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There is a similar problem with registax when using fits files, in some parts of the program it stretches the image and in other places it doesn't, this leads to a serious problem when you use the "create reference" feature, as you end up comparing stretched vs not stretched images.
personally I solved this by making pixel (0,0) "black" and pixel (0,1) "white" in my fits images, defeating anyone who tries to stretch them :-)
cheers, Bird
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