NAMIC Wiki - User contributions [en]

Paraview Support for Computational Anatomy

2010-06-24T19:52:54Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

Thanks to Curtis Lisle for converting the film to Quicktime mov format.

[[Media:LeftAmygdalaSurfaceHarmonics.mov| Click here for a quicktime video]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T18:34:12Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

<flash>file=LeftAmygdalaSurfaceHarmonics.swf|width=30|height=30</flash>

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T18:31:13Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

<flash>file=LeftAmygdalaSurfaceHarmonics.swf|width=30|height=30|quality=best</flash>

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T18:30:35Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
<flash>file=LeftAmygdalaSurfaceHarmonics.swf|width=10%|height=30|quality=best</flash>

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T18:20:01Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
[[File:LeftAmygdalaSurfaceHarmonics.swf]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T18:19:19Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
[[Media:LeftAmygdalaSurfaceHarmonics.swf]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:LeftAmygdalaSurfaceHarmonics.swf

2010-06-24T18:18:59Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-24T18:18:49Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
[[File:LeftAmygdalaSurfaceHarmonics.swf]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T18:05:06Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
[[File:LeftAmygdalaSurfaceHarmonics.flv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:LeftAmygdalaSurfaceHarmonicsNew.wmv

2010-06-24T17:01:52Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-24T17:01:41Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
[[File:LeftAmygdalaSurfaceHarmonicsNew.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T17:00:57Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[Media:LeftAmygdalaSurfaceHarmonics.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T17:00:22Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[File:LeftAmygdalaSurfaceHarmonics.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T16:56:50Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[File:LeftAmygdalaSurfaceHarmonics.mpeg]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T16:08:58Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[File:LeftAmygdalaSurfaceHarmonics.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T16:04:25Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[Media:LeftAmygdalaSurfaceHarmonics.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:LeftAmygdalaSurfaceHarmonics.wmv

2010-06-24T16:03:30Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-24T16:03:20Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[File:LeftAmygdalaSurfaceHarmonics.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T16:03:09Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.
[[File:LeftAmygdalaSurfaceHarmonics.wmv]]

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T15:50:33Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[File:LeftAmygdalaSurfaceHarmonics.ogv]]
==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-24T15:49:34Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.

Update (June 24, 2010): we managed to imbed the JHU CIS group's ITK-based Laplace-Beltrami filter into a VTK-plugin that runs on Paraview. We uncovered, along the way, a bug in the itk::QuadEdgeMesh, which was a useful exercise in itself, and we thank Alexandre Gouillard for his support in this area. Thanks to Julien Finet and Pat Marion of Kitware, who wrote a Python-based script that produces an animation from the surface harmonic outputs produced by the Laplace-Beltrami filter. Embedded here is a digital film of this animation produced with RecordMyDesktop.

[[File:LeftAmygdalaSurfaceHarmonics.ogv]]
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:VtkITKRecursiveGaussianFilter.png

2010-06-21T17:43:21Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-21T17:43:19Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:34:44Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
[[File:vtkITKRecursiveGaussianFilter.png]]
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:33:06Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface mesh.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:32:05Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
[[File:ITKSmoothPolyData.png]]
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:23:57Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:ITKSmoothPolyData.png

2010-06-21T17:23:15Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-21T17:22:20Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:ITKSmoothPolyData.png|ITK-based smoothing of surface model.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:20:18Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
Image:|ITK-based smoothing of surface model.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:16:11Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-21T17:14:47Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal.gif|Slicer scene with JHU Atlas.
Image:ParaviewScene.png|Scene instantiated under Paraview.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:SlicerSceneOriginal.gif

2010-06-21T17:13:37Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-21T17:13:07Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
[[File:SlicerSceneOriginal.gif]]|Slicer scene.
<gallery>
Image:ParaviewScene.png|Scene instantiated under Paraview.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:12:31Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
[[File:SlicerSceneOriginal.gif]]|Slicer scene.
Image:ParaviewScene.png|Scene instantiated under Paraview.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-21T17:11:07Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''
<gallery>
Image:SlicerSceneOriginal|Slicer scene.
Image:ParaviewScene.png|Scene instantiated under Paraview.
</gallery>
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

File:ParaviewScene.png

2010-06-21T17:01:47Z

MichelKitware:

Paraview Support for Computational Anatomy

2010-06-21T17:00:32Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

[[File:ParaviewScene.png]]
==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

NA-MIC NCBC Collaboration:3D Shape Analysis for Computational Anatomy

2010-06-07T18:29:47Z

MichelKitware: /* Key Personnel */

Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]

[[Image:JHUCollaboration.jpg|thumb|right|300px|Deformation of hippocampal surface in 27 patients with MDD relative to hippocampus of 42 healthy comparison subjects]]
==Abstract==
The long term goal of Computational Anatomy (CA) is to create algorithmic tools that aid basic and
clinical neuroscientists in the analysis of variability in anatomical structures at different scales. The
difficulty is the complexity of anatomical substructures and the large variation across subjects. It is
proposed to develop an open-source pipeline for 3D statistical shape analysis of anatomical
variations from a population of anatomical structures. The overall aim is to integrate 3D Slicer
application and ITK software library with the statistical shape analysis pipeline being disseminated by
the Biomedical Informatics Research Network and thus enable the wider neuroimaging community to
efficiently analyze anatomical variations in disease. The first aim is to standardize shape deformation
vectors generated by several CA methods such as the Large Deformation Diffeomorphic Metric
Mapping (LDDMM) developed at the Center for Imaging Science at Johns Hopkins University and the
Finite Element Method for Deformable Registration (FEMDR) used in ITK. This will allow shape
vectors to be used by both global metric classifier analysis in classifying diseased shapes and
Gaussian Random Field (GRF) model analysis in localizing shape changes in disease. The two
methods will be unified to provide a new metric classifier based on the data generated by GRF. In the
final stage, hypothesis testing will be used to correlate global metric classification with localized
shape changes. The second aim is to construct anatomical atlases needed for analysis of shape
vectors. These atlases will be generated from segmented hippocampal and amygdala structures in
already acquired populations of children, adolescents and young adults in neuroimaging studies of
major depression disorder (MDD) at Washington University at St Louis. As a major public health
burden, MDD provides the biological testbed for the pipeline from which probabilistic atlases will be
generated. The third aim is to integrate the software libraries with the pipeline by leveraging the
power and flexibility of the 3D Slicer software and ITK libraries developed by NA-MIC, Kitware and
others. The fourth aim is to implement modules for visualization of the analysis of shape vectors in 3D
Slicer. The fifth aim is to implement a stand-alone version of Medical Reality Markup Language
(MRML) independent of 3D Slicer. This will allow for the propagation of MRML as a standard format
for future neuroimaging applications.

==Grant#==
R01EB008171

==Key Personnel==
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the JHU: Michael Miller, PI, Joe Hennessey
*[http://www.imaging.wustl.edu/NIL/ The Neuroscience Imaging Laboratory] Washington University St. Louis
*NA-MIC: Stephen Aylward, Will Schroeder, Michel Audette ([http://www.kitware.com/ Kitware])

==Funding Duration==
05/21/2009-02/28/2013

Paraview Support for Computational Anatomy

2010-06-03T18:06:43Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK-based processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T18:06:27Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data types and file formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T18:02:17Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU CIS the work done so far at Kitware on KWScene, in relation to the data and formats routinely used in their Computational Anatomy research, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T18:01:32Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, in relation to JHU CIS data and formats routinely used in Computational Anatomy, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T18:00:10Z

MichelKitware: /* Key Investigators */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
* Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T17:59:24Z

MichelKitware: /* Key Investigators */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
# Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T17:58:55Z

MichelKitware: /* Key Investigators */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
# Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing. This library will facilitate Paraview use in the computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. In addition, support for this library is being built into Paraview, the platform of interaction of the CIS group. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T17:57:54Z

MichelKitware: /* Key Investigators */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
# Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing, in order to for Paraview use in computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. In addition, support for this library is being built into Paraview, the platform of interaction of the CIS group. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T17:53:15Z

MichelKitware: /* Key Investigators */

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Luis Ibanez, Julien Finet, Andinet Enquobahrie, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
# Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing, in order to support computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. In addition, support for this library is being built into Paraview, the platform of interaction of the CIS group. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T17:52:11Z

MichelKitware:

__NOTOC__
* Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
# Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing, in order to support computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. In addition, support for this library is being built into Paraview, the platform of interaction of the CIS group. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>

Paraview Support for Computational Anatomy

2010-06-03T17:51:49Z

MichelKitware: /* Delivery Mechanism */

__NOTOC__
#Implemented in conjunction with proposal ''3D Shape Analysis for Computational Anatomy''

==Key Investigators==
* Kitware: Michel Audette, Stephen Aylward, Will Schroeder
* Johns Hopkins: Michael Bowers, Anthony Kolasny, Michael Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
# Enable Paraview to support VTK-based visualization and ITK-based processing for 3D Shape Analysis Computational Anatomy.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Anatomical components to be manipulated as a scene composed of MRML nodes, e.g.: VolumeNode, ModelNode, etc.
# Interaction possible between Slicer and Paraview.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A new library, KWScene, is being developed based on the MRML standard to support scene graph-type manipulation of volume and surface primitives for VTK-based visualization and ITK-based processing, in order to support computation pipeline and visualization of Computational Anatomy research at Johns Hopkins Center for Imaging Science. In addition, support for this library is being built into Paraview, the platform of interaction of the CIS group. Reading and serialization is compatible with Slicer scenes.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

Summer Project Week will be used to demonstrate to JHU the work done so far at Kitware on KWScene, and to develop a VTK-plugin mechanism for ITK processing on Paraview.

==References==
* http://www.paraview.org/
* Mirza Faisal Beg, Michael I. Miller, Alain Trouvé, Laurent Younes: Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision 61(2): 139-157 (2005)
* Grenander, U. and Miller, M. I. 1998. Computational anatomy: an emerging discipline. Q. Appl. Math. LVI, 4 (Dec. 1998), 617-694.
</div>