Recent breakthroughs of deep learning algorithms in medical imaging, automated detection, and segmentation techniques for renal (kidney) in abdominal computed tomography (CT) images have been limited. Radiomics and machine learning analyses of renal diseases rely on the automatic segmentation of kidneys in CT images. Inspired by this, our primary aim is to utilize deep semantic segmentation learning models with a proposed training scheme to achieve precise and accurate segmentation outcomes. Moreover, this work aims to provide the community with an open-source, unenhanced abdominal CT dataset for training and testing the deep learning segmentation networks to segment kidneys and detect kidney stones. Five variations of deep segmentation networks are trained and tested both dependently (based on the proposed training scheme) and independently. Upon comparison, the models trained with the proposed training scheme enable the highly accurate 2D and 3D segmentation of kidneys and kidney stones. We believe this work is a fundamental step toward AI-driven diagnostic strategies, which can be an essential component of personalized patient care and improved decision-making in treating kidney diseases.