Linux x86 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
This installation includes Sun's Java Runtime Environment 1.4.2 and the complete ImageJ source code (in the src.zip).

Memory
To make more than 128MB of memory available to ImageJ, edit the 'run' script. For example, changing the script to 

./jre/bin/java -Xmx256m -cp ij.jar ij.ImageJ
makes 256MB available to ImageJ.

Upgrades
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 ImageJ and the JRE
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 compile contained in tools.jar. The Java 1.4.2 runtime included with the Linux distribution of ImageJ includes tools.jar in ImageJ/jre/lib/ext. Users of the Java SDK will need to add tools.jar to the command line. Here is an example: 
java -Xmx200m -cp ij.jar:\usr\local\jdk1.4\lib\tools.jar ij.ImageJ
Browser Support
The Help/ImageJ Web Site and Help/Online Docs commands run the Netscape browser to open 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
or
ln -s /opt/kde3/bin/konqueror /usr/local/bin/netscape