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We have one Leica TCS SP5 MP confocal system and I would like to find out 
how the size of the laser beam on the stage is controlled?

It is possible to controlled the size of the point in 2P. It's mentionned in one 
answer you have to inderfill, but never over. To do that you have to add a 
lense in the laser beam.

 When we change the pixel size to meet Nyquist criteria, does the laser focal 
point on the specimen change its size accordingly?

It's only change with the NA.

 Will the focused beam has same size to the pixels? What is the smallest focus 
size of the laser beam on the stage we can achieve?

I always obtain the same résolution with a 2P than a normal confocal but in 
deep (over 1mm in tthe brain of over weeks mouse)


 Does two photon excitation has the same scenarios? 

No because the pulse power is over a confocal and you can excite many fluo 
at the same time. You have less bleaching due to the small excitaion point. 
Infact may be the 'confocal' system if you use multi wave length 2P laser.
Thank you very much in advance for your kind advice.