Cells segmentation from 3-D confocal images of early zebrafish embryogenesis

IEEE Transactions on Image Processing

Volumn 19, Issue 3, 2010, Pages 770-781

  Zanella, Cecilia ^a   Campana, Matteo ^a   Rizzi, Barbara ^a   Melani, Camilo ^a,b   Sanguinetti, Gonzalo ^a,c   Bourgine, Paul ^d   Mikula, Karol ^e   Peyrieras, Nadine ^f   Sarti, Alessandro ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^c UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

^d Centre de Recherche en Epistemologie Appliquee Ecole Polytechnique   (France)

^e SLOVAK UNIVERSITY OF TECHNOLOGY   (Slovakia)

^f CNRS   (France)

Author keywords

Bioimaging; Confocal imaging; Image processing; Segmentation; Subjective surfaces

Indexed keywords

ALGORITHM VALIDATION; AUTOMATED ALGORITHMS; BIO-IMAGING; BIOLOGICAL PROCESS; CELL SHAPES; CLASSICAL METHODS; CONFOCAL IMAGE; CONFOCAL IMAGING; EDGE PRESERVING; EMBRYONIC CELLS; IMAGE FEATURES; MORPHODYNAMICS; QUANTITATIVE ANALYSIS; SUB-CELLULAR; ZEBRAFISH; ZEBRAFISH EMBRYOS;

CELL MEMBRANES; CYTOLOGY; IMAGE PROCESSING; IMAGING SYSTEMS; SIGNAL TO NOISE RATIO; THREE DIMENSIONAL;

EDGE DETECTION;

ALGORITHM; ANIMAL; ANIMAL EMBRYO; ARTICLE; CELL DIVISION; CELL MEMBRANE; CELL NUCLEUS; CELL SHAPE; CYTOLOGY; IMAGE PROCESSING; METHODOLOGY; PRENATAL DEVELOPMENT; REPRODUCIBILITY; ZEBRA FISH;

ALGORITHMS; ANIMALS; CELL DIVISION; CELL MEMBRANE; CELL NUCLEUS; CELL SHAPE; EMBRYO, NONMAMMALIAN; IMAGE PROCESSING, COMPUTER-ASSISTED; REPRODUCIBILITY OF RESULTS; ZEBRAFISH;

EID: 77249134601     PISSN: 10577149     EISSN: None     Source Type: Journal    
DOI: 10.1109/TIP.2009.2033629     Document Type: Article

References (39)

1. P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, "Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy," Science, vol.322, pp. 1065-1069, 2008.
2. S. J. Lockett and B. Herman, "Automatic detection of clustered, fluorescence- stained nuclei by digital image-based cytometry," Cytometry, vol.17, pp. 1-12, 1994.
3. A. I. Dow, J. M. Shafer, J. M. Kirkwood, R. A. Mascari, and A. S. Waggoner, "Automatic multiparameter florescence imaging for determining lymphocyte phenotype and activation status in Melanoma tissue sections," Cytometry, vol.25, pp. 71-81, 1996.
4. N. Malpica, C. Ortiz de Solorzano, J. J. Vaquero, A. Santos, I. Vallcorba, J. M. Garcia-Sagredo, and F. del Pozo, "Applying watershed algorithms to the segmentation of clustered nuclei," Cytometry, vol.28, pp. 289-297, 1997.
5. J. P. Rigaut, J. Vassy, P. Herlin, F. Duigou, E. Masson, D. Briane, J. Foucrier, S. Carvajal-Gonzalez, A. M. Downs, and A. M. Mandard, "Three-dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks," Cytometry, vol.12, pp. 511-524, 1991.
6. T. Irinopoulou, J. Vassy,M. Beil, E. Nicopoulou, D. Encaoua, and J. P. Rigaut, "Three-dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks of prostatic lesions," Cytometry, vol.27, pp. 99-105, 1997.
7. K. Rodenacker, M. Aubele, P. Hutzler, and P. S. Umesh Adiga, "Groping for quantitative digital 3-D image analysis: An approach to quantitative in situ hybridization in thick tissue sections of prostate carcinoma," Anal. Cell. Pathol., vol.15, pp. 19-29, 1997.
8. S. J. Lockett, D. Sudar, C. T. Thompson, D. Pinkel, and J. W. Gray, "Efficient, interactive, three-dimensional segmentation of cell nuclei in thick tissue sections," Cytometry, vol.31, pp. 275-286, 1998.
9. C. Ortiz de Solorzano, E. Garcia Rodriguez, A. Jones, D. Pinkel, J. W. Gray, D. Sudar, and S. J. Lockett, "Segmentation of confocal microscope images of cell nuclei in thick tissue section," J. Microsc., vol.193, pp. 212-226, 1999.
10. A. Sarti, C. Ortiz De Solorzano, S. Lockett, and R. Malladi, "A geometric model for 3-D confocal image analysis," IEEE Trans. Biomed. Eng., vol.47, pp. 1600-1609, 2000.
11. D. R. Padfield, J. Rittscher, T. Sebastian, N. Thomas, and B. Roysam, "Spatio-temporal cell cycle analysis using 3D level set segmentation of unstained nuclei in line scan confocal fluorescence images," in Proc. 3rd IEEE Int. Symp. Biomedical Imaging: Nano to Macro, 2006, pp. 1036-1039.
12. X. Wang, W. He, D. Metaxas, R. Mathew, and E. White, "Cell segmentation and tracking using texture-adaptive snakes," in Proc. 4th IEEE Int. Symp. Biomedical Imaging: From Nano to Macro, 2007, pp. 101-104.
13. C. Ortiz de Solorzano, R. Malladi, S. A. Leliévre, and S. J. Lockett, "Segmentation of nuclei and cells using membrane related protein markers," J. Microsc., vol.201, pp. 404-415, 2001.
14. A. Sarti, R. Malladi, and J. A. Sethian, "Subjective surfaces: A method for completing missing boundaries," Proc. Nat. Acad. Sci. United States of America, vol.12, pp. 6258-6263, 2000.
15. A. Sarti and G. Citti, "Subjective surfaces and Riemannian mean curvature flow of graphs," Acta Math. Univ. Comenianae, vol.LXX, no.1, pp. 85-103, 2001.
16. A. Sarti, R. Malladi, and J. A. Sethian, "Subjective surfaces: A geometric model for boundary completion," Int. J. Comput. Vis., vol.46, pp. 201-221, 2002.
17. C. Zanella, B. Rizzi, C. Melani, M. Campana, P. Bourgine, K. Mikula, N. Peyriéras, and A. Sarti, "Segmentation of cells from 3D confocal images of live Zebrafish embryo," in Proc. IEEE Eng. Med. Biol. Soc., 2007, pp. 6027-6030.
18. S. Megason and S. Fraser, "Digitizing life at the level of the cell: Highperformance laser-scanning microscopy and image analysis for in toto imaging of development," Mech. Dev., vol.120, pp. 1407-1420, 2003.
19. K. Dooley and L. Zon, "Zebrafish: A model system for the study of human disease," Curr. Opin. Genet. Dev., vol.10, no.3, pp. 252-256, 2000.
20. C. B. Kimmel, W. W. Ballard, S. R. Kimmel, B. Ullmann, and T. F. Schilling, "Stages of embryonic development of the zebrafish," Dev. Dyn., vol.203, pp. 253-310, 1995.
21. Z. Kriva, K. Mikula, N. Peyriéras, B. Rizzi, and A. Sarti, "3D early embryogenesys image filtering by nonlinear partial differential equations," Med. Image Anal., submitted for publication.
22. B. Rizzi, M. Campana, C. Zanella, C. Melani, R. Cunderlik, Z. Kriva, P. Bourgine, K. Mikula, N. Peyriéras, and A. Sarti, "3D zebra fish embryo images filtering by nonlinear partial differential equations," in Proc. IEEE Eng. Med. Biol. Soc., 2007, pp. 6251-6254.
23. V. Caselles, R. Kimmel, and G. Sapiro, "Geodesic active contours," Int. J. Comput. Vis., vol.22, pp. 61-79, 1997.
24. R. Malladi, J. A. Sethian, and B. C.Vemuri, "Shape modeling with front propagation: A level set approach," IEEE Trans. Pattern Anal. Mach. Intell., vol.17, pp. 158-175, 1995.
25. P. Perona and J. Malik, "Scale-space and edge detection using anisotropic diffusion," IEEE Trans. Pattern Anal. Mach. Intell., vol.12, pp. 629-639, 1990.
26. D. Ballard, "Generalizing the hough transform to detect arbitrary shapes," Pattern Recognit., vol.13, pp. 111-122, 1981.
27. C. Melani, M. Campana, B. Lombardot, B. Rizzi, F. Veronesi, C. Zanella, P. Bourgine, K. Mikula, N. Peyriéras, and A. Sarti, "Cells tracking in a live zebrafish embryo," in Proc. IEEE Eng. Med. Biol. Soc., 2007, pp. 1631-1634.
28. J. Canny, "A computational approach to edge detection," IEEE Trans. Pattern Anal. Mach. Intell., vol.PAMI-8, no.6, pp. 679-698, Jun. 1986.
29. L. C. Evans and J. Spruck, "Motion of level sets by mean curvature I," J. Diff. Geom., vol.33, pp. 635-681, 1991.
30. S. Osher and J. A. Sethian, "Front propagating with curvature dependent speed: Algorithms based on Hamilton Jacobi formulation," J. Comput. Phys., vol.79, pp. 12-49, 1988.
31. R. J. LeVeque, Finite Volume Methods for Hyperbolic Problems. Cambridge, MA: Cambridge Univ. Press, 2002.
32. K. Mikula and N. Ramarosy, "Semi-implicit finite volume scheme for solving nonlinear diffusion equations in image processing," Numer. Math., vol.89, no.3, pp. 561-590, 2001.
33. S. Corsaro, K. Mikula, A. Sarti, and F. Sgallari, "Semi-implicit co-volume method in 3D image segmentation," SIAM J. Sci. Comput., vol.28, no.6, pp. 2248-2265, 2006.
34. K. Mikula, A. Sarti, and F. Sgallari, "Co-volume level set method in subjective surface based medical image segmentation," in Handbook of Medical Image Analysis: Segmentation and Registration Models, J. Suri, Ed. et al. New York: Springer, 2005, pp. 583-626.
35. K. Mikula, A. Sarti, and F. Sgallari, "Co-volume method for Riemannian mean curvature flow in subjective surfaces multiscale segmentation," Comput. Vis. Sci., vol.9, no.1, pp. 23-31, 2006.
36. V. Caselles, R. Kimmel, and G. Sapiro, "Geodesic active contours," Int. J. Comput. Vis., vol.22, pp. 61-79, 1997.
37. M. Campana, B. Rizzi, C. Melani, P. Bourgine, N. Peyriéras, and A. Sarti, "A framework for 4D-biomedical image processing, visualization and analysis," in Proc. 3rd Int. Conf. Computer Graphics Theory and Applications, 2008, pp. 403-408.
38. J. W. Zhang, G. Q. Han, and Y.Wo, "Image registration based on generalized and mean hausdorff distances," in Proc. 4th Int. Conf. Machine Learning and Cybernetics, 2005, pp. 5117-5121.
39. P. A.Yushkewich, J. Piven, H. C. Hazlett, R. G. Smith, S. Ho, J. C. Gee, and G. Gerig, "User guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability," Neuroimage vol. 31, pp. 1116-1128, 2006 [Online]. Available: http://www. itksnap.org