As it provides the only method for mapping neural tracts in vivo, diffusion MRI tractography is gaining importance in clinical and neuroscience research. However, the precision of tractography results is influenced by many factors. In this study, we propose a highly realistic simulator based on real data acquired by synchrotron x-ray phase-contrast imaging. This imaging technique with histology-like resolution is demonstrated to reveal adequately the mouse brain in 3D by comparison with classical histology, which loses continuity along the sectioning axis. We expect that our simulator may serve as a tool for the validation and optimization of tractography algorithms.