Multi-compartment modeling of FLIP data reveals dynamics of eGFP-Q73 in inclusion bodies. A FLIP experiment was performed in CHO cells expressing eGFP-Q73 as described in legend to Figure 6. A, montage of every 20th frame of the data. Inset is a zoom of the small box pointing to an IB; a FIRE LUT is used for visualization purposes. A’, sketch of the multi-compartment (MC) model used for determining binding/dissociation parameters. B, FL kinetics for the IB (blue dots) and for a region in the cytoplasm (green dots) with overlayed fit to the MC model for the IB (compartment 1; dark blue line) and for the cytoplasm (compartment 2; dark green line). C, another FLIP sequence imaged with a total frame rate of 2.4 sec. First frame of the time series is shown in green, while selected subsequent frames are overlayed in red. This color coding visualizes movement of two IB’s at the cell edge (large one up and small one below; arrows). Tracking of the mobile IB’s and measurement of their intensity was performed using the SpotTracker plugin for ImageJ . D, x,y-plot of the trajectories of the IB’s; E, mean square displacement (MSD) calculated from the trajectories; F, step length distribution between subsequent steps; G, fluorescence intensity of eGFP-Q73 in the IB’s (blue dots = large IB; red dots = small IB) and in the cytoplasm (green dots) and fit with the MC model for the IB’s (compartments 1, dark blue and red line, respectively) as well as for the cytoplasm (compartment 2, dark green line).