Biomedical Research Foundation Academy Of AthensAcademy Of Athens
Scientific Personnel

Stamatis N. Stamatis N. Pagakis, PhD
Staff Research Scientist A'

Telephone : +30 210 6597 093
Fax : +30 210 6597 545
e-mail :

Center :

Basic Research

Core Facility Site :


Brief Bio

Stamatis Pagakis is the head of the Biological Imaging Unit (BIU).  He received his Diploma in Electrical Engineering from the University of Patras, and his MS and Ph.D. degrees in Biomedical Engineering from University of California, Davis, with specialization in cardiovascular imaging, microscopy and image analysis. He has worked with fluorescent bio-markers for more than 30 years and he has extensive experience in optical microscopy and the application of imaging techniques to visualise cellular processes in living cells. 

His Ph.D. research focused on the development of an automated microscope system for the quantitative intracellular calcium imaging and 3D visualisation to study the mechanism for the modulation of capillary blood vessel permeability in-situ. It was the first application of fluorescence dyes and image deconvolution (for the improvement of the 3D image quality) in the study of small capillary vessels (Pagakis S.N., IEEE/Eng. Medicine and Biology, 5:2034).

Dr Pagakis worked as a senior research scientist at the University Laboratory of Physiology, Oxford (1994-1997), and then at the National Institute of Medical Research (NIMR-MRC), Mill Hill, London where he was the founder and director of the Confocal and Image Analysis Laboratory (CIAL). His work was also supported by grants from the Medical Research Council (MRC) and the European Union.

He joined BRFAA in 2005 to create a modern imaging facility in the newly established institute. The Biological Imaging Unit (BIU) was therefore founded and was the first core facility in Greece operating in accordance to European standards by offering imaging services and consulting both in microscopy and Image Analysis. 

He has more than 30 publications in refereed journals.  His current interests focus on image restoration, 3D visualisation and the development of software algorithms for automatic analysis of biological microscopy images. With collaborators in Uppsala University (J. Adler; Journal of Microscopy 230, 121-133; 2008), he co-developed the RBNCC method which corrects for noise that contributes to the underestimation of the Pearson and Spearman co-localisation coefficients and improves the results of the standard co-localisation method. This algorithm is being used by commercial software packages (  He is an expert user of ImageJ/FIJI. 

Member of IEEE, the Society for Engineering in Medicine and Biology (EMBS) and the Royal Microscopical Society (RMS).

Selected Publications

2021 Pantazopoulou V., Delis A.D., Georgiou S., Pagakis S.N., Dragona E., Kloukina I., Chatzitheodoridis E., Trebicka J., Velentzas A. D., Thiele M., Gagos S., Thanos D., Tseleni S., Stravopodis D.J., Anasasiadou E.: AGO2 localizes to cytokinetic protrusions in a p38-dependent manner and is needed for accurate cell division. Commun Biol. 2021 Jun 11;4(1):726.

2021   Stergiou I.E., Kambas K., Poulaki A.,Giannouli S., Katsila T., Dimitrakopoulou A., Vidali V., Mouchtouris V., Kloukina I., Xingi E., Pagakis S.N., Probert L., Patrinow G.P., Ritis K., Tzioufas A.G., and Voulgarelis M.: Exploiting the Role of Hypoxia-Inducible Factor 1 and Pseudohypoxia in the Myelodysplastic Syndrome Pathophysiology. Int. J. Mol. Sci. 2021, 22(8), 4099. Commun Biol.

2020  Daskalakis K., Alexandraki K.I., Kloukina I., Kassi E., Felekouras E., Xingi E., Pagakis S.N., Tsolakis A.V., Andreakos E., Kaltsas G., Kambas K.: Increased autophagy/mitophagy levels in primary tumours of patients with pancreatic neuroendocrine neoplasms. Endocrine 2020 Feb29.

2013    F. Karagianni; G. Kaltsa; N. Prakoura; P. Politis; V. Kaltezioti; S. Psarras; S. Pagakis; M. Katsimboulas; C. Chatziantoniou; A. S. Charonis, Transgelin up-regulation in Obstructive Nephropathy, PLOS ONE, June 2013.

2010  E.L. Papadopoulou, A. Samara, M. Barberoglou, A. Manousaki, S.N. Pagakis, E. Anastasiadou, C. Fotakis and E. Stratakis: Silicon scaffolds promoting three-dimensional neuronal web of cytoplasmic processes. Tissue Engineering, Part C: Methods. Jun, 16(3):497-502.

2008    J. Adler, S.N. Pagakis and I. Parmryd: Replicate Based Noise Corrected Correlation for Accurate Measurements of Colocalization, J. Micrsc.,  230(1):121-133. IF1.56

2006    M. C. Coles, H. Veiga-Fernandes, K. E. Foster, T. Norton, S. N.Pagakis, B. Seddon and D. Kioussis:  Role of T, NK cells and IL7/IL7r interactions during neonatal maturation of lymph nodes  Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13457-62.

2003    Festenstein R., S.N. Pagakis, K. Hiragami, D. Lyon, A. Verrault, B. Sekali and D. Kioussis: Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science, Jan 31, 299:719-721

2003    J. Adler J. and S.N. Pagakis: Reducing image distortions due to temperature related microscope stage drift. J. Microsc. 210(2):131-136.

2002    Daly C.J., McGee A., Vila E., Briones A., Arribas S.M., Pagakis S.N., Adler J., Merle A., Maddison J., Pedersen J., McGrath J.C.:  Analysing the 3D structure of blood vessels using confocal microscopy. Microscopy & Analysis, 92:5-8.

1999     Erent M., S.N. Pagakis, J.P. Browne and P. Bayley:  Association of calmodulin with cytoskeletal structures at different stages of HeLa cell division, visualized by a calmodulin-EGFP fusion protein, Mol. Cell Biol. Res. Com., 1:209-215.

1994    Pagakis S.N. and F.E. Curry:  Imaging of Ca2+ transients in endothelial cells of single perfused capillaries: correlation of peak [Ca2+]i with sites of macromolecule leakage. Microcirculation, 1(4):213-230.


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