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ImageJ has been extended with thousands of plugins: special-purpose software components that extend ImageJ’s functionality—e.g., by offering additional commands via menu entries.
Available plugins
You can browse the list of available ImageJ extensions.
Tiers of plugins
There are four tiers of plugins:
- Core ImageJ plugins, bundled with the base ImageJ distribution. (more than 1000 as of this writing)
- Core Fiji plugins, bundled with the Fiji distribution of ImageJ. (nearly 1000 additional plugins as of this writing)
- Plugins installable from an ImageJ update site.
- Additional plugins available from various online sources, which must be manually installed.
Installing plugins
The ImageJ Updater is the best way to install and update plugins. Simply add the update site containing your plugins of interest, and they will be installed automatically for you. If the plugin is not available via update site, but packaged as .jar file, or as unpackaged directory with .class files, see Installing plugins manually below.
Advanced topics
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 a hosted update site on sites.imagej.net, to easily share and maintain updated plugins.
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
.jaror.classthen it is usually enough to simply restart ImageJ after dropping the file intoplugins(or any similar directory mentioned in the following sections). - If the file suffix is
.javathen you typically must manually compile it to a.classusing thejavacutility. For example, running the following from the directory containing your plugin:javac -cp "$IJ_DIR/jars/*" MyCoolPlugin_.java. This assumes environment variableIJ_DIRset to your ImageJ installation directories ($IJ_DIRfor MacOS/Linux,%IJ_DIR%for Windows). After running this command once you will have a.classfile that you can use as indicated above. Don’t forget the_required in the name!
User-specific plugins
In addition to looking in the plugins folder of ImageJ itself, ImageJ also looks in the .plugins folder in 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 website’s article Changing Location of Plugins Directory.
Multiple plugin directories
For ultimate control, ImageJ also provides support for manually configuring the list of plugin paths, similar to Java’s classpath, using the ij1.plugin.dirs system property. Note that the trailing double-separator, --, is required!
E.g.,
- on 64-bit Linux:
$IJ_DIR/ImageJ-linux64 -Dij1.plugin.dirs=/path/to/my/plugins -- -
On macOS:
$IJ_DIR/Contents/MacOS/ImageJ-macosx -Dij1.plugin.dirs=/path/to/my/plugins -- - On 64-bit Windows:
%IJ_DIR%\ImageJ-win64 -Dij1.plugin.dirs="C:\path\to\my\plugins" --
Where $IJ_DIR (or %IJ_DIR% on Windows) is the path to your ImageJ installation.
