To determine the developmental stage of embryonic mice, we apply a geometric morphometric approach to the changing shape of the mouse limb bud as it grows from embryonic day 10 to embryonic day 15 post-conception. As the ontogenetic sequence results in the de novo emergence of shape features not present in the early stages, we have created a standard ontogenetic trajectory for limb bud development – a quantitative characterization of shape change during limb morphogenesis. This trajectory of form as a function of time also gives us the reverse function: the ability to infer developmental stage from form, with a typical uncertainty of 2 h. We introduce eMOSS (embryonic mouse ontogenetic staging system) as a fast, reliable, convenient and freely available online tool for staging embryos from two-dimensional images of their limb buds, and illustrate its use in phenotyping early limb abnormalities.

The establishment of precise, high-resolution temporal sequences for morphogenetic events in laboratory mice remains a vexing issue in developmental biology. Mouse embryos collected at the same period of gestation, even those from the same litter, show wide variation in individual levels of progress along their developmental trajectory. Therefore, age at harvest does not provide sufficient information about developmental progress to serve as the basis for forming samples for the study of rapidly or near-simultaneously occurring events such as the sequence of ossification center formation. Here, we generate two measures of individual developmental progress (developmental age) for a large sample of mouse embryos using crown–rump lengths that measures size, and limbstaging ages produced by the embryonic Mouse Ontogenetic Staging System (eMOSS) that measure shape. Using these measures, we establish fine-grained sequences of ossification center appearance for mouse embryos. The two measures of developmental progress generate slightly different sequences of ossification center formation demonstrating that despite their tight correlation throughout the developmental period, size and shape are aspects of form that are at least partially dissociated in development.