XRay diffraction patterns are black and white. So are scanning electron microscope (SEM) images. Why is this so? At the time of measurement at the atomic level, do the atoms fail to absorb or emit colored light?
This has to do with the way the radiation is detected. X-ray diffraction, for instance, deals with electromagnetic radiation with a wavelength shorter than 10 nm. This cannot be properly assigned a color, but it is nevertheless possible to detect it using some instrument. This can result in an image, and it is up to the person carrying out the experiment to assign a color scale to that image.
Bare atoms have very specific wavelengths associated with their transitions, some of which are in the visible spectrum. Sodium, for instance, has a strong transition at 598 nm, which is the orange you often see in street lights. In labs that work with sodium, though, there is no added benefit to designing experiments such that they can see the orange color gets imaged. They might as well detect everything in grayscale and color it in afterwards.