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Master thesis: Image-based Tree Reconstruction of Single-Cell Videos

Advertising institute: IBG-1 - Biotechnology
Reference number: D086/2014, Computer science, mathematics, (bio)informatics

Background:
Single-cell analysis in combination with time-lapse microscopy provides a unique opportunity for in-depth analyses of intracellular processes. At the Institute of Bio- and Geosciences (IBG-1: Biotechnology), tailor-made microfluidic lab-on-a-chip devices are operated, capable of high-throughput cultivation of microorganisms in defined environments. Evaluating huge amounts of image data in an automated fashion requires state-of-the-art bioimage analysis techniques.

Project description:
Lineage trees visualize the development of cellular population from single cells. When working with living specimen, the image frequency is not always sufficiently high to accurately resolve all mother-daughter relationships. In this case, extra information in combination with statistical methods may render certain scenarios more likely than others. The goal of the project is to define useful measures that yield a ranking of probable lineage trees from an acquired image sequence. Furthermore, a solution for visualizing the inherent uncertainty in lineage trees is to be developed.

Requirements:
We are looking for excellent and highly motivated candidates studying computer science, mathematics, (bio)informatics, or similar. Candidates should have good practical experience in OO programming (preferably Java and Python), good communication skills and strong interest in multidisciplinary research.

About us:
The “Modeling and Simulation Group” is part of the IBG-1, located at the Research Center Jülich (Forschungszentrum Jülich GmbH). The project is an excellent example for research at the interface of biological experimentation, engineering and computational analysis. We offer a multidisciplinary and interesting research environment within a young and dynamic group.

Contact:

Dr. Katharina Nöh
Modeling and Simulation Group
IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49 2461 61-9294
E-Mail: k.noeh@fz-juelich.de

Stefan Helfrich, M.Sc.
Modeling and Simulation Group
IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49 2461 61-9067
E-Mail: s.helfrich@fz-juelich.de

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