ETH Competence Center - Competence Center for Rehabilitation Engineering and Science (RESC)| Acronym | RESC | | Homepage | https://resc.ethz.ch/ | | Country | Switzerland | | ZIP, City | | | Address | | | Phone | | | Type | Academy | | Parent organization | ETH Zurich | | Current organization | ETH Competence Center - Competence Center for Rehabilitation Engineering and Science (RESC) | | Child organizations | | | Members | |
Open OpportunitiesCombine two exploding fields in computer science: machine learning and agent-based modelling.
Based on preclinical and in vitro studies of cell behaviour and cytokine reaction-diffusion and mechanical tests we have generated an in-house biofidelic agent-based model of the human skeleton and its response to diseases and their treatments. This model reproduces the effects of several widely used osteoporosis treatments on key parameters used to quantify fracture risk. This rule-based approach involves studying bone mechanobiology at the cell scale and extrapolating this to millions of cells at the tissue scale to understand the pharmacokinetics of treatments and identify possible new therapies and approaches to patient-specific treatment.
An alternative approach to in silico prediction of response to treatment is a supervised learning approach where we simply input baseline and follow-up bone scans to a CNN with twelve layers constructed using keras. We then attempt to dive into the black box and quantify what characteristics of the input govern the response of our model. The issue is the clinical data is not big enough to do this well so we use the agent-based model as input to the ML approach to construct a proxy model! This also helps us understand, validate and quantify the uncertainty in the agent-based model. To decide which runs of the agent-based model to use as input to the ML approach to construct the proxy model we use polynomial chaos expansion. - Animal Physiology-Cell, Artificial Intelligence and Signal and Image Processing, Cell Development (incl. Cell Division and Apoptosis), Cellular Interactions (incl. Adhesion, Matrix, Cell Wall), Computation Theory and Mathematics, Modeling and Simulation, Protein Targeting and Signal Transduction
- Bachelor Thesis, Master Thesis, Semester Project
| Delayed bone healing or failed non-unions account for 5 – 10% of all bone fractures and present a challenging problem in regenerative medicine. The impact of delayed unions or non-unions can be devastating with prolonged rehabilitation, decreased quality of life and significant health care costs. Our lab has conducted fracture healing studies in young and prematurely-aged mouse models with different defect sizes. The aim of this project is to analyse data from mice which exhibit delayed unions and non-unions. - Biomaterials, Biomechanical Engineering
- Bachelor Thesis, Internship, Master Thesis, Semester Project
| Bone exhibits a remarkable ability to adapt its microstructure in response to mechanical and metabolic demands. This process involves a dynamic balance between bone-forming osteoblasts and bone-resorbing osteoclasts, with osteocytes playing a crucial role in signaling micro-mechanical cues. Disruptions in these mechanisms, as seen in conditions like postmenopausal osteoporosis, lead to decreased bone density and increased fracture risk. Sclerostin is pivotal in determining bone formation or resorption in response to mechanical stimuli and is targeted by FDA-approved osteoporosis medications. However, the drug's mechanism and its interaction with mechanical loading remain unclear. This project aims to investigate bone's response to sclerostin antibody treatment and uncover the cellular mechanisms governing bone adaptation using single-cell mechanomics cluster analysis. - Computational Biology and Bioinformatics, Engineering and Technology, Mathematical Sciences, Medical and Health Sciences, Physics
- Bachelor Thesis, Internship, Master Thesis, Semester Project
| Modern robots collect data from various sensors. When these sensors operate independently, time-synchronization through rectification of their individual clocks and correction for temporal drift is required.
In our previous work, we developed an initial version of a synchronization pipeline in Python, designed for offline data synchronization. Our current pipeline already effectively synchronizes sensors that include a common external synchronization signal. Despite already working well, our current pipeline still requires some expertise to configure the data sources. To make the pipeline widely usable, we now need to make it function seamlessly even without expert knowledge and access to external synchronization signals. This enhancement should also extend to scenarios involving continuous online data as well.
Furthermore, we want to prove the correctness of the synchronization and showcase the performance based on synthetic data.
In essence, your thesis will comprise the following key objectives:
1. Understand the challenges involved in data synchronization.
2. Familiarize yourself with the existing synchronization pipeline.
3. Innovate strategies for achieving data synchronization without relying on external synchronization signals.
4. Enhance the user interface by creating an intuitive guide for using the pipeline effectively.
5. Extend the functionality to accommodate online data streams.
6. Assess the pipeline's correctness and performance using synthetic biosignals, as well as pre-recorded biosignals from the SMS-Lab and Tohoku University.
Throughout this project, you will receive guidance from me, a 4th year PhD candidate at the Sensory-Motor Systems Lab at ETH Zurich, and researchers at Tohoku University in Sendai, Japan. As I will be in Japan from October, we will conduct the weekly meetings over Zoom.
Furthermore, in case of interest, you have the exciting opportunity to visit us in Japan. This opportunity can be pursued either through personal funding or by applying for respective scholarships, such as the Heyning-Roelli Foundation, SEMP, Spickenreuther Foundation, and others. I have received scholarships in the past and I am happy to provide guidance and support throughout the application process. - Biosensor Technologies, Data Storage Representations, Data Structures, Digital Systems, Information Storage, Retrieval and Management, Pattern Recognition, Signal Processing, Simulation and Modelling, Software Engineering
- ETH Zurich (ETHZ), Internship, Master Thesis, Semester Project
| In this project, we focus on continuous and quantitative monitoring of activities of daily living (ADL) in SCI individuals with the goal of identifying cardiovascular events and PI-related risk behaviors.
ADLs specific to SCI patients and their lifestyles shall be discussed and narrowed down in the scope of this work, therefore an autonomous camera-based system is proposed to classify ADLs.
The Current work builds on a previous project where a SlowFast network [1] was trained to identify SCI-specific classes and we aim to further improve the classification and temporal resolution for transferring to wearables' time-series data. - Computer Vision, Health Information Systems (incl. Surveillance), Intelligent Robotics, Knowledge Representation and Machine Learning, Neural Networks, Genetic Alogrithms and Fuzzy Logic, Pattern Recognition
- Bachelor Thesis, ETH Zurich (ETHZ), Internship, Master Thesis, MD
| Fracture healing is a complex process that involves inflammation, angiogenesis, and bone remodeling. The remodelling process helps maintain bone density, repair micro-damage that occurs due to everyday activities, and adapt bones to the specific needs of an individual's body. Mechanical loading is a crucial factor in the regulation of fracture healing. The forces and strains experienced by the bone during everyday activities influence the cellular responses, callus formation, bone deposition, remodelling, and, ultimately, the successful recovery of the fractured bone. The mechanisms underlying spatial cell reorganization during loading, which contributes to fracture healing, remain unclear. The project aims to investigate and explore the fracture healing process of mice using spatial transcriptome changes in response to mechanical loading. By shedding light on this aspect, the project aims to contribute to the broader understanding of fracture healing and potentially pave the way for more effective treatment strategies in the future. - Biological Mathematics, Computational Biology and Bioinformatics, Engineering and Technology, Information, Computing and Communication Sciences, Medical and Health Sciences, Physics
- Bachelor Thesis, Course Project, ETH for Development (ETH4D) (ETHZ), ETH Zurich (ETHZ), IDEA League Student Grant (IDL), Internship, Master Thesis, Semester Project
| Bone is a metabolically active, rigid connective tissue that provides structural support, facilitates movement, and protects vital organs. Micro-computed tomography (micro-CT) is a widely employed imaging technology to gain deeper insights into bone structure and function. We have recently introduced the mi-CT image data repository, an open-access platform dedicated to biomedical images obtained from micro-CT scans within our research group (https://www.mi-ct.ethz.ch/). This repository aims to facilitate research by developing an efficient online image management system, making the data easily accessible. Achieving open access to these tools necessitates the creation of interfaces between the online platform and existing Python-based preprocessing software. - Artificial Intelligence and Signal and Image Processing, Biomechanical Engineering, Computational Biology and Bioinformatics, Medical and Health Sciences, Programming Languages, Software Engineering
- Bachelor Thesis, Course Project, ETH for Development (ETH4D) (ETHZ), IDEA League Student Grant (IDL), Internship, Master Thesis, Semester Project
| This project aims to develop a pipeline to register 2D histological images to 3D micro-CT images. - Biomedical Engineering, Computational Biology and Bioinformatics, Computer Hardware, Interdisciplinary Engineering, Materials Engineering, Mathematical Sciences, Mathematical Software, Mechanical and Industrial Engineering, Medical and Health Sciences
- Bachelor Thesis, Internship, Master Thesis, Semester Project
| We seek a highly motivated Bachelor's or Master's student dedicated to developing and applying a mathematical model, simulation, optimization, and process control to deepen the scale-up of bone organoids. This project offers an opportunity to gain valuable work experience within a highly interdisciplinary and international team. - Differential, Difference and Integral Equations, Dynamical Systems, Modeling and Simulation, Optimisation, Process Control and Simulation, Stochastic Analysis and Modelling, Systems Biology and Networks, Systems Theory and Control
- Bachelor Thesis, IDEA League Student Grant (IDL), Internship, Master Thesis, Semester Project
| Current tissue engineering strategies fail to recreate the complex bone architecture where a 3D bone cell network resides in the cavities for mechano-regulation of bone remodeling. This project aims to create a 3D printed in vitro model of bone for medicine. - Biochemistry and Cell Biology, Biomaterials, Interdisciplinary Engineering, Macromolecular Chemistry, Mechanical and Industrial Engineering, Medical and Health Sciences, Polymers
- Master Thesis
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