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I'm looking at a series of particle density probabilities of proteins floating on a cell, these particles move around and also blink, so these density probabilities differ a bit from one time to another.

I also have a control, which is these proteins stuck to a surface, without the ability to move around.

Now, the two distributions are obviously different, but what interests me is how they evolve over time - I want to figure out if the distribution over time on the cell varies more due to the motion of the proteins, and not just due to the stochastic blinking, or other sources of noise.

The question is, how do I compare the variation over time of these two different distributions? How do I say that one varies more than the other in a statistically significant way?

Is comparing by Kolmogorov-Smirnov the distributions of the background and cell distances obtained by calculating the Jensen Shanon distance between density histograms of adjacent frames a sensible approach?

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