CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis

Thomas Höllt, Nicola Pezzotti, Vincent van Unen, Frits Koning, Boudewijn P.F. Lelieveldt, Anna Vilanova
IEEE Transactions on Visualization and Computer Graphics (Proceedings of Information Visualization 2017), Volume 24, Number 1 - jan 2018
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Single-cell analysis through mass cytometry has become an increasingly important tool for immunologists to study the immune system in health and disease. Mass cytometry creates a high-dimensional description vector for single cells by time-of-flight measurement. Recently, t-Distributed Stochastic Neighborhood Embedding (t-SNE) has emerged as one of the state-of-the-art techniques for the visualization and exploration of single-cell data. Ever increasing amounts of data lead to the adoption of Hierarchical Stochastic Neighborhood Embedding (HSNE), enabling the hierarchical representation of the data. Here, the hierarchy is explored selectively by the analyst, who can request more and more detail in areas of interest. Such hierarchies are usually explored by visualizing disconnected plots of selections in different levels of the hierarchy. This poses problems for navigation, by imposing a high cognitive load on the analyst. In this work, we present an interactive summary-visualization to tackle this problem. CyteGuide guides the analyst through the exploration of hierarchically represented single-cell data, and provides a complete overview of the current state of the analysis. We conducted a two-phase user study with domain experts that use HSNE for data exploration. We first studied their problems with their current workflow using HSNE and the requirements to ease this workflow in a field study. These requirements have been the basis for our visual design. In the second phase, we verified our proposed solution in a user evaluation.

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BibTex references

@Article { HPVKLV18,
  author       = "H\öllt, Thomas and Pezzotti, Nicola and Unen, Vincent van and Koning, Frits and Lelieveldt, Boudewijn P.F.
                  and Vilanova, Anna",
  title        = "CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis",
  journal      = "IEEE Transactions on Visualization and Computer Graphics (Proceedings of Information Visualization 2017)",
  number       = "1",
  volume       = "24",
  month        = "jan",
  year         = "2018",
  note         = "10.1109/TVCG.2017.2744318",
  url          = ""

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