The problem with cutting the sprites out is that, for the most part of my experience, they include anti-aliasing (semi-transparent pixels to help smoothen edges). Anti-aliasing makes accurately ripping the original sprites ni-on impossible and I doubt anyone has the time, bother and know-how to create a program that can recognise and fix anti-aliasing in any format of media.
When I was attempting to rip sprites from AE this way I had to open each sprite up, frame by frame, in Adobe Fireworks and use the rubber tool at various transparencies to replicate the anti-aliasing. This, however, was menial and heavily time-consuming and simply wasn't worth the shoddy results. The colour of the background I'd ripped the sprites off of was clearly visible around the edges of the sprites in most cases and, without pixel-by-pixel hue editing, I doubt it would be fixed.
Sorry to be the bearer of bad news.
~Blessed be
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