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MiC is an ImageJ plugin to compare segmentation masks.

it comes with 3 plugins:

• Mask instant Comparator for 2D masks or stack of 2D masks
• Mask instant Comparator 3D for 3D masks (work for single slice masks also)
• Convert Stack 2D masks to 3D mask to convert a stack of 2D masks to 3D mask i.e. check that objects keeps the same object number value along stack.