Atoms are about three orders of magnitude smaller than the wavelength of visible light. So for any optical microscope they are just point sources. The finite size spot a camera sees is only due to diffraction from the finite size of the objective. This is also why stars don't appear infinitely small in images.
> In optical engineering, the objective is the optical element that gathers light from the object being observed and focuses the light rays to produce a real image. [1]
I found this [2] article to be pretty approachable without the jargon overload like Wikipedia often suffers from.
[1] - https://en.m.wikipedia.org/wiki/Objective_(optics)
[2] - https://en.m.wikipedia.org/wiki/Diffraction-limited_system
Quantum dots are a few nanometers in size (so << the wavelength that they emit) and you can get a solution of them from Sigma Aldrich for ~$500. People mix them into their samples and then use that to deconvolve the image/volume that they acquire.
This wasn’t the correct setup though to do that. Presumably the reason you can see a single atom is because there is only one present, ie if there was a second one next to it you wouldn’t necessarily be able to see the difference in the photograph.