Abstract
Although fluorescence microscopy permeates all of cell and molecular biology, most biologists have little experience with the underlying photophysical phenomena. Understanding the principles underlying fluorescence microscopy is useful when attempting to solve imaging problems. Additionally, fluorescence microscopy is in a state of rapid evolution, with new techniques, probes and equipment appearing almost daily. Familiarity with fluorescence is a prerequisite for taking advantage of many of these developments. This review attempts to provide a framework for understanding excitation of and emission by fluorophores, the way fluorescence microscopes work, and some of the ways fluorescence can be optimized.
Access options
Subscribe to Journal
Get full journal access for 1 year
$259.00
only $21.58 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
from$8.99
All prices are NET prices.



References
- 1
Tsien, R.Y. The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544 (1998).
- 2
Valeur, B. Molecular Fluorescence: Principles and Applications. (Wiley-VCH, Weinheim, 2002).
- 3
Lakowicz, J.R., ed. Principles of Fluorescence Spectroscopy. 2nd ed. (Plenum Press, New York, 1999).
- 4
Turro, N.J. Modern Molecular Photochemistry. (University Science Books, Sausalito, California, 1991).
- 5
Irvine, D.J., Purbhoo, M.A., Krogsgaard, M. & Davis, M.M. Direct observation of ligand recognition by T cells. Nature 419, 845–849 (2002).
- 6
Wang, L., Jackson, W.C., Steinbach, P.A. & Tsien, R.Y. Evolution of new nonantibody proteins via iterative somatic hypermutation. Proc. Natl. Acad. Sci. USA 101, 16745–16749 (2004).
- 7
Deerinck, T.J. et al. Fluorescence photooxidation with eosin: a method for high resolution immunolocalization and in situ hybridization detection for light and electron microscopy. J. Cell Biol. 126, 901–910 (1994).
- 8
Suhling, K., French, P.M. & Phillips, D. Time-resolved fluorescence microscopy. Photochem. Photobiol. Sci. 4, 13–22 (2005).
- 9
Elson, D. et al. Time-domain fluorescence lifetime imaging applied to biological tissue. Photochem. Photobiol. Sci. 3, 795–801 (2004).
- 10
Jares-Erijman, E.A. & Jovin, T.M. FRET imaging. Nat. Biotechnol. 21, 1387–1395 (2003).
- 11
Mizuno, H. et al. Photo-induced peptide cleavage in the green-to-red conversion of a fluorescent protein. Mol. Cell 12, 1051–1058 (2003).
- 12
Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H. & Miyawaki, A. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl. Acad. Sci. USA 99, 12651–12656 (2002).
- 13
Mason, W.T., ed. Fluorescent and Luminescent Probes for Biological Activity: A Practical Guide for Quantitative Real-Time Analysis. (Academic Press Harcourt Brace and Co., Boston, 1993).
- 14
Periasamy, A., ed. Methods in Cellular Imaging (Oxford University Press, Oxford, 2001).
- 15
Rudolf, R., Mongillo, M., Rizzuto, R. & Pozzan, T. Looking forward to seeing calcium. Nat. Rev. Mol. Cell Biol. 4, 579–586 (2003).
- 16
Tsien, R.Y. Fluorescent indicators of ion concentrations. Methods Cell Biol. 30, 127–156 (1989).
- 17
Bassnett, S., Reinisch, L. & Beebe, D.C. Intracellular pH measurement using single excitation-dual emission fluorescence ratios. Am. J. Physiol. 258, 171–178 (1990).
- 18
Yuste, R. & Konnerth, A., eds. Imaging in Neuroscience and Development: A Laboratory Manual. (Cold Spring Harbor Laboratory Press, New York, 2005).
- 19
Zhang, J., Campbell, R.E., Ting, A.Y. & Tsien, R.Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906–918 (2002).
- 20
Griesbeck, O. Fluorescent proteins as sensors for cellular functions. Curr. Opin. Neurobiol. 14, 636–641 (2004).
- 21
Ohmichi, T. et al. DNA-based biosensor for monitoring pH in vitro and in living cells. Biochemistry 44, 7125–7130 (2005).
- 22
Grinvald, A. & Hildesheim, R. VSDI: a new era in functional imaging of cortical dynamics. Nat. Rev. Neurosci. 5, 874–885 (2004).
- 23
Kuhn, B., Fromherz, P. & Denk, W. High sensitivity of Stark-shift voltage-sensing dyes by one- or two-photon excitation near the red spectral edge. Biophys. J. 87, 631–639 (2004).
- 24
Reiff, D.F. et al. In vivo performance of genetically encoded indicators of neural activity in flies. J. Neurosci. 25, 4766–4778 (2005).
- 25
Goldman, R.D. & Spector, D.L., eds. Live Cell Imaging: A Laboratory Manual. (Cold Spring Harbor Laboratory Press, New York, 2004).
- 26
Inoué, S. & Spring, K.R. Video Microscopy. 2nd edn. (Plenum Publishing, New York, 1997).
- 27
Abramowitz, M., Spring, K.R., Keller, H.E. & Davidson, M.W. Basic principles of microscope objectives. Biotechniques 33, 772–781 (2002).
- 28
Panchuk-Voloshina, N. et al. Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright photostable conjugates. J. Histochem. Cytochem. 47, 1179–1188 (1999).
- 29
Ono, M. et al. Quantitative comparison of anti-fading mounting media for confocal laser scanning microscopy. J. Histochem. Cytochem. 49, 305–331 (2001).
- 30
Johnson, G.D. & Nogueira Araujo, G.M. A simple method of reducing the fading of immunofluorescence during microscopy. J. Immunol. Methods 43, 349–350 (1981).
- 31
Johnson, G.D. et al. Fading of immunofluorescence during microscopy: a study of the phenomenon and its remdedy. J. Immunol. Methods 55, 231–242 (1982).
- 32
Giloh, H. & Sedat, J.W. Fluorescence microscopy: reduced photobleaching of rhodamine and fluorescein protein conjugates by n-propyl gallate. Science 217, 1252–1255 (1982).
- 33
Alivisatos, A.P., Gu, W. & Larabell, C. Quantum dots as cellular probes. Annu. Rev. Biomed. Eng. 7, 55–76 (2005).
- 34
van Gijlswijk, R.P. et al. Fluorochrome-labeled tyramides: use in immunocytochemistry and fluorescence in situ hybridization. J. Histochem. Cytochem. 45, 375–382 (1997).
- 35
Cullander, C. Imaging in the far-red with electronic light microscopy: requirements and limitations. J. Microsc. 176, 281–286 (1994).
Author information
Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Rights and permissions
About this article
Cite this article
Lichtman, J., Conchello, JA. Fluorescence microscopy. Nat Methods 2, 910–919 (2005). https://doi.org/10.1038/nmeth817
Published:
Issue Date:
Further reading
-
Brief descriptions of the principles of prominent methods used to study the penetration of materials into human hair and a review of examples of their use
International Journal of Cosmetic Science (2021)
-
Trypsiligase‐Catalyzed Labeling of Proteins on Living Cells
ChemBioChem (2021)
-
Nanoprobes with aggregation-induced emission for theranostics
Materials Chemistry Frontiers (2021)
-
A short review: Comparisons of high-throughput phenotyping methods for detecting drought tolerance
Scientia Agricola (2021)
-
Entanglement Enabled Intensity Interferometry of different wavelengths of light
Annals of Physics (2021)