Tools for neuroinformatic data exchange: An XML application for neuronal morphology data

Weihong Qi; Sharon Crook

doi:10.1016/j.neucom.2004.01.171

Tools for neuroinformatic data exchange: An XML application for neuronal morphology data

Weihong Qi, Sharon Crook

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

We describe an Extensible Markup Language (XML) application that defines a common data format for the storage and processing of neuronal morphology data. The application, MorphML, is consistent with current neuronal digitization methods and is also compatible with existing simulation software environments for creating compartmental models of neurons based on morphology data. We also describe a tool, nemo2xml, which generates MorphML documents corresponding to digitized neuronal morphology files for one particular data format, the Nevin or binary branch tree syntax.

Original language	English (US)
Pages (from-to)	1091-1095
Number of pages	5
Journal	Neurocomputing
Volume	58-60
DOIs	https://doi.org/10.1016/j.neucom.2004.01.171
State	Published - Jun 2004
Externally published	Yes

Keywords

Digitized neurons
Neuronal morphology data
XML application

ASJC Scopus subject areas

Computer Science Applications
Cognitive Neuroscience
Artificial Intelligence

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10.1016/j.neucom.2004.01.171

Cite this

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title = "Tools for neuroinformatic data exchange: An XML application for neuronal morphology data",

abstract = "We describe an Extensible Markup Language (XML) application that defines a common data format for the storage and processing of neuronal morphology data. The application, MorphML, is consistent with current neuronal digitization methods and is also compatible with existing simulation software environments for creating compartmental models of neurons based on morphology data. We also describe a tool, nemo2xml, which generates MorphML documents corresponding to digitized neuronal morphology files for one particular data format, the Nevin or binary branch tree syntax.",

keywords = "Digitized neurons, Neuronal morphology data, XML application",

author = "Weihong Qi and Sharon Crook",

note = "Funding Information: The MorphML package and nemo2xml are both available at http://www.umemat.maine.edu/faculty/crook/MorphML.html . We would like to thank Robert Cannon, Hugo Cornelis, Laszlo Zaborszky, and Zoltan Nadasdy for helpful discussions of neuronal morphology and the MorphML schema design. We also gratefully acknowledge the support of the National Science Foundation through IBN 0091117. This material is also based on work supported by the National Science Foundation at the Mathematical Biosciences Institute under Agreement 0112050. Copyright: Copyright 2008 Elsevier B.V., All rights reserved.",

year = "2004",

month = jun,

doi = "10.1016/j.neucom.2004.01.171",

language = "English (US)",

volume = "58-60",

pages = "1091--1095",

journal = "Neurocomputing",

issn = "0925-2312",

publisher = "Elsevier",

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TY - JOUR

T1 - Tools for neuroinformatic data exchange

T2 - An XML application for neuronal morphology data

AU - Qi, Weihong

AU - Crook, Sharon

N1 - Funding Information: The MorphML package and nemo2xml are both available at http://www.umemat.maine.edu/faculty/crook/MorphML.html . We would like to thank Robert Cannon, Hugo Cornelis, Laszlo Zaborszky, and Zoltan Nadasdy for helpful discussions of neuronal morphology and the MorphML schema design. We also gratefully acknowledge the support of the National Science Foundation through IBN 0091117. This material is also based on work supported by the National Science Foundation at the Mathematical Biosciences Institute under Agreement 0112050. Copyright: Copyright 2008 Elsevier B.V., All rights reserved.

PY - 2004/6

Y1 - 2004/6

N2 - We describe an Extensible Markup Language (XML) application that defines a common data format for the storage and processing of neuronal morphology data. The application, MorphML, is consistent with current neuronal digitization methods and is also compatible with existing simulation software environments for creating compartmental models of neurons based on morphology data. We also describe a tool, nemo2xml, which generates MorphML documents corresponding to digitized neuronal morphology files for one particular data format, the Nevin or binary branch tree syntax.

AB - We describe an Extensible Markup Language (XML) application that defines a common data format for the storage and processing of neuronal morphology data. The application, MorphML, is consistent with current neuronal digitization methods and is also compatible with existing simulation software environments for creating compartmental models of neurons based on morphology data. We also describe a tool, nemo2xml, which generates MorphML documents corresponding to digitized neuronal morphology files for one particular data format, the Nevin or binary branch tree syntax.

KW - Digitized neurons

KW - Neuronal morphology data

KW - XML application

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SP - 1091

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JO - Neurocomputing

JF - Neurocomputing

ER -

Tools for neuroinformatic data exchange: An XML application for neuronal morphology data

Abstract

Keywords

ASJC Scopus subject areas

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