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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: https://doi.org/10.1371/journal.pone.0228091

Souhrn

SWC files are a widely used format to store neuron morphologies, and are used to share digitally reconstructed neurons using NeuroMorpho.org 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


Zdroje

1. Cannon RC, Turner DA, Pyapali GK, Wheal HV. An on-line archive of reconstructed hippocampal neurons. JNeurosciMethods. 1998;84: 49–54.

2. Stockley EW, Cole HM, Brown AD, Wheal HV. A system for quantitative morphological measurement and electronic modelling of neurons: three-dimensional reconstruction. JNeurosciMethods. 1993;47: 39–51.

3. Ascoli GA, Donohue DE, Halavi M. NeuroMorpho.Org: a central resource for neuronal morphologies. JNeurosci. 2007;27: 9247–9251.

4. Hines ML, Carnevale NT. NEURON: a tool for neuroscientists. Neuroscientist. 2001;7: 123–135. doi: 10.1177/107385840100700207 11496923

5. Hines ML, Carnevale NT. Expanding NEURON’s repertoire of mechanisms with NMODL. Neural Comput. 2000;12: 995–1007. doi: 10.1162/089976600300015475 10905805

6. Hines ML, Carnevale NT. The NEURON simulation environment. Neural Comput. 1997;9: 1179–1209. doi: 10.1162/neco.1997.9.6.1179 9248061

7. Ishizuka N, Cowan WM, Amaral DG. A quantitative analysis of the dendritic organization of pyramidal cells in the rat hippocampus. JCompNeurol. 1995;362: 17–45. doi: 10.1002/cne.903620103 8576427

8. Radman T, Ramos RL, Brumberg JC, Bikson M. Role of cortical cell type and morphology in subthreshold and suprathreshold uniform electric field stimulation in vitro. Brain Stimul. 2009;2: 215–228, 228.e1–3. doi: 10.1016/j.brs.2009.03.007 20161507

9. Feng L, Zhao T, Kim J. neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format. eNeuro. 2015;2: 10.1523/ENEURO.0049-14.2014. eCollection 2015 Jan-Feb. doi: 10.1523/ENEURO.0049-14.2014 26464967

10. Scorcioni R, Polavaram S, Ascoli GA. L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. NatProtoc. 2008;3: 866–876. doi: 10.1038/nprot.2008.51 18451794

11. Luisi J, Narayanaswamy A, Galbreath Z, Roysam B. The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions. Neuroinformatics. 2011;9: 305–315. doi: 10.1007/s12021-011-9115-0 21487683

12. SharkViewer. Available: https://github.com/JaneliaSciComp/SharkViewer


Článek vyšel v časopise

PLOS One


2020 Číslo 1
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