IJ2 is out
 Sec. 1: Introduction Up Part I: Getting Started Sec. 3: Getting Help 

2 Installing and Maintaining ImageJ

ImageJ can be downloaded from ../../download.html. Details on how to install ImageJ on Linux, Mac OS 9, Mac OS X and Windows [1] are available at ../install/ (HelpInstallation…↓ command). Specially useful are the platform-specific Troubleshooting and Known Problems sections. Fiji↓ installation is described at http://fiji.sc/wiki/index.php/Downloads.
The downloaded package may not contain the latest bug fixes so it is recommended to upgrade ImageJ right after a first installation. Updating IJ[?] consists only of running HelpUpdate ImageJ…↓, which will install the latest ij.jar in the ImageJ folder (on Linux and Windows) or inside the ImageJ.app (on Mac OS X).
HelpUpdate ImageJ…↓ can be used to upgrade (or downgrade) the ij.jar file to release updates or daily builds. Release updates are announced frequently on the IJ news website and are labelled alphabetically (e.g., v. 1.43m). Typically, these releases contain several new features and bug fixes, described in detail on the ImageJ News page. Daily builds, on the other hand, are labelled with numeric sub-indexes (e.g., v. 1.43n4) and are often released without documentation. Nevertheless, if available, release notes for daily builds can be found at ../../source/release-notes.html. When a release cycle ends (v. 1.42 ended with 1.42q, v. 1.43 with 1.43u, etc.) an installation package is created, downloadable from ../../download.html. Typically, this package is bundled with a small list of add-ons (Macros↓, Scripts↓ and Plugins↓).
Luts, Macros and Tools Updater, a macro toolset that performs live-updating of macros listed on the ImageJ web site

2.1 ImageJDistributions

ImageJ alone is not that powerful: it’s real strength is the vast repertoire of Plugins↓ that extend ImageJ’s functionality beyond its basic core. The many hundreds, probably thousands, freely available plugins from contributors around the world play a pivotal role in ImageJ’s success [102]. Running HelpUpdate ImageJ…↓, however, will not update any of the plugins you may have installed [B]  [B] Certain plugins, however, provide self-updating mechanisms (e.g., ObjectJ and the OME Bio-Formats library)..
ImageJ add-ons (Plugins↓, Scripts↓ and Macros↓) are available from several sources (ImageJ's plugins page [HelpPlugins…↓], ImageJ Information and Documentation Portal and Fiji's webpage, among others) making manual updates of a daunting task. This reason alone, makes it extremely convenient the use of ImageJDistributions↑ bundled with a pre-organized collection of add-ons.
Below is a list of the most relevant projects that address the seeming difficult task of organizing and maintaining ImageJ beyond its basics. If you are a life scientist and have doubts about which distribution to choose you should opt for Fiji↓. It is heavily maintained, offers an automatic updater, improved scripting capabilities and ships with powerful plugins. More specialized adaptations of ImageJ are discussed in Software Packages Built on Top of ImageJ↓.


Fiji (Fiji Is Just ImageJ—Batteries included) is a distribution of ImageJ together with Java, Java 3D and several plugins organized into a coherent menu structure. Citing its developers, “Fiji compares to ImageJ as Ubuntu compares to Linux”. The main focus of Fiji is to assist research in life sciences, targeting image registration, stitching, segmentation, feature extraction and 3D visualization, among others. It also supports many scripting languages (BeanScript, Clojure, Jython, Python, Ruby, see Scripting in Other Languages↓). Importantly, Fiji ships with a convenient updater that knows whether your files are up-to-date, obsolete or locally modified. Comprehensive documentation is available for most of its plugins. The Fiji project was presented publicly for the first time at the ImageJ User and Developer Conference in November 2008.

MBF ImageJ

The MBF ImageJ bundle or ImageJ for Microscopy (formerly WCIF-ImageJ) features a collection of plugins and macros, collated and organized by Tony Collins at the MacBiophotonics facility, McMaster University. It is accompanied by a comprehensive manual describing how to use the bundle with light microscopy image data. It is a great resource for microscopists but is not maintained actively, lagging behind the development of core ImageJ.
Note that you can add plugins from MBF ImageJ to Fiji, combining the best of both programs. Actually, you can use multiple ImageJ distributions simultaneously, assemble your own ImageJ bundle by gathering the plugins that best serve your needs (probably, someone else at your institution already started one?) or create symbolic links to share plugins between different installations.
Description of all ImageJ related projects at ImageDev

2.2 Related Software

2.2.1 Software Packages Built on Top of ImageJ

Bio7Bio7 is an integrated development environment for ecological modeling with a main focus on individual based modeling and spatially explicit models. Bio7 features: Statistical analysis (using R); Spatial statistics; Fast communication between R and Java; BeanShell and Groovy support; Sensitivity analysis with an embedded flowchart editor and creation of 3D OpenGL (Jogl) models (see also RImageJ in ImageJ Interoperability↓).
BoneJBoneJ is a collection of tools for trabecular geometry and whole bone shape analysis.
μManagerMicro-Manager is a software package for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers, most scientific-grade cameras and many peripherals used in microscope imaging.
MRI--CIAMRI Cell Image Analyzer, developed by the Montpellier RIO Imaging facility (CNRS), is a rapid image analysis application development framework, adding visual scripting interface to ImageJ’s capabilities. It can create batch applications as well as interactive applications. The applications include the topics “DNA combing”, “quantification of stained proteins in cells”, “comparison of intensity ratios between nuclei and cytoplasm” and “counting nuclei stained in different channels”.
ObjectJObjectJ, the successor of object-image, supports graphical vector objects that non-destructively mark images on a transparent layer. Vector objects can be placed manually or by macro commands. Composite objects can encapsulate different color-coded marker structures in order to bundle features that belong together. ObjectJ provides back-and-forth navigation between results and images. The results table supports statistics, sorting, color coding, qualifying and macro access.
SalsaJSalsaJ is a student-friendly software developed specifically for the EU-HOU project. It is dedicated to image handling and analysis of astronomical images in the classroom. SalsaJ has been translated into several languages.
TrakEM2TrakEM2 is a program for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation [6]. TrakEM2 is distributed with Fiji and capable of:

2.2.2 ImageJ Interoperability

Several packages exist that allow ImageJ to interact with other applications/environments:
Bitplane ImarisImarisXT can load and execute ImageJ plugins. bpImarisAdapter (Windows only and requiring valid licenses for Imaris and ImarisXT) allows the exchange of images between Imaris and ImageJ.
Cell ProfilerCellProfiler [9] features RunImageJ, a module that allows ImageJ plugins to be run in a CellProfiler pipeline.
IcyIcy, an open source community software for bio-imaging, executes ImageJ plugins with almost 100% plugin compatibility.
KnimeKnime ([?]Konstanz Information Miner) contains several image processing nodes ([?]KNIP) that are capable of executing ImageJ plugins and macros.
Open Microscopy Environment[?]All Open Microscopy Environment projects such as Bio-Formats, VisBio and OMERO integrate well with ImageJ.
RImageJ — R bindings for ImageJ Bindings between ImageJ and R (GNU S) — The free software environment for statistical computing and graphics. The documentation for RImageJ is available at http://cran.r-project.org/web/packages/RImageJ/RImageJ.pdf (see also Bio7 in Software Packages Built on Top of ImageJ↑).
MIJ — Matlab—ImageJ bi-directional communication A Java package for bi-directional data exchange between Matlab and ImageJ, allowing to exchange images between the two imaging software. MIJ also allows MATLAB to access all built-in functions of ImageJ as well as third-party ImageJ plugins. The developers provide more information on the MIJ and Matlab File Exchange websites. Fiji↑ features Miji.m, which makes even more convenient to use the libraries and functions provided by Fiji’s components from within Matlab.

2.3 ImageJ2

ImageJDev is a federally funded, multi-institution project dedicated to the development of the next-generation version of ImageJ: “ImageJ2”. ImageJ2 is a complete rewrite of ImageJ, that includes the current, stable version ImageJ (“ImageJ1”) with a compatibility layer so that old-style plugins and macros can run the same as they currently do in ImageJ1. Below is a summary of the ImageJDev project aims:
Be sure to follow the ImageJ2 project news and the ImageDev blog for updates on this exciting project.
 Sec. 1: Introduction Up Part I: Getting Started Sec. 3: Getting Help