OSA's Digital Library

Optics Express

Optics Express

  • Editor: Michael Duncan
  • Vol. 14, Iss. 9 — May. 1, 2006
  • pp: 3806–3829

Real-time automated 3D sensing, detection, and recognition of dynamic biological micro-organic events

Bahram Javidi, Seokwon Yeom, Inkyu Moon, and Mehdi Daneshpanah  »View Author Affiliations

Optics Express, Vol. 14, Issue 9, pp. 3806-3829 (2006)

View Full Text Article

Enhanced HTML    Acrobat PDF (2131 KB)

Browse Journals / Lookup Meetings

Browse by Journal and Year


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools



In this paper, we present an overview of three-dimensional (3D) optical imaging techniques for real-time automated sensing, visualization, and recognition of dynamic biological microorganisms. Real time sensing and 3D reconstruction of the dynamic biological microscopic objects can be performed by single-exposure on-line (SEOL) digital holographic microscopy. A coherent 3D microscope-based interferometer is constructed to record digital holograms of dynamic micro biological events. Complex amplitude 3D images of the biological microorganisms are computationally reconstructed at different depths by digital signal processing. Bayesian segmentation algorithms are applied to identify regions of interest for further processing. A number of pattern recognition approaches are addressed to identify and recognize the microorganisms. One uses 3D morphology of the microorganisms by analyzing 3D geometrical shapes which is composed of magnitude and phase. Segmentation, feature extraction, graph matching, feature selection, and training and decision rules are used to recognize the biological microorganisms. In a different approach, 3D technique is used that are tolerant to the varying shapes of the non-rigid biological microorganisms. After segmentation, a number of sampling patches are arbitrarily extracted from the complex amplitudes of the reconstructed 3D biological microorganism. These patches are processed using a number of cost functions and statistical inference theory for the equality of means and equality of variances between the sampling segments. Also, we discuss the possibility of employing computational integral imaging for 3D sensing, visualization, and recognition of biological microorganisms illuminated under incoherent light. Experimental results with several biological microorganisms are presented to illustrate detection, segmentation, and identification of micro biological events.

© 2006 Optical Society of America

OCIS Codes
(100.5010) Image processing : Pattern recognition
(100.6890) Image processing : Three-dimensional image processing
(110.6880) Imaging systems : Three-dimensional image acquisition
(170.3880) Medical optics and biotechnology : Medical and biological imaging

ToC Category:
Imaging Systems

Original Manuscript: February 1, 2006
Revised Manuscript: April 10, 2006
Manuscript Accepted: April 10, 2006
Published: May 1, 2006

Virtual Issues
Vol. 1, Iss. 6 Virtual Journal for Biomedical Optics

Bahram Javidi, Seokwon Yeom, Inkyu Moon, and Mehdi Daneshpanah, "Real-time automated 3D sensing, detection, and recognition of dynamic biological micro-organic events," Opt. Express 14, 3806-3829 (2006)

Sort:  Author  |  Year  |  Journal  |  Reset  


  1. The largely forgotten Influenza in 1918, a. k. a. "Spanish Flu" or "La Grippe" killed an estimated 40 million people worldwide, and an estimated 600,000 in the USA. It infected an estimated 20% of the world population. See Alfred Crosby, "America's Forgotten Pandemic: The Influenza of 1918," (Cambridge University Press, Cambridge, 1989).
  2. http://www.pbs.org/wgbh/amex/influenza/
  3. J. W. Lengeler, G. Drews, and H. G. Schlegel, Biology of the prokaryotes, (New York, Blackwell science, 1999).
  4. M. G. Forero, F. Sroubek, and G. Cristobal, "Identification of tuberculosis bacteria based on shape and color," Real-time Imag. 10, 251-262 (2004). [CrossRef]
  5. J. Alvarez-Borrego, R. R. Mourino-Perez, G. Cristobal-Perez, and J. L. Pech-Pacheco, "Invariant recognition of polychromatic images of Vibrio cholerae 01," Opt. Eng. 41, 827-833 (2002). [CrossRef]
  6. A. L. Amaral, M. da Motta, M. N. Pons, H. Vivier, N. Roche, M. Moda, and E. C. Ferreira, "Survey of protozoa and metazoa populations in wastewater treatment plants by image analysis and discriminant analysis," Environmentrics 15, 381-390 (2004). [CrossRef]
  7. S.-K. Treskatis, V. Orgeldinger, H. wolf, and E. D. Gilles, "Morphological characterization of filamentous microorganisms in submerged cultures by on-line digital image analysis and pattern recognition," Biotechnol. Bioeng. 53, 191-201 (1997). [CrossRef] [PubMed]
  8. T. Luo, K. Kramer, D. B. Goldgof, L. O. Hall, S. Samson, A. Remsen, and T. Hopkins, "Recognizing plankton images from the shadow image particle profiling evaluation recorder," IEEE Trans. Syst. Man. Cybern. Part B 34, 1753-1762 (2004). [CrossRef]
  9. A. Mahalanobis, R. R. Muise, S. R. Stanfill, and A. V. Nevel, "Design and application of quadratic correlation filters for target detection," IEEE Trans. Aerosp. Electron. Syst. 40, 837-850 (2004). [CrossRef]
  10. F. A. Sadjadi, "Infrared target detection with probability density functions of wavelet transform subbands," Appl. Opt. 43, 315-323 (2004). [CrossRef] [PubMed]
  11. A. K. Jain, Fundamentals of digital image processing, (Prentice Hall, 1989).
  12. R. O. Duda, P. E. Hart, and D. G. Stork, Pattern classification 2nd, (NewYork, Wiley Interscience, 2001).
  13. C. M. Bishop, Neural networks for pattern recognition, (New York, Oxford University Press, 1995).
  14. B. Javidi and P. Refregier, eds., Optical pattern recognition, (SPIE, 1994).
  15. 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]
  16. F. Sadjadi, ed., Milestones in performance evaluations of signal and image processing systems, (SPIE Press, 1993).
  17. P. Refregier, V. Laude, and B. Javidi, "Nonlinear joint transform correlation: an optimum solution for adaptive image discrimination and input noise robustness," J. Opt. Lett. 19, 405-407 (1994).
  18. F. Sadjadi, "Improved target classification using optimum polarimetric SAR signatures," IEEE Trans. Aerosp. Electron. Syst. 38, 38-49 (2002). [CrossRef]
  19. B. Javidi and F. Okano, eds., Three-dimensional television, video, and display technologies, (New York, Springer, 2002).
  20. B. Javidi, ed., Image Recognition and Classification: Algorithms, Systems, and Applications, (New York, Marcel Dekker, 2002). [CrossRef]
  21. B. Javidi and E. Tajahuerce, "Three dimensional object recognition using digital holography," Opt. Lett. 25, 610-612 (2000). [CrossRef]
  22. O. Matoba, T. J. Naughton, Y. Frauel, N. Bertaux, and B. Javidi, "Real-time three-dimensional object reconstruction by use of a phase-encoded digital hologram," Appl. Opt. 41, 6187-6192 (2002). [CrossRef] [PubMed]
  23. Y. Frauel and B. Javidi, "Neural network for three-dimensional object recognition based on digital holography," Opt. Lett. 26, 1478-1480 (2001). [CrossRef]
  24. 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]
  25. B. Javidi and D. Kim, "Three-dimensional-object recognition by use of single-exposure on-axis digital holography," Opt. Lett. 30, 236-238 (2005). [CrossRef] [PubMed]
  26. D. Kim and B. Javidi, "Distortion-tolerant 3-D object recognition by using single exposure on-axis digital holography," Opt. Express 12, 5539-5548 (2005). [CrossRef]
  27. S. Yeom and B. Javidi, "Three-dimensional object feature extraction and classification with computational holographic imaging," Appl. Opt. 43, 442-451 (2004). [CrossRef] [PubMed]
  28. B. Javidi, I. Moon, S. Yeom, and E. Carapezza, "Three-dimensional imaging and recognition of microorganism using single-exposure on-line (SEOL) digital holography," Opt. Express 13, 4492-4506 (2005). [CrossRef] [PubMed]
  29. S. Yeom, I Moon, and B. Javidi, "Real-time 3D sensing, visualization and recognition of dynamic biological micro-organisms," Proceedings of IEEE 94, 550-566 (2006). [CrossRef]
  30. S. Yeom and B. Javidi, "Three-dimensional recognition of microorganisms," J. Bio. Opt. 11, 02401718 (2006). [CrossRef]
  31. S. Yeom, I. Moon, and B. Javidi, "Two approaches of 3D microorganism recognition using single exposure on-line digital holography," in F. Sadjadi and B. Javidi (eds.), Physics of Automatic Target Recognition, (Springer, 2006).
  32. B. Javidi, I. Moon, and S. Yeom, "3D microorganism sensing, visualization and recognition using single exposure on-line digital holography," Optics and Photonics News 17, 16-21 (2006). [CrossRef]
  33. I. Moon and B. Javidi, "Shape-tolerant three-dimensional recognition of microorganisms using digital holography," Opt. Express 13, 9612-9622 (2005). [CrossRef] [PubMed]
  34. S. Kishk and B. Javidi, "Improved resolution 3D object sensing and recognition using time multiplexed computational integral imaging," Opt. Express 11, 3528-3541 (2003). [CrossRef] [PubMed]
  35. S. Yeom, B. Javidi, and E. Watson, "Photon counting passive 3D image sensing for automatic target recognition," Opt. Express 13, 9310-9330 (2005). [CrossRef] [PubMed]
  36. T. Kreis, ed., Handbook of Holographic Interferometry, (Wiley, VCH, 2005).
  37. J. W. Goodman, Introduction to Fourier Optics 2nd, (Boston, McGraw Hill, 1996). [PubMed]
  38. J. W. Goodman and R. W. Lawrence, "Digital image holograms," Appl. Phys. Lett. 11, 77-79 (1967). [CrossRef]
  39. I. Yamaguchi and T. Zhang, "Phase-shifting digital holography," Opt. Lett. 22, 1268-1270 (1997). [CrossRef] [PubMed]
  40. P. Ferraro, S. Grilli, D. Alfieri, S. D. Nicola, A. Finizio, G. Pierattini, B. Javidi, G. Coppola, and V. Striano, "Extended focused image in microscopy by digital holography," Opt. Express 13, 6738-6749 (2005). [CrossRef] [PubMed]
  41. T. Zhang and I. Yamaguchi, "Three-dimensional microscopy with phase-shifting digital holography," Opt. Lett. 23, 1221-1223 (1998). [CrossRef]
  42. B. R. Brown and A. W. Lohmann, "Complex spatial filtering with binary masks," Appl. Opt. 5, 967-969 (1966). [CrossRef] [PubMed]
  43. M. DaneshPanah and B. Javidi "Segmentation of 3D holographic images using bivariate jointly distributed region snake," Opt. Express (submitted).
  44. O. Germain and P. Refregier "Optimal snake-based segmentation of a random luminance target on a spatially disjoint background," Opt. Lett. 21, 1845 (1996). [CrossRef] [PubMed]
  45. C. Chesnaud, V. Page, and P. Refregier, "Improvement in robustness of the statistically independent region snake-based segmentation method of target-shape tracking," Opt. Lett. 23, 488-490 (1998). [CrossRef]
  46. M. Kass, A. Witkin, and D. Terzopoulus, "Snakes: Active contour models," Int. J. Comput. Vision 1, 321-331 (1987). [CrossRef]
  47. N. Mukhopadhyay, Probability and Statistical Inference, (New York, Marcel Dekker, 2000).
  48. B. Javidi and J. Wang, "Limitations of the classic definition of the signal-to-noise ratio in matched filter based optical pattern recognition," Appl. Opt. 31, 6826-6829 (1992). [CrossRef] [PubMed]
  49. B. Javidi and J. Wang, "Optimum distortion invariant filters for detecting a noisy distorted target in background noise," J. Opt. Soc. Am. 12, 2604-2614 (1995). [CrossRef]
  50. J. G. Daugman, "Uncertainty relation for resolution in space, spatial frequency, and orientation optimized by two-dimensional visual cortical filters," J. Opt. Soc. Am. 2, 1160-1169 (1985). [CrossRef]
  51. T. S. Lee, "Image representation using 2D Gabor wavelets," IEEE Trans. Pattern. Anal. Mach. Intell. 18, 959-971 (1996). [CrossRef]
  52. J. G. Daugman, "How iris recognition works," IEEE Trans. Circuits Syst. for Video.Tech. 14, 21-30, (2004). [CrossRef]
  53. M. Lades, J. C. Vorbruggen, J. Buhmann, J. Lange, C. v.d. Malsburg, R. P. Wurtz, and W. Konen, "Distortion invariant object recognition in the dynamic link architecture," IEEE Trans. Comput. 42, 300-311 (1993). [CrossRef]
  54. R. P. Wurtz, "Object recognition robust under translations, deformations, and changes in background," IEEE Trans. Pattern. Anal. Mach. Intell. 19, 769-775 (1997). [CrossRef]
  55. B. Duc, S. Fischer, and J. Bigun, "Face authentification with Gabor information on deformable graphs," IEEE Trans. Image Process. 8, 504-516 (1999). [CrossRef]
  56. S. Yeom, B. Javidi, Y. J. Roh, and H. S. Cho, "Three-dimensional object recognition using x-ray imaging," Opt. Eng. 43, 027201-1~23 (2005). [CrossRef]
  57. G.W. Snedecor and W.G. Cochran, Statistical Methods, (Iowa State University Press, 1989).
  58. M. G. Lippmann, "Epreuves reversibles donnant la sensation du relief," J. Phys. 7, 821-825 (1908).
  59. H. E. Ives, "Optical properties of a Lippmann lenticuled sheet," J. Opt. Soc. Am. 21, 171-176 (1931). [CrossRef]
  60. Okoshi, Three-Dimensional Imaging Techniques, (New York, Academic, 1976).
  61. C. B. Burckhardt, "Optimum parameters and resolution limitation of integral photography," J. Opt. Soc. Am. 58, 71-76 (1968). [CrossRef]
  62. F. Okano, H. Hoshino, J. Arai, and I. Yuyama, "Real-time pickup method for a there-dimensional image based on Integral Photography," Appl. Opt.  36, 1598-1603 (1997). [CrossRef] [PubMed]
  63. F. Jin, J. Jang, and B. Javidi, "Effects of device resolution on three-dimensional integral imaging," Opt. Lett. 29, 1345-1347 (2004). [CrossRef] [PubMed]
  64. J. S. Jang and B. Javidi, "Three-dimensional integral imaging of micro-objects," Opt. Lett. 29, 1230-1232 (2004). [CrossRef] [PubMed]
  65. R. Martínez-Cuenca, G. Saavedra, M. Martínez-Corral, and B. Javidi, "Enhanced depth of field integral imaging with sensor resolution constraints," Opt. Express 12, 5237-5242 (2004). [CrossRef] [PubMed]
  66. H. Arimoto and B. Javidi, "Integral three-dimensional imaging with digital reconstruction," Opt. Lett. 26, 157-159 (2001). [CrossRef]
  67. A. Stern and B. Javidi, "3D image sensing and reconstruction with time-division multiplexed computational integral imaging (CII)," Appl. Opt. 42, 7036-7042 (2003). [CrossRef] [PubMed]
  68. S. Hong and B. Javidi, "Improved resolution 3D object reconstruction using computational integral imaging with time multiplexing," Opt. Express 12, 4579 - 4588 (2004). [CrossRef] [PubMed]
  69. Y. Frauel, E. Tajahuerce, O. Matoba, A. Castro, and B. Javidi, "Comparison of passive ranging integral imaging and active imaging digital holography for three-dimensional object recognition", Appl. Opt. 43, 452-462 (2004). [CrossRef] [PubMed]
  70. A. Stern and B. Javidi, "Three-Dimensional image sensing, visualization, and processing using integral imaging," Proceedings of the IEEE 94, 591- 607 (2006). [CrossRef]

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.

« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited