Recent advancements in automated fluorescence microscopy has made high-content screening an essential technique for discovering novel molecular pathways in disease or potential new therapeutic treatments. Automatic morphology quantification from images of fluorescence microscopy plays an increasingly important role in high-content screens. However, there are very few freeware tools or methods which provide automatic neuronal morphology quantification for these high-content screens. To automate these morphological feature measurements, we have developed NeurphologyJ; it is capable of automatically quantifying neuronal morphology such as soma number and size, neurite length, neurite ending points and attachment points. NeurphologyJ is implemented as a plugin to ImageJ, an open-source Java-based image-processing and analysis platform.

NeurphologyJ has been accepted by the journal BMC Bioinformatics and can be found here.

Sample images of rat hippocampal neurons analyzed by NeurphologyJ are shown:

original neurite soma

attachment point endpoint merge



NeurphologyJ interactive version

Please right click on the above hyperlink and save the .txt file into the Plugins folder of ImageJ.


NeurphologyJ high-throughput version

Please save the .zip file and unzip both files into the Plugins folder of ImageJ.



This file is about 1 Mb, please be patient.


Supplemental image set 1 (hippocampal neurons)

This file is about 20 Mb, please be patient.


Supplemental image set 2 (P19 neurons)

This file is about 3 Mb, please be patient.


Supplemental image set 3 (attachment and ending points)

This file is about 120 kb, so it should download quickly.



Eric Hwang, Assistant Professor
Department of Biological Science and Technology
Room 111 Zhu-Ming Building, 75 Bo-Ai Street
Hsin-Chu, Taiwan 300
Tel: +886-3-5712121#56968
Fax: +886-3-572-9288
hwangeric (at)

All rights reserved. © 2008 Eric Hwang