Fiji (software)

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Open-source image-processing software

title: "Fiji (software)" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["computer-vision-software", "neuroimaging-software", "free-software-programmed-in-java", "software-using-the-gnu-general-public-license"] description: "Open-source image-processing software" topic_path: "technology/computing" source: "https://en.wikipedia.org/wiki/Fiji_(software)" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0

::summary Open-source image-processing software ::

::data[format=table title="Infobox software"]

FieldValue
nameFiji
logoFIJI (software) Logo.svg
logo size200px
captionFiji in action
developerJohannes Schindelin, Ignacio Arganda-Carreras, Albert Cardona, Mark Longair, Benjamin Schmid, and others
latest release version2.9.0
latest release date
operating_systemany with Java support
programming languageJava
licenseGPL v3 (some plugins have different licenses)
genreImage processing and Image analysis
repo
website
::

| name = Fiji | logo= FIJI (software) Logo.svg | logo size= 200px | screenshot = | caption = Fiji in action | developer = Johannes Schindelin, Ignacio Arganda-Carreras, Albert Cardona, Mark Longair, Benjamin Schmid, and others | latest release version = 2.9.0 | latest release date = | operating_system = any with Java support | programming language = Java | license = GPL v3 (some plugins have different licenses) | genre = Image processing and Image analysis | repo = | website = ::figure[src="https://upload.wikimedia.org/wikipedia/commons/7/7b/20221126_17_58_02-Fiji_(software)_-_Wikipedia.png" caption="Screenshot of Fiji in Windows 11"] ::

Fiji is an open source image processing package based on ImageJ2.

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.

Plugins

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.

Audience

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 registration, segmentation, and other advanced image processing algorithms.

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

Fiji was prominently featured in Nature Methods review supplement on visualization.

The lattice fringe spacing of CdSe quantum dots was analyzed using Fiji.

Development

Fiji is fully open source. Its sources live in a public Git repository.

Fiji was accepted as an organization into the Google Summer of Code 2009, and completed two projects.

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. To this end, as one of the aforementioned Google Summer of Code projects, a script editor was added with syntax highlighting and in-place code execution.

The scripting framework is included in the Fiji releases, so that advanced users can use such scripts in their common workflow.

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

Script editor

The script editor in Fiji supports rapid prototyping of scripts and ImageJ plugins, making Fiji a powerful tool to develop new image processing algorithms and explore new image processing techniques with ImageJ.

Supported platforms

Fiji runs on Windows, Linux, and Mac OS X, Intel 32-bit or 64-bit, with limited support for MacOSX/PPC.

References

References

  1. "Tags - fiji/fiji".
  2. "LICENSE.txt file".
  3. "LICENSES file".
  4. (2012). "Fiji: an open-source platform for biological-image analysis". Nature Methods.
  5. Fiji was presented publicly for the first time on the ImageJ User and Developer Conference in November 2008.
  6. link. (28 January 2021 in November 2008 and the [http://imagejconf.tudor.lu/archive/imagej-user-and-developer-conference-2010/doku.php?id=:archive:imagej-user-and-developer-conference-2010:presentations:schindelin:start 3rd ImageJ and User Developer Conference] in October 2010.)
  7. Compare with the [https://fiji.sc/Fiji_Usage Fiji Usage Map]
  8. (2011). "Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes". Bioinformatics.
  9. (April 2009). "Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions". Bioinformatics.
  10. (May 2009). "Automated classification of ''Plasmodium'' sporozoite movement patterns reveals a shift toward productive motility during salivary gland infection". Biotechnology Journal.
  11. The [https://fiji.sc/ Fiji Wiki], Retrieved 2012-11-01.
  12. (2010). "A high-level 3D visualization API for Java and ImageJ". BMC Bioinformatics.
  13. (2010). "Software for bead-based registration of selective plane illumination microscopy data". Nature Methods.
  14. (2010). "Identifying Neuronal Lineages of Drosophila by Sequence Analysis of Axon Tracts". The Journal of Neuroscience.
  15. (2010). "Visualization of image data from cells to organisms". Nature Methods.
  16. Allahverdi, Cagdas. (2025). "Analysis of The Lattice Fringe of a Quantum Dot Using Fiji". ASES.
  17. link. (7 February 2019 in October 2010)
  18. Albert Cardona's crash course [http://www.ini.uzh.ch/~acardona/fiji-tutorial/index.html ''Jython scripting with Fiji''].

::callout[type=info title="Wikipedia Source"] This article was imported from Wikipedia and is available under the Creative Commons Attribution-ShareAlike 4.0 License. Content has been adapted to SurfDoc format. Original contributors can be found on the article history page. ::

computer-vision-softwareneuroimaging-softwarefree-software-programmed-in-javasoftware-using-the-gnu-general-public-license