Spectroscopic imaging is well suited to the study of micro-samples from artworks, where the sample material is limited and the maximum amount of information needs to be obtained. In this study, a new approach to imaging elemental data from energy dispersive X-ray analysis maps was used in conjunction with micro-Raman spectroscopic imaging to characterise the paint layers within micro-samples. Cross-sections from the 16th century painting Portrait of a Youth were found to contain vermilion, lead-tin yellow type 1 and a blue-green pigment consistent with terre-verte. The mid-preparatory layer (imprimatura) contains a high proportion of elements and mineral inclusions that indicates a clay-type composition. The ground layer was identified as anhydrite with large gypsum inclusions. The pigments and composition of the preparatory layers are consistent with those used by Italian Renaissance artist Dosso Dossi.