Skip to main content

Super-Resolution Fluorescence Microscopy for Single Cell Imaging

  • Chapter
  • First Online:
Single Cell Biomedicine

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1068))

Abstract

In the past two decades, super-resolution fluorescence microscopy has undergone a dynamic evolution. Following proof-of-concept studies with stimulated emission depletion (STED) microscopy, several new approaches such as structured illumination microscopy (SIM), photoactivation localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), have been developed for imaging of nanoscale structural details and fast cellular dynamics in biological research. In this chapter, after briefly explaining their principles, we will describe the recent application of these super-resolution techniques in single cell imaging. In addition, the extension of super-resolution microscopy to 3D, multicolor, live-cell imaging and multimodal imaging are also discussed, significantly improving the precision of single cell imaging. Combining with molecular biology, biochemistry and bio-computing algorithms, super-resolution fluorescence microscopy continues to expand its capabilities and provide comprehensive insights into the details of single cells.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zheng XT, Li CM (2012) Single cell analysis at the nanoscale. Chem Soc Rev 41(6):2061–2071

    Article  CAS  PubMed  Google Scholar 

  2. Armbrecht L, Dittrich PS (2017) Recent advances in the analysis of single cells. Anal Chem 89(1):2–21

    Article  CAS  PubMed  Google Scholar 

  3. Sousa AA, Leapman RD (2012) Development and application of STEM for the biological sciences. Ultramicroscopy 123:38–49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM et al (2013) Cryo-electron microscopy-a primer for the non-microscopist. FEBS J 280(1):28–45

    Article  CAS  PubMed  Google Scholar 

  5. Stephens DJ, Allan VJ (2003) Light microscopy techniques for live cell imaging. Science 300(5616):82–86

    Article  CAS  PubMed  Google Scholar 

  6. Abbe E (1873) Beitrage zur Theorie des mikroskops und der mikroskopischen wahrnehmung. Arch Mikroskop Anat 9:413–420

    Article  Google Scholar 

  7. Huang B, Bates M, Zhuang X (2009) Super-resolution fluorescence microscopy. Annu Rev Biochem 78:993–1016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA et al (2013) Single cell optical imaging and spectroscopy. Chem Rev 113(4):2469–2527

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Fornasiero EF, Opazo F (2015) Super-resolution imaging for cell biologists: concepts, applications, current challenges and developments. BioEssays 37(4):436–451

    Article  PubMed  Google Scholar 

  10. Stone MB, Shelby SA, Veatch SL (2017) Super-resolution microscopy: shedding light on the cellular plasma membrane. Chem Rev 117(11):7457–7477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Betzig E (2015) Single molecules, cells, and super-resolution optics (Nobel Lecture). Angew Chem Int Ed 54(28):8034–8053

    Article  CAS  Google Scholar 

  12. Moerner WE (2015) Single-molecule spectroscopy, imaging, and photocontrol: foundations for super-resolution microscopy (Nobel Lecture). Angew Chem Int Ed 54(28):8067–8093

    Article  CAS  Google Scholar 

  13. Hell SW (2015) Nanoscopy with focused light (Nobel Lecture). Angew Chem Int Ed 54(28):8054–8066

    Article  CAS  Google Scholar 

  14. Hell SW, Wichmann J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett 19(11):780–782

    Article  CAS  PubMed  Google Scholar 

  15. Klar TA, Hell SW (1999) Subdiffraction resolution in far-field fluorescence microscopy. Opt Lett 24(14):954–956

    Article  CAS  PubMed  Google Scholar 

  16. Willig KI, Rizzoli SO, Westphal V, Jahn R, Hell SW (2006) STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 440(7086):935–939

    Article  CAS  PubMed  Google Scholar 

  17. Kittel RJ, Wichmann C, Rasse TM, Fouquet W, Schmidt M, Schmid A et al (2006) Bruchpilot promotes active zone assembly, Ca2+ channel clustering, and vesicle release. Science 312(5776):1051–1054

    Article  CAS  PubMed  Google Scholar 

  18. Sieber JJ, Willig KI, Kutzner C, Gerding-Reimers C, Harke B, Donnert G et al (2007) Anatomy and dynamics of a supramolecular membrane protein cluster. Science 317(5841):1072–1076

    Article  CAS  PubMed  Google Scholar 

  19. Donnert G, Keller J, Medda R, Andrei MA, Rizzoli SO, Lührmann R et al (2006) Macromolecular-scale resolution in biological fluorescence microscopy. Proc Natl Acad Sci U S A 103(31):11440–11445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kellner RR, Baier CJ, Willig KI, Hell SW, Barrantes FJ (2007) Nanoscale organization of nicotinic acetylcholine receptors revealed by stimulated emission depletion microscopy. Neuroscience 144(1):135–143

    Article  CAS  PubMed  Google Scholar 

  21. Lin W, Margolskee R, Donnert G, Hell SW, Restrepo D (2007) Olfactory neurons expressing transient receptor potential channel M5 (TRPM5) are involved in sensing semiochemicals. Proc Natl Acad Sci U S A 104(7):2471–2476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Schneider A, Rajendran L, Honsho M, Gralle M, Donnert G, Wouters F et al (2008) Flotillin-dependent clustering of the amyloid precursor protein regulates its endocytosis and amyloidogenic processing in neurons. J Neurosci 28(11):2874–2882

    Article  CAS  PubMed  Google Scholar 

  23. 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(5873):246–249

    Article  CAS  PubMed  Google Scholar 

  24. Lukinavičius G, Reymond L, D'Este E, Masharina A, Göttfert F, Ta H et al (2014) Fluorogenic probes for live-cell imaging of the cytoskeleton. Nat Methods 11(7):731–733

    Article  CAS  PubMed  Google Scholar 

  25. Honigmann A, Mueller V, Ta H, Schoenle A, Sezgin E, Hell SW et al (2014) Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells. Nat Commun 5:5412

    Article  CAS  PubMed  Google Scholar 

  26. D’Este E, Kamin D, Göttfert F, El-Hady A, Hell SW (2015) STED nanoscopy reveals the ubiquity of subcortical cytoskeleton periodicity in living neurons. Cell Rep 10(8):1246–1251

    Article  CAS  PubMed  Google Scholar 

  27. Liu Y, Lu Y, Yang X, Zheng X, Wen S, Wang F et al (2017) Amplified stimulated emission in upconversion nanoparticles for super-resolution nanoscopy. Nature 543(7644):229–233

    Article  CAS  PubMed  Google Scholar 

  28. Erdmann RS, Takakura H, Thompson AD, Rivera-Molina F, Allgeyer ES, Bewersdorf J et al (2014) Super-resolution imaging of the Golgi in live cells with a bioorthogonal ceramide probe. Angew Chem Int Ed 53(38):10242–10246

    Article  CAS  Google Scholar 

  29. Hanne J, Falk HJ, Görlitz F, Hoyer P, Engelhardt J, Sahl SJ et al (2015) STED nanoscopy with fluorescent quantum dots. Nat Commun 6:7127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gustafsson MG (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198(Pt 2):82–87

    Article  CAS  PubMed  Google Scholar 

  31. Heintzmann R, Cremer CG (1999) Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. Proc SPIE 3568:185–196

    Article  Google Scholar 

  32. Gustafsson MG, Shao L, Carlton PM, Wang CJ, Golubovskaya IN, Cande WZ et al (2008) Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 94(12):4957–4970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Heintzmann R, Jovin TM, Cremer C (2002) Saturated patterned excitation microscopy-a concept for optical resolution improvement. J Opt Soc Am A Opt Image Sci Vis 19(8):1599–1609

    Article  PubMed  Google Scholar 

  34. York AG, Parekh SH, Dalle Nogare D, Fischer RS, Temprine K, Mione M et al (2012) Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy. Nat Methods 9(7):749–754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Olshausen PV, Defeu Soufo HJ, Wicker K, Heintzmann R, Graumann PL, Rohrbach A (2013) Super-resolution imaging of dynamic MreB filaments in B. subtilis-a multiple-motor-driven transport? Biophys J 105(5):1171–1181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Schermelleh L, Carlton PM, Haase S, Shao L, Winoto L, Kner P et al (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320(5881):1332–1336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Shao L, Kner P, Rego EH, Gustafsson MG (2011) Super-resolution 3D microscopy of live whole cells using structured illumination. Nat Methods 8(12):1044–1046

    Article  CAS  PubMed  Google Scholar 

  38. Fiolka R, Shao L, Rego EH, Davidson MW, Gustafsson MG (2012) Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination. Proc Natl Acad Sci U S A 109(14):5311–5315

    Article  PubMed  PubMed Central  Google Scholar 

  39. Kner P, Chhun BB, Griffis ER, Winoto L, Gustafsson MG (2009) Super-resolution video microscopy of live cells by structured illumination. Nat Methods 6(5):339–342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Gustafsson MG (2005) Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci U S A 102(37):13081–13086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Rego EH, Shao L, Macklin JJ, Winoto L, Johansson GA, Kamps-Hughes N et al (2012) Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution. Proc Natl Acad Sci U S A 109(3):135–143

    Article  Google Scholar 

  42. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793):1642–1645

    Article  PubMed  Google Scholar 

  43. Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3(10):793–795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Hess ST, Girirajan TP, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91(11):4258–4272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Heilemann M, van de Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A et al (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed 47(33):6172–6176

    Article  CAS  Google Scholar 

  46. Lee HL, Lord SJ, Iwanaga S, Zhan K, Xie H, Williams JC et al (2010) Super-resolution imaging of targeted proteins in fixed and living cells using photoactivatable organic fluorophores. J Am Chem Soc 132(43):15099–15101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Fölling J, Belov V, Kunetsky R, Medda R, Schönle A, Egner A et al (2007) Photochromic rhodamines provide nanoscopy with optical sectioning. Angew Chem Int Ed 46(33):6266–6270

    Article  CAS  Google Scholar 

  48. Lee MK, Rai P, Williams J, Twieg RJ, Moerner WE (2014) Small-molecule labeling of live cell surfaces for three-dimensional super-resolution microscopy. J Am Chem Soc 136(40):14003–14006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Grimm JB, Sung AJ, Legant WR, Hulamm P, Matlosz SM, Betzig E et al (2013) Carbofluoresceins and carborhodamines as scaffolds for high-contrast fluorogenic probes. ACS Chem Biol 8(6):1303–1310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Tian Z, Li AD, Hu D (2011) Super-resolution fluorescence nanoscopy applied to imaging core-shell photoswitching nanoparticles and their self-assemblies. Chem Commun 47(4):1258–1260

    Article  CAS  Google Scholar 

  51. Zhang H, Wang C, Jiang T, Guo H, Wang G, Cai X et al (2015) Microtubule-targetable fluorescent probe: site-specific detection and super-resolution imaging of ultratrace tubulin in microtubules of living cancer cells. Anal Chem 87(10):5216–5222

    Article  CAS  PubMed  Google Scholar 

  52. Bates M, Huang B, Dempsey GT, Zhuang X (2007) Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317(5845):1749–1753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Huang B, Wang W, Bates M, Zhuang X (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319(5864):810–813

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Heilemann M, van de Linde S, Mukherjee A, Sauer M (2009) Super-resolution imaging with small organic fluorophores. Angew Chem Int Ed 48(37):6903–6908

    Article  CAS  Google Scholar 

  55. Lukinavičius G, Umezawa K, Olivier N, Honigmann A, Yang G, Plass T et al (2013) A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat Chem 5(2):132–139

    Article  CAS  PubMed  Google Scholar 

  56. Uno SN, Kamiya M, Yoshihara T, Sugawara K, Okabe K, Tarhan MC et al (2014) A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging. Nat Chem 6(8):681–689

    Article  CAS  PubMed  Google Scholar 

  57. Gu X, Zhao E, Lam JW, Peng Q, Xie Y, Zhang Y et al (2015) Mitochondrion-specific live-cell bioprobe operated in a fluorescence turn-on manner and a well-designed photoactivatable mechanism. Adv Mater 27(44):7093–7100

    Article  CAS  PubMed  Google Scholar 

  58. Gu X, Zhao E, Zhao T, Kang M, Gui C, Lam JW et al (2016) A mitochondrion-specific photoactivatable fluorescence turn-pn AIE-based bioprobe for localization super-resolution microscope. Adv Mater 28(25):5064–5071

    Article  CAS  PubMed  Google Scholar 

  59. Dertinger T, Colyer R, Iyer G, Weiss S, Enderlein J (2009) Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). Proc Natl Acad Sci U S A 106(52):22287–22292

    Article  PubMed  PubMed Central  Google Scholar 

  60. Dertinger T, Colyer R, Vogel R, Enderlein J, Weiss S (2010) Achieving increased resolution and more pixels with super-resolution optical fluctuation imaging (SOFI). Opt Express 18(18):18875–18885

    Article  PubMed  PubMed Central  Google Scholar 

  61. Dedecker P, Mo GC, Dertinger T, Zhang J (2012) Widely accessible method for super-resolution fluorescence imaging of living systems. Proc Natl Acad Sci U S A 109(27):10909–10914

    Article  PubMed  PubMed Central  Google Scholar 

  62. Dertinger T, Heilemann M, Vogel R, Sauer M, Weiss S (2010) Super-resolution optical fluctuation imaging with organic dyes. Angew Chem Int Ed 49(49):9441–9443

    Article  CAS  Google Scholar 

  63. Zhang X, Chen X, Zeng Z, Zhang M, Sun Y, Xi P et al (2015) Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI). ACS Nano 9(3):2659–2667

    Article  CAS  PubMed  Google Scholar 

  64. Chen X, Li R, Liu Z, Sun K, Sun Z, Chen D et al (2017) Small photoblinking semiconductor polymer dots for fluorescence nanoscopy. Adv Mater. https://doi.org/10.1002/adma.201604850

  65. Zeng Z, Chen X, Wang H, Huang N, Shan C, Zhang H et al (2015) Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging. Sci Rep 5:8359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Kisley L, Brunetti R, Tauzin LJ, Shuang B, Yi X, Kirkeminde AW et al (2015) Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging. ACS Nano 9(9):9158–9166

    Article  CAS  PubMed  Google Scholar 

  67. Godin AG, Lounis B, Cognet L (2014) Super-resolution microscopy approaches for live cell imaging. Biophys J 107(8):1777–1784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Hauser M, Wojcik M, Kim D, Mahmoudi M, Li W, Xu K (2017) Correlative super-resolution microscopy: new dimensions and new opportunities. Chem Rev 117(11):7428–7456

    Article  CAS  PubMed  Google Scholar 

  69. Watanabe S, Punge A, Hollopeter G, Willig KI, Hobson RJ, Davis MW et al (2011) Protein localization in electron micrographs using fluorescence nanoscopy. Nat Methods 8(1):80–84

    Article  CAS  PubMed  Google Scholar 

  70. Ries J, Kaplan C, Platonova E, Eghlidi H, Ewers H (2012) A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat Methods 9(6):582–584

    Article  CAS  PubMed  Google Scholar 

  71. Opazo F, Levy M, Byrom M, Schäfer C, Geisler C, Groemer TW et al (2012) Aptamers as potential tools for super-resolution microscopy. Nat Methods 9(10):938–939

    Article  CAS  PubMed  Google Scholar 

  72. Deschout H, Cella Zanacchi F, Mlodzianoski M, Diaspro A, Bewersdorf J, Hess ST et al (2014) Precisely and accurately localizing single emitters in fluorescence microscopy. Nat Methods 11(3):253–266

    Article  CAS  PubMed  Google Scholar 

  73. Klein T, Löschberger A, Proppert S, Wolter S, van de Linde S, Sauer M (2012) Live-cell dSTORM with SNAP-tag fusion proteins. Nat Methods 8(1):7–9

    Article  CAS  Google Scholar 

  74. Wombacher R, Heidbreder M, van de Linde S, Sheetz MP, Heilemann M, Cornish VW et al (2010) Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods 7(9):717–719

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors gratefully appreciate the support from the National Natural Science Foundation of China (No.81472835 and 81670091) and the National Key Clinical Specialist Construction Programs of China (2013-544).

Conflicts of Interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Xiaobo Wang .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Feng, H., Wang, X., Xu, Z., Zhang, X., Gao, Y. (2018). Super-Resolution Fluorescence Microscopy for Single Cell Imaging. In: Gu, J., Wang, X. (eds) Single Cell Biomedicine. Advances in Experimental Medicine and Biology, vol 1068. Springer, Singapore. https://doi.org/10.1007/978-981-13-0502-3_6

Download citation

Publish with us

Policies and ethics