Tavernarakis Lab bioimaging and microscopy papers
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1.
Kounakis K., Layana Castro P. E., Garcia Garvi A., Sanchez-Salmeron A.-J. and Tavernarakis N. (2025)
Automated analysis of C. elegans fluorescence images using SegElegans. Journal of Visualized Experiments , 224: e69094.(Supplementary material: 1 ) |
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2.
Layana Castro P. E., Kounakis K., García Garví A., Gkikas I., Tsiamantas I., Tavernarakis N. and Sanchez-Salmeron A.-J. (2025)
SegElegans: Instance segmentation using dual convolutional recurrent neural network decoder in Caenorhabditis elegans microscopic images. Computers in Biology and Medicine , 190: 110012. |
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3.
Sotiriou Α., Ploumi C., Charmpilas N. and Tavernarakis N. (2024)
Assessing polyglutamine tract aggregation in the nematode Caenorhabditis elegans. Methods in Cell Biology , 181: 1-15. |
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4.
Kounakis K. and Tavernarakis N. (2022)
Assessment of Neuronal Cell Death in Caenorhabditis elegans. Methods in Molecular Biology , 2515: 309-317. |
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5.
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. |
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6.
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. |
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7.
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. |
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8.
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: 1 ) |
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9.
Palikaras K., Lionaki E. and Tavernarakis N. (2019)
Mitophagy dynamics in Caenorhabditis elegans. Methods in Molecular Biology , 1880: 655-668. |
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10.
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). |
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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: 1 ) |
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12.
Palikaras K. and Tavernarakis N. (2017)
Assessing mitochondrial selective autophagy in the nematode Caenorhabditis elegans. Methods in Molecular Biology , 1567: 349-361. |
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13.
Papandreou M.-E. and Tavernarakis N. (2017)
Monitoring autophagic responses in Caenorhabditis elegans. Methods in Enzymology , 588: 429-444. |
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14.
Palikaras K. and Tavernarakis N. (2017)
In vivo mitophagy monitoring in Caenorhabditis elegans to determine mitochondrial homeostasis. Bio-protocol , 7: e2215. |
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15.
Charmpilas N., Kounakis K. and Tavernarakis N. (2017)
Monitoring mitophagy during ageing in Caenorhabditis elegans. Methods in Molecular Biology , 1759: 151-160. |
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16.
Kourtis N. and Tavernarakis N. (2017)
Protein synthesis rate assessment by fluorescence recovery after photobleaching (FRAP). Bio-protocol , 7: e2156. |
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17.
Rieckher M. and Tavernarakis N. (2017)
P-Body and Stress Granule Quantification in Caenorhabditis elegans. Bio-protocol , 7: e2108. |
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18.
Palikaras K. and Tavernarakis N. (2015)
In vivo imaging of mitophagy in Caenorhabditis elegans. Nature Protocols , DOI: 10.1038/protex.2015.090. |
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19.
Palikaras K. and Tavernarakis N. (2015)
Multiphoton fluorescence light microscopy (v. 3.0). eLS: Citable reviews in the life sciences (Jose M. Valpuesta , editor), Wiley-Blackwell, London, UK. |
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20.
Mari M., Petanidou B., Palikaras K., Fotakis C., Tavernarakis N., and Filippidis G. (2015)
Non-linear imaging techniques visualize the lipid profile of Advanced Microscopy Techniques IV; and Neurophotonics II (Emmanuel Beaurepaire , Peter T. C. So, Francesco Pavone, and Elizabeth M. Hillman, editors), SPIE Press, Bellingham, USA. |
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21.
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. |
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22.
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. |
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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. |
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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. |
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25.
Palikaras K. and Tavernarakis N. (2012)
Multiphoton fluorescence light microscopy (v. 2.0). eLS: Citable reviews in the life sciences (Jose M. Valpuesta , editor), Wiley-Blackwell, London, UK. |
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27.
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. |
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28.
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. |
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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. |
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30.
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). |
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31.
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. |
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32.
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. |
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33.
Kourtis N. and Tavernarakis N. (2009)
Cell-specific monitoring of protein synthesis in vivo. PLOS One , 4: e4547.(Supplementary material: 1 ) |
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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. |
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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. |
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36.
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. |
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37.
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. |
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38.
Tsibidis G. D. and Tavernarakis N. (2007)
Nemo: A computational tool for analyzing nematode locomotion. BMC Neuroscience , 8: 86-93.(Supplementary material: 1 ) |
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39.
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. |
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40.
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. |
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41.
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. |
Relevant non-linear optics literature
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6.
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. |
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9.
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. |
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26.
Muller M., Squier J., Wilson K.R., Brakenhoff G.J. (1998)
3D microscopy of transparent objects using third-harmonic generation Review of Scientific Instruments 72: 2855-2867. |