Optical nanoscopy: From acquisition to analysis

Annual Review of Biomedical Engineering

Volumn 14, Issue , 2012, Pages 231-254

  Gould, Travis J ^a   Hess, Samuel T ^b   Bewersdorf, Joerg ^a,c  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b University of Maine   (United States)

^c Yale University   (United States)

Author keywords

Diffraction; Fluorescence photoactivation localization microscopy; Image processing; STED microscopy; Super resolution

Indexed keywords

ANALYSIS APPROACH; BASIC PRINCIPLES; BIOLOGICAL IMAGING; CLASS OF METHODS; DIFFRACTION LIMITS; FAR-FIELD; FLUORESCENCE IMAGING; FLUORESCENT PROBE MOLECULES; PHOTOACTIVATION; PHOTOPHYSICAL PROPERTIES; SUPER RESOLUTION;

FLUORESCENCE; IMAGE PROCESSING; OPTICAL DATA PROCESSING;

DIFFRACTION;

ALGORITHM; CONCEPT ANALYSIS; DIFFRACTION; FLUORESCENCE MICROSCOPY; IMAGE ANALYSIS; IMAGE QUALITY; INTERMETHOD COMPARISON; LASER MICROSCOPY; LOCALIZATION MICROSCOPY; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MICROSCOPY; OPTICAL NANOSCOPY; POINT SPREAD FUNCTION; REVIEW; SIGNAL NOISE RATIO; STIMULATED EMISSION DEPLETION MICROSCOPY; THREE DIMENSIONAL IMAGING;

ALGORITHMS; BIOMEDICAL ENGINEERING; FLUORESCENT DYES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MICROSCOPY; MICROSCOPY, FLUORESCENCE; MODELS, STATISTICAL; NANOTECHNOLOGY; OPTICS AND PHOTONICS;

EID: 84864190680     PISSN: 15239829     EISSN: 15454274     Source Type: Book Series    
DOI: 10.1146/annurev-bioeng-071811-150025     Document Type: Review

References (106)

1. Hell SW. 2007. Far-field optical nanoscopy. Science 316:1153-58 (Pubitemid 46877470)
2. Toomre D, Bewersdorf J. 2010. A new wave of cellular imaging. Annu. Rev. Cell Dev. Biol. 26:285-314
3. Abbe E. 1873. Beiträge zur Theorie des Mikroskops und der Mikroskopischen Wahrnehmung. Arch. Mikrosk. Anat. 9:413-68
4. HellSW, Wichmann J. 1994. Breaking the diffraction resolution limit by stimulated emission: stimulatedemission-depletion fluorescence microscopy. Opt. Lett. 19:780-82
5. Hell SW. 2009. Microscopy and its focal switch. Nat. Methods 6:24-32
6. Hell SW, Jakobs S, Kastrup L. 2003. Imaging and writing at the nanoscale with focused visible light through saturable optical transitions. Appl. Phys. A 77:859-60
7. Bretschneider S, EggelingC, Hell SW. 2007. Breaking the diffraction barrier in fluorescencemicroscopy by optical shelving. Phys. Rev. Lett. 98:218103
8. Hell SW, Kroug M. 1995. Ground-state-depletion fluorescence microscopy: a concept for breaking the diffraction resolution limit. Appl. Phys. B 60:495-97
9. Dedecker P, Hotta J, Flors C, Sliwa M, Uji-i H, et al. 2007. Subdiffraction imaging through the selective donut-mode depletion of thermally stable photoswitchable fluorophores: numerical analysis and application to the fluorescent protein Dronpa. J. Am. Chem. Soc. 129:16132-41
10. Grotjohann T, Testa I, Leutenegger M, Bock H, Urban NT, et al. 2011. Diffraction-unlimited all-optical imaging and writing with a photochromic GFP. Nature 478:204-8
11. Hofmann M, Eggeling C, Jakobs S, Hell SW. 2005. Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc. Natl. Acad. Sci. USA 102:17565-69 (Pubitemid 41803537)
12. Harke B, Keller J, Ullal CK, Westphal V, Schonle A, Hell SW. 2008. Resolution scaling in STED microscopy. Opt. Express 16:4154-62 (Pubitemid 351434386)
13. Westphal V, Hell SW. 2005. Nanoscale resolution in the focal plane of an optical microscope. Phys. Rev. Lett. 94:143903
14. Barak LS, Webb WW. 1982. Diffusion of low density lipoprotein-receptor complex on human fibroblasts. J. Cell Biol. 95:846-52 (Pubitemid 13186107)
15. Schmidt T, Schutz GJ, Baumgartner W, Gruber HJ, Schindler H. 1996. Imaging of single molecule diffusion. Proc. Natl. Acad. Sci. USA 93:2926-2916.
16. Ram S, Ward ES, Ober RJ. 2006. Beyond Rayleigh's criterion: a resolution measure with application to single-molecule microscopy. Proc. Natl. Acad. Sci. USA 103:4457-62
17. Thompson RE, Larson DR, Webb WW. 2002. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 82:2775-83 (Pubitemid 34441314)
18. Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR. 2003. Myosin V walks hand-overhand: single fluorophore imaging with 1.5-nm localization. Science 300:2061-65 (Pubitemid 36760126)
19. Bornfleth H, Sätzler K, Eils R, Cremer C. 1998. High-precision distance measurements and volumeconserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy. J. Microsc. 189:118-36 (Pubitemid 28109122)
20. Lacoste TD, Michalet X, Pinaud F, Chemla DS, Alivisatos AP, Weiss S. 2000. Ultrahigh-resolution multicolor colocalization of single fluorescent probes. Proc. Natl. Acad. Sci. USA 97:9461-66 (Pubitemid 30650797)
21. Gordon MP, Ha T, Selvin PR. 2004. Single-molecule high-resolution imaging with photobleaching. Proc. Natl. Acad. Sci. USA 101:6462-65 (Pubitemid 38585996)
22. Qu X, Wu D, Mets L, Scherer NF. 2004. Nanometer-localized multiple single-molecule fluorescence microscopy. Proc. Natl. Acad. Sci. USA 101:11298-303 (Pubitemid 39038341)
23. Lagerholm BC, Averett L, Weinreb GE, Jacobson K, Thompson NL. 2006. Analysis method for measuring submicroscopic distances with blinking quantum dots. Biophys. J. 91:3050-60 (Pubitemid 44526495)
24. Lidke KA, Rieger B, Jovin TM, Heintzmann R. 2005. Superresolution by localization of quantum dots using blinking statistics. Opt. Express 13:7052-62 (Pubitemid 41305581)
25. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642-45 (Pubitemid 44414039)
26. Hess ST, Girirajan TP, MasonMD. 2006. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91:4258-72 (Pubitemid 44887284)
27. Rust MJ, Bates M, Zhuang X. 2006. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3:793-96
28. Baddeley D, Jayasinghe ID, Cremer C, Cannell MB, Soeller C. 2009. Light-induced dark states of organic fluorochromes enable 30 nm resolution imaging in standard media. Biophys. J. 96:L22-24
29. Biteen JS, ThompsonMA, TselentisNK, Bowman GR, Shapiro L, MoernerWE. 2008. Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP. Nat. Methods 5:947-49
30. Folling J, Bossi M, Bock H, Medda R, Wurm CA, et al. 2008. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat. Methods 5:943-45
31. Heilemann M, van de Linde S, SchuttpelzM, Kasper R, Seefeldt B, et al. 2008. Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew. Chem. Int. Ed. Engl. 47:6172-76
32. Vogelsang J, Cordes T, Forthmann C, Steinhauer C, Tinnefeld P. 2009. Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and superresolution microscopy. Proc. Natl. Acad. Sci. USA 106:8107-12
33. Sharonov A, Hochstrasser RM. 2006. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc. Natl. Acad. Sci. USA 103:18911-16 (Pubitemid 350002802)
34. Gould TJ, Gunewardene MS, Gudheti MV, Verkhusha VV, Yin S, et al. 2008. Nanoscale imaging of molecular positions and anisotropies. Nat. Methods 5:1027-30
35. Bossi M, Folling J, Belov VN, Boyarskiy VP, Medda R, et al. 2008. Multicolor far-field fluorescence nanoscopy through isolated detection of distinct molecular species. Nano Lett. 8:2463-68
36. Gunewardene M, Subach FV, Gould TJ, Penoncello GP, Gudheti MV, et al. 2011. Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys. J. 101:1522-28
37. Gould TJ, Myers JR, Bewersdorf J. 2011. Total internal reflection STED microscopy. Opt. Express 19:13351-57
38. Klar TA, Jakobs S, Dyba M, Egner A, Hell SW. 2000. Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc. Natl. Acad. Sci. USA 97:8206-10 (Pubitemid 30639649)
39. Juette MF, Gould TJ, Lessard MD, Mlodzianoski MJ, Nagpure BS, et al. 2008. Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat. Methods 5:527-29 (Pubitemid 351761759)
40. Huang B, WangW, Bates M, Zhuang X. 2008. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810-13 (Pubitemid 351225870)
41. Pavani SR, ThompsonMA, Biteen JS, Lord SJ, Liu N, et al. 2009. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc. Natl. Acad. Sci. USA 106:2995-99
42. Baddeley D, Cannell M, Soeller C. 2011. Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil. Nano Res. 4:589-98
43. Tang J, Akerboom J, Vaziri A, Looger LL, Shank CV. 2010. Near-isotropic 3D optical nanoscopy with photon-limited chromophores. Proc. Natl. Acad. Sci. USA 107:10068-73
44. Aquino D, Schonle A, Geisler C, Middendorff CV, Wurm CA, et al. 2011. Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores. Nat. Methods 8:353-59
45. Schmidt R, Wurm CA, Jakobs S, Engelhardt J, Egner A, Hell SW. 2008. Spherical nanosized focal spot unravels the interior of cells. Nat. Methods 5:539-44 (Pubitemid 351761762)
46. ShtengelG, Galbraith JA, GalbraithCG, Lippincott-Schwartz J, Gillette JM, et al. 2009. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc. Natl. Acad. Sci. USA 106:3125-30
47. Gugel H, Bewersdorf J, Jakobs S, Engelhardt J, Storz R, Hell SW. 2004. Cooperative 4Pi excitation and detection yields sevenfold sharper optical sections in live-cell microscopy. Biophys. J. 87:4146-52 (Pubitemid 39602918)
48. Hell S, Steltzer EHK. 1992. Properties of a 4Pi confocal fluorescence microscope. J. Opt. Soc. Am. A 9:2159-67
49. Shroff H, Galbraith CG, Galbraith JA, Betzig E. 2008. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat. Methods 5:417-23 (Pubitemid 351619100)
50. Westphal V, Rizzoli SO, Lauterbach MA, Kamin D, Jahn R, Hell SW. 2008. Video-rate far-field optical nanoscopy dissects synaptic vesicle movement. Science 320:246-49 (Pubitemid 351521423)
51. Lauterbach MA, Ullal CK, Westphal V, Hell SW. 2010. Dynamic imaging of colloidal-crystal nanostructures at 200 frames per second. Langmuir 26:14400-4
52. Eggeling C, Ringemann C, Medda R, Schwarzmann G, Sandhoff K, et al. 2009. Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 457:1159-62
53. Hess ST, Gould TJ, Gudheti MV, Maas SA, Mills KD, Zimmerberg J. 2007. Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories. Proc. Natl. Acad. Sci. USA 104:17370-75 (Pubitemid 350219826)
54. Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF, et al. 2008. High-density mapping of singlemolecule trajectories with photoactivated localization microscopy. Nat. Methods 5:155-57 (Pubitemid 351181741)
55. Jones SA, Shim SH, He J, Zhuang X. 2011. Fast, three-dimensional super-resolution imaging of live cells. Nat. Methods 8:499-508
56. Neher RA, Mitkovski M, Kirchhoff F, Neher E, Theis FJ, Zeug A. 2009. Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophys. J. 96:3791-800
57. Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J, et al. 2007. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc. Natl. Acad. Sci. USA 104:20308-13
58. Bates M, Huang B, Dempsey GT, Zhuang X. 2007. Multicolor super-resolution imaging with photoswitchable fluorescent probes. Science 317:1749-53 (Pubitemid 47461839)
59. Klein T, Loschberger A, Proppert S, Wolter S, van de Linde S, SauerM. 2011. Live-cell dSTORM with SNAP-tag fusion proteins. Nat. Methods 8:7-9
60. Testa I, Wurm CA, Medda R, Rothermel E, von Middendorf C, et al. 2010. Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength. Biophys. J. 99:2686-94
61. Donnert G, Keller J, Wurm CA, Rizzoli SO, Westphal V, et al. 2007. Two-color far-field fluorescence nanoscopy. Biophys. J. 92:L67-69 (Pubitemid 46557839)
62. Meyer L, Wildanger D, Medda R, Punge A, Rizzoli SO, et al. 2008. Dual-color STED microscopy at 30-nm focal-plane resolution. Small 4:1095-100
63. Neumann D, Buckers J, Kastrup L, Hell SW, Jakobs S. 2010. Two-color STED microscopy reveals different degrees of colocalization between hexokinase-I and the three human VDAC isoforms. PMC Biophys. 3:4
64. Pellett PA, Sun X, Gould TJ, Rothman JE, Xu MQ, et al. 2011. Two-color STED microscopy in living cells. Biomed. Opt. Express 2:2364-71
65. Buckers J, Wildanger D, Vicidomini G, Kastrup L, Hell SW. 2011. Simultaneous multi-lifetime multicolor STED imaging for colocalization analyses. Opt. Express 19:3130-43
66. Engelhardt J, Keller J, Hoyer P, Reuss M, Staudt T, Hell SW. 2011. Molecular orientation affects localization accuracy in superresolution far-field fluorescence microscopy. Nano Lett. 11:209-13
67. Rittweger E, Han KY, Irvine SE, Eggeling C, Hell SW. 2009. STED microscopy reveals crystal colour centres with nanometric resolution. Nat. Photonics 3:144-47
68. Willig KI, Keller J, Bossi M, Hell SW. 2006. STED microscopy resolves nanoparticle assemblies. New J. Phys. 8:106
69. Gould TJ, Verkhusha VV, Hess ST. 2009. Imaging biological structures with fluorescence photoactivation localization microscopy. Nat. Protoc. 4:291-308
70. Matsuda A, Shao L, Boulanger J, Kervrann C, Carlton PM, et al. 2010. Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones. PLoS ONE 5:e12768
71. Krizek P, Raska I, Hagen GM. 2011. Minimizing detection errors in single molecule localization microscopy. Opt. Express 19:3226-35
72. Cheezum MK, Walker WF, Guilford WH. 2001. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J. 81:2378-88 (Pubitemid 32917184)
73. Enderlein J, Toprak E, Selvin PR. 2006. Polarization effect on position accuracy of fluorophore localization. Opt. Express 14:8111-20 (Pubitemid 44331025)
74. Abraham AV, Ram S, Chao J, Ward ES, Ober RJ. 2009. Quantitative study of single molecule location estimation techniques. Opt. Express 17:23352-73
75. Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H. 2010. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat. Methods 7:377-81
76. Zhang B, Zerubia J, Olivo-Marin JC. 2007. Gaussian approximations of fluorescence microscope pointspread function models. Appl. Opt. 46:1819-29 (Pubitemid 46659549)
77. Ram S, Prabhat P, Chao J, Ward ES, Ober RJ. 2008. High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells. Biophys. J. 95:6025-43
78. Kao HP, Verkman AS. 1994. Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position. Biophys. J. 67:1291-300 (Pubitemid 24272983)
79. Mlodzianoski MJ, Juette MF, Beane GL, Bewersdorf J. 2009. Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy. Opt. Express 17:8264-77
80. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642-45 (Pubitemid 44414039)
81. Mlodzianoski MJ, Schreiner JM, Callahan SP, Smolkova K, Dlaskova A, et al. 2011. Sample drift correction in 3D fluorescence photoactivation localization microscopy. Opt. Express 19:15009-19
82. Holden SJ, Uphoff S, Kapanidis AN. 2011. DAOSTORM: an algorithm for high-density superresolution microscopy. Nat. Methods 8:279-80
83. Huang F, Schwartz SL, Byars JM, Lidke KA. 2011. Simultaneous multiple-emitter fitting for single molecule super-resolution imaging. Biomed. Opt. Express 2:1377-93
84. Quan T, Zhu H, Liu X, Liu Y, Ding J, et al. 2011. High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion. Opt. Express 19:16963-74
85. Henriques R, Lelek M, Fornasiero EF, Valtorta F, Zimmer C, Mhlanga MM. 2010. QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat. Methods 7:339-40
86. Wolter S, Schuttpelz M, Tscherepanow M, van de Linde S, Heilemann M, Sauer M. 2010. Real-time computation of subdiffraction-resolution fluorescence images. J. Microsc. 237:12-22
87. Quan T, Li P, Long F, Zeng S, Luo Q, et al. 2010. Ultra-fast, high-precision image analysis for localization-based super resolution microscopy. Opt. Express 18:11867-76
88. Smith CS, Joseph N, Rieger B, Lidke KA. 2010. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7:373-75
89. Wieser S, Schutz GJ. 2008. Tracking single molecules in the live cell plasma membrane-do's and don't's. Methods 46:131-40
90. Semrau S, Schmidt T. 2007. Particle image correlation spectroscopy (PICS): retrieving nanometer-scale correlations from high-density single-molecule position data. Biophys. J. 92:613-21 (Pubitemid 46145794)
91. Pyenta PS, Holowka D, Baird B. 2001. Cross-correlation analysis of inner-leaflet-anchored green fluorescent protein co-redistributed with IgE receptors and outer leaflet lipid raft components. Biophys. J. 80:2120-32 (Pubitemid 32401978)
92. Petersen NO, Hoddelius PL, Wiseman PW, SegerO, Magnusson KE. 1993. Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application. Biophys. J. 65:1135-46 (Pubitemid 23263930)
93. Diggle PJ. 1979.Onparameter estimation and goodness-of-fit testing for spatial point patterns. Biometrics 38:87-101
94. Prior IA, Muncke C, Parton RG, Hancock JF. 2003. Direct visualization of Ras proteins in spatially distinct cell surface microdomains. J. Cell Biol. 160:165-70 (Pubitemid 36254950)
95. Annibale P, Vanni S, Scarselli M, Rothlisberger U, Radenovic A. 2011. Quantitative photo activated localization microscopy: unraveling the effects of photoblinking. PLoS ONE 6:e22678
96. Annibale P, Vanni S, Scarselli M, Rothlisberger U, Radenovic A. 2011. Identification of clustering artifacts in photoactivated localization microscopy. Nat. Methods 8:527-28
97. Sengupta P, Jovanovic-TalismanT, Skoko D, Renz M, Veatch SL, Lippincott-Schwartz J. 2011. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8:969-75
98. Zacharias DA, Violin JD, Newton AC, Tsien RY. 2002. Partitioning of lipid-modifiedmonomeric GFPs into membrane microdomains of live cells. Science 296:913-16 (Pubitemid 34464897)
99. Hess ST, Kumar M, Verma A, Farrington J, Kenworthy A, Zimmerberg J. 2005. Quantitative electron microscopy and fluorescence spectroscopy of the membrane distribution of influenza hemagglutinin. J. Cell Biol. 169:965-76 (Pubitemid 41002872)
100. Gower JC, Ross GJS. 1969. Minimum spanning trees and single linkage cluster analysis. J. R. Stat. Soc. Ser. C (Appl. Stat.) 18:54-64
101. Baddeley D, Cannell MB, Soeller C. 2010. Visualization of localization microscopy data. Microsc. Microanal. 16:64-72
102. Willig KI, Rizzoli SO, Westphal V, Jahn R, Hell SW. 2006. STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 440:935-39
103. Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, et al. 2009. Self-organization of the Escherichia coli chemotaxis network imagedwith super-resolution light microscopy. PLoS Biol. 7:e1000137
104. Wu M, Huang B, Graham M, Raimondi A, Heuser JE, et al. 2010. Coupling between clathrin-dependent endocytic budding and F-BAR-dependent tubulation in a cell-free system. Nat. Cell Biol. 12:902-8
105. Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW, et al. 2010. Nanoscale architecture of integrin-based cell adhesions. Nature 468:580-84
106. Watanabe S, Punge A, Hollopeter G, Willig KI, Hobson RJ, et al. 2011. Protein localization in electron micrographs using fluorescence nanoscopy. Nat. Methods 8:80-84