INCF Endorses Digital SWC Reconstructions Describing Neuron Morphology as a Standard
8 March 2024On February 29th the INCF’s Standards and Best Practices Committee voted to endorse SWC as a new standard. SWC files (file extension of .swc) are text-based (ASCII text) files that describe three-dimensional neuronal or glial morphology.
These digital reconstructions represent morphology as a vectorized tree structure, made of a series of connected nodes. An SWC file contains a series of text-based rows where each neuron node is described by a single row of only seven space-separated values. The format is simple and intuitive; a parser of or writer to the format could be implemented by anyone with knowledge of any programming language. This is a
With a 25-year history and over 1,000 publications, the SWC format was considered a strong candidate for INCF endorsement by the INCF Standards and Best Practices Committee. It is open, has strong documentation, is well conceived and executed, and supports FAIR reasonably well. It has strong community support and use outside of the core group involved in its specification and development. Additionally, many tools have been developed to support the format.
Read more:
Articles:
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An on-line archive of reconstructed hippocampal neurons (Journal of Neuroscience Methods, 1998). https://doi.org/10.1016/s0165-0270(98)00091-0
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Design and implementation of multi-signal and time-varying neural reconstructions (Sci. Data, 2018). https://doi.org/10.1038/sdata.2017.207
SWC on GitHub: https://github.com/INCF/swc-specification
Documentation: https://swc-specification.readthedocs.io/en/latest/swc.html