Useful microscopy papers

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.


LM Basics

  1. Goodwin, PC (2015) A primer on the fundamental principles of light microscopy: Optimizing magnification, resolution, and contrast. Mol.Reprod. Dev. 82/(7-8): 502-507
  2. Zeiss publication: Capitza, HG (1997) Microscopy from the very Beginning 2nd Edn.
  3. Oldfield, R (1994) The Abbe theory of microscope image formation Chapter 3, pp 41-46 in: Light Microscopy: an illustrated guide Wolfe, ISBN 0-7234-1876-4
  4. Thorn, K (2016) A quick guide to light microscopy in cell biology Mol Biol Cell. 27/2: 219-222
  5. McNamara, G et al (2017) Microscopy & Image Analysis Curr. Protoc. Human genetics Unit 4.4
  6. North, A (2006) Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition Jour. Cell Biol. 172/1: 9-18
  7. Johnson, J (2012) Not seeing is not believing: improving the visibility of your fluorescence images Mol. Biol. Cell. 23/5: 754-757
  8. Stelzer, EHK (1998) Contrast, resolution, pixelation, dynamic range, and signal-to-noise ratio Jour. Microscopy 189/1: 15-24
  9. Plasek & Reischig, J (1998) Transmitted-light microscopy for biology: a physicist’s point of view. Part 1 and Part 2 Proc. Royal Microsc. Soc. 33/2: 121-127 & 33/3: 196-205
  10. Amos, W.B. & White J.G. (2003) How the Confocal Laser Scanning Microscope entered Biological Research Biology of the Cell 95: 335–342


Köhler illumination

  1. Evennett, PJ (1983) Köhler illumination: A simple interpretation Proc. RMS 28/4: 189-192
  2. Evennett, PJ (1996) Depth of Field and Depth of Focus Explained Proc. RMS 31/1: 64-66


Fluorescence microscopy

  1. Combs, CA & Shroff, H (2017) Fluorescence Microscopy: A Concise Guide to Current Imaging Methods Curr. Protoc. Neurosci. Unit 2.1
  2. Follain, G et al (2017) Seeing is believing – multiscale spatio-temporal imaging towards in vivo cell biology Jour. Cell Science 130/1: 23-38
  3. Sanderson, MJ et al (2014) Fluorescence Microscopy Cold Spring Harbor Protocols doi: 10.1101/pdb.top071795
  4. Lichtman, JW & Conchello, JA (2005) Fluorescence microscopy Nature Methods 2/12: 910-919
  5. Stelzer, EHK (2005) Practical limits to resolution in fluorescence light microscopy Chapter 96, pp 767-773 in: Imaging in Neuroscience and Development: a laboratory manual Yuste, R & Konnerth, A  (eds) Cold Spring Harbor Laboratory Press ISBN 978-0-879699-37-6
  6. Hong, G et al (2017) Near-infrared fluorophores for biomedical imaging Nature Biomed. Imaging 1: 0010
  7. Ward, EN & Pal, R (2017) Image scanning microscopy: an overview Jour. Microscopy 266/2: 221-228
  8. Lee, J (2017) Perspectives on bioluminescence mechanisms Photochem. & Photobiol. 93/2: 389-404
  9. Schneider, AFL & Hackenberger, CPR (2017) Fluorescent labelling in living cells Curr. Opin. Biotech. 48: 61-68
  10. Thermo Tech tip #6 Extinction coefficients

For other resources see the Fluorescence webpage and Chapters 15 – 27 in Understanding Light Microscopy


Live cell imaging

  1. Landecker, H (2009) Seeing things: from microcinematography to live cell imaging Nature Methods 6/10: 707-709
  2. Frigault, MM et al (2009) Live-cell microscopy – tips and tools Jour Cell Science 122/6: 753-767
  3. Swedlow, JR (2010) Advanced hardware and software tools for fast multidimensional imaging of living cells PNAS 107/37: 16005-16006
  4. Coutu, DL & Schroeder, T (2013) Probing cellular processes by long-term live imaging – historic problems and current solutions Jour. Cell Science 126/17: 3805-3815
  5. Watkins, SC & St. Croix, CM (2013) Building a Live Cell Microscope: What You Need and How to Do It Curr. Protoc. Cytometry Unit 2.21
  6. Lynch, AE et al (2014) Low-cost motility tracking system (LOCOMOTIS) for time-lapse microscopy applications and cell visualisation PLoS One 9/8: e103547
  7. Kang, M et al (2013) Live imaging, identifying, and tracking single cells in complex populations in vivo and ex vivo Methods Mol Biol. 1052: 109-123
  8. Landecker, H (2011) Creeping, drinking, dying: The cinematic portal and the microscopic world of the twentieth-century cell Science in Context 24/3: 381-416
  9. Carlton, PM et al (2010) Fast live simultaneous multiwavelength four-dimensional optical microscopy PNAS 107/37: 16016-16022
  10. Arigovindan, M et al (2013) High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise ratio PNAS 110/43: 17344-17349
  11. Cole, RW (2014) Live-cell Imaging Cell Adhesion & Migration 8/5: 452-459.

For other resources, see the Live Cell Imaging webpage and Chapter 28 in Understanding Light Microscopy



  1. Editorial (2013) Artifacts of Light Nature Methods 10/12: 1135
  2. Johnson, S et al (2013) Assessment of cell viability Curr. Protoc. Cytometry Unit 9.2
  3. Icha, J et al (2017)Phototoxicity in live fluorescence microscopy, and how to avoid it Bioessays 39/8. doi: 10.1002/bies.201700003
  4. Swedlow, JR (2010) Advanced hardware and software tools for fast multidimensional imaging of living cells PNAS 107/37: 16005-16006
  5. Schneckenburger, H (2012) Light exposure and cell viability in fluorescence microscopy Jour. Microscopy 245/3: 311-318
  6. Madgison, V & Khodjakov, A (2013) Circumventing photodamage in live-cell microscopy Methods Cell Biol. 114: 545-560
  7. Jemielita, M et al (2013) Comparing phototoxicity during development of zebrafish craniofacial bone using confocal and light sheet fluorescence microscopy techniques Jour. Biophotonics 6/11-12: 920-28
  8. Khodjakov, A & Rieder, CL (2006) Imaging the division process in living tissue culture cells Methods 38/1: 2-1
  9. Mountants and antifades PDF from the Wright Cell Imaging Facility, Toronto


Fluorescent Proteins

  1. Points to keep in mind when choosing an FP  and a quick overview of GFP
  2. Rodriguez, EA et al (2017) The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins Trends Biochem Sci. 42/2: 111-129
  3. Bindels, DS et al (2017) mScarlet: a bright monomeric red fluorescent protein for cellular imaging Nature Methods 14/1: 53-56
  4. Cranfill, PJ et al (2016) Quantitative assessment of fluorescent proteins Nature Methods 13/7: 557-562
  5. Heppert, JK et al (2016) Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system Mol Biol Cell. 27/22: 3385-3394
  6. Snapp, EL (2009) Fluorescent proteins: a cell biologist’s user guide Trends Cell Biol. 19/11: 649-55
  7. Costantini, LM & Snapp, EL (2013) Fluorescent proteins in cellular organelles: serious pitfalls and some solutions DNA Cell Biol. 32/11: 622-62
  8. Tiwari, DK & Nagai, T (2013) Smart fluorescent proteins: Innovation for barrier-free superresolution imaging in living cells Dev. Growth Differ. 55/4: 491-507
  9. Wiedenmann, J et al (2009) Fluorescent proteins for live-cell imaging: opportunities, limitations, challenges IUBMB Life 61/11: 1029-1042
  10. Hense, A et al (2015) Monomeric garnet, a far-red fluorescent protein for live-cell STED imaging Scientific Reports 5: 18006 and mGarnet2
  11. Chudakov, DM et al (2010) Fluorescent proteins and their applications in imaging living cells and tissues Physiol. Rev. 90/3: 1103-1163
  12. Davidson, MW & Campbell, RE (2009) Engineered fluorescent proteins: innovations & applications 6/10: 713-717
  13. Day, RN & Davidson, MW (2009) The fluorescent protein palette: tools for cellular imaging Chem. Soc. Rev. 38/10: 2887-2921
  14. Shaner, NC et al (2008) Improving the photostability of bright monomeric orange and red fluorescent proteins Nature Methods 5/6: 545-551
  15. Wang, Y; Shyy, J Y-J & Chien, S (2008) Fluorescence proteins, Live-cell imaging and mechanobiology: seeing is believing. Annu. Rev. Biomed. Eng. 10: 1-38
  16. Snapp, E (2005) Design and use of fluorescent fusion proteins in cell biology Curr. Protocols Cell Biol. Unit 21.4
  17. Ai, H-W et al (2014) Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications Nature Protocols 9/4: 910-928
  18. Enterina, JR (2015) Emerging fluorescent protein technologies Curr. Opinion Chem. Biol. 27: 10-17
  19. Eason, MG et al (2017) A structure-guided rational design of red fluorescent proteins: towards designer genetically-encoded fluorophores Curr. Opinion Struct. Biol. 45: 91-99
  20. Shu, X et al (2011) A genetically-encoded tag for correlated light and electron microscopy of intact cells tissues and organisms PLoS Biology 9/4: e1001041

For other resources see the Fluorescent proteins webpage. Also see the Nobel prize lectures, below.


Fixation & Immunofluorescence

  1. Eltoum, I et al (2001) Introduction to the Theory and Practice of Fixation of Tissues Jour. Histotechnol. 24/3: 173-190
  2. See also Chapter 2 in Biological Microtechnique
  3. Chapter 16 Nowacek, J et al (2010) Fixation & Tissue processing in the 6th Edn DAKO guide on Special stains and H&E
  4. Immunofluorescence tips and tricks  see also Specimen Prepn. & Immunology on the Useful Books page
  5. Allan, VJ (2000) Basic Immunofluorescence Chapter 1, pp 1-26, in: Protein Localization by Fluorescence Microscopy – a practical approach VJ Allan (ed) OUP, Oxford  ISBN 0-19-963740-7
  6. Taylor, CR & Rudbeck, L (2013) Immunohistochemical Staining Methods 6th Edn DAKO guide



  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


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. Helmchen, F & Denk, W (2005) Deep tissue two-photon microscopy Nature Methods 2/12: 932-940
  3. Stutzmann, GE & Parker, I (2005) Dynamic multiphoton imaging: a live view from cells to systems Physiology 20: 15-21
  4. Friedl, P et al (2007) Biological second and third harmonic generation microscopy Curr Protoc Cell Biol. Unit 4.15
  5. Campagnola, PJ & Loew, LM (2003) Second-harmonic imaging microscopy for visualizing biomolecular arrays in cells, tissues and organisms Nature Biotech. 21/11: 1356-1360
  6. Yang, W & Yuste, R (2017) In vivo imaging of neural activity Nature Methods 14/4: 349-359
  7. Ware, LA (2014) Three photons are better than two Biophotonics 57/5: 237; 239
  8. 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
  9. Yound, MD et al (2015) A pragmatic guide to multiphoton microscope design Adv. Opt. Photonics 7/2: 276-378
  10. 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
    See also the multi-photon spectra on the Fluorophore Databases page.



  1. Gigan, S (2017) Optical microscopy aims deep Nature Photonics 11/1: 14-16
  2. Chhetri, RK & Keller, PJ (2016) Imaging far and wide eLife 5: e21072 – commentary on McConnell et al (2017) below:
  3. McConnell, G et al (2016) A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout eLife 5: e18659


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.


Single molecule imaging

  1. Shashkova, S & Leake, MC (2017) Single-molecule fluorescence microscopy review: shedding new light on old problems Bioscience Reports 37/4: pii: BSR20170031
  2. Forties, RA & Wang, MD (2014) Discovering the power of single molecules Cell 157/1: 4-7
  3. Walter, NG et al (2008) Do-it-yourself guide: how to use the modern single-molecule toolkit Nature Methods 5/6: 475-489
  4. Coelho, M et al (2013) Single-molecule imaging in vivo: the dancing building blocks of the cell Integr Biol (Camb) 5/5: 748-58
  5. Sacconi, L et al (2006) Cell imaging and manipulation by nonlinear optical microscopy Cell Biochem. & Biophysics 45/3: 289-302


Light-sheet (SPIM) microscopy

  1. Power, RM & Huisken, J (2017) A guide to light-sheet fluorescence microscopy for multiscale imaging Nature Methods 14/4: 260-373
  2. Adams, MW et al (2017) Light Sheet Fluorescence Microscopy (LSFM) Curr. Protoc. Cytometry 71: Unit 12.37, 1-15
  3. Reynaud, EG et al (2015) Guide to light-sheet microscopy for adventurous biologists Nature Methods 12/1: 30-34
  4. Heddleston, JM & Chew, T-L (2016) Light sheet microscopes: Novel imaging toolbox for visualizing life’s processes Int. Jour. Biochem. Cell Biol. 80: 119-123
  5. de Medeiros, G et al (2016) Light-sheet imaging of mammalian development Seminars Cell & Dev. Biology 55: 148-155
  6. Chen, B-C et al (2014) Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution Science 346 (6208): 439; 1257998
  7. Gao, L et al (2014) 3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy Nature Protocols 9/5: 1083-1101
  8. Scherf, N & Huisken, J (2015) The smart and gentle microscope Nature Biotech. 33/8: 815-818
  9. Reynaud, EG (2008) Light sheet-based fluorescence microscopy: More dimensions, more photons, and less photodamage HFSP Journal 2/5: 266-275
  10. Stelzer, EHK (2015) Light-sheet fluorescence microscopy for quantitative biology Nature Methods 12/1: 23-26


Airyscan papers

  1. Brief explanationImaging & Microscopy articleMarch 2014
  2. Airyscan white paper – from Zeiss
  3. Further detailed explantion – from Zeiss
  4. LSM 880 fast acquisition mode – from Zeiss
  5. Comparison with super-resolution – Dr. M. Sivaguru Carl Woese Inst. Genomic Biology
  6. Korobchevskaya, K et al (2017) Exploring the potential of Airyscan microscopy for live cell imaging Photonics 4/3:41
  7. Sivaguru, M et al (2016) Comparative performance of airyscan and structured illumination superresolution microscopy in the study of the surface texture and 3D shape of pollen Microsc. Res. & Tech. doi: 10.1002/jemt.22732
  8. Li, Y et al (2017) Image scanning fluorescence emission difference microscopy based on a detector array Jour. Microscopy 266/3: 288-297
  9. Korobchevskaya, K et al (2016) Intensity weighted subtraction microscopy approach for image contrast and resolution enhancement Scientific Reports 6: 25816


Clearing Tissues

  1. Ariel, P (2017) A beginner’s guide to tissue clearing Int. Jour. Biochem & Cell Biol. 84: 35-39
  2. Vigouroux, RJ et al (2017) Neuroscience in the third dimension: shedding new light on the brain with tissue clearing Mol. Brain 10/1:33
  3. Richardson, DS & Lichtman, JW (2015) Clarifying tissue clearing Cell 162/2: 246-257
  4. Silvestri, L et al (2016) Clearing of fixed tissue: a review from a microscopist’s perspective Jour. Biomed. Optics 21/8: 081205
  5. Marx, V (2014) Microscopy: seeing through tissue Nature Methods 11/12: 1209-1214
  6. Seo, J et al (2016) Clearing and Labeling Techniques for Large-Scale Biological Tissues Mol. Cells 39/6: 439–446
  7. Höckendorf, B et al (2014) Making biology transparent Nature Biotechnology 32/11: 1104-1105
  8. Tomer, R et al (2014) Advanced CLARITY for rapid and high-resolution imaging of intact tissues Nature Protocols 9/7: 1682-1697
  9. Magliaro, C (2016) Clarifying CLARITY: Quantitative Optimization of the Diffusion Based Delipidation Protocol for Genetically Labeled Tissue Front. Neurosci. 10: 179
  10. Azaripour, A et al (2016) A survey of clearing techniques for 3D imaging of tissues withspecial reference to connective tissue Prog. Histochem. Cytochem. 51/2: 9-23.
  11. Pan, C et al (2016) Shrinkage-mediated imaging of entire organs and organisms using uDISCO Nature Methods 13/10: 859-867
  12. Treweek, JB & Gradinaru, V (2016) Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors Curr Opin Biotechnol. 40:193-207


Super-resolution imaging

  1. Zimmermann, T (2017) Superresolution microscopy Encyclopedia of Life Science Review
  2. Fessenden, M (2016) Illuminating life’s building blocks  Nature 533(7604): 565-8. = technology feature commentary
  3. Wegel, E et al (2016) Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison. Science Reports 6: 27290
  4. Demmerle, J et al (2015) Assessing resolution in super-resolution imaging Methods 88: 3-10
  5. Demmerle, J et al (2017) Strategic and practical guidelines for successful structured illumination microscopy Nature Protocols 12/5: 988-1010
  6. Lambert, TJ & Waters, JC (2017) Navigating challenges in the application of superresolution microscopy Jour. Cell Biol. 216/1: 53-63
  7. Richter, KN et al (2017) Review of combined isotopic and optical nanoscopy Neurophotonics 4/2: 020901
  8. Ward, EN & Pal, R (2017) Image scanning microscopy: an overview Jour. Microscopy 266/2: 221-228
  9. Schubert, V (2017) Super-resolution Microscopy – Applications in Plant Cell Research Front Plant Sci. 8: 531
  10. Turkowyd, B et al (2016) From single molecules to life: microscopy at the nanoscale Anal Bioanal Chem 408/25: 6885–6911
  11. Cox, S (2015) Super-resolution imaging in live cells Dev. Biol. 401/1: 175-181
  12. Montgomery, PC & Leong-Hoi, A (2015) Emerging optical nanoscopy techniques Nanotechnol Sci Appl. 8: 31-44
  13. Horrocks, MH et al (2014) The changing point‑spread function: single‑molecule‑based super‑resolution imaging Histochem. Cell Biol. 141/6: 577–585
  14. Yamanaka, M et al (2014) Introduction to super-resolution microscopy Microscopy (Oxf) 63/3: 177-192
  15. Hedde, PN & Nienhaus, GU (2014) Super-resolution localization microscopy with photoactivatable fluorescent marker proteins Protoplasma 251/2: 349-362
  16. Allen, JR et al (2014) Structured illumination microscopy for superresolution Chem. Phys. Chem. 15/4: 566-576
  17. Schropp, M et al (2017) XL-SIM: extending super-resolution into deeper layers Photonics 4/2: 33
  18. Nienhaus, K & Nienhaus GU (2014) Fluorescent proteins for live-cell imaging with super-resolution Chem. Soc. Rev. 43/4: 1088-1106
  19. Han, R et al (2013) Recent Advances in Super-Resolution Fluorescence Imaging and Its Applications in Biology Jour. Genet. Genomics 40/12: 583 – 595
  20. Cox, S & Jones, GE (2013) Imaging cells at the nanoscale Int. Jour. Biochem. & Cell Biol. 45/: 1669-1678
  21. Moerner, WE (2012) Microscopy beyond the diffraction limit using actively controlled single molecules Jour. Microscopy 246/3: 213-220
  22. Ball, G et al (2012) A cell biologist’s guide to high resolution imaging Chapter 2 in Methods Enzymology 504: 29-55
  23. Dedecker, P et al (2012) Widely accessible method for superresolution fluorescence imaging of living systems PNAS 109/27: 10909-10914
  24. Leung, BO & Cheu, KC (2011) Review of Super-Resolution Fluorescence Microscopy for Biology Appl. Spectrosc. 65/9: 967-980
  25. Galbraith, CG & Galbraith, JA (2011) Super-resolution microscopy at a glance Jour. Cell Science 124/10: 1607-1611  – slightly dated; good introduction
  26. Schermelleh, L et al (2010) A guide to super-resolution fluorescence microscopy Jour. Cell Biol. 190/2: 165-175  – slightly dated; good introduction; highly-cited paper
  27. Heintzmann, R & Ficz, G (2006) Breaking the resolution limit in light microscopy Briefings Funct. Genomics 5/4: 289-301
  28. Huang, F et al (2016) Ultra-high resolution 3D imaging of whole cells Cell 166/4: 128-140
  29. Millis, BA et al (2013) Superresolution imaging with standard fluorescent probes Curr Protoc Cell Biol. 60: Unit 21.
  30. Ouyang, W et al (2018) Deep learning massively accelerates super-resolution localization microscopy Nature Biotechnol. 2018 Apr 16. doi: 10.1038/nbt.4106. Institute Pasteur weblink
  31. Sengupta, P et al (2014) Superresolution imaging of biological systems using photoactivated localization microscopy Chem Rev. 114/6: 3189-202.
  32. Also see the Nobel prize lectures, below and this commentary.
  33. The Photonics special issue on super-resolution edited by three eminent scientists in the field, plus this video explanation by Jennifer Lippincott-Schwartz


Expansion microscopy – the new kid on the block

  1. Strack, R (2015) Bigger is better for super-resolution Nature Methods 12/3: 169 – Commentary
  2. Engerer, P et al (2016) Super-resolution microscopy writ large Nature Biotechnol. 34/9: 928-930
  3. Chen, F et al (2015) Expansion Microscopy Science 347(6221): 543-548
  4. Gao, R et al (2017) Q&A: expansion microscopy BMC Biology 15:50
  5. Chang, J-B et al (2017) Iterative expansion microscopy Nature Methods 14/6: 593-599
  6. Chozinski, TJ et al (2016) Expansion microscopy with antibodies and fluorescent proteins Nature Methods 13/6: 485-488
  7. Tillberg, PW et al (2016) Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies Nature Biotechnol. 34/9: 987-992
  8. Zhang, YS et al (2016) Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications. Scientific Reports 6: 22691


Spectral Imaging

  1. Zimmermann, T et al (2014) Clearing Up the Signal: Spectral Imaging and Linear Unmixing in Fluorescence Microscopy Chapter 5, pp 129-148 in: Methods Mol. Biol. vol. 1075 Paddock, SW (ed) Humana Press, ISBN 978-1-60761-847-8
  2. Garini, Y; Young, IT and McNamara, G (2006) Spectral imaging: principles and applications Cytometry A 69A/8: 735-747
  3. Berg, RH (2004) Evaluation of spectral imaging for plant cell analysis Jour. Microscopy 214/2: 174-181
  4. Hiraoka, Y et al (2002) Multispectral imaging fluorescence microscopy for living cells Cell Struct. Function 27/5: 367-374


Refractive Index Mismatch

  1. Visser, TD et al (1992) Refractive index and axial distance measurements in 3-D microscopy Optik 90/1: 17-19
  2. Besseling, TH et al (2015) Methods to calibrate and scale axial distances in confocal microscopy as a function of refractive index Jour. Microscopy 257/2: 142-150
  3. Hell, S et al (1992) Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index Jour. Microscopy 169/3: 391-405
  4. Ji, N (2017) Adaptive optical fluorescence microscopy Nature Methods 14/4: 374-380


Image Analysis

  1. Dr John Russ – Roadmap Guide to Image Analysis   for more on Seeing the Scientific Image, go here
  2. Meijering, E et al (2016) Imagining the future of bioimage analysis Nature Biotechnol. 34/12: 1250-1255
  3. Roeder, AHK et al (2012) A computational image analysis glossary for biologists Development 139/17: 3071-3080
  4. Bassel, GW (2015) Accuracy in Quantitative 3D Image Analysis Plant Cell 27/4: 950-953
  5. Editorial (2012) The quest for quantitative microscopy Nature Methods 9/7: 627


Digital Imaging

  1. Ossi, J (2008) Light Microscopy Digital Imaging Curr. Protoc. Cytom. Unit 2.3.
  2. Bernas, T (2005) Basics of Digital Microscopy Curr. Protoc. Cytom. Unit 12.2.
  3. Cromey, DW (2013) Digital Images Are Data: And Should Be Treated as Such Chapter 1, in: Cell Imaging Techniques: Methods and Protocols Douglas J. Taatjes, DJ & Roth, J (eds.) Methods Mol. Biol. 931: 1-27
  4. Rossner, M & K. Yamada, K (2004) What’s in a picture? The temptation of image manipulation Jour. Cell Biol. 166/1: 11-5  plus guidelines
  5. Entwistle, A (2005) Digital images in science: Fair or fraud? The Biochemist 27/5: 17-22
  6. Pawley, JB (2006) Points, Pixels and Gray Levels: Digitizing Image Data pp 59-79, Chapter 4 in: Handbook of Biology Confocal Microscopy 3rd edition. (ed.) JB Pawley. Springer, New York. ISBN = 0-387-25921-X

For further resources on digital imaging, see also the Other Links page


Stereology & Particle Tracking

  1. West, MJ (2012) Introduction to stereology Cold Spring Harbor Protocols pii: pdb.top070623. doi: 10.1101/pdb.top070623
  2. West, MJ (2013) Getting started in stereology Cold Spring Harbor Protocols doi:10.1101/pdb.top071845   see also Basic Stereology for Biologists and Neuroscientists
  3. Meijering, E et al (2012) Methods for cell and particle tracking Chapter 9 in Methods Enzymology 504: 183-200
  4. Chenouard, N et al (2014) Objective comparison of particle tracking methods Nature Methods 11/3: 281-289
  5. Hoffman, TL (2006) Counting Cells pp 21-24 Chapter 3 in: Cell Biology: a laboratory handbook vol 3 3rd edn (ed) Julio Cellis, Elsevier ISBN 978-0121647339
  6. Kloke, J & Hardin, J (2008) Introduction to Statistical Analysis Curr. Protoc. Lab. Techs. Appendix A4 1-30.


Quality control and PSF determination

  1. Hng, KI & Dormann, D (2013) ConfocalCheck – a software tool for the automated monitoring of confocal microscope performance PLoS One 8/11: e79879
  2. Zucker, RM (2004) Confocal microscopy system performance: axial resolution Microscopy Today 38: 38-40
  3. Eason, B et al (2014) Microscope maintenance and quality control:  a practical guide Microscopy: advances in scientific research and education vol. 2, pages 713-724 A. Méndez-Vilas (ed) Formatex Research Center, Extremadura  ISBN = 978-84-942134-4-1
  4. Brown, CM et al (2015) A quantitative measure of field illumination Jour. Biomolecular Techniques 26/2: 37-44
  5. Stack, RF et al (2015) Quality assurance testing for modern optical systems Microsc. Microanal. 17/4:598-606
  6. Butzlaff M et al (2015) eSIP: A Novel Solution-Based Sectioned Image Property Approach for Microscope Calibration PLoS One 10/8: e013498
  7. Schrader, M et al (1998) Ultrathin fluorescent layers for monitoring the axial resolution in confocal and two-photon fluorescence microscopy Jour. Microscopy 191/2: 135-140
  8. Kedziora, KM et al (2011) Method of calibration of a fluorescence microscope for quantitative studies Jour. Microscopy 244/1: 101-111
  9. Cole, RW et al (2011) Measuring & interpreting PSFs to determine confocal microscope resolution and ensure quality control Nature Methods 6/12: 1929-1941
  10. Not a paper, but Thermo Fisher’s source of Standards; bead suspensions, slides etc.
  11. Davis, I (2000) Visualising fluorescence in Drosophila – optimal detection in thick specimens Chapter 6, pp 133-162 in: Protein Localization by Fluorescence Microscopy, VJ Allen,  ed. OUP, Oxford.   ISBN = 0-19-963740-7    Also see this bead prep PDF from Micron, Oxford.
  12. Waters, JC (2009) Accuracy and precision in quantitative fluorescence microscopy  Jour. Cell Biology 185/7: 1135-1148.
  13. Waters, JC & Swedlow, J (2008) Interpreting Fluorescence Microscopy Images and Measurements  in: Evaluating Techniques in Biochemical Research, D. Zuk, ed. Cell Press 37-42
  14. Waters, JC & Wittmann, T (2014) Concepts in Quantitative Fluorescence Microscopy Chapter 1 in Methods in Cell Biology vol 124 Quantitative Imaging in Cell Biology Jennifer C. Waters and Torsten Wittman (eds) Elsevier, Amsterdam.  ISBN = 978-0-12-420138-5
  15. Jonkman, J et al (2014) Quantitative confocal microscopy: Beyond a pretty picture Chapter 7 in Methods in Cell Biology vol 124 Quantitative Imaging in Cell Biology Jennifer C. Waters and Torsten Wittman (eds) Elsevier, Amsterdam.  ISBN = 978-0-12-420138-5
  16. Zucker, RM & Price, O (2001) Evaluation of confocal microscopy system performance Cytometry 44/4: 273-294
  17. Zucker, RM & Price, O (2001) Statistical evaluation of confocal microscopy images Cytometry 44/4: 295-308
  18. Lee, J-S et al (2014) Calibration of wide-field deconvolution microscopy for quantitative fluorescence imaging Jour. Biomol. Tech. 25/1:31-40
  19. Terasaki, M (2006) Quantification of fluorescence in thick specimens with an application to cyclin B-GFP expression in starfish oocytes  Biol. Cell 98/4: 245-252
  20. Model, MA & Burkhardt, JK (2001) A standard for calibration and shading correction of a fluorescence microscope Cytometry 44/4: 309-16
  21. Cole, RW et al (2013) International test results for objective lens quality,resolution, spectral accuracy and spectral separation for confocal laser scanning microscopes Microsc. Microanal. 19/6:1653-56
  22.  PSF explanation A4 page from Yang & Yuste (2017)
  23. See also the section on Planning an imaging experiment, Chapter 27 of Understanding Light Microscopy.

Reflectance & Polarisation microscopy

  1. Guggenheim, EJ et al (2017) Imaging In focus: Reflected light imaging: Techniques and applications Int. Jour. Biochem. Cell Biol. 83: 65-70
  2. Montag, M et al (2011) Gamete competence assessment by polarizing optics in assisted reproduction Hum Reprod Update 17/5: 654-666
  3. Inoué, S (2002) Polarization microscopy Curr. Protoc. Cell Biology Unit 4.9  See also the biography here.

Correlative microscopy – CLEM

  1. Kopek, BG (2017) Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples Nature Protocols 12/5: 916-946
  2. van Elsland, DM et al (2017) Correlative light and electron microscopy reveals discrepancy between gold and fluorescence labelling Jour. Microscopy
  3. Karreman, MA et al (2016) Intravital correlative microscopy: imaging life at the nanoscale Trends Cell Biol. 26/11: 848-863
  4. Müller-Reichert, T & Verkade, P (2012) Correlative Light and Electron Microscopy Methods in Cell Biology vol. 111 Elsevier, Academic Press ISBN 978-0-12-416026-2
  5. Müller-Reichert, T & Verkade, P (2014) Correlative Light and Electron Microscopy II Methods in Cell Biology vol. 124 Elsevier, Academic Press ISBN 978-0-12-801075-4
  6. Müller-Reichert, T & Verkade, P (2017) Correlative Light and Electron Microscopy III Methods in Cell Biology vol. 140 Elsevier, Academic Press ISBN: 978-0-12-809975-9 (Paul & Thomas are friends from Dresden days at the MPI-GBG: they amongst the very best in the world at CLEM and electron microscopy).
  7. Perkovic, M et al (2014) Correlative Light- and Electron Microscopy with chemical tags Jour. Structural Biol. 186/: 205-213
  8. Jahn, KA et al (2012) Correlative microscopy: Providing new understanding in the biomedical and plant sciences Micron 43/5: 565-582
  9. Peddie, CJ et al (2014) Correlative and integrated light and electron microscopy of in-resin GFP fluorescence, used to localise diacylglycerol in mammalian cells Ultramicroscopy 143: 3-14
  10. Tuijtel, MW et al (2017) Inducing fluorescence of uranyl acetate as a dual-purpose contrast agent for correlative light-electron microscopy with nanometre precision Science Reports 7/1: 10442
  11. Johnson, E et al (2015) Correlative in-resin super-resolution and electron microscopy using standard flourescent protins Scientific Reports 5: 9583 also see this report on using photo-switchable fluorescent proteins.
  12. Brama, E et al (2016) UltraLM & MiniLM: locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy Wellcome Open Research 1: 26
  13. Shu, X et al (2011) A genetically-encoded tag for correlated light and electron microscopy of intact cells tissues and organisms PLoS Biology 9/4: e1001041
  14. Wiley Correlative Microscopy ebook  and this Correlative Microscopy explanation

The Nobel Prize papers

The Nobel prize in Chemistry has been awarded to those working in microscopy for the discovery and development of GFP (in 2008 to Osamu Shimomura, Martin Chalfie and Roger Y. Tsien) and again in 2014 to to Eric Betzig, W.E. Moerner and Stefan Hell for the development of super-resolved fluorescence microscopy. The Nobel lectures these men gave are worth reading.

GFP: discovery by Shimomura (Jour Microscopy article here); Use of the cloned protein as a marker by Chalfie; FP optimisation by Tsien.

Super-resolution: development of STED by Hell; development by Moerner of single molecule microscopy and its use by Betzig.

Introduction to EM

  1. Verkade, P (2013) Essential Guide to Electron microscopy (TEM & SEM) Chapter 7, pp 59-65 in: Essential Guide to Reading Biomedical Papers: Recognising and Interpreting Best Practice (ed) Langton, PD; John Wiley & Sons, New York.  ISBN: 978-1-119-95996-0
  2. Winey, M et al (2014) Conventional transmission electron microscopy Mol Biol Cell. 25/3: 319-323
  3. Hossler, F (2014) Ultrastructure Atlas of Human Tissue Wiley-Blackwell  ISBN = 978-1-118-28453-7
  4. Do, M et al (2015) Imaging and characterizing cells using tomography Arch. Biochem. Biophys. 581: 111-121
  5. Schröder, RR (2015) Advances in electron microscopy: a qualitative view of instrumentation development for macromolecular imaging and tomography Arch. Biochem. Biophys. 581: 25-38
  6. Titze, B & Genoud, C (2016) Volume scanning electron microscopy for imaging biological ultrastructure Biol. Cell 108/11: 307-323
  7. Tafti, AP et al (2015) Recent advances in 3D SEM surface reconstruction Micron 78: 54-66
  8. Wernitznig, S et al (2016) Optimizing the 3D-reconstruction technique for serial block-face scanning electron microscopy Jour. Neurosci. Methods 264: 16-24



      1. Henry Baker, author of the first microscopy laboratory manual
      2. Near-field optical microscopy review (Lereu et al 2012)
      3. Betzig near-field paper development (Betzig et al 1986)
      4. Atomic Force microscopy (Francis et al 2010)
      5. Adaptive optics explanation
      6. Michel-Lévy chart
      7. Challenge the impact factor
      8. Cells as living lasers and single cell lasers (Gather & Yun 2011)
      9. ICQ metric for colocalisation: Khanna et al. (2006)

Go to my seven favourite modern microscopy papers   

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.

As well as these papers, there is a list of microscopy books which I find helpful, use at work and lend out to others.

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