There are a few different flavors of ImageJ with very similar names, and some confusion is inevitable. Below is a table which should help to clarify the purpose of each. For the historical context of these projects, see the History of ImageJ.
| Name | Author/Maintainer(s) | Description | Initiated | Status |
| ImageJ ImageJ1 | Wayne Rasband | The current, stable version is known simply as "ImageJ"—or sometimes "ImageJ1" or "IJ1" to differentiate it from ImageJ 2.0 (still in development). | 1997 | Active |
| ImageJ2 ImageJDev | ImageJ developers | The ImageJDev project (this web site and associated community) is developing version 2.0 of ImageJ, referred to as "ImageJ2" or "IJ2" for short. It is a complete rewrite of ImageJ, but includes ImageJ1 with a compatibility layer, so that old-style plugins and macros can run the same as in IJ1. | Dec. 2009 | Active |
| ImageJA | Johannes Schindelin |
ImageJA is a project that provides a clean Git History of the ImageJ 1.* branch, with a proper 'pom.xml' file so that it can be used with Maven without hassles. It is what Fiji uses (see below) at its core. | Jul. 2005 | Active |
| Fiji | Fiji contributors |
Fiji is Just ImageJ, with extras. It is a distribution of ImageJ with many plugins useful for image analysis in the life sciences, an automatic updater, and improved scripting capabilities. It is actively maintained, with updates released often. We recommend Fiji as the preferred version of ImageJ. | Dec. 2007 | Active |
| MBF_ImageJ | Tony Collins | The MBF "ImageJ for Microscopy" bundle (formerly WCIF_ImageJ) is a collection of plugins and macros, collated and organized by the MacBiophotonics facility. It goes hand in hand with a comprehensive manual describing how to use the bundle with light microscopy image data. It is a great resource by microscopists, for microscopists. However, it is not maintained as actively as Fiji is (see above). For the most part it is possible to add specific plugins from MBF_ImageJ to a Fiji installation, combining the best of both programs. | 2005 | Last update: Dec. 2009 |
| SalsaJ | EU-HOU | SalsaJ is a fork of ImageJ1 intended for use with professional astronomy images. It was designed to be used in classrooms, and has been localized into over 30 different languages. | Unknown | Last update: Feb. 2010 |
| ImageJ2x | Rawak Software | ImageJ2x is a fork of ImageJ1, modified to use a Swing interface. It does not appear to be under active development anymore. | Unknown | Last update: Oct. 2008 |
| ImageJX | Grant Harris | ImageJX was created as a means to discuss and explore improvements to ImageJ. There was an ImageJX mailing list as well as an ImageJX software prototype. The ImageJX software prototype was a proof of concept—an attempt to reorganize ImageJ's internals to make it more flexible. The prototype demonstrated this flexibility by recasting the program in Swing. The ImageJX project formed the basis of an application to NIH for funding, which is what launched the ImageJDev project (see above). | Mar. 2009 | Superceded by ImageJ2 |
| NIH Image | Wayne Rasband | NIH Image is a public domain image processing and analysis program for the Macintosh. It is the direct predecessor of ImageJ, and is no longer under active development (though see ImageSXM below). | 1993 or earlier | Superceded by ImageJ |
| ImageSXM | Steve Barrett | Image SXM is a version of NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. | May 1993 | Active |