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Hi Ben,
I currently use SiriL and have no problems stacking my CR2's with SiriL. But I suppose you would like to process each file is that correct. Maybe stacking as one file maybe the way. Never tried it but I may do that for the exercise. I have a ned to look at each file from my last imaging session.
Otherwise I use darktable which is free to process each file and save them as TIFF's. Unfortunately Darktable does not export to FITS.
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