Fluorescent microscopy can illuminate neurons genetically engineered to express fluorescent proteins. "Two-photon" microscopy is special because it lights up the fluorescent neurons only at the focal point allowing scientists to piece together multiple sections in order to obtain a 3D image.
So how does this "two-photon" technology produce fluorescence only at the focal point if the fluorescent laser beam is penetrating all of the surrounding tissue? The theory is that the chances of two low-energy photons hitting the fluorophore at the same time with enough energy to produce a fluorescent event are extremely slim.
Imagine you're at a cocktail party and you've had a couple drinks. It's a big room and even though you're stumbling around, you haven't bumped into anyone with enough force to spill your drink. Now shrink the room a bit. People are closer so you start bumping into them one by one. But what are the odds that you'll bump into two people at the same time with enough force to spill your drink? The odds are slim to none. But when you shrink that room small enough (the focal point), the chances of bumping into two people (photons) at the same time is enough to make you spill the drink (fluorescence).