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I suggest you need to develop a workflow. Think of it like a flowchart. In simplest form it might be:
[capture data] -> [process data]
Then you break each step down and refine them bit by bit , then end result being a better final image. Depending on your definition of a better image. It could be something that accurate measurements be made from or just yet another pretty picture.
The solution is more a solution that works for YOU, it may not be the best solution but it gets you to an end result. Software will likely depend on how you capture and in what forms. There is no ultimate solution just try lots of packages and follow tutorials and take notes.
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