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The atom can't be directly imaged by bouncing light off it, it's far too small to do that (with visible light).

Instead they're shining a laser at it, which excites some of its valence electrons to higher orbitals. When those electrons drop back to their ground states they emit (visible) light, some of which reaches the camera.

The atom is effectively acting as an isotropic radiator (radiating equally in all directions). The camera lens is much larger than the atom.

There are thus multiple paths from the atom to the lens and the sensor behind. Less light will reach the camera from greater angles, so the light that goes straight towards the lens or nearly straight will impact the sensor most, and that area will appear brightest. (This is my somewhat mangled attempt to explain abberation in optics...)

Even if the light were perfectly collimated in a beam the size of the atom it would still be unable to make a dot in the final image smaller than a single pixel of the sensor. If film were used instead of a digital sensor it would expose at least one pigment grain, again much larger than the atom itself.

The apparent size is an artifact of the imaging process.



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