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Light Microscopy

How to get it right

  • Cromey, D.W., 2010. Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images
    Science and Engineering Ethics 16, pp. 639–667 source
  • Pearson, Helen, 2007: The good, the bad and the ugly
    Nature 447, 138-140 (10 May 2007) source
  • Brown, C.M., 2007: Fluorescence microscopy - avoiding the pitfalls
    J Cell Sci 120, 1703-1705 source
  • Eisenstein, Michael, 2006: Something to see
    Nature 443, 1017-1021 (26 October 2006) source
  • Pawley, Jim, 2000: The 39 Steps: A Cautionary Tale about “quantatative” 3D Fluorescence Microscopy
    BioTechniques 28-5:2-4 source

Fluorescent Proteins

  • Shcherbakova, D.M. et. al., 2013 Near-infrared fluorescent proteins for multicolor in vivo imaging
    Nature Methods 10, 751–754 source
  • Shcherbakova, D.M. et. al., 2012 Red fluorescent proteins: advanced imaging applications and future design
    Angew Chem Int Ed Engl. 51(43):10724-38 source
  • Wu, B. et. al., 2011 Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics
    Curr Opin Cell Biol. 23(3): 310–317 source
  • Goedhart, J. et. al., 2010 Bright cyan fluorescent protein variants identified by fluorescence lifetime screening
    Nature Methods 7(2):137-9 source
  • Shcherbo, D. et. al., 2009 Far-red fluorescent tags for protein imaging in living tissues.
    Biochem J. 418(3):567-74 source
  • Nienhaus, G.U. et. al., 2008: Optimized and Far-Red-Emitting Variants of Fluorescent Protein eqFP611.
    Chem Biol. 15(3):224-33. source
  • Shaner, N.C. et. al., 2007: Advances in fluorescent protein technology
    J Cell Sci 120, 4247-4260. source
  • Koushik, Srinagesh V. et. al. , 2006: Cerulean, Venus, and VenusY67C FRET Reference Standards
    Biophys J. 91(12): L99–L101. source
  • Eisenstein, Michael, 2006: Helping cells to tell a colorful tale
    Nature Methods 3, 647 - 655 source


  • Becker, W., 2012: Fluorescence lifetime imaging – techniques and applications
    J Microsc. 247(2):119-36 source
  • Weber, M., 2011: Light sheet microscopy for real-time developmental biology
    Curr Opin Genet Dev. 21(5):566-72 source
  • Truong, T.V. et. al., 2011: Deep and fast live imaging with two-photon scanned light-sheet microscopy
    Nature Methods 8, 757–760 source
  • Min, W. et. al., 2011: Coherent nonlinear optical imaging: beyond fluorescence microscopy
    Annu Rev Phys Chem. 62:507-30 source
  • Hell, S.W., 2009: Microscopy and its focal switch
    Nature Methods 6, 24 - 32 source
  • Evans, C.L., et. al. 2008: Coherent Anti-Stokes Raman Scattering Microscopy: Chemical Imaging for Biology and Medicine
    Annu Rev Anal Chem 1:883-909 source
  • Mazza, D. et. al., 2008:A New FRAP/FRAPa Method For 3-D Diffusion Measurements Based On Multi-photon Excitation Microscopy
    Biophys J. 95(7):3457-69 source
  • Göbel, Werner et. al., 2007: Imaging cellular network dynamics in three dimensions using fast 3D laser scanning
    Nature Methods - 4, 73 - 79 (2007) source
  • Edward J. Botcherby, Rimas Juskaitis, Martin J. Booth, Tony Wilson, 2007: Aberration-free optical refocusing in high numerical aperture microscopy.
    Opt Lett. 32(14):2007-9 source
  • Donnert, Gerald et al., 2006, Major signal increase in fluorescence microscopy through dark-state relaxation
    Nature Methods 4 (01), 81-86
  • Frohn, J. T. et. al., 2001: Three-dimensional resolution enhancement in fluorescence microscopy by harmonic excitation
    Optics Letters 26 (11), 828-830 source

Technical Tests

  • Cole, R.W. et. al., 2011: Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control
    Nat Protoc. 6(12):1929-41 source
  • Murray, John M. et. al., 2007: Evaluating performance in three-dimensional fluorescence microscopy
    Journal of Microscopy Volume 228 Issue 3 Page 390-405, December 2007 source
  • Zucker, Robert M., 2006: Quality Assessment of Confocal Microscopy Slide Based Systems: Performance
    Cytometry Part A 69A:659–676 (2006) source
  • Zucker, Robert M., 2006: Quality Assessment of Confocal Microscopy Slide-Based Systems: Instability
    Cytometry Part A 69A:677–690 (2006) source
  • Zucker, Robert M., 2007: Reliability of confocal microscopy spectral imaging systems: Use of multispectral beads.
    Cytometry A. 2007 Jan 31 source
  • Zucker, Robert M., 2001: Evaluation of confocal microscopy system performance.
    Cytometry 44(4):273-94 source

Image Processing and Analysis


  • Mitchel, J.A., Martin, I.S., Hoffman-Kim, D., 2013. Neurient: An algorithm for automatic tracing of confluent neuronal images to determine alignment
    Journal of Neuroscience Methods 214, pp. 210–222 source
  • Meijering, E., Dzyubachyk, O., Smal, I., 2012. Methods for Cell and Particle Tracking,
    in: Methods in Enzymology. Elsevier, pp. 183–200 source
  • Dima, A.A. et. al., 2011. Comparison of segmentation algorithms for fluorescence microscopy images of cells
    Cytometry Part A 79, pp. 545–559 source
  • Padmanabhan, K. et. al., 2010: A novel algorithm for optimal image thresholding of biological data
    Journal of Neuroscience Methods, 193:2, pp. 380-384 source


  • Dunn, K.W., Kamocka, M.M., McDonald, J.H., 2011. A practical guide to evaluating colocalization in biological microscopy
    American Journal of Physiology-Cell Physiology 300, C723–C742 source
  • Bolte, S. et. al., 2006: A guided tour into subcellular colocalization analysis in light microscopy
    Journal of Microscopy, Vol. 224, Pt 3 December 2006, pp. 213–232 source
    • Good paper to start with if you want to learn more about colocalization. Covers all relevant points.
  • Costes, Sylvain V. et. al., 2004: Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells
    Biophysical Journal Volume 86 June 2004 3993–4003 source
  • Manders, E.M.M. et. al., 1993: Measurement of co-localization of objects in dual-color confocal images
    Journal of Microscopy, Vol. 169, Pt 3, March 1993, pp. 375-382
  • Manders, E.M.M. et. al., 1992: Dynamics of three-dimensional replication patterns during the S-phase, analyzed by double labelling of DNA and confocal microscopy
    Journal of Cell Science 103, 857-862 (1992)
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