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Fiji

Fiji Is Just ImageJ — a distribution of ImageJ bundled with plugins for scientific image analysis.

Overview

Fiji packages ImageJ with a curated set of plugins for the life sciences, plus an integrated updater that keeps both Fiji and its plugins current. It runs as a standalone application (Java is bundled — no separate install needed) on Windows, macOS, and Linux.

Key features

  • Large plugin ecosystem via update sites
  • Macro recorder and scripting in ImageJ Macro, Jython, Groovy, JavaScript, BeanShell
  • Bio-Formats for reading most microscopy file formats
  • ROI Manager, 3D Viewer, stitching, registration, and deconvolution plugins

Installation

  1. Download from the Fiji download page.
  2. Extract the archive and run the executable for your OS (ImageJ-win64.exe, Fiji.app, or ImageJ-linux64).
  3. Keep it current via Help > Update... and manage extra plugin sources via Help > Update... > Manage Update Sites.

Tip

Many Cell Observatory workflows depend on the PTBIOP update site (e.g. the Cellpose wrapper). Enable it via Manage Update Sites when needed.

Scripting

Fiji can be automated at three levels of complexity:

  • Macro recorder (Plugins > Macros > Record...) — captures your GUI actions as an ImageJ Macro script. The fastest way to start automating a manual workflow.
  • ImageJ Macro Language — simple scripting for batch operations. Reference: Built-in Macro Functions.
  • Jython, Groovy, BeanShell — for more complex scripts anything the macro language can't express cleanly. See the Fiji scripting guide.

Keep scripts in a Git repository — see GitHub for a handy setup to keep track of your script changes.

Official documentation

Learning resources

Video

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