What is disclosed are a novel system and method for transforming coordinates in an image processing system. In one embodiment, image data is received in a first coordinate space and second coordinate space information is received. A first selection is made, based on a set of relative coordinate space mappings, to select at least a first transformation for mapping of the image data in the first coordinate space to an intermediate image canonical coordinate space using at least a first coordinate change matrix. The intermediate image canonical coordinate space has coordinates which are independent of the image processing system. A second selection is made, based on the set of relative coordinate space mappings, to select at least a second transformation for mapping from the intermediate image canonical coordinate space to the second coordinate space using at least a second coordinate change matrix to transform the intermediate image canonical coordinate space.