Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis

Christian Herz; Nicolas Vergnet; Sijie Tian; Abdullah H. Aly; Matthew A. Jolley; Nathanael Tran; Gabriel Arenas; Andras Lasso; Nadav Schwartz; Kathleen E. O’Neill; Paul A. Yushkevich; Alison M. Pouch

doi:10.1117/1.JMI.11.3.036001

14 May 2024 Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis

Christian Herz, Nicolas Vergnet, Sijie Tian, Abdullah H. Aly, Matthew A. Jolley, Nathanael Tran, Gabriel Arenas, Andras Lasso, Nadav Schwartz, Kathleen E. O’Neill, Paul A. Yushkevich, Alison M. Pouch

Author Affiliations +

Journal of Medical Imaging, Vol. 11, Issue 3, 036001 (May 2024). https://doi.org/10.1117/1.JMI.11.3.036001

Abstract

Purpose

Deformable medial modeling is an inverse skeletonization approach to representing anatomy in medical images, which can be used for statistical shape analysis and assessment of patient-specific anatomical features such as locally varying thickness. It involves deforming a pre-defined synthetic skeleton, or template, to anatomical structures of the same class. The lack of software for creating such skeletons has been a limitation to more widespread use of deformable medial modeling. Therefore, the objective of this work is to present an open-source user interface (UI) for the creation of synthetic skeletons for a range of medial modeling applications in medical imaging.

Approach

A UI for interactive design of synthetic skeletons was implemented in 3D Slicer, an open-source medical image analysis application. The steps in synthetic skeleton design include importation and skeletonization of a 3D segmentation, followed by interactive 3D point placement and triangulation of the medial surface such that the desired branching configuration of the anatomical structure’s medial axis is achieved. Synthetic skeleton design was evaluated in five clinical applications. Compatibility of the synthetic skeletons with open-source software for deformable medial modeling was tested, and representational accuracy of the deformed medial models was evaluated.

Results

Three users designed synthetic skeletons of anatomies with various topologies: the placenta, aortic root wall, mitral valve, cardiac ventricles, and the uterus. The skeletons were compatible with skeleton-first and boundary-first software for deformable medial modeling. The fitted medial models achieved good representational accuracy with respect to the 3D segmentations from which the synthetic skeletons were generated.

Conclusions

Synthetic skeleton design has been a practical challenge in leveraging deformable medial modeling for new clinical applications. This work demonstrates an open-source UI for user-friendly design of synthetic skeletons for anatomies with a wide range of topologies.

Citation Download Citation

Christian Herz, Nicolas Vergnet, Sijie Tian, Abdullah H. Aly, Matthew A. Jolley, Nathanael Tran, Gabriel Arenas, Andras Lasso, Nadav Schwartz, Kathleen E. O’Neill, Paul A. Yushkevich, and Alison M. Pouch "Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis," Journal of Medical Imaging 11(3), 036001 (14 May 2024). https://doi.org/10.1117/1.JMI.11.3.036001

Received: 25 August 2023; Accepted: 18 April 2024; Published: 14 May 2024

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KEYWORDS

Deformation

Anatomy

Modeling

Image segmentation

3D modeling

Human-machine interfaces

Design

Purpose

Approach

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