Abstract

With the evolving technology in CMOS integration, new classes of 2D-imaging detectors have recently become available. In particular, single photon avalanche diode (SPAD) arrays allow detection of single photons at high acquisition rates (≥ 100kfps), which is about two orders of magnitude higher than with currently available cameras. Here we demonstrate the use of a SPAD array for imaging fluorescence correlation spectroscopy (imFCS), a tool to create 2D maps of the dynamics of fluorescent molecules inside living cells. Time-dependent fluorescence fluctuations, due to fluorophores entering and leaving the observed pixels, are evaluated by means of autocorrelation analysis. The multi-τ correlation algorithm is an appropriate choice, as it does not rely on the full data set to be held in memory. Thus, this algorithm can be efficiently implemented in custom logic. We describe a new implementation for massively parallel multi-τ correlation hardware. Our current implementation can calculate 1024 correlation functions at a resolution of 10μs in real-time and therefore correlate real-time image streams from high speed single photon cameras with thousands of pixels.

© 2012 OSA

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  1. D. Magde, E. L. Elson, and W. W. Webb, “Fluorescence correlation spectroscopy i: conceptual basis and theory,” Biopolymers13, 1–27 (1974).
    [CrossRef]
  2. D. Magde, E. L. Elson, and W. W. Webb, “Fluorescence correlation spectroscopy. ii. an experimental realization,” Biopolymers13, 29–61 (1974).
    [CrossRef] [PubMed]
  3. O. Krichevsky and G. Bonnet, “Fluorescence correlation spectroscopy: the technique and its applications,” Rep. Prog. Phys.65, 251–297 (2002).
    [CrossRef]
  4. M. Engels, B. Hoppe, H. Meuth, and R. Peters, “A single chip 200 MHz digital correlation system for laser spectroscopy with 512 correlation channels,” in “ISCAS’99. Proceedings of the 1999 IEEE International Symposium on Circuits and Systems, 1999,”, vol. 5 (IEEE, 1999), vol. 5, pp. 160–163.
  5. B. Hoppe, H. Meuth, M. Engels, and R. Peters, “Design of digital correlation systems for low-intensity precision photon spectroscopic measurements,” in “IEEE Proceedings Circuits, Devices and Systems,”, vol. 148 (IET, 2001), vol. 148, pp. 267–271.
  6. M. Engels, B. Hoppe, H. Meuth, and R. Peters, “Fast digital photon correlation system with high dynamic range,” in “Proceedings of the 13th Annual IEEE International ASIC/SOC Conference, 2000,” (IEEE, 2000), pp. 18–22.
  7. M. Wahl, I. Gregor, M. Patting, and J. Enderlein, “Fast calculation of fluorescence correlation data with asynchronous time-correlated single-photon counting,” Opt. Express11, 3583–3591 (2003).
    [CrossRef] [PubMed]
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  12. M. Culbertson and D. Burden, “A distributed algorithm for multi-tau autocorrelation,” Rev. Sci. Instrum.78, 044102 (2007).
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  13. B. Tieman, S. Narayanan, A. Sandy, and M. Sikorski, “Mpicorrelator: a parallel code for performing time correlations,” Nucl. Inst. Meth. A649, 240–242 (2011).
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  23. G. Heuvelman, F. Erdel, M. Wachsmuth, and K. Rippe, “Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy,” Eur. Biophys. J.38, 813–828 (2009).
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  24. F. Bestvater, Z. Seghiri, M. S. Kang, N. Gröner, J. Y. Lee, I. Kang-Bin, and M. Wachsmuth, “EMCCD-based spectrally resolved fluorescence correlation spectroscopy,” Opt. Express18, 23818–23828 (2010).
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  25. D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-hole array correlation imaging: highly parallel fluorescence correlation spectroscopy,” Biophys. J.96, 5050–5059 (2009).
    [CrossRef] [PubMed]
  26. B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
    [CrossRef] [PubMed]
  27. 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. Express10, 10627–10641 (2010).
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  28. J. Capoulade, M. Wachsmuth, L. Hufnagel, and M. Knop, “Quantitative fluorescence imaging of protein diffusion and interaction in living cells,” Nat. Biotechnol.29, 835–839 (2011).
    [CrossRef] [PubMed]
  29. L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.
  30. M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
    [CrossRef] [PubMed]
  31. R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.
  32. C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.
  33. C. Niclass, M. Sergio, and E. Charbon, “A single photon avalanche diode array fabricated in 0.35-μm CMOS and based on an event-driven readout for TCSPC experiments,” in “Proc. SPIE,” 6372, 63720S (2006).
    [CrossRef]
  34. K. Schätzel, “Noise on photon correlation data: I. autocorrelation functions,” Quantum Opt.2, 287–305 (1990).
    [CrossRef]
  35. K. Schätzel, “New concepts in correlator design,” Inst. Phys. Conf. Ser.77, 175–184 (1985).
  36. Z. Kojro, A. Riede, M. Schubert, and W. Grill, “Systematic and statistical errors in correlation estimators obtained from various digital correlators,” Rev. Sci. Instrum.70, 4487–4496 (1999).
    [CrossRef]
  37. J. Sankaran, X. Shi, L. Ho, E. Stelzer, and T. Wohland, “ImFCS: a software for imaging FCS data analysis and visualization,” Opt. Express18, 25468–25481 (2010).
    [CrossRef] [PubMed]
  38. The diffusion coefficient was D = 20μm2/s (corresponding to an intermediately sized protein in water), the simulation timestep of the random walk, as well as the minimum lag time were Δtsim = τmin = 1μs. There were around 1.2 particles in the effective measurement volume Veff ≈ 0.4μm3 on average.
  39. T. Wocjan, J. Krieger, O. Krichevsky, and J. Langowski, “Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by brownian dynamics,” Phys. Chem. Chem. Phys.11, 10671–10681 (2009).
    [CrossRef]
  40. C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.
  41. K. Greger, J. Swoger, and E. H. K. Stelzer, “Basic building units and properties of a fluorescence single plane illumination microscope,” Rev. Sci. Instrum.78, 023705 (2007).
    [CrossRef] [PubMed]
  42. Joachim Wuttke: lmfit - a C/C++ routine for Levenberg-Marquardt minimization with wrapper for least-squares curve fitting, based on work by B. S. Garbow, K. E. Hillstrom, J. J. Moré, and S. Moshier. Version 3.2, retrieved on 2011-08-31 from http://www.messen-und-deuten.de/lmfit/ .
  43. QuickFit 3.0 can be downloaded free of charge from http://www.dkfz.de/Macromol/quickfit/ . In addition to the fitting capabilities, it also contains software implementations of the correlators described in here.
  44. S. T. Hess and W. W. Webb, “Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy,” Biophys. J.83, 2300–2317 (2002).
    [CrossRef] [PubMed]

2012 (2)

G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
[CrossRef] [PubMed]

E. Schaub, “F2cor: fast 2-stage correlation algorithm for FCS and DLS,” Opt. Express20, 2184–2195 (2012).
[CrossRef] [PubMed]

2011 (3)

B. Tieman, S. Narayanan, A. Sandy, and M. Sikorski, “Mpicorrelator: a parallel code for performing time correlations,” Nucl. Inst. Meth. A649, 240–242 (2011).
[CrossRef]

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

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

2010 (4)

2009 (3)

G. Heuvelman, F. Erdel, M. Wachsmuth, and K. Rippe, “Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy,” Eur. Biophys. J.38, 813–828 (2009).
[CrossRef] [PubMed]

T. Wocjan, J. Krieger, O. Krichevsky, and J. Langowski, “Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by brownian dynamics,” Phys. Chem. Chem. Phys.11, 10671–10681 (2009).
[CrossRef]

D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-hole array correlation imaging: highly parallel fluorescence correlation spectroscopy,” Biophys. J.96, 5050–5059 (2009).
[CrossRef] [PubMed]

2007 (3)

B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
[CrossRef] [PubMed]

M. Culbertson and D. Burden, “A distributed algorithm for multi-tau autocorrelation,” Rev. Sci. Instrum.78, 044102 (2007).
[CrossRef] [PubMed]

K. Greger, J. Swoger, and E. H. K. Stelzer, “Basic building units and properties of a fluorescence single plane illumination microscope,” Rev. Sci. Instrum.78, 023705 (2007).
[CrossRef] [PubMed]

2006 (3)

2004 (1)

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

2003 (2)

D. Magatti and F. Ferri, “25 ns software correlator for photon and fluorescence correlation spectroscopy,” Rev. Sci. Instrum.74, 1135–1144 (2003).
[CrossRef]

M. Wahl, I. Gregor, M. Patting, and J. Enderlein, “Fast calculation of fluorescence correlation data with asynchronous time-correlated single-photon counting,” Opt. Express11, 3583–3591 (2003).
[CrossRef] [PubMed]

2002 (2)

O. Krichevsky and G. Bonnet, “Fluorescence correlation spectroscopy: the technique and its applications,” Rep. Prog. Phys.65, 251–297 (2002).
[CrossRef]

S. T. Hess and W. W. Webb, “Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy,” Biophys. J.83, 2300–2317 (2002).
[CrossRef] [PubMed]

2001 (1)

1999 (2)

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “A single chip 200 MHz digital correlation system for laser spectroscopy with 512 correlation channels,” in “ISCAS’99. Proceedings of the 1999 IEEE International Symposium on Circuits and Systems, 1999,”, vol. 5 (IEEE, 1999), vol. 5, pp. 160–163.

Z. Kojro, A. Riede, M. Schubert, and W. Grill, “Systematic and statistical errors in correlation estimators obtained from various digital correlators,” Rev. Sci. Instrum.70, 4487–4496 (1999).
[CrossRef]

1990 (1)

K. Schätzel, “Noise on photon correlation data: I. autocorrelation functions,” Quantum Opt.2, 287–305 (1990).
[CrossRef]

1985 (1)

K. Schätzel, “New concepts in correlator design,” Inst. Phys. Conf. Ser.77, 175–184 (1985).

1974 (2)

D. Magde, E. L. Elson, and W. W. Webb, “Fluorescence correlation spectroscopy i: conceptual basis and theory,” Biopolymers13, 1–27 (1974).
[CrossRef]

D. Magde, E. L. Elson, and W. W. Webb, “Fluorescence correlation spectroscopy. ii. an experimental realization,” Biopolymers13, 29–61 (1974).
[CrossRef] [PubMed]

Ahmed, S.

B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
[CrossRef] [PubMed]

Anhut, T.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

Besse, P.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

Bestvater, F.

Blom, H.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

Bonnet, G.

O. Krichevsky and G. Bonnet, “Fluorescence correlation spectroscopy: the technique and its applications,” Rep. Prog. Phys.65, 251–297 (2002).
[CrossRef]

Borghetti, F.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Buchholz, J.

G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
[CrossRef] [PubMed]

Burden, D.

M. Culbertson and D. Burden, “A distributed algorithm for multi-tau autocorrelation,” Rev. Sci. Instrum.78, 044102 (2007).
[CrossRef] [PubMed]

Burkhardt, M.

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, 835–839 (2011).
[CrossRef] [PubMed]

Carrara, L.

L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.

Charbon, E.

C. Niclass, M. Sergio, and E. Charbon, “A single photon avalanche diode array fabricated in 0.35-μm CMOS and based on an event-driven readout for TCSPC experiments,” in “Proc. SPIE,” 6372, 63720S (2006).
[CrossRef]

L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.

C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Cheng, Y.

Y. Yang, J. Shen, W. Liu, and Y. Cheng, “Digital real-time correlator implemented by field programmable gate array,” in “CISP’08. Congress on Image and Signal Processing, 2008,”, vol. 1 (IEEE, 2008), vol. 1, pp. 149–151.

Colyer, R.

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

Colyer, R. A.

Cova, S.

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

R. A. Colyer, G. Scalia, I. Rech, A. Gulinatti, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array,” Biomed. Opt. Express1, 1408–1431 (2010).
[CrossRef]

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

Culbertson, M.

M. Culbertson and D. Burden, “A distributed algorithm for multi-tau autocorrelation,” Rev. Sci. Instrum.78, 044102 (2007).
[CrossRef] [PubMed]

Elson, E. L.

D. Magde, E. L. Elson, and W. W. Webb, “Fluorescence correlation spectroscopy i: conceptual basis and theory,” Biopolymers13, 1–27 (1974).
[CrossRef]

D. Magde, E. L. Elson, and W. W. Webb, “Fluorescence correlation spectroscopy. ii. an experimental realization,” Biopolymers13, 29–61 (1974).
[CrossRef] [PubMed]

Enderlein, J.

Engels, M.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “A single chip 200 MHz digital correlation system for laser spectroscopy with 512 correlation channels,” in “ISCAS’99. Proceedings of the 1999 IEEE International Symposium on Circuits and Systems, 1999,”, vol. 5 (IEEE, 1999), vol. 5, pp. 160–163.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “Fast digital photon correlation system with high dynamic range,” in “Proceedings of the 13th Annual IEEE International ASIC/SOC Conference, 2000,” (IEEE, 2000), pp. 18–22.

B. Hoppe, H. Meuth, M. Engels, and R. Peters, “Design of digital correlation systems for low-intensity precision photon spectroscopic measurements,” in “IEEE Proceedings Circuits, Devices and Systems,”, vol. 148 (IET, 2001), vol. 148, pp. 267–271.

Erdel, F.

G. Heuvelman, F. Erdel, M. Wachsmuth, and K. Rippe, “Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy,” Eur. Biophys. J.38, 813–828 (2009).
[CrossRef] [PubMed]

Favi, C.

C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.

Ferri, F.

D. Magatti and F. Ferri, “25 ns software correlator for photon and fluorescence correlation spectroscopy,” Rev. Sci. Instrum.74, 1135–1144 (2003).
[CrossRef]

D. Magatti and F. Ferri, “Fast multi-tau real-time software correlator for dynamic light scattering,” Appl. Opt.40, 4011–4021 (2001).
[CrossRef]

Fishburn, M. W.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Fore, S.

Gersbach, M.

C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Ghioni, M.

R. A. Colyer, G. Scalia, I. Rech, A. Gulinatti, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array,” Biomed. Opt. Express1, 1408–1431 (2010).
[CrossRef]

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

Gösch, M.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

Greger, K.

K. Greger, J. Swoger, and E. H. K. Stelzer, “Basic building units and properties of a fluorescence single plane illumination microscope,” Rev. Sci. Instrum.78, 023705 (2007).
[CrossRef] [PubMed]

Gregor, I.

Grill, W.

Z. Kojro, A. Riede, M. Schubert, and W. Grill, “Systematic and statistical errors in correlation estimators obtained from various digital correlators,” Rev. Sci. Instrum.70, 4487–4496 (1999).
[CrossRef]

Gröner, N.

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Gulinatti, A.

Guo, L.

B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
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C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

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G. Heuvelman, F. Erdel, M. Wachsmuth, and K. Rippe, “Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy,” Eur. Biophys. J.38, 813–828 (2009).
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Hoppe, B.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “A single chip 200 MHz digital correlation system for laser spectroscopy with 512 correlation channels,” in “ISCAS’99. Proceedings of the 1999 IEEE International Symposium on Circuits and Systems, 1999,”, vol. 5 (IEEE, 1999), vol. 5, pp. 160–163.

C. Jakob, A. T. Schwarzbacher, B. Hoppe, and R. Peters, “A FPGA optimised digital real-time mutichannel correlator architecture,” in “10th Euromicro Conference on Digital System Design Architectures, Methods and Tools, 2007. DSD 2007,” (IEEE, 2007).

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “Fast digital photon correlation system with high dynamic range,” in “Proceedings of the 13th Annual IEEE International ASIC/SOC Conference, 2000,” (IEEE, 2000), pp. 18–22.

B. Hoppe, H. Meuth, M. Engels, and R. Peters, “Design of digital correlation systems for low-intensity precision photon spectroscopic measurements,” in “IEEE Proceedings Circuits, Devices and Systems,”, vol. 148 (IET, 2001), vol. 148, pp. 267–271.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “The development of a digital multichannel correlator system for light scattering experiments,” in “Irish Signals and Systems Conference, 2006. IET,” (IET, 2006), pp. 99–103.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “A multichannel digital real-time correlator as single FPGA implementation,” in “15th International Conference on Digital Signal Processing, 2007,” (2007), pp. 276–279.

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, 835–839 (2011).
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Jakob, C.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “A multichannel digital real-time correlator as single FPGA implementation,” in “15th International Conference on Digital Signal Processing, 2007,” (2007), pp. 276–279.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “The development of a digital multichannel correlator system for light scattering experiments,” in “Irish Signals and Systems Conference, 2006. IET,” (IET, 2006), pp. 99–103.

C. Jakob, A. T. Schwarzbacher, B. Hoppe, and R. Peters, “A FPGA optimised digital real-time mutichannel correlator architecture,” in “10th Euromicro Conference on Digital System Design Architectures, Methods and Tools, 2007. DSD 2007,” (IEEE, 2007).

Kang, M. S.

Kang-Bin, I.

Kannan, B.

B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
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R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

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C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.

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, 835–839 (2011).
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Z. Kojro, A. Riede, M. Schubert, and W. Grill, “Systematic and statistical errors in correlation estimators obtained from various digital correlators,” Rev. Sci. Instrum.70, 4487–4496 (1999).
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G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
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G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
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Langowski, J.

G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
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T. Wocjan, J. Krieger, O. Krichevsky, and J. Langowski, “Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by brownian dynamics,” Phys. Chem. Chem. Phys.11, 10671–10681 (2009).
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M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
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Lee, J. Y.

Li, D.-U.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Liu, W.

Y. Yang, J. Shen, W. Liu, and Y. Cheng, “Digital real-time correlator implemented by field programmable gate array,” in “CISP’08. Congress on Image and Signal Processing, 2008,”, vol. 1 (IEEE, 2008), vol. 1, pp. 149–151.

W. Liu, J. Shen, and X. Sun, “Design of multiple-tau photon correlation system implemented by FPGA,” in “ICESS’08. International Conference on Embedded Software and Systems, 2008,” (IEEE, 2008), pp. 410–414.

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R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

Maruyama, I.

B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
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Maruyama, Y.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Meuth, H.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “A single chip 200 MHz digital correlation system for laser spectroscopy with 512 correlation channels,” in “ISCAS’99. Proceedings of the 1999 IEEE International Symposium on Circuits and Systems, 1999,”, vol. 5 (IEEE, 1999), vol. 5, pp. 160–163.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “Fast digital photon correlation system with high dynamic range,” in “Proceedings of the 13th Annual IEEE International ASIC/SOC Conference, 2000,” (IEEE, 2000), pp. 18–22.

B. Hoppe, H. Meuth, M. Engels, and R. Peters, “Design of digital correlation systems for low-intensity precision photon spectroscopic measurements,” in “IEEE Proceedings Circuits, Devices and Systems,”, vol. 148 (IET, 2001), vol. 148, pp. 267–271.

Michalet, X.

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

R. A. Colyer, G. Scalia, I. Rech, A. Gulinatti, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array,” Biomed. Opt. Express1, 1408–1431 (2010).
[CrossRef]

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

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D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-hole array correlation imaging: highly parallel fluorescence correlation spectroscopy,” Biophys. J.96, 5050–5059 (2009).
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G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
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Narayanan, S.

B. Tieman, S. Narayanan, A. Sandy, and M. Sikorski, “Mpicorrelator: a parallel code for performing time correlations,” Nucl. Inst. Meth. A649, 240–242 (2011).
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D. J. Needleman, Y. Xu, and T. J. Mitchison, “Pin-hole array correlation imaging: highly parallel fluorescence correlation spectroscopy,” Biophys. J.96, 5050–5059 (2009).
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C. Niclass, M. Sergio, and E. Charbon, “A single photon avalanche diode array fabricated in 0.35-μm CMOS and based on an event-driven readout for TCSPC experiments,” in “Proc. SPIE,” 6372, 63720S (2006).
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L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.

C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.

Patting, M.

Peters, R.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “A single chip 200 MHz digital correlation system for laser spectroscopy with 512 correlation channels,” in “ISCAS’99. Proceedings of the 1999 IEEE International Symposium on Circuits and Systems, 1999,”, vol. 5 (IEEE, 1999), vol. 5, pp. 160–163.

C. Jakob, A. T. Schwarzbacher, B. Hoppe, and R. Peters, “A FPGA optimised digital real-time mutichannel correlator architecture,” in “10th Euromicro Conference on Digital System Design Architectures, Methods and Tools, 2007. DSD 2007,” (IEEE, 2007).

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “Fast digital photon correlation system with high dynamic range,” in “Proceedings of the 13th Annual IEEE International ASIC/SOC Conference, 2000,” (IEEE, 2000), pp. 18–22.

B. Hoppe, H. Meuth, M. Engels, and R. Peters, “Design of digital correlation systems for low-intensity precision photon spectroscopic measurements,” in “IEEE Proceedings Circuits, Devices and Systems,”, vol. 148 (IET, 2001), vol. 148, pp. 267–271.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “The development of a digital multichannel correlator system for light scattering experiments,” in “Irish Signals and Systems Conference, 2006. IET,” (IET, 2006), pp. 99–103.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “A multichannel digital real-time correlator as single FPGA implementation,” in “15th International Conference on Digital Signal Processing, 2007,” (2007), pp. 276–279.

Popovic, R.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

Rech, I.

R. A. Colyer, G. Scalia, I. Rech, A. Gulinatti, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array,” Biomed. Opt. Express1, 1408–1431 (2010).
[CrossRef]

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

Resnati, D.

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

Richardson, J. A.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Riede, A.

Z. Kojro, A. Riede, M. Schubert, and W. Grill, “Systematic and statistical errors in correlation estimators obtained from various digital correlators,” Rev. Sci. Instrum.70, 4487–4496 (1999).
[CrossRef]

Rigler, R.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
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Rippe, K.

G. Heuvelman, F. Erdel, M. Wachsmuth, and K. Rippe, “Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy,” Eur. Biophys. J.38, 813–828 (2009).
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Rochas, A.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
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Sandy, A.

B. Tieman, S. Narayanan, A. Sandy, and M. Sikorski, “Mpicorrelator: a parallel code for performing time correlations,” Nucl. Inst. Meth. A649, 240–242 (2011).
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Sankaran, J.

J. Sankaran, X. Shi, L. Ho, E. Stelzer, and T. Wohland, “ImFCS: a software for imaging FCS data analysis and visualization,” Opt. Express18, 25468–25481 (2010).
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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. Express10, 10627–10641 (2010).
[CrossRef]

Scalia, G.

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

R. A. Colyer, G. Scalia, I. Rech, A. Gulinatti, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array,” Biomed. Opt. Express1, 1408–1431 (2010).
[CrossRef]

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

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Scheidegger, N.

L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.

Schubert, M.

Z. Kojro, A. Riede, M. Schubert, and W. Grill, “Systematic and statistical errors in correlation estimators obtained from various digital correlators,” Rev. Sci. Instrum.70, 4487–4496 (1999).
[CrossRef]

Schwarzbacher, A.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “A multichannel digital real-time correlator as single FPGA implementation,” in “15th International Conference on Digital Signal Processing, 2007,” (2007), pp. 276–279.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “The development of a digital multichannel correlator system for light scattering experiments,” in “Irish Signals and Systems Conference, 2006. IET,” (IET, 2006), pp. 99–103.

Schwarzbacher, A. T.

C. Jakob, A. T. Schwarzbacher, B. Hoppe, and R. Peters, “A FPGA optimised digital real-time mutichannel correlator architecture,” in “10th Euromicro Conference on Digital System Design Architectures, Methods and Tools, 2007. DSD 2007,” (IEEE, 2007).

Schwille, P.

Seghiri, Z.

Sergio, M.

C. Niclass, M. Sergio, and E. Charbon, “A single photon avalanche diode array fabricated in 0.35-μm CMOS and based on an event-driven readout for TCSPC experiments,” in “Proc. SPIE,” 6372, 63720S (2006).
[CrossRef]

Serov, A.

M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. Besse, R. Popovic, H. Blom, and R. Rigler, “Parallel single molecule detection with a fully integrated single-photon 2 × 2 CMOS detector array,” J. Biomed. Opt.9, 913 (2004).
[CrossRef] [PubMed]

Shea, H.

L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.

Shen, J.

W. Liu, J. Shen, and X. Sun, “Design of multiple-tau photon correlation system implemented by FPGA,” in “ICESS’08. International Conference on Embedded Software and Systems, 2008,” (IEEE, 2008), pp. 410–414.

Y. Yang, J. Shen, W. Liu, and Y. Cheng, “Digital real-time correlator implemented by field programmable gate array,” in “CISP’08. Congress on Image and Signal Processing, 2008,”, vol. 1 (IEEE, 2008), vol. 1, pp. 149–151.

Shi, X.

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. Express10, 10627–10641 (2010).
[CrossRef]

J. Sankaran, X. Shi, L. Ho, E. Stelzer, and T. Wohland, “ImFCS: a software for imaging FCS data analysis and visualization,” Opt. Express18, 25468–25481 (2010).
[CrossRef] [PubMed]

Sikorski, M.

B. Tieman, S. Narayanan, A. Sandy, and M. Sikorski, “Mpicorrelator: a parallel code for performing time correlations,” Nucl. Inst. Meth. A649, 240–242 (2011).
[CrossRef]

Stelzer, E.

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. Express10, 10627–10641 (2010).
[CrossRef]

K. Greger, J. Swoger, and E. H. K. Stelzer, “Basic building units and properties of a fluorescence single plane illumination microscope,” Rev. Sci. Instrum.78, 023705 (2007).
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Stoppa, D.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Sudhaharan, T.

B. Kannan, L. Guo, T. Sudhaharan, S. Ahmed, I. Maruyama, and T. Wohland, “Spatially resolved total internal reflection fluorescence correlation microscopy using an electron multiplying charge-coupled device camera,” Anal. Chem.79, 4463–4470 (2007).
[CrossRef] [PubMed]

Sun, X.

W. Liu, J. Shen, and X. Sun, “Design of multiple-tau photon correlation system implemented by FPGA,” in “ICESS’08. International Conference on Embedded Software and Systems, 2008,” (IEEE, 2008), pp. 410–414.

Swoger, J.

K. Greger, J. Swoger, and E. H. K. Stelzer, “Basic building units and properties of a fluorescence single plane illumination microscope,” Rev. Sci. Instrum.78, 023705 (2007).
[CrossRef] [PubMed]

Tieman, B.

B. Tieman, S. Narayanan, A. Sandy, and M. Sikorski, “Mpicorrelator: a parallel code for performing time correlations,” Nucl. Inst. Meth. A649, 240–242 (2011).
[CrossRef]

Tisa, S.

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

Vamosi, G.

G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vamosi, “Note: multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array,” Rev. Sci. Instrum.83, 046101 (2012).
[CrossRef] [PubMed]

Veerappan, C.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

Villa, F.

R. Colyer, G. Scalia, F. Villa, F. Guerrieri, S. Tisa, F. Zappa, S. Cova, S. Weiss, and X. Michalet, “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD,” in “Proc. SPIE,” 7905, 790503–1 (2011).

Wachsmuth, M.

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[CrossRef] [PubMed]

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Other (13)

Joachim Wuttke: lmfit - a C/C++ routine for Levenberg-Marquardt minimization with wrapper for least-squares curve fitting, based on work by B. S. Garbow, K. E. Hillstrom, J. J. Moré, and S. Moshier. Version 3.2, retrieved on 2011-08-31 from http://www.messen-und-deuten.de/lmfit/ .

QuickFit 3.0 can be downloaded free of charge from http://www.dkfz.de/Macromol/quickfit/ . In addition to the fitting capabilities, it also contains software implementations of the correlators described in here.

C. Niclass, C. Favi, T. Kluter, M. Gersbach, and E. Charbon, “A 128 × 128 single-photon imager with on-chip column-level 10b time-to-digital converter array capable of 97ps resolution,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2008), pp. 44–594.

The diffusion coefficient was D = 20μm2/s (corresponding to an intermediately sized protein in water), the simulation timestep of the random walk, as well as the minimum lag time were Δtsim = τmin = 1μs. There were around 1.2 particles in the effective measurement volume Veff ≈ 0.4μm3 on average.

R. Colyer, G. Scalia, T. Kim, I. Rech, D. Resnati, S. Marangoni, M. Ghioni, S. Cova, S. Weiss, and X. Michalet, “High-throughput multispot single-molecule spectroscopy,” in “Proceedings-Society of Photo-Optical Instrumentation Engineers,”, vol. 7571 (NIH Public Access, 2010), vol. 7571, p. 75710G.

C. Veerappan, J. A. Richardson, R. J. Walker, D.-U. Li, M. W. Fishburn, Y. Maruyama, D. Stoppa, F. Borghetti, M. Gersbach, R. K. Henderson, and E. Charbon, “A 160x128 single-photon image sensor with on-pixel 55ps 10b time-to-digital converter.” in “ISSCC, IEEE International Solid-State Circuits Conference,” (IEEE, 2011), pp. 312–314.

L. Carrara, C. Niclass, N. Scheidegger, H. Shea, and E. Charbon, “A gamma, x-ray and high energy proton radiationtolerant CMOS image sensor for space applications,” in “ISSCC, IEEE International Solid-State Circuits Conference,” (2009), pp. 40–41.

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “The development of a digital multichannel correlator system for light scattering experiments,” in “Irish Signals and Systems Conference, 2006. IET,” (IET, 2006), pp. 99–103.

C. Jakob, A. T. Schwarzbacher, B. Hoppe, and R. Peters, “A FPGA optimised digital real-time mutichannel correlator architecture,” in “10th Euromicro Conference on Digital System Design Architectures, Methods and Tools, 2007. DSD 2007,” (IEEE, 2007).

C. Jakob, A. Schwarzbacher, B. Hoppe, and R. Peters, “A multichannel digital real-time correlator as single FPGA implementation,” in “15th International Conference on Digital Signal Processing, 2007,” (2007), pp. 276–279.

Y. Yang, J. Shen, W. Liu, and Y. Cheng, “Digital real-time correlator implemented by field programmable gate array,” in “CISP’08. Congress on Image and Signal Processing, 2008,”, vol. 1 (IEEE, 2008), vol. 1, pp. 149–151.

W. Liu, J. Shen, and X. Sun, “Design of multiple-tau photon correlation system implemented by FPGA,” in “ICESS’08. International Conference on Embedded Software and Systems, 2008,” (IEEE, 2008), pp. 410–414.

M. Engels, B. Hoppe, H. Meuth, and R. Peters, “Fast digital photon correlation system with high dynamic range,” in “Proceedings of the 13th Annual IEEE International ASIC/SOC Conference, 2000,” (IEEE, 2000), pp. 18–22.

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Figures (8)

Fig. 1
Fig. 1

Hardware design of a linear correlator (a) in comparison with a multi-τ correlator (b). Panel (c) shows a schematic view of the multi-τ correlator, where the linear correlator building blocks are summarized by a single block. Corresponding channels are grouped with the same color. Global/undelayed (g) and local/delayed (l) inputs are located on the left. For autocorrelation, the global and local signal inputs to the 0-th block ( J n ( g ) = J n ( l ) = I n ) are identical. The oe-20-16-17767-e001 blocks represent delay elements, the ⊗-blocks multipliers and the oe-20-16-17767-e002 blocks accumulators.

Fig. 2
Fig. 2

Block scheduling algorithm. The counter c in the first row defines the current cycle. The second row shows the block s that is processed in the corresponding cycle. Further below the order of processing is shown: When a block s has been processed twice, the following block, s + 1, can process the sum of the two preceding s-blocks.

Fig. 3
Fig. 3

Comparison of a naïve implementation (a: one correlator per pixel) and an optimized implementation (b: reuse CorrPEs for several pixels) of a multi-pixel multi-τ correlator for a 3 × 3 SPAD array.

Fig. 4
Fig. 4

System layout and data path - from data acquisition to correlation. One USB interface is used to stream the raw images, the other for streaming (intermediate) results. The first level cache (L1, double buffered) is used to hold the context of the currently processed pixel. FIFOs for row resorting and for context storage use external memory.

Fig. 5
Fig. 5

Simulation results for different implementations of multi-τ correlators: The left panels (a,b) show simulations for a sine wave input signal I(t) = 1 + sin(2πt/(0.151ms)). The simulations on the right (c,d) were created using an FCS simulation. The top graphs (a,c) are estimates of the autocorrelation function using direct correlation from Eq. (3) (green), a multi-τ correlator with one monitor channel per lag time (blue) and our estimated normalization from Eq. (10) (magenta). Graph (a) also shows the theorectical ACF g(theoretical)(τ) = 1 + cos(2πτ/(0.151ms)) for the sine signal (light red). The lower graphs (b,d) show the absolute deviation of the estimates from g(theoretical)(τ) (b) and from a fit to the curves (d). The parameters resulting from the fit in (c) are the same within < 2.5% for all three estimates.

Fig. 6
Fig. 6

Distribution of 992 (gray) ACFs taken by our sensor (first 31 columns only), exposed to a 630 nm LED sine-modulated with a frequency of 2.5kHz. The inset shows a section of the input count rate summed over 4 samples or 40μs for each point. The correlator was running for 1.2s (131072 samples at τmin = 10μs). The gray curves with significantly lower amplitude are due to hot pixels of the SPAD array; since these SPADs fire randomly, the corresponding correlation amplitude is decreased. The median, which tends to be less sensitive towards outliers than the mean, is shown in red. The theoretical model g(theoretical)(τ) = 1+A·cos(2πf ·τ) is fitted against the median in the interval [10μs, 1ms], and is shown until τ = 2ms. The fit yields a frequency of (2502 ± 4)Hz. Compare also Fig. 5(a).

Fig. 7
Fig. 7

Results from SPIM-FCS measurements of fluorescent microspheres with diameter 40nm. The measurement duration was 20.97s.

Fig. 8
Fig. 8

Example normalized correlation curves for two different sizes of beads, with diameters 40nm (red) and 100nm (blue). The curves are an average over 16 single-pixel ACFs each and the given diffusion coefficients are the average and standard deviation from fits to these 16 single curves.

Tables (3)

Tables Icon

Table 1 Interleaved pipeline of the linear correlator design with 8 channels.

Tables Icon

Table 2 Binary representation of counter c that solves relations Eq. (8) for a given linear correlator block s. * denotes a don’t care condition.

Tables Icon

Table 3 Memory layout of a pixel context

Equations (13)

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g ( τ ) = I ( t ) I ( t + τ ) t I ( t ) t 2 , I ( t ) t : lim T ˜ 1 T ˜ 0 T ˜ I ( t ) d t
I n = 0 τ min I ( n τ min + t ) d t , n = 0 , 1 , T 1
g ^ sym ( τ k ) = 1 T τ k n = τ k T 1 I n I n τ k = : G τ k [ 1 T n = 0 T 1 I n = : M 0 ] [ 1 T τ k n = τ k T 1 I n τ k = : M τ k ]
I s , n = k = 1 m s I n k , for  s > 0
τ 0 , 0 = 0 τ s , 0 = τ s 1 , P 1 + m s 1 τ s , p = τ s , p 1 + m s = i = 1 s P + p m i 1 P ,
g ^ sym , multi τ ( τ s , p ) = g ( τ s , p τ min ) * Λ ( τ s , p , m s ) ,
1 Δ t lin 1 st lin . corr . + 1 2 Δ t lin 2 nd lin . corr . + 1 4 Δ t lin 3 rd lin . corr . + n = 0 1 2 n Δ t lin = 2 Δ t lin
s = 0 : c mod  2 1 = 0 s = 1 : c mod  2 2 = 3 s 2 : c mod  2 s + 1 = ( 2 s 3 )
g ^ sym , multi τ ( τ s , p ) = G τ s , p 2 s T M 0 M τ s , p
M τ s , p = M 0 T τ s , p T .
g ( x , y ) ( τ ) = I ( x ) ( t ) I ( y ) ( t + τ ) t I ( x ) ( t ) t I ( y ) ( t ) t
g ^ sym , multi τ ( CCF ) ( τ s , p ) = G τ s , p 2 s T M 0 ( g ) M τ s , p ( l )
g ( fit ) ( τ ) = 1 N ( 1 + τ τ D ) 1 ( 1 + τ γ 2 τ D ) 1 / 2

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