"in vivo" is Latin for "within the living."
Here, it indicates that the experiment was done in a living mouse.
It has always been challenging to perform experiments on living animals; there are many technological, practical, and ethical concerns which generally limit the precision with which experiments can be conducted.
For example, in order to see beyond the surface of mouse's brain, we have always needed to cut the brain into thin sections, and therefore need to euthanize the mouse.
With the invention of two-photon imaging, it became possible to image noninvasively (without the need to euthanize) deep into a mouse's brain, unlocking powerful experiments such as those performed in this paper.