Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

Mark Longair; Dean A. Baker; J. Douglas Armstrong

doi:10.1093/bioinformatics/btr390

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

Mark Longair, Dean A. Baker, J. Douglas Armstrong

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

Abstract

Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL.Contact: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch

Original language	English
Pages (from-to)	2453-2454
Number of pages	2
Journal	Bioinformatics
Volume	27
Issue number	17
DOIs	https://doi.org/10.1093/bioinformatics/btr390
Publication status	Published - 2011

Access to Document

10.1093/bioinformatics/btr390

http://bioinformatics.oxfordjournals.org/content/27/17/2453

Cite this

@article{2f38dfd828044ac2b337b6e91fe2e534,

title = "Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes",

abstract = "Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL.Contact: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch",

author = "Mark Longair and Baker, {Dean A.} and Armstrong, {J. Douglas}",

year = "2011",

doi = "10.1093/bioinformatics/btr390",

language = "English",

volume = "27",

pages = "2453--2454",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "17",

}

TY - JOUR

T1 - Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

AU - Longair, Mark

AU - Baker, Dean A.

AU - Armstrong, J. Douglas

PY - 2011

Y1 - 2011

N2 - Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL.Contact: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch

AB - Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL.Contact: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch

U2 - 10.1093/bioinformatics/btr390

DO - 10.1093/bioinformatics/btr390

M3 - Article

VL - 27

SP - 2453

EP - 2454

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 17

ER -

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

Abstract

Access to Document

Fingerprint

Cite this