ImageJ is still under active development, and new features and bug fixes are added to the core distribution on a regular basis. Currently, the development of a revised system for ImageJ is being developed. It is called ImageJ2. The goals of ImageJ2 are to better support multidimensional data as well as create a more extensible platform that can be used as a library instead of a standalone application. It will also create a more consistent environment for development and extension. One of the features being developed is the updating mechanism for ImageJ. Currently, it is possible to update ImageJ automatically using a central repository, and one of the goals of ImageJ2 is to expand this option to plugins and other features and allow tracking of bugs and features. However, one of the core requirements in the new ImageJ2 system is backward compatibility. This goal means that plugins developed now will stay functional in future releases of ImageJ. The current status is indicated as beta, which means the plugin is functional but may still contain bugs and is not optimized for performance yet.

Other developments related to image are those related to image formats and standards. Currently, all major commercial acquisition platforms store image data in unique proprietary file formats. The SCIFIO project is aimed at creating an extensible and integrated interface to handle images of different formats. It will support more image formats and allow for additional options to be set when importing the data, such as autoscaling, loading metadata, and loading the data in different ImageJ image types. However, it is still under active development, and some of the features do not quite work in a production environment (yet).

The OME-XML (Open Microscopy Environment-XML) project is aimed at creating a file format that contains all the image and metadata in a standardized format. This would facilitate the exchange of microscope image data, regardless of the equipment used for acquisition. It is mainly focused on the exchange of microscopy data in the field of life sciences. It contains all the experimental and setup data as well as the pixel data in a single file specification.

Besides the OME-XML format, which is focused on integrating acquisition and processing across multiple acquisition platforms, there is also active development of the plugin used to import many image formats currently in existence. This plugin, called Bio-Formats, is mostly focused on image formats from the life sciences. However, it also supports FITS data, which is used in the field of astronomy and space exploration. It currently supports (to different degrees) 140 different image formats and converts them to the OME-XML format for use in ImageJ.

When you download a copy of ImageJ, the JRE can be provided along with it. If you already have a copy of the JRE installed, you could download ImageJ without the JRE for a faster download. The minimal requirements to run ImageJ are JRE Version 1.6 or higher. For some distributions, most notably Fiji, the JRE has to be version 1.6. This limitation is due to the current implementation of the updater included with Fiji, which is not capable of updating the JRE. This problem may be resolved in the future.

As ImageJ comes with its own JRE, it can be extracted on a USB drive and run from there without installation. The only limitations on the system are dependent on the size of the images. ImageJ loads images directly into memory, so the available system memory needs to be large enough to hold the images you wish to process. When memory requirements exceed 3 GB, a 64-bit operating system with a 64-bit JRE is required.

Since ImageJ is platform independent, you could use the same version on all three platforms: Windows, OS X, and Linux. The only platform-dependent part is the JRE; for each platform, there is a specific JRE installation. The following sections will explain how to install ImageJ on each of the operating systems.

In order to install ImageJ on Windows, you can download the latest version from the ImageJ website at the NIH (http://imagej.nih.gov/ij/download.html) or for Fiji from the Fiji website (http://Fiji.sc/Downloads). When downloading from the NIH website, there are two choices: an installer for 32-bit or 64-bit systems and a ZIP archive when you wish to run ImageJ on a platform without installer privileges.

When using the installer version, it is generally not recommended that you install ImageJ in the Program Files folder. Certain files within the ImageJ folder need to be modified when using the program, so when running it as a regular user, access problems may occur. Also, when installing or creating plugins, the compiled files need to be placed in the plugins folder within ImageJ. This folder may not have write permission when it is located in the Program Files folder for regular (non-administrator) users. Alternatively, you could change the access permissions for the ImageJ folder specifically. However, this is not recommended from a security point of view.

Double-clicking on the ImageJ.exe file within the extracted folder will start ImageJ. This file is a wrapper executable that calls the ij.jar file and uses the supplied JRE to run it. The Fiji distribution comes as a ZIP archive that can be extracted on a disk and run immediately:

ImageJ is available for Mac OS X as a ZIP archive that can be extracted to a folder within the Applications folder. The Fiji distribution can be downloaded as a DMG file that can be dropped in the Applications folder. This will install the ImageJ folder and make it accessible for all registered users. It will also create a Fiji icon in the app drawer. If you wish to import or export QuickTime movies under OS X 10.10 (Yosemite), you need to download the QTJava.zip and libQTJNative.jnilib files from http://imagej.nih.gov/ij/download/qt/ into your home directory within the Library/Java/Extensions folder.

Note that in OS X 10.7 and later, you may receive a warning the first time you try to run ImageJ. This warning will say ImageJ can't be opened because it is from an unidentified developer. This can be resolved by going to the system settings and pushing the allow button in the security and privacy panel. This should prevent this warning from showing up in the future. Alternatively, you can select the Anywhere option from the Allow apps downloaded from section. The latter option is not recommended from a security point of view, as it might also allow malicious software to be executed.

Note that when ImageJ (or Fiji) is run on OS X, the menu bar is not part of the main window as in Windows:

ImageJ can be installed on Linux platforms by unpacking the distribution from the NIH website. The distribution from the NIH website is available as a ZIP file, while the Fiji distribution is available as a tar.gz file. For most Linux distributions, it is recommended that you extract the archive to a location within your home folder. This prevents problems with write permissions on the ImageJ folders. The folder contains a shell script to run ImageJ. This shell script is named ImageJ. For different desktop environments, methods exist to create a shell shortcut to this script to allow it to run from a shortcut.

The two most important folders are the macros and plugins folders. These folders will be searched for available macros and plugins when ImageJ loads. When you download a plugin and place it in the plugins folder, the plugin will be found the next time ImageJ starts. When downloading plugins, there are three different options of files that can be downloaded: a Java source file (.java), a compiled file (.class), or a Java archive (.jar). In order for plugins to be displayed in the plugins menu, the .java and .class files need to contain at least one underscore character in the filename. For .jar files, the archive needs to contain a plugins.config file that defines the location within the menu system. This has an additional advantage that plugins within a .jar archive can also be installed outside the plugins menu.Underscores are replaced by spaces in the plugins menu or removed completely if the last character is an underscore. If you place your plugins in a folder within the plugins folder, this folder name will also show up in the Plugins menu, but only if it contains at least one valid plugin. If you download the source file of a plugin, you can create an executable plugin by choosing Compile and Run from the Plugins menu and selecting the Java file. The next time ImageJ is run, the new plugin will be automatically detected.

JAR files are slightly special. They can be placed within the plugins folder, but they do not have to show up in the Plugins menu. The JAR file contains a manifest that specifies the location where the plugins within it are placed. This specification allows the developer to place the plugin in a specific submenu of the Plugins menu, regardless of the folder where the JAR file is placed. This would be especially handy if you create a group of linked or associated plugins that you wish to group within the Plugins menu.

The macros folder contains a collection of macros that come with ImageJ and is also the default location to store user-defined macros. ImageJ macros are flat text files with the .ijm extension, although this extension is not essential. Any flat text file with valid macro code can be run in ImageJ. Macros in ImageJ have their own language, which is similar to Java, but with a few minor differences. Chapter 5, Basic Measurements with ImageJ will investigate how to create macros and will explain the language constructs in ImageJ macros.