ImFCS: A software for imaging FCS data analysis and visualization

Optics Express

Volumn 18, Issue 25, 2010, Pages 25468-25481

  Sankaran, Jagadish ^a   Shi, Xianke ^a   Ho, Liang Yoong ^b   Stelzer, Ernst H K ^c   Wohland, Thorsten ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b BIOINFORMATICS INSTITUTE   (Singapore)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENCE SPECTROSCOPY; REFRACTIVE INDEX; VISUALIZATION;

ARRAY DETECTORS; CORRELATION FUNCTION; CROSS-CORRELATION FUNCTION; CROSS-CORRELATIONS; DATA ANALYSIS; FLUORESCENCE CORRELATION SPECTROSCOPY; LARGE AMOUNTS OF DATA; OBLIQUE ILLUMINATION; OPEN-SOURCE SOFTWARES; STANDARD IMAGES; STANDARD MODEL; SUB-CRITICAL; TOTAL INTERNAL REFLECTIONS;

DATA VISUALIZATION;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; COMPUTER PROGRAM; METHODOLOGY; SPECTROFLUOROMETRY;

ALGORITHMS; PATTERN RECOGNITION, AUTOMATED; SOFTWARE; SPECTROMETRY, FLUORESCENCE;

EID: 78650068830     PISSN: None     EISSN: 10944087     Source Type: Journal    
DOI: 10.1364/OE.18.025468     Document Type: Article

References (28)

1. M. Brinkmeier, K. Dorre, J. Stephan, and M. Eigen, "Two beam cross correlation: A method to characterize transport phenomena in micrometer-sized structures," Anal. Chem. 71(3), 609-616 (1999).
2. M. Gösch, A. Serov, T. Anhut, T. Lasser, A. Rochas, P. A. Besse, R. S. 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(5), 913-921 (2004).
3. B. Kannan, J. Y. Har, P. Liu, I. Maruyama, J. L. Ding, and T. Wohland, "Electron multiplying charge-coupled device camera based fluorescence correlation spectroscopy," Anal. Chem. 78(10), 3444-3451 (2006).
4. M. Burkhardt, and P. Schwille, "Electron multiplying CCD based detection for spatially resolved fluorescence correlation spectroscopy," Opt. Express 14(12), 5013-5020 (2006).
5. 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).
6. 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(12), 4463-4470 (2007).
7. L. Guo, J. Y. Har, J. Sankaran, Y. M. Hong, B. Kannan, and T. Wohland, "Molecular diffusion measurement in lipid bilayers over wide concentration ranges: a comparative study," Chem Phys Chem 9(5), 721-728 (2008).
8. 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).
9. 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).
10. M. Matsumoto, T. Sugiura, and K. Minato, "Spatially resolved fluorescence correlation spectroscopy based on electron multiplying CCD - art. no. 663017," in Confocal, Multiphoton, and Nonlinear Microscopic Imaging III, T. Wilson, and A. Periasamy, eds. (2007), pp. 63017-63017.
11. M. Matsumoto, T. Sugiura, and K. Minato, "Illumination by Near-Critical-Angle Incidence for Imaging Fluorescence Correlation Spectroscopy with Electron-Multiplying Charge-Coupled Device Camera," Jpn. J. Appl. Phys. 49(6), 060208 (2010).
12. 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).
13. 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).
14. R. Rigler, H. Vogel, Z. Petrášek, and P. Schwille, "Scanning Fluorescence Correlation Spectroscopy," in Single Molecules and Nanotechnology (Springer Berlin Heidelberg, 2008), pp. 83-105.
15. "Tiff 6.0 specification," http://partners.adobe.com/public/ developer/en/tiff/TIFF6.pdf.
16. W. S. Rasband, "ImageJ," (U. S. National Institutes of Health, Bethesda, Maryland, USA, http://rsb.info.nih.gov/ij/, 1997-2009).
17. K. Schaetzel, and R. Peters, "Noise on multiple-tau photon correlation data," S. S. Kenneth, ed., (SPIE, 1991), pp. 109-115.
18. T. Wohland, R. Rigler, and H. Vogel, "The standard deviation in fluorescence correlation spectroscopy," Biophys. J. 80(6), 2987-2999 (2001). (Pubitemid 32521670)
19. X. Shi, and T. Wohland, "Fluorescence Correlation Spectroscopy," in Nanoscopy and Multidimensional Optical Fluorescence Microscopy A. Diaspro, ed. (CRC Press, 2010).
20. W. Press, B. Flannery, S. Teukolsky, and W. Vetterling, Numerical Recipes in C: The Art of Scientific Computing (Cambridge University Press, 1992).
21. B. Zhang, J. Zerubia, and J.-C. Olivo-Marin, "Gaussian approximations of fluorescence microscope point-spread function models," Appl. Opt. 46(10), 1819-1829 (2007).
22. B. Zhang, J. Zerubia, and J. C. Olivo-Marin, "A study of Gaussian approximations of fluorescence microscopy PSF models - art. no. 60900K," in Conference on Three-Dimensional and Multidimensional Microscopy - Image Acquisition and Processing XIII, J. A. Conchello, C. J. Cogswell, and T. Wilson, eds., (SPIE, San Jose, CA, 2006), pp. K900-K900.
23. J. Ries, E. P. Petrov, and P. Schwille, "Total internal reflection fluorescence correlation spectroscopy: effects of lateral diffusion and surface-generated fluorescence," Biophys. J. 95(1), 390-399 (2008).
24. D. Freedman, and P. Diaconis, "On the histogram as a density estimator-L2 theory," Probab. Theory Relat. Fields 57, 453-476 (1981).
25. C. A. Konopka, and S. Y. Bednarek, "Variable-angle epifluorescence microscopy: a new way to look at protein dynamics in the plant cell cortex," Plant J. 53(1), 186-196 (2008).
26. M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, "Highly inclined thin illumination enables clear single-molecule imaging in cells," Nat. Methods 5(2), 159-161 (2008).
27. M. Tokunga, N. Imamoto, and K. Sakata-Sogawa, "Addendum: Highly inclined thin illumination enables clear single-molecule imaging in cells," Nat. Methods 5(5), 455-455 (2008).
28. J. Ries, M. Bayer, G. Csúcs, R. Dirkx, M. Solimena, H. Ewers, and P. Schwille, "Automated suppression of sample-related artifacts in Fluorescence Correlation Spectroscopy," Opt. Express 18(11), 11073-11082 (2010).