Methods, systems, and computer readable media for deriving a three-dimensional (3D) surface from colonoscopic video are disclosed. According to one method for deriving a 3D surface from colonoscopic video, the method comprises: performing video frame preprocessing to identify a plurality of keyframes of a colonoscopic video, wherein the video frame preprocessing includes informative frame selection and keyframe selection; generating, using a recurrent neural network and direct sparse odometry, camera poses and depth maps for the keyframes; and fusing, using SurfelMeshing and the camera poses, the depth maps into a three-dimensional (3D) surface of a colon portion, wherein the 3D surface indicates at least one region of the colon portion that was not visualized.