About this manual – Please read first
NOTE: This manual describes the MBF ImageJ collection of plugins available from the Software section of MBF website.

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs on any computer with a Java 1.1 or later virtual machine, either as an online applet or as a downloadable application. The author, Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

The best source of information about ImageJ can be found at the ImageJ homepage (http://rsb.info.nih.gov/ij/) and by subscribing to the ImageJ mailing list (details on the home page). This manual is meant to be an introduction to ImageJ for light microscopy – a small part of ImageJ’s repertoire.

ImageJ has a large number of native functions supplemented by an ever increasing number of “plugins” (optional extras needing installation). The core functions are described in detail on the ImageJ web site (follow the Documentations link). A plugin is a file (named *.class) which needs to be in the “plugins” sub-folder of the ImageJ folder, otherwise ImageJ will not load it.

In this manual, the native functions are referred to in italicised, black text, the plugins by italicised, dark-blue text. ImageJ functions can be accessed by keyboard shortcuts, or “hotkeys”. Some hotkeys are hard-wired in to ImageJ, while others are user-defined. Unlike most other Windows applications, keyboard shortcuts do not require the “control” key to be pressed (for example, in Microsoft Word, the hotkey to “copy” is Ctrl+C); in ImageJ, it is just “C”. Unless you have installed ImageJ from the Wright Cell Imaging Facility website (Manuals and Software link), the plugins referred to in this manual and some of customised the keyboard shortcuts (the “hotkeys”) may not work.

This collection of plugins has merely been collated and organised by MBF; they have all have been obtained free from the ImageJ website or elsewhere on the Internet. The credit for this work should go to the authors of the plugins (See Appendix). Please ensure that they are properly acknowledged in any publication that their work facilitates. I have attempted to include appropriate citations or contact details for each author.

This manual is intended to be an introductory overview to get you up and running, and as such, is not exhaustive. I began working on this manual while employed at the Babraham Institute, Cambridge, UK. It emerged as the popular WCIF_ImageJ collection. WCIF_ImageJ ceased to be updated in April 2006. MBF_ImageJ was first posted in Autumn 2006.