OSA's Digital Library

Virtual Journal for Biomedical Optics

Virtual Journal for Biomedical Optics


  • Editor: Gregory W. Faris
  • Vol. 2, Iss. 9 — Sep. 26, 2007

Tracking biological microorganisms in sequence of 3D holographic microscopy images

Mehdi DaneshPanah and Bahram Javidi  »View Author Affiliations

Optics Express, Vol. 15, Issue 17, pp. 10761-10766 (2007)

View Full Text Article

Enhanced HTML    Acrobat PDF (1568 KB) Open Access

Browse Journals / Lookup Meetings

Browse by Journal and Year


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools



We develop a 3D region tracking method based on Maximum A Posteriori (MAP) tracker and adapt it to digital hologram sequences to efficiently track biological microorganisms in holographic microscopy data. In our approach, the target surface is modeled as the iso-surface of a level set function which is evolved at each frame via level set Hamilton Jacobian update rule in Euler-Lagrangian framework. The statistical characteristics of the target microorganism versus the background are exploited to evolve the interface at each frame, thus the algorithm works independent of the shape or morphology of the target. We use the bivariate Gaussian distribution to model the reconstructed hologram data which enables us to take into account the correlation between the amplitude and phase of the reconstructed wavefront to obtain a more accurate tracking solution.

© 2007 Optical Society of America

OCIS Codes
(100.6890) Image processing : Three-dimensional image processing
(170.3880) Medical optics and biotechnology : Medical and biological imaging

ToC Category:
Image Processing

Original Manuscript: May 10, 2007
Revised Manuscript: July 17, 2007
Manuscript Accepted: August 1, 2007
Published: August 10, 2007

Virtual Issues
Vol. 2, Iss. 9 Virtual Journal for Biomedical Optics

Mehdi DaneshPanah and Bahram Javidi, "Tracking biological microorganisms in sequence of 3D holographic microscopy images," Opt. Express 15, 10761-10766 (2007)

Sort:  Author  |  Year  |  Journal  |  Reset  


  1. J. W. Goodman, Introduction to Fourier Optics, 3nd ed., (Roberts & Company, Englewood, Colorado, 2005).
  2. Y. Frauel, T. J. Naughton, O. Matoba, E. Tajahuerce, and B. Javidi, "Three-dimensional imaging and processing using computational holographic imaging," Proceedings. of the IEEE 94, 636-653 (2006). [CrossRef]
  3. E. Tajahuerce, O. Matoba, and B. Javidi, "Shift-Invariant Three-Dimensional Object Recognition by Means of Digital Holography," Appl. Opt. 40, 3877-3886 (2001). [CrossRef]
  4. O. Matoba, T. J. Naughton, Y. Frauel, N. Bertaux, B. Javidi, "Real-time three-dimensional object reconstruction by use of a phase-encoded digital Hologram," Appl. Opt. 41, 6187-6192 (2002). [CrossRef] [PubMed]
  5. T. Nomura, S. Murata, E. Nitanai, and T. Numata, "Phase-shifting digital holography with a phase difference between orthogonal polarizations," Appl. Opt. 45, 4873-4877 (2006). [CrossRef] [PubMed]
  6. B. Javidi, S. Yeom, I. Moon, and M. Daneshpanah, "Real-time automated 3D sensing, detection, and recognition of dynamic biological micro-organic events," Opt. Express 14, 3806-3829 (2006). [CrossRef] [PubMed]
  7. A. Stern and B. Javidi, "Theoretical analysis of three-dimensional imaging and recognition of micro-organisms with a single-exposure on-line holographic microscope," J. Opt. Soc. Am. A 24, 163-168 (2007). [CrossRef]
  8. M. DaneshPanah and B. Javidi "Segmentation of 3D holographic images using bivariate jointly distributed region snake," Opt. Express 14, 5143-5153 (2006). [CrossRef] [PubMed]
  9. P. Ferraro, G. Coppola, S. De Nicola, A. Finizio, and G. Pierattini, "Digital holographic microscope with automatic focus tracking by detecting sample displacement in real time," Opt. Lett. 28, 1257-1259 (2003). [CrossRef] [PubMed]
  10. F. Sadjadi, ed., Selected Papers on Automatic Target Recognition, SPIE-CDROM, (2000).
  11. P. Refregier, Noise Theory and Application to Physics, (Springer, 2005)
  12. F. Sadjadi and A. Mahalonobis, "Target adaptive polarimetric SAR target discrimination using MACH filters," Appl. Opt. 45, 7365-7374 (2006).
  13. H. Kwon and N. M. Nasrabadi, "Kernel RX-algorithm: a nonlinear anomaly detector for hyperspectral imagery," IEEE Trans. Geosci. Remote Sens. 43, 388-397 (2005). [CrossRef]
  14. A. Mahalonobis, R. Muise, and S. Stanfill, "Performance evaluation of quadratic correlation filters for target detection and discrimination in IR imagery," Appl. Opt. 43, 5198-5205 (2004).
  15. A. Blake, A. Yuille eds, Active Vision, MIT Press, Cambridge (1992).
  16. F. Goudail and P. Refregier, "Optimal target tracking on image sequences with a deterministic background," J. Opt. Soc. Am. A 14, 3197-3207 (1997). [CrossRef]
  17. S. C. Zhu and A. Yuille, "Region competition: unifying snakes, region growing, and bayes/mdl for multiband image segmentation," IEEE Trans. Pattern Anal. Mach. Intell. 18, 884-900 (1996). [CrossRef]
  18. A. Yilmaz, X. Li, and M. Shah, "Contour based object tracking with occlusion handling in video acquired using mobile cameras," IEEE Trans. Pattern Anal. Mach. Intell. 26, 1531-1536 (2004). [CrossRef] [PubMed]
  19. M. Kass, A. Witkin, and D. Terzopoulos, "Snakes: Active Contour Models," Proc. ICCV, 259-268 (1987).
  20. J. Sethian, Level Set Methods: Evolving Interfaces in Geometry, Fluid Mechanics Computer Vision and Material Sciences, (Cambridge Univ. Press, 1999).

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.


Fig 1. Fig 2. Fig 3.

Supplementary Material

» Media 1: MOV (332 KB)     
» Media 2: MOV (1962 KB)     

« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited