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I used to use Images Plus for processing one shot colour images.Its built form the ground up to do that. CCDstack will do it as well and I think it has been improved a lot for one shot colour cameras but in the past it did not seem particularly friendly to one shot colour.
Its been a while but Images Plus does a lot of these steps automatically once setup with which camera. I'd check if they support the FLI 8000C.
Debayering means to separate the colour data into the red green and blue separate data to enable individual processing of each colour should you want.
I think really though all you want is to do darks, flats and biases then stack. Perhaps some noise reduction with data rejection of hot and cold pixels to clean it up a bit more. I would use CCDstack for data rejection but that could be a later refinement once you are stacking colour images and getting a good image.
Greg.
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