Fig. 5.

Effective diffusion coefficients determined by PyFRAP. a Results of in vitro experiments and PyFRAP analysis for freely diffusing fluorescent dextrans of different molecular weights. Black markers indicate literature values for fluorescent dextrans, red markers the mean effective diffusion estimates obtained by in vitro experiments and PyFRAP analysis, and grey markers the theoretical estimates derived from the Einstein-Stokes equation (see Supplementary Note 3). Red error bars show the standard deviation of PyFRAP’s effective diffusion estimates, and black error bars show the standard deviation of the literature values listed in Supplementary Table 7. The grey line represents a linear regression fit to the theoretical values. b Results of FRAP/iFRAP experiments for the photoconvertible protein Dendra2. c Results of simulations investigating the influence of tortuosity on effective diffusion for differently packed bead experiments. Grey and black markers indicate 2D and 3D simulation results, respectively. d Results of fluorescent dextran experiments demonstrating the impact of tortuosity on effective diffusivities. e Results of GFP experiments to analyse the impact of tortuosity, embryonic extracelluar environment, protein production, and extracellular binding on effective diffusion estimates. Box plots in b, d, e show median (orange line), mean (black horizontal line inside box), 25% quantiles (box), and all included data points (red markers). Whiskers extend to the smallest data point within the 1.5 interquartile range of the lower quartile, and to the largest data point within the 1.5 interquartile range of the upper quartile