Development of biomechanical biopsy imaging for tumour tissue screening

Supervisor: A/Prof Irina Kabakova (UTS) 

Co-supervisor: A/Prof Thomas Cox (Garvan Institute of Medical Research) 

Stipend: UTS domestic stipend 37k p/a tax free + 5k top-up

Research allowance: UTS allowance of 2.5k p/a for publishing costs, consumables and travel

Affiliation: ARC Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS)

Eligibility requirement: citizenship or permanent residence in Australia/New Zealand

General description and project aims

In spite of tremendous progress in modern biomedical diagnostics and treatment, cancer remains one of the leading causes of death worldwide, with almost 50,000 deaths per year attributed to solid cancers in Australia alone. Despite many tests are found helpful in cancer diagnosis, it can only be confirmed via a biopsy test where a small piece of tissue is excised from the organ or tissue and used for clinical histology staining to differentiate cancerous cells from the healthy ones. The tissues need to be sent to pathology labs and the test can take up to a week to complete. A rapid or real-time test, however, would be largely beneficial for the detection of cancerous cells, especially guiding the doctor during the surgery and determining margins for the tumour excision. Such a test should ideally be label-free, non-destructive and use approaches that can be integrated with the standard microscopy systems and hand-held devices for the easy translation into medical practice. Light-based techniques are preferred since light imaging can provide microscopic resolution, at the spatial scale of the cells. 

This project will combine: 1) biological methods for tissue preparation, 2) light-based methods of Brillouin scattering for 3D micromechanical mapping, and 3) machine learning techniques for data processing and image analysis to develop and deploy a novel state-of-the-art opto-mechanical and real-time imaging biopsy for the differential detection of tumour tissues from surrounding healthy tissue.

The position offered will be primarily based at the University of Technology Sydney and is supported by Garvan Institute of Medical Research and recently established Australian Research Council (ARC) Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS). Part of the position will involve working closely with cancer biologists on site at the Garvan Institute of Medical Research in Darlinghurst.

The position is supported by a HDR stipend of $37k/year with possibility of an additional discretionary top-up for high-achieving students and $2.5k/year allowance for research related expenses and travel. 

The Ph.D. project aims are:

1. To develop and optimise novel methods for tissue preparation and imaging of complex biological material using advanced Brillouin microscopy.
2. To identify markers of pathological processes in cancer cells and tissues based on micromechanical and fluorescence imaging collected using a state-of-the-art combined Brillouin-Fluorescence microscopy system.
3. To develop novel numerical and analytical methods for processing of Brillouin and fluorescence data, including classification, principle component and clustering machine learning methods.
4. To combine all the aforementioned methods to develop and deploy a micromechanical imaging biopsy system for real-time tumour tissue diagnostics.

Research Environment:

University of Technology Sydney, School of Mathematical and Physical Sciences

 University of Technology Sydney (UTS) is #1 young University in Australia and within the top 100 Universities worldwide. The School of Mathematical and Physical Sciences @UTS has a rich research and teaching culture placing it at the forefront of technological challenge. The School’s emphasis is in the delivery of quality research-informed and practice-based higher education to produce the scientists of the future in health technologies, energy, defence and space. A/Prof Irina Kabakova is Australia’s expert in Brillouin microscopy and runs an independent research group supported by extensive portfolio of internal and external research funding. Irina’s goal is to transform biomedical diagnostics by introducing novel imaging technologies based on multimodal and Brillouin imaging.

The ARC Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS)

Optical frequency combs hold remarkable promise for reshaping the realms of precision measurements, high-speed communication, sensing, and astronomical discovery. Recent advances in nanofabrication make it possible to miniaturise bulky optical and electronic systems onto microchips, thus streamlining the production and reducing costs. This emerging Microcomb technology holds the key to unlocking the full potential of optical frequency combs. By joining the ARC Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS), you will play an important role in developing these microcomb technologies to transform science and society. COMBS is a large dynamic, diverse and inclusive community that spans across Australia and beyond. As a member of COMBS, you will have the opportunity to work with other COMBS scientists within the eight Australian Universities network, take advantage of internships with industry and our many international partners in Europe, Asia and the US. There will be many opportunities for learning through workshops, technology translation and entrepreneurship bootcamps, and access to top photonics scientists. COMBS values equity, diversity, inclusion, and access, and we recognise the importance of intersectionality. We are committed to creating an environment that embraces and harnesses these intersections to do the best science we can. We invite you to join us to become part of the diverse and inclusive COMBS community. 

Garvan Institute of Medical Research 

The Garvan Institute of Medical Research brings together world-leading researchers and clinicians, collaborating locally and globally, to improve human health. From the individual patient with rare disease, to the many thousands affected by complex, widespread illnesssuch as cancer, our researchers are pioneering discoveries across the diseases that have the deepest impact on our community. As a higher degree research student at Garvan, you’ll be immersed in a program of independent and original research and have access to Garvan’s state-of-the-art research facilities, which incorporate a range of cutting-edge equipment and expertise. A/Prof. Thomas Cox is a cancer cell biologist and one of Australia’s leaders in the field of the extracellular matrix and matrix remodelling in the progression of solid tumours. Thomas currently leads the Matrix and Metastasis Lab, part of the Cancer Ecosystems Program at the Garvan Institute and Kinghorn Cancer Centre (https://www.garvan.org.au/people/researchers/thomas-cox). The labs creative research program integrates matrix biology with precision oncology, to make fundamental advances in personalised stromal targeting of solid tumours. This unique collaboration will allow you to master skills in advanced imaging approaches and their application into the real world setting of cancer research.

How to apply: Please submit your expression of interest via email to irina.kabakova@uts.edu.au. The expression of interest must include: 1) a cover letter stating why you are interested in the position, 2) a CV to address your suitability, 3) a digital copy of your degree transcript with grades.