Deep neural networks (DNNs) are shown to be promising solutions in many challenging artificial intelligence tasks. However, it is very hard to figure out whether the low precision of a DNN model is an inevitable result, or caused by defects. This paper aims at addressing this challenging problem. We find that the internal data flow footprints of a DNN model can provide insights to locate the root cause effectively. We develop DeepMorph (DNN Tomography) to analyze the root cause, which can guide a DNN developer to improve the model.