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Another thing you might want to consider doing Chris is to scroll through the images first using the slider at the bottom and find the best overall frame. Do a SAP on that frame using a fairly large alignment box. When that is finished do a MAP using one of the first few frames in the reordered list. The initial SAP will reorder the images from best to worst and you will have better features to align on at the start.
(While it's not directly related to what you are asking for but might improve the quality results of your alignment run).
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