Fiji (software)

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Fiji Is Just ImageJ
FIJI (software) Logo.svg
Developer(s) Johannes Schindelin, Albert Cardona, Mark Longair, Benjamin Schmid, and others
Stable release 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)
Website fiji.sc

Fiji (Fiji Is Just ImageJ)[1][2] is an Open Source image processing package based on ImageJ.

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.

Plugins[edit]

Many plugins exist for ImageJ, with a wide range of applications, but also a wide range of quality.[3]

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.[4]

Audience[edit]

While Fiji was originally intended for neuro-scientists (and continues to be so[5]), it accumulated enough functionality to attract scientists from a variety of fields, such as cell biology,[6] parasitology,[7] 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.[8]

Fiji is most popular in the Life sciences community, where the 3D Viewer[9] helps visualizing data obtained through light microscopy, and for which Fiji provides registration,[10] segmentation and other advanced image processing algorithms.

The Fiji component TrakEM2 was successfully used and enhanced to analyze neuronal lineages in larval Drosophila brains.[11]

Fiji was prominently featured in Nature Methods review supplement on visualization [12]

Development[edit]

Fiji is fully Open Source; its sources live in a Git repository (see the homepage for details).

Fiji was accepted as 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[edit]

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.[13][14]

Supported platforms[edit]

Fiji runs on Windows, Linux and MacOSX, Intel 32-bit or 64-bit (not yet Itanium), with limited support for MacOSX/PPC.

References[edit]

  1. ^ 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 and Albert Cardona (2012). "Fiji: an open-source platform for biological-image analysis". Nature Methods 9(7) (7): 676–682. doi:10.1038/nmeth.2019. 
  2. ^ Fiji was presented publicly for the first time on the ImageJ User and Developer Conference in November 2008.
  3. ^ 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.
  4. ^ Compare with the Fiji Usage Map
  5. ^ 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. PMID 21727141. 
  6. ^ Preibisch S and Saalfeld S and 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. 
  7. ^ Hegge S and Kudryashev M and Smith A and 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. doi:10.1002/biot.200900007. PMID 19455538. 
  8. ^ The Fiji Wiki, accessed 2012-11-01.
  9. ^ Benjamin Schmid , Johannes Schindelin , Albert Cardona , Mark Longair and 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. 
  10. ^ Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin and 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. 
  11. ^ Albert Cardona, Stephan Saalfeld, Ignacio Arganda, Wayne Pereanu, Johannes Schindelin and 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. 
  12. ^ 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 and Jean-Karim Hériché (2010). "Visualization of image data from cells to organisms". Nature Methods 7 (3s): S26–S41. doi:10.1038/nmeth.1431. 
  13. ^ Scripting in Fiji (Fiji Is Just ImageJ) at 3rd User and Developer Conference in October 2010
  14. ^ Albert Cardona's crash course Jython scripting with Fiji.

External links[edit]

  • Official website
  • ImageJ2, a closely related project that will provide the new central piece (fully backwards-compatible to ImageJ) of Fiji in the near future.