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A Part-to-Whole Circular Cell Explorer

Siyuan Zhao, G. Elisabeta Marai

TL;DR

An interactive visual analysis system that addresses perceptual problems in the state of the art, while adding filtering, drilling, and clustering analysis capabilities to help researchers gain deeper insights into the molecular mechanisms underlying complex biological processes within tissues.

Abstract

Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the tissue image with pie charts for the cell distribution. We design an interactive visual analysis system that addresses perceptual problems in the state of the art, while adding filtering, drilling, and clustering analysis capabilities. Our approach can help researchers gain deeper insights into the molecular mechanisms underlying complex biological processes within tissues.

A Part-to-Whole Circular Cell Explorer

TL;DR

An interactive visual analysis system that addresses perceptual problems in the state of the art, while adding filtering, drilling, and clustering analysis capabilities to help researchers gain deeper insights into the molecular mechanisms underlying complex biological processes within tissues.

Abstract

Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the tissue image with pie charts for the cell distribution. We design an interactive visual analysis system that addresses perceptual problems in the state of the art, while adding filtering, drilling, and clustering analysis capabilities. Our approach can help researchers gain deeper insights into the molecular mechanisms underlying complex biological processes within tissues.

Paper Structure

This paper contains 4 sections, 2 figures.

Table of Contents

  1. Introduction
  2. Related Work
  3. Redesign
  4. Discussion and Conclusion

Figures (2)

  • Figure 1: Interactive web-based tool leveraging the redesigned encoding: (A) a control panel allows changing the opacity of the tissue image and circular slice encodings, as well as selecting a subset of genes to view and analyze; (B) tissue image view, showing here the result of t-SNE Laurens2008 clustering and gene expression, currently showing gene expression of regional THAL_lat astrocytes markers kleshchevnikov2022; (C) projection view; (D) hybrid violin plot for the distribution of each cluster, which can also be explored in tabular or heatmap form.
  • Figure 2: Pie chart, circular slices, and stacked bar chart