Stem cells develop during embryogenesis and play a key role in maintaining our bodies in a healthy state. Sometimes stem cells become abnormal and this leads to disease. Understanding how stem cells and other cells form in the embryo and how stem cells maintain themselves in the adult body could provide important new information on how stem cells can give rise to abnormal cells such as in cancer. In order to understand stem cells scientists need to study them. Often this is done in a laboratory in defined conditions. Although such studies have reveled important information about development and about stem cell biology, lab conditions do not necessarily reflect how such cells normally grow. Ideally we would be able to study stem cells where they reside and without disturbing their growth. We previously developed a method for studying stem cells in living tissues in a non-invasive way. The studies we carried out have further developed this methodology and have shown that stem cells can be studied in situ and that we can study their metabolism as they live and grow. Using these methods we should be able to develop methods for understanding how stem cells and other cells develop normally in the embryo, why that process sometimes goes wrong and how stem cells in adults sometimes go awry and give rise to cancers.