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Computational Tool Translates Complex Data Into 2-Dimensional Images


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Imaging of the progression of cancer cells.

Visual interactive Stochastic Neighbor Embedding (viSNE) reveals the progression of cancer in a sample of cells taken from a patient with acute myeloid leukemia. In figure a, the contours represent cell density in each region of the map. Each point represents a cell from the diagnosis sample (top, purple) or relapse sample (bottom, red). In figure b, cells from both diagnosis and relapse samples are shown in each map. Cells are colored according to intensity of expression of the indicated cell markers, enabling the comparison of expression patterns before and after relapse.

Credit: Dana Peer, PhD/Columbia University

Columbia University researchers have developed a computational method that enables scientists to visualize and interpret high-dimensional data produced by single-cell measurement technologies such as mass cytometry.

"Our method not only will allow scientists to explore the heterogeneity of cancer cells and to characterize drug-resistant cancer cells, but also will allow physicians to track tumor progression, identify drug-resistant cancer cells, and detect minute quantities of cancer cells that increase the risk of relapse," says Columbia University researcher Dana Pe'er.

The method, called visual interactive Stochastic Neighbor Embedding (viSNE), is based on an algorithm that translates high-dimensional data into visual representations. "Basically, viSNE provides a way to visualize very high-dimensional data in two dimensions, while maintaining the most important organization and structure of the data," Pe'er says. "Color is used as a third dimension to enable users to interactively visualize various features of the cells."

The researchers used mass cytometry and viSNE to study bone marrow cells from patients with acute myeloid leukemia, and also showed that viSNE can detect minimal residual disease.

From Columbia University
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Abstracts Copyright © 2013 Information Inc., Bethesda, Maryland, USA


 

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