The position of the sample is measured and used to correct for any off-axis motion during tomography using x-ray projection microscope system with a rotation stage system. The position is sensed using a precision-machined, low-CTE gold-coated cylinder or disc and three to five capacitive distance sensors. The correction can then be performed purely as image processing in software, by applying an appropriate shift in X and Y of the captured x-ray projections. A calibration is often necessary for each system (gold disc plus sensors plus sample stage) to account for any machining errors of the gold disc or positioning errors of the capacitive sensors. This calibration should also be repeated whenever any maintenance is performed on the metrology setup.