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Updated: May 31, 2026
Standardization of a Novel Semi-Automatic Software for Neurite Outgrowth Measurement
Published on: August 9, 2024
Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes
Mark H Longair1, Dean A Baker, J Douglas Armstrong
1Institute of Neuroinformatics, Uni/ETH Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. longair@ini.phys.ethz.ch
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.
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