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My workflow in DSS is to load up each channel into a separate group with their relevant calibration files
I load one dummy image file onto the "Main" group because it has special (unwanted) properties. But it needs one file for another group tab to appear.
Then I register everything but don't stack. This can take a while if you have lots of subs.
The best image I copy back in Windows and call "Ref.fits" and I load it onto the Main group.
Leave it unchecked, right click and Use as Reference Frame.
Remove the dummy file that was on Main group.
Then one group at a time I select all the files in the group and right click to Check them.
Then I stack that group and save the output file. Make sure you don't re-register the files.
When done I Uncheck All then move on to the next group.
Rinse and repeat for all groups
All your stacked images will now be aligned
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