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

Cytometry Part A

601-611

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 cartesian x/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 metaevaluation
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.

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