Cell therapy is a promising and emerging field for the treatment of human diseases. However, to understand and optimize cell therapy, the inability to track the cell transplants in vivo remains a major problem. Most cell transplantation techniques involve the use of histological analysis to evaluate cell transfection, proliferation, and migration after sacrifice. In this literature, for the first time an in vivo model has been developed to study stem cells. Explantation culture of chicken embryo into surrogate shells has been modified for high resolution and long term imaging. A special long distance fluorescence microscope and micromanipulation systems has been developed for in vivo application specially aiming for the injection and tracking of fluorescence labeled cells into chicken embryo and track them. By using the developed system, it was possible to image the whole period of embryonic development of chicken embryo.