It wouldn't work well at deep depths because it's interacting with the electron shell. After a few nanometer or two of tissue you'd have no signal. If you'd figured out a way to put a brain in the microscope. They tend to want samples in a vacuum, a few cm square and no more than a few mm thick including the sample mount.

You'd have to use something like neutrons, which don't interact with electrons and can be used to image internal structure. Those tend to have side-effects, though, like inducing radioactive decay in nuclei.

Don't fire electron beams at live brains, they don't like it.