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Image analysis tools in biology and biochemistry using ImageJ

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Image analysis and processing tool developments using the ImageJ software:

Thursday 2 April 2009, by Gilles Carpentier

  Table of contents  

 User tool helper:

User can customize ImageJ by adding its own programs. This can be made by using the "Java" language (plugins), or the "macro" language. While plugins are directly accessible from the "Plugins" menu, access to macros is more fastidious. A tool has been developed [2] to supress any access differences between the two methods.

The « Macro Plugin Shortcuts » tool is a very easy way to transform virtually any macro developments into plugin-like aspect. It suggests the list of the ImageJ macros library from a pop-up menu. Once chosen, a macro developement becomes accessible from the “ Plugins ” menu, after restarting ImageJ.

In the present example, the « AutoThresholdAndSegment » Macro chosen by the user (see the above screen shot), is now accessible like any other plugins. The so selected developments are organised into a sub-folder called « My Favorite Macros », making them easier to find and operate.

Once activated from « My Favorite Macros », sub-functions of the selected macro, are immediately available from the Plugin -> Macros sub-menu.


[2Carpentier G. Contribution: the Macro Plugin Shortcuts, which makes plugin shortcuts for macros and tools. ImageJ News, July 2006.

logoij ImageJ ( is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (, is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.
Gilles Carpentier, Faculte des Sciences et Technologie,
Universite Paris Est Creteil Val-de-Marne, France.

Special thanks to Alessandra Albano for the English correction of these sites.
Computer Data Acquisition
for Biochemistry Practice Works
Image analysis tools in biology
and biochemistry using ImageJ