Micro-computed tomography (Micro-CT) is an X-ray imaging technique that produces high-resolution 3D computerised virtual' models of geological specimens based on the X-ray attenuation of different materials in the specimen. The virtual' specimens are made up of voxels, the 3D equivalent of pixels, each assigned a gray value based on X-ray absorption. Micro-CT has enormous potential for allowing non-destructive, digital analysis of structure and composition when the mineralogical phases can be digitally separated. However, variation in X-ray flux between scans results in highly variable grayscale values for identical materials. Consequently, materials usually have to be segmented manually, which is subjective, inaccurate, labour-intensive and time consuming. Here we present a protocol and imaging software package that can be used to accurately and precisely extract quantifiable information in a repeatable and objective fashion. The software will allow the separation, visualisation, measurement and analysis of spatial and volumetric distribution of different mineral phases without damaging the specimen. This paper explains the potential use of this protocol and software package to ultimately allow automatic segmentation and quantification of gold in drill core samples, removing subjectivity and inaccuracies from data processing.