Yes. These are images taken by confocal microscopy, where you focus a laser scanning microscope on a plane and only see that. Then you move the focus plane up

Yes. These are images taken by confocal microscopy, where you focus a laser scanning microscope on a plane and only see that. Then you move the focus plane up by a bit and take the next picture. Super-resolution microscopy such as STORM, STED or PALM on the other hand will give you coordinates.