Skip to main content

Requirements for Samples in Super-Resolution Fluorescence Microscopy

  • Protocol
  • First Online:
Super-Resolution Microscopy Techniques in the Neurosciences

Part of the book series: Neuromethods ((NM,volume 86))

Abstract

The preparation of samples and the choice of appropriate labeling techniques have become instrumental for the development of light microscopy techniques with increasingly high resolution. Both localization microscopy and STED approaches require fluorophores with specific features, including high photostability, specific excitation–emission spectra, and selective switching of single molecules to “on” and “off” state. Additionally, at higher resolutions the limits of conventional immunostaining often become apparent, as clearly exemplified by rather fragmented stainings of continuous cellular components such as microtubules and membranous organelles. Hence, the correct exploitation of fluorescent probes is of crucial importance for successful super-resolution imaging.

Here, the most prominent techniques related to super-resolution imaging are briefly explained, followed by a more detailed technical description of fluorophores and embedding media that are required for such imaging procedures. Some relevant aspects of troubleshooting the preparation of super-resolution samples are included to offer practical support for such experiment.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Watanabe S, Punge A, Hollopeter G et al (2011) Protein localization in electron micrographs using fluorescence nanoscopy. Nat Methods 8:80–84. doi:10.1038/nmeth.1537

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Betzig E, Patterson GH, Sougrat R et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645. doi:10.1126/science.1127344

    Article  CAS  PubMed  Google Scholar 

  3. Schermelleh L, Heintzmann R, Leonhardt H (2010) A guide to super-resolution fluorescence microscopy. J Cell Biol 190:165–175. doi:10.1083/jcb.201002018

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  5. Dyba M, Jakobs S, Hell SW (2003) Immunofluorescence stimulated emission depletion microscopy. Nat Biotechnol 21:1303–1304. doi:10.1038/nbt897

    Article  CAS  PubMed  Google Scholar 

  6. Hess ST, Girirajan TPK, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258–4272. doi:10.1529/biophysj.106.091116

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Fölling J, Bossi M, Bock H et al (2008) Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat Methods 5:943–945. doi:10.1038/nmeth.1257

    Article  PubMed  Google Scholar 

  8. Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–795. doi:10.1038/nmeth929

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  11. Swedlow JR (2003) Quantitative fluorescence microscopy and image deconvolution. Methods Cell Biol 72:349–367

    Article  PubMed  Google Scholar 

  12. Airy GB (1835) On the diffraction of an object-glass with circular aperture. Trans Camb Philos Soc 5:283–291

    Google Scholar 

  13. Born M, Wolf E, Bhatia AB (1999) Principles of optics: electromagnetic theory of propagation, interference and diffraction of light, seventh edition, ISBN: 978-0-521-64222-4 (Print), page 436–443, Cambridge University Press

    Google Scholar 

  14. Pawley JB (1995) Handbook of biological confocal microscopy, second edition, ISBN: 978-0-387-25921-5 (Print) 978-0-387-45524-2 (Online), page 128–129, Springer Science+Business Media, Inc.

    Google Scholar 

  15. Barish RD, Schulman R, Rothemund PWK, Winfree E (2009) An information-bearing seed for nucleating algorithmic self-assembly. Proc Natl Acad Sci U S A 106:6054–6059. doi:10.1073/pnas.0808736106

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Steinhauer C, Jungmann R, Sobey TL et al (2009) DNA origami as a nanoscopic ruler for super-resolution microscopy. Angew Chem Int Ed Engl 48:8870–8873. doi:10.1002/anie.200903308

    Article  CAS  PubMed  Google Scholar 

  17. Sparrow CM (1916) On spectroscopic resolving power. Astrophys J 44:76–86

    Article  Google Scholar 

  18. Dawes WR (1867) Catalogue of micrometrical measurements of double stars. Mon Not R Astron Soc 27:217–238

    Google Scholar 

  19. Barakat R (1965) Rayleigh wavefront criterion. J Opt Soc Am 55:572–573

    Article  Google Scholar 

  20. Ban N, Escobar C, Garcia R et al (1994) Crystal structure of an idiotype-anti-idiotype Fab complex. Proc Natl Acad Sci U S A 91:1604–1608

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Brown JK, Pemberton AD, Wright SH, Miller HRP (2004) Primary antibody-Fab fragment complexes: a flexible alternative to traditional direct and indirect immunolabeling techniques. J Histochem Cytochem 52:1219–1230. doi:10.1369/jhc.3A6200.2004

    Article  CAS  PubMed  Google Scholar 

  22. Ries J, Kaplan C, Platonova E et al (2012) A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat Methods 9:582–584. doi:10.1038/nmeth.1991

    Article  CAS  PubMed  Google Scholar 

  23. Westphal V, Rizzoli SO, Lauterbach MA et al (2008) Video-rate far-field optical nanoscopy dissects synaptic vesicle movement. Science 320:246–249. doi:10.1126/science.1154228

    Article  CAS  PubMed  Google Scholar 

  24. Rankin BR, Hell SW (2009) STED microscopy with a MHz pulsed stimulated-Raman-scattering source. Opt Express 17:15679–15684

    Article  CAS  PubMed  Google Scholar 

  25. Nägerl UV, Bonhoeffer T (2010) Imaging living synapses at the nanoscale by STED microscopy. J Neurosci 30:9341–9346. doi:10.1523/JNEUROSCI.0990-10.2010

    Article  PubMed  Google Scholar 

  26. Wheatley SP, Wang YL (1998) Indirect immunofluorescence microscopy in cultured cells. Methods Cell Biol 57:313–332

    Article  CAS  PubMed  Google Scholar 

  27. Dempsey GT, Vaughan JC, Chen KH et al (2011) Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 1–14. doi:10.1038/nmeth.1768

  28. Heilemann M, van de Linde S, Schüttpelz M et al (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed Engl 47:6172–6176. doi:10.1002/anie.200802376

    Article  CAS  PubMed  Google Scholar 

  29. Van De Linde S, Endesfelder U, Mukherjee A et al (2009) Multicolor photoswitching microscopy for subdiffraction-resolution fluorescence imaging. Photochem Photobiol Sci Off J Eur Photochem Assoc Eur Soc Photobiol 8:465–469

    Google Scholar 

  30. Johnson GD, Davidson RS, McNamee KC et al (1982) Fading of immunofluorescence during microscopy: a study of the phenomenon and its remedy. J Immunol Methods 55:231–242. doi:10.1016/0022-1759(82)90035-7

    Article  CAS  PubMed  Google Scholar 

  31. Ono M, Murakami T, Kudo A et al (2001) Quantitative comparison of anti-fading mounting media for confocal laser scanning microscopy. J Histochem Cytochem 49:305–312

    Article  CAS  PubMed  Google Scholar 

  32. Diaspro A, Federici F, Robello M (2002) Influence of refractive-index mismatch in high-resolution three-dimensional confocal microscopy. Appl Opt 41:685–690

    Article  PubMed  Google Scholar 

  33. 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 U S A 102:17565–17569. doi:10.1073/pnas.0506010102

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Hell SW, Kroug M (1995) Ground-state-depletion fluorscence microscopy: a concept for breaking the diffraction resolution limit. Appl Phys B Lasers Opt 60:495–497. doi:10.1007/BF01081333

    Article  Google Scholar 

  35. Heintzmann R, Jovin TM, Cremer C (2002) Saturated patterned excitation microscopy—a concept for optical resolution improvement. J Opt Soc Am A 19:1599. doi:10.1364/JOSAA.19.001599

    Article  Google Scholar 

  36. Andresen M, Stiel AC, Fölling J et al (2008) Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy. Nat Biotechnol 26:1035–1040. doi:10.1038/nbt.1493

    Article  CAS  PubMed  Google Scholar 

  37. Rittweger E, Rankin BR, Westphal V, Hell SW (2007) Fluorescence depletion mechanisms in super-resolving STED microscopy. Chem Phys Lett 442:483–487. doi:10.1016/j.cplett.2007.06.017

    Article  CAS  Google Scholar 

  38. Fitzpatrick JAJ, Yan Q, Sieber JJ et al (2009) STED nanoscopy in living cells using Fluorogen Activating Proteins. Bioconjug Chem 20:1843–1847. doi:10.1021/bc900249e

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  39. Han KY, Willig KI, Rittweger E et al (2009) Three-dimensional stimulated emission depletion microscopy of nitrogen-vacancy centers in diamond using continuous-wave light. Nano Lett 9:3323–3329. doi:10.1021/nl901597v

    Article  CAS  PubMed  Google Scholar 

  40. Moneron G, Medda R, Hein B et al (2010) Fast STED microscopy with continuous wave fiber lasers. Opt Express 18:1302. doi:10.1364/OE.18.001302

    Article  CAS  PubMed  Google Scholar 

  41. Willig KI, Harke B, Medda R, Hell SW (2007) STED microscopy with continuous wave beams. Nat Methods 4:915–918. doi:10.1038/nmeth1108

    Article  CAS  PubMed  Google Scholar 

  42. Donnert G, Keller J, Wurm CA et al (2007) Two-color far-field fluorescence nanoscopy. Biophys J 92:L67–L69. doi:10.1529/biophysj.107.104497

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Westphal V, Hell S (2005) Nanoscale resolution in the focal plane of an optical microscope. Phys Rev Lett. doi:10.1103/PhysRevLett.94.143903

    PubMed  Google Scholar 

  44. Vicidomini G, Moneron G, Han KY et al (2011) sharper low-power sted nanoscopy by time gating. Nat Methods 8:1–5. doi:10.1038/nMeth.1624

    Article  Google Scholar 

  45. Moffitt JR, Osseforth C, Michaelis J (2011) Time-gating improves the spatial resolution of STED microscopy. Opt Express 19:4242–4254

    Article  PubMed  Google Scholar 

  46. Dyba M, Hell S (2002) Focal spots of size λ/23 open up far-field florescence microscopy at 33 nm axial resolution. Phys Rev Lett. doi:10.1103/PhysRevLett.88.163901

    PubMed  Google Scholar 

  47. Kelsh RN, Brand M, Jiang YJ et al (1996) Zebrafish pigmentation mutations and the processes of neural crest development. Development 123:369–389

    CAS  PubMed  Google Scholar 

  48. Staudt T, Lang MC, Medda R et al (2007) 2, 2 0-Thiodiethanol: a new water soluble mounting medium for high resolution optical microscopy. Microsc Res Tech 9:1–9. doi:10.1002/jemt

    Article  Google Scholar 

  49. Huang B, Wang W, Bates M, Zhuang X (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–813. doi:10.1126/science.1153529

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  50. Thompson RE, Larson DR, Webb WW (2002) Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82:2775–2783. doi:10.1016/S0006-3495(02)75618-X

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  51. Vogelsang J, Cordes T, Forthmann C et al (2009) Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and superresolution microscopy. Proc Natl Acad Sci U S A 106:8107–8112. doi:10.1073/pnas.0811875106

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  52. Toomre D, Bewersdorf J (2010) A new wave of cellular imaging. Annu Rev Cell Dev Biol 26:285–314. doi:10.1146/annurev-cellbio-100109-104048

    Article  CAS  PubMed  Google Scholar 

  53. Testa I, Wurm C a, Medda R et al (2010) Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength. Biophys J 99:2686–2694. doi:10.1016/j.bpj.2010.08.012

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  54. Jones SA, Shim S-H, He J, Zhuang X (2011) Fast, three-dimensional super-resolution imaging of live cells. Nat Methods 8:499–508. doi:10.1038/nmeth.1605

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  55. Giannone G, Hosy E, Levet F et al (2010) Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys J 99:1303–1310. doi:10.1016/j.bpj.2010.06.005

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  56. Axelrod D (1981) Cell-substrate contacts illuminated by total internal reflection fluorescence. J Cell Biol 89:141–145

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Lampe, M., Fouquet, W. (2014). Requirements for Samples in Super-Resolution Fluorescence Microscopy. In: Fornasiero, E., Rizzoli, S. (eds) Super-Resolution Microscopy Techniques in the Neurosciences. Neuromethods, vol 86. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-983-3_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-983-3_14

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-982-6

  • Online ISBN: 978-1-62703-983-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics