Abstract

Abstract: We developed a Digital Holographic Microscope (DHM) working with a partial coherent source specifically adapted to perform high throughput recording of holograms of plankton organisms in-flow, in a size range of 3µm-300µm, which is of importance for this kind of applications. This wide size range is achieved with the same flow cell and with the same microscope magnification. The DHM configuration combines a high magnification with a large field of view and provides high-resolution intensity and quantitative phase images refocusing on high sample flow rate. Specific algorithms were developed to detect and extract automatically the particles and organisms present in the samples in order to build holograms of each one that are used for holographic refocusing and quantitative phase contrast imaging. Experimental results are shown and discussed.

© 2014 Optical Society of America

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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]

2013 (4)

A. B. Bochdansky, M. H. Jericho, G. J. Herndl, “Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m,” Limnol. Oceanogr. Methods 11, 28–40 (2013).
[CrossRef]

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

A. El Mallahi, C. Minetti, F. Dubois, “Automated three-dimensional detection and classification of living organisms using digital holographic microscopy with partial spatial coherent source: application to the monitoring of drinking water resources,” Appl. Opt. 52(1), A68–A80 (2013).
[CrossRef] [PubMed]

A. El Mallahi, F. Dubois, “Separation of overlapped particles in digital holographic microscopy,” Opt. Express 21(5), 6466–6479 (2013).
[CrossRef] [PubMed]

2012 (3)

A. El Mallahi, A. Detavernier, C. Yourassowsky, F. Dubois, “Automated 3D detection and classification of Giardia lamblia cysts using digital holographic microscopy with partially coherent source,” Proc. SPIE 8429, 84291D (2012).
[CrossRef]

A. Schaap, T. Rohrlack, Y. Bellouard, “Optical classification of algae species with a glass lab-on-a-chip,” Lab Chip 12(8), 1527–1532 (2012).
[CrossRef] [PubMed]

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

2011 (2)

H. H. Jakobsen, J. Carstensen, “FlowCAM: Sizing cells and understanding the impact of size distributions on biovolume of planktonic community structure,” Aquat. Microb. Ecol. 65(1), 75–87 (2011).
[CrossRef]

J. Watson, “Submersible digital holographic cameras and their application to marine science,” Opt. Eng. 50(9), 091313 (2011).
[CrossRef]

2010 (4)

L. T. Nielsen, H. H. Jakobsen, P. J. Hansen, “High resilience of two coastal plankton communities to twenty-first century seawater acidification: evidence from microcosm studies,” Mar. Biol. Res. 6(6), 542–555 (2010).
[CrossRef]

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

P. Kolman, R. Chmelík, “Coherence-controlled holographic microscope,” Opt. Express 18(21), 21990–22003 (2010).
[CrossRef] [PubMed]

D. Shin, M. Daneshpanah, A. Anand, B. Javidi, “Optofluidic system for three-dimensional sensing and identification of micro-organisms with digital holographic microscopy,” Opt. Lett. 35(23), 4066–4068 (2010).
[CrossRef] [PubMed]

2009 (1)

2008 (3)

2007 (2)

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

H. M. Sosik, R. J. Olson, “Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry,” Limnol. Oceanogr. Methods 5, 204–216 (2007).
[CrossRef]

2006 (2)

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

F. Dubois, N. Callens, C. Yourassowsky, M. Hoyos, P. Kurowski, O. Monnom, “Digital holographic microscopy with reduced spatial coherence for three-dimensional particle flow analysis,” Appl. Opt. 45(5), 864–871 (2006).
[CrossRef] [PubMed]

2005 (1)

2003 (2)

2002 (2)

2000 (1)

V. Kachel, J. Wietzorrek, “Flow cytometry and integrated imaging,” Sci. Mar. 64, 247–254 (2000).

1999 (3)

1998 (2)

T. Zhang, I. Yamaguchi, “Three-dimensional microscopy with phase-shifting digital holography,” Opt. Lett. 23(15), 1221–1223 (1998).
[CrossRef] [PubMed]

C. K. Sieracki, M. E. Sieracki, C. S. Yentsch, “An imaging-in-flow system for automated analysis of marine microplankton,” Mar. Ecol. Prog. Ser. 168, 285–296 (1998).
[CrossRef]

1982 (1)

Abraham, A.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

Allano, D.

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Alquaddoomi, O.

E. Malkiel, O. Alquaddoomi, J. Katz, “Measurements of plankton distribution in the ocean using submersible holography,” Meas. Sci. Technol. 10(12), 1142–1152 (1999).
[CrossRef]

Amato-Grill, J.

Anand, A.

Barbastathis, G.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

Basiji, D. A.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Bellouard, Y.

A. Schaap, T. Rohrlack, Y. Bellouard, “Optical classification of algae species with a glass lab-on-a-chip,” Lab Chip 12(8), 1527–1532 (2012).
[CrossRef] [PubMed]

Bevilacqua, F.

Bochdansky, A. B.

A. B. Bochdansky, M. H. Jericho, G. J. Herndl, “Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m,” Limnol. Oceanogr. Methods 11, 28–40 (2013).
[CrossRef]

Buskey, E. J.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

Callens, N.

Campbell, L.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

Carapezza, E.

Carstensen, J.

H. H. Jakobsen, J. Carstensen, “FlowCAM: Sizing cells and understanding the impact of size distributions on biovolume of planktonic community structure,” Aquat. Microb. Ecol. 65(1), 75–87 (2011).
[CrossRef]

Cheong, F. C.

Chmelík, R.

Coëtmellec, S.

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Coppola, G.

Coupier, G.

Cuche, E.

Daneshpanah, M.

Davis, C.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

De Nicola, S.

Depeursinge, C.

Detavernier, A.

A. El Mallahi, A. Detavernier, C. Yourassowsky, F. Dubois, “Automated 3D detection and classification of Giardia lamblia cysts using digital holographic microscopy with partially coherent source,” Proc. SPIE 8429, 84291D (2012).
[CrossRef]

Dixon, L.

Dominguez-Caballero, J. A.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

Donaghay, P.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Dreyfus, R.

Dubois, F.

A. El Mallahi, C. Minetti, F. Dubois, “Automated three-dimensional detection and classification of living organisms using digital holographic microscopy with partial spatial coherent source: application to the monitoring of drinking water resources,” Appl. Opt. 52(1), A68–A80 (2013).
[CrossRef] [PubMed]

A. El Mallahi, F. Dubois, “Separation of overlapped particles in digital holographic microscopy,” Opt. Express 21(5), 6466–6479 (2013).
[CrossRef] [PubMed]

A. El Mallahi, A. Detavernier, C. Yourassowsky, F. Dubois, “Automated 3D detection and classification of Giardia lamblia cysts using digital holographic microscopy with partially coherent source,” Proc. SPIE 8429, 84291D (2012).
[CrossRef]

C. Minetti, N. Callens, G. Coupier, T. Podgorski, F. Dubois, “Fast measurements of concentration profiles inside deformable objects in microflows with reduced spatial coherence digital holography,” Appl. Opt. 47(29), 5305–5314 (2008).
[CrossRef] [PubMed]

F. Dubois, P. Grosfils, “Dark-field digital holographic microscopy to investigate objects that are nanosized or smaller than the optical resolution,” Opt. Lett. 33(22), 2605 (2008).
[CrossRef] [PubMed]

F. Dubois, N. Callens, C. Yourassowsky, M. Hoyos, P. Kurowski, O. Monnom, “Digital holographic microscopy with reduced spatial coherence for three-dimensional particle flow analysis,” Appl. Opt. 45(5), 864–871 (2006).
[CrossRef] [PubMed]

F. Dubois, O. Monnom, C. Yourassowsky, J.-C. Legros, “Border processing in digital holography by extension of the digital hologram and reduction of the higher spatial frequencies,” Appl. Opt. 41(14), 2621–2626 (2002).
[CrossRef] [PubMed]

F. Dubois, L. Joannes, J.-C. Legros, “Improved three-dimensional imaging with a digital holography microscope with a source of partial spatial coherence,” Appl. Opt. 38(34), 7085–7094 (1999).
[CrossRef] [PubMed]

El Mallahi, A.

Erickson, J. S.

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

Ferraro, P.

Finizio, A.

Frost, K.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Garcia-Sucerquia, J.

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

Godard, G.

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Grier, D. G.

Grosfils, P.

Hall, B. E.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Hansen, P. J.

L. T. Nielsen, H. H. Jakobsen, P. J. Hansen, “High resilience of two coastal plankton communities to twenty-first century seawater acidification: evidence from microcosm studies,” Mar. Biol. Res. 6(6), 542–555 (2010).
[CrossRef]

Hashemi, N.

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

Henrichs, D. W.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

Herndl, G. J.

A. B. Bochdansky, M. H. Jericho, G. J. Herndl, “Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m,” Limnol. Oceanogr. Methods 11, 28–40 (2013).
[CrossRef]

Hong, J.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Hoyos, M.

Hu, Q.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

Hyatt, C. J.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

Ina, H.

Jakobsen, H. H.

H. H. Jakobsen, J. Carstensen, “FlowCAM: Sizing cells and understanding the impact of size distributions on biovolume of planktonic community structure,” Aquat. Microb. Ecol. 65(1), 75–87 (2011).
[CrossRef]

L. T. Nielsen, H. H. Jakobsen, P. J. Hansen, “High resilience of two coastal plankton communities to twenty-first century seawater acidification: evidence from microcosm studies,” Mar. Biol. Res. 6(6), 542–555 (2010).
[CrossRef]

Javidi, B.

Jericho, M. H.

A. B. Bochdansky, M. H. Jericho, G. J. Herndl, “Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m,” Limnol. Oceanogr. Methods 11, 28–40 (2013).
[CrossRef]

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

W. Xu, M. H. Jericho, H. J. Kreuzer, I. A. Meinertzhagen, “Tracking particles in four dimensions with in-line holographic microscopy,” Opt. Lett. 28(3), 164–166 (2003).
[CrossRef] [PubMed]

Jericho, S. K.

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

Joannes, L.

Jüptner, W.

U. Schnars, W. Jüptner, “Digital recording and numerical reconstruction of holograms,” Meas. Sci. Technol. 13(9), R85–R101 (2002).
[CrossRef]

Kachel, V.

V. Kachel, J. Wietzorrek, “Flow cytometry and integrated imaging,” Sci. Mar. 64, 247–254 (2000).

Katz, J.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

E. Malkiel, O. Alquaddoomi, J. Katz, “Measurements of plankton distribution in the ocean using submersible holography,” Meas. Sci. Technol. 10(12), 1142–1152 (1999).
[CrossRef]

Kobayashi, S.

Kolman, P.

Kreuzer, H. J.

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

W. Xu, M. H. Jericho, H. J. Kreuzer, I. A. Meinertzhagen, “Tracking particles in four dimensions with in-line holographic microscopy,” Opt. Lett. 28(3), 164–166 (2003).
[CrossRef] [PubMed]

Kurowski, P.

Lebrun, D.

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Legros, J.-C.

Li, W.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

Liang, L.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Ligler, F. S.

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

Loomis, N.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

Malkiel, E.

E. Malkiel, O. Alquaddoomi, J. Katz, “Measurements of plankton distribution in the ocean using submersible holography,” Meas. Sci. Technol. 10(12), 1142–1152 (1999).
[CrossRef]

McFarland, M.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Meinertzhagen, I. A.

Milgram, J.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

Minetti, C.

Monnom, O.

Moon, I.

Nayak, A. R.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Nielsen, L. T.

L. T. Nielsen, H. H. Jakobsen, P. J. Hansen, “High resilience of two coastal plankton communities to twenty-first century seawater acidification: evidence from microcosm studies,” Mar. Biol. Res. 6(6), 542–555 (2010).
[CrossRef]

Olson, R. J.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

H. M. Sosik, R. J. Olson, “Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry,” Limnol. Oceanogr. Methods 5, 204–216 (2007).
[CrossRef]

Ortyn, W. E.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Paranthoën, P.

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Perry, D. J.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Pierattini, G.

Podgorski, T.

Rines, J.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Rohrlack, T.

A. Schaap, T. Rohrlack, Y. Bellouard, “Optical classification of algae species with a glass lab-on-a-chip,” Lab Chip 12(8), 1527–1532 (2012).
[CrossRef] [PubMed]

Salah, N.

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Schaap, A.

A. Schaap, T. Rohrlack, Y. Bellouard, “Optical classification of algae species with a glass lab-on-a-chip,” Lab Chip 12(8), 1527–1532 (2012).
[CrossRef] [PubMed]

Schnars, U.

U. Schnars, W. Jüptner, “Digital recording and numerical reconstruction of holograms,” Meas. Sci. Technol. 13(9), R85–R101 (2002).
[CrossRef]

Shin, D.

Sieracki, C. K.

C. K. Sieracki, M. E. Sieracki, C. S. Yentsch, “An imaging-in-flow system for automated analysis of marine microplankton,” Mar. Ecol. Prog. Ser. 168, 285–296 (1998).
[CrossRef]

Sieracki, M. E.

C. K. Sieracki, M. E. Sieracki, C. S. Yentsch, “An imaging-in-flow system for automated analysis of marine microplankton,” Mar. Ecol. Prog. Ser. 168, 285–296 (1998).
[CrossRef]

Sosik, H. M.

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

H. M. Sosik, R. J. Olson, “Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry,” Limnol. Oceanogr. Methods 5, 204–216 (2007).
[CrossRef]

Sullivan, J.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Sullivan, J. M.

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

Sun, B.

Takeda, M.

Talapatra, S.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Twardowski, M.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Venkatachalam, V.

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

Watson, J.

J. Watson, “Submersible digital holographic cameras and their application to marine science,” Opt. Eng. 50(9), 091313 (2011).
[CrossRef]

Weidemann, A. D.

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

Wietzorrek, J.

V. Kachel, J. Wietzorrek, “Flow cytometry and integrated imaging,” Sci. Mar. 64, 247–254 (2000).

Xiao, K.

Xu, W.

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

W. Xu, M. H. Jericho, H. J. Kreuzer, I. A. Meinertzhagen, “Tracking particles in four dimensions with in-line holographic microscopy,” Opt. Lett. 28(3), 164–166 (2003).
[CrossRef] [PubMed]

Yamaguchi, I.

Yentsch, C. S.

C. K. Sieracki, M. E. Sieracki, C. S. Yentsch, “An imaging-in-flow system for automated analysis of marine microplankton,” Mar. Ecol. Prog. Ser. 168, 285–296 (1998).
[CrossRef]

Yeom, S.

Yourassowsky, C.

Zhang, C.

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Zhang, T.

Anal. Chem. (1)

J. S. Erickson, N. Hashemi, J. M. Sullivan, A. D. Weidemann, F. S. Ligler, “In Situ Phytoplankton Analysis: There’s Plenty of Room at the Bottom,” Anal. Chem. 84(2), 839–850 (2012).
[CrossRef] [PubMed]

Appl. Opt. (5)

Aquat. Microb. Ecol. (1)

H. H. Jakobsen, J. Carstensen, “FlowCAM: Sizing cells and understanding the impact of size distributions on biovolume of planktonic community structure,” Aquat. Microb. Ecol. 65(1), 75–87 (2011).
[CrossRef]

Cytometry A (1)

W. E. Ortyn, D. J. Perry, V. Venkatachalam, L. Liang, B. E. Hall, K. Frost, D. A. Basiji, “Extended depth of field imaging for high speed cell analysis,” Cytometry A 71A(4), 215–231 (2007).
[CrossRef] [PubMed]

J. Opt. Soc. Am. (1)

J. Phycol. (1)

L. Campbell, R. J. Olson, H. M. Sosik, A. Abraham, D. W. Henrichs, C. J. Hyatt, E. J. Buskey, “First harmfull Dinophysis (Dinophyceae, Dinophysiales) bloom in the U.S. is revealed by automated imaging flow cytometry,” J. Phycol. 46(1), 66–75 (2010).
[CrossRef]

Lab Chip (1)

A. Schaap, T. Rohrlack, Y. Bellouard, “Optical classification of algae species with a glass lab-on-a-chip,” Lab Chip 12(8), 1527–1532 (2012).
[CrossRef] [PubMed]

Limnol. Oceanogr. Methods (2)

H. M. Sosik, R. J. Olson, “Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry,” Limnol. Oceanogr. Methods 5, 204–216 (2007).
[CrossRef]

A. B. Bochdansky, M. H. Jericho, G. J. Herndl, “Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m,” Limnol. Oceanogr. Methods 11, 28–40 (2013).
[CrossRef]

Mar. Biol. Res. (1)

L. T. Nielsen, H. H. Jakobsen, P. J. Hansen, “High resilience of two coastal plankton communities to twenty-first century seawater acidification: evidence from microcosm studies,” Mar. Biol. Res. 6(6), 542–555 (2010).
[CrossRef]

Mar. Ecol. Prog. Ser. (2)

C. K. Sieracki, M. E. Sieracki, C. S. Yentsch, “An imaging-in-flow system for automated analysis of marine microplankton,” Mar. Ecol. Prog. Ser. 168, 285–296 (1998).
[CrossRef]

S. Talapatra, J. Hong, M. McFarland, A. R. Nayak, C. Zhang, J. Katz, J. Sullivan, M. Twardowski, J. Rines, P. Donaghay, “Characterization of biophysical interactions in the water column using in situ digital holography,” Mar. Ecol. Prog. Ser. 473, 29–51 (2013).
[CrossRef]

Meas. Sci. Technol. (3)

E. Malkiel, O. Alquaddoomi, J. Katz, “Measurements of plankton distribution in the ocean using submersible holography,” Meas. Sci. Technol. 10(12), 1142–1152 (1999).
[CrossRef]

U. Schnars, W. Jüptner, “Digital recording and numerical reconstruction of holograms,” Meas. Sci. Technol. 13(9), R85–R101 (2002).
[CrossRef]

N. Salah, G. Godard, D. Lebrun, P. Paranthoën, D. Allano, S. Coëtmellec, “Application of multiple exposure digital in-line holography to particle tracking in a Bénard-von Kármán vortex flow,” Meas. Sci. Technol. 19(7), 074001 (2008).
[CrossRef]

Opt. Eng. (1)

J. Watson, “Submersible digital holographic cameras and their application to marine science,” Opt. Eng. 50(9), 091313 (2011).
[CrossRef]

Opt. Express (4)

Opt. Lett. (6)

Proc. SPIE (1)

A. El Mallahi, A. Detavernier, C. Yourassowsky, F. Dubois, “Automated 3D detection and classification of Giardia lamblia cysts using digital holographic microscopy with partially coherent source,” Proc. SPIE 8429, 84291D (2012).
[CrossRef]

Rev. Sci. Instrum. (1)

S. K. Jericho, J. Garcia-Sucerquia, W. Xu, M. H. Jericho, H. J. Kreuzer, “Submersible digital in-line holographic microscope,” Rev. Sci. Instrum. 77(4), 043706 (2006).
[CrossRef]

Sci. Mar. (1)

V. Kachel, J. Wietzorrek, “Flow cytometry and integrated imaging,” Sci. Mar. 64, 247–254 (2000).

Other (2)

N. J. Poulton and J. L. Martin, “Imaging flow cytometry for quantitative phytoplankton analysis-FlowCAM,” in Microscopic and Molecular Methods for Quantitative Phytoplankton Analysis, B. Karlson, C. Cusack, and E. Bresnan eds. (Intergovernmental Oceanographic Commission of UNESCO, 2010) 47–54.

J. A. Dominguez-Caballero, N. Loomis, W. Li, Q. Hu, J. Milgram, G. Barbastathis, C. Davis, “Advances in plankton imaging using digital holography,” dx.doi.org/10.1364/DH.2007.DMB5 (2007)

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Figures (9)

Fig. 1
Fig. 1

GG: rotating Ground Glass; L1 and L2: Lenses; BS1 and BS2: Beam Splitters; ML1-3: Microscope Lenses; M1-5: Mirrors.

Fig. 2
Fig. 2

(a) Example of a recorded hologram; the square box shows the hologram quality in a magnified zone. (b) Corrected intensity image corresponding to (a). The comparison between the two images shows the reduction of the permanent defects. Scale bar: 50µm.

Fig. 3
Fig. 3

(a) Corrected phase image corresponding to the hologram of Fig. 2a. The gray levels are ranging from 0 to 255. The phase background is set to the gray level 127. (b) Regions of interest (ROI) built around each detected particles by the described method. Note that the upper left particle is not detected, as it is located outside a mask window applied to reduce the influence of the border.

Fig. 4
Fig. 4

Individual refocusing of detected particles of Fig. 3(b). The reconstructions are performed on separated holograms for each particle. The individual holograms are built by a border processing applied on the complete hologram limited by the individual ROI’s shown by Fig. 3(b). The letter labels are corresponding to the ones of Fig. 3(b). The labels I and P identify, respectively the intensity and phase images. The background of the phase images is set to the gray level 32. The reconstruction distances d are indicated below every couple of images corresponding to one particle. Scale bar: 20 µm.

Fig. 5
Fig. 5

A missed particle by the detection process. (a) Recorded intensity, (b) refocused intensity over a distance of 20µm and (c) phase image corresponding to (b). Scale bar: 20µm.

Fig. 6
Fig. 6

3D plot of the phase map of Fig. 4 (e P).

Fig. 7
Fig. 7

A plankton organism refocused by 200 µm. (a) Intensity in the recorded plane, (b) refocused intensity and (c) phase image in the refocused plane. Scale bar: 20µm.

Fig. 8
Fig. 8

Results with Giardia lamblia cyst. (a) Out of focus intensity image (defocus distance 60µm), (b) refocused intensity image and (c) refocused phase map. Scale bar: 20µm.

Fig. 9
Fig. 9

Refocusing of a large plankton organism. (a) Intensity in the detection plane, (b) Refocused intensity image. Refocusing distance of 155µm. Scale bar: 20µm.

Equations (5)

Equations on this page are rendered with MathJax. Learn more.

g'( s',t' )=exp{ jkd } F U,V 1 exp{ j πλd( U 2 + V 2 ) n 2 e 2 } F s,t +1 g( s,t ),
i ck ( s,t )= i k ( s,t ) / i a ( s,t ) .
φ ck ( s,t )= mod 2π { φ k ( s,t ) φ a ( s,t ) }.
H( u,v )=( 1exp{ u 2 + v 2 2 σ 2 } ),
D=| ξ |NA,

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