A method and apparatus for automated vertebra localization and identification in a 3D computed tomography (CT) volumes is disclosed. Initial vertebra locations in a 3D CT volume of a patient are predicted for a plurality of vertebrae corresponding to a plurality of vertebra labels using a trained deep image-to-image network (DI2IN). The initial vertebra locations for the plurality of vertebrae predicted using the DI2IN are refined using a trained recurrent neural network, resulting in an updated set of vertebra locations for the plurality of vertebrae corresponding to the plurality of vertebrae labels. Final vertebra locations in the 3D CT volume for the plurality of vertebrae corresponding to the plurality of vertebra labels are determined by refining the updated set of vertebra locations using a trained shape-basis deep neural network.