The easiest way to upgrade to the latest version of ImageJ is to use the Help>Update ImageJ command, available in version 1.41 or later.

The Update ImageJ command downloads the latest ij.jar file (the core of ImageJ) from wsr.imagej.net/jars/ij.jar. Alternatively, it will download the "daily build" ij.jar file from wsr.imagej.net/download/daily-build if "daily build" is selected from the drop down menu. The Java source code for ImageJ is available at image.nih.gov/ij/download/src/.