The software Dave and Gail used, AstroIIDC (Mac), records the video in Quicktime format.
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Dave, I'd be curious to know if you and Gail have tried
Lynkeos to process your videos. Although I'm nowhere close to producing what you do, I do have experience with both AstroIIDC and Lynkeos. I prefer Lynkeos only because it's not quite as convoluted (to me, anyway) as AstroIIDC.