In 1981, Elliott and Dover designed an X-ray microtomography scanner as a means of measuring the local mineral concentration in teeth. Although slow, this first generation system gave accurate measurements of the X-ray linear attenuation coefficient (LAC) due to its use of energy dispersive photon counting apparatus. Attaining such accuracy with integrating detectors in third generation scanners is difficult, but has been the goal of our ongoing development. The current *MuCat 2* system uses a 6cm square CCD chip with a parallel fibre-optic faceplate coupled to a CsI scintillator. Time delay integration readout (with sliding camera) is used to eliminate ring artefacts and enable high dynamic range X-ray projections to be acquired. The beam is collimated with a moving aperture (tracking the camera) to reduce X-ray scatter. Beam hardening is reduced by the use of filtering and corrected using data from an aluminium step wedge to optimise a model of polychromatic X-ray generation, attenuation and detection. Adjustments can be made to the model to allow for known specimen composition. Projections are corrected for distortion and repeatable wobble in the rotation stage. Where high absolute accuracy of the LAC is required, a pure aluminium wire is included in the scan and used to *fine-tune* the grey level after reconstruction.