Fiji features an integrated updating system and aims to provide users with a coherent menu structure, extensive documentation in the form of detailed algorithm descriptions and tutorials, and the ability to avoid the need to install multiple components from different sources.

As stated on the official website, the primary focus is "life sciences", although Fiji provides many tools helping with scientific image analysis in general.

The Fiji component TrakEM2 was successfully used and enhanced to analyze neuronal lineages in larval Drosophila brains.

The scripting framework, which supports JavaScript, Jython, JRuby, Clojure, BeanShell, and other languages, is an integral part of the development of Fiji; many developers prototype their plugins in one of the mentioned scripting languages, and gradually turn the prototypes into proper Java code.

The development benefits from occasional hackathons, where life scientists with computational background meet and improve their respective plugins of interest.