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Check the noise on your amplifiers
You may want to adjust the bias setting on your amplifiers (e.g. if you are using Femto amplifiers) and maybe de-noise. This is easy to do from within ScanImage. Turn off the PMT power supply, bring up all the channels windows and press "Focus". Then right-click on each channel window and show the histogram. It should look something like this (click for larger version):
Ensure that the offset subtraction for each channel is switched off by unchecking the checkboxes. The roughly Gaussian distribution which you see arises from various forms of electrical noise In this case you can also see a ripple pattern that comes from the amplifier. The offset on Channel 1 is slightly negative. The digitizer we are using is 16 bit so the scale goes up to +/- 2^15 (32768).
In this case our goals are to reduce the noise and also to adjust the offsets to make them 0V, if desired. (If you wish, you could set set the offset to negative extreme of your digitization range, which would double the available dynamic range. StitchIt can calculate the actual zero offset to handle a biased amplifier.)

Tweaking the bias.

Simply turn the offset set-screw on your amp whilst imaging until the peak of the curve is at zero. On the Femto you want the offset screw not the bias screw. You may offset to a negative number to increase dynamic range.

Denoising

At least on the Femtos it's possible to get rid of the annoying ripple noise but you will need to spend a little time messing around. Things that you can try including grounding the chassis of all the amplifiers or resting them on foil which you ground. After a little messing around, we now have this (click for larger version showing all four channels):
Channel 1 is a little noisier than the others and there are some funny streaks in Channel 2, but overall things are much better. Remember: here we're looking at signals right at the low end of the digitizer's input range.