Try imregister() and imshowpair(). There are examples in the help to help you.
How to compare two parts of same image?
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I am subplotting 3 images back to back which are a part of each other with a minor difference shifted (not rotated) in certain way. I want the user to choose the most appropriate one.I read abt image registration but have no clue how to use it. Please help.
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