Sunlight can penetrate deeply into the atmosphere at this wavelength and be reflected back out, providing a view of an underlying region of the atmosphere, the lower troposphere. The second panel was taken in the blue portion of wavelengths detected by the human eye. At these wavelengths, gases in the atmosphere scatter a modest amount of sunlight, so the clouds we see tend to be at somewhat higher altitudes than in the top panel. The third panel shows near-infrared reflected sunlight at a wavelength where the gas methane, an important constituent of Jupiter's atmosphere, absorbs strongly. Dark places are regions without high-level clouds and consequently large amounts of methane accessible to sunlight.
Bright regions are locations with high clouds in the upper troposphere shielding the methane below.
The bottom panel was taken in the ultraviolet. At these very short wavelengths, the clear atmosphere scatters sunlight, and hazes in the stratosphere, above the troposphere, absorb sunlight. That makes it difficult to see into lower layers at all. The bright regions are generally free of high stratospheric hazes. A small bright spot is visible near the center of each panel.