SlicerSALT: ShapePopulationViewer for Skeletal Representations

Figure 1: ShapePopulationViewer displays s-reps of a hippocampi dataset.

We have added new functionality to the ShapePopulationViewer module in SlicerSALT for accepting skeletal representations (s-reps). Users can now use the “Add S-Rep Files” button to import s-rep files (in .xml format) into ShapePopulationViewer for viewing and interacting with multiple s-rep objects at the same time. These changes are available in SlicerSALT nightly packages starting from May 17th.

The s-rep is a form of skeletal model which is used to precisely model the structure of an anatomic object with no essential interior branches, providing a rich geometric representation with correspondence across cases. As demonstrated in the work by Pizer et al., s-reps can be well suited for probabilistic analysis. We are currently working to extend SlicerSALT with modules to perform such analysis. Once these modules are finished, together with the current s-rep modules and ShapePopulationViewer, users will be able to perform s-rep-based statistical shape analysis completely in SlicerSALT.

What is SlicerSALT

SlicerSALT is an open-source, free comprehensive software that will allow biomedical scientists to precisely locate shape changes in their imaging studies. SlicerSALT can be used to create 3D models from the landmarks and display them in various views. The software’s interface does not require a technical background to navigate, so researchers outside of computer science can use it for morphometry analysis. This software will enhance the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Potential fields of interest include pharmacology, neuroscience, paleontology and orthodontics. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies. As an offspring of 3D Slicer, SlicerSALT is free to download, and its code is open source. 

More information about SlicerSALT is available at

Current s-rep functionality in SlicerSALT

We have previously added three s-rep related modules which are categorized into “Skeleton, topology” under SlicerSALT. These modules can be used to perform s-rep-related operations on a single object. 

Module 1: “Skeletal Representation Initializer” can be used to initialize an s-rep by mean curvature flow of an object.

Module 2: “Skeletal Representation Refiner” can be used to refine an s-rep to fit an object boundary more precisely.

Module 3: “Skeletal Representation Visualizer” can be used to visualize an s-rep and its fit to the input object boundary.

For more guidance on how to used these modules, please refer to the SlicerSALT documentation.

SlicerSALT is an example of custom 3DSlicer applications that Kitware develops, funded by the National Institute of Biomedical Imaging and Bioengineering (NIBIB, grant R01EB021391). Contact us at to learn how we can help you integrate the 3DSlicer-based software into your research, processes and products.

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