3D parallel coordinate systems—A new data visualization method in the context of microscopy‐based multicolor tissue cytometry

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Abstract
Background: Presentation of multiple interactions is of vital importance in the new field of cytomics. Quantitative analysis of multi‐ and polychromatic stained cells in tissue will serve as a basis for medical diagnosis and prediction of disease in forthcoming years. A major problem associated with huge interdependent data sets is visualization. Therefore, alternative and easy‐to‐handle strategies for data visualization as well as data meta‐evaluation (population analysis, cross‐correlation, co‐expression analysis) were developed.Methods: To facilitate human comprehension of complex data, 3D parallel coordinate systems have been developed and used in automated microscopy‐based multicolor tissue cytometry (MMTC). Frozen sections of human skin were stained using the combination anti‐CD45‐PE, anti‐CD14‐APC, and SytoxGreen as well as the appropriate single and double negative controls. Stained sections were analyzed using automated confocal laser microscopy and semiquantitative MMTC‐analysis with TissueQuest 2.0. The 3D parallel coordinate plots are generated from semiquantitative immunofluorescent data of single cells. The 2D and 3D parallel coordinate plots were produced by further processing using the Matlab environment (Mathworks, USA).Results: Current techniques in data visualization primarily utilize scattergrams, where two parameters are plotted against each other on linear or logarithmic scales. However, data evaluation on cartesianx/y‐scattergrams is, in general, only of limited value in multiparameter analysis. Dot plots suffer from serious problems, and in particular, do not meet the requirements of polychromatic high‐context tissue cytometry of millions of cells. The 3D parallel coordinate plot replaces the vast amount of scattergrams that are usually needed for the cross‐correlation analysis. As a result, the scientist is able to perform the data meta‐evaluation by using one single plot. On the basis of 2D parallel coordinate systems, a density isosurface is created for representing the event population in an intuitive way.Conclusions: The proposed method opens new possibilities to represent and explore multidimensional data in the perspective of cytomics and other life sciences, e.g., DNA chip array technology. Current protocols in immunofluorescence permit simultaneous staining of up to 17 markers. Showing the cross‐correlation between these markers requires 136 scattergrams, which is a prohibitively high number. The improved data visualization method allows the observation of such complex patterns in only one 3D plot and could take advantage of the latest developments in 3D imaging. © 2006 International Society for Analytical Cytology