NeuronJ

A Java Program for Neurite Tracing and Quantification

Written by Erik Meijering

General Description

NeuronJ is an ImageJ plugin to facilitate the tracing and quantification of elongated structures in two-dimensional (2D) images (8-bit gray-scale and indexed color), in particular neurites in fluorescence microscopy images. More details on the underlying algorithms can be found in the paper referenced below.

Download

The plugin can be installed by downloading the following two files to the plugins folder of ImageJ:

> NeuronJ_.jar (version 1.4.1)
> imagescience.jar (version 2.3.0)

By downloading any of the above, you indicate your agreement with the copyright notice and disclaimer below.

The first file contains the actual plugin classes while the latter is a library of support classes (you can download its API if you are interested in using its functionality also for other purposes).

This version requires at least Java 1.5 and ImageJ 1.41g. The program was tested and found to run properly on Windows XP (Service Pack 3). I haven't had the possibility yet to test it on other platforms so I don't guarantee anything there.

The source code of NeuronJ is not available.

A description of the toolbar components can be found in the online manual.

You can also download the sample image and tracings shown above.

Check out the release notes for information on updates.

Copyright Notice and Disclaimer

Permission to copy and use the software and accompanying documentation provided on these webpages for educational, research, and not-for-profit purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following two paragraphs appear in all copies. The copyright holder is free to make upgraded or improved versions of the software available for a fee or commercially only.

IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, OF ANY KIND WHATSOEVER, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF HE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE COPYRIGHT HOLDER SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION IS PROVIDED "AS IS". THE COPYRIGHT HOLDER HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

Acknowledgments

The development of NeuronJ started while I was with the Biomedical Imaging Group (collaborating with people from the Laboratory of Cellular Neurobiology) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, and was finished while I was with the Biomedical Imaging Group Rotterdam in the Netherlands. If you publish results that are based on NeuronJ, I expect you to acknowledge my work by putting a reference to the following paper:

•	E. Meijering, M. Jacob, J.-C. F. Sarria, P. Steiner, H. Hirling, M. Unser. Design and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence Microscopy Images. Cytometry, vol. 58A, no. 2, April 2004, pp. 167-176.

NeuronJ also features in the following paper on ImageJ:

•	M. D. Abràmoff, P. J. Magalhães, S. J. Ram. Image Processing with ImageJ. Biophotonics International, vol. 11, no. 7, July 2004, pp. 36-42.

It even made the front cover of the journal!

Front Cover of July 2004 Issue of Biophotonics International

Last update on December 3, 2008.