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

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

./jre/bin/java -mx256m -cp ij.jar ij.ImageJ

Sharing ImageJ and the JRE
With ImageJ 1.24n and newer, 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 -mx128m -cp ij.jar -Dplugins.dir=/home/wayne ij.ImageJ