Accuracy and precision in quantitative fluorescence microscopy
Open accessAbstract
The light microscope has long been used to document the localization of fluorescent molecules in cell biology research. With advances in digital cameras and the discovery and development of genetically encoded fluorophores, there has been a huge increase in the use of fluorescence microscopy to quantify spatial and temporal measurements of fluorescent molecules in biological specimens. Whether simply comparing the relative intensities of two fluorescent specimens, or using advanced techniques like Förster resonance energy transfer (FRET) or fluorescence recovery after photobleaching (FRAP), quantitation of fluorescence requires a thorough understanding of the limitations of and proper use of the different components of the imaging system. Here, I focus on the parameters of digital image acquisition that affect the accuracy and precision of quantitative fluorescence microscopy measurements.
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Multiple variables can influence the quantitation of fluorophores in fixed tissue samples, so the interpretation of MBP immunofluorescence as a marker of myelination must be considered cautiously.
“Lastly, we have used MBP immunofluorescence as a marker of myelination, however, multiple variables can influence the quantitation of fluorophores in fixed tissue samples (Straight, 2007; Waters, 2009) and this interpretation must be considered cautiously.”
From The role of myelination in measures of white matter integrity: Combination of diffusion tensor imaging and two-photon microscopy of CLARITY intact brains (2017) · cites this paper as Waters, 2009
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Cumming, G., Fidler, F., & Vaux, D. L. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200611141 · Cited by 940 · see citing works
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Research works printed but not linked: 74
- Adams M.C. Salmon W.C. Gupton S.L. Cohan C.S. Wittmann T. Prigozhina N. Waterman-Storer C.M. 2003 A high-speed multispectral spinning-disk confocal microscope system for fluorescent speckle microscopy of living cells. Methods. 29: 29– 41 12543069
- Allan V.J. 2000 Protein Localization by Fluorescence Microscopy: A Practical Approach. Oxford University, New York 256 pp
- Art J. 2006 Photon detectors for confocal microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 251– 262
- Aubin J.E. 1979 Autofluorescence of viable cultured mammalian cells. J. Histochem. Cytochem. 27: 36– 43 220325
- Axelrod D. Thompson N.L. Burghardt T.P. 1983 Total internal inflection fluorescent microscopy. J. Microsc. 129: 19– 28 6827590
- Bolte S. Cordelieres F.P. 2006 A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224: 213– 232 17210054
- Cardullo R.A. Hinchcliffe E.H. 2007 Digital manipulation of brightfield and fluorescence images: noise reduction, contrast enhancement, and feature extraction. Methods Cell Biol. 81: 285– 314 17519172
- Chen H. Puhl H.L. III Koushik S.V. Vogel S.S. Ikeda S.R. 2006 Measurement of FRET efficiency and ratio of donor to acceptor concentration in living cells. Biophys. J. 91: L39– L41 16815904 PMC1544280
- Churchman L.S. Okten Z. Rock R.S. Dawson J.F. Spudich J.A. 2005 Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc. Natl. Acad. Sci. USA. 102: 1419– 1423 15668396 PMC545495
- Day R.N. 2005 Imaging protein behavior inside the living cell. Mol. Cell. Endocrinol. 230: 1– 6 15664445
- De Mey J.R. Kessler P. Dompierre J. Cordelières F.P. Dieterlen A. Vonesch J.L. Sibarita J.B. Kevin F.S. 2008 Fast 4D microscopy. Methods Cell Biol. 85: 83– 112 18155460
- Diaspro A. Chirico G. Usai C. Ramoino P. Dobrucki J. 2006 Photobleaching. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 690– 699
- Dorn J.F. Jaqaman K. Rines D.R. Jelson G.S. Sorger P.K. Danuser G. 2005 Yeast kinetochore microtubule dynamics analyzed by high-resolution three-dimensional microscopy. Biophys. J. 89: 2835– 2854 16192284 PMC1366782
- Dorn J.F. Danuser G. Yang G. Kevin F.S. 2008 Computational processing and analysis of dynamic fluorescence image data. Methods Cell Biol. 85: 497– 538 18155477
- Egner A. Hell S.W. 2006 Aberrations in confocal and multi-photon fluorescence microscopy induced by refractive index mismatch. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 404– 412
- Giepmans B.N. Adams S.R. Ellisman M.H. Tsien R.Y. 2006 The fluorescent toolbox for assessing protein location and function. Science. 312: 217– 224 16614209
- Goodwin P.C. 2007 Evaluating optical aberration using fluorescent microspheres: methods, analysis, and corrective actions. Methods Cell Biol. 81: 397– 413 17519176
- Gordon G.W. Berry G. Liang X.H. Levine B. Herman B. 1998 Quantitative fluorescence resonance energy transfer measurements using fluorescence microscopy. Biophys. J. 74: 2702– 2713 9591694 PMC1299610
- Hell S.W. Stelzer E. 1995 Lens aberrations in confocal fluorescence microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 347– 353
- Hiraoka Y. Sedat J.W. Agard D.A. 1990 Determination of three-dimensional imaging properties of a light microscope system. Partial confocal behavior in epifluorescence microscopy. Biophys. J. 57: 325– 333 2317554 PMC1280673
- Hoffman D.B. Pearson C.G. Yen T.J. Howell B.J. Salmon E.D. 2001 Microtubule-dependent changes in assembly of microtubule motor proteins and mitotic spindle checkpoint proteins at PtK1 kinetochores. Mol. Biol. Cell. 12: 1995– 2009 11451998 PMC55648
- Huang B. Wang W. Bates M. Zhuang X. 2008 Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science. 319: 810– 813 18174397 PMC2633023
- Inoue S. 2006 Foundations of confocal scanned imaging in light microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 1– 19
- Inoué S. Spring K.R. 1997 Video Microscopy: The Fundamentals. Plenum Press, New York 770 pp
- Jares-Erijman E.A. Jovin T.M. 2003 FRET imaging. Nat. Biotechnol. 21: 1387– 1395 14595367
- Jares-Erijman E.A. Jovin T.M. 2006 Imaging molecular interactions in living cells by FRET microscopy. Curr. Opin. Chem. Biol. 10: 409– 416 16949332
- Joglekar A.P. Bouck D.C. Molk J.N. Bloom K.S. Salmon E.D. 2006 Molecular architecture of a kinetochore-microtubule attachment site. Nat. Cell Biol. 8: 581– 585 16715078 PMC2867088
- Joglekar A.P. Salmon E.D. Bloom K.S. Kevin F.S. 2008 Counting kinetochore protein numbers in budding yeast using genetically encoded fluorescent proteins. Methods Cell Biol. 85: 127– 151 18155462 PMC2892121
- Johnson I. 2006 Practical considerations in the selection and application of fluorescent probes. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 353– 364
- Keller H.E. 2006 Objective lenses for confocal microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 145– 160
- Manley S. Gillette J.M. Patterson G.H. Shroff H. Hess H.F. Betzig E. Lippincott-Schwartz J. 2008 High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods. 5: 155– 157 18193054
- Mason D.W. Williams A.F. 1980 The kinetics of antibody binding to membrane antigens in solution and at the cell surface. Biochem. J. 187: 1– 20 6967725 PMC1162489
- Melan M.A. Sluder G. 1992 Redistribution and differential extraction of soluble proteins in permeabilized cultured cells. Implications for immunofluorescence microscopy. J. Cell Sci. 101: 731– 743 1527176
- Moomaw B. 2007 Camera technologies for low light imaging: overview and relative advantages. Methods Cell Biol. 81: 251– 283 17519171
- Moore J. Allan C. Burel J. Loranger B. MacDonald D. Monk J. Swedlow J.R. Kevin F.S. 2008 Open tools for storage and management of quantitative image data. Methods Cell Biol. 85: 555– 570 18155479
- Mortensen K. Larsson L.I. 2001 Quantitative and qualitative immunofluorescence studies of neoplastic cells transfected with a construct encoding p53-EGFP. J. Histochem. Cytochem. 49: 1363– 1367 11668189
- Murray J.M. 1998 Evaluating the performance of fluorescence microscopes. J. Microsc. 191: 128– 134 9767475
- Murray J.M. Appleton P.L. Swedlow J.R. Waters J.C. 2007 Evaluating performance in three-dimensional fluorescence microscopy. J. Microsc. 228: 390– 405 18045334 PMC2438600
- Nolte A. Pawley J. Horing L. 2006 Non-laser light sources for three-dimentional microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 126– 144
- North A.J. 2006 Seeing is believing? A beginners' guide to practical pitfalls in image acquisition. J. Cell Biol. 172: 9– 18 16390995 PMC2063524
- Patterson G.H. Piston D.W. 2000 Photobleaching in two-photon excitation microscopy. Biophys. J. 78: 2159– 2162 10733993 PMC1300807
- Pawley J. 2000 The 39 steps: a cautionary tale of quantitative 3-D fluorescence microscopy. Biotechniques. 28: 884– 886, 888 10818693
- Pawley J.B. 1994 Sources of noise in 3D microscopical data sets. Three-Dimensional Confocal Microscopy: Volume Investigation of Biological Systems. Stevens J.K. Mills L.R. Trogadis J.E., Academic Press, Inc., San Diego 48– 90
- Pawley J.B. 2006a Fundamental limits in confocal microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 20– 42
- Pawley J.B. 2006b Handbook of Biological Confocal Microscopy. Springer-Verlag New York, Inc., New York 985 pp
- Pawley J.B. 2006c Points, pixels, and gray levels: digitizing image data. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 59– 79
- Periasamy A. Day R.N. 2005 Molecular Imaging: FRET Microscopy and Spectroscopy. Oxford University Press 336 pp
- Ploem J.S. 1999 Fluorescence microscopy. Fluorescent and Luminescent Probes for Biological Activity. Mason W.T., editor Academic Press, London 3– 13
- Rabut G. Ellenberg J. 2005 Photobleaching techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, iFRAP, and FLIP. Live Cell Imaging: A Laboratory Manual. Goldman R.D. Spector D.L., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 101– 126 21123431
- Rasnik I. French T. Jacobson K. Berland K. 2007 Electronic cameras for low-light microscopy. Methods Cell Biol. 81: 219– 249 17519170
- Rietdorf J. Stelzer E.H.K. 2006 Special optical elements. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 43– 58
- Robbins M.S. Hadwen B.J. 2003 The noise performance of electron multiplying charge-coupled devices. IEEE Trans. Electron. Dev. 50: 1227– 1232
- Rocheleau J.V. Piston D.W. 2003 Two-photon excitation microscopy for the study of living cells and tissues. Curr. Protoc. Cell Biol. Chapter 4: Unit 4.11 18228433
- Salmon E.D. Canman J.C. 2001 Proper alignment and adjustment of the light microscope. Curr. Protoc. Cell Biol. Chapter 4: Unit 4.1 18228362
- Schaufele F. Demarco I. Day R.N. 2005 FRET imaging in the widefield microscope. Molecular Imaging: FRET Microscopy and Spectroscopy. Periasamy A. Day R.N., Oxford University Press 72– 94
- Sekar R.B. Periasamy A. 2003 Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations. J. Cell Biol. 160: 629– 633 12615908 PMC2173363
- Shaner N.C. Steinbach P.A. Tsien R.Y. 2005 A guide to choosing fluorescent proteins. Nat. Methods. 2: 905– 909 16299475
- Siegel R.M. Chan F.K. Zacharias D.A. Swofford R. Holmes K.L. Tsien R.Y. Lenardo M.J. 2000 Measurement of molecular interactions in living cells by fluorescence resonance energy transfer between variants of the green fluorescent protein. Sci. STKE. 2000: PL1 11752595
- Snapp E.L. Altan N. Lippincott-Schwartz J. 2003 Measuring protein mobility by photobleaching GFP chimeras in living cells. Curr. Protoc. Cell Biol. Chapter 21: Unit 21.1 18228432
- Sprague B.L. McNally J.G. 2005 FRAP analysis of binding: proper and fitting. Trends Cell Biol. 15: 84– 91 15695095
- Spring K.R. 2007 Cameras for digital microscopy. Methods Cell Biol. 81: 171– 186 17519168
- Straight A.F. 2007 Fluorescence protein applications in microscopy. Methods Cell Biol. 81: 93– 113 17519164
- Stryer L. 1978 Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47: 819– 846 354506
- Swedlow J.R. Hu K. Andrews P.D. Roos D.S. Murray J.M. 2002 Measuring tubulin content in Toxoplasma gondii: a comparison of laser-scanning confocal and wide-field fluorescence microscopy. Proc. Natl. Acad. Sci. USA. 99: 2014– 2019 11830634 PMC122311
- Tommre D. Pawley J.B. 2006 Disk-scanning confocal microscopy. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 221– 237
- Tsien R.Y. Ernst L. Waggoner A. 2006 Fluorophores for confocal microscopy: photophysics and photochemistry. Handbook of Biological Confocal Microscopy. Pawley J.B., editor Springer-Verlag New York, Inc., New York 338– 348
- Vogel S.S. Thaler C. Koushik S.V. 2006 Fanciful FRET. Sci. STKE. 2006: re2 16622184
- Wallace W. Schaefer L.H. Swedlow J.R. 2001 A workingperson's guide to deconvolution in light microscopy. Biotechniques. 31: 1076– 1097 11730015
- Waters J.C. 2007 Live-cell fluorescence imaging. Methods Cell Biol. 81: 115– 140 17519165
- Waters J.C. Swedlow J.R. 2007 Interpreting fluorescence microscopy images and measurements. Evaluating Techniques in Biochemical Research. Zuk D., editor Cell Press, Cambridge, MA 37– 42
- Wolf D.E. Samarasekera C. Swedlow J.R. 2007 Quantitative analysis of digital microscope images. Methods Cell Biol. 81: 365– 396 17519175
- Wu J.Q. Pollard T.D. 2005 Counting cytokinesis proteins globally and locally in fission yeast. Science. 310: 310– 314 16224022
- Yildiz A. Selvin P.R. 2005 Fluorescence imaging with one nanometer accuracy: application to molecular motors. Acc. Chem. Res. 38: 574– 582 16028892
- Zwier J.M. Van Rooij G.J. Hofstraat J.W. Brakenhoff G.J. 2004 Image calibration in fluorescence microscopy. J. Microsc. 216: 15– 24 15369479
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- Authors
- Waters, J. C.
- Affiliations
- Harvard University (US)
- Corresponding author
- Waters, Jennifer C.
- ORCID
- Waters, Jennifer C.
- Venue
- Journal of Cell Biology
- Publisher
- Rockefeller University Press
- Published
- 2009-06-29
- Volume
- 185
- Issue
- 7
- Pages
- 1135-1148
- ISSN
- 0021-9525 (ISSN-L)
- 1540-8140
- PMC
- PMC2712964
- OpenAlex
- W2141201649
- Cited by
- 613
- References
- 1
- Citations by year
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- FWCI
- 9.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-sa
- Locations
- The Journal of Cell Biology (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Physical Sciences › Engineering › Electrical and Electronic Engineering › Advanced Measurement and Detection Methods
- Keywords
- quantitative fluorescence microscopy, measurement accuracy, measurement precision, digital image acquisition, image acquisition parameters, fluorescence intensity measurement
- MeSH terms
- Fluorescent Dyes, Image Interpretation, Computer-Assisted, Light, Microscopy, Fluorescence, Sensitivity and Specificity
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