Abstract: Systems and methods for improving magnetic resonance imaging relate to reconstructing multi-slice images based on sharing the strong structural similarities between adjacent image slices. In addition, a joint denoising method exploits these structural similarities. In part the reconstruction is based on use of a residual neural networks and denoising is achieved with a deep learning based strategy. The system and method have proved useful in both simulation and in vivo brain experiments, demonstrating significant noise reduction in all images and revealing more microstructural details in quantitative diffusion maps.