Useful papers page 3

 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.

Super-resolution imaging

  1. Möckl, L & Moerner, WE (2020) Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. Jour Am Chem Soc. 142(42): 17828-17844.
  2. Schermelleh, L et al (2019) Super-resolution microscopy demystified Nature Cell Biology 21/1: 72-84 Review
  3. Vangindertael, J et al. (2018) An introduction to optical super-resolution microscopy for the adventurous biologist Methods Appl Fluoresc. 6(2): 022003 – a really good and clear review.
  4. Sahl, SJ; hell, SW & Jakobs, S (2017) Fluorescence nanoscopy in cell biology Nat Rev Mol Cell Biol. 18(11):685-701. Review.
  5. Zimmermann, T (2017) Superresolution microscopy Encyclopedia of Life Science Review
  6. Jahr, W et al. (2017) Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens Methods 174: 27-41.
  7. Kasuboski, JM et al. (2012)  Super-Resolution Microscopy: A Comparative Treatment Current Protocols in Cytometry UNIT 2.17 2.17.1-2.17.2
  8. Fessenden, M (2016) Illuminating life’s building blocks  Nature 533(7604): 565-8. = technology feature commentary
  9. Wegel, E et al (2016) Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison. Science Reports 6: 27290
  10. Demmerle, J et al (2015) Assessing resolution in super-resolution imaging Methods 88: 3-10
  11. Demmerle, J et al (2017) Strategic and practical guidelines for successful structured illumination microscopy Nature Protocols 12/5: 988-1010
  12. Lambert, TJ & Waters, JC (2017) Navigating challenges in the application of superresolution microscopy Jour. Cell Biol. 216/1: 53-63
  13. Richter, KN et al (2017) Review of combined isotopic and optical nanoscopy Neurophotonics 4/2: 020901
  14. Ward, EN & Pal, R (2017) Image scanning microscopy: an overview Jour. Microscopy 266/2: 221-228
  15. Schubert, V (2017) Super-resolution Microscopy – Applications in Plant Cell Research Front Plant Sci. 8: 531
  16. Turkowyd, B et al (2016) From single molecules to life: microscopy at the nanoscale Anal Bioanal Chem 408/25: 6885–6911
  17. Cox, S (2015) Super-resolution imaging in live cells Dev. Biol. 401/1: 175-181
  18. Montgomery, PC & Leong-Hoi, A (2015) Emerging optical nanoscopy techniques Nanotechnol Sci Appl. 8: 31-44
  19. Horrocks, MH et al (2014) The changing point‑spread function: single‑molecule‑based super‑resolution imaging Histochem. Cell Biol. 141/6: 577–585
  20. Yamanaka, M et al (2014) Introduction to super-resolution microscopy Microscopy (Oxf) 63/3: 177-192
  21. Hedde, PN & Nienhaus, GU (2014) Super-resolution localization microscopy with photoactivatable fluorescent marker proteins Protoplasma 251/2: 349-362
  22. Allen, JR et al (2014) Structured illumination microscopy for superresolution Chem. Phys. Chem. 15/4: 566-576
  23. Schropp, M et al (2017) XL-SIM: extending super-resolution into deeper layers Photonics 4/2: 33
  24. Nienhaus, K & Nienhaus GU (2014) Fluorescent proteins for live-cell imaging with super-resolution Chem. Soc. Rev. 43/4: 1088-1106
  25. Han, R et al (2013) Recent Advances in Super-Resolution Fluorescence Imaging and Its Applications in Biology Jour. Genet. Genomics 40/12: 583 – 595
  26. Cox, S & Jones, GE (2013) Imaging cells at the nanoscale Int. Jour. Biochem. & Cell Biol. 45/: 1669-1678
  27. Moerner, WE (2012) Microscopy beyond the diffraction limit using actively controlled single molecules Jour. Microscopy 246/3: 213-220
  28. Ball, G et al (2012) A cell biologist’s guide to high resolution imaging Chapter 2 in Methods Enzymology 504: 29-55
  29. Dedecker, P et al (2012) Widely accessible method for superresolution fluorescence imaging of living systems PNAS 109/27: 10909-10914
  30. Leung, BO & Cheu, KC (2011) Review of Super-Resolution Fluorescence Microscopy for Biology Appl. Spectrosc. 65/9: 967-980
  31. Galbraith, CG & Galbraith, JA (2011) Super-resolution microscopy at a glance Jour. Cell Science 124/10: 1607-1611  – slightly dated; good introduction
  32. Bates et al. (2012) Multicolor super-resolution fluorescence imaging via multi-parameter fluorophore detection. Chemphyschem. 13(1): 99-107
  33. 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
  34. Heintzmann, R & Ficz, G (2006) Breaking the resolution limit in light microscopy Briefings Funct. Genomics 5/4: 289-301
  35. Huang, F et al (2016) Ultra-high resolution 3D imaging of whole cells Cell 166/4: 128-140
  36. Millis, BA et al (2013) Superresolution imaging with standard fluorescent probes Curr Protoc Cell Biol. 60: Unit 21.
  37. 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
  38. Sengupta, P et al (2014) Superresolution imaging of biological systems using photoactivated localization microscopy Chem Rev. 114/6: 3189-202.
  39. Schnitzbauer, J et al (2017) Super-resolution microscopy with DNA-PAINT Nature Protoc. 12(6): 1198-1228.
  40. Also see the Nobel prize lectures, below and this commentary.
  41. The Photonics special issue on super-resolution edited by three eminent scientists in the field, plus this video explanation by Jennifer Lippincott-Schwartz
  42. Mund M & Ries, J (2020) How good are my data? Reference standards in super-resolution microscopy Mol Biol Cell. 31(19): 2093-2096
  43. Diekmann, R et al. (2020) Optimizing imaging speed and excitation intensity for single-molecule localization microscopy. Nat Methods 17(9): 909-912

Single molecule imaging

  1. Möckl, L & Moerner, WE (2020) Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. Jour Am Chem Soc. 142(42): 17828-17844.
  2. Shashkova, S & Leake, MC (2017) Single-molecule fluorescence microscopy review: shedding new light on old problems Bioscience Reports 37/4: pii: BSR20170031
  3. Shivanandan A et al (2014) Challenges in quantitative single molecule localization microscopy FEBS Lett. 588(19): 3595-3602.
  4. Forties, RA & Wang, MD (2014) Discovering the power of single molecules Cell 157/1: 4-7
  5. Walter, NG et al (2008) Do-it-yourself guide: how to use the modern single-molecule toolkit Nature Methods 5/6: 475-489
  6. Coelho, M et al (2013) Single-molecule imaging in vivo: the dancing building blocks of the cell Integr Biol (Camb) 5/5: 748-58
  7. Sacconi, L et al (2006) Cell imaging and manipulation by nonlinear optical microscopy Cell Biochem. & Biophysics 45/3: 289-302

Correlative super-resolution imaging

  1. Kopek, B et al (2017) Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples Nature Protoc. 12(5): 916-946
  2. Kopek BG et al (2013) Correlative photoactivated localization and scanning electron microscopy PLoS One 8(10): e77209.
  3. Johnson, E & Kaufman, R (2017) Chapter 3Preserving the photoswitching ability of standard fluorescent proteins for correlative in-resin super-resolution and electron microscopy Methods Cell Biol. 140:49-67
  4. Hoffman, DP et al. (2020) Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 367(6475):eaaz5357.
  5. Tuijtel MW et al. (2019) Correlative cryo super-resolution light and electron microscopy on mammalian cells using fluorescent proteins. Sci Rep. 9(1):1369.

Self-build super-resolution imaging

  1. Diederich, B et al (2020) Nanoscopy on the Chea(i)p

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

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

Near-field imaging

      1. Near-field optical microscopy review (Lereu et al 2012)
      2. Betzig near-field paper development (Betzig et al 1986)
      3. Atomic Force microscopy (Francis et al 2010)
      4. How the doors to the nanoworld were opened (Gerber & Lang 2006)

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.

Super-resolution: development of STED by Hell; development by Moerner of single molecule microscopy and its use by Betzig. For the GFP papers, 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.

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