BodyParts3D in Matlab

This small collection of functions can be used to load and plot items from the BodyParts3D database. This database is used for the Anatomography website.

You are currently reading the README. The nice ‘project page’ is located here.

Download BodyParts3D

To use this code, the BodyParts3D database must first be downloaded: https://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html

Download the IS-A Tree version of the "Polygon Mesh Data" collections (isa_BP3D_4.0_obj_99.zip); it has a larger number of files which corresponds to the list included in the file isa_element_parts.txt. A direct download link is: ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/LATEST/isa_BP3D_4.0_obj_99.zip (136MB)

Configuration

The file displ_body_parts.m must have two paths changed to be specific for your system. Wherever you put the folder containing the .obj files, change OBJ_PATH to that location. Then change CACHE_PATH anywhere else on your computer; this folder will be used to store cache files so that the .obj files don't need to be imported (a slow process) every time.

OBJ_PATH   = '/Users/will/Local/Biomech/BodyParts3D/v4obj/';
CACHE_PATH = '/Users/will/Local/Biomech/BodyParts3D/v4cache/';

After adding the BodyParts3D-matlab directory to your Matlab path, run load_parts_list.m in the same directory to save the parts_list.mat file. Otherwise it will be added to whichever directory you're in when you run the code, which would waste a little time and disk space.

Usage

It's pretty easy — check out the example file example_body_parts.m. Basically, run the command find_body_parts(regex) to search for body parts in the database; e.g.,

find_body_parts('bone organ .* vertebra')
find_body_parts('vocalis')

When that returns the part(s) you wish to display, add an output as so:

parts = find_body_parts('/ cervical vertebra /');
displ_body_parts(parts)

Colour and opacity can be selected using additional options to displ_body_parts().

Acknowledgement and citation

If you make use of this code in your work, please cite the original BodyParts3D Project, as well as this repository.

‘BodyParts3D: 3D structure database for anatomical concepts’

Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K
Nucleic Acids Res. 2008 Oct 3
DOI: 10.1093/nar/gkn613

‘BodyParts3D in Matlab’

W.S.P. Robertson

Copyright and licence

Distributed under the Apache License v2.

The following files are redistributed from other work: