Abstract: A non-rigid anatomy reference system can include reference markers that are rigidly attachable to separate bodies of rigid tissue connected through flexible tissue in a region of a patient forming a marker array. A tracking system can acquire movement data of the reference markers as a function of time and position. A processor can be configured to: receive the movement data, where an individual reference marker has a first number of degrees of freedom less than 6 and a second reference marker having a second number of degrees of freedom; track the marker array as a whole with a total number of degrees of freedom greater than the first and the second number; and produce an updated image of the region of the patient to maintain registration to a prior image of the region and the tracked movement of the reference markers via the function.