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The 3D Atlas of Human Embryology project was funded by the Academic Medical Center (AMC) in Amsterdam, the Netherlands, in 2009. Since then, over 75 students, under the supervision of embryologists of the Department of Anatomy, Embryology & Physiology, have contributed to this labor-intensive project, investing over 45,000 hours of work. The result of this effort is an embryology atlas with more than 15,000 manually annotated sections and a duplicate series of fully reconstructed human embryos covering the phase of organogenesis, between Carnegie stage 7 (15–17 days old embryo) and 23 (56–60 days).

The atlas is based on digital images of serial sections of 34 human embryos of the Carnegie Collection between stages 7 and 23. The software package Amira is used to align the sections and to create the 3D reconstructions of all developing organ systems. After manual segmentation in Amira, Blender was used to create smooth-surfaced models, suitable for use in 3D-PDFs, applications or games. These models are based on the original reconstructions and are without loss of necessary detail. 

The 3D models are presented in an interactive fashion, which facilitates the exploration of the complex 3D relations between the different organs. These models are 3D-PDF files that can be viewed and studied with Adobe reader version X or higher. This allows the student or researcher to develop an independent view on spatial relations. The 3D reconstructions enable the quantitative measurement of the growth of the individual organs and structures, the assessment of the changing position of organs relative to the vertebral segments during development and the verification of remaining ambiguities in the description of the development of organs.


For further information we refer you to our list of publications.

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