RTip is a tool to quantify plant root growth velocity using high-resolution microscopy image sequences at sub-pixel accuracy. The fully automated RTip tracker is designed for high-throughput analysis of plant phenotyping experiments with episodic perturbations. RTip is able to auto-skip past these manual intervention perturbation activity, i.e. when the root tip is not under the microscope, the image is distorted or blurred. RTip provides the most accurate root growth velocity results with the lowest variance (i.e. localization jitter) compared to six tracking algorithms including the top-performing unsupervised Discriminative Correlation Filter Tracker and the Deeper and Wider Siamese Network. RTip is the only tracker that is able to automatically detect and recover from (occlusion-like) varying duration perturbation events.