Useful papers page 2

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  

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

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

Phototoxicity

  1. Editorial (2013) Artifacts of Light Nature Methods 10/12: 1135
  2. Editorial (2018) Phototoxicity revisited Nature Methods 15/10: 751
  3. Laissue, PP et al (2017) Assessing photoxicity in live fluorescence imaging Nature Methods 14/7: 657-661
  4. Kiepas, A et al (2020) Optimizing live-cell fluorescence imaging conditions to minimize phototoxicity Jour. Cell Sci. 133/4:jcs242834  doi: 10.1242/jcs.242834 [see doi link for supplementary info. material]
  5. Tosheva, KL et al (2019) Between Life and Death: Reducing Phototoxicity in Super-Resolution Microscopy Preprints 2019: 2019080319
  6. Johnson, S et al (2013) Assessment of cell viability Curr. Protoc. Cytometry Unit 9.2
  7. Icha, J et al (2017)Phototoxicity in live fluorescence microscopy, and how to avoid it Bioessays 39/8. doi: 10.1002/bies.201700003
  8. Swedlow, JR (2010) Advanced hardware and software tools for fast multidimensional imaging of living cells PNAS 107/37: 16005-16006
  9. Schneckenburger, H (2012) Light exposure and cell viability in fluorescence microscopy Jour. Microscopy 245/3: 311-318
  10. Tinevez, JY et al (2012) A quantitative method for measuring phototoxicity of a live cell imaging microscope Methods Enzymol. 506:291-309
  11. Madgison, V & Khodjakov, A (2013) Circumventing photodamage in live-cell microscopy Methods Cell Biol. 114: 545-560
  12. 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
  13. Khodjakov, A & Rieder, CL (2006) Imaging the division process in living tissue culture cells Methods 38/1: 2-1
  14. Mountants and antifades PDF from the Wright Cell Imaging Facility, Toronto
  15. Mubaid, F & Brown, CM (2017) Less is more: longer exposure times with low light intensity is less photo-toxic Microscopy Today Nov 2017 https://doi.org/10.1017/S1551929517000980 See also the Kiepas (2020) paper above [4].
  16. Minimizing photodamage with LEDs (Cool-LED article)

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

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.
  7. Fazeli, E et al (2020) Automated Cell Tracking with Fiji F1000Research 2020, 9:1279
  8. Rizk, A et al (2014) Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh Nat Protoc. 9(3): 586-96

Experimental Planning

  1. Statistics – see Nature Methods series.
  2. Jost, AP-T et al., (2019) Designing a rigorous microscopy experiment: Validating methods and avoiding bias Jour. Cell Biol. 218(5): 1452-1466
  3. Lee, JY & Kitaoka, M. (2018) A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments Mol. Biol. Cell 29(13): 1519-1525
  4. Wait, EC et al (2020) Hypothesis-driven quantitative fluorescence microscopy – the importance of reverse-thinking in experimental design Jour. Cell Sci. 133/21: jcs250027.
  5. Marqués, G; Pengo, T & Sanders, MA (2020) Imaging methods are vastly underreported in biomedical research Elife 9:e55133
  6. Deagle, RC et al. (2017) Reproducibility in light microscopy: Maintenance, standards and SOPs Int J Biochem Cell Biol. 89: 120-124
  7. Mund M & Ries, J (2020) How good are my data? Reference standards in super-resolution microscopy Mol Biol Cell. 31(19): 2093-2096

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.

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. Asteriti S, Ricci V, Cangiano L. Two simple criteria to estimate an objective’s performance when imaging in non-design tissue clearing solutions. Jour. Neurosci. Methods. 332:108564.
  23.  PSF explanation A4 page from Yang & Yuste (2017)
  24. See also the section on Planning an imaging experiment, Chapter 27 of Understanding Light Microscopy.
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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