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Master thesis: Integrative Preprocessing for Time-Lapse Microscopy Videos

Advertising institute: IBG-1 - Biotechnology
Reference number: D085/2014, 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 cultivations of microorganisms in picoliter environments. Evaluating huge amounts of image data in an automated fashion requires state-of-the-art bioimage analysis techniques.

Project description:
To evaluate acquired image sequences, the first step is the detection of regions of interest (ROIs) which critically impacts the quality of the whole analysis. Having the structural information of the cultivation chambers at hand, pattern matching approaches in combination with signal/image processing techniques are to be used to eliminate device structures from acquired images while accounting for production inaccuracies. The goal of the project is to establish a robust preprocessing workflow for time-lapse videos of bacterial microcolonies in various cultivation structures. The overall performance of the approach is to be benchmarked against ground truth data sets with respect to quality, robustness, and speed.

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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