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My guess (without much practical experience) is that the near IR confocal 
will have issues in terms of detector sensitivity if you are using a point 
scanner and PMTs; Most PMTs have pretty low QE in near-IR, with just few 
exceptions. APD or camera-based detection may work better.

Whether the lower sensitivity on the detection side is offset by improved 
excitation (1-p versus 2-P) is an interesting question.


Stan Vitha
Microscopy and Imaging Center
Texas A&M University