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Did some googling today and there are a bunch of open source (and some paid programs) that do image stacking and 3d model construction , some are medically oriented e.g/ slicer4, but some are versatile generic tools that can be used in many different ways eg. ImageJ / fiji . Some of them are just 2d to 3d viewers but others allow exporting 3d formats such as obj , stl . Some are geared towards 3d printing, but once you have a 3d mesh you can do lots of interesting manipulations in a 3d program such as blender . I got some fun ideas for next halloween
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