A major obstacle to stem cell based therapies is the immune response of the patient to stem cell derived tissue, which can be recognized as foreign and attacked by the patient’s immune system. T cells orchestrate immune responses and are “educated” about self versus foreign antigen in an organ called the thymus. It may be possible to educate T cells in a patient to avoid attacking stem cell derived grafts by “re-educating” them in a thymus that contains the same material as the graft. To better understand how human T cells develop and improve the systems we currently use to mimic this process in the laboratory, we examined two complementary models of human thymocyte development: humanized immune system (HIS) mice and human thymic slices. Taking advantage of the most recent innovations in microscopic imaging, we examined and manipulated the interactions between developing human T cells and their support cells in living 3D tissues. Using small molecule inhibitors in our slice model, we identified signals immature T cells use to find their way in the thymus. Comparing our HIS model to human samples, we also found differences in non-conventional T cell development. In sum, our models provide a platform for dissecting the signals necessary for selection of diverse T cell lineages.