FIJI (Fiji Is Not ImageJ)

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...