neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format

eNeuro. 2015 Jan 2;2(1):ENEURO.0049-14.2014. doi: 10.1523/ENEURO.0049-14.2014. eCollection 2015 Jan-Feb.


Brain circuit mapping requires digital reconstruction of neuronal morphologies in complicated networks. Despite recent advances in automatic algorithms, reconstruction of neuronal structures is still a bottleneck in circuit mapping due to a lack of appropriate software for both efficient reconstruction and user-friendly editing. Here we present a new software design based on the SWC format, a standardized neuromorphometric format that has been widely used for analyzing neuronal morphologies or sharing neuron reconstructions via online archives such as We have also implemented the design in our open-source software called neuTube 1.0. As specified by the design, the software is equipped with parallel 2D and 3D visualization and intuitive neuron tracing/editing functions, allowing the user to efficiently reconstruct neurons from fluorescence image data and edit standard neuron structure files produced by any other reconstruction software. We show the advantages of neuTube 1.0 by comparing it to two other software tools, namely Neuromantic and Neurostudio. The software is available for free at, which also hosts complete software documentation and video tutorials.

Keywords: SWC; bioimage informatics; neuron tracing; user-friendly software.