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Proceedings Paper

Integration of information and volume visualization for analysis of cell lineage and gene expression during embryogenesis
Author(s): Andrej Cedilnik; Jeffrey Baumes; Luis Ibanez; Sean Megason; Brian Wylie
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Paper Abstract

Dramatic technological advances in the field of genomics have made it possible to sequence the complete genomes of many different organisms. With this overwhelming amount of data at hand, biologists are now confronted with the challenge of understanding the function of the many different elements of the genome. One of the best places to start gaining insight on the mechanisms by which the genome controls an organism is the study of embryogenesis. There are multiple and inter-related layers of information that must be established in order to understand how the genome controls the formation of an organism. One is cell lineage which describes how patterns of cell division give rise to different parts of an organism. Another is gene expression which describes when and where different genes are turned on. Both of these data types can now be acquired using fluorescent laser-scanning (confocal or 2-photon) microscopy of embryos tagged with fluorescent proteins to generate 3D movies of developing embryos. However, analyzing the wealth of resulting images requires tools capable of interactively visualizing several different types of information as well as being scalable to terabytes of data. This paper describes how the combination of existing large data volume visualization and the new Titan information visualization framework of the Visualization Toolkit (VTK) can be applied to the problem of studying the cell lineage of an organism. In particular, by linking the visualization of spatial and temporal gene expression data with novel ways of visualizing cell lineage data, users can study how the genome regulates different aspects of embryonic development.

Paper Details

Date Published: 28 January 2008
PDF: 11 pages
Proc. SPIE 6809, Visualization and Data Analysis 2008, 68090J (28 January 2008); doi: 10.1117/12.768014
Show Author Affiliations
Andrej Cedilnik, TiVo, Inc. (United States)
Jeffrey Baumes, Kitware, Inc. (United States)
Luis Ibanez, Kitware, Inc. (United States)
Sean Megason, California Institute of Technology (United States)
Brian Wylie, Sandia National Labs. (United States)


Published in SPIE Proceedings Vol. 6809:
Visualization and Data Analysis 2008
Katy Börner; Matti T. Gröhn; Jinah Park; Jonathan C. Roberts, Editor(s)

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