Neural circuits in the central nervous system build our various higher brain functions. However, little is known about mechanisms underlying neuronal information processing in the brain. Anatomical graph structures of real neural networks will provide us with fundamental views to elucidate them. We aim at developing a three-dimensional atlas of neural circuits using high resolution hard X-ray microscopy by synchrotron radiation. We stained neurons of a complete brain from a mouse by the Golgi-Cox method. The heavy metals used in our procedure enhanced X-ray absorption and phase contrast. 3D images of fibriform axons and dendrites of various neurons were reconstructed by back projection. X-ray microscopy with a Talbot interferometer demonstrated finer histological structures of pyramidal neurons in the hippocampus and the cerebral cortex. This observation probably serves as a foundation for achieving a mammalian Connectome Project (identifying complete wiring diagrams of the brain) with X-ray nano-tomography in the near future.