- Sharing the Java Runtime
- Command Line Options
- Contents of ImageJ Folder
InstallationTo install and run ImageJ, download ImageJ bundled with either 32-bit or 64-bit Java, extract the ImageJ directory from the ZIP archive, change to the ImageJ directory and double click the "ImageJ" launcher.
MemoryUse the Edit>Options>Memory & Threads command to specify the maximum amount of memory available to ImageJ, initially set to 75% of available RAM by the ImageJ launcher. To make more than 2GB available requires a 64-bit computer running a 64-bit version of Linux and a 64-bit version of Java.
UpgradingUse the Help>Update ImageJ command to update to the latest version of ImageJ.
Sharing the Java RuntimeYou 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:This example uses Java 1.6 SDK to run ImageJ from /usr/local/ImageJ with the plugin directory also located in /usr/local/ImageJ:cd /usr/local/ImageJ ./jre/bin/java -Xmx512m -jar ij.jar -ijpath /home/wayne/ImageJ/usr/java/jdk1.6/bin/java -Xmx512m -jar /usr/local/ImageJ/ij.jar -ijpath /usr/local/ImageJ
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 (don't check for another instance) -debug Runs ImageJ in debug mode
TroubleshootingHere are some common problems encountered when running ImageJ on Linux, and their solutions:
- Windows are blank or stacks are not displayed correctly on Ubuntu with compiz enabled.
Disable all effects in System Preferences > Appearance > Visual Effects.
Contents of ImageJ Folder:
- This JAR (Java Archive) file is the platform-independent core of ImageJ. It is the only file changed when you upgrade using the Help>Update ImageJ command.
- This is the ImageJ launcher.
- This folder contains the 32-bit ot 64-bit Java 1.6.0_24 runtime from Oracle.
- This folder contains example macros. The StartupMacros.txt file in this folder contains macros and macro tools that are automatically installed when ImageJ launches. To run a macro, drag and drop it on the ImageJ window and run it by pressing ctrl-r (Macros>Run Macro).
- This folder contains a small sample of the hundreds of plugins available for ImageJ. The plugins in this folder are installed in the Plugins menu when ImageJ starts.
- This folder contains LUTs (LookUp Tables) that are installed at startup in the Image>Lookup Tables menu. Use the Image>Color>Display LUTs command to view all the LUTs in this menu.
- This folder contains images used by ImageJ, such as the ImageJ icon (icon.png) and an optional custom cursor (example).
ScreenshotThis screenshot, created by pressing shift-g (Plugins>Utilities>Capture Screen), shows ImageJ running on a Linux netbook with a 800x480 screen, 512MB RAM and 4GB SSD.