Systems and methods of image processing include a processor in communication with a display and a computer readable recording medium having instructions executed by the processor to read a three-dimensional (3D) image data set from the computer-readable recording medium and automatically generate a tree structure of blood vessels based on patient images of the image data set using a neural network. Manually- and/or semi-automatically-generated 3D models of blood vessels are used to train the neural network. The systems and methods involve segmenting and classifying blood vessels in the 3D image data set using the trained neural network, closing holes, finding roots and endpoints in the segmentation, finding shortest paths between the roots and endpoints, selecting most probable paths, combining most probable paths into directed graphs, solving overlaps between directed graphs, and creating 3D models of blood vessels based on the directed graphs.