Towards a 3-dimensional atlas of the developing human embryo: the Amsterdam experience

Reprod Toxicol. 2012 Sep;34(2):225-36. doi: 10.1016/j.reprotox.2012.05.087. Epub 2012 May 26.


Knowledge of complex morphogenetic processes that occur during embryonic development is essential for understanding anatomy and to get insight in the pathogenesis of congenital malformations. Understanding these processes can be facilitated by using a three-dimensional (3D) developmental series of human embryos, which we aim to create in this project. Digital images of serial sections of 34 human embryos of the Carnegie Collection between Carnegie stages 7 (15-17 days) and 23 (56-60 days) are used to create 3D reconstructions of different organ systems. The software package Amira is used to align the sections and to create the 3D reconstructions. In this midway evaluation we show the first results of the atlas, containing 34 embryos with more than 13.500 manually annotated sections. The 3D models can be interactively viewed within a 3D-pdf. This will be the first complete digital 3D human embryology atlas of this size, containing all developing organ systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Atlases as Topic*
  • Embryo, Mammalian / anatomy & histology*
  • Embryonic Development
  • Humans
  • Image Processing, Computer-Assisted
  • Imaging, Three-Dimensional
  • Models, Anatomic*
  • Software