I may be a bit late responding, but have you considered caged compounds?
There are a number of chemicals available which are non-fluorescent until
they are hit with  UV.  The UV cleaves a piece off the molecule to release
the colored species.  Firing the laser into a cuvette a number of times, then
reading the released signal may be sensitive enough for what you want.

There aren't enough calibrated standards in microscopy.  I have worked on
developing in-house standards at our company, but keep looking for more
globally applicable solutions.

Good luck,

David
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