Games Engineering Life Sciences Initiative

Overview

The Games Engineering Life Sciences Initiative is taking on the challenges in - and briding gaps for - real-time interactive systems for biology and medicine.

We are researching interactive tools and methods for the support of fundamental and cutting-edge research. This includes interactive, agent-based modelling and simulation, the integration of current immersive display technology in data analysis, tools for the exploration, annotation, and visualization of datasets, as well as applications in teaching and training.

One key aspect of our projects is the integration with, support of, and the increase of explainability of machine learning or artificial intelligence-driven workflows.

Current Projects

Reciprocal Space: X-Ray Diffraction Data Analysis

X-ray diffraction crystallography is the main method to determine the structure of proteins. Protein structure, in turn, is key to understanding protein function. It forms an important basis for fundamental research in life sciences, such as the discovery of new vaccines. The bulk of the data processing is commonly done using automated worklfows. However, certain pathologies still pose problems to these systems, and failure to detect them can have catastrophic effects on output quality. We work on immersive tools to support the early indexing phase of the common diffraction data processing workflow. Even before extensive automated analysis, the detector data can be screened in reciprocal space, a mathematical construct can be quite revealing and many potential and actual issues can easily be spotted. The three-dimensional nature of this data makes it a natural subject to immersive visualization.

In collaboration with: Dr. Andrea Thorn, Rudolf-Virchow-Zentrum, Würzburg University

Microscopy Image Analysis: Ground Truth Data Definition for Automated Segmentation Algorithms using XR

The vast datasets created by microscopy imaging are usually processed by automated analysis tools to identify relevant features, such as different tissue types, cell nuclei, or other structural and functional features. However, each automated analytical step needs to be validated and benchmarked. For this, scientists painstakingly markup ground truth data as a validation set. This project aims to support the mark-up process of volumetric datasets using immersive visualization tools and an intuitive user experience.

In collaboration with: Prof. Dr. Sabine Fischer, CCTB, Würzburg University

Project MIONA: Multi-Immersive Onko Analysis

Multi-Cellular Tumor Spheroids (MCTS) are a common biological model for the study of the development of tumor cells and the effects of drug therapy. MIONA researches the interactive visualization and simulation of MCTS based on the MecaCell simulation platform. The project aims to provide an immersive data analysis workbench for the analysis of important spatial relationships and processes within an evolving interactive simulation.

In collaboration with: Dr. Sylvain Cussat-Blanc, Universitée Toulous

Applications in Developmental Biology

In the video, an immersive application is used to visualize expression patterns of NANOG and GATA6, obtained from a data set of an ICM organoid. These are biological model systems for mammalian pre-implantation development. The dataset was taken from Mathew et al., “Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering”, Biophysical Journal 116, 127–141, January 8, 2019.

In collaboration with: Prof. Dr. Sabine Fischer, CCTB, Würzburg University