Ureteroscopy is becoming the first surgical treatment option for the majority of urinary affections. This procedure is carried out using an endoscope which provides the surgeon with the visual and spatial information necessary to navigate inside the urinary tract. Having in mind the development of surgical assistance systems, that could enhance the performance of surgeon, the task of lumen segmentation is a fundamental part since this is the visual reference which marks the path that the endoscope should follow. This is something that has not been analyzed in ureteroscopy data before. However, this task presents several challenges given the image quality and the conditions itself of ureteroscopy procedures. In this paper, we study the implementation of a Deep Neural Network which exploits the advantage of residual units in an architecture based on U-Net. For the training of these networks, we analyze the use of two different color spaces: gray-scale and RGB data images. We found that training on gray-scale images gives the best results obtaining mean values of Dice Score, Precision, and Recall of 0.73, 0.58, and 0.92 respectively. The results obtained show that the use of residual U-Net could be a suitable model for further development for a computer-aided system for navigation and guidance through the urinary system.