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Final Year Projects for 2007
If you are interested in instrumentation, electronics, optoelectronics, lasers, or optical engineering,
and their applications in Medicine and Biology, then OBEL could be for you. Projects in OBEL will help
to develop your practical skills in the areas just mentioned as well as in systems integration,
interfacing, numerical modelling, and programming. These skills are sought in a wide range of industries
in the instrumentation, telecommunications, biomedical engineering, and biotechnology sectors.
OBEL’s final year projects fall into one or more of the following categories:
- Electronics design, implementation and testing; optoelectronics and lasers;
- Systems integration, interfacing and software design and development;
- Optical engineering – design and realization of optical systems;
- Mechanical systems – design and realisation of mechanics for endoscopic and portable hand held devices;
- Numerical modelling and associated theory – signal processing or light-tissue interactions;
- Image and data analysis, 3D reconstruction and visualization; and
- Microscopy of biological cell and tissue samples.
Your project will form a part of the group’s research and will be strongly collaborative and team based. OBEL’s staff and postgraduate students will be interested in your project, and will be eager to help you succeed. OBEL offers a range of projects of varying sizes from small well-defined implementation projects to larger research projects. Research projects are more open-ended and offer the flexibility in direction associated with real research. With either project type you will have the opportunity to work with your supervisor to define the direction, style and boundaries of your project
OBEL’s mission is to invent and develop new techniques based on optics and photonics for non-invasive interrogation of living systems, particularly the diagnosis of human diseases. Although our research is strongly motivated by these biomedical applications and based on the use of light, YOU DO NOT NEED PRIOR KNOWLEDGE OF BIOMEDICINE OR OPTICS. All project areas can accommodate two or more students. From the project descriptions alone, it may not be completely clear to you what you would actually do – come and talk to us. Contact details are on our webpage.
Available Project Areas
Choose a link to find out about the projects offered in OBEL's research areas. Each research area has several projects available, usually covering several of the categories above.
- Medical Imaging with Optical Coherence Tomography
- Modelling and Exploiting Diffuse Light Propagation in Skin Tissue
- Anatomical Endoscopic Optical Coherence Tomography
- Ultra-wide Field Optical Histology - Scattering Fourier Holography
- Intelligent Guided Needle Biopsy for Breast Cancer
- Optical Clearing and Two-Photon Microsocopy
Project Descriptions
Medical Imaging with Optical Coherence Tomography
Optical coherence tomography (OCT) is a micron-resolution, cross-sectional sub-surface medical imaging modality. OCT is providing images of unprecedented clarity of living biological entities, especially of the human retina, providing new information on a variety of diseases and conditions, and endoscopically in coronary arteries. OBEL has pioneered anatomical OCT imaging of the upper airway. OCT research at OBEL aims at understanding and improving the technique and in designing and building instruments for various applications, including skin (blood flow and microstructure of vessels, cancer detection in collaboration with dermatologists Chris Quirk and Chris Clay and histopathologist Peter Heenan, and drug uptake), and recently in animal muscle tissue (for muscular dystrophy research with Miranda Grounds at Anatomy & Human Biology). Other applications are listed under Project Areas 3 and 5 below.
Examples of possible specific projects:
- Signal processing: Model, design, construct, and demonstrate signal processing
systems for OCT, including analogue, direct digitisation, and/or DSP implementations;
- Theory: Develop a theoretical model of OCT images of specific biological structures;
- Software for spectral domain Doppler OCT: : Spectral domain OCT is known to have
several advantages over time domain OCT. You will write software to acquire and display OCT images
from a SD-OCT system and then use it to obtain Doppler information from samples by tracking the phase
in consecutive A-scans;
- Software and hardware for en-face OCT: Our current software enables imaging depth
sections (z-x). We want the option of generating transverse sections (x-y, or en-face). You will write
software to control image acquisition from a high-resolution en-face system. This work will also build
towards 3D acquisition. On the hardware side of this project, you will review current designs of OCT
sample arms, and help with the design and construction of a high NA optical system for en-face scanning.
Design criteria include aberration correction (imaging performance), compactness and incorporation of
a CCD positioning system for clinical use. Again, this work can potentially build towards a 3D imaging
system;
- Engineering compact instrumentation: Design and construct a compact OCT system for clinical use. The focus is on miniaturization of the current optical fibre-based system and involves the design and construction of portable/compact electronic and optical modules. The portability and reliability of the system will be tested under clinical conditions; and
- Muscle imaging: Early work suggests OCT may be able to differentiate between
dystrophic and non-dystrophic mice, which could reduce the need for subjects and improve the statistics
and accuracy of many experiments. You will continue investigating what OCT can provide.
What gives your skin its colour is the interplay of absorption (by melanin - brown and haemoglobin - red) and the scattering of light within your tissue, and the depths at which both occur. For some time, we have been motivated by the goal of earlier and more reliable detection of melanoma to exploit these interactions. We have built up considerable expertise in modelling light propagation in tissue, and in the development and clinical application of spectroscopic instrumentation that could provide low-cost solutions. Apart from melanoma (collaborators: Quirk, Clay and Heenan), we have emerging interests in blood oxygenation in the peripheral circulation and the spectroscopic detection of other agents.
We use a variety of modelling techniques but mainly Monte Carlo simulations. You may develop and implement new techniques (primarily working in Matlab or C), do simulation experiments using existing modelling systems, or work on physical experiments to verify the results of our models (or some combination of these). Other collaborators in this work include Jon Emery, Professor of General Practice at UWA, and groups at Oregon Health and Science University, USA and the University of Florence, Italy.
Examples of possible specific projects:
Modelling:
- Extend our spectroscopic optical models to new skin lesion pathologies and verify them
against measurement and pathology;
- Develop an optical model for the dermatoscope, a commonly used visual aid;
Instrumentation:
- Develop a reflectance spectroscopy based blood oxygenation system – build the instrument,
optimise the signal processing, and model the system to predict and optimise its performance;
- Investigate how to customise the dermatoscope to enhance its diagnostic capability –
building simple imaging instruments and measuring and modelling their performance.
We have developed an endoscopic OCT system that can image the internal anatomy of large hollow organs.
In a world first, we have used it to quantify the collapse of the upper airway in a patient with the
condition obstructive sleep apnoea. This effort is a long-term collaboration with Peter Eastwood and
David Hillman in the Department of Pulmonary Physiology, Sir Charles Gairdner Hospital. Despite its
unique capability, there remain many opportunities to further improve the whole system, including
the 2-D and 3-D presentation of results, analysis of the recorded data, and to adapt it for other
applications – a current interest is Burns patients in collaboration with Dr Fiona Wood at Royal Perth
Hospital.
Examples of possible specific projects:
- Signal Processing: Upgrade the image acquisition rate of the system, with a new
high-speed data acquisition card, improvements to the software, or better signal processing electronics;
- Image Analysis: Develop image analysis techniques to enhance the raw OCT images,
extract the airway contour information, and measure parameters (Matlab);
- 3D Reconstruction: Develop three-dimensional reconstruction techniques to convert
the data into accurate 3D models of the upper airway. (Matlab, C, or IDL);
- Clinical Measurement: Develop clinical experiments using the hollow organ profiling
system on patients at the Hospital; and
- Optical Probes: Assist with the design and construction of some novel endsocope probes. This would suit a student with an interest in mechanics.
Light scattering is the basis for most optical diagnostic techniques. One important property of light scattering is how it varies in intensity with the angle of the scattered light. We seek to measure the light scattering of living cells as they undergo processes such as division and programmed death in order to develop models for how these processes can be detected by other diagnostic systems.
OBEL has been developing equipment to measure light scattering using Fourier holography and
techniques to construct and process an image of scattering from a two-dimensional sample field.
This technique has the potential to replace the laborious and time-consuming process of microscopic
counting of cells, which is ubiquitous in medicine and biology. We are initially focussing on muscle
cells and tissues with Miranda Grounds, Anatomy and Human Biology, UWA.
Examples of possible specific projects:
- Holography System: Characterise the experimental performance of the Fourier
holographic scattering instrument and design and implement improvements to it;
- Image reconstruction software: Development of system software for the acquisition,
processing, and reconstruction of the Fourier holograms; and
- Cells and muscle tissue: Development of software for measuring and imaging muscle cells and tissues, including the implementation of digital spatial filtering and pattern recognition methods.
We have developed a method, which we call Bifocal Optical Coherence Refractometry (BOCR), to measure the refractive index of living tissue, and refractive index is sensitive to the physiological state and pathology of the tissue. We are working on a prototype in collaboration with Christobel Saunders, Professor of Surgery, UWA (SCGH) and a group at University of Illinois at Urbana-Champaign, USA, which we hope to fit inside a biopsy needle. We plan to use the technique to guide breast tissue biopsies to avoid sampling error –when the biopsy misses the tumour.
Examples of possible specific projects:
- Needle Biopsy Probe: You will work on the optics and mechanical design of the probe
itself – would suit a mechanical/mechatronics student;
- BOCR system: You will work on interfacing the probe to the endosciopic OCT
system and design interfaces and processing to extract the required refractive index information; and
- Clinical Measurements: You will perform measurements on phantoms and breast tissue samples obtained from SCGH and analyse the results to develop methods for correlating the BOCR measurement to pathology.
OBEL is a partner in the Centre for Microscopy and Microanalysis’s state-of-the-art million-dollar two-photon microscope, commissioned in 2004. A two-photon microscope uses non-linear absorption of two photons to induce fluorescence that is confined to a very small region. It is rapidly becoming widely used in biotechnology and bioengineering worldwide. OBEL has two main thrusts in this area: the development of two-photon techniques for in vivo applications – it shows extraordinary promise; and the systematic study of how to improve imaging depth and contrast in living specimens through the addition of so-called clearing and contrast agents, including biologically compatible nanoparticles. We are collaborating closely with the European Laboratory for Nonlinear Spectroscopy in Florence, Italy, as well as with the Centre for Microscopy and Microanalysis at UWA.
Examples of possible specific projects:
- Clearing agents: Examine and quantify the effects and dynamics of clearing agents
in tissues samples;
- Pilot in vivo applications: Study two-photon imaging of malignant and normal
tissue samples; and
- Benchmark studies: Compare fresh, frozen, and fixed two-photon and fluorescence lifetime images of tissue samples.
