Abstract

Abstract: Better understanding of bacteria environment interactions in the context of biofilm formation requires accurate 3-dimentional measurements of bacteria motility. Digital Holographic Microscopy (DHM) has demonstrated its capability in resolving 3D distribution and mobility of particulates in a dense suspension. Due to their low scattering efficiency, bacteria are substantially difficult to be imaged by DHM. In this paper, we introduce a novel correlation-based de-noising algorithm to remove the background noise and enhance the quality of the hologram. Implemented in conjunction with DHM, we demonstrate that the method allows DHM to resolve 3-D E. coli bacteria locations of a dense suspension (>107 cells/ml) with submicron resolutions (<0.5 µm) over substantial depth and to obtain thousands of 3D cell trajectories.

© 2014 Optical Society of America

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References

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2014 (4)

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Phys. Rev. Lett. 113(6), 068103 (2014).
[Crossref] [PubMed]

J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

A. T. Hansen, M. Hondzo, J. Sheng, and M. J. Sadowsky, “Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae,” Freshw. Biol. 59(2), 312–324 (2014).
[Crossref]

2013 (4)

A. Chengala, M. Hondzo, and J. Sheng, “Microalga propels along vorticity direction in a shear flow,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87(5), 052704 (2013).
[Crossref] [PubMed]

B. J. Gemmell, J. Sheng, and E. J. Buskey, “Morphology of seahorse head hydrodynamically aids in capture of evasive prey,” Nat. Commun. 4, 2840 (2013).

S. Talapatra and J. Katz, “Three-dimensional velocity measurements in a roughness sublayer using microscopic digital in-line holography and optical index matching,” Meas. Sci. Technol. 24(2), 024004 (2013).
[Crossref]

V. Kantsler, J. Dunkel, M. Polin, and R. E. Goldstein, “Ciliary contact interactions dominate surface scattering of swimming eukaryotes,” Proc. Natl. Acad. Sci. U.S.A. 110(4), 1187–1192 (2013).
[Crossref] [PubMed]

2012 (5)

H. C. Marcos, H. C. Fu, T. R. Powers, and R. Stocker, “Bacterial rheotaxis,” Proc. Natl. Acad. Sci. U.S.A. 109(13), 4780–4785 (2012).
[Crossref] [PubMed]

L. Gan and G. J. Jensen, “Electron tomography of cells,” Q. Rev. Biophys. 45(1), 27–56 (2012).
[Crossref] [PubMed]

A. Greenbaum, U. Sikora, and A. Ozcan, “Field-portable wide-field microscopy of dense samples using multi-height pixel super-resolution based lensfree imaging,” Lab Chip 12(7), 1242–1245 (2012).
[Crossref] [PubMed]

S. Talapatra and J. Katz, “Coherent structures in the inner part of a rough-wall channel flow resolved using holographic PIV,” J. Fluid Mech. 711, 161–170 (2012).
[Crossref]

T. W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proc. Natl. Acad. Sci. U.S.A. 109(40), 16018–16022 (2012).
[Crossref] [PubMed]

2011 (3)

O. Mudanyali, W. Bishara, and A. Ozcan, “Lensfree super-resolution holographic microscopy using wetting films on a chip,” Opt. Express 19(18), 17378–17389 (2011).
[Crossref] [PubMed]

R. Stocker, “Reverse and flick: Hybrid locomotion in bacteria,” Proc. Natl. Acad. Sci. U.S.A. 108(7), 2635–2636 (2011).
[Crossref] [PubMed]

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
[Crossref] [PubMed]

2010 (7)

N. T. Shaked, T. M. Newpher, M. D. Ehlers, and A. Wax, “Parallel on-axis holographic phase microscopy of biological cells and unicellular microorganism dynamics,” Appl. Opt. 49(15), 2872–2878 (2010).
[Crossref] [PubMed]

C. Oh, S. O. Isikman, B. Khademhosseinieh, and A. Ozcan, “On-chip differential interference contrast microscopy using lensless digital holography,” Opt. Express 18(5), 4717–4726 (2010).
[Crossref] [PubMed]

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

T. W. Su, A. Erlinger, D. Tseng, and A. Ozcan, “Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy,” Anal. Chem. 82(19), 8307–8312 (2010).
[Crossref] [PubMed]

J. Katz and J. Sheng, “Applications of holography in fluid mechanics and particle dynamics,” Annu. Rev. Fluid Mech. 42(1), 531–555 (2010).
[Crossref]

W. Bishara, T. W. Su, A. F. Coskun, and A. Ozcan, “Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution,” Opt. Express 18(11), 11181–11191 (2010).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, J. Katz, J. E. Adolf, and A. R. Place, “A dinoflagellate exploits toxins to immobilize prey prior to ingestion,” Proc. Natl. Acad. Sci. U.S.A. 107(5), 2082–2087 (2010).
[Crossref] [PubMed]

2009 (3)

I. Moon, M. Daneshpanah, B. Javidi, and A. Stern, “Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy,” Proc. IEEE 97(6), 990–1010 (2009).
[Crossref]

J. Sheng, E. Malkiel, and J. Katz, “Buffer layer structures associated with extreme wall stress events in a smooth wall turbulent boundary layer,” J. Fluid Mech. 633, 17–60 (2009).
[Crossref]

M. Bertilson, O. von Hofsten, U. Vogt, A. Holmberg, and H. M. Hertz, “High-resolution computed tomography with a compact soft x-ray microscope,” Opt. Express 17(13), 11057–11065 (2009).
[Crossref] [PubMed]

2008 (2)

J. Sheng, E. Malkiel, and J. Katz, “Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress in a turbulent boundary layer,” Exp. Fluids 45(6), 1023–1035 (2008).
[Crossref]

Y. Awatsuji, T. Tahara, A. Kaneko, T. Koyama, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel two-step phase-shifting digital holography,” Appl. Opt. 47(19), D183–D189 (2008).
[Crossref] [PubMed]

2007 (2)

M. Danesh Panah and B. Javidi, “Tracking biological microorganisms in sequence of 3D holographic microscopy images,” Opt. Express 15, 10761–10766 (2007).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

2006 (6)

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

E. Lauga, W. R. DiLuzio, G. M. Whitesides, and H. A. Stone, “Swimming in circles: Motion of bacteria near solid boundaries,” Biophys. J. 90(2), 400–412 (2006).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Digital holographic microscope for measuring three-dimensional particle distributions and motions,” Appl. Opt. 45(16), 3893–3901 (2006).
[Crossref] [PubMed]

S. K. Jericho, J. Garcia-Sucerquia, W. B. Xu, M. H. Jericho, and H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instr. 77, 043706 (2006).

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

M. K. Kim, L. F. Yu, and C. J. Mann, “Interference techniques in digital holography,” J. Opt. A 8(7), S518–S523 (2006).
[Crossref]

2005 (2)

2004 (3)

2003 (3)

2002 (2)

2000 (1)

B. Tao, J. Katz, and C. Meneveau, “Geometry and scale relationships in high Reynolds number turbulence determined from three-dimensional holographic velocimetry,” Phys. Fluids 12(5), 941–944 (2000).
[Crossref]

1998 (1)

Y. N. Xia and G. M. Whitesides, “Soft lithography,” Annu. Rev. Mater. Sci. 28(1), 153–184 (1998).
[Crossref]

1997 (2)

J. Zhang, B. Tao, and J. Katz, “Turbulent flow measurement in a square duct with hybrid holographic PIV,” Exp. Fluids 23(5), 373–381 (1997).
[Crossref]

I. Yamaguchi and T. Zhang, “Phase-shifting digital holography,” Opt. Lett. 22(16), 1268–1270 (1997).
[Crossref] [PubMed]

1995 (2)

P. D. Frymier, R. M. Ford, H. C. Berg, and P. T. Cummings, “Three-dimensional tracking of motile bacteria near a solid planar surface,” Proc. Natl. Acad. Sci. U.S.A. 92(13), 6195–6199 (1995).
[Crossref] [PubMed]

G. Greenberg and A. Boyde, “Novel method for stereo imaging in light-microscopy at high magnifications: reply,” Neuroimage 2, 86–87 (1995).
[Crossref]

1994 (1)

G. Y. Fan and M. H. Ellisman, “Stereoscopy by tilted illumination in transmission electron microscopy,” Ultramicroscopy 55(2), 155–164 (1994).
[Crossref] [PubMed]

1988 (1)

G. Q. Xiao, T. R. Corle, and G. S. Kino, “Real‐time confocal scanning optical microscope,” Appl. Phys. Lett. 53(8), 716–718 (1988).
[Crossref]

1987 (1)

1985 (1)

A. Boyde, “Stereoscopic images in confocal (tandem scanning) microscopy,” Science 230(4731), 1270–1272 (1985).
[Crossref] [PubMed]

1973 (1)

J. Adler, “A method for measuring chemotaxis and use of the method to determine optimum conditions for chemotaxis by Escherichia coli,” J. Gen. Microbiol. 74(1), 77–91 (1973).
[Crossref] [PubMed]

1972 (2)

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli Analysed by Three-dimensional Tracking,” Nature 239(5374), 500–504 (1972).
[Crossref] [PubMed]

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239(5374), 500–504 (1972).
[Crossref] [PubMed]

1971 (1)

H. C. Berg, “How to track bacteria,” Rev. Sci. Instrum. 42(6), 868–871 (1971).
[Crossref] [PubMed]

1968 (1)

Adler, J.

J. Adler, “A method for measuring chemotaxis and use of the method to determine optimum conditions for chemotaxis by Escherichia coli,” J. Gen. Microbiol. 74(1), 77–91 (1973).
[Crossref] [PubMed]

Adolf, J.

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

Adolf, J. E.

J. Sheng, E. Malkiel, J. Katz, J. E. Adolf, and A. R. Place, “A dinoflagellate exploits toxins to immobilize prey prior to ingestion,” Proc. Natl. Acad. Sci. U.S.A. 107(5), 2082–2087 (2010).
[Crossref] [PubMed]

Aslund, N.

Awatsuji, Y.

Barry, M.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Phys. Rev. Lett. 113(6), 068103 (2014).
[Crossref] [PubMed]

Belas, R.

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

Berg, H. C.

P. D. Frymier, R. M. Ford, H. C. Berg, and P. T. Cummings, “Three-dimensional tracking of motile bacteria near a solid planar surface,” Proc. Natl. Acad. Sci. U.S.A. 92(13), 6195–6199 (1995).
[Crossref] [PubMed]

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239(5374), 500–504 (1972).
[Crossref] [PubMed]

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli Analysed by Three-dimensional Tracking,” Nature 239(5374), 500–504 (1972).
[Crossref] [PubMed]

H. C. Berg, “How to track bacteria,” Rev. Sci. Instrum. 42(6), 868–871 (1971).
[Crossref] [PubMed]

Bertilson, M.

Bishara, W.

Boyde, A.

G. Greenberg and A. Boyde, “Novel method for stereo imaging in light-microscopy at high magnifications: reply,” Neuroimage 2, 86–87 (1995).
[Crossref]

A. Boyde, “Stereoscopic images in confocal (tandem scanning) microscopy,” Science 230(4731), 1270–1272 (1985).
[Crossref] [PubMed]

Brown, D. A.

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239(5374), 500–504 (1972).
[Crossref] [PubMed]

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli Analysed by Three-dimensional Tracking,” Nature 239(5374), 500–504 (1972).
[Crossref] [PubMed]

Buskey, E. J.

B. J. Gemmell, J. Sheng, and E. J. Buskey, “Morphology of seahorse head hydrodynamically aids in capture of evasive prey,” Nat. Commun. 4, 2840 (2013).

Carl, D.

Carlsson, K.

Cembella, A. D.

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

Chengala, A.

A. Chengala, M. Hondzo, and J. Sheng, “Microalga propels along vorticity direction in a shear flow,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87(5), 052704 (2013).
[Crossref] [PubMed]

Cisneros, L. H.

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
[Crossref] [PubMed]

Colomb, T.

Corle, T. R.

G. Q. Xiao, T. R. Corle, and G. S. Kino, “Real‐time confocal scanning optical microscope,” Appl. Phys. Lett. 53(8), 716–718 (1988).
[Crossref]

Coskun, A. F.

Cuche, E.

Cummings, P. T.

P. D. Frymier, R. M. Ford, H. C. Berg, and P. T. Cummings, “Three-dimensional tracking of motile bacteria near a solid planar surface,” Proc. Natl. Acad. Sci. U.S.A. 92(13), 6195–6199 (1995).
[Crossref] [PubMed]

Danesh Panah, M.

Daneshpanah, M.

I. Moon, M. Daneshpanah, B. Javidi, and A. Stern, “Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy,” Proc. IEEE 97(6), 990–1010 (2009).
[Crossref]

Debeir, O.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

Decaestecker, C.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

Depeursinge, C.

DiLuzio, W. R.

E. Lauga, W. R. DiLuzio, G. M. Whitesides, and H. A. Stone, “Swimming in circles: Motion of bacteria near solid boundaries,” Biophys. J. 90(2), 400–412 (2006).
[Crossref] [PubMed]

Drescher, K.

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
[Crossref] [PubMed]

Dubois, F.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

F. Dubois, C. Minetti, O. Monnom, C. Yourassowsky, J. C. Legros, and P. Kischel, “Pattern recognition with a digital holographic microscope working in partially coherent illumination,” Appl. Opt. 41(20), 4108–4119 (2002).
[Crossref] [PubMed]

Dunkel, J.

V. Kantsler, J. Dunkel, M. Polin, and R. E. Goldstein, “Ciliary contact interactions dominate surface scattering of swimming eukaryotes,” Proc. Natl. Acad. Sci. U.S.A. 110(4), 1187–1192 (2013).
[Crossref] [PubMed]

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
[Crossref] [PubMed]

Dürr, F.

Ehlers, M. D.

Ellisman, M. H.

G. Y. Fan and M. H. Ellisman, “Stereoscopy by tilted illumination in transmission electron microscopy,” Ultramicroscopy 55(2), 155–164 (1994).
[Crossref] [PubMed]

Emery, Y.

Erlinger, A.

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

T. W. Su, A. Erlinger, D. Tseng, and A. Ozcan, “Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy,” Anal. Chem. 82(19), 8307–8312 (2010).
[Crossref] [PubMed]

Fan, G. Y.

G. Y. Fan and M. H. Ellisman, “Stereoscopy by tilted illumination in transmission electron microscopy,” Ultramicroscopy 55(2), 155–164 (1994).
[Crossref] [PubMed]

Ford, R. M.

P. D. Frymier, R. M. Ford, H. C. Berg, and P. T. Cummings, “Three-dimensional tracking of motile bacteria near a solid planar surface,” Proc. Natl. Acad. Sci. U.S.A. 92(13), 6195–6199 (1995).
[Crossref] [PubMed]

Frymier, P. D.

P. D. Frymier, R. M. Ford, H. C. Berg, and P. T. Cummings, “Three-dimensional tracking of motile bacteria near a solid planar surface,” Proc. Natl. Acad. Sci. U.S.A. 92(13), 6195–6199 (1995).
[Crossref] [PubMed]

Fu, H. C.

H. C. Marcos, H. C. Fu, T. R. Powers, and R. Stocker, “Bacterial rheotaxis,” Proc. Natl. Acad. Sci. U.S.A. 109(13), 4780–4785 (2012).
[Crossref] [PubMed]

Gan, L.

L. Gan and G. J. Jensen, “Electron tomography of cells,” Q. Rev. Biophys. 45(1), 27–56 (2012).
[Crossref] [PubMed]

Ganguly, S.

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
[Crossref] [PubMed]

Garcia-Sucerquia, J.

S. K. Jericho, J. Garcia-Sucerquia, W. B. Xu, M. H. Jericho, and H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instr. 77, 043706 (2006).

Gemmell, B. J.

B. J. Gemmell, J. Sheng, and E. J. Buskey, “Morphology of seahorse head hydrodynamically aids in capture of evasive prey,” Nat. Commun. 4, 2840 (2013).

Goldstein, R. E.

V. Kantsler, J. Dunkel, M. Polin, and R. E. Goldstein, “Ciliary contact interactions dominate surface scattering of swimming eukaryotes,” Proc. Natl. Acad. Sci. U.S.A. 110(4), 1187–1192 (2013).
[Crossref] [PubMed]

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
[Crossref] [PubMed]

Greenbaum, A.

A. Greenbaum, U. Sikora, and A. Ozcan, “Field-portable wide-field microscopy of dense samples using multi-height pixel super-resolution based lensfree imaging,” Lab Chip 12(7), 1242–1245 (2012).
[Crossref] [PubMed]

Greenberg, G.

G. Greenberg and A. Boyde, “Novel method for stereo imaging in light-microscopy at high magnifications: reply,” Neuroimage 2, 86–87 (1995).
[Crossref]

Hansen, A. T.

A. T. Hansen, M. Hondzo, J. Sheng, and M. J. Sadowsky, “Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae,” Freshw. Biol. 59(2), 312–324 (2014).
[Crossref]

Hertz, H. M.

Holmberg, A.

Hondzo, M.

A. T. Hansen, M. Hondzo, J. Sheng, and M. J. Sadowsky, “Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae,” Freshw. Biol. 59(2), 312–324 (2014).
[Crossref]

A. Chengala, M. Hondzo, and J. Sheng, “Microalga propels along vorticity direction in a shear flow,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87(5), 052704 (2013).
[Crossref] [PubMed]

Isikman, S. O.

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

C. Oh, S. O. Isikman, B. Khademhosseinieh, and A. Ozcan, “On-chip differential interference contrast microscopy using lensless digital holography,” Opt. Express 18(5), 4717–4726 (2010).
[Crossref] [PubMed]

Javidi, B.

I. Moon, M. Daneshpanah, B. Javidi, and A. Stern, “Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy,” Proc. IEEE 97(6), 990–1010 (2009).
[Crossref]

M. Danesh Panah and B. Javidi, “Tracking biological microorganisms in sequence of 3D holographic microscopy images,” Opt. Express 15, 10761–10766 (2007).
[Crossref] [PubMed]

Jensen, G. J.

L. Gan and G. J. Jensen, “Electron tomography of cells,” Q. Rev. Biophys. 45(1), 27–56 (2012).
[Crossref] [PubMed]

Jericho, M. H.

S. K. Jericho, J. Garcia-Sucerquia, W. B. Xu, M. H. Jericho, and H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instr. 77, 043706 (2006).

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography of microspheres,” Appl. Opt. 41(25), 5367–5375 (2002).
[Crossref] [PubMed]

Jericho, S. K.

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

S. K. Jericho, J. Garcia-Sucerquia, W. B. Xu, M. H. Jericho, and H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instr. 77, 043706 (2006).

Kaneko, A.

Kantsler, V.

V. Kantsler, J. Dunkel, M. Polin, and R. E. Goldstein, “Ciliary contact interactions dominate surface scattering of swimming eukaryotes,” Proc. Natl. Acad. Sci. U.S.A. 110(4), 1187–1192 (2013).
[Crossref] [PubMed]

Katz, J.

S. Talapatra and J. Katz, “Three-dimensional velocity measurements in a roughness sublayer using microscopic digital in-line holography and optical index matching,” Meas. Sci. Technol. 24(2), 024004 (2013).
[Crossref]

S. Talapatra and J. Katz, “Coherent structures in the inner part of a rough-wall channel flow resolved using holographic PIV,” J. Fluid Mech. 711, 161–170 (2012).
[Crossref]

J. Sheng, E. Malkiel, J. Katz, J. E. Adolf, and A. R. Place, “A dinoflagellate exploits toxins to immobilize prey prior to ingestion,” Proc. Natl. Acad. Sci. U.S.A. 107(5), 2082–2087 (2010).
[Crossref] [PubMed]

J. Katz and J. Sheng, “Applications of holography in fluid mechanics and particle dynamics,” Annu. Rev. Fluid Mech. 42(1), 531–555 (2010).
[Crossref]

J. Sheng, E. Malkiel, and J. Katz, “Buffer layer structures associated with extreme wall stress events in a smooth wall turbulent boundary layer,” J. Fluid Mech. 633, 17–60 (2009).
[Crossref]

J. Sheng, E. Malkiel, and J. Katz, “Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress in a turbulent boundary layer,” Exp. Fluids 45(6), 1023–1035 (2008).
[Crossref]

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Digital holographic microscope for measuring three-dimensional particle distributions and motions,” Appl. Opt. 45(16), 3893–3901 (2006).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Single beam two-views holographic particle image velocimetry,” Appl. Opt. 42(2), 235–250 (2003).
[Crossref] [PubMed]

E. Malkiel, J. Sheng, J. Katz, and J. R. Strickler, “The three-dimensional flow field generated by a feeding calanoid copepod measured using digital holography,” J. Exp. Biol. 206(20), 3657–3666 (2003).
[Crossref] [PubMed]

B. Tao, J. Katz, and C. Meneveau, “Geometry and scale relationships in high Reynolds number turbulence determined from three-dimensional holographic velocimetry,” Phys. Fluids 12(5), 941–944 (2000).
[Crossref]

J. Zhang, B. Tao, and J. Katz, “Turbulent flow measurement in a square duct with hybrid holographic PIV,” Exp. Fluids 23(5), 373–381 (1997).
[Crossref]

Kemper, B.

Khademhosseinieh, B.

Kim, M. K.

M. K. Kim, L. F. Yu, and C. J. Mann, “Interference techniques in digital holography,” J. Opt. A 8(7), S518–S523 (2006).
[Crossref]

Kino, G. S.

G. Q. Xiao, T. R. Corle, and G. S. Kino, “Real‐time confocal scanning optical microscope,” Appl. Phys. Lett. 53(8), 716–718 (1988).
[Crossref]

Kischel, P.

Kiss, R.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

Koschitzki, F.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Koyama, T.

Kreuzer, H. J.

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

S. K. Jericho, J. Garcia-Sucerquia, W. B. Xu, M. H. Jericho, and H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instr. 77, 043706 (2006).

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography of microspheres,” Appl. Opt. 41(25), 5367–5375 (2002).
[Crossref] [PubMed]

Kubota, T.

Lauga, E.

E. Lauga, W. R. DiLuzio, G. M. Whitesides, and H. A. Stone, “Swimming in circles: Motion of bacteria near solid boundaries,” Biophys. J. 90(2), 400–412 (2006).
[Crossref] [PubMed]

Legros, J. C.

Legros, J.-C.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

Lewis, N. I.

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

Li, G. F.

J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

Limberger, H. G.

Lotz, C.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Magistretti, P. J.

Maleschlijski, S.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Malkiel, E.

J. Sheng, E. Malkiel, J. Katz, J. E. Adolf, and A. R. Place, “A dinoflagellate exploits toxins to immobilize prey prior to ingestion,” Proc. Natl. Acad. Sci. U.S.A. 107(5), 2082–2087 (2010).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Buffer layer structures associated with extreme wall stress events in a smooth wall turbulent boundary layer,” J. Fluid Mech. 633, 17–60 (2009).
[Crossref]

J. Sheng, E. Malkiel, and J. Katz, “Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress in a turbulent boundary layer,” Exp. Fluids 45(6), 1023–1035 (2008).
[Crossref]

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Digital holographic microscope for measuring three-dimensional particle distributions and motions,” Appl. Opt. 45(16), 3893–3901 (2006).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Single beam two-views holographic particle image velocimetry,” Appl. Opt. 42(2), 235–250 (2003).
[Crossref] [PubMed]

E. Malkiel, J. Sheng, J. Katz, and J. R. Strickler, “The three-dimensional flow field generated by a feeding calanoid copepod measured using digital holography,” J. Exp. Biol. 206(20), 3657–3666 (2003).
[Crossref] [PubMed]

Mann, C. J.

M. K. Kim, L. F. Yu, and C. J. Mann, “Interference techniques in digital holography,” J. Opt. A 8(7), S518–S523 (2006).
[Crossref]

Marcos, H. C.

H. C. Marcos, H. C. Fu, T. R. Powers, and R. Stocker, “Bacterial rheotaxis,” Proc. Natl. Acad. Sci. U.S.A. 109(13), 4780–4785 (2012).
[Crossref] [PubMed]

Marquet, P.

Matoba, O.

McConnell, G.

Meinertzhagen, I. A.

Meneveau, C.

B. Tao, J. Katz, and C. Meneveau, “Geometry and scale relationships in high Reynolds number turbulence determined from three-dimensional holographic velocimetry,” Phys. Fluids 12(5), 941–944 (2000).
[Crossref]

Meng, H.

Minetti, C.

Molaei, M.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Phys. Rev. Lett. 113(6), 068103 (2014).
[Crossref] [PubMed]

Monnom, O.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

F. Dubois, C. Minetti, O. Monnom, C. Yourassowsky, J. C. Legros, and P. Kischel, “Pattern recognition with a digital holographic microscope working in partially coherent illumination,” Appl. Opt. 41(20), 4108–4119 (2002).
[Crossref] [PubMed]

Moon, I.

I. Moon, M. Daneshpanah, B. Javidi, and A. Stern, “Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy,” Proc. IEEE 97(6), 990–1010 (2009).
[Crossref]

Mudanyali, O.

O. Mudanyali, W. Bishara, and A. Ozcan, “Lensfree super-resolution holographic microscopy using wetting films on a chip,” Opt. Express 19(18), 17378–17389 (2011).
[Crossref] [PubMed]

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

Newpher, T. M.

Nishio, K.

Obst, U.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Oh, C.

Ozcan, A.

T. W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proc. Natl. Acad. Sci. U.S.A. 109(40), 16018–16022 (2012).
[Crossref] [PubMed]

A. Greenbaum, U. Sikora, and A. Ozcan, “Field-portable wide-field microscopy of dense samples using multi-height pixel super-resolution based lensfree imaging,” Lab Chip 12(7), 1242–1245 (2012).
[Crossref] [PubMed]

O. Mudanyali, W. Bishara, and A. Ozcan, “Lensfree super-resolution holographic microscopy using wetting films on a chip,” Opt. Express 19(18), 17378–17389 (2011).
[Crossref] [PubMed]

W. Bishara, T. W. Su, A. F. Coskun, and A. Ozcan, “Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution,” Opt. Express 18(11), 11181–11191 (2010).
[Crossref] [PubMed]

C. Oh, S. O. Isikman, B. Khademhosseinieh, and A. Ozcan, “On-chip differential interference contrast microscopy using lensless digital holography,” Opt. Express 18(5), 4717–4726 (2010).
[Crossref] [PubMed]

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

T. W. Su, A. Erlinger, D. Tseng, and A. Ozcan, “Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy,” Anal. Chem. 82(19), 8307–8312 (2010).
[Crossref] [PubMed]

Place, A. R.

J. Sheng, E. Malkiel, J. Katz, J. E. Adolf, and A. R. Place, “A dinoflagellate exploits toxins to immobilize prey prior to ingestion,” Proc. Natl. Acad. Sci. U.S.A. 107(5), 2082–2087 (2010).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

Polin, M.

V. Kantsler, J. Dunkel, M. Polin, and R. E. Goldstein, “Ciliary contact interactions dominate surface scattering of swimming eukaryotes,” Proc. Natl. Acad. Sci. U.S.A. 110(4), 1187–1192 (2013).
[Crossref] [PubMed]

Powers, T. R.

H. C. Marcos, H. C. Fu, T. R. Powers, and R. Stocker, “Bacterial rheotaxis,” Proc. Natl. Acad. Sci. U.S.A. 109(13), 4780–4785 (2012).
[Crossref] [PubMed]

Pu, Y.

Rappaz, B.

Rosenhahn, A.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Sadowsky, M. J.

A. T. Hansen, M. Hondzo, J. Sheng, and M. J. Sadowsky, “Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae,” Freshw. Biol. 59(2), 312–324 (2014).
[Crossref]

Salathé, R. P.

Saleh, B. E. A.

J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

Schwartz, T.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Sencan, I.

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

Seo, S.

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

Shaked, N. T.

Sheng, J.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Phys. Rev. Lett. 113(6), 068103 (2014).
[Crossref] [PubMed]

A. T. Hansen, M. Hondzo, J. Sheng, and M. J. Sadowsky, “Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae,” Freshw. Biol. 59(2), 312–324 (2014).
[Crossref]

B. J. Gemmell, J. Sheng, and E. J. Buskey, “Morphology of seahorse head hydrodynamically aids in capture of evasive prey,” Nat. Commun. 4, 2840 (2013).

A. Chengala, M. Hondzo, and J. Sheng, “Microalga propels along vorticity direction in a shear flow,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87(5), 052704 (2013).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, J. Katz, J. E. Adolf, and A. R. Place, “A dinoflagellate exploits toxins to immobilize prey prior to ingestion,” Proc. Natl. Acad. Sci. U.S.A. 107(5), 2082–2087 (2010).
[Crossref] [PubMed]

J. Katz and J. Sheng, “Applications of holography in fluid mechanics and particle dynamics,” Annu. Rev. Fluid Mech. 42(1), 531–555 (2010).
[Crossref]

J. Sheng, E. Malkiel, and J. Katz, “Buffer layer structures associated with extreme wall stress events in a smooth wall turbulent boundary layer,” J. Fluid Mech. 633, 17–60 (2009).
[Crossref]

J. Sheng, E. Malkiel, and J. Katz, “Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress in a turbulent boundary layer,” Exp. Fluids 45(6), 1023–1035 (2008).
[Crossref]

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Digital holographic microscope for measuring three-dimensional particle distributions and motions,” Appl. Opt. 45(16), 3893–3901 (2006).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, and J. Katz, “Single beam two-views holographic particle image velocimetry,” Appl. Opt. 42(2), 235–250 (2003).
[Crossref] [PubMed]

E. Malkiel, J. Sheng, J. Katz, and J. R. Strickler, “The three-dimensional flow field generated by a feeding calanoid copepod measured using digital holography,” J. Exp. Biol. 206(20), 3657–3666 (2003).
[Crossref] [PubMed]

Sikora, U.

A. Greenbaum, U. Sikora, and A. Ozcan, “Field-portable wide-field microscopy of dense samples using multi-height pixel super-resolution based lensfree imaging,” Lab Chip 12(7), 1242–1245 (2012).
[Crossref] [PubMed]

Stern, A.

I. Moon, M. Daneshpanah, B. Javidi, and A. Stern, “Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy,” Proc. IEEE 97(6), 990–1010 (2009).
[Crossref]

Stocker, R.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Phys. Rev. Lett. 113(6), 068103 (2014).
[Crossref] [PubMed]

H. C. Marcos, H. C. Fu, T. R. Powers, and R. Stocker, “Bacterial rheotaxis,” Proc. Natl. Acad. Sci. U.S.A. 109(13), 4780–4785 (2012).
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E. Lauga, W. R. DiLuzio, G. M. Whitesides, and H. A. Stone, “Swimming in circles: Motion of bacteria near solid boundaries,” Biophys. J. 90(2), 400–412 (2006).
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Strickler, J. R.

E. Malkiel, J. Sheng, J. Katz, and J. R. Strickler, “The three-dimensional flow field generated by a feeding calanoid copepod measured using digital holography,” J. Exp. Biol. 206(20), 3657–3666 (2003).
[Crossref] [PubMed]

Su, T. W.

T. W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proc. Natl. Acad. Sci. U.S.A. 109(40), 16018–16022 (2012).
[Crossref] [PubMed]

T. W. Su, A. Erlinger, D. Tseng, and A. Ozcan, “Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy,” Anal. Chem. 82(19), 8307–8312 (2010).
[Crossref] [PubMed]

S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

W. Bishara, T. W. Su, A. F. Coskun, and A. Ozcan, “Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution,” Opt. Express 18(11), 11181–11191 (2010).
[Crossref] [PubMed]

Tahara, T.

Talapatra, S.

S. Talapatra and J. Katz, “Three-dimensional velocity measurements in a roughness sublayer using microscopic digital in-line holography and optical index matching,” Meas. Sci. Technol. 24(2), 024004 (2013).
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S. Talapatra and J. Katz, “Coherent structures in the inner part of a rough-wall channel flow resolved using holographic PIV,” J. Fluid Mech. 711, 161–170 (2012).
[Crossref]

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B. Tao, J. Katz, and C. Meneveau, “Geometry and scale relationships in high Reynolds number turbulence determined from three-dimensional holographic velocimetry,” Phys. Fluids 12(5), 941–944 (2000).
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J. Zhang, B. Tao, and J. Katz, “Turbulent flow measurement in a square duct with hybrid holographic PIV,” Exp. Fluids 23(5), 373–381 (1997).
[Crossref]

Tseng, D.

T. W. Su, A. Erlinger, D. Tseng, and A. Ozcan, “Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy,” Anal. Chem. 82(19), 8307–8312 (2010).
[Crossref] [PubMed]

Ura, S.

Van Ham, P.

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
[Crossref] [PubMed]

Vater, S. M.

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
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Wax, A.

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S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
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Wernicke, G.

Whitesides, G. M.

E. Lauga, W. R. DiLuzio, G. M. Whitesides, and H. A. Stone, “Swimming in circles: Motion of bacteria near solid boundaries,” Biophys. J. 90(2), 400–412 (2006).
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J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

Xu, W.

Xu, W. B.

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
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Xue, L.

T. W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proc. Natl. Acad. Sci. U.S.A. 109(40), 16018–16022 (2012).
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Yamaguchi, I.

Ye, Y. T.

J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

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F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
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F. Dubois, C. Minetti, O. Monnom, C. Yourassowsky, J. C. Legros, and P. Kischel, “Pattern recognition with a digital holographic microscope working in partially coherent illumination,” Appl. Opt. 41(20), 4108–4119 (2002).
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M. K. Kim, L. F. Yu, and C. J. Mann, “Interference techniques in digital holography,” J. Opt. A 8(7), S518–S523 (2006).
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J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

J. Zhang, B. Tao, and J. Katz, “Turbulent flow measurement in a square duct with hybrid holographic PIV,” Exp. Fluids 23(5), 373–381 (1997).
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S. Seo, S. O. Isikman, I. Sencan, O. Mudanyali, T. W. Su, W. Bishara, A. Erlinger, and A. Ozcan, “High-throughput lens-free blood analysis on a chip,” Anal. Chem. 82(11), 4621–4627 (2010).
[Crossref] [PubMed]

T. W. Su, A. Erlinger, D. Tseng, and A. Ozcan, “Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy,” Anal. Chem. 82(19), 8307–8312 (2010).
[Crossref] [PubMed]

Annu. Rev. Fluid Mech. (1)

J. Katz and J. Sheng, “Applications of holography in fluid mechanics and particle dynamics,” Annu. Rev. Fluid Mech. 42(1), 531–555 (2010).
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Annu. Rev. Mater. Sci. (1)

Y. N. Xia and G. M. Whitesides, “Soft lithography,” Annu. Rev. Mater. Sci. 28(1), 153–184 (1998).
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Appl. Opt. (10)

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T. Colomb, F. Dürr, E. Cuche, P. Marquet, H. G. Limberger, R. P. Salathé, and C. Depeursinge, “Polarization microscopy by use of digital holography: application to optical-fiber birefringence measurements,” Appl. Opt. 44(21), 4461–4469 (2005).
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F. Dubois, C. Minetti, O. Monnom, C. Yourassowsky, J. C. Legros, and P. Kischel, “Pattern recognition with a digital holographic microscope working in partially coherent illumination,” Appl. Opt. 41(20), 4108–4119 (2002).
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J. Sheng, E. Malkiel, and J. Katz, “Digital holographic microscope for measuring three-dimensional particle distributions and motions,” Appl. Opt. 45(16), 3893–3901 (2006).
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G. Q. Xiao, T. R. Corle, and G. S. Kino, “Real‐time confocal scanning optical microscope,” Appl. Phys. Lett. 53(8), 716–718 (1988).
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Biophys. J. (1)

E. Lauga, W. R. DiLuzio, G. M. Whitesides, and H. A. Stone, “Swimming in circles: Motion of bacteria near solid boundaries,” Biophys. J. 90(2), 400–412 (2006).
[Crossref] [PubMed]

Exp. Fluids (2)

J. Sheng, E. Malkiel, and J. Katz, “Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress in a turbulent boundary layer,” Exp. Fluids 45(6), 1023–1035 (2008).
[Crossref]

J. Zhang, B. Tao, and J. Katz, “Turbulent flow measurement in a square duct with hybrid holographic PIV,” Exp. Fluids 23(5), 373–381 (1997).
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Freshw. Biol. (1)

A. T. Hansen, M. Hondzo, J. Sheng, and M. J. Sadowsky, “Microscale measurements reveal contrasting effects of photosynthesis and epiphytes on frictional drag on the surfaces of filamentous algae,” Freshw. Biol. 59(2), 312–324 (2014).
[Crossref]

J. Biomed. Opt. (1)

F. Dubois, C. Yourassowsky, O. Monnom, J.-C. Legros, O. Debeir, P. Van Ham, R. Kiss, and C. Decaestecker, “Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration,” J. Biomed. Opt. 11(5), 054032 (2006).
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E. Malkiel, J. Sheng, J. Katz, and J. R. Strickler, “The three-dimensional flow field generated by a feeding calanoid copepod measured using digital holography,” J. Exp. Biol. 206(20), 3657–3666 (2003).
[Crossref] [PubMed]

J. Fluid Mech. (2)

S. Talapatra and J. Katz, “Coherent structures in the inner part of a rough-wall channel flow resolved using holographic PIV,” J. Fluid Mech. 711, 161–170 (2012).
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J. Sheng, E. Malkiel, and J. Katz, “Buffer layer structures associated with extreme wall stress events in a smooth wall turbulent boundary layer,” J. Fluid Mech. 633, 17–60 (2009).
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J. Opt. Soc. Am. A (2)

Lab Chip (1)

A. Greenbaum, U. Sikora, and A. Ozcan, “Field-portable wide-field microscopy of dense samples using multi-height pixel super-resolution based lensfree imaging,” Lab Chip 12(7), 1242–1245 (2012).
[Crossref] [PubMed]

Meas. Sci. Technol. (1)

S. Talapatra and J. Katz, “Three-dimensional velocity measurements in a roughness sublayer using microscopic digital in-line holography and optical index matching,” Meas. Sci. Technol. 24(2), 024004 (2013).
[Crossref]

Nat. Commun. (1)

B. J. Gemmell, J. Sheng, and E. J. Buskey, “Morphology of seahorse head hydrodynamically aids in capture of evasive prey,” Nat. Commun. 4, 2840 (2013).

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J. Zhang, Y. Xie, G. F. Li, Y. T. Ye, and B. E. A. Saleh, “Single-shot phase-shifting digital holography,” Opt. Eng. 53, 86884 (2014).

Opt. Express (7)

Opt. Lett. (1)

Phycologia (1)

N. I. Lewis, W. B. Xu, S. K. Jericho, H. J. Kreuzer, M. H. Jericho, and A. D. Cembella, “Swimming speed of three species of Alexandrium (Dinophyceae) as determined by digital in-line holography,” Phycologia 45(1), 61–70 (2006).
[Crossref]

Phys. Fluids (1)

B. Tao, J. Katz, and C. Meneveau, “Geometry and scale relationships in high Reynolds number turbulence determined from three-dimensional holographic velocimetry,” Phys. Fluids 12(5), 941–944 (2000).
[Crossref]

Phys. Rev. E Stat. Nonlin. Soft Matter Phys. (1)

A. Chengala, M. Hondzo, and J. Sheng, “Microalga propels along vorticity direction in a shear flow,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87(5), 052704 (2013).
[Crossref] [PubMed]

Phys. Rev. Lett. (1)

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Phys. Rev. Lett. 113(6), 068103 (2014).
[Crossref] [PubMed]

PLoS ONE (1)

S. M. Vater, S. Weisse, S. Maleschlijski, C. Lotz, F. Koschitzki, T. Schwartz, U. Obst, and A. Rosenhahn, “Swimming behavior of Pseudomonas aeruginosa studied by holographic 3D tracking,” PLoS ONE 9(1), e87765 (2014).
[Crossref] [PubMed]

Proc. IEEE (1)

I. Moon, M. Daneshpanah, B. Javidi, and A. Stern, “Automated three-dimensional identification and tracking of micro/nanobiological organisms by computational holographic microscopy,” Proc. IEEE 97(6), 990–1010 (2009).
[Crossref]

Proc. Natl. Acad. Sci. U.S.A. (8)

T. W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proc. Natl. Acad. Sci. U.S.A. 109(40), 16018–16022 (2012).
[Crossref] [PubMed]

J. Sheng, E. Malkiel, J. Katz, J. Adolf, R. Belas, and A. R. Place, “Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates,” Proc. Natl. Acad. Sci. U.S.A. 104(44), 17512–17517 (2007).
[Crossref] [PubMed]

K. Drescher, J. Dunkel, L. H. Cisneros, S. Ganguly, and R. E. Goldstein, “Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering,” Proc. Natl. Acad. Sci. U.S.A. 108(27), 10940–10945 (2011).
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V. Kantsler, J. Dunkel, M. Polin, and R. E. Goldstein, “Ciliary contact interactions dominate surface scattering of swimming eukaryotes,” Proc. Natl. Acad. Sci. U.S.A. 110(4), 1187–1192 (2013).
[Crossref] [PubMed]

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Figures (7)

Fig. 1
Fig. 1

Setup of Digital Holography Microscopy (DHM) and microfluidics platform.

Fig. 2
Fig. 2

Portion of original and de-noised sample holograms of (Left) E. coli and (Right) solid particles. (a & d): Original holograms. (b & e); holograms de-noised with the conventional time-averaging technique; (c & f): holograms processed with the correlation-based ensemble-averaging technique.

Fig. 3
Fig. 3

The correlation coefficient profiles smoothed by a 3-point moving average. (a) The correlation coefficient profile calculated with Eq. (3) between the hologram recorded at t o =80s and its neighboring holograms within the temporal shift, τ, ranging ±450 s. (b) The correlation profiles for holograms recorded at various time frames shown on top of each profile. The main horizontal axis shows the absolute recording time, t 0 . Inset axes show the time delay, τ[90, 90] , with respect to the selected time frame, t 0 , shown the Inset vertical axes as τ=0 . Only axes corresponding to profile centered at t 0 =120 & 295s are shown for clarity.

Fig. 4
Fig. 4

Reconstructions of bacterial hologram shown in Fig. 2(c). (a-c) reconstructed images at 10, 100, and 210μm away from the hologram plane. (d) Superimposed reconstructions at the interval of 0.5μm of the sample volume from 90μm to 110μm away from the hologram plane. (e) 3D distribution of particles. (f) Superimposed images reconstructed at the depth varying from 10μm to 15μm at the interval of 0.5μm over 0.33s, totaling 5 time frames.

Fig. 5
Fig. 5

Numerically reconstructed images of a single E. coli cell recorded by DHM at the magnification of 40X with the range of ±7μm at the interval of 3.5 μm . The center image, i.e. z= z 0 , is the in-focus image. The distance from the in-focus plane is marked on each sub image. The bottom row shows microscopic images of an E. coli at the corresponding planes from the in-focus location recorded by Nikon TiE with a Nikon Plan Fluor 40X objectives.

Fig. 6
Fig. 6

Intensity distribution of an ensemble averaged E. coli reconstruction. (a) Normalized 3D Intensity distribution of the ensemble averaged cell. Black lines show the iso-surface of intensity distribution threshold at 0.8. Two intersecting planes are x-y and x-z contour plots respectively. (b) The one-dimensional intensity distribution along the z axis. The width of the profile indicates the depth of focus of bacterial DHM.

Fig. 7
Fig. 7

Sample 3D trajectories obtained by DHM: (a) A sample 3D trajectory showing a E. coli cell swimming in circle. The trajectory is superimposed by the corresponding reconstructed in-focus images. (b) Collection of 3D trajectories over one minute DHM recordings. Only half of the trajectories are shown. Color: the swimming speed.

Tables (1)

Tables Icon

Table 1 Motility characteristics of wild-type E. coli in the bulk compared to earlier results in the bulk [65]. The tumbling angle is the angle between two consecutive runs. Statistics were compiled over 2,750 trajectories, excluding cells immobilized on surfaces and represent mean ± standard deviation. (adopted and modified from ref [1].)

Equations (8)

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I H (x,y;t)= I N (x,y;t)+ I B (x,y;t),
I N (x,y;t)= I N,sp + I N,sys .
I N (x,y,t) I N,sys = I H ^ = I H f δ x , δ y .
Cr( t 0 ,  τ )= I N ( x,y; t 0 ) I N ( t 0 +τ )dxdy I N 2 ( x,y; t 0 )dxdy I N 2 ( x,y; t 0 +τ )dxdy I H ^ ( x,y; t 0 ) I H ^ ( x,y; t 0 +τ )dxdy I H ^ 2 ( x,y; t 0 )dxdy I H ^ 2 ( x,y; t 0 +τ )dxdy .
I N ( x,y )= 1 T 0 T I H ( x,y;t )dt= 1 N 1 N I H (x,y).
I N ( x,y; t 0 ) I H (x,y; t 0 +τ)|Cr( t 0 ,τ )> C r th τ .
I p ( x,y;t )= I H ( x, y; t ) I H (x,y;t+τ) |Cr( t,τ )> C r th τ .
I ¯ ( r )=1 1 N 1 N [ I( r + x c n )I( x c n ) ] [ I max ( r + x c n )I( x c n ) ] ,

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