%0 Journal Article
%T JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases
%A Guangjie Feng
%A Nick Burton
%A Bill Hill
%A Duncan Davidson
%A Janet Kerwin
%A Mark Scott
%A Susan Lindsay
%A Richard Baldock
%J BMC Bioinformatics
%D 2005
%I BioMed Central
%R 10.1186/1471-2105-6-47
%X We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture.We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.Three-dimensional (3D) images are now commonplace in biomedical research. Techniques for direct capture of 3D data are widespread and new techniques are becoming available, [1,2] to complement existing sectioning methods [3], confocal and micro-CT/MRI [4]. In addition such data is being stored in databases that can be accessed freely (EADHB[5], EMAP[6], BIOIMAGE[7], and MRIMA[8]) and many more such atlases and bioinformatics resources will become available. There are a number of tools available for browsing such data, but they are either commercial with a significant cost for the user (e.g. AVS/Express, VolRen, Amira, Analyse) or free but tied to a specific architecture. Systems based purely on an architecture neutral language such as Java (e.g. ImageJ[9]) can be slow when processing large 3D volume images and have not been developed with the 3D atlas browsing application in mind. The purpose of this work is to combine the machine-architecture independence of Java, with a highly portable, freely available fast and efficient C-coded image proces
%U http://www.biomedcentral.com/1471-2105/6/47