Skeleton3D

Calculates the 3D skeleton of an arbitrary binary volume using parallel medial axis thinning.

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Actualizado 5 Dec 2018

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Skeleton3D: Parallel medial axis thinning of a 3D binary volume
This code calculates the 3D medial axis skeleton of an arbitrary 3d binary volume. It is an optimized MATLAB implementation of the homotopic thinning algorithm described in [1]. We developed it to quantify the network of cell processes in bone [2], but it should work on images of any tubular or filamentous structures. An example volume (testvol.mat) is included, along with an example script (Test_Skeleton3D.m). Any comments, corrections or suggestions are highly welcome.
Usage:
skel = Skeleton3D(bin)
where "bin" is a 3D binary image, and "skel" the resulting image containing only the skeleton voxels, or
skel = Skeleton3D(bin,mask)

to mask all foreground voxels in 'mask' from skeletonization, e.g. to preserve certain structures in a image volume.

For additional cleanup, e.g. pruning of short branches, please use my Skel2Graph3D package on MATLAB File Exchange.

This code is inspired by the ITK implementation by Hanno Homann [3] and the Fiji/ImageJ plugin by Ignacio Arganda-Carreras [4]. If you include this in your own work, please cite our original publicaton [2].

Philip Kollmannsberger 09/2013
philipk@gmx.net

References:

[1] Ta-Chih Lee, Rangasami L. Kashyap and Chong-Nam Chu
"Building skeleton models via 3-D medial surface/axis thinning algorithms."
Computer Vision, Graphics, and Image Processing, 56(6):462–478, 1994.

[2] Kollmannsberger, Kerschnitzki et al.,
"The small world of osteocytes: connectomics of the lacuno-canalicular network in bone."
New Journal of Physics 19:073019, 2017.

[3] http://hdl.handle.net/1926/1292

[4] http://fiji.sc/wiki/index.php/Skeletonize3D

Citar como

Kollmannsberger, Kerschnitzki et al., "The small world of osteocytes: connectomics of the lacuno-canalicular network in bone." New Journal of Physics 19:073019, 2017.

Compatibilidad con la versión de MATLAB
Se creó con R2010b
Compatible con cualquier versión
Compatibilidad con las plataformas
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Versión Publicado Notas de la versión
1.12.0.1

updated reference

1.12.0.0

Fixed title

1.11.0.0

Linked to github

1.1.0.0

Removed designation of global variables, and added H1 line for help. For cleaning noise such as short artifacts, please use my Skel2Graph3D package.

1.0.0.0

Para consultar o notificar algún problema sobre este complemento de GitHub, visite el repositorio de GitHub.
Para consultar o notificar algún problema sobre este complemento de GitHub, visite el repositorio de GitHub.