If you’ve ever noticed the 3D images of brain structures on Wikipedia, you may have been curious where they are sourced from.


It turns out that they are generated from a freely accessible Japanese database, the Life Sciences Database Archive. This database is licensed under Creative Commons.

It includes anatomical models that can be downloaded as well as other public databases including gene expression databases. The anatomical models can be downloaded and browsed online at the Body Parts 3D site.

The database is organised with a formal ontology which uses the same structure as University of Washington’s Foundational Model Explorer.

The object library is extensive, with over 4000 objects, I imported the brain objects into a 3D rendering program for example:

brain_wireframe.jpg brain_render.jpg

It’s fantastic to see this level of anatomical data available for free, thanks to the scientists and data managers at the University of Tokyo,

also see this paper:

Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K. BodyParts3D: 3D structure database for anatomical concepts. Nucleic Acids Res. 2009 Jan;37(Database issue):D782-5. Epub 2008 Oct 3. PMID: 18835852

Edit 4 Sept ‘14

The BioDigital Human project is a web-based 3D anatomical browser. Unfortunately, it’s not open source and doesn’t allow export of 3D data but it is free to use for the time being. The authors have produced a very intuitive and powerful anatomical browser that also includes animated pathological demonstrations. It’s a very useful teaching tool. Hopefully they will see fit to open up the licensing a little in the future.