Methods and systems for deep learning based image reconstruction are disclosed herein. An example method includes receiving a set of imaging projections data, identifying a voxel to reconstruct, receiving a trained regression model, and reconstructing the voxel. The voxel is reconstructed by: projecting the voxel on each imaging projection in the set of imaging projections according to an acquisition geometry, extracting adjacent pixels around each projected voxel, feeding the regression model with the extracted adjacent pixel data to produce a reconstructed value of the voxel, and repeating the reconstruction for each voxel to be reconstructed to produce a reconstructed image.