Windows Installation

Installation
Memory
Troubleshooting
Drag and Drop
Upgrading Java
Contents of ImageJ folder
Command Line Options

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.
If the "ImageJ" window is too small, set "GUI scale" in the Edit>Options>Appearance dialog to a value greater then 1.0.
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>Compatibility 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".

I installed the Windows 10 Creators Update and now ImageJ freezes when I try to open an image.

Enable "Use JFileChooser to open/save" in Edit>Options>Input/Output.

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:

Download and install the latest JDK from www.oracle.com/technetwork/java/javase/downloads/
Go to the ImageJ folder and delete or rename the jre folder
Delete the ImageJ.cfg file
Restart ImageJ and the launcher (ImageJ.exe) will generate a new ImageJ.cfg that uses the Java you just installed.

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

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