Segmentation of ascidian notochord cells in DIC timelapse images

Microscopy Research and Technique

Volumn 74, Issue 8, 2011, Pages 727-734

  Obara, Boguslaw ^a,b   Veeman, Michael ^c   Choi, Jae Hyeok ^a   Smith, William ^b   Manjunath, B S ^a  

^a University of California   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cell segmentation; Differential interference contrast microscopy; Image analysis and processing; Morphogenesis; Notochord

Indexed keywords

CYTOLOGY; IMAGE ENHANCEMENT; IMAGE SEGMENTATION;

CELL EDGES; CELL SEGMENTATION; DIFFERENTIAL INTERFERENCE CONTRAST; DIFFERENTIAL INTERFERENCE CONTRAST MICROSCOPY; IMAGE-ANALYSIS; IMAGES PROCESSING; MORPHOGENESIS; NETWORK SNAKES; NOTOCHORD; TIME LAPSE IMAGES;

CELLS;

ASCIDIA;

EID: 79960603202     PISSN: 1059910X     EISSN: 10970029     Source Type: Journal    
DOI: 10.1002/jemt.20950     Document Type: Article

References (23)

1. Butenuth M. 2006.Segmentation of imagery using network snakes. International Archives of Photogrammetry, Remote Sensing and Spatial Information Sciences XXXVI, 20-22 September, Bonn, Germany, 3: 1-6.
2. Canny J. 1986. A computational approach to edge detection. Pattern Anal Mach Intell 8: 679-698.
3. Chaudhuri S, Chatterjee S, Katz N, Nelson M, Goldbaum M. 1989. Detection of blood vessels in retinal images using two-dimensional matched filters. IEEE Trans Med Imaging 8: 263-269.
4. Desolneux A, Moisan L, Morel J. 2008. From gestalt theory to image analysis: A probabilistic approach. New York: Springer-Verlag.
5. Gelasca E, Obara B, Fedorov D, Kvilekval K, Manjunath B. 2009. A biosegmentation benchmark for evaluation of bioimage analysis methods. BMC Bioinformatics 10.
6. Heise B, Sonnleitner A, Klement E. 2005. DIC image reconstruction on large cell scans. Microscopy Res Tech 55: 312-320.
7. Jiang D, Smith W. 2007. Ascidian notochord morphogenesis. Dev Dyn 236: 1748-1757.
8. Jiang K, Liao Q.-M, Xiong Y. 2006. A novel white blood cell segmentation scheme based on feature space clustering. Soft Comput, 10: 12-19.
9. Kass M, Witkin A, Terzopoulos D. 1988. Snakes: Active contour models. J Comput Vision 1: 321-331.
10. Kvilekval K, Fedorov D, Obara B, Singh AK, Manjunath BS. 2010. Bisque: A platform for bioimage analysis and management. Bioinformatics 26: 544-552.
11. Munro E, Odell G. 2002. Polarized basolateral cell motility underlies invagination and convergent extension of the ascidian notochord. Development 129: 13-24.
12. Murphy D. 2001. Differential interference contrast (DIC) microscopy and modulation contrast microscopy. Fundamentals of Light Microscopy and Digital Imaging. New York: Wiley-Liss.
13. Ning F, Delhomme D, LeCun Y, Piano F, Bottou L, Barbano P. 2005. Toward automatic phenotyping of developing embryos from videos. IEEE Trans Image Process 14: 1360-1371.
14. Passamaneck Y, Gregorio A. 2005. Ciona intestinalis: chordate development made simple. Dev Dyn 233: 1-19.
15. Preza C, Snyder D, Rosenberger F, Markham J, Conchello J. 1997.Phase estimation from transmitted-light DIC images using rotational diversity. Image Reconstruction and Restoration II, Proc. SPIE, Vol 3170. San Diego, CA. pp. 97-107.
16. Sankaran P, Asari VK. 2006. Adaptive thresholding based cell segmentation for cell-destruction activity verification. Proceedings of the 35th Applied Imagery and Pattern Recognition Workshop, IEEE Computer Society. Washington, DC. pp. 14
17. Shribak M, Inoue S. 2006. Orientation-independent differential interference contrast microscopy. Appl Opt 45: 460-469.
18. Stemple D. 2005. Structure and function of the notochord: An essential organ for chordate development. Development 132: 2503-2512.
19. Sumengen B, Manjunath B. 2006. Graph partitioning active contours (GPAC) for image segmentation. IEEE Trans Pattern Anal Mach Intell 21: 509-521.
20. Wahlby C, Sintorn I, Erlandsson F, Borgefors G, Bengtsson E. 2004. Combining intensity, edge and shape information for 2d and 3d segmentation of cell nuclei in tissue sections. J Microscopy 215: 67-76.
21. Wallingford J, Fraser S, Harland R. 2002. Convergent extension: the molecular control of polarized cell movement during embryonic development. Dev Cel 2: 695-706.
22. Yasuda T, Bannai H, Onami S, Miyano S, Kitano H. 1999.Towards automatic construction of cell-lineage of C. elegans from Nomarski DIC microscope images. Genome Informatics Workshop, Vol 10, Tokyo, Japan. pp 144-154.
23. Young D, Glasbey C, Gray A, Martin N. 1998. Towards automatic cell identification in dic microscopy. J Microscopy 192: 186-193.