Abstract

We describe various methods to process the data collected with a digital confocal microscope (DCM) in order to get more information than what we could get from a conventional confocal system. Different metrics can be extracted from the data collected with the DCM in order to produce images that reveal different features of the sample. The integrated phase of the scattered field allows for the three-dimensional reconstruction of the refractive index distribution. In a similar way, the integration of the field intensity yields the absorption coefficient distribution. The deflection of the digitally reconstructed focus reveals the sample-induced aberrations and the RMS width of the focus gives an indication on the local scattering coefficient. Finally, in addition to the conventional confocal metric, which consists in integrating the intensity within the pinhole, the DCM allows for the measurement of the phase within the pinhole. This metrics is close to the whole-field integrated phase and thus gives a qualitative image of the refractive index distribution.

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  1. M. Minsky, “Microscopy apparatus,” U.S. patent 3,013,467 (1961).
  2. C. J. R. Sheppard and A. Coudhury, “Image formation in the scanning microscope,” Opt. Acta24(10), 1051–1073 (1977).
    [CrossRef]
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    [CrossRef]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef]
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    [CrossRef]
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    [CrossRef] [PubMed]
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    [CrossRef]
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    [CrossRef]
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    [CrossRef]
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    [CrossRef]
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    [CrossRef] [PubMed]
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    [CrossRef]

2012 (1)

2010 (2)

K. Dillon and Y. Fainman, “Depth sectioning of attenuation,” J. Opt. Soc. Am. A27, 1347–1354 (2010).
[CrossRef]

K. Dillon and Y. Fainman, “Computational confocal tomography for simultaneous reconstruction of objects, occlusions and aberrations,” App. Opt.49(13), 2529–2538 (2010).
[CrossRef]

2008 (3)

2007 (2)

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods4, 717–719 (2007).
[CrossRef] [PubMed]

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

2006 (2)

2004 (1)

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

2003 (1)

2000 (1)

E. Cuche, P. Marquet, and C. Depeursinge, “Spatial filtering for zero-order and twin-image elimination in digital off-axis holography,” App. Opt.39, 4070–4075 (2000).
[CrossRef]

1999 (1)

1991 (1)

A. E. Dixon, S. Damaskinos, and M. R. Atkinson, “A scanning confocal microscope for transmission and reflection imaging,” Nature351, 551–553 (1991).
[CrossRef]

1988 (2)

R. M. Goldstein, H. A. Zebken, and C. L. Werner, “Satellite radar interferometry: two-dimensional phase unwrapping,” Radio Sci.23(4), 713–720 (1988).
[CrossRef]

M. D. Feit and J. A. Fleck, “Beam nonparaxiality, filament formation, and beam breakup in the self-focusing of optical beams,” J. Opt. Soc. Am. B5(3), 633–640 (1988).
[CrossRef]

1977 (1)

C. J. R. Sheppard and A. Coudhury, “Image formation in the scanning microscope,” Opt. Acta24(10), 1051–1073 (1977).
[CrossRef]

Arnison, M. R.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Atalick, S.

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

Atkinson, M. R.

A. E. Dixon, S. Damaskinos, and M. R. Atkinson, “A scanning confocal microscope for transmission and reflection imaging,” Nature351, 551–553 (1991).
[CrossRef]

Badizadegan, K.

Balberg, M.

Barbastathis, G.

Brady, D. J.

Charrière, F.

Choi, W.

Cogswell, C. J.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Colomb, T.

Coudhury, A.

C. J. R. Sheppard and A. Coudhury, “Image formation in the scanning microscope,” Opt. Acta24(10), 1051–1073 (1977).
[CrossRef]

Cuche, E.

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

E. Cuche, P. Marquet, and C. Depeursinge, “Spatial filtering for zero-order and twin-image elimination in digital off-axis holography,” App. Opt.39, 4070–4075 (2000).
[CrossRef]

Damaskinos, S.

A. E. Dixon, S. Damaskinos, and M. R. Atkinson, “A scanning confocal microscope for transmission and reflection imaging,” Nature351, 551–553 (1991).
[CrossRef]

Dasari, R. R.

Debailleul, M.

M. Debailleul, B. Simon, V. Georges, O. Haeberle, and V. Lauer, “Holographic microscopy and diffractive microtomography of transparent samples,” Meas. Sci. Technol.19, 074009 (2008).
[CrossRef]

Depeursinge, C.

Dillon, K.

K. Dillon and Y. Fainman, “Computational confocal tomography for simultaneous reconstruction of objects, occlusions and aberrations,” App. Opt.49(13), 2529–2538 (2010).
[CrossRef]

K. Dillon and Y. Fainman, “Depth sectioning of attenuation,” J. Opt. Soc. Am. A27, 1347–1354 (2010).
[CrossRef]

Dixon, A. E.

A. E. Dixon, S. Damaskinos, and M. R. Atkinson, “A scanning confocal microscope for transmission and reflection imaging,” Nature351, 551–553 (1991).
[CrossRef]

Fainman, Y.

K. Dillon and Y. Fainman, “Computational confocal tomography for simultaneous reconstruction of objects, occlusions and aberrations,” App. Opt.49(13), 2529–2538 (2010).
[CrossRef]

K. Dillon and Y. Fainman, “Depth sectioning of attenuation,” J. Opt. Soc. Am. A27, 1347–1354 (2010).
[CrossRef]

Fang-Yen, C.

Feit, M. D.

Fekete, P. W.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Feld, M. S.

Fleck, J. A.

Georges, V.

M. Debailleul, B. Simon, V. Georges, O. Haeberle, and V. Lauer, “Holographic microscopy and diffractive microtomography of transparent samples,” Meas. Sci. Technol.19, 074009 (2008).
[CrossRef]

Goldstein, R. M.

R. M. Goldstein, H. A. Zebken, and C. L. Werner, “Satellite radar interferometry: two-dimensional phase unwrapping,” Radio Sci.23(4), 713–720 (1988).
[CrossRef]

Goy, A.

Haeberle, O.

M. Debailleul, B. Simon, V. Georges, O. Haeberle, and V. Lauer, “Holographic microscopy and diffractive microtomography of transparent samples,” Meas. Sci. Technol.19, 074009 (2008).
[CrossRef]

Helgason, S.

S. Helgason, The Radon Transform, 2nd ed. (Birkhauser, 1999).

Herring, R.

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

Jacquemin, P.

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

Kuehn, J.

Lai, S.

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

Landkof, N. S.

N. S. Landkof, Foundation of Modern Potential Theory (Springer Verlag, 1972).

Lauer, V.

M. Debailleul, B. Simon, V. Georges, O. Haeberle, and V. Lauer, “Holographic microscopy and diffractive microtomography of transparent samples,” Meas. Sci. Technol.19, 074009 (2008).
[CrossRef]

Levin, G. G.

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

Likhachev, A. V.

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

Lue, N.

N. Lue, W. Choi, K. Badizadegan, R. R. Dasari, M. S. Feld, and G. Popescu, “Confocal diffraction phase microscopy of live cells,” Opt. Lett.33, 2074–2076 (2008).
[CrossRef] [PubMed]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods4, 717–719 (2007).
[CrossRef] [PubMed]

Marian, A.

Marquet, P.

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

E. Cuche, P. Marquet, and C. Depeursinge, “Spatial filtering for zero-order and twin-image elimination in digital off-axis holography,” App. Opt.39, 4070–4075 (2000).
[CrossRef]

McLeod, R. A.

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

Mertz, J.

Minaev, V. L.

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

Minsky, M.

M. Minsky, “Microscopy apparatus,” U.S. patent 3,013,467 (1961).

Montfort, F.

OByrne, J. W.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Oh, S.

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods4, 717–719 (2007).
[CrossRef] [PubMed]

Pavillon, N.

Philp, D.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Pickalov, V. V.

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

Popescu, G.

Psaltis, D.

Serrano, M.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Sheppard, C.

C. Sheppard and D. Shotton, Confocal Laser Scanning Microscopy (BIOS Scientific Publishers, 1997).

Sheppard, C. J. R.

C. J. R. Sheppard and A. Coudhury, “Image formation in the scanning microscope,” Opt. Acta24(10), 1051–1073 (1977).
[CrossRef]

Shotton, D.

C. Sheppard and D. Shotton, Confocal Laser Scanning Microscopy (BIOS Scientific Publishers, 1997).

Simon, B.

M. Debailleul, B. Simon, V. Georges, O. Haeberle, and V. Lauer, “Holographic microscopy and diffractive microtomography of transparent samples,” Meas. Sci. Technol.19, 074009 (2008).
[CrossRef]

Sudiarta, W.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

Vishnyakov, G. N.

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

Werner, C. L.

R. M. Goldstein, H. A. Zebken, and C. L. Werner, “Satellite radar interferometry: two-dimensional phase unwrapping,” Radio Sci.23(4), 713–720 (1988).
[CrossRef]

Yang, C.

Zebken, H. A.

R. M. Goldstein, H. A. Zebken, and C. L. Werner, “Satellite radar interferometry: two-dimensional phase unwrapping,” Radio Sci.23(4), 713–720 (1988).
[CrossRef]

Zhao, H.

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

App. Opt. (2)

E. Cuche, P. Marquet, and C. Depeursinge, “Spatial filtering for zero-order and twin-image elimination in digital off-axis holography,” App. Opt.39, 4070–4075 (2000).
[CrossRef]

K. Dillon and Y. Fainman, “Computational confocal tomography for simultaneous reconstruction of objects, occlusions and aberrations,” App. Opt.49(13), 2529–2538 (2010).
[CrossRef]

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

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

Meas. Sci. Technol. (1)

M. Debailleul, B. Simon, V. Georges, O. Haeberle, and V. Lauer, “Holographic microscopy and diffractive microtomography of transparent samples,” Meas. Sci. Technol.19, 074009 (2008).
[CrossRef]

Microscopy and Analysis (1)

G. N. Vishnyakov, G. G. Levin, V. L. Minaev, V. V. Pickalov, and A. V. Likhachev, “Tomographic interference microscopy of living cells,” Microscopy and Analysis18, 15–17 (2004).

Nat. Methods (1)

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods4, 717–719 (2007).
[CrossRef] [PubMed]

Nature (1)

A. E. Dixon, S. Damaskinos, and M. R. Atkinson, “A scanning confocal microscope for transmission and reflection imaging,” Nature351, 551–553 (1991).
[CrossRef]

Opt. Acta (1)

C. J. R. Sheppard and A. Coudhury, “Image formation in the scanning microscope,” Opt. Acta24(10), 1051–1073 (1977).
[CrossRef]

Opt. Express (2)

Opt. Lett. (5)

Radio Sci. (1)

R. M. Goldstein, H. A. Zebken, and C. L. Werner, “Satellite radar interferometry: two-dimensional phase unwrapping,” Radio Sci.23(4), 713–720 (1988).
[CrossRef]

Ultramicroscopy (1)

S. Lai, R. A. McLeod, P. Jacquemin, S. Atalick, and R. Herring, “An algorithm for 3-D refractive index measurement in holographic confocal microscopy,” Ultramicroscopy107, 196–201 (2007).
[CrossRef]

Other (5)

M. Minsky, “Microscopy apparatus,” U.S. patent 3,013,467 (1961).

C. Sheppard and D. Shotton, Confocal Laser Scanning Microscopy (BIOS Scientific Publishers, 1997).

J. W. OByrne, P. W. Fekete, M. R. Arnison, H. Zhao, M. Serrano, D. Philp, W. Sudiarta, and C. J. Cogswell, “Adaptive optics in confocal microscopy,” in Proceedings of the 2nd International Workshop on Adaptive Optics for Industry and Medicine, G. D. Love, ed. (World Scientific, 1999).

S. Helgason, The Radon Transform, 2nd ed. (Birkhauser, 1999).

N. S. Landkof, Foundation of Modern Potential Theory (Springer Verlag, 1972).

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