Localisation microscopy with quantum dots using non-negative matrix factorisation

Optics Express

Volumn 22, Issue 20, 2014, Pages 24594-24605

  Mandula, Ondřej ^a,e   Šestak, Ivana Šumanovac ^b,c   Heintzmann, Rainer ^b,c,d   Williams, Christopher K I ^e  

^a Fondation Nanosciences   (France)

^b LEIBNIZ INSTITUTE OF PHOTONIC TECHNOLOGY   (Germany)

^c FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^d KING'S COLLEGE LONDON   (United Kingdom)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FACTORIZATION; FLUOROPHORES; NANOCRYSTALS;

HIGH RESOLUTION IMAGE; LOCALISATION; NON-NEGATIVE MATRIX FACTORISATION; SUPER RESOLUTION IMAGING;

SEMICONDUCTOR QUANTUM DOTS;

FLUORESCENT DYE; QUANTUM DOT;

ALGORITHM; DIAGNOSTIC IMAGING; DIAGNOSTIC USE; FLUORESCENCE MICROSCOPY; HUMAN; PROCEDURES; THEORETICAL MODEL;

ALGORITHMS; DIAGNOSTIC IMAGING; FLUORESCENT DYES; HUMANS; MICROSCOPY, FLUORESCENCE; MODELS, THEORETICAL; QUANTUM DOTS;

EID: 84907708334     PISSN: None     EISSN: 10944087     Source Type: Journal    
DOI: 10.1364/OE.22.024594     Document Type: Article

References (26)

1. A. Small and S. Stahlheber, "Fluorophore localization algorithms for super-resolution microscopy," Nat. Methods 11(3), 267-279 (2014).
2. A. R. Small, "Theoretical limits on errors and acquisition rates in localizing switchable fluorophores," Biophys. J. 96(2), 16-8 (2009).
3. U. Resch-Genger, M. Grabolle, S. Cavaliere-Jaricot, R. Nitschke, and T. Nann, "Quantum dots versus organic dyes as fluorescent labels," Nat. Methods 5(9), 763-775 (2008).
4. F. D. Stefani, J. P. Hoogenboom, and E. Barkai, "Beyond quantum jumps: blinking nanoscale light emitters," Phys. Today 62(2), 34 (2009).
5. F. Huang, S. L. Schwartz, J. M. Byars, K. A. Lidke, and F. Huang, "Simultaneous multiple-emitter fitting for single molecule super-resolution imaging," Biomed. Opt. Express 2(5), 1377-1393 (2011).
6. S. J. Holden, S. Uphoff, and A. N. Kapanidis, "DAOSTORM: An algorithm for high-density super-resolution microscopy," Nat. Methods 8(4), 279-280, (2011).
7. L. Zhu, W. Zhang, D. Elnatan, and B. Huang, "Faster STORM using compressed sensing," Nat. Methods 9(7), 721-723 (2012).
8. K. A. Lidke, B. Rieger, T. M. Jovin, and R. Heintzmann, "Superresolution by localization of quantum dots using blinking statistics," Opt. Express 13(18), 7052 (2005).
9. A. Barsic and R. Piestun, "Super-resolution of dense nanoscale emitters beyond the diffraction limit using spatial and temporal information," Appl. Phys. Lett. 102(23), 231103 (2013).
10. S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, "Bayesian localization microscopy reveals nanoscale podosome dynamics," Nat. Methods 9(2), 195-200, (2011).
11. S. Geissbuehler, N. L. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, "Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI)," Opt. Nanoscopy 1(1), 4 (2012).
12. D. D. Lee and H. S. Seung, "Algorithms for non-negative matrix factorization," Adv. Neural Inf. Process. Syst. 13, 556-562 (2001).
13. O. Mandula, "Super-resolution methods for fluorescence microscopy," PhD thesis, University of Edinburgh (2012).
14. J. Kim and H. Park, "Toward Faster Nonnegative Matrix Factorization: A New Algorithm and Comparisons," 2008 Eighth IEEE International Conference on Data Mining (2008), pp. 353-362.
15. P. O. Hoyer, "Non-negative matrix factorization with sparseness constraints," J. Mach. Learn. Res. 5, 1457-1469 (2004).
16. MATLAB. (2010). version 7.10.0 (R2010a). Natick, Massachusetts: The MathWorks Inc.
17. https://www.dropbox.com/s/731u3u4htpdndgr/inmf.zip
18. https://github.com/aludnam/inmf
19. A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, "Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes," Nat. Methods 8(4), 327-333 (2011).
20. T. Dertinger, R. Colyera, G. Iyera, S. Weissa, and J. Enderleind, "Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). Supporting Information," PNAS 106(52), 22287-22292 (2009).
21. http://bigwww.epfl.ch/smlm/datasets/index.html?p=real-hd
22. N. Olivier, D. Keller, P. Gonczy, and S. Manley, "Resolution doubling in 3D-STORM imaging through improved buffers," PLoS One 8(7), (2013).
23. M. Everingham, L. Gool, C. K. I.Williams, J.Winn, and A. Zisserman, "The Pascal Visual Object Classes (VOC) Challenge," Int. J. Comput. Vis. 88(2), 303-338 (2009).
24. 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).
25. A. Hyvärinen and E. Oja, "Independent component analysis: Algorithms and applications," Neural Netw. 13(4-5), 411-430 (2000).
26. D. Baddeley, M. B. Cannell, and C. Soeller, "Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil," Nano Res. 4(6), 589-598 (2011).