A QuickTime movie being played in the QT4D Player plugin within ImageJ under Macintosh OS X 10.3, Java virtual machine 1.4.2, and QuickTime for Java 6.1. [Original footage - Mark Sheffield; software development: Jeff Hardin]

Developing freely available, open source software for 4d microscopy

We are developing plugins that run within the public domain program, ImageJ, to acquire, process, and play back 4d microscopy data as an outgrowth of our own imaging needs. When beta testing of these plugins is complete, they will be posted as a free download at the ImageJ web site. Plugins are currently in beta testing for "crunching" raw datasets into QuickTime movies (QT4D Writer), browsing raw datasets consisting of single image files (Browse 4D), aciled movies (QT4D Player). Other batch processing plugins are in alpha testing that produce rotated, 3d reconstructions of confocal and multiphoton datasets, and that interconvert raw data from spinning disk confocal datasets for use with the freely available Voxx visualization package from the Indiana University Schcool of Medicine. The advantage of this software suite is that is free(!), and that it allows 4d daatasets to be viewed without special, proprietary software.

voxx-sample Click the thumbnail to see a movie generated by Voxx, using data generated by Abbi Cox. Red = muscle; green = epithelial cells.


Questions? Contact Jeff at: jdhardin@wisc.edu