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An automated parsing pipeline system and method for anatomical localization and condition classification is disclosed. The system comprises an input even source, a memory unit and processor including a volumetric image processor, a voxel parsing engine, localization layer and a detection module. The volumetric image processor is configured to receive volumetric image from the input source and parse the received volumetric image. The voxel parsing engine is configured to assign each voxel a distant anatomical structure. The localization layer is configured to crop a defined anatomical structure with surroundings. The detection module is configured to classify conditions for each defined anatomical structure within the cropped image. The disclosed system and method provide accurate localization of a tooth and detects several common conditions in each tooth.