One of the factors that limits the depth at which one can image brain tissue in vivo with two-photon imaging is out-of-plane fluorescence. Although the excitation falls off as the square of the distance from the focal plane, some highly fluorescent samples can add to background even if they’re out-of-plane. For example, the dura mater fluoresces quite well with 810 nm excitation, and as power is increased to see deeper into the brain, the dura can generate green photons even if it is not in the plane of focus.
Experimenters using brightly labeled layer 5 neurons have noted that they can easily image deep into the brain, partially due to the decreased background fluorescence at 910 nm.
So why not use three photon excitation? The excitation photons have even lower energy (1500+ nm), and the probability of excitation falls off as the power of 4. Horton, Wang, Kobat et al. did just that.