Interpretation of image from a STM mircroscope

Pardon my apparent cluelessness on this subject. My curiosity peaked after watching a video of (apparently) atoms. What I saw was essentially areas of black white or grey. I do understand that the microscope does not use visible light in discovering the atoms particles due to the relative large size of photons.
I'm rather curious about what one should interpret the black and white areas, and the grey spheres as. I mean, does the black areas mean that it's an area that's a vacuum?

Well, the way a STM works is that it can 'sense' when an object is near by sparking a current through the vacuum in between (it's a little more complicated than that, but it's a close enough analogy). The closer the object is, the more current will flow. So what you're actually seeing is patches of an object getting close, so that the current can run through, and patches of nothing being near. To make it easier to interpret, I'm guessing they color the 'high current' areas white and 'low current' areas black. And greyscale accordingly in-between.

I hope this answers your question.

The STM microscope essentailly measures the charge density of electrons at the surface of a material. The lightness/darkness of the image simply indicates the charge density.

Depending on how the image-processing is set up, the dark areas probably mean low electron charge density. But colours could equally well have been used - see link.

I know more about who invented the Scanning Tunneling Microscope (Gerd Binnig and Heinrich Rohrer) than how one works. (Actually, I know more about the guy who invented the best in his time- Adam Cohen- age 18- in 1998).

Maybe Wikipedia might be of some assistance?
It is a bit complicated.