The surface temperature means just what you think it does, but you may not have encountered the word emissivity before. Emissivity is the ratio of thermal energy emission of the target object, over the thermal energy emission of a true blackbody at the same temperature.
Everything in nature emits electromagnetic radiation that is a function of its temperature, and not (in theory) a function of what it is made out of. That radiation is what we call thermal radiation. In the case of a perfect black body, which absorbs 100% of all radiation that hits it, the thermal radiation emitted is a function of the temperature only. Furthermore, no object will emit purely thermal radiation with more intensity than a true blackbody, so its emission is a maximum. But most of the real stuff in the real world, as you probably already know, is not perfect. In the case of real world stuff, what it is made out of does make a difference, and nature expresses that difference by a sort of efficiency; some things will emit more thermal radiation, even though they are at the same temperature as something else. High emissivity material emits more thermal radiation, and low emissivity material emits less thermal radiation, at any given temperature. Emissivity is always expressed as a number between zero and one.
The ASTER TIR instrument will measure the thermal radiation coming out of the top of the atmosphere. My atmospheric correction algorithms will remove the effect of the atmosphere, as best we can (it would be better to call this atmospheric compensation, but atmospheric correction is already the officially enshrined title). We will then be left with the thermal radiation leaving the ground surface. From that we will derive both the temperature and the emissivity.
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