Unleashing Insights: A Powerful Visualization Tool for Single-Cell Data

Antibiotic resistance is increasing globally, posing significant challenges to healthcare systems. To address this issue, it’s essential to understand how and why certain bacteria develop resistance. Variations in bacterial gene expression — the process of reading information from genes — may hold important insights. Single-cell RNA sequencing, or “scRNA-seq,” has emerged as a critical tool for examining these differences. This technique offers a comprehensive view of gene expression in individual cells at specific moments. Nevertheless, the substantial amount of data generated makes it difficult for researchers to visualize and analyze effectively, indicating a pressing need for innovative tools and methods to better display and comprehend this information.

The team at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, part of the Helmholtz Centre for Infection Research (HZI) in Braunschweig, has worked alongside designers at the Technical University of Applied Sciences Würzburg-Schweinfurt (THWS) to create a new tool. Their desktop application, named sCIRCLE (single-Cell Interactive Real-time Computer visualization for Low-dimensional Exploration), allows users to interactively visualize scRNA-seq data in 3D. Users can examine single cells enriched with metadata from various viewpoints and in real-time. Different filters and settings let researchers focus on specific genes expressed in individual cells at designated times, enhancing their ability to study particular cell types or genes. “sCIRCLE also serves as an effective communication tool for teams working together to analyze data sets or present findings,” explains Lars Barquist, a computational biologist who led the development of the tool at HIRI and is also a professor at the University of Toronto, Canada. Furthermore, sCIRCLE is already compatible with virtual reality devices, indicating progress towards more immersive 3D data visualization experiences.

An Innovative Collaborative Approach

The ease of use of sCIRCLE is noteworthy: “The interface is straightforward and designed to be intuitive. This makes sCIRCLE especially useful for biologists who might not have a strong background in bioinformatics,” adds Barquist. The collaboration between designers and bioinformaticians aimed to present the data in a simple and visually appealing manner: “The collaboration between bioinformatics and design is crucial as our data sets continue to expand and we require new ways to make them comprehensible,” Barquist notes.

To bring the project to fruition, THWS Master’s student Maximilian Seeger had the chance to work closely with HIRI researchers. He explained, “This experience helped me grasp what researchers wanted to achieve with their data, allowing me to develop an interface that could facilitate that exploration.” The research team conducted trial runs with data from HIRI scientists, gathering insights and feedback on the tool. The outcomes have been published in the journal NAR Genomics and Bioinformatics.

“The collaborative development of sCIRCLE highlights the significance of interdisciplinary and inter-institutional partnerships. I am thrilled that we successfully combined the expertise of two operating institutions in Würzburg for this project, and I am eager to see future collaborations,” says Erich Schöls, a professor of interactive media at THWS, who collaborated with Lars Barquist in supervising Seeger. “This is just the initial step towards crafting intuitive, interactive tools for data analysis,” says Barquist with optimism. “We plan to build upon this groundwork to enhance our tools, making them even more engaging and user-friendly.” Currently, while the application has basic virtual reality integration, the team aspires to develop additional, easy-to-navigate virtual environments for exploring data in the future.