Rank: 289 based on 421 downloads (last 30 days) and 1 file submitted
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Yan Zhang

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Company/University
University of Central Lancashire

Personal Profile:

Awarded PhD degree in 2006 in the areas of computer vision and pattern recognition at the University of Central Lancashire. Since then, working as a postdoc at the same institute focusing on multi-dimensional and multi-modality medical data processing dedicated to image guided radiotherapy.

Professional Interests:
medical image processing, computer vision, variational/PDE models for data processing, pattern recognition and machine learning

 

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03 Sep 2009 Screenshot 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang active contoursurface, aos, levelset, 2d and 3d fast marchi..., curvature flow, hybrid snake model 421 22
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4.7 | 7 ratings
Comments and Ratings by Yan View all
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22 Nov 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang

Hi Alex,

The problem has been fully discussed before, please see the previous comments for the details. In brief, go to the source file ac_distance_transform_3d.cpp, and get rid of the string in std::exception.

16 Oct 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang

Hi Eran,

To answer your first question, let' s use u to represent the level-set, normally we use curvature flow to smooth the curve
u_t = div(\nabla u/|\nabla u|)
In my implementation, I do this in two steps:
(1) Make |\nabla u| = 1 using reinitialization (ac_reinit).
(2) With (1) the above equation can be simplified to
u_t = div(\nabla u) = \del u (the Laplacian of u)
which describes the linear diffusion of the level-set.
It's more efficient than solving the more general PDE
u_t = div(g \nabla u/|\nabla u|)
which leads to the answer to your second question --- you should look into the codes in "ac_GAC_model" (AOS implementation for geodesic active contour) that tells exactly how to integrate edge information.

08 Sep 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang

Hi Marco,

Thanks for your advices. For your Point 1, it's a strange problem, the file did pass my gcc 4.4 compiler on MacOSX. Then I tried to compile it on Ubuntu with the same compiler and it failed as you pointed out. As for Point 2, it's totally my fault.
28 Aug 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang

Hi, Ning. One more thing: please don't use LCC compiler, it only supports C, NOT C++.
28 Aug 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang

Hi, Ning. Can you tell me which compiler are you using? It looks to me that the compiler doesn't support C++ (can't recognize keywords 'new', 'delete' and operator overloads). If you are using gcc, make sure link to the standard c++ library using '-lstdc++' or directly use g++.

If you are using Windows system, a more complete version of the toolbox can be downloaded from the following link:
http://ecson.org/resources/software/_AOSLevelsetSegmentationToolbox.zip
which includes all the pre-compiled mex files in the right place meaning you can use the toolbox directly without having to compile the c++ source files by yourself.

Hope this can help.
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22 Nov 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang Zhang, Yan

Hi Alex,

The problem has been fully discussed before, please see the previous comments for the details. In brief, go to the source file ac_distance_transform_3d.cpp, and get rid of the string in std::exception.

19 Nov 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang Kararg, Alex

Cannot compile running the compile_mex_codes.m . The output is :

expr: syntax error
/Applications/MATLAB_R2008a/bin/util/mex/mexutil.sh: line 13: [: too many arguments
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
ld warning: duplicate dylib /Applications/MATLAB_R2008a/bin/maci/libz.1.dylib
BinaryHeap.h: In member function 'void CBinaryHeapMinSort<IndexType, WeightType>::Insert(IndexType, WeightType) [with IndexType = int, WeightType = double]':
ac_distance_transform_3d.cpp:27: instantiated from 'void DistanceTransform3D(const InputType*, OutputType*, const int*) [with InputType = unsigned char, OutputType = double]'
ac_distance_transform_3d.cpp:115: instantiated from here
BinaryHeap.h:56: error: no matching function for call to 'std::exception::exception(const char [1])'
/usr/include/c++/4.0.0/exception:57: note: candidates are: std::exception::exception()
/usr/include/c++/4.0.0/exception:55: note: std::exception::exception(const std::exception&)

    mex: compile of ' "ac_distance_transform_3d.cpp"' failed.

??? Error using ==> mex at 207
Unable to complete successfully.

Error in ==> compile_mex_codes at 7
mex ac_distance_transform_3d.cpp

Any help to run the compile_mex_codes.m would be really appreciated. Thank you!
12 Nov 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang Khin

Hi Yan Zhang, When I read your 'test_ChanVese_model_3d.m' and 'test_hybrid_model_3d.m', I have a problem that cannot read head_ct.mat file. It's showing error "??? Error using ==> load Unable to read MAT file head_ct.mat. File may be corrupt." is it because of version different? I am using Matlab 6.5 please advise. thanks

27 Oct 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang Jenny

Hi,Zhang yan.Thank you for your toolbox.I have a problem.I'm trying to use your box to segment my own MRI head datas which are a series of JPEG or DICOM forms.Is your tool possible to segment this form of data.Or I must convert these formats to the supported formats.And how to?Thank you very much!
16 Oct 2009 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang Zhang, Yan

Hi Eran,

To answer your first question, let' s use u to represent the level-set, normally we use curvature flow to smooth the curve
u_t = div(\nabla u/|\nabla u|)
In my implementation, I do this in two steps:
(1) Make |\nabla u| = 1 using reinitialization (ac_reinit).
(2) With (1) the above equation can be simplified to
u_t = div(\nabla u) = \del u (the Laplacian of u)
which describes the linear diffusion of the level-set.
It's more efficient than solving the more general PDE
u_t = div(g \nabla u/|\nabla u|)
which leads to the answer to your second question --- you should look into the codes in "ac_GAC_model" (AOS implementation for geodesic active contour) that tells exactly how to integrate edge information.

Top Tags Applied by Yan
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2d and 3d fast marching, 2d3d image segmentation, active contoursurface, aos, chanvese model
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Updated   File Tags Downloads
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03 Sep 2009 Screenshot 2D/3D image segmentation toolbox 2D/3D image segmentation using level-set based active contour/surface with AOS scheme Author: Yan Zhang active contoursurface, aos, levelset, 2d and 3d fast marchi..., curvature flow, hybrid snake model 421 22
  • 4.71429
4.7 | 7 ratings
 

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