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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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>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\u2013diffusion simulations, that the StrExp function can describe both, binding\/barrier\u2013limited 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\u2019s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB\u2019s 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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-296","type":"journal-article","created":{"date-parts":[[2013,1,28]],"date-time":"2013-01-28T05:14:26Z","timestamp":1359350066000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation"],"prefix":"10.1186","volume":"13","author":[{"given":"Daniel","family":"W\u00fcstner","sequence":"first","affiliation":[]},{"given":"Lukasz M","family":"Solanko","sequence":"additional","affiliation":[]},{"given":"Frederik W","family":"Lund","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Sage","sequence":"additional","affiliation":[]},{"given":"Hans J","family":"Schroll","sequence":"additional","affiliation":[]},{"given":"Michael A","family":"Lomholt","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,11,13]]},"reference":[{"key":"5625_CR1","doi-asserted-by":"publisher","first-page":"3303","DOI":"10.1083\/jcb.109.6.3303","volume":"109","author":"KW Dunn","year":"1989","unstructured":"Dunn KW, McGraw TE, Maxfield FR: Iterative fractionation of recycling receptors from lysosomally destined ligands in an early sorting endosome. 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