Difference between revisions of "2014 Summer Project Week:Slicer Murin Shape Analysis"

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<li> Modalities: <b> Optical Projection Tomography</b> [[File:Sample OPT Mouse embryo.zip]]    <br>
 
<li> Modalities: <b> Optical Projection Tomography</b> [[File:Sample OPT Mouse embryo.zip]]    <br>
  <B> Micro Computed Tomography </b> [[File:Stained registered sample mCT.zip]] <br>\
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  <B> Micro Computed Tomography </b> [[File:Stained registered sample mCT.zip]] <br>
 
[[Image:OPT Crossection.PNG|100px]]
 
[[Image:OPT Crossection.PNG|100px]]
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<li> Shape Analysis
 
<ul>
 
<ul>
<li>We use landmarks to identify the anatomical regions across our samples which vary hugely in development.  
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<li>We use landmarks to identify the anatomical regions across our developmental series of fetal samples.  
<li>We want to be able segment brains from about 600 volumes and do a coupled analysis of facial and brain phenotypes ([[Image:Fetus variation picture.PNG|200px]]).
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<li>We want to be able segment brains from about 600 volumes and do a coupled analysis of facial and brain phenotypes. <br>
 +
([[Image:Fetus variation picture.PNG|200px]])  
 
</ul>
 
</ul>
  

Revision as of 15:18, 24 June 2014

Home < 2014 Summer Project Week:Slicer Murin Shape Analysis

Key Investigators

  • Murat Maga (Seattle Children's Research Institute & University of Washington Dept. of Pediatrics)
  • Ryan Young (Seattle Children's Research Institute)


Project Description

  • Research: Changes in development due to Fetal Alcohol Exposure and how this affects the development of the craniofacial complex.
    • Face is the major diagnostic feature to identify
    • Brain and the CNS are affected primarily.
    • What's the earliest time we begin to detect changes in the face?
    • How does the brain volumes (and gross morphology) relate to changes in the face?
  • Modalities: Optical Projection Tomography File:Sample OPT Mouse embryo.zip
    Micro Computed Tomography File:Stained registered sample mCT.zip
    OPT Crossection.PNG
  • Shape Analysis
    • We use landmarks to identify the anatomical regions across our developmental series of fetal samples.
    • We want to be able segment brains from about 600 volumes and do a coupled analysis of facial and brain phenotypes.
      (Fetus variation picture.PNG)
  • Challenges in Slicer with our datasets due to small voxel sizes (6-35 micron). Specifically visualization, recording coordinates of anatomical landmarks, segmentation and registration. (File:Project week question.txt)
  • Goals for Project Week:
    • Meet the community and learn
    • Implement the landmark based Procrustes Analysis in Slicer


    Objective

    • Create a GPA/PCA shape analysis and visualization module for Slicer.
  • Approach, Plan

    • Impliment GPA/PCA shape analysis in python
    • Visualize the deformation of a reference volume along the principle components using thin plate splines(TPS.png)
    • Ability to create semi-landmarks to increase spatial coverage.
      • User will a uniformly sampled point cloud by entering the number of semi-landmarks. Existing “hard” landmarks will be used for their distribution. This will serve as the template to be transferred to all remaining volumes (atlas)
      • The template will be transferred to a new surface. Existing “hard” landmarks will allow for correspondence. The transferred points will then be moved along the surface of the volume by optimizing the bending energy function.
      • The coordinates of the slid landmarks will be saved into a new fiducial list, from which the GPA analysis can be conducted.

    Progress

    • Generalized Procrustes Alignment
    • Principal Component and Singular Value Decomposition of the Procrustes aligned coordinates
    • Thin Plate Spline visualization of the shape variables from PCA and/or SVD (by either morphing a reference volume along the shape variable, or visualizing the TPS grid using Transformation Visualizer module).

    File:PowerPoint.pdf