Interactive Visual Analysis of Toponome Data

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In Toponomics, the function protein pattern in cells or tissue (the toponome) is imaged and analyzed for applications in toxicology, new drug development and patient-drug-interaction. The most advanced imaging technique is robot-driven multi-parameter fluorescence microscopy. This technique is capable of co-mapping hundreds of proteins and their distribution and assembly in protein clusters across a cell or tissue sample by running cycles of fluorescence tagging with monoclonal antibodies or other affinity reagents, imaging, and bleaching in situ. The imaging results in complex multi-parameter data composed of one slice or a 3D volume per affinity reagent. Biologists are particularly interested in the localization of co-occurring proteins, the frequency of co-occurrence and the distribution of co-occurring proteins across the cell. The goal of this project is to develop an interactive visual analysis approach which supports the biologists in evaluating the multi-parameter fluorescence microscopy data.

The project is carried out in close collaboration with Walter Schubert and Reyk Hillert from the molecular pattern recognition working group at the University of Magdeburg. The graph-based visual analysis was developed together with Helmut Doleisch and Wolfgang Freiler from CD-adapco, Vienna and implemented within the SimVis framework.

Contact

Name Dr.-Ing. Steffen Oeltze-Jafra
Doz. Dr. Walter Schubert
Adress Otto-von-Guericke-Universität Magdeburg
Fakultät für Informatik / ISG, PSF 4120
39016 Magdeburg
Phone (+49-391) 67-1 2527
Fax (+49 391) 67-1 11 64

Images

Publications


Steffen Oeltze-Jafra, Franz Pieper, Reyk Hillert, Bernhard Preim, Walter Schubert
Proc. of Eurographics Workshop on Visual Computing for Biology and Medicine (EG VCBM), pp. 79-88, 2014
BIBTeX
@InProceedings{Oeltze_2014_VCBMa,
Title = {{Interactive Labeling of Toponome Data}},
Author = {Steffen Oeltze-Jafra and Franz Pieper and Reyk Hillert and Bernhard Preim and Walter Schubert},
Booktitle = {{Proc. of Eurographics Workshop on Visual Computing for Biology and Medicine (EG VCBM)}},
Year = {2014},
Address = {Wien},
Month = {04.-05. September},
Pages = {79--88},
Owner = {schumann},
Timestamp = {2014.08.19}
}
Steffen Oeltze, Paul Klemm, Reyk Hillert, Bernhard Preim, Walter Schubert
2nd IEEE Symposium on Biological Data Visualization (BioVis), in print, 2012
BIBTeX
@InProceedings{Oeltze_2012_BioVis,
Title = {{Visualization and Exploration of 3D Toponome Data}},
Author = {Steffen Oeltze and Paul Klemm and Reyk Hillert and Bernhard Preim and Walter Schubert},
Booktitle = {{2nd IEEE Symposium on Biological Data Visualization (BioVis)}},
Year = {2012},
Pages = {to appear},
Owner = {schumann},
Timestamp = {2012.10.09}
}
Steffen Oeltze, Paul Klemm, Reyk Hillert, Bernhard Preim, Walter Schubert
VCBM 2012 - Eurographics Workshop on Visual Computing for Biology and Medicine, pp. 115-122, 2012
BIBTeX
@InProceedings{Oeltze_2012_VCBM,
Title = {{Visualization and Exploration of 3D Toponome Data}},
Author = {Steffen Oeltze and Paul Klemm and Reyk Hillert and Bernhard Preim and Walter Schubert},
Booktitle = {{VCBM 2012 - Eurographics Workshop on Visual Computing for Biology and Medicine}},
Year = {2012},
Address = {Norrköping},
Month = {September},
Pages = {115--122},
Owner = {schumann},
Timestamp = {2012.10.09}
}
Steffen Oeltze, Wolfgang Freiler, Reyk Hillert, Helmut Doleisch, Bernhard Preim, Walter Schubert
IEEE Transactions on Visualization and Computer Graphics (TVCG), 17(12), pp. 1882-1891, 2011
BIBTeX
Media
@Article{Oeltze_2011_VIS,
Title = {{Interactive, Graph-Based Visual Analysis of High-Dimensional, Multi-Parameter Fluorescence Microscopy Data in Toponomics}},
Author = {Steffen Oeltze and Wolfgang Freiler and Reyk Hillert and Helmut Doleisch and Bernhard Preim and Walter Schubert},
Journal = {{IEEE Transactions on Visualization and Computer Graphics (TVCG)}},
Year = {2011},
Note = {to appear},
Pages = {1882--1891},
Volume = {17(12)},
Comment = {to appear},
Keywords = {VIS, d},
Owner = {Steffen Oeltze},
Timestamp = {2011.08.16}
}
Interactive Visual Analysis of Toponome Data
Interactive, graph-based visual analysis of toponome data. This special kind of data depicts the location and topological distribution of proteins in a cell or tissue sample. The particular data shown in the video represents a probe containing lymphocytes. The visual analysis framework supports the biologist in detecting and understanding a cell's function protein patterns.