Fiji (software)

Fiji^[4][5] is an open source image processing package based on ImageJ2.

Fiji

Developer(s)	Johannes Schindelin, Ignacio Arganda-Carreras, Albert Cardona, Mark Longair, Benjamin Schmid, and others
Stable release	2.9.0 / September 14, 2022; 2 years ago (2022-09-14)[1]
Repository	github.com/fiji/fiji
Written in	Java
Operating system	any with Java support
Type	Image processing and Image analysis
License	GPL v3[2] (some plugins have different licenses[3])
Website	fiji.sc

Screenshot of Fiji in Windows 11

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.^[6]

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.^[7]

Audience

While Fiji was originally intended for neuroscientists (and continues to be so^[8]), it accumulated enough functionality to attract scientists from a variety of fields, such as cell biology,^[9] parasitology,^[10] 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.^[11]

Fiji is most popular in the life sciences community, where the 3D Viewer^[12] helps visualizing data obtained through light microscopy, and for which Fiji provides registration,^[13] segmentation, and other advanced image processing algorithms.

The Fiji component TrakEM2 was successfully used and enhanced to analyze neuronal lineages in larval Drosophila brains.^[14]

Fiji was prominently featured in Nature Methods review supplement on visualization.^[15]

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.^[16][17]

Supported platforms

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

References

1. "Tags - fiji/fiji". Retrieved 26 November 2022 – via GitHub.
2. "LICENSE.txt file". Retrieved 25 November 2022 – via GitHub.
3. "LICENSES file". Retrieved 25 November 2022 – via GitHub.
4. Primary reference: Johannes Schindelin; Ignacio Arganda-Carreras; Erwin Frise; Verena Kaynig; Mark Longair; Tobias Pietzsch; Stephan Preibisch; Curtis Rueden; Stephan Saalfeld; Benjamin Schmid; Jean-Yves Tinevez; Daniel James White; Volker Hartenstein; Kevin Eliceiri; Pavel Tomancak; Albert Cardona (2012). "Fiji: an open-source platform for biological-image analysis". Nature Methods. 9 (7): 676–682. doi:10.1038/nmeth.2019. PMC 3855844. PMID 22743772.
5. Fiji was presented publicly for the first time on the ImageJ User and Developer Conference in November 2008.
6. Compare the presentations at the 2nd ImageJ User and Developer Conference Archived 28 January 2021 at the Wayback Machine in November 2008 and the 3rd ImageJ and User Developer Conference in October 2010.
7. Compare with the Fiji Usage Map
8. Longair Mark; Baker DA; Armstrong JD. (2011). "Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes". Bioinformatics. 27 (17): 2453–4. doi:10.1093/bioinformatics/btr390. hdl:20.500.11850/39228. PMID 21727141.
9. Preibisch S, Saalfeld S, Tomancak P (April 2009). "Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions". Bioinformatics. 25 (11): 1463–5. doi:10.1093/bioinformatics/btp184. PMC 2682522. PMID 19346324.^{[dead link‍]}
10. Hegge S, Kudryashev M, Smith A, Frischknecht F (May 2009). "Automated classification of Plasmodium sporozoite movement patterns reveals a shift toward productive motility during salivary gland infection". Biotechnology Journal. 4 (6): 903–13. doi:10.1002/biot.200900007. PMID 19455538. S2CID 7371409. Archived from the original on 1 August 2009.
11. The Fiji Wiki, Retrieved 2012-11-01.
12. Benjamin Schmid; Johannes Schindelin; Albert Cardona; Mark Longair; Martin Heisenberg (2010). "A high-level 3D visualization API for Java and ImageJ". BMC Bioinformatics. 11: 274. doi:10.1186/1471-2105-11-274. PMC 2896381. PMID 20492697.
13. Stephan Preibisch; Stephan Saalfeld; Johannes Schindelin; Pavel Tomancak (2010). "Software for bead-based registration of selective plane illumination microscopy data". Nature Methods. 7 (6): 418–419. doi:10.1038/nmeth0610-418. PMID 20508634. S2CID 39609830.
14. Albert Cardona; Stephan Saalfeld; Ignacio Arganda; Wayne Pereanu; Johannes Schindelin; Volker Hartenstein (2010). "Identifying Neuronal Lineages of Drosophila by Sequence Analysis of Axon Tracts". The Journal of Neuroscience. 30 (22): 7538–7553. doi:10.1523/JNEUROSCI.0186-10.2010. PMC 2905806. PMID 20519528.
15. Thomas Walter; David W Shattuck; Richard Baldock; Mark E Bastin; Anne E Carpenter; Suzanne Duce; Jan Ellenberg; Adam Fraser; Nicholas Hamilton; Steve Pieper; Mark A Ragan; Jurgen E Schneider; Pavel Tomancak; Jean-Karim Hériché (2010). "Visualization of image data from cells to organisms". Nature Methods. 7 (3s): S26–S41. doi:10.1038/nmeth.1431. PMC 3650473. PMID 20195255.
16. Scripting in Fiji (Fiji Is Just ImageJ) at 3rd User and Developer Conference Archived 7 February 2019 at the Wayback Machine in October 2010
17. Albert Cardona's crash course Jython scripting with Fiji.

External links

• Official website
• fiji on GitHub
• ImageJ2, the version of ImageJ upon which Fiji is built
• Fiji tutorial for Scientists, Easy Fiji (https://www.youtube.com/@easyfiji4858/featured) - Video tutorials for scientists on using Fiji macro.