Hybrid pixel cameras are new X-ray detectors working in a photon counting mode rather than in the standard integration mode used in conventional radiography systems. This novel approach presents advantages, in particular the absence of dark noise and the ability to set an energy threshold on the detected photons. This ability is of uppermost importance for the development of K-edge imaging approaches, which exploit spectral information on the counted photons. We investigate the capability to perform K-edge imaging by using the new XPAD3 hybrid pixel detector with 500 kpixels of 130 μm incorporated in the micro-CT demonstrator PIXSCAN II. K-edge images are obtained from three sets of projections acquired from the same subject under three different energy thresholds around the K-shell binding energy of a contrast agent. To minimize time dependent changes of the biological samples between the three acquisitions, we have developed a composite pixel protocol allowing simultaneous acquisitions of the projections under three different energy thresholds. This methodology reduces the acquisition time and dose by a factor 3 at the expense of a corresponding loss of spatial resolution. We nevertheless demonstrate the validity of the method on different phantoms and finally on mice. Indeed, K-edge imaging with PIXSCAN II allows for the unambiguous identification of voxels containing iodine in the body of a mouse.