Bioengineering

At the Murdoch Children's Research Institute, internationally recognised Clinicians and Biomedical Scientists are looking to work with Engineering, Mathematics and Physics graduates in multi-disciplinary projects to drive innovation in many different areas of research.

Project are available for students studying towards a PhD, Masters, Honours or 4th Year placements. Contact Supervisors about the project to find out more details.

Our website has more information about studying Honours, Masters and PhD.

Bioengineer Researchers desireable skills: 

Computer programming

Mathematical modelling

Fluid Dynamics

Scientific computing

Electronics

Human movement science – Biomechanics

Developing software to capture and analyse data

Electrical Engineering

Biomedical Engineering (Chemistry or Biochemistry)

Chemical Engineering

Mechanical engineering

Treatment and analysis of image/imaging

Scientific writing

Bioengineering Project List:

B1. Prospective motion correction for MRI

B4. Development of a neuroimaging toolbox to understand typical and atypical development of the infant brain

B5. Heart structure and mechanics in children with a single ventricle

B6. Modelling cardiovascular instability at birth in vulnerable infants

B7. Childhood cardiovascular development and adaptation

B8. 4D flow MRI for assessment of childhood aortic abnormalities

B9. SMART Nappy: Novel low cost point-of-care diagnostics for premature babies

B10. Inhaled Vaccines: Aerosol delivery of novel vaccines to the infant lung

B11. LaxCal- an APP to calculate laxative dose

B12. Multimodal Neuroimaging of Children - Projects in Typical Brain Development Or ADHD

Bioengineering Project Descriptions:
B1. Prospective motion correction for MRI.

Dr Richard Beare

Senior Research Officer

Clinical Sciences

Developmental Imaging

richard.beare@mcri.edu.au
 

MRI scans are very badly affected by patient movement, with even small amounts of movement leading to useless scans. This is an even bigger problem with new scanning protocols that can run for many minutes.

Real time tracking of a patient's head can be used to provide extra information to the MRI scanner that corrects for some of this motion. However MRI is a challenging environment for traditional optical trackers, with MRI safety and compatibility, clinical practicality and limited space all being problems.

This project will involve modelling and design of head tracking systems using non-standard optical sensors. Initial stages will examine the types of information that can be extracted using these sensors and will construct a lab prototype.

 

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B4. Development of a neuroimaging toolbox to understand typical and atypical development of the infant brain

The aim of this study is to develop software tools that will easily and accurately measure infant brain regions, structures and tissues from magnetic resonance imaging (MRI) scans.

Current MRI methods are mostly fine-tuned for adult brain images, and do not easily translate to infants. There is no available software specific for infants that can assess the structural characteristics of multiple brain tissues and regions.

Due to a lack of research tools to evaluate the infant brain, many important developmental diseases are understudied. This is despite the fact that early intervention will give the best chance of minimising the effects of brain abnormality and injury to improve outcomes for the child.

Development of novel MRI analysis tools is currently being undertaken by the Victorian Infant Brain Studies (VIBeS) neuroimaging team, led by Dr Deanne Thompson in collaboration with the Developmental Imaging group at the Murdoch Children's Research Institute. A morphology-driven automatic neonatal brain segmentation, MANTiS, has just been developed, which classifies a T2 structural MRI of the brain into white matter, cortical gray matter, cerebrospinal fluid, deep nuclear gray matter, brainstem, hippocampus, amygdala, and cerebellum (Beare et al., Frontiers in Neuroinformatics, 2016).

A first-of-its-kind neonatal atlas of regional brain structures, the Melbourne Children’s Regional Infant Brain (M-CRIB) atlas, has also been developed (Alexander et al, NeuroImage, Under Revision). Application of this atlas to MRI scans will allow the sub-division and measurement of 100 neonatal brain regions, including 34 cortical regions per hemisphere based on the Desikan-Killiany adult brain atlas available in the commonly used ‘FreeSurfer’ software (Desikan et al., NeuroImage, 2006), the basal ganglia and thalamus, and vermis and hemispheres of the cerebellum.

This project will involve programming our segmentation and brain sub-division techniques into an easy to use software toolbox. Ultimately this software toolbox will be made available to researchers and clinicians, leading to better diagnosis of brain conditions in high-risk infants, and may inform new treatment and intervention strategies.

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B5. Heart structure and mechanics in children with a single ventricle

Each year, at least 30 children are born in Australia with a form of congenital heart disease that means only one of the two heart pumps (ventricles) is functionally viable. Currently, the best chance of survival comes with a series of three complex operations that result in a Fontan circulation, where a single ventricle pumps blood to the body, and the major veins are connected directly to the pulmonary arteries to supply lung blood flow. Although medium-term survival is improving, these patients have reduced exercise capacity and a significant risk of heart failure.

In this project, the student will analyse magnetic resonance imaging data acquired at the Royal Children’s Hospital before and after exercise in children with a Fontan circulation. Three-dimensional models of the contracting heart and its chambers will be constructed from patient data in collaboration with the Department of Mechanical Engineering (University of Melbourne). Heart deformation will be assessed to quantify cardiac strain patterns, with the aim of improving clinical assessment of heart function and risk of complications in this complex disease.

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B6. Modelling cardiovascular instability at birth in vulnerable infants

Birth is arguably the most crucial and most complex event of life. Immediately after birth, rapid and profound changes occur in the cardiovascular system to facilitate the shift from placental respiration to breathing with the lungs. However, premature birth, congenital heart disease and/or birth complications (such as fetal or newborn asphyxia) can cause problems with the birth transition that may have long lasting consequences for the child (e.g. brain damage, requirements for intensive care, greater long-term risk of cardiovascular disease). The precise nature of the perinatal cardiovascular complications, and how they might be treated better or avoided altogether, are very difficult to study in human babies due to ethical and practical constraints.

In this PhD project, the student will develop a state-of-the-art computational modelling platform for studying the birth transition and challenges encountered by vulnerable infants. A key benefit of a modelling approach is the lack of ethical constraints and great flexibility in studying the problem. The project will be integrated with world-leading work by our group on fetal modelling and experimental studies of the birth transition in lambs, and will benefit from our links with the neonatal intensive care unit at the Royal Children’s Hospital.

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B7. Childhood cardiovascular development and adaptation

It is increasingly being recognised that the precursors to adult cardiovascular disease begin in childhood. However, we currently have limited information about the normal development of the cardiovascular system during childhood and how this normal development is interrupted by problems such as congenital heart disease. One-dimensional modelling is a powerful tool for investigating the cardiovascular system but, surprisingly, no models of the growing circulation exist.

Based on existing state-of-the-art models of the adult and newborn cardiovascular systems, the student will develop methods for incorporating childhood growth and physiological development. The model will be validated against measurements in children. The resulting model will allow simulation of blood pressure and flow throughout the circulation of a representative normal child at any time during childhood. By perturbing parameters of the normal development model, new insights will be gained into problems faced by children with congenital heart disease and why some children have a high risk of developing cardiovascular disease as adults.

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B8. 4D flow MRI for assessment of childhood aortic abnormalities

In many forms of congenital heart disease, disturbed blood flow patterns arise from abnormal vascular anatomy or heart function. This causes two fundamental and interrelated haemodynamic problems, 1) flow turbulence, which causes dissipation of fluid energy and harms endothelial cells that form the inner lining of vessel walls and 2) pressure losses, which increase workload on the heart, increase stress on vessel walls, and/or reduce or adversely redistribute blood flow to organs and tissues. These factors in turn lead to secondary cardiovascular diseases or complications. While routine clinical imaging techniques may in some cases detect turbulence or implicate pressure losses, they cannot accurately map and quantify them. Two recently described magnetic resonance imaging (MRI) techniques enable quantitative mapping of turbulence and relative pressure in 2 or 3 dimensions over time, promising unprecedented insights into disturbed flow patterns.

In this project, the student will develop and validate computational tools for calculating turbulence and relative pressure maps from 4D (i.e. 3D + time) phase-contrast MRI in patients with congenital heart disease. The key aim will be developing novel MRI-based measurements that provide added value to cardiologists who are treating cardiovascular disease in childhood.

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B9. SMART Nappy: Novel low cost point-of-care diagnostics for premature babies

Honours/Masters:

THE PROBLEM:  Accurate, low-cost, point-of-care diagnostics for premature babies are severely lacking in resource-limited rural settings. This leads to poor monitoring and late diagnoses of high risk premature babies that could otherwise have a healthy start to life. This type of diagnostics will radically change the way health care is delivered by shifting the focus from a lab-based diagnostic paradigm to an onsite, real-time diagnosis.

THE PROJECT: To improve rural health care for newborns is to develop accurate, low-cost diagnostics for newborns that will be used to detect and enable proper clinical management of the disorders. These point-of-care diagnostics require only a drop of blood or urine and require no additional steps beyond applying the sample. This means that they can be utilized by minimally-trained individuals in communities or clinics in rural settings to allow better patient management.

TECHNIQUES:  The student will use biochemical sensing methods to quantify the biomarkers. The techniques developed will be validated against gold standard methods of diagnosis.  This project is a collaborative effort between Engineering, Chemistry and Clinical sciences. There may be an opportunity to develop clean room techniques related to nanofabrication. Candidates with a strong background in Biomedical Engineering (Chemistry or Biochemistry) or other relevant Chemical Engineering expertise is encouraged to apply.

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B10. Inhaled Vaccines: Aerosol delivery of novel vaccines to the infant lung

Honours/Masters:

THE PROBLEM: The development of a safe and effective aerosol vaccine delivery platform that would be comparable to intravenous delivery has been a considerable challenge to the health care industry. Potentially, this represents a rapid response solution to pandemic disease outbreaks, especially in the developing world.  Existing aerosol delivery systems struggle to maintain biomolecule stability and ensure retention of the structure as per regulatory requirements.  Our team has developed a novel aerosol delivery system does not produce these disruptive processes, and we have shown that the nebuliser can efficiently deliver pulmonary vaccines in an adult sheep model.

THE PROJECT:  The student will conduct studies to determine if vaccine delivery via the aerosol route will induce a strong mucosal immune response, within the lung, and a robust systemic immune response compared to alternative routes of delivery in an infant lamb model.

TECHNIQUES: The student will use immunological assays such as ELISA and molecular assays to validate the immune responses.  Students will work closely with a team of molecular biologists, clinicians (neonatologists) and engineers. Candidates with a strong background in biomedical Engineering (interest in immunology) or other relevant engineering expertise is encouraged to apply.

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B11. LaxCal- an APP to calculate laxative dose

How do you know how much laxative to take each day? If you or your child has chronic constipation, this is an ongoing problem. The wrong dose means not enough poo and the problem gets bigger. Poo builds up in your rectum.

We have developed a program that calculates the dose based on:

  • How much poo you did yesterday
  • How hard the poo was
  • How much laxative you took.

We have tested it as part of a trial of over 100 children with chronic constipation. Parents found it very helpful and wish to keep using it.

We developed it in the software that the statisticians use for clinical trials. As you can expect, this is not a widely used program. Parents have called for a mobile device version.

This project will take the program from stats to APPS.

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B12. Multimodal Neuroimaging of Children - Projects in Typical Brain Development Or ADHD

Projects are available on the NICAP dataset (Neuroimaging of the Children’s Attention Project). Using state-of–art methods for multi-modal MRI neuroimaging, with detailed neuropsychological data of a large sample of children with ADHD and healthy controls. Projects are available in modeling how brain structure and function develops, or is different in children with ADHD. We seek students with a strong academic track record and interest/experience in neuroimaging analysis.

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