X-ray imaging and classification of volume defects within a three-dimensional structure includes identifying one or more volume defects within a three-dimensional structure of a sample and acquiring, with a transmission-mode x-ray diffraction imaging tool, one or more coherent diffraction images of the one or more identified volume defects. The process includes classifying the one or more volume defects within a volume of the three-dimensional structure based on the one or more coherent diffraction images, and training an additional optical or electron-based inspection tool based on the one or more classified defects.