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NA-MIC Project Weeks

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SlicerMorph Geometric Morphometric Toolset

Key Investigators

Project Description

This project aims to produce a flexible toolset for analysis of shape and form from image data using landmark-based Geometric Morphometric Methods (GMM). This toolset will be capable of handling a broad range of data and file types and will provide support for the full analysis workflow within 3D Slicer.


  1. Develop a Slicer extension with modules to support each task in the shape analysis workflow from image import through visualization of statistical output.

Approach and Plan

  1. Provide image import tools that support a broad range of image modalities and filetypes, including non-DICOM image outputs from research microCT scanners.
  2. Support common preprocessing steps, that may be required before analysis, including downsampling very large files produced by research microCT scanners.
  3. Develop a module to implement Generalized Procrustes Analysis (GPA) and Principal Component Analysis (PCA) and visualize output statistics.

Progress and Next Steps

  1. Custom image import tool
  2. Custom landmark file import tool
  3. Module to downsize images on import, optimized for speed.
  4. Module to downsize images on import, optimized for memory usage.
  5. Module to load large images, crop blank space, and saving ROI.
  6. Module to perform GPA, PCA, and visualize statistical output


  1. Added custom layout and display refinements
  2. Tested GPA module and fixed bugs
  3. Discussed method for comparing original volume to PCA warped volume. Each will be shown in one of the 3D volume viewers and a button will be added to toggle view.
  4. Discussed improving 2D vector plots. Plan to implement in VTK and add functionality to Slicer.


SlicerMorph GPA Screenshot SlicerMorph GPA Screenshot2

Background and References