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. 2023 Oct:14350:201-210.
doi: 10.1007/978-3-031-46914-5_16. Epub 2023 Oct 31.

SlicerSALT: From Medical Images to Quantitative Insights of Anatomy

Jared Vicory  1 , Ye Han  1 , Juan Carlos Prieto  2 , David Allemang  1 , Mathieu Leclercq  2 , Connor Bowley  1 , Harald Scheirich  1 , Jean-Christophe Fillion-Robin  1 , Steve Pizer  2 , James Fishbaugh  1 , Guido Gerig  3 , Martin Styner  2 , Beatriz Paniagua  1
Affiliations

SlicerSALT: From Medical Images to Quantitative Insights of Anatomy

Jared Vicory et al. Shape Med Imaging (2023). 2023 Oct.

Abstract

Three-dimensional (3D) shape lies at the core of understanding the physical objects that surround us. In the biomedical field, shape analysis has been shown to be powerful in quantifying how anatomy changes with time and disease. The Shape AnaLysis Toolbox (SALT) was created as a vehicle for disseminating advanced shape methodology as an open source, free, and comprehensive software tool. We present new developments in our shape analysis software package, including easy-to-interpret statistical methods to better leverage the quantitative information contained in SALT's shape representations. We also show SlicerPipelines, a module to improve the usability of SALT by facilitating the analysis of large-scale data sets, automating workflows for non-expert users, and allowing the distribution of reproducible workflows.

Keywords: Open-source software; Shape analysis; Statistics.

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Figures

Fig. 1.
Fig. 1.
Skeletal representations module in SlicerSALT with an s-rep visualization.
Fig. 2.
Fig. 2.
Corresponding femur models computed via registration-based correspondence. Similar coloring at similar anatomical locations show the quality of the correspondence.
Fig. 3.
Fig. 3.
ShapePopulationViewer displaying a set of 15 s-reps.
Fig. 4.
Fig. 4.
A screenshot of the SVA module in SlicerSALT. The left panel shows controls, the middle shows a mean shape (gray, transparent) alongside a shape (blue) deformed along its first principal component, and the right shows a PCA scree plot. (Color figure online)
Fig. 5.
Fig. 5.
The Tutorials panel showing a link to an online tutorial as well as sample data download buttons.
See this image and copyright information in PMC

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