K-Edge Subtraction (KES) imaging is a technique able to map a specific element such as e.g. a contrast agent within the tissues, by exploiting the sharp rise of its absorption coefficient at the K-Edge energy. Whereas mainly explored at synchrotron radiation sources, the energy discrimination properties of modern X-ray Photon Counting Detectors (XPCDs) pave the way for an implementation of single-shot KES imaging with conventional polychromatic sources. In this work we present an X-ray CT imaging system based on the innovative Pixie-III detector and discrete reconstruction. The results reported here show that a reliable automatic localization of Barium (above a certain concentration) is possible with a few dozens of tomographic projections for a volume having an axial slice of 512×512 pixels. The final application is a routine high-fidelity 3D mapping of a specific element ready for further morphological quantification by means of X-ray CT with potential promising applications in vivo.