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When shooting with a DSLR always shoot in RAW and make sure the colourspace is set to Adobe RGB. Some say this doesnt matter (rgb) but I don't know for sure so I set it anyway.
CCDs save there files at Fits files. AFAIK this is the standard file format for CCD Cameras and all astro progs should work with them.
Simple solution, buy the business a 550D and keep the 40D.
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