Hi Niels!
I think this is a great improvement over the previous system 
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Some thoughts:
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On “ToDo 3” : maybe start with the definition of Circle into the Hough file, and see afterward if there is really a need for other filters to use it ?
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Circles are found by an index center, but defined as a point afterward, leading to a confusing representation. An user that doesn’t check the code will think that the circle is defined in world coordinates, but the radius and center are in fact in continuous indexes. I think it should be harmonized, either by making the center an index, or putting all values in world coordinates (I think the latter is preferable).
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On “ToDo 2” : it depends on the previous choice. If the circle is in index system, there is no need for template.
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Since the return type of GetCircles() will change, I wonder if a vector is not preferable over a list. The syntax to access circles with lists is heavier in my opinion.
Anyway thanks for the time you put into making this!