Abstract
Accurate non-invasive identification of hydroxyapatite (HA) deposits is important for diagnosing calcific musculoskeletal disease and quantifying vascular calcification, but conventional and dual-energy CT often struggle to distinguish HA from iodinated contrast because of overlapping attenuation, noise, and beam-hardening artifacts. Spectral photon-counting CT (SPCCT) offers improved energy resolution and spatial fidelity, yet most deep-learning approaches in spectral CT focus on continuous density regression or anatomical segmentation rather than direct voxel-wise material labeling. We developed SPFF-UNet, a spectral-preserving 3D segmentation model for direct classification of HA and iodine concentrations from five-bin SPCCT volumes without material-decomposition preprocessing. A cylindrical phantom containing twelve materials was scanned at 0.1 mm isotropic resolution, including five HA concentrations, three iodine concentrations, three soft-tissue equivalents, and water. SPFF-UNet integrates spectral squeeze-excitation, EnergyFiLM, and FourierGate to preserve and exploit multi-energy information throughout the network. The model was trained for thirteen-class voxel-wise segmentation and compared with five established 3D architectures under matched training conditions. SPFF-UNet achieved the best macro-averaged performance on a held-out phantom scan (Dice 0.72 ± 0.01, IoU 0.59 ± 0.01, sensitivity 0.73 ± 0.01, precision 0.71 ± 0.01), outperforming the strongest comparator, ResUNet++ (Dice 0.66 ± 0.02, IoU 0.46 ± 0.02, sensitivity 0.67 ± 0.02, precision 0.61 ± 0.03). Performance gains were concentrated in mid/low-contrast HA and low-concentration iodine, with reduced slice-wise variability and fewer HA-iodine misclassifications. These results suggest that preserving spectral information and applying targeted spectral modulation can improve concentration-aware voxel classification from SPCCT. This phantom-based proof-of-concept provides a basis for future in vivo validation.