Optical coherence tomography angiography (OCTA) is a relatively new imaging modality that generates microvasculature map. Meanwhile, deep learning has been recently attracting considerable attention in image-to-image translation, such as image denoising, super-resolution and prediction. In this paper, we propose a deep learning based pipeline for OCTA. This pipeline consists of three parts: training data preparation, model learning and OCTA predicting using the trained model. To be mentioned, the datasets used in this work were automatically generated by a conventional system setup without any expert labeling. Promising results have been validated by in-vivo animal experiments, which demonstrate that deep learning is able to outperform traditional OCTA methods. The image quality is improved in not only higher signal-to-noise ratio but also better vasculature connectivity by laser speckle eliminating, showing potential in clinical use. Schematic description of the deep learning based optical coherent tomography angiography pipeline.