Biological research on small animals is constantly demanding for imaging devices with higher performances like combined scanners enabling multiple modality data acquisition. In this context, we consider the concept of using hybrid X-ray pixel detectors (XPAD) with the clearPET to build a prototype of microPET/CT. The system will permit simultaneous acquisition of the anatomical and functional modalities. Thanks to the placement of the XPAD in front of the gamma detectors. It is foreseen to place the X-ray source outside the PET ring, thus involving a non-conventional off-centered circular geometry for the CT data acquisition. In a first step, a series of acquisitions were performed with a microCT, built with the XPAD2 detector. Our work consists first, in the investigation of several CT reconstruction methods for these acquisitions. We hereby compare the reconstruction results obtained with two variants of the Feldkamp and two analytical methods developed to compensate for some artifacts. Second, the reconstruction issue in the off-centered geometry is addressed by testing the same algorithms on numerical simulations. It appears that, if the next generation of XPAD detectors using smaller pixels is needed to obtain high resolution images, the reconstruction method employed, plays an important role and can efficiently improve the quality of the results.