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Brightness Units
Flux
A measure of the amount of energy striking our telescope. It is typically given in units of a Jansky, abbreviated Jy. One Jy represents 1.0x10-26 W/(m2 Hz), which is a tiny amount of power (Watts), per unit area of our telescope (m2), per each frequency unit measured (Hz).

Flux Normalized to 4.04 AU

This is just the flux, adjusted to what it would be if the object was 4.04 AU away. To understand why we make this adjustment, imagine the headlights of a car approaching you at night. As the car gets closer and closer, the headlights look brighter and brighter to you. (This is explained by the inverse square law, which some of you may have studied.) The headlights themselves aren't changing, only their distance from you is changing. Similarly, since all the planets are moving, the flux we receive from them increases when they get closer, and decreases when they get farther away. Since we are interested in measuring true changes on the planet rather than just the changes due to distance, we sometimes adjust flux measurements to a common distance. When looking at Jupiter, we generally chose 4.04 AU because that is the closest Jupiter and Earth ever get. 
     Why don't we bother normalizing fluxes when we look at things very far away, like quasars? The reason is that they are so far away, the motions of the Earth and the quasar do not change the distance an appreciable amount even over many years. (The difference between something being 100,000,000,000,000,000,000 miles away and 100,000,000,000,100,000,000 miles away is not much!)

Brightness Temperature
Brightness Temperature is another way of measuring the amount of energy coming from an object. All objects naturally emit energy in a process called "thermal emission" or "blackbody emission." (Everything around you - planets, your chair, and even you - emit this energy.) In the simplest case, the amount of energy emitted depends only on the physical temperature of the object. So, when we say something has a brightness temperature of 100 Kelvin, we mean it is giving off as much energy as something that is at a temperature of 100 K. The brightness temperature, however, is not always the true physical temperature of an object! Some materials emit slightly more or less energy than other materials even when they are at the same temperature, and sometimes things emit energy by other means in addition to thermal emission. This can make their brightness temperature much higher than their physical temperature. The emission from Jupiter at S-band is an example of this.
     Brightness temperature is most often used when talking about planets. One reason for this is that it sometimes gives us an idea of the true physical temperature of the planet. Another reason is that, just as Normalized Flux described above, brightness temperature accounts for the changing distance of the planet.
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