Abstract

We demonstrate the use of two-color digital holographic microscopy (DHM) for imaging microbiological subjects. The use of two wavelengths significantly reduces artifacts present in the reconstructed data, allowing us to image weakly-scattering objects in close proximity to strongly-scattering objects. We demonstrate this by reconstructing the shape of the flagellum of a unicellular eukaryotic parasite Leishmania mexicana in close proximity to a more strongly-scattering cell body. Our approach also yields a reduction of approximately one third in the axial position uncertainty when tracking the motion of swimming cells at low magnification, which we demonstrate with a sample of Escherichia coli bacteria mixed with polystyrene beads. The two-wavelength system that we describe introduces minimal additional complexity into the optical system, and provides significant benefits.

© 2017 Optical Society of America

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  48. J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
    [Crossref]

2017 (2)

A. Wang, R. F. Garmann, and V. N. Manoharan, “Tracking e. coli runs and tumbles with scattering solutions and digital holographic microscopy,” Opt. Express 24, 23719–23725 (2017).
[Crossref]

S. Bianchi, F. Saglimbeni, and R. Di Leonardo, “Holographic imaging reveals the mechanism of wall entrapment in swimming bacteria,” Phys. Rev. X 7, 011010 (2017).

2016 (5)

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” Adv. Exp. Med. Biol. 915, 17–32 (2016).
[Crossref] [PubMed]

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
[Crossref]

J. L. Nadeau, Y. B. Cho, J. Kühn, and K. Liewer, “Improved tracking and resolution of bacteria in holographic microscopy using dye and fluorescent protein labeling,” Front. Chem. 4, 17 (2016).
[Crossref] [PubMed]

L. M. De Pablos, T. R. Ferreira, and P. B. Walrad, “Developmental differentiation in leishmania lifecycle progression: post-transcriptional control conducts the orchestra,” Curr. Opin. Microbiol. 34, 82–89 (2016).
[Crossref] [PubMed]

Y. Wu, Y. Zhang, W. Luo, and A. Ozcan, “Demosaiced pixel super-resolution for multiplexed holographic color imaging,” Sci. Rep.-UK 6, 28601 (2016).
[Crossref]

2015 (2)

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
[Crossref] [PubMed]

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

2014 (4)

G. DiCaprio, A. El Mallahi, P. Ferraro, R. Dale, G. Coppola, B. Dale, G. Coppola, and F. Dubois, “4d tracking of clinical seminal samples for quantitative characterization of motility parameters,” Biomed. Opt. Express 5, 690–700 (2014).
[Crossref]

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed escape: Solid surfaces prevent tumbling of escherichia coli,” Phys. Rev. Lett. 113, 068103 (2014).
[Crossref] [PubMed]

C. B. Giuliano, R. Zhang, and L. G. Wilson, “Digital inline holographic microscopy (dihm) of weakly-scattering subjects,” J. Vis. Exp. 84, e50488 (2014).

F. Saglimbeni, S. Bianchi, A. Lepore, and R. Di Leonardo, “Three-axis digital holographic microscopy for high speed volumetric imaging,” Opt. Express 22, 13710–13718 (2014).
[Crossref] [PubMed]

2013 (2)

A. El Mallahi, C. Minetti, and 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. Optics 52, A68–A80 (2013).
[Crossref]

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proc. Natl. Acad. Sci. USA 110, 18769–18774 (2013).
[Crossref] [PubMed]

2012 (8)

G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
[Crossref]

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

D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
[Crossref] [PubMed]

M. H. Jericho, H. J. Kreuzer, M. Kanka, and R. Riesenberg, “Quantitative phase and refractive index measurements with point-source digital in-line holographic microscopy,” Appl. Opt. 51, 1503–1515 (2012).
[Crossref] [PubMed]

D. G. Abdelsalam and D. Kim, “Real-time dual-wavelength digital holographic microscopy based on polarizing separation,” Opt. Commun. 285, 233–237 (2012).
[Crossref]

L. Wilson and R. Zhang, “3d localization of weak scatterers in digital holographic microscopy using rayleigh-sommerfeld back-propagation,” Opt. Express 20, 16735–16744 (2012).
[Crossref]

S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
[Crossref] [PubMed]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

2011 (1)

2010 (2)

M. Kim, “Principles and techniques of digital holographic microscopy,” SPIE Rev. 1, 018005 (2010).

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
[Crossref]

2009 (1)

Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
[Crossref]

2008 (2)

2007 (6)

2006 (2)

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

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
[Crossref]

2005 (1)

C. Ó. S. Sorzano, P. Thévenaz, and M. Unser, “Elastic registration of biological images using vector-spline regularization,” IEEE T. Bio-Med. Eng. 52, 652–663 (2005).
[Crossref]

2003 (2)

2001 (2)

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography for biological applications,” Proc. Natl. Acad. Sci. 98, 11301–11305 (2001).
[Crossref] [PubMed]

I. Yamaguchi, J.-I. Kato, S. Ohta, and J. Mizuno, “Image formation in phase-shifting digital holography and applications to microscopy,” Appl. Optics 40, 6177–6186 (2001).
[Crossref]

1999 (1)

1994 (1)

1992 (1)

1972 (1)

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

1967 (1)

J. Goodman and R. W. Lawrence, “Digital image formation from electronically detected holograms,” Appl. Phys. Lett. 11, 77–79 (1967).
[Crossref]

Abdelsalam, D. G.

D. G. Abdelsalam and D. Kim, “Real-time dual-wavelength digital holographic microscopy based on polarizing separation,” Opt. Commun. 285, 233–237 (2012).
[Crossref]

Adolf, J.

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

Alvarez, L.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Antonucci, A.

G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
[Crossref]

Arganda-Carreras, I.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Awatsuji, Y.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
[Crossref]

Barry, M.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed escape: Solid surfaces prevent tumbling of escherichia coli,” Phys. Rev. Lett. 113, 068103 (2014).
[Crossref] [PubMed]

Belas, R.

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

Berg, H. C.

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

Bevilacqua, F.

Bianchi, S.

S. Bianchi, F. Saglimbeni, and R. Di Leonardo, “Holographic imaging reveals the mechanism of wall entrapment in swimming bacteria,” Phys. Rev. X 7, 011010 (2017).

F. Saglimbeni, S. Bianchi, A. Lepore, and R. Di Leonardo, “Three-axis digital holographic microscopy for high speed volumetric imaging,” Opt. Express 22, 13710–13718 (2014).
[Crossref] [PubMed]

Boss, D.

D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
[Crossref] [PubMed]

Boyer, K.

Brenker, C.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Brown, D. A.

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

Cardona, A.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Carter, L. M.

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proc. Natl. Acad. Sci. USA 110, 18769–18774 (2013).
[Crossref] [PubMed]

Charrière, F.

Cheong, F. C.

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
[Crossref]

Cho, S.-H.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
[Crossref] [PubMed]

Cho, Y. B.

J. L. Nadeau, Y. B. Cho, J. Kühn, and K. Liewer, “Improved tracking and resolution of bacteria in holographic microscopy using dye and fluorescent protein labeling,” Front. Chem. 4, 17 (2016).
[Crossref] [PubMed]

Colin, R.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Colomb, T.

Congestri, R.

G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
[Crossref]

Coppola, G.

Coskun, A. F.

S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
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Cui, Y.

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F. Saglimbeni, S. Bianchi, A. Lepore, and R. Di Leonardo, “Three-axis digital holographic microscopy for high speed volumetric imaging,” Opt. Express 22, 13710–13718 (2014).
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G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
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A. El Mallahi, C. Minetti, and 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. Optics 52, A68–A80 (2013).
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G. DiCaprio, A. El Mallahi, P. Ferraro, R. Dale, G. Coppola, B. Dale, G. Coppola, and F. Dubois, “4d tracking of clinical seminal samples for quantitative characterization of motility parameters,” Biomed. Opt. Express 5, 690–700 (2014).
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A. El Mallahi, C. Minetti, and 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. Optics 52, A68–A80 (2013).
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J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Ferreira, T. R.

L. M. De Pablos, T. R. Ferreira, and P. B. Walrad, “Developmental differentiation in leishmania lifecycle progression: post-transcriptional control conducts the orchestra,” Curr. Opin. Microbiol. 34, 82–89 (2016).
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K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” Adv. Exp. Med. Biol. 915, 17–32 (2016).
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J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
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Gadelha, C.

C. Gadelha, B. Wickstead, and K. Gull, “Flagellar and ciliary beating in trypanosome motility,” Cell Mot. Cytoskel. 64, 629–643 (2007).
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F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
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Garcia-Sucerquia, J.

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
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Giuliano, C. B.

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J. Goodman and R. W. Lawrence, “Digital image formation from electronically detected holograms,” Appl. Phys. Lett. 11, 77–79 (1967).
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S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
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Grier, D. G.

Groves, R. M.

Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
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M. Wiese, D. Kuhn, and C. G. Grünfelder, “Protein kinase involved in flagellar-length control,” Eukaryot. Cell 2, 769–777 (2003).
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Gull, K.

C. Gadelha, B. Wickstead, and K. Gull, “Flagellar and ciliary beating in trypanosome motility,” Cell Mot. Cytoskel. 64, 629–643 (2007).
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Hadwiger, M.

K. Engel, M. Hadwiger, J. M. Kniss, C. Rezk-Salama, and D. Weiskopf, Real-time volume graphics (A.K. Peters Ltd., 2006).
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J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
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D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
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Isikman, S. O.

S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
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Jericho, M. H.

M. H. Jericho, H. J. Kreuzer, M. Kanka, and R. Riesenberg, “Quantitative phase and refractive index measurements with point-source digital in-line holographic microscopy,” Appl. Opt. 51, 1503–1515 (2012).
[Crossref] [PubMed]

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
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W. Xu, M. H. Jericho, H. J. Kreuzer, and I. A. Meinertzhagen, “Tracking particles in four dimensions with in-line holographic microscopy,” Opt. Lett. 28, 164–166 (2003).
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W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography for biological applications,” Proc. Natl. Acad. Sci. 98, 11301–11305 (2001).
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Jericho, S. K.

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
[Crossref]

Jikeli, J. F.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
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Jüptner, W.

Kakue, T.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
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Kanka, M.

Kato, J.-I.

I. Yamaguchi, J.-I. Kato, S. Ohta, and J. Mizuno, “Image formation in phase-shifting digital holography and applications to microscopy,” Appl. Optics 40, 6177–6186 (2001).
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Katz, D. M.

Katz, J.

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

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

Kaupp, U. B.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
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Kaynig, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Kemper, B.

Kenney, L. J.

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
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D. G. Abdelsalam and D. Kim, “Real-time dual-wavelength digital holographic microscopy based on polarizing separation,” Opt. Commun. 285, 233–237 (2012).
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Kim, K.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
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M. Kim, “Principles and techniques of digital holographic microscopy,” SPIE Rev. 1, 018005 (2010).

Kim, S.-H.

Kim, Y.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
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Klages, P.

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
[Crossref]

Kniss, J. M.

K. Engel, M. Hadwiger, J. M. Kniss, C. Rezk-Salama, and D. Weiskopf, Real-time volume graphics (A.K. Peters Ltd., 2006).
[Crossref]

Kreuzer, H. J.

M. H. Jericho, H. J. Kreuzer, M. Kanka, and R. Riesenberg, “Quantitative phase and refractive index measurements with point-source digital in-line holographic microscopy,” Appl. Opt. 51, 1503–1515 (2012).
[Crossref] [PubMed]

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
[Crossref]

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

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography for biological applications,” Proc. Natl. Acad. Sci. 98, 11301–11305 (2001).
[Crossref] [PubMed]

Kubota, T.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
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Kuhn, D.

M. Wiese, D. Kuhn, and C. G. Grünfelder, “Protein kinase involved in flagellar-length control,” Eukaryot. Cell 2, 769–777 (2003).
[Crossref] [PubMed]

Kühn, J.

Langehanenberg, P.

Lawrence, R. W.

J. Goodman and R. W. Lawrence, “Digital image formation from electronically detected holograms,” Appl. Phys. Lett. 11, 77–79 (1967).
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Lee, S.

Lee, S.-E.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
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Lee, S.-H.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
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S.-H. Lee and D. G. Grier, “Holographic microscopy of holographically trapped three-dimensional structures,” Opt. Express 15, 1505–1512 (2007).
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H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
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Lepore, A.

Liewer, K.

J. L. Nadeau, Y. B. Cho, J. Kühn, and K. Liewer, “Improved tracking and resolution of bacteria in holographic microscopy using dye and fluorescent protein labeling,” Front. Chem. 4, 17 (2016).
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Lim, C. T.

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
[Crossref]

Longair, M.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Longworth, J. W.

Luo, W.

Y. Wu, Y. Zhang, W. Luo, and A. Ozcan, “Demosaiced pixel super-resolution for multiplexed holographic color imaging,” Sci. Rep.-UK 6, 28601 (2016).
[Crossref]

S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
[Crossref] [PubMed]

Magistretti, P. J.

D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
[Crossref] [PubMed]

Malkiel, E.

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

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

Manoharan, V. N.

Marquet, P.

Martin, K. E.

Matoba, O.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
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McGorty, R.

McPherson, A.

Meinertzhagen, I. A.

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

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography for biological applications,” Proc. Natl. Acad. Sci. 98, 11301–11305 (2001).
[Crossref] [PubMed]

Minetti, C.

A. El Mallahi, C. Minetti, and 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. Optics 52, A68–A80 (2013).
[Crossref]

Mizuno, J.

I. Yamaguchi, J.-I. Kato, S. Ohta, and J. Mizuno, “Image formation in phase-shifting digital holography and applications to microscopy,” Appl. Optics 40, 6177–6186 (2001).
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M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed escape: Solid surfaces prevent tumbling of escherichia coli,” Phys. Rev. Lett. 113, 068103 (2014).
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Nadeau, J. L.

J. L. Nadeau, Y. B. Cho, J. Kühn, and K. Liewer, “Improved tracking and resolution of bacteria in holographic microscopy using dye and fluorescent protein labeling,” Front. Chem. 4, 17 (2016).
[Crossref] [PubMed]

Nai, M. H.

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
[Crossref]

Nishio, K.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
[Crossref]

Ohta, S.

I. Yamaguchi, J.-I. Kato, S. Ohta, and J. Mizuno, “Image formation in phase-shifting digital holography and applications to microscopy,” Appl. Optics 40, 6177–6186 (2001).
[Crossref]

Osten, W.

Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
[Crossref]

Ozcan, A.

Y. Wu, Y. Zhang, W. Luo, and A. Ozcan, “Demosaiced pixel super-resolution for multiplexed holographic color imaging,” Sci. Rep.-UK 6, 28601 (2016).
[Crossref]

S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
[Crossref] [PubMed]

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

Park, H.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
[Crossref] [PubMed]

Park, S.

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
[Crossref]

Park, Y.

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
[Crossref] [PubMed]

Pascal, R.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Pedrini, G.

Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
[Crossref]

Perry, R. W.

Pichlo, M.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Pietzsch, T.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Place, A. R.

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

Preibisch, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Rappaz, B.

D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
[Crossref] [PubMed]

F. Charrière, B. Rappaz, J. Kühn, T. Colomb, P. Marquet, and C. Depeursinge, “Influence of shot noise on phase measurement accuracy in digital holographic microscopy,” Opt. Express 15, 8818–8831 (2007).
[Crossref] [PubMed]

Reece, S. E.

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proc. Natl. Acad. Sci. USA 110, 18769–18774 (2013).
[Crossref] [PubMed]

Rennhack, A.

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Rezk-Salama, C.

K. Engel, M. Hadwiger, J. M. Kniss, C. Rezk-Salama, and D. Weiskopf, Real-time volume graphics (A.K. Peters Ltd., 2006).
[Crossref]

Rhodes, C. K.

Riesenberg, R.

Roichman, Y.

Rueden, C.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Saalfeld, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Saglimbeni, F.

S. Bianchi, F. Saglimbeni, and R. Di Leonardo, “Holographic imaging reveals the mechanism of wall entrapment in swimming bacteria,” Phys. Rev. X 7, 011010 (2017).

F. Saglimbeni, S. Bianchi, A. Lepore, and R. Di Leonardo, “Three-axis digital holographic microscopy for high speed volumetric imaging,” Opt. Express 22, 13710–13718 (2014).
[Crossref] [PubMed]

Schindelin, J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Schmid, B.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Schnars, U.

Sheng, J.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed escape: Solid surfaces prevent tumbling of escherichia coli,” Phys. Rev. Lett. 113, 068103 (2014).
[Crossref] [PubMed]

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

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

Solem, J. C.

Sorzano, C. Ó. S.

C. Ó. S. Sorzano, P. Thévenaz, and M. Unser, “Elastic registration of biological images using vector-spline regularization,” IEEE T. Bio-Med. Eng. 52, 652–663 (2005).
[Crossref]

Stefano, L. D.

G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
[Crossref]

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G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
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M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed escape: Solid surfaces prevent tumbling of escherichia coli,” Phys. Rev. Lett. 113, 068103 (2014).
[Crossref] [PubMed]

Su, T.

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

Tahara, T.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
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Thévenaz, P.

C. Ó. S. Sorzano, P. Thévenaz, and M. Unser, “Elastic registration of biological images using vector-spline regularization,” IEEE T. Bio-Med. Eng. 52, 652–663 (2005).
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Thornton, K. L.

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” Adv. Exp. Med. Biol. 915, 17–32 (2016).
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Tinevez, J. Y.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Tomancal, P.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Tommasi, E. D.

G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
[Crossref]

Unser, M.

C. Ó. S. Sorzano, P. Thévenaz, and M. Unser, “Elastic registration of biological images using vector-spline regularization,” IEEE T. Bio-Med. Eng. 52, 652–663 (2005).
[Crossref]

Ura, S.

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
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van Blaaderen, A.

van de Ville, D.

D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
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van Oostrum, P.

von Bally, G.

Walrad, P. B.

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” Adv. Exp. Med. Biol. 915, 17–32 (2016).
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L. M. De Pablos, T. R. Ferreira, and P. B. Walrad, “Developmental differentiation in leishmania lifecycle progression: post-transcriptional control conducts the orchestra,” Curr. Opin. Microbiol. 34, 82–89 (2016).
[Crossref] [PubMed]

Wang, A.

Weiskopf, D.

K. Engel, M. Hadwiger, J. M. Kniss, C. Rezk-Salama, and D. Weiskopf, Real-time volume graphics (A.K. Peters Ltd., 2006).
[Crossref]

White, D. J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
[Crossref]

Wickstead, B.

C. Gadelha, B. Wickstead, and K. Gull, “Flagellar and ciliary beating in trypanosome motility,” Cell Mot. Cytoskel. 64, 629–643 (2007).
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M. Wiese, D. Kuhn, and C. G. Grünfelder, “Protein kinase involved in flagellar-length control,” Eukaryot. Cell 2, 769–777 (2003).
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Wilson, L.

Wilson, L. G.

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” Adv. Exp. Med. Biol. 915, 17–32 (2016).
[Crossref] [PubMed]

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

C. B. Giuliano, R. Zhang, and L. G. Wilson, “Digital inline holographic microscopy (dihm) of weakly-scattering subjects,” J. Vis. Exp. 84, e50488 (2014).

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proc. Natl. Acad. Sci. USA 110, 18769–18774 (2013).
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Wong, C. C.

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
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Y. Wu, Y. Zhang, W. Luo, and A. Ozcan, “Demosaiced pixel super-resolution for multiplexed holographic color imaging,” Sci. Rep.-UK 6, 28601 (2016).
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Xu, W.

J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
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W. Xu, M. H. Jericho, H. J. Kreuzer, and I. A. Meinertzhagen, “Tracking particles in four dimensions with in-line holographic microscopy,” Opt. Lett. 28, 164–166 (2003).
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W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography for biological applications,” Proc. Natl. Acad. Sci. 98, 11301–11305 (2001).
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Xue, L.

T. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3d tracking of human sperms reveals rare statistics of helical trajectories,” Proc. Natl. Acad. Sci. 109, 16018–16022 (2012).
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I. Yamaguchi, J.-I. Kato, S. Ohta, and J. Mizuno, “Image formation in phase-shifting digital holography and applications to microscopy,” Appl. Optics 40, 6177–6186 (2001).
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Yi, G.-R.

Zhang, R.

C. B. Giuliano, R. Zhang, and L. G. Wilson, “Digital inline holographic microscopy (dihm) of weakly-scattering subjects,” J. Vis. Exp. 84, e50488 (2014).

L. Wilson and R. Zhang, “3d localization of weak scatterers in digital holographic microscopy using rayleigh-sommerfeld back-propagation,” Opt. Express 20, 16735–16744 (2012).
[Crossref]

Zhang, Y.

Y. Wu, Y. Zhang, W. Luo, and A. Ozcan, “Demosaiced pixel super-resolution for multiplexed holographic color imaging,” Sci. Rep.-UK 6, 28601 (2016).
[Crossref]

3D Research (1)

T. Tahara, T. Kakue, Y. Awatsuji, K. Nishio, S. Ura, T. Kubota, and O. Matoba, “Parallel phase-shifting color digital holographic microscopy,” 3D Research 1, 25 (2010).
[Crossref]

Adv. Exp. Med. Biol. (1)

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” Adv. Exp. Med. Biol. 915, 17–32 (2016).
[Crossref] [PubMed]

Appl. Opt. (5)

Appl. Optics (4)

B. Kemper and G. von Bally, “Digital holographic microscopy for live cell applications and technical inspection,” Appl. Optics 47, A52–A61 (2008).
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J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, “Digital in-line holographic microscopy,” Appl. Optics 45, 836–850 (2006).
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A. El Mallahi, C. Minetti, and 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. Optics 52, A68–A80 (2013).
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I. Yamaguchi, J.-I. Kato, S. Ohta, and J. Mizuno, “Image formation in phase-shifting digital holography and applications to microscopy,” Appl. Optics 40, 6177–6186 (2001).
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Appl. Phys. Lett. (1)

J. Goodman and R. W. Lawrence, “Digital image formation from electronically detected holograms,” Appl. Phys. Lett. 11, 77–79 (1967).
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Biomed. Opt. Express (1)

Biophys. J. (1)

F. C. Cheong, C. C. Wong, Y. F. Gao, M. H. Nai, Y. Cui, S. Park, L. J. Kenney, and C. T. Lim, “Rapid, high-throughput tracking of bacterial motility in 3d via phase-contrast holographic video microscopy,” Biophys. J. 108, 1248–1256 (2016).
[Crossref]

Cell Mot. Cytoskel. (1)

C. Gadelha, B. Wickstead, and K. Gull, “Flagellar and ciliary beating in trypanosome motility,” Cell Mot. Cytoskel. 64, 629–643 (2007).
[Crossref]

Curr. Opin. Microbiol. (1)

L. M. De Pablos, T. R. Ferreira, and P. B. Walrad, “Developmental differentiation in leishmania lifecycle progression: post-transcriptional control conducts the orchestra,” Curr. Opin. Microbiol. 34, 82–89 (2016).
[Crossref] [PubMed]

Eukaryot. Cell (1)

M. Wiese, D. Kuhn, and C. G. Grünfelder, “Protein kinase involved in flagellar-length control,” Eukaryot. Cell 2, 769–777 (2003).
[Crossref] [PubMed]

Front. Chem. (1)

J. L. Nadeau, Y. B. Cho, J. Kühn, and K. Liewer, “Improved tracking and resolution of bacteria in holographic microscopy using dye and fluorescent protein labeling,” Front. Chem. 4, 17 (2016).
[Crossref] [PubMed]

IEEE T. Bio-Med. Eng. (1)

C. Ó. S. Sorzano, P. Thévenaz, and M. Unser, “Elastic registration of biological images using vector-spline regularization,” IEEE T. Bio-Med. Eng. 52, 652–663 (2005).
[Crossref]

J. Biophotonics (1)

G. DiCaprio, G. Coppola, L. D. Stefano, M. D. Stefano, A. Antonucci, R. Congestri, and E. D. Tommasi, “Shedding light on diatom photonics by means of digital holography,” J. Biophotonics 7, 341–350 (2012).
[Crossref]

J. Vis. Exp. (1)

C. B. Giuliano, R. Zhang, and L. G. Wilson, “Digital inline holographic microscopy (dihm) of weakly-scattering subjects,” J. Vis. Exp. 84, e50488 (2014).

Nat. Commun. (1)

J. F. Jikeli, L. Alvarez, B. M. Friedrich, L. G. Wilson, R. Pascal, R. Colin, M. Pichlo, A. Rennhack, C. Brenker, and U. B. Kaupp, “Sperm navigation along helical paths in 3d chemoattractant landscapes,” Nat. Commun. 6, 7985 (2015).
[Crossref] [PubMed]

Nature (1)

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

Nature Met. (1)

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancal, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Met. 9, 676–682 (2012).
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Opt. Commun. (1)

D. G. Abdelsalam and D. Kim, “Real-time dual-wavelength digital holographic microscopy based on polarizing separation,” Opt. Commun. 285, 233–237 (2012).
[Crossref]

Opt. Express (8)

S. Lee, Y. Roichman, G.-R. Yi, S.-H. Kim, S.-M. Yang, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Opt. Express 15, 18275–18282 (2007).
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J. Fung, K. E. Martin, R. W. Perry, D. M. Katz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Opt. Express 19, 8051–8065 (2011).
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S.-H. Lee and D. G. Grier, “Holographic microscopy of holographically trapped three-dimensional structures,” Opt. Express 15, 1505–1512 (2007).
[Crossref] [PubMed]

F. Saglimbeni, S. Bianchi, A. Lepore, and R. Di Leonardo, “Three-axis digital holographic microscopy for high speed volumetric imaging,” Opt. Express 22, 13710–13718 (2014).
[Crossref] [PubMed]

A. Wang, R. F. Garmann, and V. N. Manoharan, “Tracking e. coli runs and tumbles with scattering solutions and digital holographic microscopy,” Opt. Express 24, 23719–23725 (2017).
[Crossref]

F. Charrière, B. Rappaz, J. Kühn, T. Colomb, P. Marquet, and C. Depeursinge, “Influence of shot noise on phase measurement accuracy in digital holographic microscopy,” Opt. Express 15, 8818–8831 (2007).
[Crossref] [PubMed]

L. Wilson and R. Zhang, “3d localization of weak scatterers in digital holographic microscopy using rayleigh-sommerfeld back-propagation,” Opt. Express 20, 16735–16744 (2012).
[Crossref]

J. Kühn, T. Colomb, F. Montfort, F. Charrière, Y. Emery, E. Cuche, P. Marquet, and C. Depeursinge, “Real-time dual-wavelength digital holographic microscopy with a single hologram acquisition,” Opt. Express 15, 7231–7242 (2007).
[Crossref] [PubMed]

Opt. Laser. Eng. (1)

Y. Fu, G. Pedrini, B. M. Hennelly, R. M. Groves, and W. Osten, “Dual-wavelength image-plane digital holography for dynamic measurement,” Opt. Laser. Eng. 47, 552–557 (2009).
[Crossref]

Opt. Lett. (2)

Phys. Rev. Lett. (1)

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed escape: Solid surfaces prevent tumbling of escherichia coli,” Phys. Rev. Lett. 113, 068103 (2014).
[Crossref] [PubMed]

Phys. Rev. X (1)

S. Bianchi, F. Saglimbeni, and R. Di Leonardo, “Holographic imaging reveals the mechanism of wall entrapment in swimming bacteria,” Phys. Rev. X 7, 011010 (2017).

PLoS One (2)

D. Boss, A. Hoffmann, B. Rappaz, C. Depeursinge, P. J. Magistretti, D. van de Ville, and P. Marquet, “Spatially-resolved eigenmode decomposition of red blood cells membrane fluctuations questions the role of atp in flickering,” PLoS One 7, e40667 (2012).
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S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLoS One 7, e45044 (2012).
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Proc. Natl. Acad. Sci. (3)

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

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, “Digital in-line holography for biological applications,” Proc. Natl. Acad. Sci. 98, 11301–11305 (2001).
[Crossref] [PubMed]

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

Proc. Natl. Acad. Sci. USA (1)

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proc. Natl. Acad. Sci. USA 110, 18769–18774 (2013).
[Crossref] [PubMed]

Sci. Rep. (1)

H. Park, S.-H. Lee, K. Kim, S.-H. Cho, W.-J. Lee, Y. Kim, S.-E. Lee, and Y. Park, “Characterizations of individual mouse red blood cells parasitized by babesia microti using 3-d holographic microscopy,” Sci. Rep. 5, 10827 (2015).
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Sci. Rep.-UK (1)

Y. Wu, Y. Zhang, W. Luo, and A. Ozcan, “Demosaiced pixel super-resolution for multiplexed holographic color imaging,” Sci. Rep.-UK 6, 28601 (2016).
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SPIE Rev. (1)

M. Kim, “Principles and techniques of digital holographic microscopy,” SPIE Rev. 1, 018005 (2010).

Other (1)

K. Engel, M. Hadwiger, J. M. Kniss, C. Rezk-Salama, and D. Weiskopf, Real-time volume graphics (A.K. Peters Ltd., 2006).
[Crossref]

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Figures (6)

Fig. 1
Fig. 1 Optical layout for our simplified dual wavelength setup. A wavelength division multiplexer (WDM) is used to couple the two illumination wavelengths into a single fiber, which is directed onto a free-space coupler (FSC). An objective lens (OL) and tube lens (TL) produce an image of the sample at the microscope image plane, indicated as a vertical dashed line. The DualView apparatus (DV) images this plane with unit magnification onto a CMOS camera, spatially separating images created by the two illumination sources (see text).
Fig. 2
Fig. 2 Example two-color holographic images of a mixture of E. coli cells and polystyrene beads (see text), showing intermediate processing steps. Panels (a) and (b) show raw holographic data. The images in panels (c) and (d) show the same data, but with the static background removed (see text). The bottom row shows the maximum intensity projection of the intensity gradient stacks Igrad (x, y, z; t); this data can be used either for image registration or for object localization. The scale bars represent 25 μm in all panels.
Fig. 3
Fig. 3 Combining images of a mixture of E. coli cells and polystyrene beads (see text). (a) A superposition of images from red and green channels. The green image is shifted to the right, and suffers a slight stretching in the same direction. (b) A superposition of the red channel with the transformed green channel. The scale bar in panel (b) represents 30 μm. The scale in panel (a) is approximately the same, although red and green channels differ in scale by approximately 1.5% (see text).
Fig. 4
Fig. 4 Signal-to-noise ratio improvements using two-color DHM on a mixture of E. coli cells and polystyrene beads. Panels (a) and (b) show maximum intensity projections of gradient stacks from the red and green channels, respectively. Panel (c) shows the effect of multiplying the channels together. Panels (a–c) are displayed using a linear mapping from black for the minimum value, to white for the maximum value. Panel (d) shows a line profile along the path indicated with a light blue line in panels (a–c). The data in panel (d) have been scaled to have a maximum of 1, and fitted with a Gaussian curve (see text), to demonstrate improvements in the SNR. The scale bars in panels (a–c) represent 25 μm.
Fig. 5
Fig. 5 (a) A three-dimensional reconstruction of the swimming trajectory of bacterial cell, color-coded with instantaneous swimming speed. The total track duration is 40 seconds. (b) Five seconds of data showing the z-position as a function of time from the red channel only (bottom), the green channel only (middle, offset by 2 μm) and using both channels combined (top, offset by 5 μm). The black lines through the data points show the spline-smoothed track used to characterize the localization noise (see text). (c–e) Histograms of residuals when a spline fit is removed from the three-dimensional trajectory shown in (a). The one- and two-color systems achieve similar accuracy in the plane normal to the optical axis (Δx and Δy), but the two-color method reduces uncertainty in the axial coordinate (Δz), shown by the narrower histogram in panel (e).
Fig. 6
Fig. 6 Example data acquired from a subject with heterogeneous scattering properties: a promastigote L. mexicana cell. (a) and (b) show the red and green maximum intensity projection images, respectively (scale bar = 10 μm in each). Panel (c) shows a color image with the red and green channels combined, so that the artifacts can be seen to lie in different positions in each channel. Panel (d) shows the maximum intensity projection of the registered ‘joint’ image (scale bar = 10 μm), and panel (e) shows two orthogonal projections of the cell, demonstrating the three-dimensional reconstruction of the flagellum, the hair-like projection at the top of the cell (scale bar = 2 μm).

Equations (2)

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I g ( x , y , z , ; t ) = I im ( x , y , z ; t ) S z ( x , y , z ) ,
S z ( x , y , 0 ) = ( 1 2 1 2 4 2 1 2 1 ) S z ( x , y , 1 ) = ( 0 0 0 0 0 0 0 0 0 ) S z ( x , y , 2 ) = ( 1 2 1 2 4 2 1 2 1 ) .

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