A surgical specimen imaging system includes a micro-X-ray computed tomography (CT) unit for CT imaging of the specimen and a structured light imaging (SLI) unit for optical imaging at multiple wavelengths, multiple phase offsets, and multiple structured-light pattern periods including unstructured light. The system's image processing unit receives CT and optical images and is configured by firmware in memory to co-register the images and process the optical images to determine texture at multiple subimages of the optical images, determined textures forming a texture map. The texture map is processed by a machine-learning-based classifier to determine a tissue type map of the specimen, and the tissue type map is processed with the CT images to give a 3D tissue-type map. In embodiments, the firmware extracts optical properties including scattering and absorption at multiple wavelengths and the classifier also uses these properties in generating the tissue type map.