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I think K3CCDTools is aimed more towards video camera recording of movie files for planetary imaging more-so than deep sky. At least that's what I use it for. I'm sure it's capable of deep sky stuff, but don't think it's as intuitive.
Nebulosity is more set up for deep sky, long exposure image capture of still cameras rather than video cameras.
I don't have any experience with long exposure modded webcams, so not sure how/where that would fit into the equation. I'm sure they'd be compatible with K3CCDTools, not sure about Neb.
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