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You can't do that with CCDsoft. So you would need to do that as Lodestar can have hot pixels/artifacts that need to be dark subtracted out to be useful.
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What am I not understanding here? CCDSoft can do bias or dark subtracts for the Lodestar using an image reduction group (see "CCDSoftV5->Image->Reduce->Image Reduction->Autoguider" and "CCDSoftV5->Take Image->Autoguider->Image->Reduction bias, dark, flat->Group Autoguider"). I do exactly that with CCDSoft to eliminate hot pixels. The Lodestar doesn't work at all as an autoguider if you don't eliminate those pesky hot pixels.