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SlicerSALT

Key Investigators

  • Beatriz Paniagua (Kitware)
  • Jean-Christophe Fillion-Robin (Kitware)
  • Jared Vicory (Kitware)
  • Laura Pascal (Kitware)
  • Junpyo Hong (University of North Carolina)
  • Chao Huang (University of North Carolina)
  • Juan Carlos Prieto (University of North Carolina)
  • Mahmoud Mostapha (University of North Carolina)
  • Zhiyuan Liu (University of North Carolina)
  • Loïc Michoud (University of Michigan)
  • James Fishbaugh (NYU Tandon School of Engineering)

Project Description

Slicer Shape AnaLysis Toolbox (SlicerSALT) is the dissemination vehicle of powerful shape analysis methodology based on 3D Slicer open-source software. SlicerSALT will enhance the intuitiveness and ease of use 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.

SlicerSALT will be used to:

  • Compute Point Distributed Models (PDM) using Spherical Harmonic Representation on spherical topology objects (Extension alrealdy available in SlicerSALT: SPHARM-PDM Extension)
  • Compute estimating shape correspondence for population of objects with complex topology
  • Run 4D regression in a collection of 3D PDMs associated to a linear variable (i.e. age) (Extension soon available in SlicerSALT: Shape Regression Extension)
  • Perform correspondence optimization using study-wise shape analysis
  • Fit skeletal representations (s-reps) to a collection of binary volumes
  • Compute image-based correspondence in binary volumes of different topologies

Objective

  1. Work on the new SlicerSALT release
  2. Work on the methodology for the estimation of shape correspondence for population of objects with complex topology

Approach and Plan

  1. SlicerSALT's Project:
  • Update of the Slicer version used by SlicerSALT to the new release
  • Incorporation of Shape Regression Extension in the new SlicerSALT release
  • Test of the new extensions
  1. Project for the estimation of shape correspondence for population of objects with complex topology:
  • Comparison of the three methods already existing
  • Investigation in order to universalize the Deformetrica method (issue with the use of Cuda/GPU)
  • Investigation in order to find a more efficient method (new tools, new algorithms, etc..)

Progress and Next Steps

  • Update of the Slicer version used by SlicerSALT to the new release
  • Shape Regression Extension:
    • Fixing of some bugs on the shape regression computation
    • Adding of some tests
    • Test of the slicer extension package on Windows and Mac (Issue on Linux) -> Almost ready to be integrated in SlicerSALT
  • Estimation of shape correspondence for population of objects with complex topology:
    • Comparison of the three methods already existing
    • Abandon of the ThinShellDemon method due to the generated results not enough accurate
    • Next Steps:
      • Improvement of the Deformetrica method in order to accelerate the computation
      • Tests on new data

Illustrations

Shape Regression Extension:

Estimation of shape correspondence for population of objects with complex topology:

Background and References