A method of aligning masks for phase imaging or phase contrast imaging in X-ray apparatus using a pixel-type X-ray detector makes use of non-idealities of all real detectors. A mask may be provided before the sample to generate beams, adjacent to the pixels of the detector or both. The method includes moving the mask into a plurality of translational position increments and identifying the increment for which the intensity has a maximum or minimum. The identified value of the increment may vary over the pixels of the detector. Alignment positions are selected in which steps in a plot of the increment over the area of the detector are minimized and/or aligned with the rows and columns of pixels.