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An ImageJ Plugin for Automated Quantification of Axon Regeneration in Spinal Cord Tissue


AxonTracer is a freely available open-source tool for automated analysis of regenerating axons following spinal cord injury. An interactive user interface provides detection-parameter adjustment, which does not require prior image analysis experience. Raw data as well as normalized results are stored in an excel file and axon tracings are superimposed on raw images allowing for subjective visual verification. This software allows for automated, unbiased analysis of hundreds of images with thousands of labeled axons, thus providing a useful tool in enabling in vivo screens of axon regeneration following spinal cord injury.

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Axon Tracer

AxonTracer quantifies the sum of all axons within the image and identifies them by superimposed tracings in yellow. It offers 4 analysis options.

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Axon Tracer Detail

AxonTracerDetail quantifies the length of individual axons and identifies them by multicolor tracings within the entire image that is analysed.

Please Cite AxonTracer in Your Publications

Patel A, Li Z, Canete P, Strobl H, Dulin J, Kadoya K, Gibbs D, Poplawski GHD. AxonTracer: a novel ImageJ plugin for automated quantification of axon regeneration in spinal cord tissue. BMC Neurosci. 2018 Mar 9;19(1):8. doi: 10.1186/s12868-018-0409-0. PubMed PMID: 29523078; PubMed Central PMCID: PMC5845359.

Associated Files

ImageJ Java 1.6 bundle

Download ImageJ bundled with Java 1.6.0 to assure correct ROI detection when utilizing AxonTracer's analysis option "3" and "4".

Required ImageJ Plugins

AxonTracer requires installing of FeatureJ.jar and imagescience.jar 
(Copyright © 1996 - 2018 Erik Meijering)

Example Images

To test the functionality of AxonTracer you can download example images here, optimized for the individual analysis conditions.

Figures Of Manuscript

High resolution Figures of the AxonTracer manuscript can be downloaded here.


License under GNU GENERAL PUBLIC LICENSE Version 3


The AxonTracer Manuscript can be downloaded here.

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