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Greg,
I use PI for everything starting with calibration and registration. To do this combination the easiest way is to use the BatchPreprocessing script. If you just want to do registration then StarAlignment is the tool of choice.
The FITS format has some weaknesses as a standard so you'll find there are issues with moving files between applications like CCDStack and PI. These can be resolved (PI has a lot of flexibility if you mess with the preferences) but it is generally more difficult to skip between applications.
Cheers,
Rick.
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