Useful papers page 4

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.

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
  11. The Nature Methods collection of articles


  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

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

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
  5. Diel, EE et al (2020) Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy. Nature Protocols 15/9: 2773-2784. See also the companion Nature Protocols paper Jonkman et al (2020) Tutorial on confocal here and poster.

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



  1. Barlow, AL et al (2010) Colocalization Analysis in Fluorescence Micrographs: Verification of a More Accurate Calculation of Pearson’s Correlation Coefficient Microscopy and Microanalysis 16/6: 710-724.
  2. Adler, J & Parmryd, I (2021) Quantifying colocalization: The case for discarding theManders overlap coefficient CytometryA Mar 15. doi: 10.1002/cyto.a.24336: 1-11.
  3. Adler, J & Parmryd I (2010) Quantifying colocalization by correlation: the Pearson correlation coefficient is superior to the Mander’s overlap coefficient. Cytometry A 77(8): 733-42.
  4. Sheng, H et al. (2016) Systematic and general method for quantifying localization in microscopy images. Biol Open 5(12): 1882-1893.
  5. Dunn KW et al. (2011) A practical guide to evaluating colocalization in biological microscopy. Am J Physiol Cell Physiol. 300(4): C723-42
  6. McDonald, JH & Dunn KW (2013) Statistical tests for measures of colocalization in biological microscopy. J Microsc. 252(3): 295-302.
  7. Lagache T et al. (2015) Statistical analysis of molecule colocalization in bioimaging. Cytometry A 87(6): 568-79.
  8. Lavancier, F et al. (2020) Testing independence between two random sets for the analysis of colocalization in bioimaging. Biometrics 76(1): 36-46.
  9. Aaron, JS, Taylor, AB & Chew TL (2018) Image co-localization – co-occurrence versus correlation. Jour Cell Sci. 131 (3): jcs211847. But also see the correspondence from Adler/Parmryd here.

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
  6. Fazeli, E et al (2020) Automated Cell Tracking with Fiji F1000Research 2020, 9:1279
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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