Local tissue stem cells are known to exist in mammalian lungs but their role in epithelial maintenance remains unclear. We therefore developed murine aggregation chimera and wholemount imaging techniques to assess the contribution of these cells to lung homeostasis and repair. In this chapter we provide further details regarding the generation of murine aggregation chimera mice and their subsequent use in wholemount lung imaging. We also describe methods related to the interpretation of this data that allows for quantitative assessment of airway stem cell activation versus quiescence. Using these techniques, it is possible to compare the growth and differentiation capacity of various lung epithelial cells in normal, repairing, and diseased states.