Abstract

Despite recent advances in optical super-resolution, we lack a method that can visualize the path followed by diffusing molecules in the cytoplasm or in the nucleus of cells. Fluorescence correlation spectroscopy (FCS) provides molecular dynamics at the single molecule level by averaging the behavior of many molecules over time at a single spot, thus achieving very good statistics but at only one point in the cell. Earlier image-based methods including raster-scan and spatiotemporal image correlation need spatial averaging over relatively large areas, thus compromising spatial resolution. Here, we use spatial pair-cross-correlation in two dimensions (2D-pCF) to obtain relatively high resolution images of molecular diffusion dynamics and transport in live cells. The 2D-pCF method measures the time for a particle to go from one location to another by cross-correlating the intensity fluctuations at specific points in an image. Hence, a visual map of the average path followed by molecules is created.

© 2017 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]

2017 (1)

2016 (1)

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

2015 (2)

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination,” Sci. Rep. 4(1), 7048 (2015).
[Crossref] [PubMed]

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
[Crossref] [PubMed]

2014 (6)

M. Baum, F. Erdel, M. Wachsmuth, and K. Rippe, “Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells,” Nat. Commun. 5, 4494 (2014).
[Crossref] [PubMed]

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
[Crossref] [PubMed]

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

M. Guo, H. Gelman, and M. Gruebele, “Coupled Protein Diffusion and Folding in the Cell,” PLoS One 9(12), e113040 (2014).
[Crossref] [PubMed]

2013 (6)

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

L. Potvin-Trottier, L. F. Chen, A. R. Horwitz, and P. W. Wiseman, “A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells,” New J. Phys. 15(8), 085006 (2013).
[Crossref]

J. E. Purvis and G. Lahav, “Encoding and Decoding Cellular Information through Signaling Dynamics,” Cell 152(5), 945–956 (2013).
[Crossref] [PubMed]

C. Di Rienzo, E. Gratton, F. Beltram, and F. Cardarelli, “Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes,” Proc. Natl. Acad. Sci. U.S.A. 110(30), 12307–12312 (2013).
[Crossref] [PubMed]

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, K. M. Hahn, and E. Gratton, “Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM,” Proc. Natl. Acad. Sci. U.S.A. 110(1), 135–140 (2013).
[Crossref] [PubMed]

2012 (5)

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[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]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus,” Biophys. J. 102(3), 691–697 (2012).
[Crossref] [PubMed]

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

2011 (4)

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

F. Cardarelli, L. Lanzano, and E. Gratton, “Fluorescence correlation spectroscopy of intact nuclear pore complexes,” Biophys. J. 101(4), L27–L29 (2011).
[Crossref] [PubMed]

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol. 29(9), 835–839 (2011).
[Crossref] [PubMed]

2010 (5)

N. Gröner, J. Capoulade, C. Cremer, and M. Wachsmuth, “Measuring and imaging diffusion with multiple scan speed image correlation spectroscopy,” Opt. Express 18(20), 21225–21237 (2010).
[Crossref] [PubMed]

T. Wohland, X. Shi, J. Sankaran, and E. H. K. Stelzer, “Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments,” Opt. Express 18(10), 10627–10641 (2010).
[Crossref] [PubMed]

Z. Petrásek, J. Ries, and P. Schwille, “Scanning FCS for the Characterization of Protein Dynamics in Live Cells,” Methods Enzymol. 472, 317–343 (2010).
[Crossref] [PubMed]

A. Kinkhabwala and P. I. Bastiaens, “Spatial aspects of intracellular information processing,” Curr. Opin. Genet. Dev. 20(1), 31–40 (2010).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow,” Proc. Natl. Acad. Sci. U.S.A. 107(38), 16560–16565 (2010).
[Crossref] [PubMed]

2009 (6)

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

M. A. Digman and E. Gratton, “Imaging Barriers to Diffusion by Pair Correlation Functions,” Biophys. J. 97(2), 665–673 (2009).
[Crossref] [PubMed]

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-Hole Array Correlation Imaging: Highly Parallel Fluorescence Correlation Spectroscopy,” Biophys. J. 96(12), 5050–5059 (2009).
[Crossref] [PubMed]

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

2008 (2)

J. W. D. Comeau, D. L. Kolin, and P. W. Wiseman, “Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy,” Mol. Biosyst. 4(6), 672–685 (2008).
[Crossref] [PubMed]

M. Weiss, “Probing the interior of living cells with fluorescence correlation spectroscopy,” Ann. N. Y. Acad. Sci. 1130(1), 21–27 (2008).
[Crossref] [PubMed]

2007 (1)

P. D. Moens and L. A. Bagatolli, “Profilin binding to sub-micellar concentrations of phosphatidylinositol (4,5) bisphosphate and phosphatidylinositol (3,4,5) trisphosphate,” Biochim. Biophys. Acta 1768(3), 439–449 (2007).
[Crossref] [PubMed]

2006 (3)

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

D. L. Kolin, D. Ronis, and P. W. Wiseman, “k-Space image correlation spectroscopy: A method for accurate transport measurements independent of fluorophore photophysics,” Biophys. J. 91(8), 3061–3075 (2006).
[Crossref] [PubMed]

J. Ries and P. Schwille, “Studying slow membrane dynamics with continuous wave scanning fluorescence correlation spectroscopy,” Biophys. J. 91(5), 1915–1924 (2006).
[Crossref] [PubMed]

2004 (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Ahrar, S.

Arevalo, R.

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

Bagatolli, L. A.

P. D. Moens and L. A. Bagatolli, “Profilin binding to sub-micellar concentrations of phosphatidylinositol (4,5) bisphosphate and phosphatidylinositol (3,4,5) trisphosphate,” Biochim. Biophys. Acta 1768(3), 439–449 (2007).
[Crossref] [PubMed]

Bastiaens, P. I.

A. Kinkhabwala and P. I. Bastiaens, “Spatial aspects of intracellular information processing,” Curr. Opin. Genet. Dev. 20(1), 31–40 (2010).
[Crossref] [PubMed]

Baum, M.

M. Baum, F. Erdel, M. Wachsmuth, and K. Rippe, “Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells,” Nat. Commun. 5, 4494 (2014).
[Crossref] [PubMed]

Belov, V. N.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Beltram, F.

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

C. Di Rienzo, E. Gratton, F. Beltram, and F. Cardarelli, “Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes,” Proc. Natl. Acad. Sci. U.S.A. 110(30), 12307–12312 (2013).
[Crossref] [PubMed]

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
[Crossref] [PubMed]

Berkovich, R.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Bianchini, P.

P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
[Crossref] [PubMed]

Bizzarri, R.

P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
[Crossref] [PubMed]

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
[Crossref] [PubMed]

Boucher, Y.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Brown, E. B.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Capoulade, J.

J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol. 29(9), 835–839 (2011).
[Crossref] [PubMed]

N. Gröner, J. Capoulade, C. Cremer, and M. Wachsmuth, “Measuring and imaging diffusion with multiple scan speed image correlation spectroscopy,” Opt. Express 18(20), 21225–21237 (2010).
[Crossref] [PubMed]

Cardarelli, F.

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
[Crossref] [PubMed]

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

C. Di Rienzo, E. Gratton, F. Beltram, and F. Cardarelli, “Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes,” Proc. Natl. Acad. Sci. U.S.A. 110(30), 12307–12312 (2013).
[Crossref] [PubMed]

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (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]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus,” Biophys. J. 102(3), 691–697 (2012).
[Crossref] [PubMed]

F. Cardarelli, L. Lanzano, and E. Gratton, “Fluorescence correlation spectroscopy of intact nuclear pore complexes,” Biophys. J. 101(4), L27–L29 (2011).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow,” Proc. Natl. Acad. Sci. U.S.A. 107(38), 16560–16565 (2010).
[Crossref] [PubMed]

Cecchini, M.

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
[Crossref] [PubMed]

Chauhan, V. P.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Chen, L. F.

L. Potvin-Trottier, L. F. Chen, A. R. Horwitz, and P. W. Wiseman, “A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells,” New J. Phys. 15(8), 085006 (2013).
[Crossref]

Comeau, J. W. D.

J. W. D. Comeau, D. L. Kolin, and P. W. Wiseman, “Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy,” Mol. Biosyst. 4(6), 672–685 (2008).
[Crossref] [PubMed]

Cremer, C.

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Di Luca, M.

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
[Crossref] [PubMed]

Di Rienzo, C.

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

C. Di Rienzo, E. Gratton, F. Beltram, and F. Cardarelli, “Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes,” Proc. Natl. Acad. Sci. U.S.A. 110(30), 12307–12312 (2013).
[Crossref] [PubMed]

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
[Crossref] [PubMed]

Diaspro, A.

P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
[Crossref] [PubMed]

Digman, M. A.

E. Hinde, M. A. Digman, K. M. Hahn, and E. Gratton, “Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM,” Proc. Natl. Acad. Sci. U.S.A. 110(1), 135–140 (2013).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus,” Biophys. J. 102(3), 691–697 (2012).
[Crossref] [PubMed]

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow,” Proc. Natl. Acad. Sci. U.S.A. 107(38), 16560–16565 (2010).
[Crossref] [PubMed]

M. A. Digman and E. Gratton, “Imaging Barriers to Diffusion by Pair Correlation Functions,” Biophys. J. 97(2), 665–673 (2009).
[Crossref] [PubMed]

Diop-Frimpong, B.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Dross, N.

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

Eggeling, C.

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Ehrlich, M.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Eisenberg, S.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Erdel, F.

M. Baum, F. Erdel, M. Wachsmuth, and K. Rippe, “Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells,” Nat. Commun. 5, 4494 (2014).
[Crossref] [PubMed]

Gaus, K.

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
[Crossref] [PubMed]

Gelman, H.

M. Guo, H. Gelman, and M. Gruebele, “Coupled Protein Diffusion and Folding in the Cell,” PLoS One 9(12), e113040 (2014).
[Crossref] [PubMed]

Gratton, E.

P. N. Hedde, L. Malacrida, S. Ahrar, A. Siryaporn, and E. Gratton, “sideSPIM - selective plane illumination based on a conventional inverted microscope,” Biomed. Opt. Express 8(9), 3918–3937 (2017).
[Crossref] [PubMed]

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination,” Sci. Rep. 4(1), 7048 (2015).
[Crossref] [PubMed]

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
[Crossref] [PubMed]

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

C. Di Rienzo, E. Gratton, F. Beltram, and F. Cardarelli, “Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes,” Proc. Natl. Acad. Sci. U.S.A. 110(30), 12307–12312 (2013).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, K. M. Hahn, and E. Gratton, “Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM,” Proc. Natl. Acad. Sci. U.S.A. 110(1), 135–140 (2013).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus,” Biophys. J. 102(3), 691–697 (2012).
[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]

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

F. Cardarelli, L. Lanzano, and E. Gratton, “Fluorescence correlation spectroscopy of intact nuclear pore complexes,” Biophys. J. 101(4), L27–L29 (2011).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow,” Proc. Natl. Acad. Sci. U.S.A. 107(38), 16560–16565 (2010).
[Crossref] [PubMed]

M. A. Digman and E. Gratton, “Imaging Barriers to Diffusion by Pair Correlation Functions,” Biophys. J. 97(2), 665–673 (2009).
[Crossref] [PubMed]

Graves, C.

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

Gröner, N.

Gruebele, M.

M. Guo, H. Gelman, and M. Gruebele, “Coupled Protein Diffusion and Folding in the Cell,” PLoS One 9(12), e113040 (2014).
[Crossref] [PubMed]

Guo, L.

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

Guo, M.

M. Guo, H. Gelman, and M. Gruebele, “Coupled Protein Diffusion and Folding in the Cell,” PLoS One 9(12), e113040 (2014).
[Crossref] [PubMed]

Hahn, K. M.

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, K. M. Hahn, and E. Gratton, “Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM,” Proc. Natl. Acad. Sci. U.S.A. 110(1), 135–140 (2013).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[Crossref] [PubMed]

Hedde, P. N.

P. N. Hedde, L. Malacrida, S. Ahrar, A. Siryaporn, and E. Gratton, “sideSPIM - selective plane illumination based on a conventional inverted microscope,” Biomed. Opt. Express 8(9), 3918–3937 (2017).
[Crossref] [PubMed]

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination,” Sci. Rep. 4(1), 7048 (2015).
[Crossref] [PubMed]

Hein, B.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Hell, S. W.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Henis, Y. I.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Hinde, E.

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, K. M. Hahn, and E. Gratton, “Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM,” Proc. Natl. Acad. Sci. U.S.A. 110(1), 135–140 (2013).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus,” Biophys. J. 102(3), 691–697 (2012).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow,” Proc. Natl. Acad. Sci. U.S.A. 107(38), 16560–16565 (2010).
[Crossref] [PubMed]

Honigmann, A.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

Horwitz, A. R.

L. Potvin-Trottier, L. F. Chen, A. R. Horwitz, and P. W. Wiseman, “A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells,” New J. Phys. 15(8), 085006 (2013).
[Crossref]

Hufnagel, L.

J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol. 29(9), 835–839 (2011).
[Crossref] [PubMed]

Huisken, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Jacchetti, E.

C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
[Crossref] [PubMed]

Jain, R. K.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Keller, J.

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

Kershner, A.

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

Kimble, J.

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

Kinkhabwala, A.

A. Kinkhabwala and P. I. Bastiaens, “Spatial aspects of intracellular information processing,” Curr. Opin. Genet. Dev. 20(1), 31–40 (2010).
[Crossref] [PubMed]

Klafter, J.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Knop, M.

J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol. 29(9), 835–839 (2011).
[Crossref] [PubMed]

Kolin, D. L.

J. W. D. Comeau, D. L. Kolin, and P. W. Wiseman, “Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy,” Mol. Biosyst. 4(6), 672–685 (2008).
[Crossref] [PubMed]

D. L. Kolin, D. Ronis, and P. W. Wiseman, “k-Space image correlation spectroscopy: A method for accurate transport measurements independent of fluorophore photophysics,” Biophys. J. 91(8), 3061–3075 (2006).
[Crossref] [PubMed]

Kraut, R.

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

Krieger, J.

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

Lahav, G.

J. E. Purvis and G. Lahav, “Encoding and Decoding Cellular Information through Signaling Dynamics,” Cell 152(5), 945–956 (2013).
[Crossref] [PubMed]

Lander, A. D.

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

Langowski, J.

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

Lanning, R. M.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[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]

F. Cardarelli, L. Lanzano, and E. Gratton, “Fluorescence correlation spectroscopy of intact nuclear pore complexes,” Biophys. J. 101(4), L27–L29 (2011).
[Crossref] [PubMed]

Lo, W. C.

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

Lomholt, M. A.

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

Lund, F. W.

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

Malacrida, L.

Manna, M.

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

McAllister, R.

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

Medda, R.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Mitchison, T. J.

D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-Hole Array Correlation Imaging: Highly Parallel Fluorescence Correlation Spectroscopy,” Biophys. J. 96(12), 5050–5059 (2009).
[Crossref] [PubMed]

Moens, P. D.

P. D. Moens and L. A. Bagatolli, “Profilin binding to sub-micellar concentrations of phosphatidylinositol (4,5) bisphosphate and phosphatidylinositol (3,4,5) trisphosphate,” Biochim. Biophys. Acta 1768(3), 439–449 (2007).
[Crossref] [PubMed]

Mok, W.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Mueller, V.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

Müller, G.

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

Needleman, D. J.

D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-Hole Array Correlation Imaging: Highly Parallel Fluorescence Correlation Spectroscopy,” Biophys. J. 96(12), 5050–5059 (2009).
[Crossref] [PubMed]

Nie, Q.

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

Padera, T. P.

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

Pernus, A.

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

Petrásek, Z.

Z. Petrásek, J. Ries, and P. Schwille, “Scanning FCS for the Characterization of Protein Dynamics in Live Cells,” Methods Enzymol. 472, 317–343 (2010).
[Crossref] [PubMed]

Piazza, V.

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

Polyakova, S.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Potvin-Trottier, L.

L. Potvin-Trottier, L. F. Chen, A. R. Horwitz, and P. W. Wiseman, “A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells,” New J. Phys. 15(8), 085006 (2013).
[Crossref]

Purvis, J. E.

J. E. Purvis and G. Lahav, “Encoding and Decoding Cellular Information through Signaling Dynamics,” Cell 152(5), 945–956 (2013).
[Crossref] [PubMed]

Ries, J.

Z. Petrásek, J. Ries, and P. Schwille, “Scanning FCS for the Characterization of Protein Dynamics in Live Cells,” Methods Enzymol. 472, 317–343 (2010).
[Crossref] [PubMed]

J. Ries and P. Schwille, “Studying slow membrane dynamics with continuous wave scanning fluorescence correlation spectroscopy,” Biophys. J. 91(5), 1915–1924 (2006).
[Crossref] [PubMed]

Ringemann, C.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Rippe, K.

M. Baum, F. Erdel, M. Wachsmuth, and K. Rippe, “Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells,” Nat. Commun. 5, 4494 (2014).
[Crossref] [PubMed]

Ronis, D.

D. L. Kolin, D. Ronis, and P. W. Wiseman, “k-Space image correlation spectroscopy: A method for accurate transport measurements independent of fluorophore photophysics,” Biophys. J. 91(8), 3061–3075 (2006).
[Crossref] [PubMed]

Sadeghi, S.

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

Sage, D.

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

Sandhoff, K.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Sankaran, J.

T. Wohland, X. Shi, J. Sankaran, and E. H. K. Stelzer, “Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments,” Opt. Express 18(10), 10627–10641 (2010).
[Crossref] [PubMed]

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

Schoenle, A.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

Schönle, A.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Schroll, H. J.

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

Schwarzmann, G.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Schwille, P.

Z. Petrásek, J. Ries, and P. Schwille, “Scanning FCS for the Characterization of Protein Dynamics in Live Cells,” Methods Enzymol. 472, 317–343 (2010).
[Crossref] [PubMed]

J. Ries and P. Schwille, “Studying slow membrane dynamics with continuous wave scanning fluorescence correlation spectroscopy,” Biophys. J. 91(5), 1915–1924 (2006).
[Crossref] [PubMed]

Sezgin, E.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

Shi, X.

Singh, A. P.

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

Siryaporn, A.

Sisan, D. R.

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

Solanko, L. M.

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

Spriet, C.

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

Stakic, M.

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination,” Sci. Rep. 4(1), 7048 (2015).
[Crossref] [PubMed]

Stelzer, E. H. K.

T. Wohland, X. Shi, J. Sankaran, and E. H. K. Stelzer, “Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments,” Opt. Express 18(10), 10627–10641 (2010).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Suhalim, J. L.

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

Swoger, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Ta, H.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

Urbach, J. S.

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

Urbakh, M.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Vink, R.

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
[Crossref] [PubMed]

von Middendorff, C.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
[Crossref] [PubMed]

Wachsmuth, M.

M. Baum, F. Erdel, M. Wachsmuth, and K. Rippe, “Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells,” Nat. Commun. 5, 4494 (2014).
[Crossref] [PubMed]

J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol. 29(9), 835–839 (2011).
[Crossref] [PubMed]

N. Gröner, J. Capoulade, C. Cremer, and M. Wachsmuth, “Measuring and imaging diffusion with multiple scan speed image correlation spectroscopy,” Opt. Express 18(20), 21225–21237 (2010).
[Crossref] [PubMed]

Waldeck, W.

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

Weiss, M.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

M. Weiss, “Probing the interior of living cells with fluorescence correlation spectroscopy,” Ann. N. Y. Acad. Sci. 1130(1), 21–27 (2008).
[Crossref] [PubMed]

Welch, C.

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[Crossref] [PubMed]

Wiseman, P. W.

L. Potvin-Trottier, L. F. Chen, A. R. Horwitz, and P. W. Wiseman, “A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells,” New J. Phys. 15(8), 085006 (2013).
[Crossref]

J. W. D. Comeau, D. L. Kolin, and P. W. Wiseman, “Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy,” Mol. Biosyst. 4(6), 672–685 (2008).
[Crossref] [PubMed]

D. L. Kolin, D. Ronis, and P. W. Wiseman, “k-Space image correlation spectroscopy: A method for accurate transport measurements independent of fluorophore photophysics,” Biophys. J. 91(8), 3061–3075 (2006).
[Crossref] [PubMed]

Wittbrodt, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Wohland, T.

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

T. Wohland, X. Shi, J. Sankaran, and E. H. K. Stelzer, “Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments,” Opt. Express 18(10), 10627–10641 (2010).
[Crossref] [PubMed]

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

Wolfenson, H.

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
[Crossref] [PubMed]

Wüstner, D.

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
[Crossref] [PubMed]

Xu, Y.

D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-Hole Array Correlation Imaging: Highly Parallel Fluorescence Correlation Spectroscopy,” Biophys. J. 96(12), 5050–5059 (2009).
[Crossref] [PubMed]

Yokomori, K.

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
[Crossref] [PubMed]

Zhou, S.

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

Zwerger, M.

N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
[Crossref] [PubMed]

Ann. N. Y. Acad. Sci. (1)

M. Weiss, “Probing the interior of living cells with fluorescence correlation spectroscopy,” Ann. N. Y. Acad. Sci. 1130(1), 21–27 (2008).
[Crossref] [PubMed]

Biochim. Biophys. Acta (1)

P. D. Moens and L. A. Bagatolli, “Profilin binding to sub-micellar concentrations of phosphatidylinositol (4,5) bisphosphate and phosphatidylinositol (3,4,5) trisphosphate,” Biochim. Biophys. Acta 1768(3), 439–449 (2007).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

Biophys. J. (13)

C. Di Rienzo, F. Cardarelli, M. Di Luca, F. Beltram, and E. Gratton, “Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells,” Biophys. J. 111(4), 841–851 (2016).
[Crossref] [PubMed]

D. R. Sisan, R. Arevalo, C. Graves, R. McAllister, and J. S. Urbach, “Spatially resolved fluorescence correlation spectroscopy using a spinning disk confocal microscope,” Biophys. J. 91(11), 4241–4252 (2006).
[Crossref] [PubMed]

D. L. Kolin, D. Ronis, and P. W. Wiseman, “k-Space image correlation spectroscopy: A method for accurate transport measurements independent of fluorophore photophysics,” Biophys. J. 91(8), 3061–3075 (2006).
[Crossref] [PubMed]

J. Ries and P. Schwille, “Studying slow membrane dynamics with continuous wave scanning fluorescence correlation spectroscopy,” Biophys. J. 91(5), 1915–1924 (2006).
[Crossref] [PubMed]

V. P. Chauhan, R. M. Lanning, B. Diop-Frimpong, W. Mok, E. B. Brown, T. P. Padera, Y. Boucher, and R. K. Jain, “Multiscale Measurements Distinguish Cellular and Interstitial Hindrances to Diffusion In Vivo,” Biophys. J. 97(1), 330–336 (2009).
[Crossref] [PubMed]

D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-Hole Array Correlation Imaging: Highly Parallel Fluorescence Correlation Spectroscopy,” Biophys. J. 96(12), 5050–5059 (2009).
[Crossref] [PubMed]

J. Sankaran, M. Manna, L. Guo, R. Kraut, and T. Wohland, “Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy,” Biophys. J. 97(9), 2630–2639 (2009).
[Crossref] [PubMed]

A. P. Singh, J. Krieger, A. Pernus, J. Langowski, and T. Wohland, “SPIM-FCCS: A Novel Technique to Quantitate Protein-Protein Interaction in Live Cells,” Biophys. J. 104(2), 61a (2013).
[Crossref]

E. Hinde, F. Cardarelli, M. A. Digman, A. Kershner, J. Kimble, and E. Gratton, “The Impact of Mitotic versus Interphase Chromatin Architecture on the Molecular Flow of EGFP by Pair Correlation Analysis,” Biophys. J. 100(7), 1829–1836 (2011).
[Crossref] [PubMed]

E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus,” Biophys. J. 102(3), 691–697 (2012).
[Crossref] [PubMed]

M. A. Digman and E. Gratton, “Imaging Barriers to Diffusion by Pair Correlation Functions,” Biophys. J. 97(2), 665–673 (2009).
[Crossref] [PubMed]

E. Hinde, M. A. Digman, C. Welch, K. M. Hahn, and E. Gratton, “Millisecond Spatiotemporal Dynamics of FRET Biosensors by the Pair Correlation Function and the Phasor Approach to FLIM,” Biophys. J. 102(3), 198a–199a (2012).
[Crossref] [PubMed]

F. Cardarelli, L. Lanzano, and E. Gratton, “Fluorescence correlation spectroscopy of intact nuclear pore complexes,” Biophys. J. 101(4), L27–L29 (2011).
[Crossref] [PubMed]

BMC Bioinformatics (1)

D. Wüstner, L. M. Solanko, F. W. Lund, D. Sage, H. J. Schroll, and M. A. Lomholt, “Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation,” BMC Bioinformatics 13(1), 296 (2012).
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Cell (1)

J. E. Purvis and G. Lahav, “Encoding and Decoding Cellular Information through Signaling Dynamics,” Cell 152(5), 945–956 (2013).
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Curr. Biol. (1)

S. Zhou, W. C. Lo, J. L. Suhalim, M. A. Digman, E. Gratton, Q. Nie, and A. D. Lander, “Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc,” Curr. Biol. 22(8), 668–675 (2012).
[Crossref] [PubMed]

Curr. Opin. Genet. Dev. (1)

A. Kinkhabwala and P. I. Bastiaens, “Spatial aspects of intracellular information processing,” Curr. Opin. Genet. Dev. 20(1), 31–40 (2010).
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eLife (1)

A. Honigmann, S. Sadeghi, J. Keller, S. W. Hell, C. Eggeling, and R. Vink, “A lipid bound actin meshwork organizes liquid phase separation in model membranes,” eLife 3, e01671 (2014).
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Methods Enzymol. (1)

Z. Petrásek, J. Ries, and P. Schwille, “Scanning FCS for the Characterization of Protein Dynamics in Live Cells,” Methods Enzymol. 472, 317–343 (2010).
[Crossref] [PubMed]

Mol. Biosyst. (1)

J. W. D. Comeau, D. L. Kolin, and P. W. Wiseman, “Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy,” Mol. Biosyst. 4(6), 672–685 (2008).
[Crossref] [PubMed]

Nat. Biotechnol. (1)

J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol. 29(9), 835–839 (2011).
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Nat. Commun. (3)

M. Baum, F. Erdel, M. Wachsmuth, and K. Rippe, “Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells,” Nat. Commun. 5, 4494 (2014).
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A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin, S. W. Hell, and C. Eggeling, “Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells,” Nat. Commun. 5, 5412 (2014).
[Crossref] [PubMed]

C. Di Rienzo, V. Piazza, E. Gratton, F. Beltram, and F. Cardarelli, “Probing short-range protein Brownian motion in the cytoplasm of living cells,” Nat. Commun. 5, 5891 (2014).
[Crossref] [PubMed]

Nature (1)

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, “Direct observation of the nanoscale dynamics of membrane lipids in a living cell,” Nature 457(7233), 1159–1162 (2009).
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New J. Phys. (1)

L. Potvin-Trottier, L. F. Chen, A. R. Horwitz, and P. W. Wiseman, “A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells,” New J. Phys. 15(8), 085006 (2013).
[Crossref]

Opt. Express (2)

PLoS One (3)

M. Guo, H. Gelman, and M. Gruebele, “Coupled Protein Diffusion and Folding in the Cell,” PLoS One 9(12), e113040 (2014).
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N. Dross, C. Spriet, M. Zwerger, G. Müller, W. Waldeck, and J. Langowski, “Mapping eGFP Oligomer Mobility in Living Cell Nuclei,” PLoS One 4(4), e5041 (2009).
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P. Bianchini, F. Cardarelli, M. Di Luca, A. Diaspro, and R. Bizzarri, “Nanoscale Protein Diffusion by STED-Based Pair Correlation Analysis,” PLoS One 9(6), e99619 (2014).
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Proc. Natl. Acad. Sci. U.S.A. (4)

E. Hinde, M. A. Digman, K. M. Hahn, and E. Gratton, “Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM,” Proc. Natl. Acad. Sci. U.S.A. 110(1), 135–140 (2013).
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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).
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E. Hinde, F. Cardarelli, M. A. Digman, and E. Gratton, “In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow,” Proc. Natl. Acad. Sci. U.S.A. 107(38), 16560–16565 (2010).
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C. Di Rienzo, E. Gratton, F. Beltram, and F. Cardarelli, “Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes,” Proc. Natl. Acad. Sci. U.S.A. 110(30), 12307–12312 (2013).
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Sci. Rep. (3)

E. Hinde, K. Yokomori, K. Gaus, K. M. Hahn, and E. Gratton, “Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation,” Sci. Rep. 4(1), 4219 (2015).
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C. Di Rienzo, E. Jacchetti, F. Cardarelli, R. Bizzarri, F. Beltram, and M. Cecchini, “Unveiling LOX-1 receptor interplay with nanotopography: mechanotransduction and atherosclerosis onset,” Sci. Rep. 3(1), 1141 (2013).
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P. N. Hedde, M. Stakic, and E. Gratton, “Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination,” Sci. Rep. 4(1), 7048 (2015).
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Science (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
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Traffic (1)

R. Berkovich, H. Wolfenson, S. Eisenberg, M. Ehrlich, M. Weiss, J. Klafter, Y. I. Henis, and M. Urbakh, “Accurate Quantification of Diffusion and Binding Kinetics of Non-integral Membrane Proteins by FRAP,” Traffic 12(11), 1648–1657 (2011).
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Figures (9)

Fig. 1
Fig. 1 Pictorial representation of the principle of the 2D-pCF to detect molecular transport in cells guided by obstacles and molecular interactions. A) Camera image time stack of the same focal plane (5,000 to 50,000 images) giving access to a grid of points where fluctuations due to the underlying molecular flow can be measured. B) The 2D-pCF is computed between every pair of points of the image and at a given distance. In an isotropic environment. Starting from a point, all the correlation functions should be equal and independent of the direction. The pCF correlation functions can have a maximum. C) If the environment is anisotropic, molecules could take longer to reach a given distance depending on the direction. D) The polar image resulting from plotting all the correlation functions as a function of the angle (2D-pCF) is analyzed using the first and second central moment (Eqs. (2)-(7)). E) The 2D-pCF is plotted using only the long axis of the ellipses shown in D. The definition of the axes lengths is given in Eq. (5). F) By joining the segments corresponding to the long axis we obtain the connectivity map that delineates the presence of barriers shown in red. G) If an underlying structure is present, shown schematically by a maze, the spatial connectivity can be obtained using different radii for the calculation of the 2D-pCF. H) The 2D-pCF function at a distance of 3 pixels for this maze reveals connected points at a small scale. I) The 2D-pCF calculated at a larger distance (4 pixels) show paths connected at a larger scale in the maze, and where there is an obstacle (center of the maze). The distance for the calculation of the 2D-pCF is used to reveal different barriers.
Fig. 2
Fig. 2 Simulated experiment of diffusion in disconnected regions crossed by a narrow channel. A) A channel (300 nm wide) with impenetrable walls where molecules can diffuse surrounded by two regions which are mutually disconnected. The 2D-pCF is calculated according to Eq. (1) using 32 angles at a distance of 4 pixels. B) Intensity of a single image. C) Average intensity of all images D) 2D-pCF at one pixel from the right border of the image at point 1. E) 2D-pCF in a region far from the borders at point 2. F) 2D-pCF at 2 pixels from the left border at point 3. G) 2D-pCF at 2 pixels below the channel, point 4. H) 2D-pCF in the channel at point 5. I) 2D-pCF at 1 pixel above the channel, point 6. The presence of the discontinuity due to the channel can be seen in panels G, H and I although the walls of the channel are invisible since they are not labeled. J) Computed analysis of the shape of the 2D-pCF according to Eqs. (2)-(7) using the pattern of panel H. For this simulation the PSF was 300 nm, the pixel size was 114 nm and the total field of view was 7.2 µm. The image has 64x64 pixels and 32,768 images were simulated; the particle density for this simulation was 10 molecules/μm2, which is a low value compared to experimental situations. Note that the 2D-pCF gives different patterns by moving the center of the calculation by one pixel as shown in panels D and F. Panels D-J show an image representing the 2D-pCF in a polar plot. The axes are in log-delay time. The maximum delay time is equal to 164s.
Fig. 3
Fig. 3 Simulation of molecules diffusing in a plane with a 300 nm wide channel along the diagonal. For this simulation the pixel size was 114 nm and 32,768 frames were simulated. The molecules have a diffusion coefficient of 1 μm2/s and the frame rate was 100 frames/s. A) Average intensity of the 32,768 frames. The channel is invisible in the intensity image since the molecular density is uniform. B) Eccentricity map obtained using the algorithms of the analysis of the shape of the 2D-pCF. C) the histogram of the eccentricity values obtained for all pixels in the image. D) The direction of the major axis of the eccentricity polar plot, E) The histogram of the direction for all pixels with eccentricity above the threshold value marked by the red vertical line in C). The angle is in degrees and the scale is red to blue (horizontal-vertical. F) Connectivity map obtained by drawing segments in the direction given by the direction map and length proportional to the eccentricity values. Only segments with eccentricities larger than the threshold value are shown. The black regions in panel D and F correspond to isotropic diffusion. The color of the eccentricity and angle map is the same color used for the histogram values.
Fig. 4
Fig. 4 2D pCF and iMSD analysis of a 10 nM EGFP solution. A total of 8,192 frames (128 x 128 pixels) were acquired at a rate of 125 frames/s using selective plane illumination as described in the Appendix with 488 nm light (1 mW). A) Histogram of the eccentricity values; the average eccentricity was 0.31 ± 0.08 (mean ± SD). B) From the same data, the anisotropy was calculated according to the equations Eqs. (2-7) in the manuscript. The histogram is shown in the middle panel (0.06 ± 0.03). This shows that, even in the absence of barriers, obstacles or directed motion, we get an eccentricity value >0. This is because in Eq. (5) the values of λ1 is always greater than λ2. This value of 0.3 obtained in the case of random motion in the absence of barriers was used as lower threshold for regions of random motion for data visualization. C) To demonstrate that the fluorescence fluctuations were caused by free diffusion of EGFP in solution, the iMSD of the same data was calculated as shown on the right hand side, the resulting diffusion coefficient was 114 µm2/s, which is in within the range of values found for EGFP in solution. This example shows that the data used for the 2D-pCF could also be used far from obstacles to measure the diffusion coefficient.
Fig. 5
Fig. 5 Simulation of molecules moving in a plane where there is an impenetrable box. The size of the box is 0.8 μm x 0.8 μm, comparable to structures found in the cell nucleus and large vesicles. The particle density for this simulation is 8.7 molecules/μm2. Local diffusion coefficient is 10 μm2/s both inside and outside the box. The box is impenetrable. The 2D-pCF was calculated for a distance of 4 pixels. In the simulation the waist of the PSF was 200 nm. The camera frame rate was set to 100 frames/s and a total of 16,384 frames were analyzed. A) The eccentricity map obtained using the algorithms in the manuscript. The noise is due to the low particle density. B) Connectivity map using a threshold of 0.45 for the eccentricity values to be included in the connectivity map. Note that in this structure and at regions of high curvature there are connectivity lines perpendicular to the box side in addition to connectivity lines parallel to the box sides. C) Eccentricity histogram color coded using the same colors in the eccentricity map.
Fig. 6
Fig. 6 Measuring the connectivity maps in testing samples. A 30 nM solution of EGFP is spread on top of a slide with grooves 450 nm deep and 450 nm wide. A cover glass is on top of the sample to maintain the solution in the grooves. The image was acquired in a wide field microscope equipped with an EMCCD camera at 100 frames/s; a total of 10,000 frames was collected for a total time of 100 s. The 2D-pCF algorithms were used to calculate the eccentricity and the connectivity maps. A) EM images of the grooves. B) The grooves containing a 30 nM EGFP solution. C) Eccentricity map. D) Connectivity map. EGFP molecules only diffuse in the groove as shown by the connectivity map. E) Intensity image of a GUV membrane labeled with DiOC16 in the sideSPIM microscope equipped with a sCMOS camera. F) Eccentricity map. G) Connectivity map. For the connectivity maps the eccentricity threshold was 0.45.
Fig. 7
Fig. 7 U2OS cell labeled with DiOC18 imaged with a widefield microscope with epi-fluorescence lamp illumination. A) Intensity image. White arrow indicate an obstacle. B) Eccentricity calculated according to Eq. (6). C) Connectivity map for the pCF calculated at 4 pixel distance (0.456 µm) and D) Connectivity map for the pCF (8 pixels, 0.916 μm). E) Schematic representation of a two cells junction of panel A. F) The cells are very thin at this location so that wide field illumination does not produce much out-of-focus background. G) Zoom of the flow of molecules generated by the structure indicated by the white arrow in panel A and B. Obstacle seen after computing the 2D-pCF at a distance of 4 pixels. H) The same obstacle indicated by the white arrow but after computing the 2D-pCF at a distance of 8 pixels. I) Schematic representation of the expected flow for nearby membrane structures. White lines are representing the connectivity along the membrane structures and the red line represents a barrier. See Fig. 5 for a simulation of molecules moving around or inside a box that show that connectivity lines departing from a surface can be observed if the surface has high curvature. J) At pixel resolution the image shows the diffusion of the dye along the membrane at the junction between the two cells. K) The same junction explored at a longer distance (pCF at 8 pixels). L) Schematic representation of the flow expected at the two cell junction and plasma membrane where red is the barriers and the white lines indicate the connectivity. M) Envelope of histograms of eccentricity for pCF(4) and pCF(8). The vertical line indicates the threshold used for the connectivity maps shown in C and D. For this experiment 10,000 images were collected within a total time of 100 s. The background colors in the zoomed images G,H,J and K are the values of the anisotropy.
Fig. 8
Fig. 8 MB231 cell transfected with EGFP growing in collagen I. Measurements obtained on the sideSPIM microscope at 100 frames/s. Schematic representation of the cell view with respect to the light sheet. A) View from the side. B) View from the top, this view is the image taken by the camera. C) Intensity image. D column) Eccentricity calculated at 4, 8 and 12 pixel distance. E column) Connectivity map for 4, 8, and 12 pixel distance (0.432, 0.864 and 1.296 µm, respectively). The white arrow in E) indicates an obstacle that forces the molecules to go around. F) Expected connectivity pattern for an obstacle of a size of several microns with high curvature and in for the cell membrane.
Fig. 9
Fig. 9 Connectivity map overlap to the center of mass shift (CMS) image for Fig. 8. A) The connectivity maps (dark lines) were plotted on top of the CMS at pCF(4) in a MB231 cell transfected with EGFP. B) CMS at pCF(4) in a MB231 cell expressing EGFP. C) Schematic representation of the CMS concept. The pink stick represents an impenetrable barrier and the hemi circle represents the 2D-pCF. The CMS is defined as the displacement of the first order moment of the pCF distribution. The displacement of the center of mass of the 2D-pCF distribution will occur in the proximity of a barrier since the cross-correlation between on point in one side of the barrier and another point in the other part of the barrier will be zero.

Equations (7)

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pCF=G( τ, r 0 , r 1 )= F( t, r 0 )F( t+τ, r 1 ) F( t, r 0 )F( t, r 1 ) 1.
M ij = x y x i y j I( x,y ) x y I( x,y )
μ pq = x y ( x x ¯ ) p ( y y ¯ ) q I( x,y )
θ= 1 2 arctan( 2 μ 11 μ 20 μ 02 )
λ i = μ 20 + μ 02 2 ± 4 μ 11 2 + ( μ 20 μ 02 ) 2 2
Eccentricity= 1 λ 2 λ 1
Anisotropy= λ 1 λ 2 λ 1 + λ 2

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