|Developer(s)||Johannes Schindelin, Albert Cardona, Mark Longair, Benjamin Schmid, and others|
Madison / 7 March 2011 (official release, plugins continuously updated)
|Operating system||Any (Java-based)|
|Type||Image processing & Image analysis|
|License||GPL v2 (the plugin interface is excluded from that license; some plugins have different licenses)|
Fiji's main purpose is to provide a distribution of ImageJ 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 and other scripting languages, as well as Just-In-Time Java development.
Further, some plugins require specific versions of ImageJ, specific versions of third-party libraries, or additional Java components such as the Java compiler or Java3D.
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 neuro-scientists (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, material 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.
Fiji is fully Open Source; its sources live in a Git repository (see the homepage for details).
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.
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.
Fiji runs on Windows, Linux and Mac OSX, Intel 32-bit or 64-bit, with limited support for MacOSX/PPC.
- 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. PMC . PMID 22743772. doi:10.1038/nmeth.2019.
- Fiji was presented publicly for the first time on the ImageJ User and Developer Conference in November 2008.
- Compare the presentations at the 2nd ImageJ User and Developer Conference in November 2008 and the 3rd ImageJ and User Developer Conference in October 2010.
- Compare with the Fiji Usage Map
- 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. PMID 21727141. doi:10.1093/bioinformatics/btr390.
- Preibisch S, Saalfeld S, Tomancak P (April 2009). "Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions". Bioinformatics. 25 (11): 1463–5. PMC . PMID 19346324. doi:10.1093/bioinformatics/btp184.
- Hegge S, Kudryashev M, Smith A, Frischknecht F (May 2009). "Automated classification of Plasmodium sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection". Biotechnology Journal. 4 (6): 903–13. PMID 19455538. doi:10.1002/biot.200900007.
- The Fiji Wiki, accessed 2012-11-01.
- 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. PMC . PMID 20492697. doi:10.1186/1471-2105-11-274.
- 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. PMID 20508634. doi:10.1038/nmeth0610-418.
- 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. PMC . PMID 20519528. doi:10.1523/JNEUROSCI.0186-10.2010.
- 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.
- Scripting in Fiji (Fiji Is Just ImageJ) at 3rd User and Developer Conference in October 2010
- Albert Cardona's crash course Jython scripting with Fiji.