6/25/23, 2:39 PM Windows Installation

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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.

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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
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6/25/23, 2:39 PM Windows Installation

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
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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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