Abstract

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

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2006 (4)

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]

S. Yeom and B. Javidi, "Three-dimensional recognition of microorganisms," J. Bio. Opt. 11, 02401718 (2006).
[CrossRef]

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]

A. Stern and B. Javidi, "Three-Dimensional image sensing, visualization, and processing using integral imaging," Proceedings of the IEEE 94, 591- 607 (2006).
[CrossRef]

2005 (7)

2004 (11)

F. A. Sadjadi, "Infrared target detection with probability density functions of wavelet transform subbands," Appl. Opt. 43, 315-323 (2004).
[CrossRef] [PubMed]

S. Yeom and B. Javidi, "Three-dimensional object feature extraction and classification with computational holographic imaging," Appl. Opt. 43, 442-451 (2004).
[CrossRef] [PubMed]

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]

J. S. Jang and B. Javidi, "Three-dimensional integral imaging of micro-objects," Opt. Lett. 29, 1230-1232 (2004).
[CrossRef] [PubMed]

F. Jin, J. Jang, and B. Javidi, "Effects of device resolution on three-dimensional integral imaging," Opt. Lett. 29, 1345-1347 (2004).
[CrossRef] [PubMed]

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]

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]

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]

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]

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]

J. G. Daugman, "How iris recognition works," IEEE Trans. Circuits Syst. for Video.Tech. 14, 21-30, (2004).
[CrossRef]

2003 (2)

2002 (3)

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]

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]

F. Sadjadi, "Improved target classification using optimum polarimetric SAR signatures," IEEE Trans. Aerosp. Electron. Syst. 38, 38-49 (2002).
[CrossRef]

2001 (3)

2000 (1)

1999 (1)

B. Duc, S. Fischer, and J. Bigun, "Face authentification with Gabor information on deformable graphs," IEEE Trans. Image Process. 8, 504-516 (1999).
[CrossRef]

1998 (2)

1997 (4)

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]

I. Yamaguchi and T. Zhang, "Phase-shifting digital holography," Opt. Lett. 22, 1268-1270 (1997).
[CrossRef] [PubMed]

R. P. Wurtz, "Object recognition robust under translations, deformations, and changes in background," IEEE Trans. Pattern. Anal. Mach. Intell. 19, 769-775 (1997).
[CrossRef]

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]

1996 (2)

T. S. Lee, "Image representation using 2D Gabor wavelets," IEEE Trans. Pattern. Anal. Mach. Intell. 18, 959-971 (1996).
[CrossRef]

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]

1995 (1)

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]

1994 (1)

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).

1993 (1)

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]

1992 (1)

1987 (1)

M. Kass, A. Witkin, and D. Terzopoulus, "Snakes: Active contour models," Int. J. Comput. Vision 1, 321-331 (1987).
[CrossRef]

1985 (1)

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]

1968 (1)

1967 (1)

J. W. Goodman and R. W. Lawrence, "Digital image holograms," Appl. Phys. Lett. 11, 77-79 (1967).
[CrossRef]

1966 (1)

1931 (1)

1908 (1)

M. G. Lippmann, "Epreuves reversibles donnant la sensation du relief," J. Phys. 7, 821-825 (1908).

Alfieri, D.

Alvarez-Borrego, J.

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]

Amaral, A. L.

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]

Arai, J.

Arimoto, H.

Bertaux, N.

Bigun, J.

B. Duc, S. Fischer, and J. Bigun, "Face authentification with Gabor information on deformable graphs," IEEE Trans. Image Process. 8, 504-516 (1999).
[CrossRef]

Brown, B. R.

Buhmann, J.

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]

Burckhardt, C. B.

Carapezza, E.

Castro, A.

Chesnaud, C.

Coppola, G.

Cristobal, G.

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]

Cristobal-Perez, G.

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]

da Motta, M.

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]

Daugman, J. G.

J. G. Daugman, "How iris recognition works," IEEE Trans. Circuits Syst. for Video.Tech. 14, 21-30, (2004).
[CrossRef]

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]

Duc, B.

B. Duc, S. Fischer, and J. Bigun, "Face authentification with Gabor information on deformable graphs," IEEE Trans. Image Process. 8, 504-516 (1999).
[CrossRef]

Ferraro, P.

Ferreira, E. C.

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]

Finizio, A.

Fischer, S.

B. Duc, S. Fischer, and J. Bigun, "Face authentification with Gabor information on deformable graphs," IEEE Trans. Image Process. 8, 504-516 (1999).
[CrossRef]

Forero, M. G.

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]

Frauel, Y.

Germain, O.

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]

Goldgof, D. B.

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]

Goodman, J. W.

J. W. Goodman and R. W. Lawrence, "Digital image holograms," Appl. Phys. Lett. 11, 77-79 (1967).
[CrossRef]

Grilli, S.

Hall, L. O.

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]

Hong, S.

Hopkins, T.

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]

Hoshino, H.

Ives, H. E.

Jang, J.

Jang, J. S.

Javidi, B.

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]

A. Stern and B. Javidi, "Three-Dimensional image sensing, visualization, and processing using integral imaging," Proceedings of the IEEE 94, 591- 607 (2006).
[CrossRef]

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]

S. Yeom and B. Javidi, "Three-dimensional recognition of microorganisms," J. Bio. Opt. 11, 02401718 (2006).
[CrossRef]

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]

I. Moon and B. Javidi, "Shape-tolerant three-dimensional recognition of microorganisms using digital holography," Opt. Express 13, 9612-9622 (2005).
[CrossRef] [PubMed]

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]

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]

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]

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]

J. S. Jang and B. Javidi, "Three-dimensional integral imaging of micro-objects," Opt. Lett. 29, 1230-1232 (2004).
[CrossRef] [PubMed]

S. Yeom and B. Javidi, "Three-dimensional object feature extraction and classification with computational holographic imaging," Appl. Opt. 43, 442-451 (2004).
[CrossRef] [PubMed]

F. Jin, J. Jang, and B. Javidi, "Effects of device resolution on three-dimensional integral imaging," Opt. Lett. 29, 1345-1347 (2004).
[CrossRef] [PubMed]

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]

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]

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]

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]

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]

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]

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]

H. Arimoto and B. Javidi, "Integral three-dimensional imaging with digital reconstruction," Opt. Lett. 26, 157-159 (2001).
[CrossRef]

Y. Frauel and B. Javidi, "Neural network for three-dimensional object recognition based on digital holography," Opt. Lett. 26, 1478-1480 (2001).
[CrossRef]

B. Javidi and E. Tajahuerce, "Three dimensional object recognition using digital holography," Opt. Lett. 25, 610-612 (2000).
[CrossRef]

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]

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).

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]

Jin, F.

Kass, M.

M. Kass, A. Witkin, and D. Terzopoulus, "Snakes: Active contour models," Int. J. Comput. Vision 1, 321-331 (1987).
[CrossRef]

Kim, D.

Kishk, S.

Kramer, K.

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]

Kwon, H.

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]

Lades, M.

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]

Lange, J.

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]

Laude, V.

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).

Lawrence, R. W.

J. W. Goodman and R. W. Lawrence, "Digital image holograms," Appl. Phys. Lett. 11, 77-79 (1967).
[CrossRef]

Lee, T. S.

T. S. Lee, "Image representation using 2D Gabor wavelets," IEEE Trans. Pattern. Anal. Mach. Intell. 18, 959-971 (1996).
[CrossRef]

Lippmann, M. G.

M. G. Lippmann, "Epreuves reversibles donnant la sensation du relief," J. Phys. 7, 821-825 (1908).

Lohmann, A. W.

Luo, T.

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]

Mahalanobis, A.

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]

Martínez-Corral, M.

Martínez-Cuenca, R.

Matoba, O.

Moda, M.

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]

Moon, I

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]

Moon, I.

Mourino-Perez, R. R.

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]

Muise, R. R.

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]

Nasrabadi, N. M.

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]

Naughton, T. J.

Nevel, A. V.

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]

Nicola, S. D.

Okano, F.

Orgeldinger, V.

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]

Page, V.

Pech-Pacheco, J. L.

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]

Pierattini, G.

Pons, M. N.

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]

Refregier, P.

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]

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]

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).

Remsen, A.

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]

Roche, N.

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]

Saavedra, G.

Sadjadi, F.

F. Sadjadi, "Improved target classification using optimum polarimetric SAR signatures," IEEE Trans. Aerosp. Electron. Syst. 38, 38-49 (2002).
[CrossRef]

Sadjadi, F. A.

Samson, S.

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]

Sroubek, F.

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]

Stanfill, S. R.

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]

Stern, A.

A. Stern and B. Javidi, "Three-Dimensional image sensing, visualization, and processing using integral imaging," Proceedings of the IEEE 94, 591- 607 (2006).
[CrossRef]

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]

Striano, V.

Tajahuerce, E.

Terzopoulus, D.

M. Kass, A. Witkin, and D. Terzopoulus, "Snakes: Active contour models," Int. J. Comput. Vision 1, 321-331 (1987).
[CrossRef]

Treskatis, S.-K.

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]

Vivier, H.

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]

Vorbruggen, J. C.

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]

Wang, J.

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]

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]

Watson, E.

Witkin, A.

M. Kass, A. Witkin, and D. Terzopoulus, "Snakes: Active contour models," Int. J. Comput. Vision 1, 321-331 (1987).
[CrossRef]

Wurtz, R. P.

R. P. Wurtz, "Object recognition robust under translations, deformations, and changes in background," IEEE Trans. Pattern. Anal. Mach. Intell. 19, 769-775 (1997).
[CrossRef]

Yamaguchi, I.

Yeom, S.

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]

S. Yeom and B. Javidi, "Three-dimensional recognition of microorganisms," J. Bio. Opt. 11, 02401718 (2006).
[CrossRef]

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]

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]

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]

S. Yeom and B. Javidi, "Three-dimensional object feature extraction and classification with computational holographic imaging," Appl. Opt. 43, 442-451 (2004).
[CrossRef] [PubMed]

Yuyama, I.

Zhang, T.

Appl. Opt. (9)

B. R. Brown and A. W. Lohmann, "Complex spatial filtering with binary masks," Appl. Opt. 5, 967-969 (1966).
[CrossRef] [PubMed]

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]

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]

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]

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]

F. A. Sadjadi, "Infrared target detection with probability density functions of wavelet transform subbands," Appl. Opt. 43, 315-323 (2004).
[CrossRef] [PubMed]

S. Yeom and B. Javidi, "Three-dimensional object feature extraction and classification with computational holographic imaging," Appl. Opt. 43, 442-451 (2004).
[CrossRef] [PubMed]

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]

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]

Appl. Phys. Lett. (1)

J. W. Goodman and R. W. Lawrence, "Digital image holograms," Appl. Phys. Lett. 11, 77-79 (1967).
[CrossRef]

Biotechnol. Bioeng. (1)

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]

Environmentrics (1)

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]

IEEE Trans. Aerosp. Electron. Syst. (2)

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]

F. Sadjadi, "Improved target classification using optimum polarimetric SAR signatures," IEEE Trans. Aerosp. Electron. Syst. 38, 38-49 (2002).
[CrossRef]

IEEE Trans. Comput. (1)

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]

IEEE Trans. Geosci. Remote Sens. (1)

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]

IEEE Trans. Image Process. (1)

B. Duc, S. Fischer, and J. Bigun, "Face authentification with Gabor information on deformable graphs," IEEE Trans. Image Process. 8, 504-516 (1999).
[CrossRef]

IEEE Trans. Pattern. Anal. Mach. Intell. (2)

R. P. Wurtz, "Object recognition robust under translations, deformations, and changes in background," IEEE Trans. Pattern. Anal. Mach. Intell. 19, 769-775 (1997).
[CrossRef]

T. S. Lee, "Image representation using 2D Gabor wavelets," IEEE Trans. Pattern. Anal. Mach. Intell. 18, 959-971 (1996).
[CrossRef]

IEEE Trans. Syst. Man. Cybern. Part B (1)

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]

Int. J. Comput. Vision (1)

M. Kass, A. Witkin, and D. Terzopoulus, "Snakes: Active contour models," Int. J. Comput. Vision 1, 321-331 (1987).
[CrossRef]

J. Bio. Opt. (1)

S. Yeom and B. Javidi, "Three-dimensional recognition of microorganisms," J. Bio. Opt. 11, 02401718 (2006).
[CrossRef]

J. Opt. Lett. (1)

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).

J. Opt. Soc. Am. (4)

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]

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).
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H. E. Ives, "Optical properties of a Lippmann lenticuled sheet," J. Opt. Soc. Am. 21, 171-176 (1931).
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C. B. Burckhardt, "Optimum parameters and resolution limitation of integral photography," J. Opt. Soc. Am. 58, 71-76 (1968).
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J. Phys. (1)

M. G. Lippmann, "Epreuves reversibles donnant la sensation du relief," J. Phys. 7, 821-825 (1908).

Opt. Eng. (1)

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]

Opt. Express (9)

M. DaneshPanah and B. Javidi "Segmentation of 3D holographic images using bivariate jointly distributed region snake," Opt. Express (submitted).

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]

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]

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]

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]

I. Moon and B. Javidi, "Shape-tolerant three-dimensional recognition of microorganisms using digital holography," Opt. Express 13, 9612-9622 (2005).
[CrossRef] [PubMed]

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]

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]

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]

Opt. Lett. (10)

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]

J. S. Jang and B. Javidi, "Three-dimensional integral imaging of micro-objects," Opt. Lett. 29, 1230-1232 (2004).
[CrossRef] [PubMed]

F. Jin, J. Jang, and B. Javidi, "Effects of device resolution on three-dimensional integral imaging," Opt. Lett. 29, 1345-1347 (2004).
[CrossRef] [PubMed]

Y. Frauel and B. Javidi, "Neural network for three-dimensional object recognition based on digital holography," Opt. Lett. 26, 1478-1480 (2001).
[CrossRef]

H. Arimoto and B. Javidi, "Integral three-dimensional imaging with digital reconstruction," Opt. Lett. 26, 157-159 (2001).
[CrossRef]

B. Javidi and E. Tajahuerce, "Three dimensional object recognition using digital holography," Opt. Lett. 25, 610-612 (2000).
[CrossRef]

I. Yamaguchi and T. Zhang, "Phase-shifting digital holography," Opt. Lett. 22, 1268-1270 (1997).
[CrossRef] [PubMed]

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[CrossRef]

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[CrossRef]

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[CrossRef] [PubMed]

Optics and Photonics News (1)

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]

Proceedings of IEEE (1)

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]

Proceedings of the IEEE (1)

A. Stern and B. Javidi, "Three-Dimensional image sensing, visualization, and processing using integral imaging," Proceedings of the IEEE 94, 591- 607 (2006).
[CrossRef]

Tech. (1)

J. G. Daugman, "How iris recognition works," IEEE Trans. Circuits Syst. for Video.Tech. 14, 21-30, (2004).
[CrossRef]

Other (18)

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]

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T. Kreis, ed., Handbook of Holographic Interferometry, (Wiley, VCH, 2005).

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[PubMed]

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).

http://www.pbs.org/wgbh/amex/influenza/

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Figures (15)

Fig. 1.
Fig. 1.

Diagram of the approach for 3D sensing, visualization and recognition of microbiological objects using SEOL holographic microscopy, (a) 3D morphology-based recognition, (b) shape-tolerant 3D recognition.

Fig. 2.
Fig. 2.

Experimental setup for recording SEOL digital hologram of 3D microorganisms; Ar: Argon laser, BS1, BS2: beam splitter; M1, M2: mirror; MO: microscope objective; CCD: charge-coupled device array.

Fig. 3:
Fig. 3:

Schematic diagram of the primary stochastic minimization algorithm.

Fig. 4.
Fig. 4.

The design procedure for shape independent 3D recognition of biological microorganisms. The sampling segments are extracted in the reconstructed 3D image using SEOL digital hologram.

Fig. 5.
Fig. 5.

Coordinate system for the SEOL digital hologram and the shift-invariant 3D recognition of microorganisms.

Fig. 6.
Fig. 6.

(a) Magnitude images of two diatom algae on which the snake is initialized with 4 points, (b) the final segmentation carried out by bivariate region snake after 1500 iterations, (c) the trace of the optimization criterion during the iteration.

Fig. 7.
Fig. 7.

(a) Magnitude image of an out-of-focus sphacelaria alga reconstructed from a SEOL hologram and the 5 point snake initialization,. (b) the segmented microorganism, (c) the trace of the optimization criterion during the iteration.

Fig. 8.
Fig. 8.

(a) Magnitude image of computationally reconstructed SEOL hologram of diatom algae, (b) segmentation result, (c) the final binary windows w for the target, (d) optimization profile showing mutations as small peaks.

Fig. 9.
Fig. 9.

Each image is composed of different components of the node vector in Eq. (11) when (a) u = 1, (b) u = 2, (c) u = 3.

Fig. 10.
Fig. 10.

Recognition of sphacelaria alga, (a) reference sample A1 with the graph R, (b) graph matching result of unknown input sample A9, (c) number of detections, (d) maximum similarity and minimum difference cost, (a) and (b) are presented by contrast reversal for better visualization.

Fig. 11.
Fig. 11.

Recognition of tribonema aequale alga, (a) reference sample B1 with the graph R, (b) graph matching result of unknown input sample B2, (c) number of detections, (d) maximum similarity and minimum difference cost, (a) and (b) are presented by contrast reversal for better visualization.

Fig. 12.
Fig. 12.

The magnified intensity images at the distance d = 270 mm of microorganisms by use of a 100 × microscope objective, (a) oscillatoria bacteria, (b) diatom alga.

Fig. 13.
Fig. 13.

Experimental result of correlation coefficient calculated between the intensity image of reference and the volume intensity image of unknown input versus reconstruction distance.

Fig. 14.
Fig. 14.

Experimental setup for 3D II recording of microorganisms

Fig. 15.
Fig. 15.

Reconstructed volumetric images of sphacelaria alga at different depths, (a)d = 214 μm, (b)d = 290 μm.

Tables (3)

Tables Icon

Table 1. (a) F-test (normal distribution), (b) Levene's test (any continuous distribution) for the equality of the dispersion parameter between two sampling segments versus a sample size.

Tables Icon

Table 2. (a) T-test (normal distribution) for the equality of the location parameter, (b) Mann-whitney test (nonparametric) for comparing the median between two sampling segments versus a sample size.

Tables Icon

Table 3. K-S test (distribution-free) for comparing the cumulative distribution between two sampling segments versus a sample size.

Equations (24)

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O H ( x , y ) = d 0 δ 2 d 0 + δ 2 exp [ j 2 πz λ ] jλz exp [ j π λz ( x 2 + y 2 ) ] ×
{ ∫∫ O ( ε , η ; z ) exp [ j π λz ( ε 2 + η 2 ) ] exp [ j 2 π λz ( + y η ) ] dεdη } dz ,
H ( x , y ) = O H ( x , y ) + R ( x , y ) 2 O H 2 R 2 ,
O ( ξ , η ; τ = d 0 ) = IFrT { H ( x , y ) } τ = d 0 = A o ( x , y ) exp [ j Φ o ( x , y ) ] ,
f u ( α i , φ i ) = 1 σ φ u Φ ( φ i μ φ u σ φ u ) × 1 σ α φ u Φ ( α i μ α φ u σ α φ u ) ,
μ α φ u = μ α u + ρ u σ α u ( φ μ φ u ) σ φ u , σ α φ u 2 = σ α 2 ( 1 ρ u 2 ) .
P ( S H w , Θ ) = i = 1 N f t ( α i , φ i ) · w i × i = 1 N f b ( α i , φ i ) · ( 1 w i ) ,
μ ̂ α u = 1 N u ( w ) i∊ Ω u α i , μ ̂ φ u = 1 N u ( w ) i∊ Ω u φ i ,
σ ̂ α u = { 1 N u ( w ) i∊ Ω u ( α i μ α u ) 2 } 1 2 , σ ̂ φ u = { 1 N u ( w ) i∊ Ω u ( φ i μ φ u ) 2 } 1 2 ,
ρ ̂ u = 1 N u ( w ) σ α u σ φ u i∊ Ω u ( α i μ α u ) ( φ i μ α u ) ,
J ( S H w , Θ ) = N t ( w ) log ( σ ̂ φ t σ ̂ α t 1 ρ ̂ t 2 ) + N b ( w ) log ( σ ̂ φ b σ ̂ α b 1 ρ ̂ b 2 ) .
g uv ( X ) = K uv 2 σ 2 exp ( K uv 2 X 2 2 σ 2 ) [ exp ( j K uv · x ) exp ( σ 2 2 ) ] ,
y uv ( x , y ) = x′ = 1 N x y′ = 1 N y g uv ( x x′ , y y′ ) Ô ( x′ , y′ ) ,
V [ x ] = [ ν = 1 V y 1 ν [ x ] ν = 1 V y [ x ] ] t .
x k ( P r , θ r ) = A θ r ( x k o x c o ) + P r , A θ = [ cos θ sin θ sin θ cos θ ] , k = 1 , K ,
Γ RS ( P s , θ s ) = 1 K k = 1 K V R [ X k ( P r , θ r ) ] , V S [ X k ( P s , θ s ] V R [ X k ( P r , θ r ) ] V S [ X k ( P s , θ s ) ] ,
C RS ( P s , θ s ) = 1 K k = 1 K V R [ X k ( P r , θ r ) ] V S [ X k ( P s , θ s ) ] .
Γ RS ( P s , θ ̂ s ) > α Γ and C RS ( P s , θ ̂ s ) < α c ,
F ( N X 1 ) , ( N Y 1 ) = { N Y N Y 1 } V [ Y ] { N X N X 1 } V [ X ] = V ̂ [ Y ] V ̂ [ X ] ,
W = ( N X + N Y 2 ) [ N x ( Z X ̅ Z ̅ ) 2 + N Y ( Z Y ̅ Z ̅ ) 2 ] j = 1 N X ( Z X j Z ̅ X ) 2 + j = 1 N Y ( Z Y j Z ̅ Y ) 2 ,
T = 1 V P ̅ E [ X ] E [ Y ] { ( N X ) 1 + ( N Y ) 1 } 1 2 ,
U = N X N Y + N X ( N X + 1 ) 2 R X ,
J = max < u < { F X ( u ) F Y ( u ) } ,
Corr ( x , y , p ) = FT 1 { [ U X ( x , y , p ) ] × FT * [ U Y ( x , y ) ] } ,

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