, they can be used nondestructively and can thus follow one or more individual cells in culture or in an intact organism over time.