Fiji

Web Page: http://pacific.mpi-cbg.de/wiki/index.php/SoC2009Ideas

Mailing List: fiji-devel@googlegroups.com

Fiji stands for "Fiji is Just ImageJ". ImageJ is a public domain scientific image processing application sponsored by the National Institute of Health. ImageJ runs on the Java Virtual Machine and thus has direct access to numerous and diverse public java libraries.

All Fiji project founders and contributors have written large plugin collections and ImageJ-centric applications. At some point, it was inevitable to merge our projects into a centralized and organized framework, which includes consistent and updated documentation for all its components.

For the creation of Fiji, beyond our own ImageJ-centric applications, we selected and tested a subset of the literally thousands of open source plugins that exist for ImageJ, and integrated them along with several open source libraries into a consistent framework. Plugins added capabilities beyond mere image processing, including image segmentation, image registration, 3D visualization of image volumes, and support for a variety of JVM-supported scripting languages (so far: javascript, jython, jruby, clojure and beanshell).

Fiji as a community is supported by a variety of scientific research institutions with vested interests on image processing, including but not limited to the Howard Hughes Medical Institute Janelia Farm, the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, and the Institute of Neuroinformatics of the University of Zurich and ETH Zurich.

Projects

• Fiji Plugin Manager Fiji is an Image Processing tool with great potential for further development to improve usability and thus boost task efficiency. This project will implement a new plugin manager for convenient installation and tracking of Java plugins which serve as add-on utilities. The Plugin Manager will be able to manage the list of plugins that are visible on the menu, effectively taking charge of enabling and disabling of these plugins, and the updating/installation of these utilities.
• Minimal Text Editor for ImageJ:Sumit Dubey This project aims to build a minimal script editor for ImageJ which includes 1)Writing text and scripts ,compiling and running Java,Javascript and other scripts like Jython and Jruby. 2)Syntax Highlighting and auto-indentation feature for Java,Javascript,Jython and Jruby 3)Autocompletion for the above mentioned languages 4)Minimal debugging features like higlighting the lines which could not be compiled.