Linux Installation

Installation
Memory
Upgrading
Sharing the Java Runtime
Compiling Plugins
Browser Support
Command Line Options
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. The ImageJ Documentation Wiki FAQs have instructions on how to make up to 8GB available to ImageJ on a 64-bit computer running a 64-bit version of Linux and a 64-bit version of Java.

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 -ijpath option. 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 runs ImageJ from /usr/local/ImageJ using a plugins directory at /home/wayne/ImageJ/plugins:
cd /usr/local/ImageJ
./jre/bin/java -Xmx512m -jar ij.jar -ijpath /home/wayne/ImageJ
This example uses 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 -Xmx512m -cp /usr/local/ImageJ/ij.jar:/usr/java/jdk1.5/lib/tools.jar -ijpath /usr/local/ImageJ
It adds tools.jar to the classpath, which is required for the Plugins>Compile and Run command to work.
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.
Command Line Options
ImageJ recognizes the following command line options:
  "file-name"
     Opens a file
     Example 1: blobs.tif
     Example 2: /Users/wayne/images/blobs.tif
     Example3: e81*.tif

  -ijpath path
     Specifies the path to the directory containing the plugins directory
     Example: -ijpath /Applications/ImageJ

  -port
     Specifies the port ImageJ uses to determine if another instance is running
     Example 1: -port1 (use default port address + 1)
     Example 2: -port2 (use default port address + 2)
     Example 3: -port0 (do not check for another instance)

  -macro path [arg]
     Runs a macro, passing it an optional argument
     Example 1: -macro analyze.ijm
     Example 2: -macro analyze /Users/wayne/images/stack1

  -batch path [arg]
    Runs a macro in batch (no GUI) mode, passing it an optional argument.
    ImageJ exits when the macro finishes.

  -eval "macro code"
     Evaluates macro code
     Example 1: -eval "print('Hello, world');"
     Example 2: -eval "return getVersion();"

  -run command
     Runs an ImageJ menu command
     Example: -run "About ImageJ..."
Creating a Gnome (Ubuntu) Launcher
Edit the file named 'run' in the ImageJ directory, changing it to either
~/ImageJ/jre/bin/java -Xmx512m -jar ~/ImageJ/ij.jar -ijpath ~/ImageJ
if using the Java bundled with the ImageJ distribution or to
 java -Xmx512m -jar ~/ImageJ/ij.jar -ijpath ~/ImageJ
if using the Java installed on your system. Note, these examples assume that the ImageJ directory is in your home directory.
Next make sure the file executable:
$ cd ~/ImageJ/
$ chmod +x run
Then follow these steps:

If it is not already in the ImageJ directory, download the icon at rsb.info.nih.gov/ij/images/ImageJ.png.
Copy it to /usr/share/pixmaps.
In the Gnome panel, at the top of the screen, 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 (an antique brass microscope).
Alternatively, the System>Preferences>Menus & Toolbars command will let you add a menu entry in the Gnome menus.