Dropbox link:

FRAPmanual7bdir.pdf

My FRAP curve best bits a double exponential fit, but I get two tau values by using a double exponential fit, one small and one large. My question is which tau value do I use? Only the small tau value makes sense in my experiments, am I allowed just simply to ignore the large tau value?

The double exponential fits almost any FRAP curve (even for diffusion-only recovery). This causes problems in the interpretation of data: it could be that kinetics being is nothing to do with the double exponential.

If you know pretty well that the kinetics you are analyzing is indeed a double exponential reaction and doing the experiment correctly, you could interpret that there are reactions with fast and slow kinetics and could use those values to discuss differences.

If such a condition is not met, forget about the model behind the recovery. Then all you could do is compare the half-max time (1/2 tau). This is rather qualitative but still valid and scientific.