Cytosplore: Rapid Single Cell Analysis
- Theme: Visual Analysis, Bio-/Medical Visualization
- People: Thomas Höllt, Nicola Pezzotti, Elmar Eisemann, Anna Vilanova (TU Delft), Boudewijn Lelieveldt, Vincent van Unen, Frits Koning (LUMC)
Cytosplore is an interactive visual analysis system for understanding how the immune system works. The goal of the analysis framework is to provide a clear picture of the immune systems cellular compositon and the cells’ corresponding properties and functionality. Cytosplore is targeted at the analysis of mass cytometry (CyToF) data. Mass cytometry is a novel technique to determine the properties of single-cells with unprecedented detail. This amount of detail allows for much finer differentiation but also comes at the cost of more complex analysis.
A screenshot of the Cytosplore application. We implement a coordinated multiple linked views application to show different facets of the data. From the left to right the visualizations show a force directed layout of the results of high dimensional clustering (a) using [SPADE], an embedding (b) (scatterplot visualization of dimensionality reduced data) computed using our approximated version of [tSNE] and a heat map view (c), showing median expressions of the computed clustering.
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Available Master Thesis Projects
We have open projects within the Cytosplore project including a project on classification of cellular expression data through dimensionality reduction. If you’re interested in working with me on this or other projects involving biological visualisation for your master thesis project, please contact me directly, or Dr. A. Vilanova to discuss the possibilities.
- Exploring new dimensions of the immune system. Interview with Medical Delta, Dec. 2016.
 Cytosplore: Interactive Immune Cell Phenotyping for Large Single-Cell Datasets, Thomas Höllt, Nicola Pezzotti, Vincent van Unen, Frits Koning, Elmar Eisemann, Boudewijn Lelieveldt, and Anna Vilanova, Computer Graphics Forum, 35(3), (Proceedings EG/VGTC Conference on Visualization), 2016. Paper Preprint pdf. Conference Slides.
-  Approximated and User Steerable tSNE for Progressive Visual Analytics, Nicola Pezzotti, Boudewijn P.F. Lelieveldt, Laurens van der Maaten, Thomas Höllt, Elmar Eisemann, and Anna Vilanova, IEEE Transactions on Visualization and Computer Graphics, to appear, 2016.
-  Mass Cytometry of the Human Mucosal Immune System Identifies Tissue- and Disease-Associated Immune Subsets, Vincent van Unen, Na Li, Ilse Molendijk, Temurhan Mine, Thomas Höllt, Andrea E van der Meulen-de Jong, Hein W Verspaget, M Luisa Mearin, Chris J Mulder, Jeroen van Bergen, Boudewijn P.F. Lelieveldt, and Frits Koning, Immunity, 44(5), 1227–1239, 2016.