Deconvolution methods for structured illumination microscopy

Journal of the Optical Society of America A: Optics and Image Science, and Vision

Volumn 33, Issue 7, 2016, Pages B12-B20

  Chakrova, Nadya ^a   Rieger, Bernd ^a   Stallinga, Sjoerd ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DECONVOLUTION; IMAGE PROCESSING; PERIODIC STRUCTURES;

DECONVOLUTION APPROACH; DECONVOLUTION METHOD; GENERALIZED WIENERS; ISOLATED STRUCTURES; RANDOM ILLUMINATION; RESOLUTION IMPROVEMENT; STRUCTURED ILLUMINATION MICROSCOPIES (SIM); STRUCTURED ILLUMINATION MICROSCOPY;

IMAGE RECONSTRUCTION;

EID: 84979784737     PISSN: 10847529     EISSN: 15208532     Source Type: Journal    
DOI: 10.1364/JOSAA.33.000B12     Document Type: Article

References (37)

1. P. J. Verveer, M. J. Gemkow, and T. M. Jovin, "A comparison of image restoration approaches applied to three-dimensional confocal and wide-field fluorescence microscopy," J. Microsc. 193, 50-61 (1999).
2. P. Sarder and A. Nehorai, "Deconvolution methods for 3-D fluorescence microscopy images," IEEE Signal Process. Mag. 23(3), 32-45 (2006).
3. W. Wallace, L. H. Schaefer, and J. R. Swedlow, "A working person's guide to deconvolution in light microscopy," Biotechniques 31, 1076-1097 (2001).
4. L. Schermelleh, R. Heintzmann, and H. Leonhardt, "A guide to super-resolution fluorescence microscopy," J. Cell Biol. 190, 165-175 (2010).
5. R. Heintzmann and C. Cremer, "Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating," Proc. SPIE 3568, 185-196 (1999).
6. M. G. L. Gustafsson, "Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy," J. Microsc. 198, 82-87 (2000).
7. G. E. Cragg and P. T. So, "Lateral resolution enhancement with standing evanescent waves," Opt. Lett. 25, 46-48 (2000).
8. J. T. Frohn, H. F. Knapp, and A. Stemmer, "True optical resolution beyond the Rayleigh limit achieved by standing wave illumination," Proc. Natl. Acad. Sci. USA 97, 7232-7236 (2000).
9. M. G. L. Gustafsson, L. Shao, P. M. Carlton, C. J. R. Wang, I. N. Golubovskaya, W. Z. Cande, A. D. Agard, and J. W. Sedat, "Three-dimensional desolution doubling in wide-field fluorescence microscopy by structured illumination," Biophys. J. 94, 4957-4970 (2008).
10. M. Ingaramo, A. G. York, E. Hoogendoorn, M. Postma, H. Shroff, and G. H. Patterson, "Richardson-Lucy deconvolution as a general tool for combining images with complementary strengths," ChemPhysChem 15, 794-800 (2014).
11. F. Ströhl and C. F. Kaminski, "A joint Richardson-Lucy deconvolution algorithm for the reconstruction of multifocal structured illumination microscopy data," Methods Appl. Fluoresc. 3, 014002 (2015).
12. S. Dong, P. Nanda, R. Shiradkar, K. Guo, and G. Zheng, "High-resolution fluorescence imaging via pattern-illuminated Fourier ptychography," Opt. Express 22, 20856-20870 (2014).
13. N. Chakrova, R. Heintzmann, B. Rieger, and S. Stallinga, "Studying different illumination patterns for resolution improvement in fluorescence microscopy," Opt. Express 23, 31367-31383 (2015).
14. K. Wicker, O. Mandula, G. Best, R. Fiolka, and R. Heintzmann, "Phase optimisation for structured illumination microscopy," Opt. Express 21, 2032-2049 (2013).
15. F. Orieux, E. Sepulveda, V. Loriette, and B. Dubertret, and J. C. Olivo-Marin, "Bayesian estimation for optimized structured illumination microscopy," IEEE Trans. Image Process. 21, 601-614 (2012).
16. E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, "Structured illumination microscopy using unknown speckle patterns," Nat. Photonics 6, 312-315 (2012).
17. T. Lukeš, P. Křížek, Z. Švindrych, J. Benda, M. Ovesný, K. Fliegel, M. Klíma, and G. M. Hagen, "Three-dimensional super-resolution structured illumination microscopy with maximum a posteriori probability image estimation," Opt. Express 22, 29805-29817 (2014).
18. A. Jost, E. Tolstik, P. Feldmann, K. Wicker, A. Sentenac, and R. Heintzmann, "Optical sectioning and high resolution in single-slice Structured Illumination Microscopy by thick slice blind-SIM reconstruction," PLoS One 10, e0132174 (2015).
19. A. G. York, S. H. Parekh, D. Dalle Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, "Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy," Nat. Methods 9, 749-754 (2012).
20. C. J. R. Sheppard, "Super-resolution in confocal imaging," Optik 80, 53-54 (1988).
21. C. B. Müller and J. Enderlein, "Image Scanning Microscopy," Phys. Rev. Lett. 104, 198101 (2010).
22. G. M. R. De Luca, R. M. P. Breedijk, R. A. J. Brandt, C. H. C. Zeelenberg, B. E. de Jong, W. Timmermans, L. N. Azar, R. A. Hoebe, S. Stallinga, and E. M. M. Manders, "Re-scan confocal microscopy: scanning twice for better resolution," Biomed. Opt. Express 4, 2644-2656 (2013).
23. S. Roth, C. J. Sheppard, K. Wicker, and R. Heintzmann, "Optical photon reassignment microscopy (OPRA)," Opt. Nanoscopy 2, 1-6 (2013).
24. A. G. York, P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis, and H. Shroff, "Instant super-resolution imaging in live cells and embryos via analog image processing," Nat. Methods 10, 1122-1126 (2013).
25. F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, "Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms," Nat. Methods 10, 653-658 (2013).
26. H. M. Hudson and R. S. Larkin, "Ordered subsets of projection data," IEEE Trans. Med. Imaging 13, 601-609 (1994).
27. F. Benvenuto, A. La Camera, C. Theys, A. Ferrari, H. Lanteri, and M. Bertero, "The study of an iterative method for the reconstruction of images corrupted by Poisson and Gaussian noise," Inverse Probl. 24, 035016 (2008).
28. B. Eicke, "Iteration methods for convexly constrained ill-posed problems in Hilbert space," Numer. Funct. Anal. Optim. 13, 413-429 (1992).
29. W. Richardson, "Bayesian-based iterative method of image restoration," J. Opt. Soc. Am. 62, 55-59 (1972).
30. L. B. Lucy, "An iterative technique for the rectification of observed distributions," Astron. J. 79, 745-754 (1974).
31. T. Wilson, R. Juskaitis, and P. D. Higdon, "The imaging of dielectric point scatterers in conventional and confocal polarisation microscopes," Opt. Commun. 141, 298-313 (1997).
32. P. Török, P. D. Higdon, and T. Wilson, "Theory for confocal and conventional microscopes imaging small dielectric scatterers," J. Mod. Opt. 45, 1681-1698 (1998).
33. 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, 557-562 (2013)
34. R. Heintzmann, "Estimating missing information by maximum likelihood deconvolution," Micron 38, 136-144 (2007).
35. T. J. Holmes, "Maximum-likelihood image restoration adapted for noncoherent optical imaging," J. Opt. Soc. Am. A 5, 666-673 (1988).
36. N. Chakrova, B. Rieger, and S. Stallinga, "Development of a DMD-based fluorescence microscope," Proc. SPIE 9330, 933008 (2015).
37. C. H. Righolt, J. A. Slotman, I. T. Young, S. Mai, L. J. van Vliet, and S. Stallinga, "Image filtering in structured illumination microscopy using the Lukosz bound," Opt. Express 21, 24431-24451 (2013).