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.

Go to my top ten useful microscopy papers   

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. Salmon, ED & Canman, JC (1998) Proper alignment and adjustment of the light microscope  Curr. Protoc. Cell Biology Unit 4.1
4. 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
5. Thorn, K (2016) A quick guide to light microscopy in cell biology Mol Biol Cell. 27/2: 219-222
6. McNamara, G et al (2017) Microscopy & Image Analysis Curr. Protoc. Human Genetics Unit 4.4
7. North, A (2006) Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition Jour. Cell Biol. 172/1: 9-18
8. Johnson, J (2012) Not seeing is not believing: improving the visibility of your fluorescence images Mol. Biol. Cell. 23/5: 754-757
9. Stelzer, EHK (1998) Contrast, resolution, pixelation, dynamic range, and signal-to-noise ratio Jour. Microscopy 189/1: 15-24
10. 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
11. Amos, W.B. & White J.G. (2003) How the Confocal Laser Scanning Microscope entered Biological Research Biology of the Cell 95: 335-342
12. Rayleigh, Lord (John Strutt) 1896 XV. On the Theory of Optical Images, with Special Reference to the Microscope Philosophical Mag. Series 5, 42: 167-195
13. Airy, GB (1835) On the Diffraction of an Object-glass with Circular Aperture Trans. Camb. Philos. Soc. 5: 283-291
14. Gray, N (2009) Milestone 3: Knowing the limit – (1873) Diffraction limit theory Nature Milestones.
15. Lauterbach, MA (2012) Finding, defining and breaking the diffraction barrier in microscopy – a historical perspective Optical Nanoscopy 1(1): 8

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            
   For further resources on Köhler illumination, also see here

Confocal Tutorial and Spherical Aberration Tutorial

1. Tutorial on confocal: Jonkman, J; Brown, CM; Wright, GD; Anderson, KI & North, AJ (2020) Tutorial: guidance for quantitative confocal microscopy. Nature Protocols 15/5:1585-1611   and poster.
2. Tutorial on Spherical Aberration: Diel, EE; Lichtman, JW & Richardson, DS (2020) Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy. Nature Protocols 15/9 :2773-2784.  Supplementary data.

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. Mertz, J (2019) Strategies for volumetic imaging with a fluorescence microscope Optica 6/10: 1261-1268
6. Fischer, RS et al (2011) Microscopy in 3D: a biologist’s toolbox Trends Cell Biology 21/12: 682-691
7. 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
8. Hong, G et al (2017) Near-infrared fluorophores for biomedical imaging Nature Biomed. Imaging 1: 0010
9. Ward, EN & Pal, R (2017) Image scanning microscopy: an overview Jour. Microscopy 266/2: 221-228
10. Lee, J (2017) Perspectives on bioluminescence mechanisms Photochem. & Photobiol. 93/2: 389-404
11. Schneider, AFL & Hackenberger, CPR (2017) Fluorescent labelling in living cells Curr. Opin. Biotech. 48: 61-68
12. Thermo Tech tip #6 Extinction coefficients
13. Baharlou, H et al. (2020) AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images Bioinformatics 2020 Sep 15:btaa780.

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

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
21. Scandella, V et al. (2020) A novel protocol to detect green fluorescent protein in unfixed, snap-frozen tissue Sci Rep. 10(1):14642.

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

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

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. For the super-resolution paprs, go here

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.

Go to my top ten useful microscopy papers 

Go to Useful Papers Page Two here

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