Because of the ease in generating transgenic/gene knock out models and accessibility to early stages of embryogenesis, mouse and rat models have become invaluable to studying the mechanisms that underlie human birth defects. To study precisely how structural birth defects arise, Ultrasound, MRI, microCT, Optical Projection Tomography (OPT), Optical Coherence Tomography (OCT) and histological methods have all been used for imaging mouse/rat embryos. However, of these methods, only OCT enables live, functional imaging with high spatial and temporal resolution. However, one of the major limitations of conventional OCT imaging is the light depth penetration, which limits acquisition of structural information from the whole embryo. Here we introduce new imaging scheme by OCT imaging from different sides of the embryos that extend the depth penetration of OCT to permit high-resolution imaging of 3D and 4D volumes.