Image registration is described. In an embodiment an image registration system executes automatic registration of images, for example medical images. In an example, semantic information is computed for each of the images to be registered comprising information about the types of objects in the images and the certainty of that information. In an example a mapping is found to register the images which takes into account the intensities of the image elements as well as the semantic information in a manner which is weighted by the certainty of that semantic information. For example, the semantic information is computed by estimating posterior distributions for the locations of anatomical structures by using a regression forest and transforming the posterior distributions into a probability map. In an example the mapping is found as a global point of inflection of an energy function, the energy function having a term related to the semantic information.