This last item deserves a section on its own. You might have found interesting some of the plugins that we showed you previously, and might be willing to try them on your sample images. If that is the case, you would have to download and install every one of them individually in your system. If you want to try many different plugins, this can take some time.

Fortunately for us, there is a solution, Fiji (Fiji Is Just ImageJ) is an ImageJ distribution, much alike Linux distributions, which includes the core ImageJ functionalities, in addition to many extra plugins, an auto-updating system and some extra niceties. You can access the entire list of included plugins at http://fiji.sc/Category:Plugins.

You can download and install Fiji from http://fiji.sc/Downloads. Choose the right version for your operating system and unpack the compressed file to the folder of your choice. Inside, you will see the Fiji's executable file. Below you can see the main ImageJ and Fiji windows one on top of another. They are virtually the same, but notice the number of Fiji commands printed on its status bar:

If you install it, try the different menu options. You will see that there are many more than in ImageJ, as the plugins it includes are distributed among the different menus, not only in the Plugins one. Also, try creating a new macro (by navigating to Plugins | New | Macro...). The Fiji editor is much more flexible than the basic ImageJ editor, as it has syntax coloring and many other features that make macro editing, a much pleasant experience. Everything we have explained about ImageJ so far can be done with Fiji in exactly the same way.