Congratulations to Hamed Karimi, who defended his doctoral thesis, Development of Computational and Statistical Methods for Fluorescence-Based Diffusion Measurements, at TalTech on 12 May 2026.
Molecular diffusion is fundamental to cell physiology, but measuring it accurately in living cells is difficult: long fluorescence-microscopy measurements can damage cells, while commonly used analysis methods can underestimate uncertainty. Hamed's thesis developed two complementary computational approaches to address these challenges.
The first, IOCBIO FCS, is an open-source platform for fluorescence correlation spectroscopy and raster image correlation spectroscopy. It combines fast GPU-based calculations with statistical methods that account for the properties of experimental data. The second, fluorescence intensity trace statistical analysis (FITSA), uses Bayesian analysis of fluorescence intensity traces directly. FITSA can estimate diffusion coefficients using fewer photons, enabling shorter measurements and reducing phototoxicity in live-cell experiments.
Together, these methods improve the reliability and practicality of fluorescence-based diffusion measurements in complex cellular environments.
Hamed was supervised by Marko Vendelin and co-supervised by Martin Laasmaa.