1. Konstantinidis G. and Tavernarakis N. (2024) In vivo monitoring of nucleophagy in Caenorhabditis elegans. Methods in Molecular Biology, 2845: 67-77.
   
   
2. Sotiriou A., Ploumi C., Charmpilas N., and Tavernarakis N. (2024) Assessing polyglutamine tract aggregation in the nematode Caenorhabditis elegans. Methods in Cell Biology, 181: 1-15.
   
   
3. Kounakis K. and Tavernarakis N. (2022) Assessment of Neuronal Cell Death in Caenorhabditis elegans.Methods in Molecular Biology, 2515: 309-317.
   
   
4. Palikaras K., SenGupta T., Nilsen H. and Tavernarakis N. (2022) Assessment of dopaminergic neuron degeneration in a C. elegans model of Parkinson's disease. STAR Protocols, 3: 101264.
   
   
5. Tsafas V., Giouroukou K., Kounakis K., Mari M., Fotakis C., Tavernarakis N. and Filippidis G. (2021) Monitoring ageing-associated structural alterations in Caenorhabditis elegans striated muscles via PSHG measurements. Journal of Biophotonics, 14: e202100173.
   
   
6. Ploumi C., Sotiriou A. and Tavernarakis N. (2021) Monitoring autophagic flux in Caenorhabditis elegans using p62/SQST-1 reporters. Methods in Cell Biology, 165: 73-87.
   
   
7. Papandreou M.-E., Palikaras K. and Tavernarakis N. (2020) Assessment of de novo protein synthesis rates in Caenorhabditis elegans. Journal of Visualized Experiments, 163: e61170.
      (Supplementary material)
   
   
8. Palikaras K., Lionaki E. and Tavernarakis N. (2019) Mitophagy dynamics in Caenorhabditis elegans. Methods in Molecular Biology, 1880: 655-668.
   
   
9. Rieckher M., Psycharakis S. E., Ancora  D., Liapis E., Zacharopoulos A., Ripoll J., Tavernarakis N., and Zacharakis G. (2018) Demonstrating improved multiscale imaging capabilities of light sheet microscopy in the quantification of fluorescence dynamics. Biotechnology Journal, 13: 1700419 (1-7).
   
   
10. Charmpilas N., Kounakis K. and Tavernarakis N. (2017) Monitoring mitophagy during ageing in Caenorhabditis elegans. Methods in Molecular Biology, 1759: 151-160.
    
    
11. Fang E. F., Palikaras K., Sun N., Fivenson E. M., Spangler R. D., Kerr J. S., Cordonnier S. A., Hou Y., Dombi E., Kassahun H., Tavernarakis N., Poulton J., Nilsen H. and Bohr V. A. (2017) In vitro and in vivo detection of mitophagy in human cells, C. elegans, and mice. Journal of Visualized Experiments, 129: e56301.
       (Supplementary material)
    
    
12. Palikaras K. and Tavernarakis N. (2017) In vivo mitophagy monitoring in Caenorhabditis elegans to determine mitochondrial homeostasis. Bio-protocol, 7: e2215.
    
    
13. Palikaras K. and Tavernarakis N. (2017) Assessing mitochondrial selective autophagy in the nematode Caenorhabditis elegans. Methods in Molecular Biology, 1567: 349-361.
    
    
14. Papandreou M.-E. and Tavernarakis N. (2017) Monitoring autophagic responses in Caenorhabditis elegans. Methods in Enzymology, 588: 429-444.
    
    
15. Kourtis N. and Tavernarakis N. (2017) Protein synthesis rate assessment by fluorescence recovery after photobleaching (FRAP). Bio-protocol, 7: e2156.
    
    
16. Rieckher M. and Tavernarakis N. (2017) P-Body and Stress Granule Quantification in Caenorhabditis elegans. Bio-protocol, 7: e2108.
    
    
17. Palikaras K. and Tavernarakis N. (2015) Multiphoton fluorescence light microscopy (v. 3.0). In eLS: Citable reviews in the life sciences (Jose M. Valpuesta, editor), Wiley-Blackwell, London, UK.
    
    
18. Palikaras K. and Tavernarakis N. (2015) In vivo imaging of mitophagy in Caenorhabditis elegans. Nature Protocols, DOI: 10.1038/protex.2015.090.
    
    
19. Mari M., Petanidou B., Palikaras K., Fotakis C., Tavernarakis N., and Filippidis G. (2015) Non-linear imaging techniques visualize the lipid profile of C. elegans. In Advanced Microscopy Techniques IV; and Neurophotonics II (Emmanuel Beaurepaire, Peter T. C. So, Francesco Pavone, and Elizabeth M. Hillman, editors), SPIE Press, Bellingham, USA.

20. Rieckher M., Kyparissidis-Kokkinidis I., Zacharopoulos A., Kourmoulakis G., Tavernarakis N., Ripoll J. and Zacharakis G. (2015) A customized light sheet microscope to measure spatio-temporal protein dynamics in small organisms. PLoS One, 10: e0127869.

21. Mari M., Filippidis G., Palikaras K., Petanidou B., Fotakis C. and Tavernarakis N. (2015) Imaging ectopic fat deposition in Caenorhabditis elegans muscles using nonlinear microscopy. Microscopy Research and Technique, 78: 523-528.

22. Palikaras K. and Tavernarakis N. (2012) Multiphoton fluorescence light microscopy (v. 2.0). In eLS: Citable reviews in the life sciences (Jose M. Valpuesta, editor), Wiley-Blackwell, London, UK.

23. Tserevelakis G., Megalou E. V., Filippidis G., Petanidou B., Fotakis C. and Tavernarakis N. (2014) Label-free imaging of lipid depositions in C. elegans using third-harmonic generation microscopy. PLoS One, 9: e84431.

24. Zhu S., Dong D., Birk U. J., Rieckher M., Tavernarakis N., Qu X., Liang J., Tian J. and Ripoll J. (2012) Automated motion correction for in vivo Optical Projection Tomography. IEEE Transactions on Medical Imaging, 31: 1358-1371.
    
    
25. Rieckher M., Meyer H., Ripoll J. and Tavernarakis N. (2011) Microscopic optical projection tomography in vivo. PLoS One, 6: e18963.

26. Tserevelakis G. J., Filippidis, G., Megalou E., Fotakis C. and Tavernarakis N. (2011) Cell tracking studies in live Caenorhabditis elegans embryos via Third Harmonic Generation imaging microscopy measurements. Journal of Biomedical Optics, 16: 046019/1-6.

27. Birk U. J., Rieckher M., Konstantinides N., Darrell A., Sarasa-Renedo A., Meyer H., Tavernarakis N. and Ripoll J. (2010) Correction for specimen movement and rotation errors for in vivo optical projection tomography. Biomedical Optics Express, 1: 87-96.

28. Aviles-Espinosa R., Tserevelakis G. J., C. O. Santos S. I., Filippidis G., Krmpot A. J., Vlachos M., Tavernarakis N. , Brodschelm A., Kaenders W., Artigas D. and Loza-Alvarez P. (2010) Cell division stage in C. elegans imaged using third harmonic generation microscopy. In Biomedical Optics, OSA Technical Digest (Optical Society of America, 2010).

29. Tserevelakis G. J., Filippidis G., Krmpot A. J., Vlachos M., Fotakis C. and Tavernarakis N. (2010) Imaging Caenorhabditis elegans embryogenesis by Third-Harmonic Generation microscopy. Micron, 41: 444-447.

30. Filippidis G., Gualda E. J., Mari M., Troulinaki K., Fotakis C. and Tavernarakis N. (2009) In vivo imaging of cell morphology and cellular processes in Caenorhabditis elegans using non-linear phenomena. Micron, 40: 876-880.

31. Filippidis G., Troulinaki K., Fotakis C. and Tavernarakis N. (2009) In vivo polarization-dependant Second and Third harmonic generation imaging of Caenorhabditis elegans pharyngeal muscles. Laser Physics, 19: 1475-1479.

32. Kourtis N. and Tavernarakis N. (2009) Cell-specific monitoring of protein synthesis in vivo. PLOS One, 4: e4547.

33. Gualda E. J., Filippidis G., Mari M., Voglis G., Vlachos M., Fotakis C. and Tavernarakis N. (2008) In vivo imaging of neurodegeneration in Caenorhabditis elegans by third harmonic generation microscopy.  Journal of Microscopy, 232: 270-275.

34. Filippidis G., Gualda E. J., Mari M., Voglis G., Vlachos M., Fotakis C. and Tavernarakis N. (2008) In vivo imaging of cellular structures and processes in Caenorhabditis elegans using non-linear microscopy.  IEEE Proceedings, Imaging Systems and Techniques.

35. Kourtis N. and Tavernarakis N. (2008) Monitoring protein synthesis by fluorescence recovery after photobleaching (FRAP) in vivo. Nature Protocols, DOI: 10.1038/nprot.2008.84.
    
    
36. Gualda E. J., Filippidis G., Voglis G., Mari M., Fotakis C. and Tavernarakis N. (2008) In vivo imaging of cellular structures in Caenorhabditis elegans by combined TPEF, SHG and THG microscopy. Journal of Microscopy, 229: 141-150.

37. Gualda E. J., Filippidis G., Voglis G., Mari M., Fotakis C. and Tavernarakis N. (2007) In vivo imaging of anatomical features of the nematode Caenorhabditis elegans using non-linear (TPEF-SHG-THG) microscopy.  In Confocal, Multiphoton and Nonlinear Microscopic Imaging III (Tony Wilson and Ammasi Periasamy, editors), SPIE Press, Bellingham, USA.

38. Tsibidis G. D. and Tavernarakis N. (2007) Nemo: A computational tool for analyzing nematode locomotion. BMC Neuroscience, 8: 86-93.

39. Filippidis G., Kouloumentas C., Kapsokalyvas D., Voglis G, Tavernarakis N. and Papazoglou T. G. (2005) Imaging of Caenorhabditis elegans samples and sub-cellular localization of new generation photosensitizers for photodynamic therapy, using non-linear microscopy. Journal of Physics D: Applied Physics, 38: 2625-2632.

40. Filippidis G., Kouloumentas C., Voglis G., Zacharopoulou F., Papazoglou T. G. and Tavernarakis N. (2005) Imaging of Caenorhabditis elegans neurons by second-harmonic generation and two-photon excitation fluorescence. Journal of Biomedical Optics, 10: 24015/1-8.

---

• Campagnola P.J., Loew L.M. (2003) Second-harmonic imaging microscopy for visualizing biomolecular arrays in cells, tissues and organisms. Nature Biotechnology 21: 1356-1360.

• Strachan C. J., Windbergs M., Offerhaus H. L. (2011) Pharmaceutical applications of non-linear imaging. Int J Pharm. 417: 163-172.

• Schmolze D. B., Standley C., Fogarty K. E., Fischer A. H. (2011) Advances in microscopy techniques. Arch Pathol Lab Med. 135: 255-263.

• Scheibe S., Dorostkar M. M., Seebacher C., Uhl R., Lison F., Herms J. (2011) 4D in in vivo 2-photon laser scanning fluorescence microscopy with sample motion in 6 degrees of freedom. J Neurosci Methods. 200: 47-53.

• Chu S.W., Chen S.Y., Tsai T.H., Liu T.M., Lin C.Y., Tsai H.J., Sun C.K. (2003) In vivo developmental biology study using noninvasive multi-harmonic generation microscopy. Optics Express 11: 3093-3099.

• Muller M., Squier J., Wilson K.R., Brakenhoff G.J. (1998) 3D microscopy of transparent objects using third-harmonic generation. Journal of Microscopy 191: 266-274.

• Squier J., Muller M. (2001) High resolution nonlinear microscopy: a review of sources and methods for achieving optimal imaging. Review of Scientific Instruments 72: 2855-2867.

• Zipfel W.R., Williams R.M., Webb W.W. (2003) Nonlinear magic: multiphoton microscopy in the biosciences. Nature Biotechnology 21: 1369-1377.

• Mohler W., Millard A.C., Campagnola P.J. (2003) Second harmonic generation imaging of endogenous structural proteins. Methods 29: 97-109.

• Moreaux L., Sandre O., Blanchard-Desce M.,  Mertz J. (2000) Membrane imaging by simultaneous second-harmonic and two-photon microscopy. Opt. Lett. 25: 320-322.

• Xu C., Zipfel W., Shear J.B., Williams R.M., Webb W.W. (1996) Multiphoton fluorescence excitation: new spectral windows for biological nonlinear microscopy. Proc. Natl. Acad. Sci.U.S.A. 93: 10763-10768.

• Yelin D., Silberberg Y. (1999) Laser scanning third-harmonic generation microscopy in biology. Opt. Express 5: 169-175.

• Zipfel W.R., Williams R.M., Christie R., Nikitin A.Y., Hyman B.T., Webb W.W. (2003) Live tissue intrinsic emission microscopy using multiphoton-excited native fluorescence and second harmonic generation.  Proc. Natl. Acad. Sci. U.S.A. 100: 7075-7080.

• Zoumi A., Yeh A., Tromberg B.J. (2002) Imaging cells and extracellular matrix in vivo by using second-harmonic generation and two-photon excited fluorescence.  Proc. Natl. Acad. Sci. U.S.A. 99: 11014-11019.

• Cox G., Sheppard C.J.R. (2004)  Practical limits of resolution in confocal and non-linear microscopy. Microsc. Res. Tech. 63: 18-22.

• Patterson G.H., Piston D.W. (2000) Photobleaching in two-photon excitation microscopy. Biophys J.  78: 2159-2162.

• Diaspro A, Bianchini P, Vicidomini G, Faretta M, Ramoino P, Usai C. (2006) Multi-photon excitation microscopy. Biomed Eng Online 5: 36.

• Biskup C, Zimmer T, Kelbauskas L, Hoffmann B, Klocker N, Becker W, Bergmann A, Benndorf K. (2007) Multi-dimensional fluorescence lifetime and FRET measurements.  Microsc Res Tech 70: 442-51.

• Debarre D., Supatto W., Beaurepaire E. (2005) Structure sensitivity in third harmonic generation microscopy. Optics Letters 30: 2134-2136.

• Friedl P., Wolf K., von Andrian U.H., Harms G. (2007) Biological second and third harmonic generation microscopy.  Curr Protoc Cell Biol. Chapter 4, Unit 4.15.

• Debarre D., Supatto W., Pena A.M., Fabre A., Tordjmann T., Combettes L., Schanne-Klein M.C., Beaurepaire E. (2006) Imaging lipid bodies in cells and tissues using third-harmonic generation microscopy. Nat Methods 3: 47-53.

• Williams R.M., Zipfel W.R., Webb W.W. (2001) Multiphoton microscopy in biological research. Curr Opin Chem Biol. 5: 603-608.

• Schaller R.D., JohnsonJ.C., Saykally R.J. (2003) Time-Resolved Second Harmonic Generation Near-Field Scanning Optical Microscopy. ChemPhysChem 4: 1243-1247.

• Sacconi L., Dombeck D.A., Webb W.W. (2005) Overcoming photodamage in second-harmonic generation microscopy: Real-time optical recording of neuronal action potentials. Proc. Natl. Acad. Sci. U.S.A. 103: 3124-3129.

• Faez S., Johnson P.M., Mazurenko D.A., Lagendijk A. (2009) Experimental observation of second-harmonic generation and diffusion inside random media. J. Opt. Soc. Am. B 26: 235-243.

• Yew E.Y.S., Sheppard C.J.R. (2007) Second harmonic generation polarization microscopy with tightly focused linearly and radially polarized beams. Optics Communications 275: 453-457.

• Yelin D., Silberberg Y. (1999) Laser scanning third-harmonic-generation microscopy in biology.  Opt. Express 5: 169-175.

• Muller M., Squier J., Wilsons K.R., Brakenhoff G.J. (1998) 3D microscopy of transparent objects using third-harmonic generation.  Journal of Microscopy 191: 266-274.

• Barad Y., Eisenberg H., Horowitz M., Silberberg Y. (1997) Nonlinear scanning laser microscopy by third harmonic generation. Appl. Phys. Lett. 70: 922-924.

• Assanto G., Stegeman G. I. (2001) Nonlinear Optics, Basics - Cascading. Encyclopedia of Materials: Science and Technology ISBN: 0-08-0431526: 6255-6259.

• Yang S., Zhan Q. (2008) Third-harmonic generation microscopy with tightly focused radial polarization. Journal of Optics A: Pure and Applied Optics 10: 125103.

• Batchelder D.N., Cheng C., Pitt G.D. (1993) Molecular Imaging by Raman Microscopy. Advanced Materials 3: 566-568.

---

• LSM 7 Live

• Photomanipulation with Laser Scanning Microscopes

• Localized Photoactivation

---