Fiji (Fiji Is Just ImageJ) is an open source image processing package based on .
Fiji's main purpose is to provide a distribution of ImageJ2 with many bundled plugins. 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.
Fiji is also targeted at developers, through the use of a version control system, an issue tracker, dedicated development channels, and a rapid-prototyping infrastructure in the form of a script editor which supports BeanShell, Jython, JRuby, Clojure, Groovy, JavaScript, and other scripting languages, as well as just-in-time Java development.
Many plugins exist for ImageJ, that have a wide range of applications, but also a wide range of quality.
Further, some plugins require specific versions of ImageJ, specific versions of third-party libraries, or additional Java components such as the Java compiler or Java 3D.
One of Fiji's principal aims is to make the installation of ImageJ, Java, Java 3D, the plugins, and further convenient components, as easy as possible. As a consequence, Fiji enjoys more and more active users.
While Fiji was originally intended for neuroscientists (and continues to be so), it accumulated enough functionality to attract scientists from a variety of fields, such as cell biology, parasitology, genetics, life sciences in general, materials science, etc. As stated on the official website, the primary focus is "life sciences", although Fiji provides many tools helping with scientific image analysis in general.
Fiji is most popular in the life sciences community, where the 3D Viewer helps visualizing data obtained through light microscopy, and for which Fiji provides , , and other advanced image processing algorithms.
The Fiji component TrakEM2 was successfully used and enhanced to analyze neuronal lineages in larval Drosophila brains.
