Linux Installation

Installation
Memory
Upgrading
Sharing the Java Runtime
Compiling Plugins
Browser Support
Creating a Gnome Launcher

Installation
To install and run ImageJ, download the Linux x86 .tar.gz file, extract the ImageJ directory, change to the ImageJ directory, and execute the 'run' script.
Here is an example:
gunzip ij123-x86.tar.gz
tar xvf ij123-x86.tar
cd ImageJ
./run
On newer versions of Linux you can run ImageJ by double clicking on on the 'run' script.
This installation includes Sun's Java Runtime Environment 1.5 (in the jre directory) and the complete ImageJ source code (in src.zip).

Memory
To make more than 256MB of memory available to ImageJ, edit the 'run' script. For example, changing the script to
./jre/bin/java -Xmx512m -jar ij.jar
makes 512MB available to ImageJ.

Upgrading
To upgrade to the latest version of ImageJ, replace the ij.jar JAR file in the ImageJ directory with a newer one from http://rsb.info.nih.gov/ij/upgrade/.

Sharing the Java Runtime
You can specify the location of the plugins directory from the command line using the -D option to set the "plugins.dir" property. This allows ImageJ to be in a common location (e.g., /usr/local/ImageJ) and run from the users home directory using a shell script. This example script runs ImageJ from /usr/local/ImageJ using a plugins directory at /home/wayne/ImageJ/plugins:
cd /usr/local/ImageJ
./jre/bin/java -Xmx128m -cp ij.jar -Dplugins.dir=/home/wayne ij.ImageJ
This example uses the Java 1.5 SDK to run ImageJ from /usr/local/ImageJ with the plugin directory also located in /usr/local/ImageJ:
/usr/java/jdk1.5/bin/java -Dplugins.dir=/usr/local/ImageJ -Xmx500m
-cp /usr/local/ImageJ/ij.jar:/usr/java/jdk1.5/lib/tools.jar ij.ImageJ
Compiling Plugins
The Plugins/Compile and Run command uses the javac compiler contained in the tools.jar file included with the Java Development Kit (JDK). The Java runtime included with the Linux distribution of ImageJ includes tools.jar in ImageJ/jre/lib/ext. Users who install the JDK separately must add tools.jar to the command line. Here is an example:
java -Xmx200m -cp ij.jar:\usr\local\jdk1.5\lib\tools.jar ij.ImageJ
Browser Support
Most commands in the Help menu run the Netscape browser to open pages on the ImageJ website. If Netscape is not installed, you will need to brovide a symbolic link such as
ln -s /usr/local/bin/mozilla /usr/local/bin/netscape
With ImageJ 1.38k and later, Help menu commands expect one of the following browsers to be installed (tested in this order): netscape, firefox, konqueror, mozilla, opera, epiphany or lynx. If you prefer a particular browser, make a symbolic link to 'netscape', as outlined above.
Creating a Gnome Launcher
Edit the small file named 'run' in the ImageJ directory, changing it to either
</path/to>/ImageJ/jre/bin/java -Xmx512m -jar </path/to>/ImageJ/ij.jar
if using the Java bundled with the ImageJ distribution or to
 java -Xmx512m -jar </path/to>/ImageJ/ij.jar
if using the Java installed on your system. Then make sure the file executable:
$ cd ~/ImageJ/
$ chmod +x run
Then follow these steps:

Download the icon at rsb.info.nih.gov/ij/images/ImageJ.png.
(Optional) Copy the icon to /usr/share/pixmaps if you wish to store it with the rest of your Gnome icons.
In the Gnome panel, right click and choose "Add to panel...".
Select Custom Application Launcher.
Push the "Browse" button, find the 'run' script and select it.
Click on the "No Icon" button and select the ImageJ icon, or browse to the icon's location.
Alternatively, the System>Preferences>Menus & Toolbars command will let you add a menu entry in the Gnome menus.