BodyParts3D

This repository contains a collection of 3D models of human anatomy. The 3D models are stl files which have been converted from the original .obj files from the BodyParts3D/Anatomography project.

Getting started

• The stl files are contained in the stl folder.
• To aid model discovery images are provided for each model in the png folder
• Most files are named using their Foundational Model of Anatomy Ontology (FMA) representation, which follows the format: FMA<FMAID>.stl.
• In an effort to create a human-readable list to interogate the files, the csv file FMA_ID_label_obj.csv collects the FMAID for each obj file as well as the preferredName from the ontology. An example from this list is provided here:

• For more information search the original website: http://lifesciencedb.jp/bp3d/
• The obj folder contains some sample obj-files. A full set of obj files was too large for this GitHub repository. Hence the obj files are provided here to test the obj->stl conversion process.
• Code based interfaces to interogate the model database are under development.

Why STL files

The BodyParts3D/Anatomography project provides OBJ rather than STL files. The benefit of OBJ files is that they are human-readable plain text files, in which one recognises entries like vertices and faces. However, these plain text files are too large for hosting on a plain GitHub repository (in particular models like for the skin were over 100 Mb). In this repository binary STL files are chosen since these are signigicantly smaller in size compared to plain text OBJ files (although no longer human-readable). Furthermore, GitHub is able to render STL files in the browser which aids to preview models (provided the STL file size is not too large).

Contributing

Contributions are welcome! Please post issues and pull requests or email: [email protected].

Contributions are especially welcome in relation to the following:

• Improving the means for users to retrieve content from this database. Currently only the FMAID code and preferredNameare listed. However, it remains challenging to retrieve and find files unless one is very familiar with the codes or the anatomical naming conventions.
• Adding code based database interrogation and model geometry processing code for the following languages:
  • MATLAB/Octave
  • Julia
  • Python
• Some models are currently more suitable for "display purposes" than computational biomechanics work. Some processing of these model may be needed to provide valid/merged(or separated)/cured files. An example is the skin surface FMA7163 which contains a complex mix of outer and inner surfaces (and non-manifold triagles). Isolation of the outer surface, curing of "holes", removal of non-manifold triangles, is needed to use the skin for applications like finite element mesh development.

Licenses

Derived geometry and 3D model licenses

The materials provided under the BodyParts3D/Anatomography project, and any derivatives made available here (either directly or indirectly through posts-processing functionality), are licensed under the the following license: Creative Commons License Creative Commons Attribution-Inheritance 2.1 Japan (CC BY-SA)

Please adhere to the license conditions when using/reusing the content shared from this resource.

The license can be viewed on the Life Science Integrated Database Center website and is also reproduced in this repository

BodyParts3D, Copyrightc 2008 Life Science Integrated Database Center licensed by CC Display-Inheritance 2.1 Japan

Software license

All software/code provided here, e.g. to interogate and process the geometry or image files, caries the permissive MIT open source software license.

Citing this repository

This repository should be cited in any research that employs either the model content or the codes provided.