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Stitching images with overlays

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I am stitching one large imaq image from several smaller images using image to image copy.  The small images each have several overlays.  After the image to image copy the overlays from the small images are lost. How can this be avoided.  Or at least how can I get the overlay image information to manipulate it and reapply the data.

Is this possible, it seems that it should be.

 


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