Abstract: An X-ray microscopy system and method for phase contrast and dark-field imaging utilize a partially coherent X-ray beam generated by a micro-focused X-ray source with a small focal spot size. A spatial beam modulator such as a random phase object, e.g., silicon carbide sandpaper, is placed between the source and the sample to create a random granular speckle pattern. The system employs a high-resolution detection setup with a thin scintillator and a spatially resolved detector with small pixel size to capture shifts in the speckle pattern caused by the sample's refraction effects. By analyzing these shifts, the system computes phase gradients and integrates them to produce detailed phase images, enhancing contrast in low-atomic-number materials like soft tissues and polymers. The compact design reduces source-to-detector distance, improving flux efficiency and system throughput while enabling high-resolution, three-dimensional tomographic imaging.