Difference between revisions of "Documentation/Nightly/Extensions/SkeletalRepresentation"
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== Extension Description == | == Extension Description == | ||
| − | This extension is an open source tool to | + | 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:<br /> |
| − | * | + | * Initialize an s-rep by mean curvature flow of an object boundary<br /> |
| − | * Refine an s-rep to fit an object boundary | + | * Refine an s-rep to fit an object boundary<br /> |
| + | * 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> | <gallery> | ||
SkeletalRepresentation.png|Icon of the extension | SkeletalRepresentation.png|Icon of the extension | ||
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== Modules == | == Modules == | ||
* Skeletal Representation Initializer | * Skeletal Representation Initializer | ||
| − | * Skeletal Representation | + | * Skeletal Representation Refiner |
* Skeletal Representation Visualizer | * Skeletal Representation Visualizer | ||
| + | |||
== Use Cases == | == Use Cases == | ||
Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here].<br /> | Sample data can be found [https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/master/SkeletalRepresentationVisualizer/Testing/test_data/hippo.m3d here].<br /> | ||
Latest revision as of 01:16, 23 October 2019
Home < Documentation < Nightly < Extensions < SkeletalRepresentationContents
Introduction and Acknowledgements
Acknowledgements: This work is part of Slicer Shape Analysis Toolbox (SlicerSALT), funded by NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects), as well as the 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 initialize, refine and visualize 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.
Icon of the extension
Modules
- Skeletal Representation Initializer
- Skeletal Representation Refiner
- Skeletal Representation Visualizer
Use Cases
Sample data can be found here.
The surface mesh of hippocampus
Visualize the s-rep of the hippocampus
Initialize the s-rep of the hippocampus
Tutorials
Tutorial for visualization
Tutorial for initialization
Tutorial for refinement
Similar Extensions
NA
References
- Stephen M. Pizer, Junpyo Hong, Jared Vicory, J. S. Marron, and others, "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
