A method and system for automatically labeling a spine image is disclosed. The method includes receiving an input spine image and analyzing image features of the input spine image by a deep neural network. The method further includes generating a mask image corresponding to the input spine image by the deep neural network based on image characteristics of a training image dataset. A region of interest in the mask image comprises vertebral candidates of the spine. The training image dataset comprises a plurality of spine images and a plurality of corresponding mask images. The method further includes associating labels with a plurality of image components of the mask image and labeling the input spine image based on labels associated with the mask image.