Useful papers page 5

NB Please only use the downloadable resources and academic papers on this website for your own personal study and tuition.
They are not to be multiply-distributed, or exploited for commercial use.

Two-photon & Multi-photon

  1. Denk, W. & Svoboda, K. (1997) Photon Upmanship: Why Multiphoton Imaging is more than a Gimmick. Neuron 18: 351-35
  2. Zipfel, WR; Williams, RM & Webb, WW (2003) Non-linear magic: multiphoton microscopy in the biosciences Nature Biotechnology 21/11: 1369-1377.
  3. Helmchen, F & Denk, W (2005) Deep tissue two-photon microscopy Nature Methods 2/12: 932-940
  4. Stutzmann, GE & Parker, I (2005) Dynamic multiphoton imaging: a live view from cells to systems Physiology 20: 15-21
  5. Friedl, P et al (2007) Biological second and third harmonic generation microscopy Curr Protoc Cell Biol. Unit 4.15
  6. Campagnola, PJ & Loew, LM (2003) Second-harmonic imaging microscopy for visualizing biomolecular arrays in cells, tissues and organisms Nature Biotech. 21/11: 1356-1360
  7. Yang, W & Yuste, R (2017) In vivo imaging of neural activity Nature Methods 14/4: 349-359
  8. Ware, LA (2014) Three photons are better than two Biophotonics 57/5: 237; 239
  9. Norris, G et al (2012) A promising new wavelength region for three-photon fluorescence microscopy of live cells for Jour. Microscopy 246/3: 266-273
  10. Yound, MD et al (2015) A pragmatic guide to multiphoton microscope design Adv. Opt. Photonics 7/2: 276-378
  11. Amor, A et al (2016) Widefield two-photon excitation without scanning: live cell microscopy with high time resolution and low photo-bleaching PLoS One 11/1: e0147115
  12. Diaspro, A et al. (2005) Two-photon fluorescence excitation and related techniques in biological microscopy. Q Rev Biophys. 38(2): 97-166
    See also the multi-photon spectra on the Fluorophore Databases page.

TIRF – Total Internal Reflection Fluorescence

  1. Martin-Fernandez, ML; Tynan, CJ and Webb, SED (2013) A ‘pocket guide’ to total internal reflection fluorescence Jour. Microscopy 252/1: 16-22
  2. Vizcay-Barrena, G et al (2011) Subcellular and single-molecule imaging of plant fluorescent proteins using TIRFM Jour. Exp. Botany 62/15: 5419-5428
  3. Mattheyses, AL et al (2010) Imaging with total internal reflection fluorescence microscopy for the cell biologist Jour. Cell Science 123/21: 3621-3628.


  1. Sprague, BL & McNally, JG (2005) FRAP analysis of binding: proper and fitting Trends in Cell Biology 15/2: 84-91.
    See also the follow-up paper: Mueller et al (2010) Curr. Opin. Cell Biology 22/3: 403-411
  2. Day, CA et al (2012) Analysis of protein and lipid dynamics using confocal fluorescence recovery after photobleaching (FRAP) Curr Protoc Cytom. Unit 2.19
  3. Kang, M et al  (2012) Simplified Equation to Extract Diffusion Coefficients from Confocal FRAP Data Traffic 13/12: 1589-1600
  4. Mueller, F et al (2010) FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol. 22/3: 403-411
  5. Dunn, GA et al (2004) Fluorescence localization after photobleaching (FLAP) Curr Protoc Cell Biol. Unit 21.2
  6. Basics of FRET microscopy
  7. Shrestha, D et al (2016) Understanding FRET as a Research Tool for Cellular Studies Int. Jour. Mol. Studies 16: 6718-6756
  8. Bajar, BT (2016) A guide to fluorescent protein FRET pairs Sensors 16/9 pii: E1488
  9. Sarkar, P et al (2009) Photophysical properties of Cerulean and Venus Fluorescent Proteins Jour. Biomed Opt. 14/3: 034047
  10. Vogel, SS et al (2014) Estimating the distance separating fluorescent protein FRET pairs Methods 66/2: 131-138
  11. Shamirian, A et al (2015) QD-Based FRET Probes at a Glance Sensors 15/6: 13028-13051
  12. Arai, Y & Nagai, T (2013) Extensive use of FRET in biological imaging Microscopy (Oxf) 62/4: 419-428
  13. Pietraszewska-Bogiel, A & Gadella, TWJ (2010) FRET microscopy: from principle to routine technology in cell biology Jour. Microscopy 241/2: 111-118
  14. Sahoo, H (2011) Förster resonance energy transfer – A spectroscopic nanoruler: Principle and applications Jour. Photochem. Photobiol. C: Photochemistry Reviews 12/1: 20-30
  15. Piston, DW & Kramers, G-J (2007) Fluorescent protein FRET: the good, the bad and the ugly Trends Biochem. Sci. 32/9: 407-414
  16. See the Acceptor FRET and Sensitized-emisison FRET under protocols on the Edinburgh imaging facility website
  17. Chart of images required for FRET processing
  18. Ambrose, B et al. (2020) The smfBox is an open-source platform for single-molecule FRET Nature Commun. 11/1: 5641
  19. Review: Skruzny, M et al. (2019) FRET Microscopy in Yeast Biosensors 9/4: 122
  20. Deal, J et al. (2020) Milestones in the development and implementation of FRET-based sensors of intracellular signals: A biological perspective of the history of FRET. Cell Signal. 75:109769

FLIM reviews

1. Datta, R et al (2020) Fluorescence lifetime imaging microscopy: fundamentals and advances in instrumentation, analysis, and applications. Jour.  Biomed. Opt. 25(7): 1-43

2. Becker, W (2012) Fluorescence lifetime imaging-techniques and applications. Jour. Microsc. 247(2): 119-136

3. Gao, D et al (2020) FLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysis. PLoS One 15(12): e0238327

A LEGO microscope

Vos, BE et al (2021) Designing a high-resolution LEGO-based microscope for an educational setting BioRχiv pre-print

NB Please only use the downloadable resources and academic papers on this website for your own personal study and tuition.
They are not to be multiply-distributed, or exploited for commercial use.

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