Fluorescence and bioluminescence imaging play a central role in the characterization of stem cells both in vitro and in vivo. The physical principles and application of bioluminescence imaging are reviewed in Chapter 13. This chapter thus focuses largely on the principles and applications of ¨uorescence imaging. Particular attention is placed on the recent development of noninvasive ¨uorescence techniques, such as ¨uorescence tomography (FMT), and their application in the cardiovascular system. The principles and challenges discussed, however, apply equally to the imaging of other organ systems and regions of the body.