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Segmentation of Cells from 3-D Confocal Images of Live Embryo

Received: 10 October 2014     Accepted: 14 October 2014     Published: 27 October 2014
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Abstract

Partial-differential-equation- based segmentation has been employed to accurately extract the shapes of membranes and nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. This strategy is a prerequisite for an accurate quantitative analysis of cell shape and morphodynamics during organogenesis and is the basis for an integrated understanding of biological processes. This data will also serve for the measurement of the variability between individuals in a population. The segmentation of cellular structures is achieved by first using an edge-preserving image filtering method for noise reduction and then applying an algorithm for cell shape reconstruction based on the Subjective Surfaces technique.

Published in International Journal of Intelligent Information Systems (Volume 3, Issue 6-1)

This article belongs to the Special Issue Research and Practices in Information Systems and Technologies in Developing Countries

DOI 10.11648/j.ijiis.s.2014030601.18
Page(s) 45-48
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2014. Published by Science Publishing Group

Keywords

Partial Differential Equations, Segmentation, Confocal Images, Morphodynamics

References
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[2] S. Megason and S. Fraser,”Digitizing life at the level of the cell: high- performance laser-scanning microscopy and image analysis for in toto imaging of development,” Mech. Dev., vol. 120, pp. 1407-1420, 2003.
[3] C. B. Kimmel, W. W. Ballard, S. R. Kimmel, B. Ullmann, and Th. F. Schilling, ”Stages of embryonic development of the zebrafish,” Dev. Dyn., vol. 203 , pp. 253-310, 1995.
[4] B. Rizzi., ”3D Zebra Fish Embryo Images Filtering by Nonlinear Partial Differential Equations,” 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.
[5] A. Sarti, R. Malladi, and J. A. Sethian, ”Subjective Surfaces: A Method for Completing Missing Boundaries,” Proceedings of the National Academy of Sciences of the United States of America, vol. 12, pp.6258-6263, 2000.
[6] A. Sarti, R. Malladi, and J. A. Sethian,”Subjective Surfaces: A Geometric Model for Boundary Completion,” International Journal of Computer Vision, vol. 46, pp. 201-221, 2002.
[7] 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.
[8] V. Caselles, R. Kimmel, and G. Sapiro, ”Geodesic Active Contours,” International Journal of Computer Vision, vol. 22, pp. 61-79, 1997.
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[11] W. Schroeder, K. Martin, and B. Lorensen, The Visualization Toolkit: An Object-Oriented Approach To 3D Graphics, 2nd ed., Prentice Hall, 1997.
[12] M. Campana., ”A Framework for 4D-Biomedical Image Process- ing, Visualization and Analysis,” 29th Annual International Confer- ence of the IEEE Engineering in Medicine and Biology Society.
[13] J. D. Ballard,”Generalizing the Hough Transform to Detect Arbitrary Shapes,” Pattern Recognition, vol. 13, pp. 111-122, 1981.
[14] C. Melani.,”Tracking cells in a live zebrafish embryo,” 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.
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  • APA Style

    Ali Zeynali Aaq Qaleh, Seyyed Mahdi Haji Mirahmadi. (2014). Segmentation of Cells from 3-D Confocal Images of Live Embryo. International Journal of Intelligent Information Systems, 3(6-1), 45-48. https://doi.org/10.11648/j.ijiis.s.2014030601.18

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    ACS Style

    Ali Zeynali Aaq Qaleh; Seyyed Mahdi Haji Mirahmadi. Segmentation of Cells from 3-D Confocal Images of Live Embryo. Int. J. Intell. Inf. Syst. 2014, 3(6-1), 45-48. doi: 10.11648/j.ijiis.s.2014030601.18

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    AMA Style

    Ali Zeynali Aaq Qaleh, Seyyed Mahdi Haji Mirahmadi. Segmentation of Cells from 3-D Confocal Images of Live Embryo. Int J Intell Inf Syst. 2014;3(6-1):45-48. doi: 10.11648/j.ijiis.s.2014030601.18

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  • @article{10.11648/j.ijiis.s.2014030601.18,
      author = {Ali Zeynali Aaq Qaleh and Seyyed Mahdi Haji Mirahmadi},
      title = {Segmentation of Cells from 3-D Confocal Images of Live Embryo},
      journal = {International Journal of Intelligent Information Systems},
      volume = {3},
      number = {6-1},
      pages = {45-48},
      doi = {10.11648/j.ijiis.s.2014030601.18},
      url = {https://doi.org/10.11648/j.ijiis.s.2014030601.18},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijiis.s.2014030601.18},
      abstract = {Partial-differential-equation- based segmentation has been employed to accurately extract the shapes of membranes and nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. This strategy is a prerequisite for an accurate quantitative analysis of cell shape and morphodynamics during organogenesis and is the basis for an integrated understanding of biological processes. This data will also serve for the measurement of the variability between individuals in a population. The segmentation of cellular structures is achieved by first using an edge-preserving image filtering method for noise reduction and then applying an algorithm for cell shape reconstruction based on the Subjective Surfaces technique.},
     year = {2014}
    }
    

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  • TY  - JOUR
    T1  - Segmentation of Cells from 3-D Confocal Images of Live Embryo
    AU  - Ali Zeynali Aaq Qaleh
    AU  - Seyyed Mahdi Haji Mirahmadi
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    DO  - 10.11648/j.ijiis.s.2014030601.18
    T2  - International Journal of Intelligent Information Systems
    JF  - International Journal of Intelligent Information Systems
    JO  - International Journal of Intelligent Information Systems
    SP  - 45
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    PB  - Science Publishing Group
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    UR  - https://doi.org/10.11648/j.ijiis.s.2014030601.18
    AB  - Partial-differential-equation- based segmentation has been employed to accurately extract the shapes of membranes and nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. This strategy is a prerequisite for an accurate quantitative analysis of cell shape and morphodynamics during organogenesis and is the basis for an integrated understanding of biological processes. This data will also serve for the measurement of the variability between individuals in a population. The segmentation of cellular structures is achieved by first using an edge-preserving image filtering method for noise reduction and then applying an algorithm for cell shape reconstruction based on the Subjective Surfaces technique.
    VL  - 3
    IS  - 6-1
    ER  - 

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Author Information
  • Faculty of Engineering, Islamic Azad University, Qom, Iran

  • Software Engineer, Young Researchers and Elite Club, Qazvin Branch, Islamic Azad University, Qazvin, Iran

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