1. A method of investigating a specimen using a tomographic imaging apparatus comprising: a specimen holder, for holding the specimen; a source, for producing a beam of radiation that can be directed at the specimen; a detector, for detecting a flux of radiation transmitted through the specimen from the source; a stage apparatus, for producing relative motion of the source with respect to the specimen, so as to allow the source and detector to image the specimen along a series of different viewing axes; and a processing apparatus, for assembling output from the detector into a tomographic image of at least part of the specimen, the method comprising: acquiring a set of input images of the specimen taken at a corresponding set of source positions relative to the specimen, which source positions are intended to lie on an ideal locus but are instead caused by positioning errors to lie on a distorted locus; using said input images to construct an initial tomographic image; dissociating said initial tomographic image into a set of reference images referenced to said ideal locus; comparing given input images to corresponding reference images, and calculating a set of transformations necessary to map the former onto the latter; and using said set of transformations to construct a modified tomographic image.