Volume 5 issue 6 June 2004
VisBio: a Computational Tool for Visualization of Multidimensional Biological Image Data
C. Rueden, K. W. Eliceiri* and J. G. White Laboratory for Optical and Computational Instrumentation University of Wisconsin-Madison

*corresponding author: eliceiri@wisc.edu

Running title – VisBio: an application and toolkit for visualization and analysis of large, multidimensional, biological image data of any dimensionality—including multispectral, lifetime, and other imaging modalities—with features such as arbitrary slicing, volume rendering, flexible color mapping, 3D measurements and data export.

Keywords – VisBio, multidimensional, imaging, visualization, analysis software, open source, Java, VisAD.

Abstract – New laser scanning microscopy techniques enable biologists to acquire larger, more complex image datasets. Emerging imaging modalities such as multispectral, harmonic, and fluorescence lifetime can generate data with six or more dimensions; however, existing software is not well suited to the visualization or analysis of such data. To address these concerns, we have developed VisBio, an application and toolkit for visualization and analysis of multidimensional, biological image data of any dimensionality.

Movie 1 (visbio1.mov): Volume rendering of a C. elegans embryo undergoing cell fusion and imaged by multiphoton microscopy. Dataset provided by Dr. William Mohler of the University of Connecticut-Farmington.

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Movie 2 (visbio2.mov): Three-dimensional reconstruction of human embryonic kidney cells (HEK293) that were transfected with a plasmid construct which expresses GFP. Cells were fixed with 3% paraformaldehyde and observed under a laser scanning confocal microscope. The GFP signal is observed throughout the cell. Dataset provided by Dr. Carrie Graveel, Mr. Lance Rodenkirch and Dr. Peggy Farnham of the University of Wisconsin-Madison.

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