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ImageJ has been extended with thousands of plugins!

Types of plugins

There are four tiers of plugins:

  1. Core ImageJ plugins, bundled with the base ImageJ distribution. (449 as of this writing)
  2. Core Fiji plugins, bundled with the Fiji distribution of ImageJ. (811 as of this writing)
  3. Plugins installable from an ImageJ update site.
  4. Additional plugins available for manual installation only.

Using an ImageJ update site

The Fiji distribution of ImageJ includes the ImageJ Updater: a painless way to install and update plugins. Simply add the update site containing your plugins of interest, and they will be installed automatically for you.

Installing plugins manually

If the plugin you want is not distributed via an ImageJ update site, please encourage the plugin's maintainer to do so! Anyone can create their own personal update site hosted on, freeing plugin authors from the burden of distribution and server maintenance.

In the meantime, to install a plugin manually, follow the plugin's installation instructions, if any. The plugin will consist of one or more files which must be downloaded and (typically) placed in ImageJ's plugins folder:

  • If the file suffix is .jar or .class then it is usually enough to simply restart ImageJ after dropping the file into plugins.
  • If the file suffix is .java then you typically must execute the Compile and Run command on the file to first compile it to a .class. After running this command once and restarting ImageJ, the plugin will become available in ImageJ's Plugins menu.

User-specific plugins

The Fiji distribution of ImageJ, in addition to looking for plugins in the plugins subfolder, also looks in the .plugins subfolder of the current user's home folder. This is useful if you want to install some of your own plugins without affecting the system-wide ImageJ installation.

Configuring where ImageJ looks for plugins

Power users may wish to configure exactly which folder(s) ImageJ scans for plugins. The default folder is the plugins folder of the ImageJ installation. However, this can be overridden using the plugins.dir system property. See the ImageJ web site's article Changing Location of Plugins Directory.

Multiple plugin directories

For ultimate control, Fiji also provides support for manually configuring the list of plugin paths, similar to Java's classpath, using the ij1.plugin.dirs system property.

E.g., on 64-bit Linux:

$FIJI/ImageJ-linux64 -Dij1.plugin.dirs=$FIJI/jars:$FIJI/plugins:$HOME/.plugins

On OS X:

$FIJI/Contents/MacOS/ImageJ-macosx -Dij1.plugin.dirs=$FIJI/jars:$FIJI/plugins:$HOME/.plugins

On 64-bit Windows:

%FIJI%\ImageJ-win64 -Dij1.plugin.dirs=%FIJI%\jars;%FIJI%\plugins;%HOMEDRIVE%%HOMEPATH%\.plugins

Where $FIJI (or %FIJI% on Windows) is the path to your Fiji installation.