Photon Science Applications/Biophotonics Group

Foundation for Research and Technology (FORTH)
Contact Person: Prof. Costas Fotakis
Telephone: (+30) 2810 391316



 – Non-linear microscopy group

Our research interest concerns the development and optimization of a prototype workstation for imaging biological samples in vivo at microscopic level. The developed apparatus provides complementary, unique information for the elucidation of basic molecular mechanisms and fundamental biological activities for a variety of specimens by employing non linear imaging microscopy measurements (MPEF-SHG-THG). Specifically, these advanced imaging modalities have been successfully used for the in vivo sub-cellular investigation of complex biological processes (embryogenesis, neuronal degeneration, ageing) and the extraction of valuable structural information from various samples (cancer cells, mouse embryos, C. elegans). Additionally, femtosecond laser assisted nanosurgery for the selective disruption of sub-cellular organelles (lipid bodies, mitochondria) without causing any undesirable damage to the surrounding regions has been achieved. The group is also use non linear imaging techniques as novel diagnostic tool for Cultural Heritage studies.

– Tissue engineering

Research is focused on the implementation of laser based micro- and nano-processing methodologies for the engineering 3D biomaterials or materials relevant to tissue engineering applications. The techniques deployed include two-photon polymerization (2PP), ultrafast laser micro/nano structuring (ULMNS) and single pulse UV laser irradiation of biopolymers (UVLIB). The influence of the topographical features of the fabricated scaffolds on cell behaviour, related to viability, proliferation, motility, adhesion, morphology, cytoskeletal arrangement and gene expression, is examined. Furthermore in each case, control over the topography and surface chemistry of the prepared structures is demonstrated which allows further study of cell response and its dependence on the surface energy of the scaffold. The aforementioned studies on the bioactivity of the fabricated scaffolds were performed by culturing various types of cell lines as well as primary neurons and stem cells. The ultimate goal of the research team is to study basic biological and biophysical processes at the molecular and cellular level, to understand the processes that take place at the interface between cells and biomaterials in micro / nano scale and to examine potential medical and/or clinical applications of optimized artificial tissue scaffolds.

– In vivo optical imaging lab (IVIL)

The research activities of IVIL concern the design, development and application of novel tomographic photonic technologies for in-vivo imaging in living systems. This is achieved by both applied and fundamental research on novel photonics devices and new theory development. The aim being the design and realization of key enabling technologies and tools for end users in Biology and in Clinical practice and advancing our knowledge on light – biological-tissue interactions. In particular we are interested in the non-invasive visualization of specific molecular targets and pathways by exploiting light-tissue interactions, e.g. the fluorescence signal emitted by contrast agents attached to cells or molecules. The group is also active in theoretical research concerning the development of novel tools for the accurate modeling of light propagation in tissue-like media. At the same time another important aspect of our research concerns the development of image processing and visualization tools for the analysis of images obtained by the systems and the representation of three-dimensional maps of acquired signals.


  1. A. Zelmer, P. Carroll, N. Andreu, K. Hagens, J. Mahlo, N. Redinger, B. D. Robertson, S. Wiles, T. H. Ward, T. Parish, J. Ripoll, G. J. Bancroft, and U. E. Schaible, A new in vivo model to test anti-tuberculosis drugs using fluorescence imaging., The Journal of antimicrobial chemotherapy 67.8, pp. 1948–60, (2012)
  2. Notas G, Alexaki VI, Kampa M, Pelekanou V, Charalampopoulos I, Sabour-Alaoui S, Pediaditakis I, Dessirier V, Gravanis A, Stathopoulos EN, Tsapis A, Castanas E, APRIL Binding to BCMA Activates a JNK2-FOXO3-GADD45 Pathway and Induces a G2/M Cell Growth Arrest in Liver Cells, J Immunol. 2012 Oct 15. [Epub ahead of print], (2012)
  3. Ioannou M, Alissafi T, Lazaridis I, Deraos G, Matsoukas J, Gravanis A, Mastorodemos V, Plaitakis A, Sharpe A, Boumpas D, Verginis P, Crucial role of granulocytic myeloid-derived suppressor cells in the regulation of central nervous system autoimmune disease, J Immunol. 188:1136-1146, (2012)
  4. Charalampopoulos I., Vicario A., Pediaditakis I., Gravanis A., Simi A., Ibanez CF, Genetic Dissection of Neurotrophin Signaling through the p75 Neurotrophin Receptor, Cell Reports 2, 1563-1570, (2012)
  5. J. P.-J. Abascal, J. Aguirre, J. Chamorro-Servent, M. Schweiger, S. R. Arridge, J. Ripoll, J. J. Vaquero, and M. Desco, Influence of absorption and scattering on the quantification of fluorescence diffuse optical tomography using normalized data, J. Biomed. Opt. 17.3, p. 036013, (2012)
  6. R. Favicchio, G. Zacharakis, K. Oikonomaki, A. Zacharopoulos, C. Mamalaki, and J. Ripoll, Kinetics of T-cell receptor-dependent antigen recognition determined in vivo by multi-spectral normalized epifluorescence laser scanning, Journal of Biomedical Optics 17.7, p. 076013, (2012)
  7. R. Favicchio, G. Zacharakis, K. Oikonomaki, A. Zacharopoulos, C. Mamalaki and J. Ripoll,, Kinetics of TCR-dependent Antigen Recognition Determined by Multi-Spectral Normalised Epifluorescence In vivo Laser Scanning,, J. Biom. Opt. 17, 076013, (2012)
  8. D. Vats, H. Wang, D. Esterhazy, K. Dikaiou, C. Danzer, M. Honer, F. Stuker, H. Matile, C. Migliorini, E. Fischer, J. Ripoll, R. Keist, W. Krek, R. Schibli, M. Stoffel, and M. Rudin, Multimodal imaging of pancreatic beta cells in vivo by targeting transmembrane protein 27 (TMEM27)., Diabetologia 27, pp. 2407–2416, (2012)
  9. Gravanis A, Calogeropoulou T, Panoutsakopoulou V, Thermos K, Neophytou C, Charalampopoulos I, Neurosteroids and Microneurotrophins Signal Through NGF Receptors to Induce Prosurvival Signaling in Neuronal Cells, Science Signaling. 16,5(246):pt8, (2012)
  10. A. Kokolakis, G. Zacharakis, K. Krasagakis, K. Lasithiotakis, R. Favicchio, G. Spiliopoulos, E. Giannikaki, J. Ripoll, and A. Tosca, Prehistological evaluation of benign and malignant pigmented skin lesions with optical computed tomography., Journal of biomedical optics 17.6, p. 066004, (2012)


Foundation for Research and Technology - Hellas, Heraklion, Greece

Research Field