2014 Summer Project Week:Slicer Murin Shape Analysis - Revision history

Muratmaga at 15:46, 24 June 2014

2014-06-24T15:46:30Z

2014-06-24T15:37:52Z

2014-06-24T15:36:06Z

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@@ Line 19: / Line 19: @@
 <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>
-[[Image:OPT Crossection.PNG|100px]]
+[[Image:OPT Crossection.PNG|100px]] [[Image:Registered mCT scans.png|100px]]
 <li> Shape Analysis
 <ul>

@@ Line 52: / Line 52: @@
 <li>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.
 <li>The coordinates of the slid landmarks will be saved into a new fiducial list, from which the GPA analysis can be conducted.</b>
 </ul>
 </ul>

@@ Line 58: / Line 58: @@
 <h3>Progress</h3>
 <ul>
-<li> Generalized Procrustes Alignment</li>
+<li> Generalized Procrustes Alignment (implemented)</li>
-<li> Principal Component and Singular Value Decomposition of the Procrustes aligned coordinates</li>
+<li> Principal Component and Singular Value Decomposition of the Procrustes aligned coordinates (implemented)</li>
-<li> 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).</li>
+<li> Thin Plate Spline visualization of the shape variables from PCA and/or SVD (implemented).</li>
 </ul>

@@ Line 31: / Line 31: @@
 <li> Goals for Project Week:
 <ul>
-<li>Meet the community and learn
+<li> Meet the community and learn from them!
-<li>Implement the landmark based Procrustes Analysis in Slicer
+<li> Raise awareness about issues in using Slicer in high-resolution small animal imaging.
 </ul>
@@ Line 46: / Line 47: @@
 [[Image:TPS.png|400px]])</li>
-<li> <b>Ability to create semi-landmarks to increase spatial coverage. </b>
+<li> <b>Ability to create semi-landmarks to increase coverage in regions where anatomial landmarks are sparse. </b>
 <ul>
 <li><b>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)

@@ Line 43: / Line 43: @@
 <ul>
 <li>Implement GPA/PCA shape analysis in python</li>
-<li>Visualize the deformation of a reference volume along the principle components using thin plate splines([[Image:TPS.png|400px]])</li>
+<li>Provide an interactive tool to visualize the decomposition along the principle components of shape variation using thin plate splines.<br>
 <li> <b>Ability to create semi-landmarks to increase spatial coverage. </b>

@@ Line 42: / Line 42: @@
 <h3>Approach, Plan</h3>
 <ul>
-<li>Impliment GPA/PCA shape analysis in python</li>
+<li>Implement GPA/PCA shape analysis in python</li>
 <li>Visualize the deformation of a reference volume along the principle components using thin plate splines([[Image:TPS.png|400px]])</li>

@@ Line 24: / Line 24: @@
 <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. <br>
-([[Image:Fetus variation picture.PNG|200px]])
+[[Image:Fetus variation picture.PNG|400px]]
 </ul>

@@ Line 12: / Line 12: @@
 <ul>
 <li> Face is the major diagnostic feature to identify
-<li> But brain and the CNS are affected primarily()
+<li> Brain and the CNS are affected primarily.
 </ul>
-<li> Modalities: <b> Optical Projection Tomography</b> [[File:Sample OPT Mouse embryo.zip]]    <br>[[Image:OPT Crossection.PNG|100px]]<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]])
+  <B> Micro Computed Tomography </b> [[File:Stained registered sample mCT.zip]] <br>\
 <ul>
 <li>We use landmarks to identify the anatomical regions across our samples which vary hugely in development.

@@ Line 1: / Line 1: @@
 ==Key Investigators==
-* Murat Maga
+* Murat Maga (Seattle Children's Research Institute & University of Washington Dept. of Pediatrics)
-* Ryan Young
+* Ryan Young (Seattle Children's Research Institute)
@@ Line 12: / Line 12: @@
 <ul>
 <li> Face is the major diagnostic feature to identify
-<li> But brain and the CNS are affected primarily([[File:Sample OPT Mouse embryo.zip]])
+<li> But brain and the CNS are affected primarily()
 </ul>
-<li> Modalities: Optical Projection Tomography([[Image:OPT Crossection.PNG|100px]]) & Micro Computed Tomography ([[File:Stained registered sample mCT.zip]])
+<li> Modalities: <b> Optical Projection Tomography</b> [[File:Sample OPT Mouse embryo.zip]]    <br>[[Image:OPT Crossection.PNG|100px]]<br>
 <ul>
 <li>We use landmarks to identify the anatomical regions across our samples which vary hugely in development.