Tomographic/tomosynthetic image reconstruction systems and methods in the framework of machine learning, such as deep learning, are provided. A machine learning algorithm can be used to obtain an improved tomographic image from raw data, processed data, or a preliminarily reconstructed intermediate image for biomedical imaging or any other imaging purpose. In certain cases, a single, conventional, non-deep-learning algorithm can be used on raw imaging data to obtain an initial image, and then a deep learning algorithm can be used on the initial image to obtain a final reconstructed image. All machine learning methods and systems for tomographic image reconstruction are covered, except for use of a single shallow network (three layers or less) for image reconstruction.