Slicer Wiki - User contributions [en]

User:Zhiy

2019-10-23T01:20:40Z

Zhiy: update intro

My name is Zhiyuan Liu. It's a little bit hard to pronounce it. But the first name sounds like "J-one", while the last name "Leo". I'm a Ph.D student of the Dept. Computer Science in UNC at Chapel Hill, researching on shape analysis. I'm co-advised by Stephen M. Pizer, James N. Damon and J. S. Marron. My research interest mainly falls on the shape analysis, computer vision and machine learning. In the field of shape analysis, we are now researching skeletal model and making it more stable and powerful in shape analysis. Additionally, we also invented some statistical approaches that are suitable for both high dimension low sample size situation, such as shape analysis on biomedical images, and data objects living in non-Euclideanized space. Here, we are providing such methodology to the world by developing toolkit based on Slicer. Please refer to my [http://www.cs.unc.edu/~zhiy/ home page] for more information.

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-10-23T01:16:47Z

Zhiy: update terms

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' [http://www.cs.unc.edu/~zhiy/ Zhiyuan Liu] 
'''Contributors:''' Pablo Hernandez-Cerdan, [https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin], [https://www.kitware.com/beatriz-paniagua/ Beatriz Paniagua], [https://www.kitware.com/jared-vicory/ Jared Vicory], Junpyo Hong, [http://www.cs.unc.edu/~smp/ Stephen M. Pizer] 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to initialize, refine and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Initialize an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary 
* Visualize the s-rep
S-reps have a number of advantages in shape analysis of human organs. Some previous research has shown the superiority of using s-reps to perform hypothesis testing, classification and shape distribution analysis.
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Refiner
* Skeletal Representation Visualizer

== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
Srep_tutorial.png|Tutorial for initialization
Srep_tutorial.png|Tutorial for refinement
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.
* Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-10-23T01:16:27Z

Zhiy: update terminology of features in this extension

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' [http://www.cs.unc.edu/~zhiy/ Zhiyuan Liu] 
'''Contributors:''' Pablo Hernandez-Cerdan, [https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin], [https://www.kitware.com/beatriz-paniagua/ Beatriz Paniagua], [https://www.kitware.com/jared-vicory/ Jared Vicory], Junpyo Hong, [http://www.cs.unc.edu/~smp/ Stephen M. Pizer] 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to initialize, refine and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Initialize an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary 
* Visualize the s-rep
S-reps have a number of advantages in shape analysis of human organs. Some previous research has shown the superiority of using s-reps to perform hypothesis testing, classification and shape distribution analysis.
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
Srep_tutorial.png|Tutorial for initialization
Srep_tutorial.png|Tutorial for refinement
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.
* Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-10-23T01:11:29Z

Zhiy: add home page to contributors

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' [http://www.cs.unc.edu/~zhiy/ Zhiyuan Liu] 
'''Contributors:''' Pablo Hernandez-Cerdan, [https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin], [https://www.kitware.com/beatriz-paniagua/ Beatriz Paniagua], [https://www.kitware.com/jared-vicory/ Jared Vicory], Junpyo Hong, [http://www.cs.unc.edu/~smp/ Stephen M. Pizer] 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
Srep_tutorial.png|Tutorial for initialization
Srep_tutorial.png|Tutorial for refinement
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.
* Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-01-02T19:53:22Z

Zhiy: /* Tutorials */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
Srep_tutorial.png|Tutorial for initialization
Srep_tutorial.png|Tutorial for refinement
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.
* Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-01-02T19:52:58Z

Zhiy: /* References */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
Srep_tutorial.png|Tutorial for initialization
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.
* Source code can be found https://github.com/KitwareMedical/SlicerSkeletalRepresentation

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-01-02T19:50:01Z

Zhiy:

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
Srep_tutorial.png|Tutorial for initialization
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-01-02T19:43:55Z

Zhiy: /* Tutorials */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Tutorial for visualization
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

Documentation/Nightly/Extensions/SkeletalRepresentation

2019-01-02T19:32:22Z

Zhiy: /* Use Cases */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
Initialize.png|Initialize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Download tutorial
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

File:Initialize.png

2019-01-02T19:30:00Z

Zhiy: The result of initialization of an hippocampus surface mesh

The result of initialization of an hippocampus surface mesh

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2018-09-26T19:25:23Z

Zhiy: /* Shape Analysis */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
33 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_DICOM|DICOM]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Digital_Pathology|Digital Pathology]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Remote|Remote]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Virtual_Reality|Virtual Reality]]
* [[#Extensions_by_category_Web_System_Tools|Web System Tools]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest_Imaging_Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]]

== DICOM ==
* [[Documentation/Nightly/Extensions/DCMQI|DCMQI]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]]
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]]

== Digital Pathology ==
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]]

== Filtering ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]

== IGT ==
* [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer TrackerStabilizer]
* [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]]
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]]
* [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]]
* [[Documentation/Nightly/Extensions/iGyne|iGyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]]
* [[Documentation/Nightly/Extensions/mpReview|mpReview]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]]
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]


== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]]
* [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]]
* [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]]
* [[Documentation/Nightly/Extensions/PkModeling|PkModeling]]
* [[Documentation/Nightly/Extensions/ShapeVariationAnalyzer|ShapeVariationAnalyzer]]


== Radiotherapy ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis]
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis]

== Registration ==
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/MultiLevelRegistration|MultiLevelRegistration]]


== Remote ==
* [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]]

== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment]
* [http://www.nitrc.org/projects/abc ABC]
* [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice]
* [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]]
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects]
* [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation]
* [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect]
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/EasyClip|EasyClip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint PickAndPaintExtension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics MeshStatisticsExtension]
* [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SpharmPdm SPHARM-PDM]
* [[Documentation/Nightly/Extensions/SkeletalRepresentation|SkeletalRepresentation]]


== Tractography ==
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]]

== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]


==Virtual Reality==
* [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]]


== Web System Tools ==
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]]
__NOTOC__

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T18:07:23Z

Zhiy: /* Extension Description */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary
<gallery>
SkeletalRepresentation.png|Icon of the extension
</gallery>

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Download tutorial
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

File:SkeletalRepresentation.png

2018-09-26T18:06:50Z

Zhiy: The icon of SkeletalRepresentation extension. Credit to Beatriz Paniagua

The icon of SkeletalRepresentation extension. Credit to Beatriz Paniagua

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:58:48Z

Zhiy: Initial commit

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu

== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Download tutorial
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:56:40Z

Zhiy: /* Tutorials */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu
== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Download tutorial
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:55:48Z

Zhiy: /* Tutorials */

== Introduction and Acknowledgements ==
'''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the [https://www.slicer.org/ Slicer community]. 

'''Author:''' Zhiyuan Liu 
'''Contributors:''' Pablo Hernandez-Cerdan, Jean-Christophe Fillion-Robin, Beatriz Paniagua, Jared Vicory, Junpyo Hong, Stephen M. Pizer 
'''Contact:''' Zhiyuan Liu, zhiy at cs dot unc dot edu
== Extension Description ==
This extension is an open source tool to establish, optimize and visualize [http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf skeletal representation] (abbreviated as s-rep) of 3D objects in biomedical images. The main features of this extension include: 
* Establish an s-rep by mean curvature flow of an object boundary 
* Refine an s-rep to fit an object boundary

== Modules ==
* Skeletal Representation Initializer
* Skeletal Representation Optimizer
* Skeletal Representation Visualizer
== Use Cases ==
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here]. 
<gallery>
Hippo_mesh.png|The surface mesh of hippocampus
New_srep.png|Visualize the s-rep of the hippocampus
</gallery>

== Tutorials ==
<gallery>
Srep_tutorial.png|Download the tutorial
</gallery>

== Similar Extensions ==
NA
== References ==
* Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "[http://midag.cs.unc.edu/pubs/papers/xavier_book_2019.pdf Object Shape Representation via Skeletal Models (s-reps) and Statistical Analysis]" in Riemannian Geometric Statistics in Medical Image Analysis, no. (Xavier Pennec, Stefan Sommer, and Tom Fletcher, eds.), 2019.

File:Srep tutorial.png

2018-09-26T17:54:37Z

Zhiy:

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:51:45Z

Zhiy: /* Use Cases */

File:Hippo mesh.png

2018-09-26T17:50:54Z

Zhiy:

File:New srep.png

2018-09-26T17:48:34Z

Zhiy:

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:39:47Z

Zhiy: /* References */

User:Zhiy

2018-09-26T17:36:22Z

Zhiy:

I'm a Ph.D student of the Dept. Computer Science in UNC at Chapel Hill, researching on shape analysis. I'm advised by Stephen M. Pizer Ph.D. My research interest mainly falls on the shape analysis, computer vision and machine learning. In the field of shape analysis, we are now researching skeletal model and making it more stable and powerful in shape analysis. Additionally, we also invented some statistical approaches that are suitable for both high dimension low sample size situation, such as shape analysis on biomedical images, and data objects living in non-Euclideanized space. Here, we are providing such methodology to the world by developing toolkit based on Slicer.

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:18:55Z

Zhiy: /* Use Cases */

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T17:08:51Z

Zhiy: /* Extension Description */

Documentation/Nightly/Extensions/SkeletalRepresentation

2018-09-26T16:57:31Z

Zhiy: Created page with "== Introduction and Acknowledgements == '''Acknowledgements:''' This work is part of Slicer Shape Analysis Toolbox ([http://salt.slicer.org/ SlicerSALT]), funded by NIH NIBIB..."