FijiImageJ

Fiji, short for Fiji Is Just ImageJ, is an open-source distribution of the ImageJ platform tailored for biological image analysis. It provides a ready-to-use environment that bundles ImageJ and ImageJ2, a curated set of plugins, and an integrated update system to streamline installation, version control, and workflow sharing. By combining core ImageJ functionality with an extensive plugin suite, Fiji aims to reduce setup time and promote reproducible image analyses in microscopy and related fields.

Major components include Bio-Formats for reading hundreds of image formats, TrackMate for particle and feature tracking, 3D Viewer and BigDataViewer for visualization of large datasets, and tools for scripting and automation. Fiji also exposes a flexible updater that resolves dependencies and ensures consistent plugin versions across users. Users can script in ImageJ macro, JavaScript, Python, and other languages, and can combine ImageJ2 plugins with classic ImageJ features.

Fiji is maintained by a community of researchers and developers and is distributed with cross-platform support for Windows, macOS, and Linux. It emphasizes reproducible workflows by providing pre-installed workflows and documented best practices, and it is updated through a central update system rather than manual plugin installation.

Since its inception, Fiji has become a widely adopted tool in life sciences for image segmentation, quantification, 3D reconstruction, and time-lapse analysis, serving as a bridge between novice users and advanced image analysis pipelines through its accessible interface and extensive plugin ecosystem.