CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis

Thomas Hollt, Nicola Pezzotti, Vincent van Unen, Frits Koning, Boudewijn P.F. Lelieveldt, Anna Vilanova

Research output: Contribution to journalArticleScientificpeer-review

19 Citations (Scopus)


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.

Original languageEnglish
Article number8017575
Pages (from-to)739-748
Number of pages10
JournalIEEE Transactions on Visualization and Computer Graphics
Issue number1
Publication statusPublished - 2018


  • Hierarchical Data
  • HSNE
  • Single-Cell Analysis
  • Visual Guidance


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