Fast compressed sensing analysis for superresolution imaging using L1-homotopy

Optics Express

Volumn 21, Issue 23, 2013, Pages 28583-28596

  Babcock, Hazen P ^a   Moffitt, Jeffrey R ^a   Cao, Yunlong ^b   Zhuang, Xiaowei ^a  

^a HARVARD UNIVERSITY   (United States)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPRESSED-SENSING; COMPUTATIONAL COSTS; COMPUTATIONAL TIME; FLUORESCENT EMITTERS; INTERIOR POINT METHODS; ORDERS OF MAGNITUDE; SUPER RESOLUTION IMAGING; SUPER-RESOLUTION IMAGE RECONSTRUCTION;

IMAGE RECONSTRUCTION; IMAGING TECHNIQUES; PERSONAL COMPUTERS;

OPTICAL RESOLVING POWER;

ALGORITHM; DIAGNOSTIC IMAGING; FLUORESCENCE MICROSCOPY; HUMAN; IMAGE ENHANCEMENT; IMAGE PROCESSING; PROCEDURES;

ALGORITHMS; DIAGNOSTIC IMAGING; HUMANS; IMAGE ENHANCEMENT; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, FLUORESCENCE;

EID: 84888272028     PISSN: None     EISSN: 10944087     Source Type: Journal    
DOI: 10.1364/OE.21.028583     Document Type: Article

References (27)

1. M. J. Rust, M. Bates, and X. Zhuang, "Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)," Nat. Methods 3(10), 793-796 (2006).
2. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, "Imaging intracellular fluorescent proteins at nanometer resolution," Science 313(5793), 1642-1645 (2006).
3. S. T. Hess, T. P. Girirajan, and M. D. Mason, "Ultra-high resolution imaging by fluorescence photoactivation localization microscopy," Biophys. J. 91(11), 4258-4272 (2006).
4. H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, "Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics," Nat. Methods 5(5), 417-423 (2008).
5. B. Huang, H. P. Babcock, and X. Zhuang, "Breaking the diffraction barrier: Super-resolution imaging of cells," Cell 143(7), 1047-1058 (2010).
6. S. A. Jones, S.-H. Shim, J. He, and X. Zhuang, "Fast, three-dimensional super-resolution imaging of live cells," Nat. Methods 8(6), 499-505 (2011).
7. R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, "Measuring image resolution in optical nanoscopy," Nat. Methods 10(6), 557-562 (2013).
8. S.-H. Shim, C. Xia, G. Zhong, H. P. Babcock, J. C. Vaughan, B. Huang, X. Wang, C. Xu, G.-Q. Bi, and X. Zhuang, "Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes," Proc. Natl. Acad. Sci. U.S.A. 109(35), 13978-13983 (2012).
9. 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).
10. F. Huang, S. L. Schwartz, J. M. Byars, and K. A. Lidke, "Simultaneous multiple-emitter fitting for single molecule super-resolution imaging," Biomed. Opt. Express 2(5), 1377-1393 (2011).
11. 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).
12. T. Quan, H. Zhu, X. Liu, Y. Liu, J. Ding, S. Zeng, and Z.-L. Huang, "High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion," Opt. Express 19(18), 16963- 16974 (2011).
13. H. P. Babcock, Y. M. Sigal, and X. Zhuang, "A high-density 3D localization algorithm for stochastic optical reconstruction microscopy," Optical Nanoscopy 1(1), 6-10 (2012).
14. E. A. Mukamel, H. P. Babcock, and X. Zhuang, "Statistical Deconvolution for Superresolution Fluorescence Microscopy," Biophys. J. 102(10), 2391-2400 (2012).
15. L. Zhu, W. Zhang, D. Elnatan, and B. Huang, "Faster STORM using compressed sensing," Nat. Methods 9(7), 721-723 (2012).
16. M. R. Osborne, B. Presnell, and B. A. Turlach, "A new approach to variable selection in least squares problems," IMA J. Numer. Anal. 20(3), 389-403 (2000).
17. D. M. Malioutov, M. Cetin, and A. S. Willsky, "Homotopy continuation for sparse signal representation," ICASSP 5, 733-736 (2005).
18. D. L. Donoho and Y. Tsaig, "Fast Solution of the L1-norm Minimization Problem When the Solution May be Sparse," IEEE Trans. Inf. Theory 54(11), 4789-4812 (2008).
19. A. Y. Yang and S. S. Sastry, "Fast l1-minimization algorithms and an application in robust face recognition: a review," Proceedings of 2010 IEEE 17th International Conference on Image Processing, 1849-1852 (2010).
20. A. Y. Yang, Z. Zhou, A. Ganesh, S. S. Shankar, and Y. Ma, "Fast L1-Minimization Algorithms For Robust Face Recognition," IEEE Trans. Image Process. 22(8), 3234-3246 (2012).
21. E. van den Berg and M. P. Friedlander, "Probing the Pareto frontier for basis pursuit solutions," SIAM J. Sci. Comput. 31(2), 890-912 (2009).
22. A. Beck and M. Teboulle, "A fast iterative shrinkage-thresholding algorithm for linear inverse problems," SIAM Journal on Imaging Sciences 2(1), 183-202 (2009).
23. M. C. Grant and S. P. Boyd, "CVX: Matlab software for disciplined convex programming, version 2.0 beta," http://cvxr.com/cvx (2013).
24. M. Bates, B. Huang, G. T. Dempsey, and X. Zhuang, "Multicolor super-resolution imaging with photoswitchable fluorescent probes," Science 317(5845), 1749-1753 (2007).
25. B. Huang, W. Wang, M. Bates, and X. Zhuang, "Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy," Science 319(5864), 810-813 (2008).
26. M. Grant, S. Boyd, and Y. Ye, "CVX: Matlab Software for Disciplined Convex Programming, Version 1.0 beta 3," Recent Advances in Learning and Control}, 95-110 (2006).
27. K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, "Optimized localization analysis for singlemolecule tracking and super-resolution microscopy," Nat. Methods 7(5), 377-381 (2010).