A method for tracking position of features of a moving organ from at least one sequence of image frames of the moving organ involves identifying at least a first feature and a second feature of the organ in a reference image frame. Positions of the first and second features in other image frames are tracked in order to learn motion patterns of the first and second features. A dynamic geometric relation between the first and second features is determined. In the event that the first feature of the organ is obscured in a given image frame, position of the first feature in the given image frame is determined using position of the second feature in the given image frame and the dynamic geometric relation between the first and second features.