ImageJ 1.40

The ImageJ website is at rsb.info.nih.gov/ij/, the release notes are at rsb.info.nih.gov/ij/notes.html and the installation notes are at rsb.info.nih.gov/ij/docs/install/.

Contents of ImageJ folder:

ij.jar
This JAR (Java Archive) file is the platform-independent core of ImageJ. It is the only file that needs to be changed to upgrade to a newer version of ImageJ. Use the Plugins>Utilities>Upgrade ImageJ command to download newer versions of this file.
ImageJ.app
This is the ImageJ launcher for Mac OS X.
ImageJ.exe
This is the ImageJ launcher for Windows.
run
This is a shell script that runs ImageJ.
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. The plugins in this folder are installed in the Plugins menu when ImageJ starts.
luts
This folder contains LUTs (LookUp Tables) that are installed at startup in the Image>Lookup Tables menu and in the "Lut" toolbar menu. To open a LUT file, drag and drop it on the ImageJ window.