MedianTexture - Revision history

Palani at 23:32, 24 June 2010

2010-06-24T23:32:12Z

Arnaudgelas at 22:38, 20 June 2010

2010-06-20T22:38:09Z

Palani at 22:14, 20 June 2010

2010-06-20T22:14:17Z

Megason at 15:04, 10 June 2010

2010-06-10T15:04:44Z

Megason: Created page with 'sdasd'

2010-06-10T15:04:03Z

Created page with 'sdasd'

New page

sdasd

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 __NOTOC__
 <gallery>
 Image:2TS0005_stack0001frame0005.png|Original PCNA-GFP fluorescence confocal microscope image for cell cycle marker studies.
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 Image:Mask_2TS0005_-1NU.png|MBP Non-Uniform pattern class.
 </gallery>
 ==Key Investigators==
@@ Line 49: / Line 49: @@
 <h3>Progress</h3>
-We have completed C++ and Matlab implementation of 2D median binary patterns and have a preliminary ITK version that needs to be tested and evaluated for correctness. Histograms of MBPs can be plotted using VTK widgets.
+We have completed C++ and Matlab implementation of 2D median binary patterns and have a preliminary ITK version that needs to be tested and evaluated for correctness.
 </div>

@@ Line 1: / Line 1: @@
 __NOTOC__
-[[File:MBP-definition.jpg|400px|thumb|left|Definition of MBP]]]
+[[File:MBP-definition.jpg|400px|thumb|left|Definition of MBP]]
 <gallery>
 Image:2TS0005_stack0001frame0005.png|Original PCNA-GFP fluorescence confocal microscope image for cell cycle marker studies.

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
+Image:2TS0005_stack0001frame0005.png|Original PCNA-GFP fluorescence confocal microscope image for cell cycle marker studies.
-Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
+Image:FGPAC_mask_101iter_stack0001frame0005.png|Multiphase GPAC segmentation mask.
-Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
+Image:Masked-bkg mbp+2.png|Distribution of MBPs shown with each pattern mapped to a unique color.
 </gallery>
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* ENSI-Bourges, France: Lucas Menand, Sarah Portugais, Adel Hafiane
-* Utah: Tom Fletcher, Ross Whitaker
+* Air Force Research Lab: Guna Seetharaman
 <div style="margin: 20px;">
-<div style="width: 27%; float: left; padding-right: 3%;">
+<div style="width: 40%; float: left; padding-right: 3%;">
 <h3>Objective</h3>
-We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
+Median binary patterns (MBP) are robust feature descriptors for characterizing natural and biological textures. MBPs can be used for cell segmentation, characterizing nuclei and membrane textures and for cell classification.
 </div>
-<div style="width: 27%; float: left; padding-right: 3%;">
+<div style="width: 40%; float: left; padding-right: 3%;">
 <h3>Approach, Plan</h3>
+MBPs is a robust alternative to the local binary pattern (LBP) texture descriptors that uses the local median instead of the central pixel intensity as the reference value to create a binary pattern. MBPs (and LBPs) have the attractive properties of noise-resistance, rotation invariance and shift-invariance and provide a powerful feature set for cell segmentation and classification. Using a 3x3 median window there are nine special median uniform patterns and a set of non-uniform patterns that we assign to a separate category.
 </div>
@@ Line 43: / Line 49: @@
 <h3>Progress</h3>
-Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
+We have completed C++ and Matlab implementation of 2D median binary patterns and have a preliminary ITK version that needs to be tested and evaluated for correctness. Histograms of MBPs can be plotted using VTK widgets.
 </div>
@@ Line 53: / Line 57: @@
 ==Delivery Mechanism==
-This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
+This work will be delivered to the NA-MIC Kit as an:
 #ITK Module
 ==References==
-*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
+*A. Hafiane, G. Seetharaman, K. Palaniappan, B. Zavidovique, “Rotationally invariant hashing of median patterns for texture classification”, Lecture Notes in Computer Science (ICIAR), Vol. 5112, 2008, pp. 619-629. <http://www.ncbi.nlm.nih.gov/pubmed/19116672>
-* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
-* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
+*A. Hafiane, Seetharaman, G., Zavidovique, B.: Median binary pattern for textures classification. Lecture Notes in Computer Science CIAR, 2007, pp. 387–398.
-* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
 </div>

← Older revision		Revision as of 15:04, 10 June 2010
Line 1:		Line 1:
−	~~sdasd~~	+	__NOTOC__
		+	<gallery>
		+	Image:PW-MIT2010.png\|[[2010_Summer_Project_Week#Projects\|Projects List]]
		+	Image:genuFAp.jpg\|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
		+	Image:genuFA.jpg\|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
		+	</gallery>
		+
		+	==Instructions for Use of this Template==
		+	#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
		+	#Copy the entire text of this page into the page created above
		+	#Link the created page into the list of projects for the project event
		+	#Delete this section from the created page
		+	#Send an email to tkapur at bwh.harvard.edu if you are stuck
		+
		+	==Key Investigators==
		+	* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
		+	* Utah: Tom Fletcher, Ross Whitaker
		+
		+	<div style="margin: 20px;">
		+	<div style="width: 27%; float: left; padding-right: 3%;">
		+
		+	<h3>Objective</h3>
		+	We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
		+
		+
		+
		+
		+
		+
		+	</div>
		+
		+	<div style="width: 27%; float: left; padding-right: 3%;">
		+
		+	<h3>Approach, Plan</h3>
		+
		+	Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.
		+
		+	Our plan for the project week is to first try out <bar>,...
		+
		+	</div>
		+
		+	<div style="width: 40%; float: left;">
		+
		+	<h3>Progress</h3>
		+	Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure\|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
		+
		+
		+	</div>
		+	</div>
		+
		+	<div style="width: 97%; float: left;">
		+
		+	==Delivery Mechanism==
		+
		+	This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
		+
		+	#ITK Module
		+	#Slicer Module
		+	##Built-in
		+	##Extension -- commandline
		+	##Extension -- loadable
		+	#Other (Please specify)
		+
		+	==References==
		+	*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
		+	* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
		+	* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
		+	* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
		+
		+	</div>