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AI in Physics: Convolutional neural networks for dark-field X-ray CT reconstruction |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Grating-based X-ray dark-field imaging uses scattering of X-rays to create an image of an object, rather than conventional X-ray attenuation. The combination of X-ray scattering with imaging allows us to map information about structures that are much smaller than the resolution of the imaging system over a large field of view. X-ray dark-field imaging can be combined with computed tomography (CT) to create three-dimensional images of the scattering distribution inside an object. DF-CT was recently implemented for the first time into a clinical CT here at TUM (https://www.bioengineering.tum.de/en/news/details/new-technology-for-clinical-ct-scans). The goal of this project is to use convolutional neural networks (CNNs) to remove sampling artefacts in DF-CT images. Due to the unavailability of training data from the DF-CT machine, a technologically similar experimental setup and apply transfer learning will be used. The student will acquire, process and prepare training data, as well as train and apply CNNs. Character of thesis work: mainly computational physics & image processing For more information, please contact: Dr. Florian Schaff (florian.schaff@tum.de), or Prof. Franz Pfeiffer (franz.pfeiffer@tum.de).
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Biophysical characterization of biomagnetic structures using a quantum diamond microscope |
Westmeyer |
- Research group
- Associate Professorship of Neurobiological Engineering (Prof. Westmeyer)
- Description
Are you interested in the prospects to manipulate biological structures with magnetic fields to intervene in central cellular processes relevant in biomedicine? Then you should be interested in this joint Master’s project between the Bucher Lab https://www.bucherlab.org/ and Westmeyer Lab https://www.westmeyerlab.org/ on using quantum technology based on nitrogen-vacancy (NV-)centers [1,2] to characterize and optimize biomagnetic nanostructures [3,4] in living mammalian cells.
Summary
NV-magnetometry to characterize and optimize biomagnetic nanostructures in mammalian cells
Your Profile
● an excellent and recent Bachelors's degree in (bio-)physics, biochemistry, biological engineering, biomedical engineering, or related academic programs,
● genuine interest in the powerful applications of NV-centers (https://en.wikipedia.org/wiki/Nitrogen-vacancy_center)
● previous experience with microscopy and mammalian cell culture,
● the ability to be self-motivated and work with an interdisciplinary team of bioengineers, biochemists, neuroscientists, and data scientists,
● excellent English language and organizational skills. ● an openness and mobility to collaborate with our partners at Max Planck Institutes, MIT, Caltech, and the University of Washington.
Please send your letter of motivation and your complete CV to Dominik Bucher (dominik.bucher@tum.de) and Felix Sigmund (felix.sigmund@tum.de).
References:
[1] Bucher, D.B., Glenn, D.R., Park, H., Lukin, M.D., Walsworth, R.L., 2020. Hyperpolarization-Enhanced NMR Spectroscopy with Femtomole Sensitivity Using Quantum Defects in Diamond. Physical Review X 10, 021053. https://doi.org/10.1103/PhysRevX.10.021053
[2] Bucher, D.B., Craik, D.P.L.A., Backlund, M.P., Turner, M.J., Dor, O.B., Glenn, D.R., Walsworth, R.L., 2019. Quantum diamond spectrometer for nanoscale NMR and ESR spectroscopy. Nat Protoc 14, 2707–2747. https://doi.org/10.1038/s41596-019-0201-3
[3] Sigmund, F., Massner, C., Erdmann, P., Stelzl, A., Rolbieski, H., Desai, M., Bricault, S., Wörner, T.P., Snijder, J., Geerlof, A., Fuchs, H., Hrabe de Angelis, M., Heck, A.J.R., Jasanoff, A., Ntziachristos, V., Plitzko, J., Westmeyer, G.G., 2018. Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nat Commun 9, 1990. https://doi.org/10.1038/s41467-018-04227-3
[4] Sigmund, F., Pettinger, S., Kube, M., Schneider, F., Schifferer, M., Schneider, S., Efremova, M.V., Pujol-Martí, J., Aichler, M., Walch, A., Misgeld, T., Dietz, H., Westmeyer, G.G., 2019. Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. ACS Nano 13, 8114–8123. https://doi.org/10.1021/acsnano.9b03140
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Construction of a magnetic nerve stimulation device |
Gleich |
- Research group
- Munich Institute of Biomedical Engineering (MIBE)
- Description
Magnetic stimulation is an established method for diagnostic and therapeutical applications. Depending on whether stimulation is applied to the brain, the neck or any other part of the human body, requirements to the hardware can differ significantly. We want to design and construct a device which can be easily adapted for different stimulation methods. Besides a generic processing unit, modules should be exchangeable and extensible.
Character of thesis work:
This work includes the design and construction of different modules which are assembled to a complete and operational device. Hardware layout and tests are required as well as the programming of a microprocessor. Different operation modes should be tested and evaluated.
You should bring:
Basic knowledge in circuit design and programming (C, C++)
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Dark-field Chest X-ray Imaging: Advanced image processing for clinical applications |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Dark-field radiography exploits the scattering of X-rays to visualize structures below the resolution limit. Currently, several initial clinical patient studies are underway on a worldwide first prototype we recently realized at Klinikum rechts der Isar. Within the framework of this project, the special algorithms for image post-processing of these first clinical data will be further optimized and used together with the participating radiologists for the evaluation of better direction of lung diseases.
Character of thesis work: mainly computational physics & image processing
For more information, please contact: Rafael Schick (rafael.schick@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de).
- Contact person
- Rafael Christian Schick
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Dark-field Chest X-ray Imaging: Development of registration algorithms for the analysis of functional lung images |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Dark-field radiography exploits the scattering of X-rays to reveal structures in lung tissue that cannot be visualized with conventional imaging. Currently, several initial clinical patient studies are underway on a worldwide first prototype we recently realized at Klinikum rechts der Isar. Within the scope of this project, special registration algorithms are to be developed that can register thorax images in inhalation and exhalation and allow local differences between ventilation states (for example in certain lung diseases).Character of thesis work: mainly computational physics & image processing
For more information, please contact: Rafael Schick (rafael.schick@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de).
- Contact person
- Rafael Christian Schick
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Dark-field Chest X-ray Imaging: Monte Carlo based simulation of Compton scattering |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Dark-field radiography is a novel X-ray imaging technique that is being tested for the first time in clinical patient studies on a worldwide first prototype recently completed by us at the TUM Klinikum rechts der Isar. Within the scope of this project, Monte Carlo based Compton simulations will be developed, which will allow an exact modelling of the Compton scattering and thus a better correction of the image artifacts.
Character of thesis work: experimental physics (50%) & computational physics (50%).
For more information, please contact: Theresa Urban (theresa.urban@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de).
- Contact person
- Theresa Urban
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Dark-field X-ray microCT: Pre-clinical research on improved lung disease detection |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Dark-field computed tomography uses the wave property of X-rays to provide complementary contrasts in X-ray imaging. In this project, an existing prototype for dark-field CT in mice will be used to explore the use of dark-field contrast in pre-clinical research for improved detection of lung diseases in collaboration with the Helmholtz Center for Health. In addition to experimental work to support the conduct of the preclinical studies, algorithmic research to reduce image noise and dose is planned.
Character of thesis work: experimental medical physics (60%) & image processing (40%).
For more information, please contact: Benedikt Guenther (benedikt.guenther@mytum.de), Simon Zandarco (simon.zandarco@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de).
- Contact person
- Benedikt Günther
- Simon Zandarco
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Design and fabrication of a microfluidic single-cell array platform |
Destgeer |
- Research group
- Assistant Professorship of Control and Manipulation of Microscale Living Objects (Prof. Destgeer)
- Description
- Many lung diseases are diagnosed by observing defective movements in ciliated cells. This procedure is time consuming and relies on the subjective opinion of highly trained experts, therefore preventing the unbiased assessment of disease severity and treatment success. To improve accuracy and enable statistical analysis of patient data, we are developing a microfluidic chip paired with automated image acquisition and analysis of ciliary kinematics that could become a point-of-care device in research and the clinic. We are looking for a highly motivated candidates for conducting a master thesis in our interdisciplinary team of engineers and biologists. The candidate will be designing, building, and testing a microfluidic device that will sort and position the cells for imaging. The candidate should be interested to design microfluidic device using a CAD software (e.g. AutoCAD), work in a clean room to fabricate, etc. A prior experience in the above is welcomed.
Contact: ghulam.destgeer@tum.de or janna.nawroth@helmholtz-muenchen.de
Posted on: 25.01.2023
Link: https://www.ee.cit.tum.de/en/mml/open-positions/
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Design and fabrication of a microfluidic single-cell array platform |
Destgeer |
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Design of an electric field measurement device on a milli meter scale |
Gleich |
- Research group
- Munich Institute of Biomedical Engineering (MIBE)
- Description
Comparisons of magnetic coils for inductive nerve stimulation are challenging and are mostly based on simulations. Those simulations rely on approximations and assumptions and often ignore issues like skin effect or proximity effect. Further, such calculations are time consuming and limited in accuracy and resolution. To determine the spatial field distribution along a nerve, we want to design a device that scans the electric field induced by a coil on a millimeter scale.
Character of thesis work:
Literature research on different field measurement methods and evaluate suitability; Design and construction of the device, including custom circuits and measurement environment; Evaluation of the device and exemplary measurement for different coil designs.
Question and tasks:
What methods are suitable to evaluate the electric field on a millimeter scale? Design and built the device; Determine the spatial field distribution for different coil designs; Investigate ohmic losses for solid coil wire and high frequency litz wire.
You should bring:
Interest in literature research, hardware design, experimental setup design.
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Mikrofluidische Untersuchung der Integrin-Kondensat-Assemblierung |
Bausch |
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Munich Compact Light Source: Development of an algorithmic framework for high-sensitivity grating-based phase-contrast imaging |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Using phase-contrast as alternative imaging contrast for X-rays can considerably improve the imaging results for biomedical specimens. This project will focus on the development of an algorithmic framework for a high-sensitivity and high-resolution grating-based phase-contrast micro-tomography setup at the Munich Compact Light Source for investigating soft-tissue biomedical samples, such biopsies.
Character of thesis work: mainly computational (image processing/ reconstruction)
For more information, please contact: Martin Dierolf (martin.dierolf@tum.de), Johannes Brantl (johannes.brantl@tum.de), or Franz Pfeiffer (franz.pfeiffer@tum.de)
- Contact person
- Martin Dierolf
- Johannes Brantl
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Munich Compact Light Source: Distortion correction for high-resolution quantitative X-ray imaging detectors |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
X-ray imaging detectors - in particular for high-resolution microscopy applications - may suffer from distortions, which degrade the image quality. This can have severe negative effects for quantitative applications, such as 3D micro-computed tomography. This project focuses on the characterisation of distortions of several X-ray imaging detectors at the Munich Compact Light Source, and the subsequent development of suitable correction methods.
Character of thesis work: mainly computational (image processing)
For more information, please contact: Martin Dierolf (martin.dierolf@tum.de), Johannes Melcher (johannes.melcher@tum.de), or Franz Pfeiffer (franz.pfeiffer@tum.de)
- Contact person
- Martin Dierolf
- Johannes Melcher
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Nanodosimetrie in der Bestrahlungsplanung für die Ionentherapie |
Wilkens |
- Research group
- Associate Professorship of Medical Radiation Physics (Prof. Wilkens)
- Description
- Radiation therapy for cancer patients with ions (for example carbon) is biologically more effective compared to conventional therapy with photons. However, reasons for the higher effectiveness are not yet fully understood. Nanodosimetry is a promising technique for discovering the underlying mechanisms of the higher potential to kill tumor cells.
Nanodosimetry counts ionizations in volumes of the size of a DNA segment. The distribution of ionization cluster sizes might explain the occurrence of DNA damage and contribute to the understanding of biological effectiveness.
In the case of carbon ion therapy, several fragments are present and cells are exposed to a mixed radiation field. Therefore, the nanodosimetric track structure characteristics have to be determined for each fragment species.
In this work, you will perform Monte Carlo simulations of clinical setups and track structure simulations for the nanodosimetric characteristics of the clinical beam (TOPAS). The overall goal is the implementation of the nanodosimetric results in a research treatment planning system and the investigation of calculated treatments plans regarding their distribution of nanodosimetric parameters.
Character of thesis work: 100 % computational. You will closely work together with your supervisor at Klinikum rechts der Isar.
Contact:
Frauke Alexander, Frauke.alexander@tum.de, 089-4140-9428
- Contact person
- Frauke Alexander
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New gene reporters for molecular imaging with optoacoustic tomography |
Westmeyer |
- Research group
- Associate Professorship of Neurobiological Engineering (Prof. Westmeyer)
- Description
Are you interested in discovering dynamic patterns of cellular processes across entire organs in living organisms ? Then you should be interested in this joint Master’s project between the Westmeyer Lab https://www.westmeyerlab.org/ and the Stiel Lab https://www.helmholtz-muenchen.de/ibmi/laboratories/cell-engineering/index.html on using new genetically controlled reporters for multispectral optoacoustic tomography (MSOT), an innovative technique to obtain “color information” with deeper tissue penetration than any other optical method.
Summary
Development and validation of new gene reporters for in vivo optoacoustic tomography.
Your Profile
● an excellent and recent Bachelors's degree in (bio-)physics, biochemistry, biological engineering, biomedical engineering, or related academic programs,
● genuine interest in the powerful applications of MSOT (https://en.wikipedia.org/wiki/Multispectral_optoacoustic_tomography)
● previous experience with microscopy and mammalian cell culture, and ideally work in animal models
● the ability to be self-motivated and work with an interdisciplinary team of bioengineers, biochemists, neuroscientists, and data scientists,
● excellent English language and organizational skills.
Please send your letter of motivation and your complete CV to Felix Sigmund (felix.sigmund@tum.de).
References:
[1] Stiel A.C., Deán-Ben X.L., Jiang Y., Ntziachristos V., Razansky D. and Westmeyer G.G. High-contrast imaging of reversibly switchable fluorescent proteins via temporally unmixed multispectral optoacoustic tomography. Optics Letters 40(3):367-370, 2015 https://www.osapublishing.org/ol/abstract.cfm?URI=ol-40-3-367
[2] Sigmund, F., Massner, C., Erdmann, P., Stelzl, A., Rolbieski, H., Desai, M., Bricault, S., Wörner, T.P., Snijder, J., Geerlof, A., Fuchs, H., Hrabe de Angelis, M., Heck, A.J.R., Jasanoff, A., Ntziachristos, V., Plitzko, J., Westmeyer, G.G., 2018. Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nat Commun 9, 1990. https://doi.org/10.1038/s41467-018-04227-3
[3] Weidenfeld, I., Zakian, C., Duewell, P., Chmyrov, A., Klemm, U., Aguirre, J., Ntziachristos, V. and Stiel, AC. Homogentisic acid-derived pigment as a biocompatible label for optoacoustic imaging of macrophages. Nat Commun 10, 5056 (2019) https://doi:10.1038/s41467-019-13041-4
[4] Mishra K., Stankevych M., Fuenzalida-Werner JP., Grassmann S., Gujrati V., Huang Y., Klemm U., Buchholz VR., Ntziachristos V., Stiel AC. Multiplexed whole-animal imaging with reversibly switchable optoacoustic proteins. Science Advances 2020-06 (2020). DOI: 10.1126/sciadv.aaz6293
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Simulation of peripheral electric and magnetic stimulation and experimental verification |
Gleich |
- Research group
- Munich Institute of Biomedical Engineering (MIBE)
- Description
Regression of the diaphragm muscle during artificial respiration leads to severe problems with breathing for many patients. To avoid such regression, stimulation of the phrenic nerve is a promising solution. Magnetic stimulation of the phrenic nerve has been demonstrated. However, devices are too large and complex and hence, optimization is required. We want to adapt parameters like pulse shape and coil design to stimulate the phrenic nerve with minimum energy. Further, we want to evaluate the possibility of electric stimulation and compare it to the magnetic approach. Those problems can be addressed using simulations. To verify our results, we want to design an experimental setup involving the stimulation of the sciatic nerve in the forearm.
Character of thesis work:
Extensive literature research on different simulation approaches; Extend and adapt a software environment to implement simulations for magnetic and electric simulation; Calculate field data using FEM and similar methods; Data processing using python; Design an experimental setup to verify simulations;
Question and Tasks:
What is the optimal configuration to stimulate the phrenic nerve? How are magnetic and electric stimulation different on a cellular level and how can they be simulated? How precise are our simulations? How can we verify our results?
You should bring:
Basic data science skills, ideally familiar with python and git; Good understanding of field theory; Interest in literature research
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Spectral photon counting X-ray detectors: Application to panoramic and cone-beam dental CT imaging |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
This project will explore the use of latest hybrid-pixel photon-counting detectors for improving the image quality in 3D (cone-beam CT) dental imaging applications. More specifically, the project aims at the experimental evaluation of the potential benefits of applying spectral material decomposition for dental CT application. The work will include preclinical experiments using dedicated anthropomorphic head phantoms and subsequent image analysis and interpretation. The project will be carried out in close collaboration with the Department of Radiology at the TUM Klinikum Rechts der Isar and with an external industrial collaborator located in the Munich area.
Character of thesis work: experimental physics (30%) & image processing (70%)
For more information, please contact: Daniel Berthe (daniel.berthe@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de)
- Contact person
- Daniel Berthe
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Spectral photon counting X-ray detectors: Characterisation of detector performance |
Pfeiffer |
- Research group
- Biomedical Physics
- Description
Hybrid pixel photon-counting detectors have been developed in the past in high-energy physics and are currently used in various medical imaging applications. They offer higher spatial resolution and additional energy resolution and therefore have significant potential for future improvements in radiography and CT. This work will investigate some basic physical properties of the detectors and, in particular, explore the response of such detectors to oblique radiation, which is very important for some spectral imaging applications.
The project is carried out in close collaboration with external partners from industry.
Character of the work: experimental physics (70%) & image processing (30%).
For more information, please contact: Daniel Berthe (daniel.berthe@tum.de) or Franz Pfeiffer (franz.pfeiffer@tum.de)
- Contact person
- Daniel Berthe
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