Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data

Soumyadeep Basu, Jeroen Eggermont, Thomas Kroes, Nicholas L. Jorstad, Trygve Bakken, Ed Lein, Boudewijn P.F. Lelieveldt, Thomas Höllt
Eurographics Workshop on Visual Computing for Biology and Medicine, page 111-120 - Sep 2023
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With the rapid advances in single-cell sequencing technologies, novel types of studies into the cell-type makeup of the brain have become possible. Biologists often analyze large and complex single-cell transcriptomic datasets to enhance knowledge of the intricate features of cellular and molecular tissue organization. A particular area of interest is the study of whether cell types and their gene regulation are conserved across species during evolution. However, in-depth comparisons across species of such high-dimensional, multi-modal single-cell data pose considerable visualization challenges. This paper introduces Cytosplore Simian Viewer, a visualization system that combines various views and linked interaction methods for comparative analysis of single-cell transcriptomic datasets across multiple species. Cytosplore Simian Viewer enables biologists to help gain insights into the cell type and gene expression differences and similarities among different species, particularly focusing on comparing human data to other species. The system validation in discovery research on real-world datasets demonstrates its utility in visualizing valuable results related to the evolutionary development of the middle temporal gyrus.

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@InProceedings { BEKJBLLH23,
  author       = "Basu, Soumyadeep and Eggermont, Jeroen and Kroes, Thomas and Jorstad, Nicholas L. and Bakken, Trygve and Lein,
                  Ed and Lelieveldt, Boudewijn P.F. and H\öllt, Thomas",
  title        = "Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data",
  booktitle    = "Eurographics Workshop on Visual Computing for Biology and Medicine",
  pages        = "111-120",
  month        = "Sep",
  year         = "2023",
  publisher    = "The Eurographics Association",
  doi          = "10.2312/vcbm.20231219",
  url          = ""