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UW-SIG Downloadable Software

FMA: the Foundational Model of Anatomy ontology
The Foundational Model of Anatomy ontology (FMA) is now OPEN SOURCE and available for general use. We have also removed the password protection from the FMA browser, the Foundational Model Explorer (FME), so that it can now be freely used to investigate the FMA knowledge base. The FME homepage can be found at

MindSeer: 3D Brain Visualization using Java
MindSeer is a visualization tool for multi-modality neuroimaging data. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets.

WIX: Web Interface for XQuery
WIX (Web Interface for XQuery) is a simple service that allows users to submit an XQuery to query an XML document. The servlet interface for submitting XQueries is simple and efficient and can easily be called from any programming language, other instances of XQuery, or an HTML form. Runs on Apache Tomcat.

Web Interfacing Repository Manager (WIRM)
This is a set of open source perl scripts that can be used to create web-based multimedia database systems. Developed by Rex Jakobovits while on his computer science PhD as part of the UW Brain Project, it is the basis for the brain project Language Map Experiment Management System.

Since graduating from the UW Rex has set up a company, called Vivalog Technologies, that uses this toolkit to create other content management systems.

Customizable Electronic Laboratory Online (CELO)
Customizable Electronic Laboratory Online (CELO) is a Web-based Data Management System Builder for Biomedical Research Laboratories. The system was developed by Christine Fong, while a student in the University of Washington's Structural Informatics Group. It is built on top of the Web Interfacing Repository Manager (WIRM) toolkit. SIG.

AnnoteImage v2.6 (src)
AnnoteImage is a Java tool for creating IML, an XML format for storing textual annotations to images. The annotation model is one of outlined regions, identified by labels, and colored 'strings' and 'pins'. The IML schema also allows for some limited metadata about the annotations. IML was based on an existing lisp-like format used in the Digital Anatomist Interactive Atlases.

Interactive Atlases v5.2.5
The software that drives the Digital Anatomist Interactive Atlases. This package contains a set of CGI and Java programs that allow the creation of digital atlases containing annotated images. Within each atlas the images can be arranged in a hierarchy of chapters and sections. A Java-based authoring tool allows authors to upload GIF images from their personal workstation, then to draw outlines on the images and either label the outlines with structure names, or link the outlines to other images. Once an atlas has been created and placed in the proper location on a Web server, the images may be accessed from anywhere on the Web.