In this case, "in and out of focus" is actually variations in the amplitude of the probability function for the electron density projected onto a single plane (to a first approximation). Sometimes the wave functions of all the electrons interfere constructively, so you see a bright spot, and sometimes deconstructively, so you see dark. Depending on the orientation of things, this results in the images of "atoms" that you see in the picture. As the crystal changes shape and size, the interference patterns change, which partially explains why it disappears and reappears a few times. There's a bit more going on than that, but the physics of what's happening in a TEM image is really neat.
Most of the electrons in a NaCl crystal are quite localized (all the core electrons od Na+ and Cl-, and it's not a good conductor, so the valence band is full). So I don't expect too much interesting interference patterns. It looks like a problem with vibrations that make it go out of focus.
Wow, mind blown. Thanks for correcting me. Amazing to learn that the wave function is so directly sampled by TEM that the image we get shows Moiré patterns caused by its phase :)
