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In the markup stage, what do I do when the limb is out of the image or behind something else?

A All of these cases are discussed with illustrated examples in the help panel on the left hand side. Press on the relevant header to get more information about the particular case. If the limb is inside the image, but completely occluded, then you can mark it as such during the skeleton stage by pressing the 'h' key or by clicking on the widget in the right hand panel. The only effect this has is to completely discard this limb from any further processing.