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Yves De Deene Homepage: Engineering Thesis Projects

Engineering Thesis Projects

These subjects can be choosen as part of the unit of study in the Major of Engineering (ENG411 or related). The order in which they are listed is entirely arbitrary. Many of these projects can be continued in a Master of Research and PhD program.

Subject 1: Construction of an antropomorphic radiation sensitive thorax phantom for the simulation of image guided radiotherapy

In image guided radiotherapy, radiation beams are synchronised with the patients organ motion (e.g. during breathing or heart beating) which is imaged in real time using medical imaging technologies (CT, X-rays, MRI, ultrasound). Our research group has developed a deformable elastomer that changes colour when it is exposed to ionizing radiation. The radiation induced colour change is proportional to the amount of radiation dose. This elastic material can be poured into a mold of the lung or heart. The simulated organs can be actuated by pneumatic or hydraulic pumps, hence simulating the organ motion. These automated phantoms can be used to simulate the patient during an image guided radiotherapy and the radiation dose delivered to the 'dummy' patient can be read out through optical CT scanning. This project targets at further optimising an antropomorphic thorax phantom with beating heart and lung inserts in order to better mimic human organ motion and image guided radiotherapy treatment.

Thoracic deformable dosimeter

Deformable thoracic 3D radiation dosimeter (left) that can be read out with optical CT scanning (right).

Click here for a movie of a first prototype.

This project involves hands-on mechatronics and image processing.

Subject 2: Construction of a miniaturized theragnostic irradiator with motion feedback

In image guided radiotherapy, radiation beams are synchronised with the patients organ motion (e.g. during breathing or heart beating) which is imaged in real time using medical imaging technologies (CT, X-rays, MRI, ultrasound). During the delivery of a beam of ionizing radiation on the patient, organ motion can be tracked with medical imaging. The images are then feed back into the treatment modality. The radiation beam can thus follow the organ motion. This provides more precise treatment delivery. In this project, we will develop a miniaturized prototype of such a theragnostic irradiator with motion feedback. The system can be validated with a 3D dosimetry technique developed in house.

Click here to watch a movie of a gated radiotherapy delivery to a lung tumour.

Theragnostic irradiator

Miniaturized theragnostic irradiator with image guided feedback.

This project involves hands-on mechatronics and image processing.

Subject 3: 3D radiation dosimetry with polymer gel dosimeters: Fast quantitative magnetic resonance imaging (MRI) techniques

Many radiotherapy centres have started with the implementation of high-precision conformal radiation treatments such as intensity-modulated radiotherapy (IMRT) with the aim to tailor the radiation dose distribution to the tumour shape. From a safety point-of-view, the complexity of the treatments has increased the need for three dimensional (3D) dosimetric quality assurance (QA) of the whole treatment chain. In order to safeguard the patient treatment, three dimensional dosimetry can be performed with radiation sensitive hydrogels, in which acrylic monomers are dissolved. These gels can be poured in a humanoid body shape. Upon irradiation, a polymerization reaction occurs inside the gel. By scanning the irradiated gels with quantitative magnetic resonance imaging (MRI) sequences, radiation dose maps can be acquired.

MRI of gel dosimeter

MR scanning of polymer gel dosimeters (left) involves the application of radiofrequency pulses and magnetic field gradients (right).

In this study, several new fast MRI pulse sequences will be tested in order to obtain more precise dose maps in a reasonable scanning time. A good understanding of the basic principles of magnetic resonance imaging (MRI) is an advantage. Another skill that is desirable is being able to write an image-processing program in Matlab.

Subject 4: Optical scanning of 3D radiation dosimeters: Optimization and performance analysis of optical computerized tomography (CT) reconstruction techniques.

Many radiotherapy centres have started with the implementation of high-precision conformal radiotherapy such as intensity-modulated radiotherapy (IMRT) with the aim to tailor the radiation dose distribution to the shape of the tumour. From a safety point-of-view, the complexity of the treatments has increased the need for three dimensional (3D) dosimetric quality assurance (QA) of the whole treatment chain. In order to safeguard the patient treatment, three dimensional dosimetry can be performed using plastics or hydrogel systems that change colour upon irradiation. These radiation sensitive plastics can be imaged using optical CT scanning. Different optical scanners have been developed by the research group. The dose images are obtained from either transmission (1D) profiles or entire transmission images (2D) that are acquired from different angles. Different reconstruction methods to reconstruct 3D dose distributions from the transmission data (1D or 2D) have been proposed in the scientific literature for X-ray CT medical imaging but the optimum image reconstruction algorithm has not yet been defined and implemented for optical scanning. These algorithms differ in speed and accuracy.

Filtered Backprojection

CT image reconstruction by filtered backprojection.

The aim of this project is to implement and investigate the performence of different CT reconstruction methods on scanned optical transmission data.

Subject 5: Construction of a desktop Hybrid low-field MRI-Irradiator for Preclinical and Radiobiological Research: The MRI Unit.

The goal of this project is to develop a Hybrid low-field (0.3 Tesla) nuclear Magnetic Resonance Imaging (MRI) – Scanner / Irradiator for dedicated preclinical and radiation biology research. A novel aspect of the proposed equipment is that it will be a down-scaled 'desktop' version of the ambitious MRI-Linac that is currently under construction at the Ingham institute (Liverpool Hospital). The benchtop system can provide a more accessible and cost-effective solution for research institutes. The Hybrid MRI-Irradiator will enable radiobiological studies in real time with MRI read-out, the optimization and development of new imaging techniques (e.g. MRI pulse sequences) for the next generation of human MRI-Linac’s that are currently under development and the implementation and preclinical evaluation of image guided adaptive treatment technologies based on real-time acquired MRI data. A challenging problem faced by all Hybrid MRI-Irradiator designs is to minimize the interaction of the magnetic field of the MRI unit with the ionizing radiation source while achieving a sufficiently high and homogeneous magnetic field inside the MRI unit. A magnet design based on a Hallbach arrangement of permanent Neodymium-Iron-Boron (NdFeB) permanent magnets is currently under construction. In this project, the focus is on the desktop MRI unit.

The project involves HF electronic design and 'hands-on' practical realization. A good knowledge of electro-magnetism and Matlab is recommended.

Subject 6: Hyperpolarized gas MRI: Optimization of a spin-exchange optical pumping (SEOP) hyperpolarised gas generator

Increasing the sensitivity in magnetic resonance imaging (MRI) by a factor of 50,000 through hyperpolarisation will enable imaging of inert gasses such as Helium-3 and Xenon-129. These inert gases can be inhaled passively by the patient and allow an improved regional diagnosis of the lungs of asthma and COPD patients without exposure to ionizing radiation. A hyperpolarised gas generator for gas MRI is currently under construction. The hyperpolarised gas generator makes use of the principle of spin-exchange optical pumping (SEOP) where the electron spin magnetization of Rubidium atoms is enhanced by use of high-power laser diodes. Through collisions of the Rubidium atoms with the gas molecules, the electron spin of the Rubidium atoms is transferred to the nuclear spin of the gas molecules. The efficiency of this process depends on several factors such as gas pressure, temperature, optical laser power and composition of the gas mixture. The goal in this project is to increase the efficiency of the hyperpolarised gas generator by optimization and implementation of through flow and a condensation trap.

Hyperpolarized gas generator

Hyperpolarized gas generator under construction.

The project involves 'hands-on' electronics and physics experimentation. A good knowledge of physics is recommended.

Subject 7: Numerical simulation of MRI measured molecular self-diffusion of water in tumours using CUDA GPU programming.

The molecular self-diffusion of water molecules in biological cells can be measured by use of magnetic resonance imaging (MRI). In addition, with MRI, the apparent diffusion coefficient (ADC) can be measured for different diffusion times hence probing the tissue microstructure. It has been demonstrated that the MRI measured ADC is a potential non-invasive and endogenous biomarker of radiotherapy treatment response of tumours. However, the physical basis of this response is only qualitatively described. Computational modelling based on random walking water molecules restricted by biocellular structures can be performed to describe the measured diffusion behaviour and gain more insights into the changes in tissue microstructure upon therapy. In this study, a computer program of random walkers in a confined geometry will be extended and sophisticated to better simulate the diffusion process in biological tissue.

Random walk model

Modeling molecular self-diffusion by random walkers.

This subject is targeted to a student who is interested in computational modelling and involves programming in Matlab or C/C++ code. An interest in physics is recommended.

Subject 8: Measuring the restricted water mobility in biological cells using nuclear magnetic resonance diffusion.

The molecular mobility (self-diffusion) of water molecules in biological cells can be measured by use of magnetic resonance imaging (MRI). In addition, the apparent diffusion coefficient (ADC) can be measured for different diffusion times hence probing the microstructure of human tissues. MRI measured diffusion weighted images have been suggested as potential non-invasive and endogenous biomarkers of cancer and cancer treatment response. In this project, the biophysical mechanism between restricted water mobility in cells will be studied in normal cell cultures and cell cultures that are exposed to ionising radiation. Measurements will be performed in a benchtop 0.5 Tesla NMR relaxometer and a 9.4 Tesla NMR spectrometer. The effect of diffusion time on the measured ADC in biological cells will be compared with theoretical models and results from computational simulations.

Molecular self-diffusion

Molecular self-diffusion in biological cells is restricted and can be measured with nuclear magnetic resonance imaging.

This subject is targeted to a student who is interested in experimental measurement techniques. The subject involves physics of mass transport. Basic programming and data analysis in Matlab.

Subject 9: Quantitative magnetic susceptibility mapping with magnetic resonance imaging (MRI)

The magnetic susceptibility (χ) of human tissue is strongly influenced by the presence of strong paramagnetic components such as iron. Recently, a new magnetic resonance imaging (MRI) method to make in vivo maps of magnetic susceptibility has been proposed in the scientific literature. We expect that the implementation of a new method to quantitatively map the magnetic susceptibility will enable the quantitative assessment of iron deposits in the liver and in the brain. Quantitative susceptibility mapping is based on the perturbation of the MRI phase images by the locally disturbed magnetic field and a mathematical inversion method based on a regularization approach using spatial prior information from the MRI magnitude images. The method has promising applications in the brain to characterize iron content in hemangioma patients, in defining microbleeds and in discriminating morphological regions which are distinguished by their different iron content. In this study, magnetic susceptibility mapping will be implemented on a clinical MRI scanner and will be evaluated using test objects.

The project involves the implementation of algebraic methods in Matlab or C/C++ code to reconstruct quantitative images. Skills in numerical computation and image processing are an advantage. Good mathematical skills are required.

Subject 10: Measuring visco-elastic properties of biological tissue by use of magnetic resonance imaging (MRI) elastography

Several pathologies are associated with changes in the visco-elastic properties of tissue. For example, calcifications in the breast may be indicative of breast cancer. In liver cirrhosis, the liver tissue becomes infiltrated with more fibrous connective tissue which also leads to a significant increase in mechanical stiffness. With a new magnetic resonance imaging (MRI) technique called magnetic resonance elastography (MRE), a map of tissue elasticity can be obtained non-invasively. In MRE a mechanical MR compatible actuator is placed on the patients skin inside the MRI scanner. The MRE actuator generates harmonic low-frequency (10 Hz – 1 kHz) acoustic transverse waves that propagate in the patient. At this moment, our research group is constructing a shear-wave applicator for MR elastography (MRE). The waves cause small cyclic displacements (in the order of 100 nm) of tissue as they propagate. The tiny displacements in the tissue can be measured with a motion-sensitized MRI imaging technique that is synchronized with the generated acoustic waves. From the acquired motion-sensitized MR images, “wave images” can be constructed from which a displacement vector map and finally an elasticity map can be reconstructed. This involves image processing techniques based on algebraic inversions.

The project involves some programming in Matlab, hands-on electronics and medical image processing.

Subject 11: Quantitative nuclear magnetic resonance (NMR) spectroscopy: Development of methods and phantoms for assessing cancer metabolites in vitro

It is well known that in cancer progression, metabolite concentrations change as a result of changes in cellular pathways (i.e. protein expression). This has triggered the development of techniques to assess metabolite concentrations in vivo using magnetic resonance imaging (MRI) scanners. Clinical MRI scanners operate at field strengths of up to 3 Tesla. The spectral resolution increases with magnetic field strength. NMR spectrometers with field strengths in the order of 9.4 Tesla are able to resolve NMR peaks in vitro much better than at lower field strengths. The aim of this study is to develop metabolite solutions and hydrogel test phantoms that are realistic for carcinogenic tissue and to analyse these phantoms with NMR spectroscopy on a 9.4 Tesla NMR spectrometer and on an MRI scanner. Eventually, the phantoms will find use in benchmarking the accuracy of MR spectroscopy in vivo. Special attention will also be paid to the stability of the phantoms and the influence of the medium on the NMR relaxation times. This subject involves the construction of phantoms, hands-on NMR spectroscopy on the NMR spectrometer and a clinical MRI scanner and the physical interpretation of NMR spectra. NMR spectra will be fitted using different fitting algorithms and corresponding metabolite concentrations will be derived.

NMR spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy can be performed in vitro and in vivo and can help in the assessment of cancer.

Working with Matlab, interest in physics and chemistry, signal processing

Subject 12: Construction of an optically stimulated luminescence optical fibre radiation dosimeter for clininical radiation dosimetry

Luminescence is a physical phenomenon by which light is emitted from certain materials by a mechanism different than from the absorption of heat. In optically stimulated luminescence (OSL), the emission is stimulated by a pulse of light absorbed by the luminescent material of a different wavelength than the emitted light. When OSL materials are irradiated with ionizing radiation, electron-hole pairs are created. The electrons get entrapped in electron or hole traps. When the OSL material is subsequently exposed to light, the electrons are released from the traps and luminescent light is emitted. In this project, an OSL optical fibre device will be constructed. OSL material (Aluminium oxide) will be glued on the tip of an optical fibre which will be connected to a read out unit that will also be constructed. The readout unit consists of a stimulating light source, a photomultiplier tube, optical filters and and a half-reflecting mirror to split the outgoing stimulating and the incoming luminescent light. This project involves electronics and applied physics.

The project involves hands-on electronics and applied physics (fibre optics).

Subject 13:Construction of a phased array thoracic coil for hyperpolarized gas MRI of the lungs.

With hyperpolarised gas magnetic resonance imaging, scans of the human lung filling (ventilation and perfusion scans) can be acquired. In hyperpolarized gas MRI, the nucleus of Xenon-gas atoms is magnetized in a hyperpolarized gas generator. The nuclear magnetization of Xenon-gas atoms is several orders of magnitude higher than that in conventional hydrogen proton MRI. To acquire medical images from the hyperpolarized Xenon atoms that are inhaled by the patient, a dedicated radiofrequency resonator is used. In this project, a special designed phased array coil will be developed to acquire images of the lung with high sensitivity. This project involves electromagnetic design and highfrequency electronics. The coil design will be simulated first using Finite-difference time-domain algorithms or other 3D EM simulation software.

Thoracic RF coil development

Construction of a birdcage thoracic rf coil.

The project involves hands-on electronics and high-frequency design.

Subject 14: 3D radiation dosimetry with polymer gel dosimeters: Increasing the sensitivity of PAGAT gel dosimeters

Many radiotherapy centres have started with the implementation of high-precision conformal radiation treatments such as intensity-modulated radiotherapy (IMRT) with the aim to tailor the radiation dose distribution to the tumour shape.

IMRT of brain tumour MRI scanned dose maps

Gel dosimeter phantom irradiated according to a conformal radiotherapy treatment (left). The white region is the result of irradiation induced polymerization in the hydrogel. Maps of absorbed radiation dose are obtained by use of high-accuracy quantitative R2 nuclear magnetic resonance imaging on a clinical MRI scanner (right).

From a safety point-of-view, the complexity of the treatments has increased the need for three dimensional (3D) dosimetric quality assurance (QA) of the whole treatment chain. In order to safeguard the patient treatment, three dimensional dosimetry can be performed with radiation sensitive hydrogels, in which acrylic monomers are dissolved. These gels can be poured in a humanoid body shape. Upon irradiation, a polymerization reaction occurs inside the gel. By scanning the irradiated gels with quantitative magnetic resonance imaging (MRI) sequences, radiation dose maps can be acquired.

In this study, several gel dosimeters with various compositions will be fabricated, irradiated and measured with magnetic resonance imaging (MRI). Several radiation properties and the temperature sensitivity will be investigated for the different gel dosimeters and an optimal gel dosimeter formulation will be derived. This work involves the fabrication of gel dosimeters in a chemical laboratory, the irradiation of the gel dosimeters at a clinical linear accelerator and the readout of the gel dosimeters at an MRI scanner and/or benchtop NMR relaxometer. To convert the raw MR images to quantitative dose maps, image processing with Matlab will be performed.

Subject 15: 3D radiation dosimetry with polymer gel dosimeters: A lung equivalent gel dosimeter.

Many radiotherapy centres have started with the implementation of high-precision conformal radiation treatments such as intensity-modulated radiotherapy (IMRT) with the aim to tailor the radiation dose distribution to the tumour shape. From a safety point-of-view, the complexity of the treatments has increased the need for three dimensional (3D) dosimetric quality assurance (QA) of the whole treatment chain. In order to safeguard the patient treatment, three dimensional dosimetry can be performed with radiation sensitive hydrogels, in which acrylic monomers are dissolved. These gels can be poured in a humanoid body shape. Upon irradiation, a polymerization reaction occurs inside the gel. By scanning the irradiated gels with quantitative magnetic resonance imaging (MRI) sequences, radiation dose maps can be acquired. Recently, our research group has developed several concepts for a lung equivalent gel dosimeter. With this dosimeter, dose registration in the lungs would become feasible.

Lung dosimeter

Radiation sensitive hydrogel foam that mimics lung tissue on the microscopic level.

This study involves the fabrication, irradiation and MRI scanning of lung equivalent gel dosimeters. In addition, the MRI signal attenuation through diffusion in microscopic magnetic field inhomogeneities will be analysed through a random walk diffusion model. A good understanding of the basic principles of magnetic resonance imaging (MRI) is an advantage. Another skill that is desirable is being able to write an image-processing program in Matlab.