These color-coded mouse embryos represent a breakthrough for understanding early mammalian development. A powerful new computer-assisted microscope has for the first time let researchers observe how a mouse embryo develops primitive organs, following the fate of individual cells along the way.
The microscope, described today in Cell, shines a sheet of laser light through the embryo, allowing researchers to see the cells deep inside. Earlier versions of the microscope were able to analyze zebrafish and fruit fly embryos, but mouse embryos are much more difficult. They are not only harder to keep alive in the lab, they are also much larger—making it much more difficult to see all the way through them. The microscope uses new machine learning techniques—a form of artificial intelligence in which computers learn from data—to track the embryo and keep it in focus as it drifts in its culture medium and grows by an order of magnitude from day 6 to day 8 of development. It also uses advanced algorithms to sort through millions of images to track cells as they move and divide.
The researchers combined their analysis of several embryos to create a “digital mouse embryo,” which they have made publicly available along with the software and directions for building the microscope. In the image above, blue cells will become part of the heart and green cells will become the neural tube, which later forms the brain and spinal cord.
The new view will help scientists better understand the genes and other factors that shape organs during development. That, in turn, could help them improve their attempts to coax stem cells in the lab to do the same thing.