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 20x 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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  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).
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    [CrossRef]
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    [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).
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  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).
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2006 (2)

2005 (4)

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]

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]

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

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).

2003 (1)

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).

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]

2000 (1)

A. Barty, K.A. Nugent, A. Roberts, 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, 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).

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, G. G. Levin, "Optical microtomography of phase objects, " Opt. Spectrosc. 85, 73-77 (1998).

1995 (2)

1992 (1)

1979 (1)

J. Bereiter-Hahn, CecilH. Fox and BO Thorell, "Quantitative reflection contrast microscopy of living cells," J. Cell Biol. 82, 767-779 (1979).
[CrossRef]

J. Bereiter-Hahn, CecilH. Fox and BO Thorell, "Quantitative reflection contrast microscopy of living cells," J. Cell Biol. 82, 767-779 (1979).
[CrossRef]

1970 (1)

R.  Dändliker, 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).

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, 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).

Bereiter-Hahn, J.

J. Bereiter-Hahn, CecilH. Fox and BO Thorell, "Quantitative reflection contrast microscopy of living cells," J. Cell Biol. 82, 767-779 (1979).
[CrossRef]

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).

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).

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).

Cecil, J.

J. Bereiter-Hahn, CecilH. Fox and BO Thorell, "Quantitative reflection contrast microscopy of living cells," J. Cell Biol. 82, 767-779 (1979).
[CrossRef]

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.

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.

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).

Dändliker, R.

R.  Dändliker, 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).

Depeursinge, C.

Depeursinge, Ch.

Emery, Y.

Felice, C. J.

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

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).

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).

Kawata, S.

Kühn, J.

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]

Levin, G. G.

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

G. N. Vishnyakov, 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, 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]

Magistretti, P.

Magistretti, P. J.

Marian, A.

Marquet, P.

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).

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).

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).

Nugent, K.A.

A. Barty, K.A. Nugent, A. Roberts, D. Paganin, "Quantitative phase tomography," Opt. Commun. 175, 329-336 (2000).
[CrossRef]

Paganin, D.

A. Barty, K.A. Nugent, A. Roberts, D. Paganin, "Quantitative phase tomography," Opt. Commun. 175, 329-336 (2000).
[CrossRef]

Pikalov, V. V.

G. N. Vishnyakov, G. G. Levin, A. V. Likhachev, 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).

A. Barty, K.A. Nugent, A. Roberts, D. Paganin, "Quantitative phase tomography," Opt. Commun. 175, 329-336 (2000).
[CrossRef]

Singer, W.

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).

Vishnyakov, G. N.

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

G. N. Vishnyakov, 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, 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)

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