In our dual-modality microCT/microXRF system, the two sub-systems are combined in one machine, sharing a
travelling sample holder. The microXRF, based on a pin-hole collimator and a photon-counting energysensitive 2D-detector, obtains 3D chemical composition maps of a sample. These images often lack structural information. With the built-in microCT, 3D structural information of the sample can be obtained. The two subsystems need to be properly calibrated and aligned. This calibration and alignment procedure needs to be done for all pin-hole collimators, but only need to be performed once after the system is assembled. The two modalities are calibrated separately, by analyzing projection images of a 3-ball phantom. The phantom is made of a very thin plastic cylinder, on which 3 copper balls are attached at well-chosen locations. The same phantom is used for both sub-systems and is scanned sequentially. We have evaluated this calibration method on various CT scanners and it has proven to be very effective. But it is more challenging for the XRF subsystem due to the strong absorptions. The two imaging spaces are calibrated relative to their own coordinate systems. To align the two sub-systems, the centers of the balls in reconstructed volumes are determined and then aligned using a rigid transformation. Repeated tests have shown that the mechanical movements are stable and the reconstructed image volumes can
be well co-registered.