A chicken embryo is the developmental biology’s oldest model organism. In ovo development of the chicken embryo closely mirrors human embryo development. The relatively large size, ease of access, and lack of maternal motion generated in pregnant mammals are distinct advantages the chicken embryo model provides. The chicken embryo provides an excellent platform for monitoring morphology and metabolism of central neural system (CNS) by using MRI or NMR spectroscopy over the course of development. In this presentation our recent work on monitoring Zika virus induced microcephaly and tracking stem cells are presented.