Module for SWC neuron morphology file validation and correction enabled for high throughput batch processing

Autoři: Damien M. O’Halloran aff001
Působiště autorů: Department of Biological Sciences, The George Washington University, Washington D.C., United States of America aff001
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0228091


SWC files are a widely used format to store neuron morphologies, and are used to share digitally reconstructed neurons using as well as predict functional attributes using simulation environments such as NEURON. Here we set out to develop an easily accessible tool to validate and correct SWC formatted files with an emphasis on high throughput batch processing. SWC_BATCH_CHECK is a package that provides a suite of methods to parse and correct the syntactic structure of a directory of SWC files. This tool ensures that user specified structures such as the soma or basal dendrite are correctly connected while fixing morphological features. This tool will report on missing or invalid data values while also returning basic statistical features for each file. SWC_BATCH_CHECK was validated and tested using thousands of individual SWC files to benchmark runtime performance and efficacy in both reporting on and correcting disparate SWC file features. SWC_BATCH_CHECK is open source and freely available to all users without restriction with guidelines and requirements provided to ensure straightforward installation and execution.

Klíčová slova:

Axons – Dendritic structure – Neuronal dendrites – Neurons – Pyramidal cells – Syntax – Vision – Neuronal morphology


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2020 Číslo 1