NeuronJ: A Java Program for Neurite Tracing and Quantification
General Description
NeuronJ is an ImageJ plugin to facilitate the tracing and quantification of elongated image structures.
The plugin can handle only two-dimensional (2D) images of type 8-bit gray-scale or indexed color.
More details on the underlying algorithms can be found in the paper referenced below.
Download Information
Installation is accomplished by downloading the following two jar-files to the plugins folder of ImageJ.
By downloading any of these files you indicate your agreement to the Terms and Conditions below.
> NeuronJ_.jar (version 1.4.2)
> imagescience.jar (version 2.4.1)
The API of the second file (the support library) is also available in case you are interested.
Also available, for the purpose of testing the software, are the image and tracings shown above.
See the online manual for information on how to use the plugin.
See the release notes for information on the present and past versions.
The source code will become available after completion of my wish list for this plugin.
Terms and Conditions
Copyright (C) Erik Meijering. Permission to use this software and corresponding documentation for educational, research, and not-for-profit purposes, without a fee and without a signed licensing agreement, is granted, subject to the following terms and conditions.
IT IS NOT ALLOWED TO REDISTRIBUTE, SELL, OR LEASE THIS SOFTWARE, OR DERIVATIVE WORKS THEREOF, WITHOUT PERMISSION IN WRITING FROM THE COPYRIGHT HOLDER. THE COPYRIGHT HOLDER IS FREE TO MAKE 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 ADVISED OF THE POSSIBILITY THEREOF.
THE COPYRIGHT HOLDER SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND CORRESPONDING 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 me by citing 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 Part A, vol. 58, no. 2, April 2004, pp. 167-176.
You may also want to cite a recent survey paper on neuron tracing:
- E. Meijering. Neuron Tracing in Perspective. Cytometry Part A, vol. 77, no. 7, July 2010, pp. 693-704.
NeuronJ also appears 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!
