Summer2009:The Vascular Modeling Toolkit in 3D Slicer - Revision history

Haehn: /* Key Investigators */

2009-06-26T16:09:18Z

Key Investigators

Haehn: /* Key Investigators */

2009-06-26T14:09:02Z

Key Investigators

Haehn: /* Key Investigators */

2009-06-26T04:22:15Z

Key Investigators

Haehn: /* Key Investigators */

2009-06-26T04:20:46Z

Key Investigators

Tkapur at 02:34, 22 June 2009

2009-06-22T02:34:55Z

Haehn at 01:31, 19 May 2009

2009-05-19T01:31:36Z

Haehn: Created page with 'NOTOC Image:PW2009-v3.png|Project Week Main Page File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a t...'

2009-05-19T01:13:27Z

Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a t...'

New page

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a tumor using VMTK in 3D Slicer
File:Screenshot-VMTK_in_3D_Slicer2.png|Example segmentation of vessels in an arm bearing a vascular access for hemodialysis
</gallery>

==Key Investigators==
* Daniel Haehn (Student of Medical Informatics, University of Heidelberg)

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<h3>Objective</h3>
The Vascular Modeling Toolkit ([http://vmtk.org VMTK]) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. It should be very interesting to offer such techniques in 3D Slicer.

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<h3>Approach, Plan</h3>
To provide VMTK tools in 3D Slicer the ''vtkVmtk'' library has to be available as an add-on.
With the connection of VMTK and 3D Slicer processing pipelines
between VMTK code and other algorithms can be established. <br><br>
The plan is to clean-up existing ''VMTK in 3D Slicer'' code, provide additional VMTK functionality in 3D Slicer as well as to optimize the work-flow between the existing VMTK modules. This includes more level set evolution methods and variable calculation of feature images during level set segmentation.

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<h3>Progress</h3>
The library of VMTK was made available in 3D Slicer using a GUI-less loadable module approach in order to
provide a flexible way of distributing and including it. Therefore all VMTK functions are available to 3D Slicer developers. <br><br>Python scripted modules offering VMTK level set segmentation methods and VMTK vessel enhancement filters within 3D Slicer were created. These include the following algorithms:
* Colliding Fronts and Fast Marching Upwind Gradient initialization
* Geodesic Active Contour and Curves evolution
* FrangiVesselness, SatoVesselness and VesselEnhancingDiffusion filters
<br><br>
The created modules are available at the VMTK in 3D Slicer NITRC page:
http://www.nitrc.org/projects/slicervmtklvlst/

</div>
</div>

==References==
*Antiga L, Piccinelli M, Botti L, EneIordache B, Remuzzi A, Steinmann DA. (2008) An imagebased modeling framework for patientspecific computational hemodynamics. Med Biol Eng Comput 46(11):10971112
*Antiga L, Steinman DA (2008) The Vascular Modeling Toolkit. http://www.vmtk.org/
*Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.

@@ Line 41: / Line 41: @@
 '''Summer Project Week Update:'''
 * Fast Marching Upwind Gradient initialization: target points were made optional and the algorithm can run with one or more source points (seeds).
 * Level-set initialization can now be performed on an enhanced vesselness image. During evolution stage this initial level set can be inflated within the original volume to avoid the loss of information.
-* For using the gui-less VMTK library module as a Slicer3 extension, necessary updates to the CMake files of VMTK were performed to remove deprecated INSTALL_FILES and INSTALL_TARGET calls. These changes make vtkVmtk Slicer3 compliant by using CMake 2.6, will be send to Luca Antiga and hopefully be in the official VMTK release soon.
+* For using the gui-less VMTK library module as a Slicer3 extension, necessary updates to the CMake files of VMTK were performed to remove deprecated INSTALL_FILES and INSTALL_TARGET calls. These changes make vtkVmtk Slicer3 compliant by using CMake 2.6, were sent to Luca Antiga and hopefully be in the official VMTK release soon :D.
 </div>

@@ Line 42: / Line 42: @@
 '''Summer Project Week Update:'''
 * Fast Marching Upwind Gradient initialization: target points were made optional and the algorithm can run with one or more source points (seeds).
-* Level-set initialization can now be performed on an enhanced vesselness image. During evolution stage this initial level set can be inflated within a feature image based on the original volume to avoid the loss of information.
+* Level-set initialization can now be performed on an enhanced vesselness image. During evolution stage this initial level set can be inflated within the original volume to avoid the loss of information.
 * For using the gui-less VMTK library module as a Slicer3 extension, necessary updates to the CMake files of VMTK were performed to remove deprecated INSTALL_FILES and INSTALL_TARGET calls. These changes make vtkVmtk Slicer3 compliant by using CMake 2.6, will be send to Luca Antiga and hopefully be in the official VMTK release soon.

@@ Line 42: / Line 42: @@
 '''Summer Project Week Update:'''
 * Fast Marching Upwind Gradient initialization: target points were made optional and the algorithm can run with one or more source points (seeds).
-* The initialization can now be performed on an enhanced vesselness image. During evolution stage this initial level set can be inflated within a feature image based on the original volume to avoid the loss of information.
+* Level-set initialization can now be performed on an enhanced vesselness image. During evolution stage this initial level set can be inflated within a feature image based on the original volume to avoid the loss of information.
 * For using the gui-less VMTK library module as a Slicer3 extension, necessary updates to the CMake files of VMTK were performed to remove deprecated INSTALL_FILES and INSTALL_TARGET calls. These changes make vtkVmtk Slicer3 compliant by using CMake 2.6, will be send to Luca Antiga and hopefully be in the official VMTK release soon.

@@ Line 36: / Line 36: @@
 * Geodesic Active Contour and Curves evolution
 * FrangiVesselness, SatoVesselness and VesselEnhancingDiffusion filters
-<br><br>
+<br>
 The created modules are available at the VMTK in 3D Slicer NITRC page:
 http://www.nitrc.org/projects/slicervmtklvlst/
 </div>
 </div>
 ==References==

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
+Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
 File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a tumor using VMTK in 3D Slicer
 File:Screenshot-VMTK_in_3D_Slicer2.png|Example segmentation of vessels in an arm bearing a vascular access for hemodialysis

@@ Line 7: / Line 7: @@
 ==Key Investigators==
-* Daniel Haehn (Student of Medical Informatics, University of Heidelberg)
+* [[User:haehn |Daniel Haehn]] (Student of Medical Informatics, University of Heidelberg)
 <div style="margin: 20px;">

Summer2009:The Vascular Modeling Toolkit in 3D Slicer - Revision history

Haehn: /* Key Investigators */

Haehn: /* Key Investigators */

Haehn: /* Key Investigators */

Haehn: /* Key Investigators */

Tkapur at 02:34, 22 June 2009

Haehn at 01:31, 19 May 2009

Haehn: Created page with '__NOTOC__ Image:PW2009-v3.png|Project Week Main Page File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a t...'

Haehn: Created page with 'NOTOC Image:PW2009-v3.png|Project Week Main Page File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a t...'