The Color Segmentation Tool for ImageJ

The Color Segmentation Tool for ImageJ


This plugin is designed to allow user friendly color separation in biological images. This plugin is Free Software (also known as Open Source software) distributed under the GNU General Public License, for more info see


Download the Color_Segmenter.jar file here. To install the plugin paste it into the plugins folder in the FIJI home directory and restart FIJI. After the plugin is installed it can be run from "Plugins > Color Segmenter" in the FIJI top menu.


Questions, comments, and any bugs you find can emailed to mwwoodfin at .

Supplemental Resources

The following should help you begin separating colored features using this plugin.

For a quick video demonstrating the plugin's use go here.

An example image which you can use to test the program can be found here (right click, Save Link As...).