Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Methodology article

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

Daniel Wüstner1*, Lukasz M Solanko1, Frederik W Lund1, Daniel Sage2, Hans J Schroll3 and Michael A Lomholt4

Author Affiliations

1 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK-5230, Denmark

2 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland

3 Institute for Mathematics and Computer Science (IMADA), University of Southern Denmark, Odense M, DK-5230, Denmark

4 Department of Physics, Chemistry and Pharmacy, MEMPHYS Center for Biomembrane Physics, University of Southern Denmark, Odense M, DK-5230, Denmark

For all author emails, please log on.

BMC Bioinformatics 2012, 13:296  doi:10.1186/1471-2105-13-296

Published: 13 November 2012



Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings.


We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments.


We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport.

Mathematical model; Crowding; Protein aggregation; Fractal kinetics; Rate coefficient; Multi-compartment; Neurodegeneration