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I've always used Photoshop to blend in the seams between panels. I register the panels with Registar. For the colour differences between panels I do the colour balance in CCD Stack with pixel maths on the FITS prior to save them to 16bit TIFF then do the stitching. You have to treat every panel as a stand alone process. The end file is usually too big to handle in RAM and do any major changes.
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