Abstract

3D orbital particle tracking is a versatile and effective microscopy technique that allows following fast moving fluorescent objects within living cells and reconstructing complex 3D shapes using laser scanning microscopes. We demonstrated notable improvements in the range, speed and accuracy of 3D orbital particle tracking by replacing commonly used piezoelectric stages with Electrically Tunable Lens (ETL) that eliminates mechanical movement of objective lenses. This allowed tracking and reconstructing shape of structures extending 500 microns in the axial direction. Using the ETL, we tracked at high speed fluorescently labeled genomic loci within the nucleus of living cells with unprecedented temporal resolution of 8ms using a 1.42NA oil-immersion objective. The presented technology is cost effective and allows easy upgrade of scanning microscopes for fast 3D orbital tracking.

© 2015 Optical Society of America

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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  3. T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
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  4. J. Enderlein, “Tracking of fluorescent molecules diffusing within membranes,” Appl. Phys. B 71(5), 773–777 (2000).
    [Crossref]
  5. K. Kis-Petikova and E. Gratton, “Distance measurement by circular scanning of the excitation beam in the two-photon microscope,” Microsc. Res. Tech. 63(1), 34–49 (2004).
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  17. A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
    [Crossref] [PubMed]
  18. J. B. Sibarita, “Deconvolution microscopy,” Adv. Biochem. Eng. Biotechnol. 95, 201–243 (2005).
    [Crossref] [PubMed]
  19. V. Dion and S. M. Gasser, “Chromatin movement in the maintenance of genome stability,” Cell 152(6), 1355–1364 (2013).
    [Crossref] [PubMed]
  20. C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
    [Crossref] [PubMed]
  21. F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
    [Crossref] [PubMed]
  22. H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
    [Crossref] [PubMed]

2014 (4)

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

A. Anzalone, P. Annibale, and E. Gratton, “3D orbital tracking in a modified two-photon microscope: an application to the tracking of intracellular vesicles,” J. Vis. Exp. 92, e51794 (2014).
[PubMed]

P. Annibale and E. Gratton, “Advanced fluorescence microscopy methods for the real-time study of transcription and chromatin dynamics,” Transcription 5, e28425 (2014).

J. M. Jabbour, B. H. Malik, C. Olsovsky, R. Cuenca, S. Cheng, J. A. Jo, Y. S. Cheng, J. M. Wright, and K. C. Maitland, “Optical axial scanning in confocal microscopy using an electrically tunable lens,” Biomed. Opt. Express 5(2), 645–652 (2014).
[Crossref] [PubMed]

2013 (3)

V. Dion and S. M. Gasser, “Chromatin movement in the maintenance of genome stability,” Cell 152(6), 1355–1364 (2013).
[Crossref] [PubMed]

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

C. L. Chiu, M. A. Digman, and E. Gratton, “Measuring actin flow in 3D cell protrusions,” Biophys. J. 105(8), 1746–1755 (2013).
[Crossref] [PubMed]

2012 (2)

F. Cardarelli, L. Lanzano, and E. Gratton, “Capturing directed molecular motion in the nuclear pore complex of live cells,” Proc. Natl. Acad. Sci. U.S.A. 109(25), 9863–9868 (2012).
[Crossref] [PubMed]

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

2011 (5)

B. F. Grewe, F. F. Voigt, M. van ’t Hoff, and F. Helmchen, “Fast two-layer two-photon imaging of neuronal cell populations using an electrically tunable lens,” Biomed. Opt. Express 2(7), 2035–2046 (2011).
[Crossref] [PubMed]

Dupont and D. C. Lamb, “Nanoscale three-dimensional single particle tracking,” Nanoscale 3(11), 4532–4541 (2011).
[Crossref] [PubMed]

H.-C. Lin, M.-S. Chen, and Y.-H. Lin, “A Review of Electrically Tunable Focusing Liquid Crystal Lenses,” Transactions on Electrical and Electronic Materials 12(6), 234–240 (2011).
[Crossref]

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

2006 (1)

T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
[Crossref] [PubMed]

2005 (3)

V. Levi, Q. Ruan, and E. Gratton, “3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells,” Biophys. J. 88(4), 2919–2928 (2005).
[Crossref] [PubMed]

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

J. B. Sibarita, “Deconvolution microscopy,” Adv. Biochem. Eng. Biotechnol. 95, 201–243 (2005).
[Crossref] [PubMed]

2004 (2)

H. Oku, K. Hashimoto, and M. Ishikawa, “Variable-focus lens with 1-kHz bandwidth,” Opt. Express 12(10), 2138–2149 (2004).
[Crossref] [PubMed]

K. Kis-Petikova and E. Gratton, “Distance measurement by circular scanning of the excitation beam in the two-photon microscope,” Microsc. Res. Tech. 63(1), 34–49 (2004).
[Crossref] [PubMed]

2000 (1)

J. Enderlein, “Tracking of fluorescent molecules diffusing within membranes,” Appl. Phys. B 71(5), 773–777 (2000).
[Crossref]

1996 (1)

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Albert, B.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Annibale, P.

A. Anzalone, P. Annibale, and E. Gratton, “3D orbital tracking in a modified two-photon microscope: an application to the tracking of intracellular vesicles,” J. Vis. Exp. 92, e51794 (2014).
[PubMed]

P. Annibale and E. Gratton, “Advanced fluorescence microscopy methods for the real-time study of transcription and chromatin dynamics,” Transcription 5, e28425 (2014).

Anzalone, A.

A. Anzalone, P. Annibale, and E. Gratton, “3D orbital tracking in a modified two-photon microscope: an application to the tracking of intracellular vesicles,” J. Vis. Exp. 92, e51794 (2014).
[PubMed]

Bancaud, A.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Belmont, A. S.

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Blau, H. M.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Bystricky, K.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Cardarelli, F.

F. Cardarelli, L. Lanzano, and E. Gratton, “Capturing directed molecular motion in the nuclear pore complex of live cells,” Proc. Natl. Acad. Sci. U.S.A. 109(25), 9863–9868 (2012).
[Crossref] [PubMed]

Cardinale, J.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Carrivain, P.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Carthel, C.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Celler, K.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Chen, M.-S.

H.-C. Lin, M.-S. Chen, and Y.-H. Lin, “A Review of Electrically Tunable Focusing Liquid Crystal Lenses,” Transactions on Electrical and Electronic Materials 12(6), 234–240 (2011).
[Crossref]

Cheng, S.

Cheng, Y. S.

Chenouard, N.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Chiu, C. L.

C. L. Chiu, M. A. Digman, and E. Gratton, “Measuring actin flow in 3D cell protrusions,” Biophys. J. 105(8), 1746–1755 (2013).
[Crossref] [PubMed]

Cohen, A. R.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Coraluppi, S.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Cuenca, R.

Dan, H. W.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

de Chaumont, F.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Digman, M. A.

C. L. Chiu, M. A. Digman, and E. Gratton, “Measuring actin flow in 3D cell protrusions,” Biophys. J. 105(8), 1746–1755 (2013).
[Crossref] [PubMed]

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

Dion, V.

V. Dion and S. M. Gasser, “Chromatin movement in the maintenance of genome stability,” Cell 152(6), 1355–1364 (2013).
[Crossref] [PubMed]

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Duncan, J.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Dupont,

Dupont and D. C. Lamb, “Nanoscale three-dimensional single particle tracking,” Nanoscale 3(11), 4532–4541 (2011).
[Crossref] [PubMed]

Enderlein, J.

J. Enderlein, “Tracking of fluorescent molecules diffusing within membranes,” Appl. Phys. B 71(5), 773–777 (2000).
[Crossref]

Federici, F.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Fwu, P.

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

Gadal, O.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Gasser, S. M.

V. Dion and S. M. Gasser, “Chromatin movement in the maintenance of genome stability,” Cell 152(6), 1355–1364 (2013).
[Crossref] [PubMed]

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Gehlen, L. R.

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Giral, H.

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

Godinez, W. J.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Goiffon, I.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Gong, Y.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Gratton, E.

P. Annibale and E. Gratton, “Advanced fluorescence microscopy methods for the real-time study of transcription and chromatin dynamics,” Transcription 5, e28425 (2014).

A. Anzalone, P. Annibale, and E. Gratton, “3D orbital tracking in a modified two-photon microscope: an application to the tracking of intracellular vesicles,” J. Vis. Exp. 92, e51794 (2014).
[PubMed]

C. L. Chiu, M. A. Digman, and E. Gratton, “Measuring actin flow in 3D cell protrusions,” Biophys. J. 105(8), 1746–1755 (2013).
[Crossref] [PubMed]

F. Cardarelli, L. Lanzano, and E. Gratton, “Capturing directed molecular motion in the nuclear pore complex of live cells,” Proc. Natl. Acad. Sci. U.S.A. 109(25), 9863–9868 (2012).
[Crossref] [PubMed]

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
[Crossref] [PubMed]

V. Levi, Q. Ruan, and E. Gratton, “3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells,” Biophys. J. 88(4), 2919–2928 (2005).
[Crossref] [PubMed]

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

K. Kis-Petikova and E. Gratton, “Distance measurement by circular scanning of the excitation beam in the two-photon microscope,” Microsc. Res. Tech. 63(1), 34–49 (2004).
[Crossref] [PubMed]

Grewe, B. F.

Hajjoul, H.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Haseloff, J.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Hashimoto, K.

Helmchen, F.

Huang, H.

T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
[Crossref] [PubMed]

Ishikawa, M.

Jabbour, J. M.

Jaldén, J.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Jo, J. A.

Kalaidzidis, Y.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Kervrann, C.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Kis-Petikova, K.

K. Kis-Petikova and E. Gratton, “Distance measurement by circular scanning of the excitation beam in the two-photon microscope,” Microsc. Res. Tech. 63(1), 34–49 (2004).
[Crossref] [PubMed]

Lamb, D. C.

Dupont and D. C. Lamb, “Nanoscale three-dimensional single particle tracking,” Nanoscale 3(11), 4532–4541 (2011).
[Crossref] [PubMed]

Lanzano, L.

F. Cardarelli, L. Lanzano, and E. Gratton, “Capturing directed molecular motion in the nuclear pore complex of live cells,” Proc. Natl. Acad. Sci. U.S.A. 109(25), 9863–9868 (2012).
[Crossref] [PubMed]

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

Levi, M.

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

Levi, V.

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

V. Levi, Q. Ruan, and E. Gratton, “3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells,” Biophys. J. 88(4), 2919–2928 (2005).
[Crossref] [PubMed]

Li, G.

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Liang, L.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Lin, H.-C.

H.-C. Lin, M.-S. Chen, and Y.-H. Lin, “A Review of Electrically Tunable Focusing Liquid Crystal Lenses,” Transactions on Electrical and Electronic Materials 12(6), 234–240 (2011).
[Crossref]

Lin, Y.-H.

H.-C. Lin, M.-S. Chen, and Y.-H. Lin, “A Review of Electrically Tunable Focusing Liquid Crystal Lenses,” Transactions on Electrical and Electronic Materials 12(6), 234–240 (2011).
[Crossref]

Magnusson, K. E.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Maitland, K. C.

Maizel, A.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Malik, B. H.

Maška, M.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Mathon, J.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Meijering, E.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Mozziconacci, J.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Murray, A.

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Neumann, F. R.

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Oku, H.

Olivo-Marin, J. C.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Olsovsky, C.

Ortiz de Solórzano, C.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Paul-Gilloteaux, P.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Plutz, M.

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

Ragan, T.

T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
[Crossref] [PubMed]

Ranchon, H.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Robinett, C. C.

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Rohr, K.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Roudot, P.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Ruan, Q.

V. Levi, Q. Ruan, and E. Gratton, “3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells,” Biophys. J. 88(4), 2919–2928 (2005).
[Crossref] [PubMed]

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

Sbalzarini, I. F.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Schmid, R.

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Shen, H.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Shorte, S. L.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Sibarita, J. B.

J. B. Sibarita, “Deconvolution microscopy,” Adv. Biochem. Eng. Biotechnol. 95, 201–243 (2005).
[Crossref] [PubMed]

Smal, I.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

So, P.

T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
[Crossref] [PubMed]

Stelzer, E. H.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Straight, A.

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Sudlow, G.

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Taddei, A.

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Tinevez, J. Y.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Tsai, Y. S.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Tsai-Pflugfelder, M.

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

van ’t Hoff, M.

van Wezel, G. P.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Victor, J. M.

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

Voigt, F. F.

von Wangenheim, D.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Waharte, F.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Willemse, J.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Willhelm, C.

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

Winter, M.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Wright, J. M.

Xu, Y.

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Adv. Biochem. Eng. Biotechnol. (1)

J. B. Sibarita, “Deconvolution microscopy,” Adv. Biochem. Eng. Biotechnol. 95, 201–243 (2005).
[Crossref] [PubMed]

Appl. Phys. B (1)

J. Enderlein, “Tracking of fluorescent molecules diffusing within membranes,” Appl. Phys. B 71(5), 773–777 (2000).
[Crossref]

Biomed. Opt. Express (2)

Biophys. J. (3)

V. Levi, Q. Ruan, and E. Gratton, “3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells,” Biophys. J. 88(4), 2919–2928 (2005).
[Crossref] [PubMed]

C. L. Chiu, M. A. Digman, and E. Gratton, “Measuring actin flow in 3D cell protrusions,” Biophys. J. 105(8), 1746–1755 (2013).
[Crossref] [PubMed]

V. Levi, Q. Ruan, M. Plutz, A. S. Belmont, and E. Gratton, “Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope,” Biophys. J. 89(6), 4275–4285 (2005).
[Crossref] [PubMed]

Cell (1)

V. Dion and S. M. Gasser, “Chromatin movement in the maintenance of genome stability,” Cell 152(6), 1355–1364 (2013).
[Crossref] [PubMed]

Genes Dev. (1)

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-Pflugfelder, R. Schmid, A. Taddei, and S. M. Gasser, “Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination,” Genes Dev. 26(4), 369–383 (2012).
[Crossref] [PubMed]

Genome Res. (1)

H. Hajjoul, J. Mathon, H. Ranchon, I. Goiffon, J. Mozziconacci, B. Albert, P. Carrivain, J. M. Victor, O. Gadal, K. Bystricky, and A. Bancaud, “High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome,” Genome Res. 23(11), 1829–1838 (2013).
[Crossref] [PubMed]

J Biophotonics (1)

L. Lanzano, M. A. Digman, P. Fwu, H. Giral, M. Levi, and E. Gratton, “Nanometer-scale imaging by the modulation tracking method,” J Biophotonics 4(6), 415–424 (2011).
[Crossref] [PubMed]

J. Cell Biol. (1)

C. C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A. S. Belmont, “In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition,” J. Cell Biol. 135(6), 1685–1700 (1996).
[Crossref] [PubMed]

J. Fluoresc. (1)

T. Ragan, H. Huang, P. So, and E. Gratton, “3D particle tracking on a two-photon microscope,” J. Fluoresc. 16(3), 325–336 (2006).
[Crossref] [PubMed]

J. Vis. Exp. (1)

A. Anzalone, P. Annibale, and E. Gratton, “3D orbital tracking in a modified two-photon microscope: an application to the tracking of intracellular vesicles,” J. Vis. Exp. 92, e51794 (2014).
[PubMed]

Microsc. Res. Tech. (1)

K. Kis-Petikova and E. Gratton, “Distance measurement by circular scanning of the excitation beam in the two-photon microscope,” Microsc. Res. Tech. 63(1), 34–49 (2004).
[Crossref] [PubMed]

Nanoscale (1)

Dupont and D. C. Lamb, “Nanoscale three-dimensional single particle tracking,” Nanoscale 3(11), 4532–4541 (2011).
[Crossref] [PubMed]

Nat. Methods (1)

N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. Magnusson, J. Jaldén, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J. Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H. W. Dan, Y. S. Tsai, C. Ortiz de Solórzano, J. C. Olivo-Marin, and E. Meijering, “Objective comparison of particle tracking methods,” Nat. Methods 11(3), 281–289 (2014).
[Crossref] [PubMed]

Opt. Express (1)

Plant J. (1)

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (1)

F. Cardarelli, L. Lanzano, and E. Gratton, “Capturing directed molecular motion in the nuclear pore complex of live cells,” Proc. Natl. Acad. Sci. U.S.A. 109(25), 9863–9868 (2012).
[Crossref] [PubMed]

Transactions on Electrical and Electronic Materials (1)

H.-C. Lin, M.-S. Chen, and Y.-H. Lin, “A Review of Electrically Tunable Focusing Liquid Crystal Lenses,” Transactions on Electrical and Electronic Materials 12(6), 234–240 (2011).
[Crossref]

Transcription (1)

P. Annibale and E. Gratton, “Advanced fluorescence microscopy methods for the real-time study of transcription and chromatin dynamics,” Transcription 5, e28425 (2014).

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Figures (5)

Fig. 1
Fig. 1 a) Picture and schematics of the casing of the electrical lens, that allows it to be installed at the rear of any RMS objective. b) The focal length changes with the Current, with a slope depending on the magnifying power of the objective. A 20x objective yields an axial field of view of over one mm, which reduces to 200 μm if a 60x objective is used.
Fig. 2
Fig. 2 Comparative performances of an objective piezo-stage and of the electrical lens. a) Schematics of the orbital tracking configuration. A full 3D tracking period is achieved by performing 4 radial periods: 2 above and 2 below the particle. b) Piezo and lens performance compared for an orbit period of 8.192 ms. The up-down period for orbital tracking 32.77 ms. Comparing the displacement of the focal plane achieved by movement of the objective (Piezo, blue line, 2) and by the use of the ETL (Lens, red line, 1) c) Comparing piezo and lens performance for an orbital period of 2.048 ms. d) Demodulation of the piezo response for decreasing orbit period. The ideal square wave response turns to a triangular wave response, as the device is not able to perform the entire axial excursion in the required time e) Lens focal offset of ETL response for increasing axial frequency (i.e. decreasing orbit period, as indicated in the top axis). A resonance at about 500Hz is observed.
Fig. 3
Fig. 3 a) Reconstructed trajectory of a 1 μm fluorescent bead moved in a periodic 3D spiral pattern by the stepper-motor stage over a FOV of 15 μm (x-y) and 30 μm (z). Axial tracking is performed using the objective piezo-stage. b) Reconstructed trajectory of a 1 μm fluorescent bead moved in a periodic 3D spiral pattern by the stepper-motor stage over a FOV of 15 μm (x-y) and 30 μm (z). Axial tracking is performed using the ETL. For both experiments reported in a and b a 40x 0.8 NA water objective was used. c) Frequency distribution (log-scale) of the measured distance between scanners position and localized particle position for the test trajectories generated in a and b. d) Sedimentation profile of a 15 μm fluorescent bead over an axial range of 350 μm followed using the electrical lens and a 20x 0.4NA objective.
Fig. 4
Fig. 4 Bottom-up Picture of Arabidopsis Thaliana plants rooting in an agar plate with a glass-bottom. b) 3D reconstruction of a portion of the root from a 2-photon excitation z-stack performed by using 750 nm excitation. c) Trajectory of the root axis reconstructed from 3D orbital particle tracking, performed by ramping the position of the collimated laser beam along the axial direction using the ETL over a range exceeding 400 μm. d) Z-Section of a root highlighting a root hair protrusion. e) Pattern of the rosette orbit performed in the XZ plane to reconstruct the shape of the root hair. f) nSpiro reconstruction of the root hair. All experiments were performed with a 20x 0.4NA objective.
Fig. 5
Fig. 5 a) Trajectory of two fluorescently labeled DNA loci tracked in 3D using a 60x 1.42 NA oil immersion objective in combination with the ETL. b) Mean Squared Displacement (MSD) of the distance difference between the two loci.

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