Virtual Platelets

Open Computer Science Games Engineering Bachelor Master Project Thesis Games Research Lab

Background

The Virtual Platelet Project combines the fields of systems biology, translational imaging, and games engineering to create a virtual environment that replicates the natural habitat of blood and immune cells. This environment aims to simulate key aspects of the blood and immune cells’ natural habitat:

• Blood Vessels: Simulating the pathways for blood flow and cell transport, crucial for understanding cell movement and function.
• Cellular Interactions: Reproducing how blood and immune cells interact with each other and their surroundings, vital for immune response and other bodily functions.
• Bone Marrow Environment: Modeling where blood cells are produced, an essential aspect of understanding cell life cycles.
• Cell Signaling Networks: Simulating the communication pathways between cells, critical for replicating accurate cell behavior.

This project is significant for its potential to enhance our understanding of cellular behaviors and interactions in their natural settings.

Core Components:

• Systems Biology: Investigates cellular interaction networks and their responses to stimuli.
• Super-resolution 3D Imaging: Provides detailed 3D images of cells and their environments.
• Games Engineering: Utilizes gaming technology to create dynamic, interactive simulations of cellular processes.

Task

As part of the Virtual Platelet Project, you can work on the following smaller tasks as your respective thesis:

Option 1: The Model-Pipeline Integration focuses on bridging high-definition 3D imaging with the game engine, ensuring optimal performance.

• Import System: Create a user-friendly drag-and-drop UI for importing 3D models, supporting various file formats.
• Optimization Features: Develop sliders for dynamic modification of model attributes like polygon count and texture resolution, and implement Level of Detail systems.
• Model Information: Provide detailed information (text display) about imported models and process logs.
• Texture/Shader Selection: Refine the visual quality of the models by deploying apt textures and shaders to attain a balance between visual fidelity and performance efficiency.

Option 2: This subproject is dedicated to enhancing the realism and interactivity of platelet simulations, focusing on behavioral animations and the simulation of complex interactions within blood vessels.

• Enhance Behavioral Animations & Simulations: Improve existing animations and simulations related to platelet behavior, focusing on refining object collisions and flow dynamics within vessel systems.
• Platelet Object Generation & Behavior: Create virtual platelets with specific behaviors such as adhesion, morphological changes, and secondary messenger release.
• Input-Output Behavior Rules: Establish a system to define and translate input values into specific platelet behaviors.
• Sensing and Response Mechanisms: Implement features enabling platelets to detect and respond to environmental changes, like concentration gradients of secondary metabolites.
• Collaboration & API Development: Work closely with the bioinformatics team to coordinate network models and ensure seamless API communication for future integration.
• Expandable Behavior Framework: Develop a flexible framework to facilitate the easy addition of new platelet behaviors in future updates.

Option 3: The softbodies task focuses on simulating the physical properties of cellular components in a realistic manner, specifically targeting the challenges associated with the accurate representation of soft body dynamics in a virtual environment.

• Entity Designation: Develop a feature in Godot that allows users to easily identify and classify entities as softbodies, complete with clear feedback upon successful designation.
• Parameter Configuration: Build a configuration interface for manipulating physical properties of softbodies such as stiffness and elasticity, ensuring realistic simulations.
• Interaction Mechanism: Create mechanisms for softbodies to interact with each other and their environment, including actions like fusion, separation, and deformation on impact, based on established calculations and models.
• Visualization Modes: Implement modes that allow the graphical representation of softbody structures, providing insightful visual feedback on stress points, deformation regions, etc., using color gradations or shaders.

Option 4: The VR Toolbox is dedicated to the development of interactive tools and environments within a virtual reality (VR) setting.

• Modular Toolbox: Design a modular, VR-based toolbox with drag-and-drop prefabs and configurable parameters for diverse interaction tools.
• Object Interaction: Implement VR tools for users to grab, rotate, and interact with objects, including a ‘Cellular Zoom’ feature for detailed exploration and an ‘Info Tooltip’ for object-related information.
• Environment Manipulation: Develop VR sliders to adjust environmental conditions such as pH and temperature, and include lighting adjusters and time-lapse controls for visualizing biological processes.
• Basic Blood Vessel Simulation in VR: Create a simple VR simulation of a blood vessel to visualize cell movements and interactions, focusing more on simple visual representation than biological accuracy.

Prerequisites

• Required Skills: Experience in Unity, Unreal or Godot

Contact Persons at the University Würzburg