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The Big Bang By Balloon
StartsWithABang writes If you want to map the entire sky — whether you're looking in the visible, ultraviolet, infrared or microwave, your best bet is to go to space. Only high above the Earth's atmosphere can you map out the entire sky, with your vision unobscured by anything terrestrial. But that costs millions of dollars for the launch alone! What if you've got new technology you want to test? What if you still want to defeat most of the atmosphere? (Which you need to do, for most wavelengths of light.) And what if you want to make observations on large angular scales, something by-and-large impossible from the ground in microwave wavelengths? You launch a balloon! The Spider telescope has just completed its data-taking operations, and is poised to take the next step — beyond Planck and BICEP2 — in understanding the polarization of the cosmic microwave background.
That is correct. Ozone can (and is) measured in microwave spectral bands. For example, the Microwave Limb Sounder (MLS) on the AURA satellite retrieves Ozone around 240 GHz. Actually, every Microwave sounder that I know of can measure Ozone, so I have no doubt that Ozone signatures in the upper atmosphere (just as from other trace gases) could affect microwave space observation.
But it's not the main reason why they fly there I believe. If they want to do long duration flights, everywhere else, they will have to cross large water masses and cross various airspaces. I believe it would be difficult to do the same in the north hemisphere (crossing Russian airspace). Furthermore, in the polar summer, you do not need to worry about day-night cycles, which makes power supply system simpler. If they need sun for power (always the case I guess over a 48h float), a flight in the polar winter cannot work. The only alternative could be equatorial flight, but getting the overflight permits is complex and there are, to my knowledge, no active balloon bases in equatorial/tropical regions these days.