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Research ArticleMethods/New Tools, Novel Tools and Methods

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

Linqing Feng, Ting Zhao and Jinhyun Kim
eNeuro 2 January 2015, 2 (1) ENEURO.0049-14.2014; https://doi.org/10.1523/ENEURO.0049-14.2014
Linqing Feng
1Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, 136-791, Korea
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Ting Zhao
2Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147
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Jinhyun Kim
1Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, 136-791, Korea
3Neuroscience Program, University of Science and Technology, Daejeon, 305-350, Korea
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Abstract

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 NeuroMorpho.org. 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 http://www.neutracing.com, which also hosts complete software documentation and video tutorials.

  • bioimage informatics
  • neuron tracing
  • SWC
  • user-friendly software

Footnotes

  • ↵1 Authors report no conflict of interest.

  • ↵3 This work was supported by the KIST Institutional Program (Project No. 2E24210) and WCI Program (NRF Grant Number: WCI 2009-003). T.Z. is supported by Howard Hughes Medical Institute.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

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neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format
Linqing Feng, Ting Zhao, Jinhyun Kim
eNeuro 2 January 2015, 2 (1) ENEURO.0049-14.2014; DOI: 10.1523/ENEURO.0049-14.2014

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neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format
Linqing Feng, Ting Zhao, Jinhyun Kim
eNeuro 2 January 2015, 2 (1) ENEURO.0049-14.2014; DOI: 10.1523/ENEURO.0049-14.2014
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Keywords

  • bioimage informatics
  • neuron tracing
  • SWC
  • user-friendly software

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