AxonTracker is useful to semi-automatically track and label axon structures from the motor axon connectome datasets. It is a parameter-free software, and hence can be used over a broad range of datasets.The software is designed with ease of use in mind. The interface is simple and includes a 3D visualization of the dataset along with a real-time overlay of the tracking results. A 2D view of the dataset is also provided in order to interact with the software. Three orthogonal views are provided with a provision for back-tracking the results. Points can be added/deleted from the tracking results to provide guidance in case of an error.