Documentation/Nightly/Extensions/SkeletalRepresentation

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.

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  Icon of the extension

Modules

• Skeletal Representation Initializer
• Skeletal Representation Optimizer
• Skeletal Representation Visualizer

Use Cases

Sample data can be found here.

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  The surface mesh of hippocampus

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  Visualize the s-rep of the hippocampus

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  Initialize the s-rep of the hippocampus

Tutorials

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  Tutorial for visualization

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  Tutorial for initialization

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  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