phi-max-skeleton3d-matlab-v1.1-0-gc534cab
所属分类:其他
开发工具:matlab
文件大小:16KB
下载次数:6
上传日期:2018-01-24 02:22:01
上 传 者:
tariq
说明: This code calculates the 3D medial axis skeleton of an arbitrary 3d binary volume
文件列表:
phi-max-skeleton3d-matlab-c534cab (0, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\FillEulerLUT.m (2037, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\Skeleton3D.m (5498, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\Test_Skeleton3D.m (599, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\license.txt (1322, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\p_EulerInv.m (3284, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\p_is_simple.m (1497, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\p_oct_label.m (13938, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\pk_get_nh.m (405, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\pk_get_nh_idx.m (382, 2016-04-19)
phi-max-skeleton3d-matlab-c534cab\testvol.mat (6958, 2016-04-19)
# skeleton3D-matlab: 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] Kerschnitzki, Kollmannsberger et al.,
"Architecture of the osteocyte network correlates with bone material quality."
Journal of Bone and Mineral Research, 28(8):1837-1845, 2013.
[3] http://hdl.handle.net/1926/1292
[4] http://fiji.sc/wiki/index.php/Skeletonize3D
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