Neuron_Morpho plugin Homepage

This plugin is no longer supported. Please see "Other tools" below.

Author: Giampaolo D'Alessandro (
22 June 2001 (Version 1.0.1 Beta)
27 July 2001 (Version 1.1 Beta) - Added on line help
6 August 2001 (Version 1.1.1 Beta) - Fixed bug that allowed false measurements to be taken if the control-key and the mouse were pressed in the wrong order.
10 August 2001 (Version 1.1.2 Beta) - The data is acquired using the Shift key and the mouse instead of the Control key. This change was needed because on Macs the control key pops up a menu that covers the section to be measured.
Fixed bug that makes the plugin crash if the ImageJ preference file does not exist.
13 September 2001 (Version 1.1.3) - The plugin now computes the radius instead of the diameter of the sections in accord with the swc format.
9 February 2002 (Version 1.1.4) - The lines that identify the measured sections of the neuron are drawn correctly at all magnifications.
12 July 2002 (Version 1.1.5) - The length of the data table has been increased to 10000 lines.
25 May 2007 (Version 1.1.6) - When a line is deleted all the nodes are re-numbered in sequential order. This eliminates a conflict with cvapp.
Installation: Download to the plugins folder, unzip it and restart ImageJ. The plugin requires either Java 2 or JDK 1.1 plus the swingall.jar jar file. If you use a Mac pre-OS X read this this page.
Description: The Neuron_Morpho plugin allows the user to measure the coordinates and the diameter of a section of a neuron together with other information that can be used to reconstruct the neuron morphology.
Citation: This plugin is free to use, but I would be grateful if you could cite the following paper in your research publications:

K. Brown, D. Donohue, G. D'Alessandro and G. Ascoli, A Cross-Platform Freeware Tool for Digital Reconstruction of Neuronal Arborizations from Image Stacks, Neuroinformatics 3, 343-360 (2005). DOI: 10.1385/NI:3:4:343
Bug fixes: I no longer support this plugin. See "Other tools" below.
Documentation: A full set of instructions is available in PDF format or in HTML format. A zipped archive of the documentation is included in the file, but you can also download it separately by clicking here. If you would like to reproduce the example used in the documentation, you can download the stack of images and data files by clicking here.
Other tools: I no longer actively support this plugin. You may want to try to use Neuromantic, a new tool that seems to be more powerful than NeuronMorpho and with more extensive help.

Screen shot of the Neuron_Morpho plugin (left), the online Help window (centre), ImageJ (top right) and a Manduca Sexta olfactory projection neuron (bottom right, courtesy of Tom Christensen, Univ. of Arizona).

Page mantained by G. D'Alessandro. Last updated November 02, 2018.