The mouse embryo has long been central to the study of mammalian development. We developed a light-sheet microscope that adapts itself to the dramatic changes in size, shape and optical properties of the post-implantation mouse embryo and captures its development from gastrulation to early organogenesis at the cellular level. We furthermore developed a computational framework for reconstructing long-term cell tracks, cell divisions, dynamic fate maps and maps of tissue morphogenesis across the entire embryo. By jointly analyzing cellular dynamics in multiple embryos registered in space and time, we built a dynamic atlas of post-implantation mouse development that, together with our microscopy and computational methods, is provided as a resource.
All movies were encoded using the H.264 video compression standard. They are provided in the form of MPEG-4 files as part of the paper (McDole et al. 2018, Cell), as well as in the form of a combined zip file containing all 28 movies.
We furthermore provide a complete blueprint of the adaptive multi-view light-sheet microscope for mouse imaging, including technical drawings of the microscope’s 77 types of custom mechanical components, assembly illustrations for the microscope’s 28 types of multi-part assemblies, and parts list of all custom and commercial mechanical microscope components.
In addition to the individual software modules listed above, we provide a comprehensive practical software guide with detailed instructions and preconfigured code for all software modules as well as example data.
Some of the data sets listed below include large CSV files that are not suitable for opening/browsing with standard editors such as Microsoft Excel or LibreOffice. We recommend opening these data tables in a software environment designed for handling large data structures, such as Python or Matlab.