ITK GPAC level set - Revision history

Palani at 23:45, 24 June 2010

2010-06-24T23:45:05Z

Palani at 23:36, 20 June 2010

2010-06-20T23:36:37Z

Palani at 22:19, 20 June 2010

2010-06-20T22:19:52Z

Palani: /* Resources */

2010-06-20T21:23:47Z

Resources

Palani at 16:37, 20 June 2010

2010-06-20T16:37:27Z

Palani at 16:32, 20 June 2010

2010-06-20T16:32:53Z

Palani at 16:19, 20 June 2010

2010-06-20T16:19:55Z

Arnaudgelas at 20:30, 3 June 2010

2010-06-03T20:30:55Z

Arnaudgelas: /* Key Investigators */

2010-06-03T20:16:17Z

Key Investigators

Arnaudgelas: Created page with '==Key Investigators== * University of Missouri: K. Palaniappan * Harvard Medical School: Kishore Mosaliganti

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 <h3>Progress</h3>
 Preliminary multiphase Chan-Vese level set segmentation algorithm has been developed using a Matlab reference implementation. Test cases with synthetic and microscopy imagery have been completed. Need to finish implementation for N-classes, extension to 3D and develop suite of test cases.
-</div>
+<h3>NA-MIC Progress</h3>
 </div>

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 <h3>Approach, Plan</h3>
-Extend the level set class to support multiphase level sets with two and three level sets cases. Multiphase methods model <math>N</math> classes using <math>\log N</math> phases. Each phase can segment any number of objects. Develop a multiphase coupling for multichannel data (i.e. nuclear and membrane channels). Include support for 2D and 3D multiphase curve and surface evolution.
+Extend the current ITK level set class to handle multiphase level sets with support for two, three or a general number of level sets cases. Multiphase methods model <math>N</math> classes using <math>\log N</math> phases. Each phase can be used to segment any number of objects. We plan to develop a mechanism for multiphase coupling of multichannel data (i.e. nuclear and membrane channels) with scalar or vector-based energy functions.  We plan to include support for 2D and 3D multiphase curve and surface evolution.
 </div>

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 #ITK Module
-#Slicer Module
+#Slicer Module (possibly)
 ==References==

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 A small introduction to git : [http://sourceforge.net/apps/trac/gofigure2/wiki/GIT here]
 * Data sets:
-  HeLa cell cycle phase analysis from Cristina Cardos (Technical Univ of Darmstadt).
+  HeLa cell cycle phase analysis from Cristina Cardoso (Technical Univ of Darmstadt).
   Prostate carcinoma from Michael Feldman (Univ of Pennsylvania).
   Zebrafish embryogenesis 3D confocal multichannel imagery from Sean Megason.

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 ==References==
 *I. Ersoy, F. Bunyak, V. Chagin, M. C. Cardoso, K. Palaniappan, “Segmentation and classification of cell cycle phases in fluorescence imaging”, Lecture Notes in Computer Science (MICCAI), Vol. 5762 (Part II), pp. 617-624, 2009.
 *F. Bunyak, K. Palaniappan, V. Chagin, M. C. Cardoso, "Cell Segmentation in time-lapse fluorescence microscopy with temporally varying sub-cellular fusion protein patterns", 31st Int. Conf. IEEE Engineering in Medicine and Biology Society (EMBC), Minneapolis, Minnesota, Sep. 2009, pp. 1424-1428.
 *K. Palaniappan, F. Bunyak, S. Nath, J. Goffeney, “Parallel processing strategies for cell motility and shape analysis”, High-Throughput Image Reconstruction and Analysis, Ed. C.R. Rao and G. A. Cecchi, Artech, Chapter 3, 2009.
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 *A. Mosig, S. Jaeger, W. Chaofeng, I. Ersoy, S. K. Nath, K. Palaniappan, S.S. Chen, “Tracking cells in live cell imaging videos using topological alignments”, Algorithms in Molecular Biology, Vol. 4, 10p., 2009.
 *F. Bunyak, K. Palaniappan, "Efficient segmentation using feature-based graph partitioning active contours", 12th IEEE Int. Conf. Computer Vision (ICCV), Sep. 29-Oct. 2 2009, Kyoto, Japan, pp. 873-880.
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 *A. Hafiane, F. Bunyak, K. Palaniappan, “Clustering initiated multiphase active contours and robust separation of nuclei groups for tissue segmentation”, IEEE Int. Conf. Pattern Recognition, 2008.
 *I. Ersoy, K. Palaniappan, “Multi-feature contour evolution for automatic live cell segmentation in time lapse imagery”, 30th IEEE Int. Conf. Engineering in Medicine and Biology (EMBC), pp. 371-374, 2008.
 <div style="width: 97%; float: left;">

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 ==Resources==
 * Source code :
-  git@github.com:antonin07130/NAMICSeeding.git
 We shall use [http://git-scm.com/ git] for version control :
 A small introduction to git : [http://sourceforge.net/apps/trac/gofigure2/wiki/GIT here]
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 *F. Bunyak, A. Hafiane, K. Palaniappan, Histopathology tissue segmentation by combining fuzzy clustering with multiphase vector level sets. Software Tools and Algorithms for Biological Systems, Springer, 2010.
 *F. Bunyak, K. Palaniappan, "Level set-based fast graph partitioning active contours using constant memory", Lecture Notes in Computer Science (ACIVS), Vol. 5807, pp. 145-155, 2009.
 *A. Hafiane, F. Bunyak, K. Palaniappan, “Fuzzy clustering and active contours for histopathology image segmentation and nuclei detection”, Lecture Notes in Computer Science (ACIVS), Vol. 5259, pp. 903-914, 2008.
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 *S. K. Nath, K. Palaniappan, “Fast graph partitioning active contours for image segmentation using histograms”, EURASIP Journal on Image and Video Processing, 9p., 2009, Article ID 820986 (doi:10.1155/2009/820986).
 <div style="width: 97%; float: left;">

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 ==Key Investigators==
-* University of Missouri: K. Palaniappan
+* University of Missouri: Ilker Ersoy, Filiz Bunyak, K. Palaniappan
 * Harvard Medical School: Kishore Mosaliganti, Sean Megason
 ==Project==
 <div style="margin: 20px;">
-<div style="width: 27%; float: left; padding-right: 3%;">
 <h3>Objective</h3>
 </div>
-<div style="width: 27%; float: left; padding-right: 3%;">
+<div style="width: 40%; float: left; padding-right: 3%;">
 <h3>Approach, Plan</h3>
 </div>
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 <h3>Progress</h3>
 </div>
 </div>
 <div style="width: 97%; float: left;">