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Windows Installation

Installation

The Windows version of ImageJ is available bundled with 32-bit and 64-bit versions of Java, and without Java. The version bundled with 64-bit Java requires Windows XP x64 or Windows Vista 64-bit. Both versions bundled with Java include the javac compiler needed by the Plugins>Compile and Run command. All versions include ImageJ.exe, a Windows program contributed by George Silva that launches ImageJ (ij.jar).

ImageJ.exe supports file-associations, drag and drop, auto-configuration and command line operation. If the jre folder (the Java runtime) is missing, ImageJ.exe detects the latest installed Java, generates the configuration file (ImageJ.cfg) and sets the memory limit to 2/3 of installed memory or 640MB, whichever is lower. Refer to the ImageJ.exe README for more information.

On Windows Vista, ImageJ should be installed in a directory that the user has permission to write to, such as the user's home directory, Documents or Desktop. Write permission to the ImageJ directory is required to generate the ImageJ.cfg file (if it is missing), to set the memory limit, to install plugins and macros, to update ImageJ, and to save preferences.

Use the Help>Update Image command to upgrade to newer versions of ImageJ.

Memory

Use the Edit>Options>Memory command to make more than the default 128MB available to ImageJ. Note that setting the "Maximum Memory" value to more than about 75% of real RAM may result in poor perfomance due to virtual memory "thrashing". The Edit>Options>Memory command modifies the third line in the ImageJ.cfg file in the ImageJ folder, which must be writable. This is what ImageJ.cfg looks like with "Maximum Memory" set to 700MB: 
    .
    jre\bin\javaw.exe 
    -Xmx700m -cp ij.jar ij.ImageJ
Note that this only works when you run ImageJ by double clicking on ImageJ.exe. No more than 64MB is available when you run ImageJ by double clicking on ij.jar.

You may get an error message that looks something like this: 

    Unable to update the file "ImageJ.cfg
    C:\ Program Files\ImageJ\ImageJ.cfg (Access denied)
This error is the result of not have write access to the folder containing ImageJ. You need to either run ImageJ as an administrator, or to install it in a folder that you do have write access to, for example the Documents folder.

The maximum amount of memory that can be allocated on a 32-bit Windows system running a Sun JVM (Java Virtual Machine) is ~1.5GB. Windows 64 with a 64-bit JVM does not have this limit, and BEA's JRockit JVM is reported to support up to ~3GB on 32-bit systems. More information is available on the ImageJ Documentation Wiki.

64-bit Windows

To use more than ~1.5GB of memory with a JVM from Sun requires a 64-bit CPU (AMD64, Intel Core 2 Duo, etc.), a 64-bit OS (Window XP x64 or Windows Vista 64-bit), a 64-bit version of Java, and 3GB or more of RAM. A Windows version of ImageJ bundled with 64-bit Java is available on the Download page. The title of the Memory & Threads dialog box changes to "Memory (64-bit)" when ImageJ is running on a 64-bit version of Java.

Use the Edit>Options>Memory & Threads command to allocate more than the default 640MB of memory. This requires that you are running ImageJ as an administrator or have installed it in a directory you have write access to, such as the Documents folder.

Troubleshooting

Here are some common problems encountered when running ImageJ on Windows, and their solutions:
  • ImageJ does not start.

    Delete the ImageJ.cfg file in the ImageJ folder.

  • Cannot increase memory in Edit>Options>Memory & Threads or ImageJ unexpectedly runs out of memory.

    Install ImageJ in a directory that you have write access to, such as "Documents" or "Desktop".

  • ImageJ displays blank windows or windows filled with garbage.

    Update video card driver.

  • Multiple copies of ImageJ are started when I open images by double clicking on them or by dragging and dropping them on the ImageJ icon.

    Enable "Run Socket Listener" in Edit>Options>Misc.

  • Selections flicker when I move them.

    Enable "Double Buffer Selections" in Edit>Options>Appearance.

    • Drag and Drop

    The Windows version of ImageJ opens images, text files, ROIs and LUTs dropped on the "ImageJ" window. On Windows 2000/XP, it also opens files dropped on the ImageJ icon.

    Appearance

    On Windows XP, Activate Clear Type to improve the quality of text displayed in menus, dialog boxes, text windows, and in the status bar. To use a larger menu font, choose "Large Fonts" or "Extra Large Fonts" in the "Font Size:" drop down menu in the Appearance tab of the Display Properties control panel. Check "Antialiased Tool Icons" in ImageJ's Edit>Options>Misc dialog to improve the appearance of the tool icons.

    Here is what ImageJ looks like with Clear Type enabled, "Extra Large Fonts" and antialiased tool icons.

         ImageJ window

    Known Problems

    1. Java 1.4.2 crashes when running ImageJ. This bug has been reported to Sun and is fixed in Java 1.5 (aka Java 5.0).
    2. On 32-bit systems and a Sun JVM, ImageJ cannot use more than about 1.7GB of memory, regardless of how much RAM is installed.
    3. The text cursor is sometimes used instead of the cross hair. As a work around, check "Use Pointer Cursor" in Edit>Options>Misc or change the Windows XP cursor scheme in Control Panel/Mouse/Pointers to "(None)".
    4. JFileChooser, used by the getDirectory() macro function, does not work with Java 1.5 on Vista. To work around this problem, upgrade to Java 1.6

    Compiling Plugins

    The Plugins>Compile and Run command uses the javac compiler contained in the tools.jar file included with Sun's Java Development Kit (JDK). Compile and Run works with the version of ImageJ bundled with Java because it includes a copy of tools.jar in ImageJ/jre/lib/ext. It does not work if you use the version that is not bundled with Java and you have not installed the JDK. To fix this problem, uninstall the Java Runtime Environment (JRE), download and install the JDK, delete the Image\ImageJ.cfg file, and restart ImageJ. Compile and Run will not work if you launch ImageJ by double clicking on ij.jar.

    Upgrading to a Newer Version of Java

    This is what you need to do to upgrade to a newer version of Java: This method requires an ImageJ 1.35 or later distribution (ImageJ folder) that includes George Silva's auto-configuring launcher (ImageJ.exe).

    Adding a JAR File

    Some plugins require a Java code library contained in a JAR file (e.g., Jama.jar). ImageJ's plugin class loader automatically loads code from such libraries as long as the JAR file is in the plugins folder or an immediate subfolder. The Plugins>Compile and Run command in ImageJ 1.39 and later also supports JAR file libraries located in the plugins folder or a subfolder. Note that Compile and Run will not recognize the JAR file if the name does not end in ".jar" or if the name contains an underscore.

    About the Installer

    The ImageJ Windows installer is created using the Inno Setup installer generator.

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