Tool unveiled for single-cell data visualization

Modern cutting-edge research generates enormous amounts of data, which presents scientists with the challenge of visualizing and analyzing them. Researchers from the Helmholtz Institute for RNA-Based Infection Research (HIRI) in Würzburg and the Technical University of Applied Sciences Würzburg-Schweinfurt (THWS) have developed a tool for visualizing large datasets. The sCIRCLE tool allows users to explore single-cell analysis data in an interactive and user-friendly way. Their results have been published in the journal NAR Genomics and Bioinformatics.

Antibiotic resistance is increasing worldwide and poses a major challenge to healthcare systems. Understanding the underlying processes that explain how and why some bacteria develop such defenses is critical. Differences in bacterial gene expression (where the information contained in a gene is read) could provide clues. Single-cell bacterial RNA sequencing, or scRNA-seq, has become a critical tool for analyzing these variations. This technology provides a detailed picture of gene expression in a single cell at a specific time. However, the method generates huge amounts of data that researchers struggle to visualize and analyze. Therefore, there is a great need for new approaches and tools to display and understand this information.

Researchers at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, a site of the Helmholtz Center for Infection Research (HZI) in Brunswick, in cooperation with the Julius-Maximilians-University of Würzburg (JMU) and developers at the Technical University of Applied Sciences Würzburg-Schweinfurt (THWS), have now developed such a tool. Their desktop application, called sCIRCLE (single-Cell Interactive Real-time Computer visualization for Low-dimensional Exploration), enables interactive 3D visualization of scRNA-seq data. It allows users to view individual cells, enriched with metadata, from different angles and in real time. A variety of filters and parameters can be used to explore which genes were expressed in particular cells at specific time points. This capability allows researchers to focus on specific cell populations or genes of interest. “sCIRCLE is also a valuable communication tool for collaboratively examining datasets or presenting results,” says Lars Barquist. Barquist, a computational biologist who initiated the study, leads a research group at the Helmholtz Institute in Würzburg. Barquist is also a professor at the University of Toronto in Canada. In addition, sCIRCLE is already compatible with virtual reality devices, marking a step towards immersive 3D data visualization and interaction.

An interdisciplinary collaboration looking to the future

sCIRCLE’s user-friendliness is remarkable: “The interface is easy to use and intuitively designed. This makes sCIRCLE particularly useful for biologists who do not have a deep background in bioinformatics,” adds Barquist. The designers and bioinformaticians worked together to make the data as simple and visually appealing as possible: “Collaboration between the disciplines of bioinformatics and design is extremely important because our datasets continue to grow and we need new ways to make them understandable,” says Barquist.

To carry out the project, Maximilian Seeger, a master’s student at THWS, spent some time in the HIRI research group. He had the opportunity to work directly with the scientists. “This allowed me to understand what they wanted to explore in their data and to develop an interface that would make this possible,” says Maximilian Seeger. In tests with data collected by HIRI researchers from different groups, the scientists tested the tool and provided feedback. The research team published the results in the journal NAR Genomics and Bioinformatics.

“The joint development of sCIRCLE shows the importance of interdisciplinary and interinstitutional cooperation. I am very pleased that we have succeeded in combining the expertise of two Würzburg institutions in this project and look forward to continuing this collaboration,” says Erich Schöls, Professor of Interactive Media at THWS, who supervised Max Seeger together with Lars Barquist. “We hope that this is just a first step towards developing intuitive and interactive tools for data analysis,” says Barquist optimistically. “We will build on this foundation to make our tools even more immersive and user-friendly.” Although this application currently only offers basic integration of VR, the team plans to create other easy-to-use virtual spaces for data exploration in the future.

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