Skip to main content

Laser Scanning Confocal Microscopy: History, Applications, and Related Optical Sectioning Techniques

  • Protocol
  • First Online:
Confocal Microscopy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1075))

Abstract

Confocal microscopy is an established light microscopical technique for imaging fluorescently labeled specimens with significant three-dimensional structure. Applications of confocal microscopy in the biomedical sciences include the imaging of the spatial distribution of macromolecules in either fixed or living cells, the automated collection of 3D data, the imaging of multiple labeled specimens and the measurement of physiological events in living cells. The laser scanning confocal microscope continues to be chosen for most routine work although a number of instruments have been developed for more specific applications. Significant improvements have been made to all areas of the confocal approach, not only to the instruments themselves, but also to the protocols of specimen preparation, to the analysis, the display, the reproduction, sharing and management of confocal images using bioinformatics techniques.

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 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
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. Conchello JA, Lichtman JW (2005) Optical sectioning microscopy. Nat Methods 2:920–931

    Article  CAS  PubMed  Google Scholar 

  2. Paddock SW (1999) Protocols in Confocal Microscopy. Methods Mol Biol 122. Humana Press, Totowa, NJ

    Google Scholar 

  3. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC (1994) Green fluorescent protein as a marker for gene expression. Science 263:802–805

    Article  CAS  PubMed  Google Scholar 

  4. Fraser SE (2003) Crystal gazing in optical microscopy. Nat Biotechnol 21:1272–1273

    Article  CAS  PubMed  Google Scholar 

  5. Walter T et al (2010) Visualization of image data from cells to organisms. Nat Methods 7:S26–S41

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Hibbs AR (2004) Confocal microscopy for biologists. Springer, New York

    Book  Google Scholar 

  7. Price R, Jerome WG (2011) Basic confocal microscopy. Springer, New York

    Book  Google Scholar 

  8. Minsky M (1988) Memoir on inventing the confocal scanning microscope. Scanning 10:128–138

    Article  Google Scholar 

  9. Minsky M (1957) Microscopy apparatus U.S. Patent no. 3013467

    Google Scholar 

  10. Brakenhoff GJ, van der Voort HTM, van Spronsen EA, Linnemans WAM, Nanninga N (1985) Three-dimensional chromatin distribution in neuroblastoma nuclei shown by confocal laser scanning laser microscopy. Nature 317:748–749

    Article  CAS  PubMed  Google Scholar 

  11. Pawley JB (2006) Handbook of Biological Confocal Microscopy, 3rd edn. Plenum Press, New York

    Book  Google Scholar 

  12. Amos WB, White JG (2003) How the confocal laser scanning microscope entered biological research. Biol Cell 95:335–342

    Article  CAS  PubMed  Google Scholar 

  13. White JG, Amos WB (1987) Confocal microscopy comes of age. Nature 328:183–184

    Article  Google Scholar 

  14. White JG, Amos WB, Durbin R, Fordham M (1990) Development of a confocal imaging system for biological epifluorescence application in "Optical Microscopy For Biology". Wiley-Liss Inc, New York, NY, pp 1–18

    Google Scholar 

  15. White JG, Amos WB, Fordham M (1987) An evaluation of confocal versus conventional imaging of biological structures by fluorescence light microscopy. J Cell Biol 1987(105):41–48

    Article  Google Scholar 

  16. Wilson T (1995) The role of the pinhole in confocal imaging system. Plenum Press, New York, pp 167–182

    Google Scholar 

  17. Paddock SW (2002) Confocal imaging of Drosophila embryos. In: Matsumoto B (ed) Cell biological applications of confocal microscopy, 2nd edn. Methods Cell Biol 70:355–372

    Google Scholar 

  18. Kosman D, Mizutani CM, Lemons D, Cox WG, McGinnis W, Bier E (2004) Multiplex detection of RNA expression in Drosophila embryos. Science 305:846

    Article  CAS  PubMed  Google Scholar 

  19. Brelje TC, Wessendorf MW, Sorenson RL (1993) Multicolor laser scanning confocal immunofluorescence microscopy: practical applications and limitations. Methods Cell Biol 38:98–177

    Google Scholar 

  20. Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW (2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450:56–62

    Article  CAS  PubMed  Google Scholar 

  21. Murray JM, Appleton PL, Swedlow JR, Waters JC (2007) Evaluating performance in three-dimensional fluorescence microscopy. J Microsc 228:390–405

    Article  PubMed Central  PubMed  Google Scholar 

  22. Van Roessel P, Brand A (2002) Imaging into the future: visualizing gene expression and protein interactions with fluorescent proteins. Nat Cell Biol 4:E15–E20

    Article  PubMed  Google Scholar 

  23. Paddock SW (2001) A brief history of time-lapse. Biotechniques 30:283–289

    CAS  PubMed  Google Scholar 

  24. Pawley JB (2000) The 39 steps: a cautionary tale of quantitative 3-D fluorescence microscopy. Biotechniques 28:884–887

    CAS  PubMed  Google Scholar 

  25. Heim R, Tsien RY (1996) Engineering green fluorescent protein for improved brightness, longer wavelength and fluorescence energy transfer. Curr Biol 6:178–182

    Article  CAS  PubMed  Google Scholar 

  26. Shaner NC, Patterson GH, Davidson MW (2007) Advances in fluorescent protein technology. J Cell Sci 120:4247–4260

    Article  CAS  PubMed  Google Scholar 

  27. Tsien RY (1998) The green fluorescent protein. Annu Rev Biochem 67:509–544

    Article  CAS  PubMed  Google Scholar 

  28. Giepmans BNG, Adams SR, Ellisman MH, Tsien RY (2006) The fluorescent toolbox for assessing protein location and function. Science 312:217–224

    Article  CAS  PubMed  Google Scholar 

  29. Fiala A, Suska A, Schulter OM (2010) Optogenetic approaches in neuroscience. Curr Biol 20:R897–R903

    Article  CAS  PubMed  Google Scholar 

  30. Mohler WA, White JG (1998) Stereo-4-D reconstruction and animation from living fluorescent specimens. Biotechniques 24:1006–1012

    CAS  PubMed  Google Scholar 

  31. Provenzano PP, Eliceiri KW, Keely PJ (2009) Shining new light on 3D cell motility and the metastatic process. Trends Cell Biol 19:638–48

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Paddock SW (2002) Confocal reflection microscopy; the “other” confocal mode. Biotechniques 32:274–278

    CAS  PubMed  Google Scholar 

  33. Paddock SW, Mahoney S, Minshall M, Smith LC, Duvic M, Lewis D (1991) Improved detection of in situ hybridisation by laser scanning confocal microscopy. Biotechniques 11:486–494

    CAS  PubMed  Google Scholar 

  34. Gaietta G, Deerinck TJ, Adams SR, Bouwer J, Tour O, Laird DW, Sosinsky GE, Tsien RY, Ellisman MH (2002) Multicolor and electron microscopic imaging of connexin trafficking. Science 296:503–507

    Article  CAS  PubMed  Google Scholar 

  35. Deerinck TJ, Martone ME, Lev-Ram V, Green DPL, Tsien RY, Spector DL, Huang S, Ellisman MH (1994) Fluorescence photooxidation with eosin: a method for high-resolution immunolocalisation and in situ hybridisation detection for light and electron microscopy. J Cell Biol 126:901–910

    Article  CAS  PubMed  Google Scholar 

  36. Piston DW, Kremers GJ (2007) Fluorescent protein FRET: the good, the bad and the ugly. Trends Biochem Sci 32:407–414

    Article  CAS  PubMed  Google Scholar 

  37. Pietraszewska-Bogiel A, Gadella TWJ (2010) FRET microscopy: from principle to routine technology in cell biology. J Microsc 240:111–118

    Article  Google Scholar 

  38. Bastiaens PI, Squire A (1999) Fluorescence lifetime imaging microscopy: spatial resolution of biochemical processes in the cell. Trends Cell Biol 9:48–52

    Article  CAS  PubMed  Google Scholar 

  39. Borst JW, Visser AJWG (2010) Fluorescence lifetime imaging microscopy in life sciences. Meas Sci Technol 21:1–21

    Article  Google Scholar 

  40. Conklin MW, Provenzano PP, Eliceiri KW, Sullivan R, Keely PJ (2009) Fluorescence lifetime imaging of endogenous fluorophores in histopathology sections reveals differences between normal and tumor epithelium in carcinoma in situ of the breast. Cell Biochem Biophys 53:145–57

    Article  CAS  PubMed  Google Scholar 

  41. van Royen ME, Dinant C, Farla P, Trapman J, Houtsmuller AB (2009) FRAP and FRET methods to study nuclear receptors in living cells. Methods Mol Biol 505:69–96

    Article  PubMed  Google Scholar 

  42. Lippincott-Schwartz J, Altan-Bonnet N, Patterson GH (2003) Photobleaching and photoactivation: following protein dynamics in living cells. Nat Cell Biol 2003:S7–14

    Google Scholar 

  43. Weigel A, Schild D, Zeug A (2009) Resolution in the ApoTome and the confocal laser scanning microscope: comparison. J BioMed Opt 14. Online article #014023

    Google Scholar 

  44. Wallace W, Schaefer LH, Swedlow JR (2001) A workingperson's guide to deconvolution in light microscopy. Biotechniques 5:1076–1080

    Google Scholar 

  45. Svoboda K, Yasuda R (2006) Principles of two-photon excitation microscopy and its applications to neuroscience. Neuron 50:823–839

    Article  CAS  PubMed  Google Scholar 

  46. Zipfel WR, Williams RM, Webb W (2002) Nonlinear magic: multiphoton microscopy in the biosciences. Nat Biotechnol 21:1369–1377

    Article  Google Scholar 

  47. Helmchen F, Denk W (2005) Deep tissue two-photon microscopy. Nat Methods 2:932–919

    Article  CAS  PubMed  Google Scholar 

  48. Campagnola PJ, Loew LM (2003) Second-harmonic imaging microscopy for visualizing biomolecular arrays in cells, tissues and organisms. Nat Biotechnol 21:1356–1360

    Article  CAS  PubMed  Google Scholar 

  49. Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK (2008) Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322:1065–1069

    Article  CAS  PubMed  Google Scholar 

  50. Keller PJ, Schimdt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EHK (2010) Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat Methods 7:637–642

    Article  CAS  PubMed  Google Scholar 

  51. Axelrod D (2003) Total internal reflection fluorescence microscopy in cell biology. Methods Enzymol 361:1–33

    CAS  PubMed  Google Scholar 

  52. Schermelleh L, Heintzmann R, Leonhardt H (2010) A guide to super-resolution fluorescence microscopy. J Cell Biol 190:165–175

    Article  CAS  PubMed  Google Scholar 

  53. Sharpe A, Ahlgren U, Perry P, Hill B, Ross a, Hecksher-Sorensen J, Baldock R, Davidson D (2002) Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 296:541–545

    Article  CAS  PubMed  Google Scholar 

  54. St. Croix C, Zipfel WR, Watkins SC (2007) Potential solutions for confocal imaging of living animals. Biotechniques 43:14–19

    Article  Google Scholar 

  55. Paddock SW (2001) Channel surfing: creating different colour combinations from multi-label images. Biotechniques 30:756–761

    CAS  PubMed  Google Scholar 

  56. Waters JC, Swedlow JR (2007) Interpreting fluorescence microscopy images and measurements. Cell Online 37–42

    Google Scholar 

  57. Swedlow JR, Lewis SE, Goldberg IG (2006) Modelling data across labs, genomes, space and time. Nat Cell Biol 8:1190–1194

    Article  CAS  PubMed  Google Scholar 

  58. Swedlow JR, Goldberg I, Brauner E, Sorger PK (2003) Informatics and quantitative analysis in biological imaging. Science 300:100–102

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  59. Peng H (2008) Bioimage informatics: a new era of engineering biology. Bioinformatics 24:1827–1836

    Article  CAS  PubMed  Google Scholar 

  60. Swedlow J.R., Goldberg I.G., Eliceiri K.W., and the OME Consortium (2009) Bioimage informatics for experimental biology. Annu Rev Biophys 38:327–346

    Article  Google Scholar 

  61. Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, Macdonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri KW, Swedlow JR (2010) Metadata matters: access to image data in the real world. J Cell Biol 189:777–782

    Article  CAS  PubMed  Google Scholar 

  62. Conn PM (2010) Techniques in confocal microscopy (reliable Lab solutions). Academic, New York

    Google Scholar 

  63. Goldman RD, Spector DL, Swedlow JR (2009) Live cell imaging: a laboratory manual. Cold Spring Harbor Press, New York

    Google Scholar 

  64. Murphy DB, Davidson MW (2012) Fundamentals of light microscopy and electronic imaging. Wiley-Blackwell, Hoboken, NJ

    Google Scholar 

  65. Fischer RS, Wu Y, Kanchanawong P, Shroff H, Waterman CM (2011) Microscopy in 3D: a biologist’s toolbox. Trends Cell Biol 21:682–691

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  66. Swedlow JR (2012) Innovation in biological microscopy: current status and future directions. Bioessays 34:333–340

    Article  PubMed Central  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 New York

About this protocol

Cite this protocol

Paddock, S.W., Eliceiri, K.W. (2014). Laser Scanning Confocal Microscopy: History, Applications, and Related Optical Sectioning Techniques. In: Paddock, S. (eds) Confocal Microscopy. Methods in Molecular Biology, vol 1075. Humana Press, New York, NY. https://doi.org/10.1007/978-1-60761-847-8_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-847-8_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-58829-351-0

  • Online ISBN: 978-1-60761-847-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics