Abstract

We use in-line digital holographic microscopy to image freely swimming E. coli. We show that fitting a light scattering model to E. coli holograms can yield quantitative information about the bacterium’s body rotation and tumbles, offering a precise way to track fine details of bacterial motility. We are able to extract the cell’s three-dimensional (3D) position and orientation and recover behavior such as body angle rotation during runs, tumbles, and pole reversal. Our technique is label-free and capable of frame rates limited only by the camera.

© 2016 Optical Society of America

Full Article  |  PDF Article
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References

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  1. H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239, 500–504 (1972).
    [Crossref] [PubMed]
  2. B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
    [Crossref]
  3. K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  6. K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” in “Biophysics of Infection,” C. M. Leake, ed. (Springer International Publishing, Cham, 2016), pp. 17–32.
    [Crossref]
  7. J. L. Nadeau, Y. B. Cho, and C. A. Lindensmith, “Use of dyes to increase phase contrast for biological holographic microscopy,” Optics Letters 40, 4114 (2015).
    [Crossref] [PubMed]
  8. L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proceedings of the National Academy of Sciences 110, 18769–18774 (2013).
    [Crossref]
  9. T.-W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proceedings of the National Academy of Sciences 109, 16018–16022 (2012).
    [Crossref]
  10. 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,” Nature Communications 6, 7985 (2015).
    [Crossref] [PubMed]
  11. Y. Pu and H. Meng, “Intrinsic aberrations due to Mie scattering in particle holography,” Journal of the Optical Society of America A 20, 1920–1932 (2003).
    [Crossref]
  12. F. C. Cheong, B. J. Krishnatreya, and D. G. Grier, “Strategies for three-dimensional particle tracking with holographic video microscopy,” Optics Express 18, 13563–13573 (2010).
    [Crossref] [PubMed]
  13. S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
    [Crossref] [PubMed]
  14. S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
    [Crossref] [PubMed]
  15. B. Ovryn and S. H. Izen, “Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope,” Journal of the Optical Society of America A 17, 1202–1213 (2000).
    [Crossref]
  16. C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
    [Crossref] [PubMed]
  17. C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
    [Crossref]
  18. J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
    [Crossref] [PubMed]
  19. R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
    [Crossref]
  20. B. Ovryn, “Three-dimensional forward scattering particle image velocimetry applied to a microscopic field-of-view,” Experiments in Fluids 29, S175–S184 (2000).
    [Crossref]
  21. D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
    [Crossref]
  22. S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
    [Crossref] [PubMed]
  23. J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
    [Crossref]
  24. M. A. Yurkin and A. G. Hoekstra, “The discrete-dipole-approximation code ADDA: capabilities and known limitations,” Journal of Quantitative Spectroscopy and Radiative Transfer 112, 2234–2247 (2011).
    [Crossref]
  25. A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
    [Crossref]
  26. J. Saragosti, P. Silberzan, and A. Buguin, “Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis,” PLoS ONE 7, e35412 (2012).
    [Crossref] [PubMed]
  27. N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
    [Crossref]
  28. H. C. Berg and L. Turner, “Cells of Escherichia coli swim either end forward,” Proceedings of the National Academy of Sciences 92, 477–479 (1995).
    [Crossref]
  29. S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
    [Crossref]
  30. P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
    [Crossref]

2016 (2)

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

2015 (5)

S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
[Crossref]

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
[Crossref] [PubMed]

J. L. Nadeau, Y. B. Cho, and C. A. Lindensmith, “Use of dyes to increase phase contrast for biological holographic microscopy,” Optics Letters 40, 4114 (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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

2014 (4)

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Physical Review Letters 113, 068103 (2014).
[Crossref] [PubMed]

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

2013 (1)

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proceedings of the National Academy of Sciences 110, 18769–18774 (2013).
[Crossref]

2012 (4)

T.-W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proceedings of the National Academy of Sciences 109, 16018–16022 (2012).
[Crossref]

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

J. Saragosti, P. Silberzan, and A. Buguin, “Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis,” PLoS ONE 7, e35412 (2012).
[Crossref] [PubMed]

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

2011 (2)

M. A. Yurkin and A. G. Hoekstra, “The discrete-dipole-approximation code ADDA: capabilities and known limitations,” Journal of Quantitative Spectroscopy and Radiative Transfer 112, 2234–2247 (2011).
[Crossref]

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

2010 (1)

F. C. Cheong, B. J. Krishnatreya, and D. G. Grier, “Strategies for three-dimensional particle tracking with holographic video microscopy,” Optics Express 18, 13563–13573 (2010).
[Crossref] [PubMed]

2007 (2)

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
[Crossref]

2006 (1)

S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
[Crossref] [PubMed]

2005 (1)

S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
[Crossref] [PubMed]

2003 (1)

Y. Pu and H. Meng, “Intrinsic aberrations due to Mie scattering in particle holography,” Journal of the Optical Society of America A 20, 1920–1932 (2003).
[Crossref]

2000 (2)

B. Ovryn and S. H. Izen, “Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope,” Journal of the Optical Society of America A 17, 1202–1213 (2000).
[Crossref]

B. Ovryn, “Three-dimensional forward scattering particle image velocimetry applied to a microscopic field-of-view,” Experiments in Fluids 29, S175–S184 (2000).
[Crossref]

1995 (1)

H. C. Berg and L. Turner, “Cells of Escherichia coli swim either end forward,” Proceedings of the National Academy of Sciences 92, 477–479 (1995).
[Crossref]

1972 (1)

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239, 500–504 (1972).
[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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Arlt, J.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Ayi, T.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

Barry, M.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Physical Review Letters 113, 068103 (2014).
[Crossref] [PubMed]

Berg, H. C.

N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
[Crossref]

H. C. Berg and L. Turner, “Cells of Escherichia coli swim either end forward,” Proceedings of the National Academy of Sciences 92, 477–479 (1995).
[Crossref]

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239, 500–504 (1972).
[Crossref] [PubMed]

Bianchi, S.

S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
[Crossref]

Bourouina, T.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Brenner, M. P.

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

Breuer, K. S.

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

Brown, D. A.

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239, 500–504 (1972).
[Crossref] [PubMed]

Buguin, A.

J. Saragosti, P. Silberzan, and A. Buguin, “Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis,” PLoS ONE 7, e35412 (2012).
[Crossref] [PubMed]

Carter, L. M.

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proceedings of the National Academy of Sciences 110, 18769–18774 (2013).
[Crossref]

Chaikin, P. M.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

Chaudhary, K.

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

Cheong, F. C.

F. C. Cheong, B. J. Krishnatreya, and D. G. Grier, “Strategies for three-dimensional particle tracking with holographic video microscopy,” Optics Express 18, 13563–13573 (2010).
[Crossref] [PubMed]

Chin, L.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

Cho, Y. B.

J. L. Nadeau, Y. B. Cho, and C. A. Lindensmith, “Use of dyes to increase phase contrast for biological holographic microscopy,” Optics Letters 40, 4114 (2015).
[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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Darnton, N. C.

N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
[Crossref]

Dawson, A.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Di Leonardo, R.

S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
[Crossref]

DiLuzio, W. R.

S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
[Crossref] [PubMed]

Dimiduk, T. G.

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

Findlay, R. C.

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” in “Biophysics of Infection,” C. M. Leake, ed. (Springer International Publishing, Cham, 2016), pp. 17–32.
[Crossref]

Friedrich, B. 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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Fung, J.

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

Grier, D. G.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

F. C. Cheong, B. J. Krishnatreya, and D. G. Grier, “Strategies for three-dimensional particle tracking with holographic video microscopy,” Optics Express 18, 13563–13573 (2010).
[Crossref] [PubMed]

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

Gude, S.

K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
[Crossref] [PubMed]

Guerra, R. E.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

Guerrero-García, G. I.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

Gulino, M.

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

Hoekstra, A. G.

M. A. Yurkin and A. G. Hoekstra, “The discrete-dipole-approximation code ADDA: capabilities and known limitations,” Journal of Quantitative Spectroscopy and Radiative Transfer 112, 2234–2247 (2011).
[Crossref]

Hollingsworth, A. D.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

Izen, S. H.

B. Ovryn and S. H. Izen, “Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope,” Journal of the Optical Society of America A 17, 1202–1213 (2000).
[Crossref]

Jepson, A.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[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,” Nature Communications 6, 7985 (2015).
[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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Kaz, D. M.

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

Kelleher, C. P.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

Khan, S.

S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
[Crossref] [PubMed]

Kim, S.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
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Kreis, T.

T. Kreis, Handbook of Holographic Interferometry (Wiley-VCH Verlag GmbH & Co. KGaA, 2005).

Kretzschmar, I.

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

Krishnatreya, B. J.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
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F. C. Cheong, B. J. Krishnatreya, and D. G. Grier, “Strategies for three-dimensional particle tracking with holographic video microscopy,” Optics Express 18, 13563–13573 (2010).
[Crossref] [PubMed]

Lee, S.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

Lepore, A.

S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
[Crossref]

Leprince-Wang, Y.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

Lindensmith, C. A.

J. L. Nadeau, Y. B. Cho, and C. A. Lindensmith, “Use of dyes to increase phase contrast for biological holographic microscopy,” Optics Letters 40, 4114 (2015).
[Crossref] [PubMed]

Liu, B.

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

Liu, P.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

Mani, M.

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

Manoharan, V. N.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

Martin, K. E.

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

Martinez, V. A.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

McGorty, R.

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

Meng, G.

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

Meng, H.

Y. Pu and H. Meng, “Intrinsic aberrations due to Mie scattering in particle holography,” Journal of the Optical Society of America A 20, 1920–1932 (2003).
[Crossref]

Miroli, D.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Molaei, M.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Physical Review Letters 113, 068103 (2014).
[Crossref] [PubMed]

Morse, M.

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

Nadeau, J. L.

J. L. Nadeau, Y. B. Cho, and C. A. Lindensmith, “Use of dyes to increase phase contrast for biological holographic microscopy,” Optics Letters 40, 4114 (2015).
[Crossref] [PubMed]

Ovryn, B.

B. Ovryn and S. H. Izen, “Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope,” Journal of the Optical Society of America A 17, 1202–1213 (2000).
[Crossref]

B. Ovryn, “Three-dimensional forward scattering particle image velocimetry applied to a microscopic field-of-view,” Experiments in Fluids 29, S175–S184 (2000).
[Crossref]

Ozcan, A.

T.-W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proceedings of the National Academy of Sciences 109, 16018–16022 (2012).
[Crossref]

Parkinson, J. S.

S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
[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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Perry, R. W.

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
[Crossref] [PubMed]

Philips, L. A.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Pilizota, T.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Poon, W. C.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Powers, T. R.

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

Pu, Y.

Y. Pu and H. Meng, “Intrinsic aberrations due to Mie scattering in particle holography,” Journal of the Optical Society of America A 20, 1920–1932 (2003).
[Crossref]

Razavi, S.

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

Reece, S. E.

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proceedings of the National Academy of Sciences 110, 18769–18774 (2013).
[Crossref]

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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

Roichman, Y.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

Rojevsky, S.

N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
[Crossref]

Ruffner, D. B.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

Saglimbeni, F.

S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
[Crossref]

Saragosti, J.

J. Saragosti, P. Silberzan, and A. Buguin, “Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis,” PLoS ONE 7, e35412 (2012).
[Crossref] [PubMed]

Schwarz-Linek, J.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Ser, W.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

Seung-Man, Y.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

Sheng, J.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Physical Review Letters 113, 068103 (2014).
[Crossref] [PubMed]

Shimizu, T. S.

K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
[Crossref] [PubMed]

Silberzan, P.

J. Saragosti, P. Silberzan, and A. Buguin, “Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis,” PLoS ONE 7, e35412 (2012).
[Crossref] [PubMed]

Stocker, R.

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Physical Review Letters 113, 068103 (2014).
[Crossref] [PubMed]

Stutt, A.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

Su, T.-W.

T.-W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proceedings of the National Academy of Sciences 109, 16018–16022 (2012).
[Crossref]

Takeuchi, S.

S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
[Crossref] [PubMed]

Tang, J. X.

B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
[Crossref]

Tans, S. J.

K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
[Crossref] [PubMed]

Taute, K. M.

K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
[Crossref] [PubMed]

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,” in “Biophysics of Infection,” C. M. Leake, ed. (Springer International Publishing, Cham, 2016), pp. 17–32.
[Crossref]

Turner, L.

N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
[Crossref]

H. C. Berg and L. Turner, “Cells of Escherichia coli swim either end forward,” Proceedings of the National Academy of Sciences 92, 477–479 (1995).
[Crossref]

van Blaaderen, A.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

van Oostrum, P.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

Vissers, T.

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Walia, B.

S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
[Crossref] [PubMed]

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,” in “Biophysics of Infection,” C. M. Leake, ed. (Springer International Publishing, Cham, 2016), pp. 17–32.
[Crossref]

Wang, A.

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
[Crossref]

A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

Wang, C.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

Ward, M. D.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

Weibel, D. B.

S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
[Crossref] [PubMed]

Whitesides, G. M.

S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
[Crossref] [PubMed]

Wilson, L. G.

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,” Nature Communications 6, 7985 (2015).
[Crossref] [PubMed]

L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proceedings of the National Academy of Sciences 110, 18769–18774 (2013).
[Crossref]

K. L. Thornton, R. C. Findlay, P. B. Walrad, and L. G. Wilson, “Investigating the swimming of microbial pathogens using digital holography,” in “Biophysics of Infection,” C. M. Leake, ed. (Springer International Publishing, Cham, 2016), pp. 17–32.
[Crossref]

Wright, S.

S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
[Crossref] [PubMed]

Xue, L.

T.-W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proceedings of the National Academy of Sciences 109, 16018–16022 (2012).
[Crossref]

Yap, P.

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
[Crossref]

Yi, G.

S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
[Crossref] [PubMed]

Yurkin, M. A.

M. A. Yurkin and A. G. Hoekstra, “The discrete-dipole-approximation code ADDA: capabilities and known limitations,” Journal of Quantitative Spectroscopy and Radiative Transfer 112, 2234–2247 (2011).
[Crossref]

Zhong, X.

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
[Crossref] [PubMed]

Colloids and Surfaces B: Biointerfaces (1)

J. Schwarz-Linek, J. Arlt, A. Jepson, A. Dawson, T. Vissers, D. Miroli, T. Pilizota, V. A. Martinez, and W. C. Poon, “Escherichia coli as a model active colloid: A practical introduction,” Colloids and Surfaces B: Biointerfaces 137, 2–16 (2016).
[Crossref]

Experiments in Fluids (1)

B. Ovryn, “Three-dimensional forward scattering particle image velocimetry applied to a microscopic field-of-view,” Experiments in Fluids 29, S175–S184 (2000).
[Crossref]

Faraday Discussions (1)

R. W. Perry, G. Meng, T. G. Dimiduk, J. Fung, and V. N. Manoharan, “Real-space studies of the structure and dynamics of self-assembled colloidal clusters,” Faraday Discussions 159, 211–234 (2012).
[Crossref]

Journal of bacteriology (1)

N. C. Darnton, L. Turner, S. Rojevsky, and H. C. Berg, “On torque and tumbling in swimming Escherichia coli,” Journal of bacteriology 189, 1756–1764 (2007).
[Crossref]

S. Wright, B. Walia, J. S. Parkinson, and S. Khan, “Differential activation of Escherichia coli chemoreceptors by blue-light stimuli,” Journal of Bacteriology 188, 3962–3971 (2006).
[Crossref] [PubMed]

Journal of Pharmaceutical Sciences (1)

C. Wang, X. Zhong, D. B. Ruffner, A. Stutt, L. A. Philips, M. D. Ward, and D. G. Grier, “Holographic characterization of protein aggregates,” Journal of Pharmaceutical Sciences 105, 1074–1085 (2016).
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Journal of Quantitative Spectroscopy and Radiative Transfer (2)

M. A. Yurkin and A. G. Hoekstra, “The discrete-dipole-approximation code ADDA: capabilities and known limitations,” Journal of Quantitative Spectroscopy and Radiative Transfer 112, 2234–2247 (2011).
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A. Wang, T. G. Dimiduk, J. Fung, S. Razavi, I. Kretzschmar, K. Chaudhary, and V. N. Manoharan, “Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles,” Journal of Quantitative Spectroscopy and Radiative Transfer 146, 499–509 (2014).
[Crossref]

Journal of the Optical Society of America A (2)

B. Ovryn and S. H. Izen, “Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope,” Journal of the Optical Society of America A 17, 1202–1213 (2000).
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Y. Pu and H. Meng, “Intrinsic aberrations due to Mie scattering in particle holography,” Journal of the Optical Society of America A 20, 1920–1932 (2003).
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Nano Letters (1)

S. Takeuchi, W. R. DiLuzio, D. B. Weibel, and G. M. Whitesides, “Controlling the shape of filamentous cells of Escherichia coli,” Nano Letters 5, 1819–1823 (2005).
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Nature (1)

H. C. Berg and D. A. Brown, “Chemotaxis in Escherichia coli analysed by three-dimensional tracking,” Nature 239, 500–504 (1972).
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Nature Communications (2)

K. M. Taute, S. Gude, S. J. Tans, and T. S. Shimizu, “High-throughput 3D tracking of bacteria on a standard phase contrast microscope,” Nature Communications 6, 8776 (2015).
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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,” Nature Communications 6, 7985 (2015).
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Nature Materials (1)

D. M. Kaz, R. McGorty, M. Mani, M. P. Brenner, and V. N. Manoharan, “Physical ageing of the contact line on colloidal particles at liquid interfaces,” Nature Materials 11, 138–142 (2012).
[Crossref]

Optics Express (3)

J. Fung, K. E. Martin, R. W. Perry, D. M. Kaz, R. McGorty, and V. N. Manoharan, “Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy,” Optics Express 19, 8051–8065 (2011).
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S. Lee, Y. Roichman, G. Yi, S. Kim, Y. Seung-Man, A. van Blaaderen, P. van Oostrum, and D. G. Grier, “Characterizing and tracking single colloidal particles with video holographic microscopy,” Optics Express 15, 18275–18282 (2007).
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F. C. Cheong, B. J. Krishnatreya, and D. G. Grier, “Strategies for three-dimensional particle tracking with holographic video microscopy,” Optics Express 18, 13563–13573 (2010).
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Optics Letters (1)

J. L. Nadeau, Y. B. Cho, and C. A. Lindensmith, “Use of dyes to increase phase contrast for biological holographic microscopy,” Optics Letters 40, 4114 (2015).
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Phys. Rev. E (2)

C. P. Kelleher, A. Wang, G. I. Guerrero-García, A. D. Hollingsworth, R. E. Guerra, B. J. Krishnatreya, D. G. Grier, V. N. Manoharan, and P. M. Chaikin, “Charged hydrophobic colloids at an oil-aqueous phase interface,” Phys. Rev. E 92, 062306 (2015).
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S. Bianchi, F. Saglimbeni, A. Lepore, and R. Di Leonardo, “Polar features in the flagellar propulsion of E. coli bacteria,” Phys. Rev. E 91, 062705 (2015).
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Physical Review Letters (1)

M. Molaei, M. Barry, R. Stocker, and J. Sheng, “Failed Escape: Solid Surfaces Prevent Tumbling of Escherichia coli,” Physical Review Letters 113, 068103 (2014).
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PLoS ONE (1)

J. Saragosti, P. Silberzan, and A. Buguin, “Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis,” PLoS ONE 7, e35412 (2012).
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Procedia Engineering (1)

P. Liu, L. Chin, W. Ser, T. Ayi, P. Yap, T. Bourouina, and Y. Leprince-Wang, “Real-time measurement of single bacterium’s refractive index using optofluidic immersion refractometry,” Procedia Engineering 87, 356–359 (2014).
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Proceedings of the National Academy of Sciences (4)

H. C. Berg and L. Turner, “Cells of Escherichia coli swim either end forward,” Proceedings of the National Academy of Sciences 92, 477–479 (1995).
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L. G. Wilson, L. M. Carter, and S. E. Reece, “High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms,” Proceedings of the National Academy of Sciences 110, 18769–18774 (2013).
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T.-W. Su, L. Xue, and A. Ozcan, “High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories,” Proceedings of the National Academy of Sciences 109, 16018–16022 (2012).
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B. Liu, M. Gulino, M. Morse, J. X. Tang, T. R. Powers, and K. S. Breuer, “Helical motion of the cell body enhances caulobacter crescentus motility,” Proceedings of the National Academy of Sciences 111, 11252–11256 (2014).
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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,” in “Biophysics of Infection,” C. M. Leake, ed. (Springer International Publishing, Cham, 2016), pp. 17–32.
[Crossref]

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Figures (4)

Fig. 1
Fig. 1

a) Holograms are captured on an in-line holography setup, shown at top. Our sample cells (bottom) consist of two square coverslips glued with epoxy to a larger coverslip. A droplet of tryptone broth (blue) is placed in between the smaller coverslips. A smaller droplet of cells (pink) is placed on the smaller coverslip. A top coverslip is sealed in place with vacuum grease (gray). b) We define the orientation and position of the E. coli cell relative to the laboratory frame. A unit vector u points along the long axis of the cell in the direction of travel. The angle between u and the imaging axis (z-axis) is defined to be the polar angle θ. We define another unit vector p that is a projection of u onto the x-y plane. The angle that p makes with the laboratory y-axis is the azimuthal angle ϕ.

Fig. 2
Fig. 2

We capture holograms of freely swimming E. coli in a time series. Two frames are shown in the left column, where the asymmetry in the fringes is noticeably different between the frames. The best-fit holograms are shown in the middle, and three-dimensional renderings from the best-fit holograms are shown on the right.

Fig. 3
Fig. 3

a) We capture holograms of freely swimming E. coli in a time series and fit a scattering model to them to recover the trajectory. The blue square represents the position at the start of the time series. The circle marks the position at the end. b) We plot the direction u points on a unit sphere for the duration of the trajectory in a) to show how u precesses as the cell swims.

Fig. 4
Fig. 4

a) Center-of-mass trajectory of a cell’s runs and tumbles. The blue square represents the position at the start of the time series. The circle marks the position at the end. The red squares mark the two tumbles shown in panel (b). b) We plot where u points on a sphere and indicate the tumbles in red. The gray part of the trajectory on the right, near the end, lies on the rear hemisphere. The square represents the start of the trajectory, the circle marks the end, and the arrows indicate the direction of motion.

Tables (1)

Tables Icon

Table 1 Properties of AW405 cells determined from fitting holograms of ten cells, compared to values from Darnton et al. [27] unless otherwise specified. The errors are standard deviations from the mean of measurements of ten different cells.

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