Caption: "Image of surface reconstruction on a clean gold (Au(100)) surface, as visualized using scanning tunneling microscopy (STM). The individual atoms composing the material are visible. Surface reconstruction causes the surface atoms to deviate from the bulk crystal structure, and arrange in columns several atoms wide with regularly-spaced pits between them."
The image is ∼ 100 X 100 Angstroms (Å) = 10 X 10 nanometers (nm), where 1 nm = 10 Å = 10**(-9) m
Features:
The brighter columns are higher and the darker ones are lower.
So why gold color? It's gold.
They look like fuzzy little balls. Why?
Because atoms are fuzzy little balls. The electrons that make up almost all the size of atoms exist in a continuum superposition of positions according to quantum mechanics. Thus, there is a continuously varying electron density in atoms with NO sharp edges or jumps in electron density.
The actual electron density depends on the particular physical state of the electrons. Images of atoms give only limited knowledge of this state and quantum mechanics calculations must be done to obtain it to high accuracy/precision.