Hiwi Position: Virtual Reality Visualization of Complex Multi-Dimensional Relationships of Biological Phenomena

[Subtitle]
Supervision by: Dr. Ulrich Eck
Due date:

Objective

The objective of this project is to visualize complex multi-dimensional relationships of biological phenomena using a Virtual Reality (VR) application and a commodity Head-Mounted-Display (HMD). The Institute for Computational Biology (ICB) at the Helmholtz Institute develops machine learning algorithms to cluster single cell images of flow cytometry (link). As shown in the referenced video [[][link]]. As one goes deeper into the Convolutional Neuronal Network (CNN) layer, single cells of different types are better grouped into different clusters. We plan to show this classification process in 3D and enable interactive exploration of clusters and to display information about single cells such as their image, cell cycle phase, label, and topology. Additionally, we plan to visualize other datasets, for example the results of a recent article in Nature (link).

The VR system will be implemented using a game engine (Unity or Unreal Engine). The main focus of the VR application will be on the visualization and the interactive exploration of the dataset. Users will be immersed in virtual scene that allows them to navigate in the dataset, to control the visualization parameters interactively using tracked hand controllers. A focus will be on high quality 3D rendering with minimal latency and user-friendly interaction.

Tasks

• Benchmarking of different game engines to verify that they are able to handle the visualization of datasets with a large number of individual elements
• Develop a HMD-based application using a game engine (Unity/Unreal) with high quality rendering and minimal latency
• Import/Interface with ICB datasets (precomputed or realtime)
• Design visualization for the provided dataset
• Design interactions for navigating the dataset
• Implementing inspector panels for detailed information on the individual cells

Requirements

• Advanced C++ or C# skills
• Good understanding of linear algebra
• Experience with computer graphics (OpenGL^?, SceneGraphs^?, Dataflow)
• Proficient English language skills to communicate with our international team
• Beneficial: Experience with Unity or Unreal

Contact

If you are interested please contact Dr. Ulrich Eck