SWC
Overview
SWC is a text-based file format for describing three-dimensional neuronal and glial morphology as digitally reconstructed from microscopy images. Each morphology is represented as a vectorised tree structure in which every node is encoded by seven values: a sample number (the node’s unique integer index), a type identifier, three spatial coordinates (x, y, z), a radius, and a reference to the parent node’s sample number. The format was introduced in 1998 by Cannon et al. in the context of an online archive of reconstructed hippocampal neurons, and its simplicity and wide adoption have made it a standard interchange format for neuronal morphology data across databases, simulation tools, and analysis pipelines. INCF endorsed the SWC specification in February 2024 and hosts it on GitHub.
Connections
- endorsedBy: INCF (INCFSN-24-02, 2024)
- relatedTo: NeuroMorpho.Org (SWC is the standard format for all morphological reconstructions archived in NeuroMorpho.Org)
Resources
- https://swc-specification.readthedocs.io/en/latest/swc.html (specification)
- https://github.com/INCF/swc-specification
- https://www.incf.org/swc (INCF endorsement page)
- https://doi.org/10.1016/s0165-0270(98)00091-0 (Cannon et al. 1998, J. Neurosci. Methods)