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I used to do that with a combination of programs - VirtualDub, Phatch and Ninox - before feeding into Registax (AutoStakkert would never work for me with either discrete images or AVI's out of VirtualDub). PIPP would make that a whole lot easier and save a lot of disk space used for intermediate files.
Or, with a Canon EOS, Backyard EOS saves AVI's in RGB24 format that can be used by AutoStakkert directly.
If you use Backyard EOS for capture, use 5x zoom in Planetary mode, and that's almost exactly a 1:1 pixel crop - that makes for good quality video that works well in AutoStakkert. You can still use Registax for wavelets just as before.
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