Outcome focused, interdisciplinary research using light to perform imaging, sensing and diagnosis in biomedical applications.
Our projects are designed to contribute to our research which has an international profile. As a result they can be challenging and extremely rewarding. We offer projects in one or more of the following subjects:
- Optical engineering – design and realization of optical systems.
- Theoretical optics and electromagnetic theory – development of theory underlying the imaging techniques we employ.
- Instrumentation, electronics and system integration.
- Image processing – improving the quality of images and extracting new types of information.
- Numerical modelling – modelling of image formation.
- Biology and medicine – interpretation of images and application of techniques.
- Software engineering – development of robust software systems to drive our imaging systems.
It is not a prerequisite that you be experienced in these fields to undertake a project. You would be supervised by one of OBEL’s research staff and given the opportunity to learn the valuable transferable skills required to complete your project. OBEL has a team ethos and you would be actively encouraged to work as part of a team.
OBEL has a tradition of undertaking quality research in optical and biomedical engineering. We attract high calibre honours students who go on to be employed by leading companies. For example, recent graduates of OBEL have gone on to work in companies such as Google, Delloite, Schlumberger and Finisar and universities such as MIT, University of Illinois and ANU. Recent honours students have also published original work in academic journals such as:
OBEL’s microscope in a needle was a finalist at the 2012 Australian Museum Eureka Prizes for Innovative Use of Technology. In actively seeking to commercialise out work, we regularly patent novel technology developed within the group.
The OBEL team is composed of a mixture of research staff and PhD students:
Research staff: A/Prof Barry Cense.
PhD Students: Hadi Afsharan, Qiang Wang and Michael Hackmann.
In addition to our staff and students, we collaborate with international researchers based in, for example, the USA, South-Korea, Poland and the UK.
All project areas can accommodate two or more students. It may not be completely clear to you what you would actually do from the project description alone. Please take the opportunity to come and talk to us so that we can define a project around your skills. Contact details can be found on our webpage.
1) Medical imaging with optical coherence tomography
Optical coherence tomography (OCT) is an ultra-high resolution medical imaging modality. Conceptually, it is similar to ultrasound imaging, except that reflections of light are detected rather than sound. This enables a much finer scale of image than is possible with ultrasound. OCT is providing images of unprecedented clarity of living biological entities and is providing new information on a variety of diseases and conditions, including cancer and muscular dystrophy.
OCT research at OBEL aims at understanding and improving the technique and in designing and building instruments for various applications, including breast cancer (with surgeons at Sir Charles Gairdner Hospital and Royal Perth Hospital), skin (scar assessment with Royal Perth Hospital), and animal muscle tissue (for muscular dystrophy research with Miranda Grounds at UWA Anatomy & Human Biology).
Examples of possible projects:
- Instrumentation Design: 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;
- Image Processing of medical images: OBEL is currently exploring the use of several image processing techniques, including segmentation and registration, to extract new types of information from high resolution medical images, Projects include developing new algorithms to analyse images of breast cancer, lung disease and burn scars. This is a software-based project and will require knowledge of either Matlab or C++.
2) OCT needle probes
We have developed a number of prototype needle probes, where the miniaturised optics of the OCT system are encased in a medical hypodermic needle. These probes will enable surgeons to more accurately detect cancer during surgery, and provide new ways to assess lung diseases.
We are actively exploring new probe designs, and possible projects will focus on the optics and mechanical design of the probe itself. These are hardware-based projects that involve researching a new probe design, fabrication of the optics and assessment of the probe.
3) High resolution elastography
Elastography is a new imaging technique which creates an image of what tissue ‘feels’ like. It can be used to differentiate between healthy and diseased tissue by measuring the elastic properties of the tissue. We have combined this technique with optical coherence tomography to achieve high resolution elastography. Examples of possible projects are:
- Signal processing to estimate strain: We implement elastography by placing the tissue under mechanical load and measuring the resulting displacement using optical coherence tomography. The strain introduced to the tissue is then determined from the spatial derivative of displacement. We are exploring new algorithms to improve the strain estimation and to remove artefacts from our images. Possible projects in this area include the development of phase unwrapping algorithms and the acquisition and analysis of the Doppler spectrum.
- Handheld probe design and implementation: We are developing handheld probes to allow clinicians to perform elastography measurements on patients. This involves design of an optical fibre probe and loading mechanism. The loading mechanism must be synchronised with the image acquisition. Also, it is important to measure the force exerted by the probe on the tissue. Your project could involve working in part of the team aiming to develop the first handheld optical elastography probe.
4) Optical theory and modelling
Modelling is a very important part of the development and interpretation of imaging techniques. This includes modelling of the imaging system as well as modelling of how light interacts with tissue. We offer the following projects in this area:
- Rigorous modelling of light tissue interaction for large volumes of tissue. We have expertise in using rigorous techniques such as the finite difference time domain method to model light scattering however we would like to extend this technique to be able to model larger volumes of tissue. We intend to make use of a technique which makes use of Fourier transforms to calculate spatial and temporal derivatives which allows a substantial reduction in the field sampling density. This project would require a student with, or a desire to develop, skills in electromagnetic theory and C/C++ programming.
- Another way of extending the volumes of tissue which we can model is to parallelise our current finite difference time domain code. This code could run on iVEC’s cluster computer. Again, this project would require a student with, or a desire to develop, skills in electromagnetic theory and C/C++ programming.
- OCT uses a partially coherent light source. Coherent light is produced by a point source emitting a single frequency of light. Incoherent light is produced, to a close approximation, by a source emitting a very wide band of frequencies and having a finite extent. Partially coherent sources fall somewhere in between. Generally speaking, numerical models of light scattering such as the finite element method and finite difference time domain method can model only coherent or completely incoherent light sources. However, a partially coherent source can be modelled by a decomposition of coherent modes. These modes result from the solution to an integral equation. These modes allow image formation in partially coherent imaging systems to be modelled. This project is quite challenging, but fascinating and rewarding.
- We have a number of other modelling problems to solve, please come and discuss with us if you would like to do a modelling project but don’t particularly like those mentioned above.
5) Investigation of optical properties of biological samples
One goal in OCT is to measure the optical properties of different tissue samples. This includes measuring how rapidly light attenuates and the directionality of optical scattering. It is important to benchmark optical property measurements in OCT using independent techniques. A possible project would involve building optical setups using components such as lasers, optical fibres, goniometers and integrating spheres to allow this benchmarking to be performed. Another possible project would involve characterisation of nanocrystals for use in optical spectroscopy.
6) Visualisation and rendering
A large component of our research involves efficient handling of large 3D datasets. Possible project in this area are related to visualisation, feature extraction or GPGPU (General Purpose Graphics Processing Unit) development. This could involve real-time 3D rendering for our optical imaging systems.
7) Improving OCT image quality
OCT images are subject to a granular or mottled appearance, similar to ultrasound, due to speckle. We are interested in developing techniques to reduce speckle and improve image quality, whilst maintaining high resolution. A possible project would involve developing new techniques and comparing existing techniques to achieve this.
One technique that we are keen to investigate uses sparse image representations. This technique has already been demonstrated in photography and has great potential for denoising and feature extraction in optical imaging.