SlicerSALT for Biomedical and Biomechanical Research

Speakers: Beatriz Paniagua

Workshop Description

Quantitative morphologic assessment of individual anatomical structures in Medical Imaging is often based on volumetric measurements.Volume changes are intuitive features as they might explain atrophy or dilation due to illness. On the other hand, structural changes at specific locations are not sufficiently reflected in volume measurements. Shape analysis has thus become of increasing interest to the Medical Imaging community due to its potential to precisely locate morphological changes between healthy and pathological structures.

Slicer Shape AnaLysis Toolbox (SlicerSALT) is an open-source, free comprehensive software that allows biomedical scientists to precisely locate shape changes in their imaging studies. SlicerSALT enhances the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies.

In this course we present best practices for taking advantage of SlicerSALT in any morphologic biomedical research. We will first show how each one of the different SlicerSALT modules work and how they can be used for morphometric imaging research. We will then provide data examples that will be used in interactive hands-on-demos that attendees can run on their laptops during the course. We will also cover the opportunities and challenges while performing shape analysis accurately for research applications.

Finally, we will support this learning experience with excellent, multidisciplinary, multimedia training materials oriented to teach new users of SlicerSALT about the methodology and how to apply it, regardless of scientific background.

Learning Outcomes

Introduction to SlicerSALT, its user interface and all the different functionality. Usage of SlicerSALT via its interactive, graphic interface or via non-interactive scripting Processing medical images using SlicerSALT methods Establishing a lasting, high-quality shape representation and analysis development foundation for any research projects

Intended Audience

 * Graduate students and faculty in biomedical engineering or computer science working on biomechanical modeling or related disciplines

* Engineers, software developers, and laboratory technologists and managers in academic and commercial settings where shape analysis is used to solve biomedical and biomechanical questions

Course Level

First half is introductory, with a focus on basic shape analysis research and methods as well as introduction to SlicerSALT GUI and simple non-interactive scripts (basic familiarity with Python scripting is needed). Second half is oriented towards understanding how to run SlicerSALT, and it will cover in detail necessary inputs, outputs and how to perform interpretation of results.


 * Beatriz Paniagua (Ph.D., Technical Lead, Kitware) serves as Principal Investigator of SlicerSALT. She has taught numerous hands-on-workshops to clinicians using Slicer products. She also leads academic and commercial projects at Kitware, using shape analysis to solve challenging, practical problems.