A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns

Gerth, Victor E.; Vize, Peter D.

doi:10.1093/bioinformatics/bti120

Cited by 5 publications

(2 citation statements)

References 3 publications

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“…In examples where surface deformation is not required, for example when two samples are extremely similar in shape, we have written two different systems for manual alignment of gene expression data. The first of these is known as the Interactive 3D Gene Expression viewer (Gerth and Vize, 2005; http://www.xenbase.org/3DModels/release2/release2.html/). This is a customized Java based applet based on the IDX3D software by Peter Walser (http://www.idx3d.ch/idx3d/idx3d.html).…”

Section: Volumetric Datamentioning

confidence: 99%

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

Vize

Gerth

2007

SPIE Proceedings

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Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

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Section: Volumetric Datamentioning

confidence: 99%

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

Vize

Gerth

2007

SPIE Proceedings

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“…The second class comprises numerous genomic tools (Edgar et al, 2002;Zeeberg et al, 2003;Gentleman et al, 2004;Kasprzyk et al, 2004), most of which lack the anatomical imaging component and therefore remain poorly integrated with day-to-day efforts of medical educators. Several research projects around the world attempt to merge geneexpression data with anatomical data, but do so only for nonhuman organisms (Burger et al, 2002;Gerth and Vize, 2005;Luengo Hendriks et al, 2006;McCarthy, 2006).…”

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confidence: 99%

CAVEman: Standardized anatomical context for biomedical data mapping

Turinsky

Fanea

Trinh

et al. 2007

Anatomical Sciences Ed

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The authors have created a software system called the CAVEman, for the visual integration and exploration of heterogeneous anatomical and biomedical data. The CAVEman can be applied for both education and research tasks. The main component of the system is a three-dimensional digital atlas of the adult male human anatomy, structured according to the nomenclature of Terminologia Anatomica. The underlying data-indexing mechanism uses standard ontologies to map a range of biomedical data types onto the atlas. The CAVEman system is now used to visualize genetic processes in the context of the human anatomy and to facilitate visual exploration of the data. Through the use of Javatrade mark software, the atlas-based system is portable to virtually any computer environment, including personal computers and workstations. Existing Java tools for biomedical data analysis have been incorporated into the system. The affordability of virtual-reality installations has increased dramatically over the last several years. This creates new opportunities for educational scenarios that model important processes in a patient's body, including gene expression patterns, metabolic activity, the effects of interventions such as drug treatments, and eventually surgical simulations.

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Visualization of Biological Data

Hochheiser¹,

Eliceiri²,

Goldberg³

2007

Bioinformatics‐From Genomes to Therapies

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A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns

Abstract: The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT.

Cited by 5 publications

References 3 publications

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

CAVEman: Standardized anatomical context for biomedical data mapping

Visualization of Biological Data

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