Online conversion of reconstructed neural morphologies into standardized SWC format.
Where this comes from
- Record sourced from PubMed, PMID 37973857.
- Also identified by DOI 10.1038/s41467-023-42931-x and PMC identifier 10654402.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Digital reconstructions provide an accurate and reliable way to store, share, model, quantify, and analyze neural morphology. Continuous advances in cellular labeling, tissue processing, microscopic imaging, and automated tracing catalyzed a proliferation of software applications to reconstruct neural morphology. These computer programs typically encode the data in custom file formats. The resulting format heterogeneity severely hampers the interoperability and reusability of these valuable data. Among these many alternatives, the SWC file format has emerged as a popular community choice, coalescing a rich ecosystem of related neuroinformatics resources for tracing, visualization, analysis, and simulation. This report presents a standardized specification of the SWC file format. In addition, we introduce xyz2swc, a free online service that converts all 26 reconstruction formats (and 72 variations) described in the scientific literature into the SWC standard. The xyz2swc service is available open source through a user-friendly browser interface ( https://neuromorpho.org/xyz2swc/ui/ ) and an Application Programming Interface (API).
Medical subject headings
- Ecosystem
- Software