Can you please explain me phenomenon of reflection at subatomic level? When we see atoms under an electron microscope, what exactly are we seeing? I mean, these spheres that we know as atoms are electron clouds and that is what we are seeing, am I right? 
https://www.youtube.com/watch?v=pGWSX6pStd0
Can you please explain to me, how exactly our eyes are able to see those spheres that we know as atoms? Like photons are hitting those constantly moving electrons and then they reflect back and hit the retina of our eyes where it gets absorbed. That’s fine. But I want to know, how exactly photons are interacting with those constantly moving electrons of an atom of an object from which they are being reflected?
 A: The linked video shows a TEM image. In transmission electron microscopy, you have a parallel beam of electrons incident on the material, which gets scattered by the atoms in the material. Note that, it is not just the electron cloud, but the potential formed by the atomic core (nucleus+ core electrons) and the valence electrons together, that scatter the incident electrons. To visually see the image one can use a scintillator to capture the electrons, which results in the emission of photons. One can also use a CCD system for this purpose and get a digital image.
Since electrons have a wavelength much lower than visible light, they can be used to probe extremely small length scales and can achieve atomic resolution in the images. 
During the scattering process, there are both elastically and inelastically scattered electrons. The elastically scattered electrons are useful in forming diffraction patterns, which can be used to study atomic structures. The inelastically scattered electrons can be used for characterization of the material in EELS, EDX etc. 
