Each dot is fluorescence from a single trapped barium ion. Excitation/fluorescence is at 493 nm, so the false-color map in the video is almost realistic.
My company makes an Scanning Probe Microscope (more commonly known as an AFM) which goes into a Zeiss Scanning Electron Microscope. You can unlock some really neat applications with the combination - scanning areas which would be hard to locate, observing the tip interaction with the sample and using the Focused Ion Beam to remove material from the sample.
With SPM, you can do a variety of measurements - measure the topology, measure the electrical properties, surface potential, conductivity, etc.
One thing that I don't quite get. If a single atom is the smallest thing (other than quantum foam etc), then what is it resting on in this movie. IE what is the background made of?
"Copper plate:
The scientists used copper 111 as the surface of the animation — the same material they used 10 years ago when they built the first computer that performed digital computation operations.
Carbon monoxide (CO): ok
The scientists chose carbon monoxide molecules to move around the plate. Carbon monoxide has one carbon atom and one oxygen atom, stacked on top of each other."
One thing I don't understand with that quote: it seems to imply this video was made only ten years after "first computer that performed digital computation operations". Is this a typo in the original or are they referring to something else?
Smoothness is likely due to the grounding of the backplate.
If anything I would posture that they’ve filmed the backplate and the A
atoms are the shadow from the scattering of the electrons that didn’t hit the backplate.
It's not like normal photography, it's more of a visualization of an electrical current sensor. The background is just the area of the plane they were scanning that didn't have any atoms.
Other atoms, but further away. Effectively the background is blurred because it's out of focus. The depth of field is thin enough that this works. (These are analogies. It's not strictly correct.)
It's so far from correct as to be not a useful analogy.
The real question is, how is the microscope's output converted into a visual picture? Hint, it isn't by lensing light. Thus there is no "focus" to be out of.
An atomic force microscope produces images by sensing atoms with a probe. It scans in a planar layer, analogous to a very narrow depth of field for a film camera. The background atoms do exert force on the probe, but much more weakly.
https://avsteele.com/index.html#science (scroll down a little)
Each dot is fluorescence from a single trapped barium ion. Excitation/fluorescence is at 493 nm, so the false-color map in the video is almost realistic.
More details are in the figure caption.