AbstractMaterial decomposition and virtual monochromatic imaging are the two major forms of spectral imaging in CT implemented via either energy-integration or photon-counting detection. With technological advancement in X-ray photon-counting detection, the research and development in photon-counting spectral CT is gaining the momentum towards clinical applications. Compared to its energy-integration counterpart, the photon-counting spectral CT has the freedom in spectral channelization to support multi-material (three and beyond) decomposition for spectral imaging, in which the selection of base materials plays a pivotal role in determining the imaging performance. Aimed at providing guidelines on its design and implementation, we present the physical fundamentals of multi-material decomposition (m-MD) based spectral imaging in photon-counting CT, with an emphasis on the conditioning of basis materials and spectral channelization, and its impact on the performance of spectral imaging in photon-counting CT. Towards soft tissue differentiation in clinical and preclinical applications, we demonstrate the potential performance, including contrast, noise and contrast-to-noise ratio (CNR), of m-MD based spectral imaging and its variation over base material selection, via phantom studies carried out by simulating a photon-counting CT at energy going down to 18 keV.KeywordsSpectral CTPhoton-counting spectral CTDimensionality of material spaceConditioning of basis functionsConditioning of basis materialsMaterial decomposition and virtual monochromatic imaging