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Hi Trevor,
You may not have done this:
After you have a stack each for the L, R, G, and B, you need to go into the BATCH menu and select ALIGN AND COMBINE, and in that menu tick SAVE EACH FILE and then the method - TRANSLATION - ROTATION - SCALE. Select the 4 stacked files. Press okay and you will get 4 new files created with ALIGNED in the name.
Then use LRGB Colour Synthesis using these 4 "aligned" files.
Craig
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