Segmenting Gene Expression Patterns of Early-stage Drosophila Embryos

Mathematics and Visualization

Volumn , Issue , 2008, Pages 313-327

  Huang, Min Yu ^a,c   Rübel, Oliver ^a,b,c   Weber, Gunther H ^c   Hendriks, Cris L Luengo ^c   Biggin, Mark D ^c   Hagen, Hans ^b   Hamann, Bernd ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

edge detection; gene expression pattern; pattern segmentation; ridge detection; three dimensional gene expression; thresholding

Indexed keywords

IMAGE SEGMENTATION; TRANSCRIPTION;

DROSOPHILA EMBRYOS; DROSOPHILLA; GENE EXPRESSION PATTERNS; GENE REGULATORY NETWORKS; GENES EXPRESSION; PATTERN SEGMENTATION; RIDGE DETECTIONS; THREE-DIMENSIONAL GENE EXPRESSION; THRESHOLDING; TRANSCRIPTION NETWORKS;

EDGE DETECTION;

EID: 84884172666     PISSN: 16123786     EISSN: 2197666X     Source Type: Book Series    
DOI: 10.1007/978-3-540-72630-2_18     Document Type: Chapter

References (16)

1. John F. Canny. A computational approach to edge detection. IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 8(6):679–698, 1986.
2. Guoyi Fu, S.A.Hojjat, and A.C.F. Colchester. Integrating watersheds and critical point analysis for object detection in discrete 2D images. Medical Image Analysis, 8(3):177–185, Sep 2004.
3. Soile V. E. Keränen, Charless C. Fowlkes, Cris L. Luengo Hendriks, Damir Sudar, David W. Knowles, Jitendra Malik, and Mark D. Biggin. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: Dynamics. Genome Biology, 7(12):R124, 2006.
4. Josef Kittler, John Illingworth, and J. Föglein. Threshold selection based on a simple image statistic. Computer Vision, Graphics, and Image Processing, 30(2):125–147, 1985.
5. Sudhir Kumar, Karthik Jayaraman, Sethuraman Panchanathan, Rajalakshmi Gurunathan, Ana Marti-Subirana, and Stuart J. Newfeld. BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics, 162(4):2037–2047, Dec 2002.
6. + 06] Cris L. Luengo Hendriks, Soile V. E. Keränen, Charless C. Fowlkes, Lisa Simirenko, Gunther H. Weber, Angela H. DePace, Clara Henriquez, David W. Kaszuba, Bernd Hamann, Michael B. Eisen, Jitendra Malik, Damir Sudar, Mark D. Biggin, and David W. Knowles. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: Data acquisition pipeline. Genome Biology, 7(12):R123, 2006.
7. Antonio M. López, Davis Lloret, and Joan Serrat. Multilocal creaseness based on the level-set extrinsic curvature. Technical Report 26, Centre de Visió per Computador, Dept. d’Informàtica, Universitat Autònoma de Barcelona, Spain, 1997.
8. James B. MacQueen. Some methods for classification and analysis of multivariate observations. In Lucien M. Le Cam and Jerzy Neyman, editors, Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, volume 1, pages 281–297, Berkely, CA, USA, 1967. University of California Press.
9. Geoffrey McLachlan and David Peel. Finite Mixture Models. Wiley, 2000.
10. J.B. Antoine Maintzy, Petra A. van den Elsen, and Max A. Viergever. Evaluation of ridge seeking operators for multimodality medical image matching. IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 18(4):353–365, Apr 1996.
11. Lee R. Nackman. Two-dimensional critical point configuration graphs. IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 6(4):442–449, 1984.
12. Hanchuan Peng and Eugene W. Myers. Comparing in situ mRNA expression patterns of Drosophila embryos. In RECOMB ’04: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology, pages 157–166, New York, NY, USA, 2004. ACM Press.
13. Paul L. Rosin, Alan C. F. Colchester, and Davis J. Hawkes. Early image representation using regions defined by maximum gradient paths between singular points. Pattern Recognition, 25(7):695–711, 1992.
14. Paul L. Rosin. Unimodal thresholding. Pattern Recognition, 34(11):2083–2096, 2001.
15. Oliver Rübel, Gunther H. Weber, Soile V. E. Keränen, Charless C. Fowlkes, Cris L. Luengo Hendriks, Nameeta Y. Shah, Mark D. Biggin, Hans Hagen, David W. Knowles, Jitendra Malik, Damir Sudar, and Bernd Hamann. PointCloudXplore: Visual analysis of 3D gene expression data using physical views and parallel coordinates. In Thomas Ertl, Ken Joy, and Beatriz Sousa Santos, editors, Proceedings of the EUROGRAPHICS-IEEE VGTC Symposium on Visualization 2006, pages 203–210, Lisbon, Portugal, May 2006.
16. Michael H. F. Wilkinson. Optimizing edge detectors for robust automatic threshold selection: coping with edge curvature and noise. Graph. Models Image Process., 60(5):385–401, 1998.