Do you really need that much dynamic range?
I can get away with the 10 bits I have now, was curious if it was possible to extend.
In the really low (pwm 1-5) the steps are very noticable. (even 10 or 20 % per step)
Why 50 flashes?
I don't have exact control over when the camera shutter starts and stops. So if I have at least 50 flashes during the 1 ms exposure I chan have max variation of 2% in brightness of the image. Between the individual camera captures.
So you are OK with 2% variations, but want 16 bit resolution?
This doesn't make much sense.
Your problem is one of aliasing, not resolution. Your sample window is defined by the exposure time and the thing you are sampling is your LED drive waveform.
One way to make your life easier is to use pulse density modulation rather than pulse width modulation. You should be able to get to unnoticeable brightness variations in your images with much lower clock rates than what would be required for PWM.