Windows Installation

Installation

The Windows version of ImageJ is available bundled with either Java 6 or Java 8, and without Java. 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.

When launching ImageJ for the first time, you may get a message saying that the Java Virtual Machine (JVM) cannot be found, in which case you will need to find the javaw.exe command in the file system, at a location something like "C:\Program Files\Java\jdk8\bin\javaw.exe".

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 640MB 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 1500MB:
    .
    jre\bin\javaw.exe 
    -Xmx1500m -cp ij.jar ij.ImageJ
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.

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.

  • The "ImageJ" window is tiny on my high resolution screen.

    Upgrade to Windows 8.1 or later, open the ImageJ.exe>Properties>Compatability panel and uncheck "Disable display scaling on high DPI settings".

  • 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 or try running the nVidia Fix plugin

  • 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 single instance listener" in Edit>Options>Misc.

  • I installed a 64-bit version of Java but ImageJ is using the 32-bit version.

    Edit the second line of ImageJ.cfg to point to the 64-bit version of Java. For example, change "C:\Program Files (x86)\Java\jre7\bin" to "C:\Program Files\Java\jre7\bin".

  • Drag and Drop

    The Windows version of ImageJ opens images, folders of images, text files, ROIs and LUTs dropped on the "ImageJ" window or on the the ImageJ application icon.

    Upgrading to a Newer Version of Java

    This is what you need to do to upgrade to a newer version of Java:

    Contents of ImageJ Folder

    ij.jar
    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.
    ImageJ.exe
    This is the ImageJ launcher.
    jre (optional)
    This folder contains the Java runtime.
    macros
    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).
    plugins
    This folder contains a small sample of the hundreds of plugins available for ImageJ. Plugins, macros and scripts in this folder, and immediate sub-folders, are installed in the Plugins menu when ImageJ launches.
    luts
    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.

    Command Line Options

    To run ImageJ from the command line, open a Command window, change to the ImageJ directory, and enter a command something like this:
    jre\bin\java -jar -Xmx1024m ij.jar
    
    The -Xmx1024m switch specifies that ImageJ will have available a maximum of 1024MB (1GB) of RAM.

    ImageJ recognizes the following command line options:

      "file-name"
         Opens a file
         Example 1: blobs.tif
         Example 2: /Users/wayne/images/blobs.tif
         Example 3: e81*.tif
    
      -macro path [arg]
         Runs a macro or script (JavaScript, BeanShell or Python), passing an
         optional string argument, which the macro or script can be retrieve
         using the getArgument() function. The macro or script is assumed to 
         be in the ImageJ/macros folder if 'path' is not a full directory path.
         Example 1: -macro analyze.ijm
         Example 2: -macro script.js /Users/wayne/images/stack1
         Example 2: -macro script.py '1.2 2.4 3.8'
    
      -batch path [arg]
        Runs a macro or script (JavaScript, BeanShell or Python) 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..."
         
      -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 (don't check for another instance)
    
      -debug
         Runs ImageJ in debug mode