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Firstly acquisition. Try to take each panel at the same time of night and under the same moon conditions.
Take each panel up to an early processing step and do each the same way.
Use Photoshop panorama tool (its ok sometimes and other times not) and stitch them together. Perhaps PT Gui, Microsoft ICE or some other stitching program.
Then process it further as a whole. You may still need to balance the subs with each other with regards to colour, lightness. Burn and dodge tools come into play at obvious border differences as does levels..
Greg.
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