Projects/Slicer3/2007 Project Week Support for electron microscopy - Revision history

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2007-06-29T07:53:36Z

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Wbsmith at 21:46, 8 June 2007

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Wbsmith at 21:42, 8 June 2007

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Wbsmith at 21:40, 8 June 2007

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Wbsmith at 21:23, 8 June 2007

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{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* UCSD/NCMIR: W. Bryan Smith, Mark Ellisman
* Isomics: Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Dendritic spines are the primary sites of excitatory neuronal communication in the brain. It is of fundamental interest to cellular neurobiologists to understand how the number, size, and shape of dendritic spines varies across brain regions, and as a function of experimental treatment within a given region. We would like to assess morphological properties of spines using Slicer.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Spines have been manually segmented from tilt-series electron tomograms. The spines need to be registered to a common coordinate system, and then a variety of measurements must be made on the size and shape of each spine in an effort to cluster the spines according to their morphologies.

The plan for the project week is to first try out 3D skeletonization filters in ITK to define the medial axis of each spine.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

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<br style="clear: both;" />

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===References===
* Insert some refs here

@@ Line 32: / Line 32: @@
 <h1>Progress</h1>
-* Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
+* Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]), but it creates planes rather than lines in parts of some spines.
 * Obtained code from Martin Styner (via Stephen Aylward).  Will implement and see if works.

@@ Line 32: / Line 32: @@
 <h1>Progress</h1>
-Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
+* Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
 but it creates planes rather than lines in parts of some spines.
-Obtained code from Martin Styner (via Stephen Aylward).  Will implement and see if works.
+* Obtained code from Martin Styner (via Stephen Aylward).  Will implement and see if works.
-Suggestion to try CorCTA module in Slicer2; Crashes
+* Suggestion to try CorCTA module in Slicer2; Crashes
 </div>

← Older revision		Revision as of 07:52, 29 June 2007
Line 35:		Line 35:
	but it creates planes rather than lines in parts of some spines.		but it creates planes rather than lines in parts of some spines.

		+	Obtained code from Martin Styner (via Stephen Aylward). Will implement and see if works.

		+	Suggestion to try CorCTA module in Slicer2; Crashes

	</div>		</div>

← Older revision		Revision as of 07:45, 29 June 2007
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	<h1>Progress</h1>		<h1>Progress</h1>
		+	Attempted itk::BinaryThinningImageFilter ([http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html Doxygen Link]),
		+	but it creates planes rather than lines in parts of some spines.

@@ Line 1: / Line 1: @@
 {|
 |[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
-|[[Image:Spines01.jpg|thumb|320px]]
+|[[Image:Spines01.jpg|thumb|320px|A small fragment of a dendrite (gray) with segmented spines (color).]]
-|[[Image:SpineSample.jpg|thumb|520px]]
+|[[Image:SpineSample.jpg|thumb|520px|A sample of spines plotted into individual axes.]]
 |}