The immune system involves complex interactions of many different cells and tissues, in which timing is essential. In order to assess a patient’s immunological status, follow the results of treatment, and facilitate the development of new therapeutic and vaccine agents, it is vital to be able to measure and/or visualize the components of the immune response at work and at the same time assess and characterize the overall immune state and immune function of a patient. New capabilities in methods such as fluorescence and magnetic resonance imaging, positron emission tomography, resonance Raman spectroscopy, and imaging mass spectrometry have been developed recently by Georgia Tech scientists, in collaboration with health providers in several Atlanta area hospitals. This has led to key advancements including characterizations at the single cell level, such as microfluidic trapping and fluorescence imaging of single immune cells, to whole animal characterizations, including PET imaging of immune cell localization within infectious disease models.