A system and method for accounting for motion of a target in a medical procedure includes an endoscope (302) including a tracking mechanism (304) for tracking positions and orientations of the endoscope. Memory storage (310) is configured to record the positions of the endoscope when positioned at or near moving target tissue. A motion sensor (312) is configured to track cyclical motion of an organ such that the cyclical motion of the organ can be correlated to the recorded positions of the endoscope and the target tissue.
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