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 first set of input images of the specimen, each input image being acquired while maintaining the source at a different position relative to the specimen, wherein the different positions are intended to lie on an ideal locus but instead lie on a distorted locus as a result of positioning error; using said input images to construct an initial tomographic image; dissociating said initial tomographic image into a second set of images and forward projecting the second set of images onto the ideal locus as a third set of reference images, the reference images corresponding to different input images of the first set of input images, wherein a collection of first features shown in at least a subset of the input images is also present in the reference images corresponding to the subset, and wherein each first feature is: associated with a positional error that indicates a positional deviation between representations of the first feature in a corresponding pair of input and reference images, and sufficiently small in size that the positional deviation for each first feature is observable and quantifiable from a comparison of the representations of the first feature in the corresponding pair of input and reference images; determining the positional errors for the collection of first features by performing the comparisons and quantifying the positional deviations observed therefrom; using the positional errors to calculate a set of transformations by which input images of the first set of input images can be mapped onto corresponding reference images; and using said set of transformations to construct a modified tomographic image.