A false-color scanning electron micrograph I took the other day of a B. subtilis bacterium peeking through a polycarbonate filter.
Magnification: 40,000X (the bacterium is about 0.5 micrometers in diameter; compare that with the average width of a human hair, which is 70 micrometers--this bacterium is 140 times smaller!). To the naked eye, this filter just looks like a perfectly smooth surface, and you'd never come even close to seeing that there were bacteria on it!
Since electron microscopy uses electrons instead of light to look at a specimen, there is no color in an image straight from the machine. Thus, color is often applied after the fact to make the image more interesting to look at.