Lineage mapping the pre-implantation mouse embryo by two-photon microscopy, new insights into the segregation of cell fates

► We utilize two-photon microscopy to image pre-implantation development. ► We have created specialized tracking and reconstruction algorithms. ► We identify and characterize a third, intermediate cell type in the 16-cell stage embryo. ► We provide new insights into the origins of cell fates. ► Cdx2 expression is not solely regulated by cell surface exposure.