General Data description: The following are hyperspectral (energy-resolved) X-ray CT datasets for a set of mouse limb specimens, each stained with multiple contrast agents. All scans were acquired with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The following data contains all the files necessary for reconstruction of each dataset. The biological specimens were produced as they each contain multiple contrast agents, with distinct spectral markers. When measured by an energy-sensitive detector, each contrast agent may be identified and segmented individually following spectral analysis. A mouse hindlimb was double-stained with elemental iodine and BaSO4. A mouse forelimb was triple-stained with I2KI, BaSO4 and PTA. File descriptions: Contained are two HDF5 (.h5) data files, as well as two (.txt) metadata files and a MATLAB (.mat) file. Hindlimb_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the double-stained hindlimb. Forelimb_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the triple-stained forelimb. DS_Mouse_hindlimb_sinogram.h5 contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the double-stained hindlimb specimen. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied. TS_Mouse_forelimb_sinogram.h5 contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the triple-stained forelimb specimen. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied. Energy_axis.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning.