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Roger,
For sure if you just stack all the grey scale images from the camera the resulting image will not give colour. If you do the suggestion I said earlier in CCDStack you can easily convert all the Bayer masked images directly to colour and then stack those.
I'm betting that a guy like Adam Block would not say to separate the RGB frames and stack individually if there were not some significant advantage. It's a lot of extra work so I'm thinking there must be something gained. He does a tutorial as part of the CCDSoft tutorials just on this subject so I may watch it again and see if he spells out the reason.
Peter
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