Abstract

This paper presents an optical diffraction tomography technique based on digital holographic microscopy. Quantitative 2-dimensional phase images are acquired for regularly-spaced angular positions of the specimen covering a total angle of π, allowing to built 3-dimensional quantitative refractive index distributions by an inverse Radon transform. A 20× magnification allows a resolution better than 3 μm in all three dimensions, with accuracy better than 0.01 for the refractive index measurements. This technique is for the first time to our knowledge applied to living specimen (testate amoeba, Protista). Morphometric measurements are extracted from the tomographic reconstructions, showing that the commonly used method for testate amoeba biovolume evaluation leads to systematic under evaluations by about 50%.

© 2006 Optical Society of America

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  1. A. Dunn, Light scattering properties of cells, PhD Diss., Univ. of Texas, Austin, 1997.
  2. J. Bereiter-Hahn, Cecil H. Fox, and BO Thorell, “Quantitative reflection contrast microscopy of living cells,” J. Cell Biol. 82, 767–779 (1979).
    [CrossRef] [PubMed]
  3. C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
    [CrossRef]
  4. B. Rappaz, P. Marquet, E. Cuche, Y. Emery, C. Depeursinge, and P. Magistretti, “Measurement of the integral refractive index and dynamic cell morphometry of living cells with digital holographic microscopy,” Opt. Express 13, 9361–9373 (2005).
    [CrossRef] [PubMed]
  5. E. Wolf, “Three-dimensional structure determination of semi-transparent object from holographic data,” Opt. Commun. 1, 153–156 (1969).
    [CrossRef]
  6. R. Dändliker and K. Weiss, “Reconstruction of three-dimensional refractive index from scattered waves,“ Opt. Commun. 1, 323–328 (1970).
    [CrossRef]
  7. V. Lauer, “New approach to optical diffraction tomography yielding a vector equation of diffraction tomography and a novel tomographic microscope,” J. Microsc. 205, 165–176 (2002).
    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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  14. E. A. D. Mitchell, D. J. Charman, and B. G. Warner, “Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future,” Biodivers. Conserv. (to be published).
  15. H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).
  16. R. E. Madrid and C. J. Felice, “Microbial biomass estimation,“ Crit. Rev. Biotechnol.,  25, 97–112 (2005).
    [CrossRef] [PubMed]
  17. D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
    [CrossRef]
  18. E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).
  19. E. Cuche, P. Marquet, and C. Depeursinge, “Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of Fresnel off-axis holograms,” Appl. Opt. 38, 6994–7001 (1999).
    [CrossRef]
  20. T. Colomb, E. Cuche, F. Charrière, J. Kühn, N. Aspert, F. Montfort, P. Marquet, and Ch. Depeursinge, “Automatic procedure for aberration compensation in digital holographic microscopy and applications to specimen shape compensation,“ Appl. Opt. 45, 851–863 (2006).
    [CrossRef] [PubMed]
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  22. P. Marquet, B. Rappaz, P. J. Magistretti, E. Cuche, Y. Emery, T. Colomb, and C. Depeursinge, “Digital holographic microscopy: a noninvasive contrast imaging technique allowing quantitative visualization of living cells with subwavelength axial accuracy,” Opt. Lett. 30, 468–470 (2005).
    [CrossRef] [PubMed]
  23. P. Marquet, “Développement d’une nouvelle technique de microscopie optique tridimensionnelle, la microscopie holographique digitale. Perspective pour l’étude le la plasticité neuronale,” MD-PhD Thesis Dissertation (Chapt. 5), UNI-Lausanne, 2003.
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  27. E. A. Paul and F. E. Clark, Soil microbiology and biochemistry, (Second Edition, Academic Press, San Diego, CA. 1996).
  28. M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
    [CrossRef]
  29. Dr. Enrique Lara, Swiss Federal Research Institute WSL and Laboratory of Ecological Systems, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland. (personnal communication, 2006).

2006 (4)

F. Charrière, F. Montfort, J. Kühn, T. Colomb, A. Marian, E. Cuche, P. Marquet, and Ch. Depeursinge, “Cell refractive index tomography by digital holographic microscopy,” Opt. Lett. 31, 178–180 (2006).
[CrossRef] [PubMed]

T. Colomb, E. Cuche, F. Charrière, J. Kühn, N. Aspert, F. Montfort, P. Marquet, and Ch. Depeursinge, “Automatic procedure for aberration compensation in digital holographic microscopy and applications to specimen shape compensation,“ Appl. Opt. 45, 851–863 (2006).
[CrossRef] [PubMed]

F. Charrière, E. Cuche, P. Marquet, and C. Depeursinge, “Biological cell (pollen grain) refractive index tomography with digital holographic microscopy.“ in Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII, J.-A. Conchello, C.J. Cogswell, T. Wilson, eds., Proc. SPIE 6090, 22–29 (2006).

Dr. Enrique Lara, Swiss Federal Research Institute WSL and Laboratory of Ecological Systems, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland. (personnal communication, 2006).

2005 (4)

2003 (2)

P. Marquet, “Développement d’une nouvelle technique de microscopie optique tridimensionnelle, la microscopie holographique digitale. Perspective pour l’étude le la plasticité neuronale,” MD-PhD Thesis Dissertation (Chapt. 5), UNI-Lausanne, 2003.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

2002 (2)

M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
[CrossRef]

V. Lauer, “New approach to optical diffraction tomography yielding a vector equation of diffraction tomography and a novel tomographic microscope,” J. Microsc. 205, 165–176 (2002).
[CrossRef] [PubMed]

2001 (1)

A. C. Kak and M. Slaney. Principles of Computerized Tomographic Imaging. Soc. of Ind. and Appl. Math. SIAM, 2001.

2000 (1)

A. Barty, K.A. Nugent, A. Roberts, and D. Paganin, “Quantitative phase tomography,” Opt. Commun. 175, 329–336 (2000).
[CrossRef]

1999 (3)

E. A. D. Mitchell, A. Buttler, B. Warner, and J.-M. Gobat, “Ecology of testate amoebae (Protozoa: Rhizopoda) in Sphagnum-dominated peatlands in the Jura Mountains, Switzerland and France,” Ecoscience 6, 565–576 (1999).

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, and V. V. Pikalov, “Phase Tomography of 3D Biological Microobjects: Numerical Simulation and Experimental Results,” Opt. Spectrosc. 87, 413–419 (1999).

E. Cuche, P. Marquet, and C. Depeursinge, “Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of Fresnel off-axis holograms,” Appl. Opt. 38, 6994–7001 (1999).
[CrossRef]

1998 (2)

D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
[CrossRef]

G. N. Vishnyakov and G. G. Levin, “Optical microtomography of phase objects, ” Opt. Spectrosc. 85, 73–77 (1998).

1995 (2)

1992 (1)

1979 (1)

J. Bereiter-Hahn, Cecil H. Fox, and BO Thorell, “Quantitative reflection contrast microscopy of living cells,” J. Cell Biol. 82, 767–779 (1979).
[CrossRef] [PubMed]

1970 (1)

R. Dändliker and K. Weiss, “Reconstruction of three-dimensional refractive index from scattered waves,“ Opt. Commun. 1, 323–328 (1970).
[CrossRef]

1969 (1)

E. Wolf, “Three-dimensional structure determination of semi-transparent object from holographic data,” Opt. Commun. 1, 153–156 (1969).
[CrossRef]

Allman, B. E.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Amblard, C.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
[CrossRef]

Aspert, N.

Badot, P. M.

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Barty, A.

A. Barty, K.A. Nugent, A. Roberts, and D. Paganin, “Quantitative phase tomography,” Opt. Commun. 175, 329–336 (2000).
[CrossRef]

Bellair, C. J.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Bereiter-Hahn, J.

J. Bereiter-Hahn, Cecil H. Fox, and BO Thorell, “Quantitative reflection contrast microscopy of living cells,” J. Cell Biol. 82, 767–779 (1979).
[CrossRef] [PubMed]

Bernard, N.

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Bloem, J.

M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
[CrossRef]

Bölter, M.

M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
[CrossRef]

Bourdier, G.

D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
[CrossRef]

Buttler, A.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

E. A. D. Mitchell, A. Buttler, B. Warner, and J.-M. Gobat, “Ecology of testate amoebae (Protozoa: Rhizopoda) in Sphagnum-dominated peatlands in the Jura Mountains, Switzerland and France,” Ecoscience 6, 565–576 (1999).

Charman, D. J.

E. A. D. Mitchell, D. J. Charman, and B. G. Warner, “Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future,” Biodivers. Conserv. (to be published).

Charrière, F.

Clark, F. E.

E. A. Paul and F. E. Clark, Soil microbiology and biochemistry, (Second Edition, Academic Press, San Diego, CA. 1996).

Colomb, T.

Cortet, J.

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Cuche, E.

F. Charrière, E. Cuche, P. Marquet, and C. Depeursinge, “Biological cell (pollen grain) refractive index tomography with digital holographic microscopy.“ in Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII, J.-A. Conchello, C.J. Cogswell, T. Wilson, eds., Proc. SPIE 6090, 22–29 (2006).

T. Colomb, E. Cuche, F. Charrière, J. Kühn, N. Aspert, F. Montfort, P. Marquet, and Ch. Depeursinge, “Automatic procedure for aberration compensation in digital holographic microscopy and applications to specimen shape compensation,“ Appl. Opt. 45, 851–863 (2006).
[CrossRef] [PubMed]

F. Charrière, F. Montfort, J. Kühn, T. Colomb, A. Marian, E. Cuche, P. Marquet, and Ch. Depeursinge, “Cell refractive index tomography by digital holographic microscopy,” Opt. Lett. 31, 178–180 (2006).
[CrossRef] [PubMed]

P. Marquet, B. Rappaz, P. J. Magistretti, E. Cuche, Y. Emery, T. Colomb, and C. Depeursinge, “Digital holographic microscopy: a noninvasive contrast imaging technique allowing quantitative visualization of living cells with subwavelength axial accuracy,” Opt. Lett. 30, 468–470 (2005).
[CrossRef] [PubMed]

B. Rappaz, P. Marquet, E. Cuche, Y. Emery, C. Depeursinge, and P. Magistretti, “Measurement of the integral refractive index and dynamic cell morphometry of living cells with digital holographic microscopy,” Opt. Express 13, 9361–9373 (2005).
[CrossRef] [PubMed]

E. Cuche, P. Marquet, and C. Depeursinge, “Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of Fresnel off-axis holograms,” Appl. Opt. 38, 6994–7001 (1999).
[CrossRef]

Curl, C. L.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Dändliker, R.

R. Dändliker and K. Weiss, “Reconstruction of three-dimensional refractive index from scattered waves,“ Opt. Commun. 1, 323–328 (1970).
[CrossRef]

Delbridge, L. M. D.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Depeursinge, C.

Depeursinge, Ch.

Dunn, A.

A. Dunn, Light scattering properties of cells, PhD Diss., Univ. of Texas, Austin, 1997.

Emery, Y.

Felice, C. J.

R. E. Madrid and C. J. Felice, “Microbial biomass estimation,“ Crit. Rev. Biotechnol.,  25, 97–112 (2005).
[CrossRef] [PubMed]

Fox, Cecil H.

J. Bereiter-Hahn, Cecil H. Fox, and BO Thorell, “Quantitative reflection contrast microscopy of living cells,” J. Cell Biol. 82, 767–779 (1979).
[CrossRef] [PubMed]

Francez, A.-J.

D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
[CrossRef]

Gilbert, D.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
[CrossRef]

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Gobat, J.-M.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

E. A. D. Mitchell, A. Buttler, B. Warner, and J.-M. Gobat, “Ecology of testate amoebae (Protozoa: Rhizopoda) in Sphagnum-dominated peatlands in the Jura Mountains, Switzerland and France,” Ecoscience 6, 565–576 (1999).

Grosvernier, P.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

Harris, P. J.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Harris, T.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Kak, A. C.

A. C. Kak and M. Slaney. Principles of Computerized Tomographic Imaging. Soc. of Ind. and Appl. Math. SIAM, 2001.

Kawata, S.

Kühn, J.

Lara, Dr. Enrique

Dr. Enrique Lara, Swiss Federal Research Institute WSL and Laboratory of Ecological Systems, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland. (personnal communication, 2006).

Lauer, V.

V. Lauer, “New approach to optical diffraction tomography yielding a vector equation of diffraction tomography and a novel tomographic microscope,” J. Microsc. 205, 165–176 (2002).
[CrossRef] [PubMed]

Levin, G. G.

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, and V. V. Pikalov, “Phase Tomography of 3D Biological Microobjects: Numerical Simulation and Experimental Results,” Opt. Spectrosc. 87, 413–419 (1999).

G. N. Vishnyakov and G. G. Levin, “Optical microtomography of phase objects, ” Opt. Spectrosc. 85, 73–77 (1998).

Likhachev, A. V.

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, and V. V. Pikalov, “Phase Tomography of 3D Biological Microobjects: Numerical Simulation and Experimental Results,” Opt. Spectrosc. 87, 413–419 (1999).

Madrid, R. E.

R. E. Madrid and C. J. Felice, “Microbial biomass estimation,“ Crit. Rev. Biotechnol.,  25, 97–112 (2005).
[CrossRef] [PubMed]

Magistretti, P.

Magistretti, P. J.

Marian, A.

Marquet, P.

F. Charrière, F. Montfort, J. Kühn, T. Colomb, A. Marian, E. Cuche, P. Marquet, and Ch. Depeursinge, “Cell refractive index tomography by digital holographic microscopy,” Opt. Lett. 31, 178–180 (2006).
[CrossRef] [PubMed]

T. Colomb, E. Cuche, F. Charrière, J. Kühn, N. Aspert, F. Montfort, P. Marquet, and Ch. Depeursinge, “Automatic procedure for aberration compensation in digital holographic microscopy and applications to specimen shape compensation,“ Appl. Opt. 45, 851–863 (2006).
[CrossRef] [PubMed]

F. Charrière, E. Cuche, P. Marquet, and C. Depeursinge, “Biological cell (pollen grain) refractive index tomography with digital holographic microscopy.“ in Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII, J.-A. Conchello, C.J. Cogswell, T. Wilson, eds., Proc. SPIE 6090, 22–29 (2006).

B. Rappaz, P. Marquet, E. Cuche, Y. Emery, C. Depeursinge, and P. Magistretti, “Measurement of the integral refractive index and dynamic cell morphometry of living cells with digital holographic microscopy,” Opt. Express 13, 9361–9373 (2005).
[CrossRef] [PubMed]

P. Marquet, B. Rappaz, P. J. Magistretti, E. Cuche, Y. Emery, T. Colomb, and C. Depeursinge, “Digital holographic microscopy: a noninvasive contrast imaging technique allowing quantitative visualization of living cells with subwavelength axial accuracy,” Opt. Lett. 30, 468–470 (2005).
[CrossRef] [PubMed]

P. Marquet, “Développement d’une nouvelle technique de microscopie optique tridimensionnelle, la microscopie holographique digitale. Perspective pour l’étude le la plasticité neuronale,” MD-PhD Thesis Dissertation (Chapt. 5), UNI-Lausanne, 2003.

E. Cuche, P. Marquet, and C. Depeursinge, “Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of Fresnel off-axis holograms,” Appl. Opt. 38, 6994–7001 (1999).
[CrossRef]

Meiners, K.

M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
[CrossRef]

Minami, S.

Mitchell, E. A. D.

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

E. A. D. Mitchell, A. Buttler, B. Warner, and J.-M. Gobat, “Ecology of testate amoebae (Protozoa: Rhizopoda) in Sphagnum-dominated peatlands in the Jura Mountains, Switzerland and France,” Ecoscience 6, 565–576 (1999).

E. A. D. Mitchell, D. J. Charman, and B. G. Warner, “Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future,” Biodivers. Conserv. (to be published).

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Möller, R.

M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
[CrossRef]

Montfort, F.

Nguyen-Viet, H.

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Noda, T.

Nugent, K. A.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Nugent, K.A.

A. Barty, K.A. Nugent, A. Roberts, and D. Paganin, “Quantitative phase tomography,” Opt. Commun. 175, 329–336 (2000).
[CrossRef]

Paganin, D.

A. Barty, K.A. Nugent, A. Roberts, and D. Paganin, “Quantitative phase tomography,” Opt. Commun. 175, 329–336 (2000).
[CrossRef]

Paul, E. A.

E. A. Paul and F. E. Clark, Soil microbiology and biochemistry, (Second Edition, Academic Press, San Diego, CA. 1996).

Pikalov, V. V.

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, and V. V. Pikalov, “Phase Tomography of 3D Biological Microobjects: Numerical Simulation and Experimental Results,” Opt. Spectrosc. 87, 413–419 (1999).

Rappaz, B.

Roberts, A.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

A. Barty, K.A. Nugent, A. Roberts, and D. Paganin, “Quantitative phase tomography,” Opt. Commun. 175, 329–336 (2000).
[CrossRef]

Singer, W.

Slaney, M.

A. C. Kak and M. Slaney. Principles of Computerized Tomographic Imaging. Soc. of Ind. and Appl. Math. SIAM, 2001.

Stamnes, J. J.

Stewart, A. G.

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Thorell, BO

J. Bereiter-Hahn, Cecil H. Fox, and BO Thorell, “Quantitative reflection contrast microscopy of living cells,” J. Cell Biol. 82, 767–779 (1979).
[CrossRef] [PubMed]

Vishnyakov, G. N.

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, and V. V. Pikalov, “Phase Tomography of 3D Biological Microobjects: Numerical Simulation and Experimental Results,” Opt. Spectrosc. 87, 413–419 (1999).

G. N. Vishnyakov and G. G. Levin, “Optical microtomography of phase objects, ” Opt. Spectrosc. 85, 73–77 (1998).

Warner, B.

E. A. D. Mitchell, A. Buttler, B. Warner, and J.-M. Gobat, “Ecology of testate amoebae (Protozoa: Rhizopoda) in Sphagnum-dominated peatlands in the Jura Mountains, Switzerland and France,” Ecoscience 6, 565–576 (1999).

Warner, B. G.

E. A. D. Mitchell, D. J. Charman, and B. G. Warner, “Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future,” Biodivers. Conserv. (to be published).

Wedberg, T. C.

Weiss, K.

R. Dändliker and K. Weiss, “Reconstruction of three-dimensional refractive index from scattered waves,“ Opt. Commun. 1, 323–328 (1970).
[CrossRef]

Wolf, E.

E. Wolf, “Three-dimensional structure determination of semi-transparent object from holographic data,” Opt. Commun. 1, 153–156 (1969).
[CrossRef]

Appl. Opt. (4)

Biodivers. Conserv. (1)

E. A. D. Mitchell, D. J. Charman, and B. G. Warner, “Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future,” Biodivers. Conserv. (to be published).

Biol. Fert. Soils (1)

M. Bölter, J. Bloem, K. Meiners, and R. Möller, “Enumeration and biovolume determination of microbial cells - a methodological review and recommendations for applications in ecological research,“ Biol. Fert. Soils 36, 249–259 (2002).
[CrossRef]

Crit. Rev. Biotechnol. (1)

R. E. Madrid and C. J. Felice, “Microbial biomass estimation,“ Crit. Rev. Biotechnol.,  25, 97–112 (2005).
[CrossRef] [PubMed]

Cyt. A (1)

C. L. Curl, C. J. Bellair, T. Harris, B. E. Allman, P. J. Harris, A. G. Stewart, A. Roberts, K. A. Nugent, and L. M. D. Delbridge, “Refractive index measurement in viable cells using quantitative phase-amplitude microscopy and confocal microscopy,” Cyt. A 65, 88 (2005).
[CrossRef]

Ecoscience (1)

E. A. D. Mitchell, A. Buttler, B. Warner, and J.-M. Gobat, “Ecology of testate amoebae (Protozoa: Rhizopoda) in Sphagnum-dominated peatlands in the Jura Mountains, Switzerland and France,” Ecoscience 6, 565–576 (1999).

J. Cell Biol. (1)

J. Bereiter-Hahn, Cecil H. Fox, and BO Thorell, “Quantitative reflection contrast microscopy of living cells,” J. Cell Biol. 82, 767–779 (1979).
[CrossRef] [PubMed]

J. Microsc. (1)

V. Lauer, “New approach to optical diffraction tomography yielding a vector equation of diffraction tomography and a novel tomographic microscope,” J. Microsc. 205, 165–176 (2002).
[CrossRef] [PubMed]

J. Opt. Soc. Am. A (1)

MD-PhD Thesis Dissertation (1)

P. Marquet, “Développement d’une nouvelle technique de microscopie optique tridimensionnelle, la microscopie holographique digitale. Perspective pour l’étude le la plasticité neuronale,” MD-PhD Thesis Dissertation (Chapt. 5), UNI-Lausanne, 2003.

Microbial Ecol. (3)

D. Gilbert, C. Amblard, G. Bourdier, and A.-J. Francez, “The microbial loop at the surface of a peatland: Structure, function, and impact of nutrient input,” Microbial Ecol. 35, 83–93 (1998).
[CrossRef]

E. A. D. Mitchell, D. Gilbert, A. Buttler, P. Grosvernier, C. Amblard, and J.-M. Gobat, “Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment,” Microbial Ecol. 16, 187–199 (2003).

H. Nguyen-Viet, N. Bernard, E. A. D. Mitchell, J. Cortet, P. M. Badot, and D. Gilbert, “Relationship between testate amoebae and atmospheric heavy metals (Pb, Cd, Zn, Ni, Cu, Mn and Fe) accumulated in the moss Barbula indica Hanoi, Vietnam,” Microbial Ecol. (to be published).

Opt. Commun. (3)

A. Barty, K.A. Nugent, A. Roberts, and D. Paganin, “Quantitative phase tomography,” Opt. Commun. 175, 329–336 (2000).
[CrossRef]

E. Wolf, “Three-dimensional structure determination of semi-transparent object from holographic data,” Opt. Commun. 1, 153–156 (1969).
[CrossRef]

R. Dändliker and K. Weiss, “Reconstruction of three-dimensional refractive index from scattered waves,“ Opt. Commun. 1, 323–328 (1970).
[CrossRef]

Opt. Express (1)

Opt. Lett. (2)

Opt. Spectrosc. (2)

G. N. Vishnyakov and G. G. Levin, “Optical microtomography of phase objects, ” Opt. Spectrosc. 85, 73–77 (1998).

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, and V. V. Pikalov, “Phase Tomography of 3D Biological Microobjects: Numerical Simulation and Experimental Results,” Opt. Spectrosc. 87, 413–419 (1999).

Proc. SPIE (1)

F. Charrière, E. Cuche, P. Marquet, and C. Depeursinge, “Biological cell (pollen grain) refractive index tomography with digital holographic microscopy.“ in Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII, J.-A. Conchello, C.J. Cogswell, T. Wilson, eds., Proc. SPIE 6090, 22–29 (2006).

Soc. of Ind. and Appl. Math. SIAM (1)

A. C. Kak and M. Slaney. Principles of Computerized Tomographic Imaging. Soc. of Ind. and Appl. Math. SIAM, 2001.

Other (3)

E. A. Paul and F. E. Clark, Soil microbiology and biochemistry, (Second Edition, Academic Press, San Diego, CA. 1996).

Dr. Enrique Lara, Swiss Federal Research Institute WSL and Laboratory of Ecological Systems, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland. (personnal communication, 2006).

A. Dunn, Light scattering properties of cells, PhD Diss., Univ. of Texas, Austin, 1997.

Supplementary Material (2)

» Media 1: AVI (1300 KB)     
» Media 2: AVI (1695 KB)     

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Figures (4)

Fig. 1.
Fig. 1.

Images of the testate amoebae Hyalosphenia papilio: (a) bright-field microscope image illustrating the amoeba itself and its content, P pseudostome (opening through which the amoeba pseudopods emerge), AS algal symbionts, PV phagocytic vacuoles; (b) SEM image illustrating the shell.

Fig. 2.
Fig. 2.

Holographic microscope for transmission imaging: NF neutral density filter; PBS polarizing beam splitter; BE beam expander with spatial filter; λ/2 half-wave plate; MO microscope objective; FL field lens; M mirror; BS beam splitter; O object wave; R reference wave; MP micropipette; CS coverslip; S specimen; IL immersion liquid. Inset: a detail showing the off-axis geometry at the incidence on the CCD.

Fig. 3.
Fig. 3.

Cuts in the tomographic reconstructions of 2 different Hyalosphenia papilio. Discrete values of the measured refractive index n are coded in false colors, the color-coding scales being displayed on the right part of each corresponding cut.

Fig. 4.
Fig. 4.

Animations [1.3MB (a), 1.7MB (b)] through the tomographic reconstructions of two selected Hyalosphenia papilio presenting some clearly visible inner structures tentatively identified as algal symbionts (AS) and phagocytic vacuoles (PV). The gray-level scales of the measured refractive index n are displayed on the right part of each corresponding cut.

Tables (1)

Tables Icon

Table 1. Estimated biovolumes for Hyalosphenia papilio.

Equations (2)

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φ x y = 2 π λ Δ n x y z dz ,
V = 4 3 π w l d 1 8 ,

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