Institute of Applied Physics - Biophysics
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Thesis Opportunities

We offer students opportunities to do a project work, a bachelor thesis or a master thesis. We are looking for highly motivated students with an interest to work at the interface of cell biology, biophysics and biochemistry. Further working fileds are data simulation and the improvement of microscopy setups. If you are interested and for further information, don't hesitate to contact us.

Thesis opportunities include, but are not limited to the following subjects:


Image of a fluorescence microscope

Development of an autonomous microscopy system for adaptive experimentation

Master Thesis

Joint project with Prof. Radu Grosu, Faculty of Informatics

Biological cells react dynamically to biochemical and biophysical stimuli provided by their environment, such as the presence and spatial organization of specific ligands, the dynamical behavior of the matrix or its rigidity. Typically, microscopists have to observe attentively the experiment and intervene manually, whenever appropriate. In this project, we will go beyond the state of the art by developing an autonomous microcopy system, which enables the automated interpretation of cell biological images, and – based on a set of user-defined rules – a corresponding response exerted on the cell by the microscopy system. We will employ machine learning methods to automate the image interpretation and control the hardware response.

Field: Technical Physics, Biomedical Engineering, Data Science, Informatics
Contact: schuetz@iap.tuwien.ac.at / radu.grosu@tuwien.ac.at

 


Cryo-stage for fluorescence microscopy

Assessing the properties of fluorescent dyes at cryo temperatures

Bachelor or Master Thesis

Fluorescent dyes behave differently at room temperature and low (cryogenic) temperatures. Performing super resolution microscopy at low temperatures requires a full understanding of the fluorescent dyes properties. In this project, we will examine the behaviour of different dyes at low temperatures and will characterize its photoblinking/photoswitching capabilities, establishing a library of dyes suitable for cryo super resolution microscopy.

Field: Technical Physics, Biomedical Engineering, Technical Chemistry
Contact:  lopez-martinez@iap.tuwien.ac.at / schuetz@iap.tuwien.ac.at


CHO cells incubated on a EM grid

Evaluating the suitability of different cells for super resolution microscopy at cryogenic temperatures

Bachelor or Masters thesis

Cryofixation is considered an ideal fixation technique for biological structures. It combines complete immobilization with total preservation of the live state of the cell. In this project we will evaluate different parameters and protocols for criofixating a variety of cell lines, with the aim of designing an optimized protocol for their study with super resolution microscopy.

Field: Technical Physics, Biomedical Engineering, Technical Chemistry
Contact: lopez-martinez@iap.tuwien.ac.at/ schuetz@iap.tuwien.ac.at


Scheme of a focus hold system

Construction of an automated focus hold system for cryo super resolution microscopy

Bachelor thesis

Super resolution microscopy measurements often take from few minutes to several tens of minutes for a single measurement to be done. In such long measurements, the focus of the optical system may move, which means we often need manual repositioning of the objective. In this project we will construct an automated system that continuously tracks the position of the focus and repositions the objective using a piezoelectric positioner.

Field: Technical Physics, Technical Chemistry
Contact: lopez-martinez@iap.tuwien.ac.at / schuetz@iap.tuwien.ac.at


Drift correction concept

Design of a drift correction method based on tracking of fiducial markers

Bachelor thesis

Typical super resolution microscopy measurements take several tens of minutes. During these long measuring times, the microscope can suffer from mechanical drift, which deteriorates the final resolution of the images. To attain the potential resolution of tens of nms, the mechanical drift needs to be corrected. In this project, we will design a strategy for drift correction based on tracking the displacement of fixed fiducial markers distributed all over the field of view. Their individual trajectories will be analysed and used to correct the movement of the whole system, and, this way, obtain a drift-corrected image.

Field: Technical Physics, Biomedical Engineering, Technical Chemistry
Contact: lopez-martinez@iap.tuwien.ac.at / schuetz@iap.tuwien.ac.at