Bioluminescence from murine stem cells tagged with the luciferase gene reporter and distributed within three-dimensional scaffolds of two different materials is quantified in vitro and in vivo. The luminescence emitted from cells adhering to the scaffolds tested is monitored noninvasively using a bioluminescence imaging system. Monitoring the kinetics of luciferase expression via bioluminescence enables real-time assessment of cell survival and proliferation on scaffolds both in vitro and in vivo over prolonged (8 weeks) periods of time.