Summer projects in the Auckland Bioengineering Institute

Search for Summer Research Scholarships projects in the Auckland Bioengineering Institute (ABI).

Next generation drug injectors


Project code: ABI001

Our Bioinstrumentation laboratory has developed needle-free liquid drug injectors that are actuated by controllable, quiet, and reversible linear motors. We tightly control the motion of the motor throughout the entire process of injection; this approach allows us excellent control over the speed and volume of jet drug delivery.

In this project we plan to explore some novel, exciting and potentially very valuable ideas for reducing the size/mass of our devices, and controlling the way that our fluid jets interact with the tissues that they penetrate. This work will involve designing and prototyping devices in our well-equipped bioinstrumentation laboratory, and testing their performance using high-speed imaging. You will work as part of a dynamic team of postgraduate students, with support from technical staff. This work would particularly suit a student of Engineering Science, Biomedical Engineering, or Mechanical/Mechatronics Engineering.

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Electronically controllable model of the heart’s vasculature


Project code: ABI002

During each heart-beat, the left ventricle develops pressure against the fluid impedance presented by the systemic vasculature. We have created an electronic system that computes a hardware-based lumped parameter model of the vasculature. We now wish to use the output of this model to regulate, in real-time and beat-by-beat, the flow leaving the left ventricle of an isolated beating rat heart. We will achieve this by using the model output to control an electronic valve that you will develop, or purchase, and which will be added to our working-heart apparatus.

This is an exciting project which will be suitable for an Biomedical Engineering student, or similar, who wants to learn about real-time programming, motor control and data acquisition in LabVIEW RealTime and FPGA environments. The project will provide the opportunity for you to work with physiologists, and see the outcomes of your project applied to a living experimental specimen in a laboratory environment.

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Needle-free Diabetes Management


Project code: ABI003

Diabetes is a worldwide health problem; on a high level, it is a condition that results in blood glucose concentrations higher or lower than the normal range. A tight monitoring of the blood glucose concentration is necessary for management of this disease. Today, self-monitoring devices used for this purpose require patients to lance their finger to obtain the required blood sample. This lancing process is associated with pain, scarring, and the risk of infection, leading to poor patient compliance with recommended testing regimens.

We have developed a jet injection process that can allow for the injection of drugs and/or the extraction of blood without the use of a needle or lancet. Thus, we are developing a jet injection instrument that can combine the processes of extraction of blood, measurement of glucose concentration and insulin therapy. All these processes are performed through a single orifice. This device first uses a jet of fluid to penetrate the skin and disrupt the capillary bed. Suction is then applied, extracting a mixture of blood and injected fluid whose glucose concentration is measured by a sensor. If the glucose concentration is higher than normal, insulin would be delivered using a second jet. The goal of this summer project is to integrate the sensor with the jet injector instrument.

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Curation and annotation of mathematical models and simulation experiments


Project code: ABI004

At the 38th World Congress of International Union of Physiological Sciences, to be held August 2017 in Brazil, the IUPS will launch the PHYSIOME journal. The primary goals for establishing PHYSIOME are to encourage and reward scientists for making their biomedical models available in a reproducible and reusable form. This is achieved by encoding the models and associated simulation experiments in standard formats, and annotating those data with sufficient biological knowledge to ensure other scientists are able to make informed decisions when reusing published models.

 

The Auckland Bioengineering Institute has been involved in establishing PHYSIOME, as well as contributing to the development of the required standard formats. The ABI manages the repository which will form the core archiving and distribution platform for PHYSIOME. In preparation for the launch next August, we have embarked on a process of curating and annotating the more than 600 mathematical models already published in the repository in the standard CellML format. We are also now starting to add descriptions of the simulation experiments in the standard SED-ML format to supplement the models and make them truly reproducible.

This project will require the student to work with scientists at the ABI to curate published CellML models and annotate them with biological knowledge from the original literature. The project will suit students who are keen to gain an exposure to a wide range of domains across the physiological sciences, varied modelling techniques, and numerical simulation algorithms.

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Estimating diffusion coefficient in lung acinus


Project code: ABI005

Skills needed: Mathematical modelling; Computer simulation.

Early-stage lung disease often affects lung alveoli, which are too small to see in clinical imaging. If we could detect this early disease using simple tests we could potentially better manage disease and avoid misdiagnosis. Apparent diffusion coefficients (ADC) of gases in the lungs aim to provide direct measure of lung disease and can be correlated with abnormalities in lung structure. Interpretations of ADC measurements are currently difficult, because the theory that compares ADC to lung structure is highly simplified. This project aims to compute ADC in geometries reflective of the lung’s micro-structure. You will assess how ADC is influenced by alveolar size and shape to determine to what extent it is possible to classify patients based on ADC in the young and aging populations.

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Develop a LEAP Motion Controller-based Virtual Reality application


Project code: ABI006

Supervisor

Dr Harvey Ho

The Leap Motion system recognizes and tracks hands and fingers. Its motion controller uses optical sensors and infrared light. The system functions well when the controller has a clear, high-contrast view of an object's silhouette. This feature has been used in many virtual reality (VR) applications (for examples please refer to https://developer.leapmotion.com/gallery).

The aim of this project is to develop a VR application based on the Leap Motion SDK. In the application a surgeon's hands and fingers will be simulated to interact with a virtual organ (e.g., a liver). The student is expected to do some programming (in C++, Unity or Python) and to operate a Leap motion controller and an Oculus Kit provided. A background in computer science or relevant engineering disciplines is desirable. Pilot studies have been performed in our group in this area so the student can learn from these previous projects.

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A novel approach to measure the energy efficiency of the biventricular working rat heart


Project code: ABI007

With each beat, the heart performs pressure‑volume work while consuming oxygen. Thus, its efficiency is simply the ratio of work output to energy consumed. However, the anatomy of the rat heart presents a difficulty to allow oxygen consumption to be measured while both of the ventricles are working. This is because the coronary venous effluent is mixed with the fluid pumped out by the right ventricle. An approach to resolve this limitation would be to design a cannula system inserted into the rat heart in order to separate the coronary effluent from the right‑ventricular outflow.

 

If successful, this cannula system would be the first to allow the efficiency of the rat heart to be quantified while its ventricles are simultaneously pumping. Such a novel apparatus would open many new and exciting areas of enquiry in the field of cardiac energetics.

This project is suitable for a Biomedical Engineering student, or similar, who has a strong interest in bio‑instrumentation design and in living‑specimen experimentation. It will provide the opportunity for you to perform experiments using our working‑heart rig, to design and implement a cannula system for the rat heart, to measure work output and oxygen consumption, and hence to be the first to measure the mechanical efficiency of the biventricular‑working rat heart. Journal publications will surely follow.

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Structural Characterization of Explanted Intact Human Atria


Project code: ABI008

Supervisor

Dr. Jichao Zhao

Atrial fibrillation (AF) is the most common heart rhythm disturbance in industrialized countries, and structural remodelling plays a crucial role in sustaining AF. Estimating the structural characteristics across the two atrial chambers is a challenging task in the past due to extremely complex and thin atrial wall and low resolution of human atria acquired clinically.

 

This work is made possible by the collaboration with our overseas collaborators for accessing explanted intact human hearts with a history of AF or heart failure using high resolution gadolinium enhanced (GE-MRI) (9.4T). In this project, the student will systematically analyse one human heart imaged using GE-MRI: 1) 3D human atrial myofibre architecture; 2) fibrosis distribution; and 3) wall thickness variation. More importantly, the student needs to compare the results from this heart to the two human atria we have studied recently.

This project will be suitable for students interested in imaging, programming and analysis using a computer software, particularly Matlab.

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Quantification of colonic motility patterns in response to neuromodulation


Neuromodulation is becoming an increasing therapy for chronic conditions. One of the recent application of neurostimulation is in treating fecal incontinence, which affects up to 12% of the population. It is an effective therapy with up to 80% success rate, however the mechanism involve in treatment is still debated. It is anticipated that with an improved understating of the effects of neurostimulation, the success rates could be improved. Recent developments in manometry has allowed for high-resolution spatial recordings which is starting to allow to define normal and pathophysiological mechanisms in the colonic system

The aim of the project is to develop automated methods to define and classify colonic motor patters. The challenge will to be analyse high-resolution data over a long period of time (e.g 2 to 5 days) and display the results in an intuitive format. The outcome will be an important step towards a clinical system that will be used in a hospital setting.

The student should have strong programming skills, preferably in Matlab, Python and/or C++, with interest in machine learning and classification, and signal and image processing. It would be ideal if the student has some exposure to physiology and interest in experimental techniques, but not necessary.

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Many eyes make light work


Project code: ABI010

Stereo imaging systems typically consist of a pair of closely-spaced cameras designed to image objects from slightly different directions. This leads to significant inaccuracies in depth estimation because the two views are similar and the algorithms used to correlate the images perform relatively poorly. We have recently developed an image registration algorithm that is considerably more accurate, robust, and efficient than any other published method. This project will explore the use of this new algorithm on a multicamera (≥4) imaging system to obtain very accurate geometric measurements. The outcome will be an imaging device that will accept an object and return an accurate representation of its geometry.

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Torques softly


Project code: ABI011

Measurement of dynamic forces and torques generated by the foot striking the ground are of great interest to both sport science and clinicians assessing the gait of patients with problems of movement. Current force platforms are expensive, putting them beyond the reach of most trainers and clinics. We have developed a new method for measuring force, based on highly anisotropic elastomers constraining a volume of incompressible fluid. These devices are cheap to construct and may be readily arranged into a configuration that can simultaneously measure all 6 components of force and torque. The outcome of this project will be a relatively inexpensive, low-profile platform capable of measuring dynamic forces and torques generated by the foot.

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Effects of gastric pacing with varying frequencies on underlying slow wave activity


Project code: ABI012

Stomach motility (contractions) is initiated in part by an underlying biological electrical activity called slow waves. Gastric motility disorders have been associated with abnormal slow wave electrical activity (gastric dysrhythmias). Gastric pacing is a potential therapy for gastric dysrhythmias; however, new pacing protocols are required that can effectively modulate motility patterns, while being power efficient.

Mathematical and computer models of organs are being used to help understand underlying electrophysiology of different organs. The aim of the project is to mathematically model and validate the effects of external pacing of varying protocols such as frequency and amplitude on underlying electrical activity on a sample tissue model.

Prerequisite

The student should have an interest in mathematics, biophysical modelling, experimental data-analysis, and high-performance computing.

The student should have some experience or interests in finite-element analysis, object oriented programming (e.g. C++), interests in mathematical modelling and electrophysiology.

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Investigating the effects of muscle fibres on slow wave activity generated by Interstitial Cells of Cajal network


Project code: ABI013

Motility in the stomach is initiated in part by an underlying biological electrical activity called slow waves. The slow waves are generated and actively propagated by specialised pacemaker cells called Interstitial Cells of Cajal. The activity is passively conducted to surrounding smooth muscle layers resulting in contractions.

Understanding the effects of the different muscle layer orientations on the underlying slow wave patterns is important to identify diagnostic and predictive tools for therapeutic purposes.

Mathematical and computer models of organs are used to help understand human health. Slow wave activity simulations over anatomically realistic stomach geometry have been proposed to identify underlying physiological mechanism and relate to the pathophysiology in diseased states.

The aim of the project is to investigate mathematically the effects of gastric muscle fibres in the wall of the stomach on underlying slow wave activity.

Prerequisite

The student should have an interest in mathematics, biophysical modelling, high performance computing and large data analysis.

The student should have some experience or interests in finite-element analysis, object oriented programming (e.g. C++), interests in mathematical modelling and electrophysiology.

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New visualisation methods for high-resolution electrical mapping data from the gastrointestinal tract


Project code: ABI014

Slow wave activation map

Figure 1: Slow wave activation map (right) from a recording of normal propagation, according with the electrode array position.

Contractions of the gastrointestinal (GI) tract are controlled by rhythmic, propagating electrical events, termed ‘slow waves’. Recent development and translation of high-resolution GI mapping, where slow wave activity is recorded simultaneously across a dense array of hundreds of electrodes placed directly on the stomach, has helped develop a vastly improved understanding of spatial slow wave conduction patterns. The recent discovery and classification of abnormal slow wave conduction (‘dysrhythmias’) associated with severe gastric diseases has now fuelled interest toward developing a wider range of diagnostic devices for gastric mapping.

To accurately visualise the high-resolution mapping data, spatial maps of the activation times must be constructed across the geometry of the electrode array (Figure 1). Current mapping algorithms rely on a regular grid of uniform electrode spacing, and represent the propagation as distinct temporal colour bands.

This project aims to improve the current mapping algorithms by developing visualisation techniques to map slow wave propagation from electrode arrays of non-uniform spacing, and also to ‘smooth’ the activation colour map. Applicants should ideally have a strong interest and background in bioengineering, programming and mathematics with experimental validation, and experimental electrophysiology. The successful applicant will have the opportunity to work closely with leading bioengineers and clinicians at the Auckland Bioengineering Institute, primarily working with Drs Tim Angeli and Niranchan Paskaranandavadivel.

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Physical Simulations for Training in Robotic Surgery


Physical Simulations for Training in Robotic Surgery

Project code:  MHS031

Department

  • Surgery

Location

Auckland

The University of Auckland Bioengineering Institute has been gifted a Da Vinci Surgical Robot after it was decomissioned from a local private hospital. This gift could provide an opportunity for surgical students and trainees to gain basic experience and skills in robotic surgery, including use of controls, tissue handling, and suturing, before beginning to use robotic surgery in patients. In order to make use of this opportunity, validated physical simulations are required for use in effective training exercises.

The aim of this studentship will be to:
1. Conduct a review of physical (i.e. real and not ‘virtual’ or software-based) simulation systems and ‘games’ currently in use for training in minimally-invasive and robotic surgery.
2. Develop low-cost physical simulations for training in robotic surgery, e.g. for learning handling, grasping, stacking, suturing skills.
3. Validate the educational utility of the developed simulations with the help of medical student and surgical trainee volunteers.
 

Skills

This is a surgical / clinical education project, teaching simulation development, skills training and educational validation.  The use of surgical simulators is a rapidly developing field, and the studentship offers the chance to experience this area of research.  The project would suit students with a strong practical aptitude, and an interest in surgery, education, and bioengineering.

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How do changes in geometrical complexity and landmark of the crystalline lens influence its fluid dynamics?


How do changes in geometrical complexity and landmark of the crystalline lens influence its fluid dynamics?

Project code:  MHS033

Department

Optometry and Vision Science

Location

Auckland

Supervisor

Ehsan Vaghefi

The crystalline lens plays an important role in allowing light to be fine focused onto the retina which allows us to perceive the world around us.
The complexity and distinct geometrical features of the crystalline lens is what allows this to happen.
We have already implemented a base model of the crystalline lens anatomy and fluid dynamics.
We are now interested in improving the model by adding more ultra-structural details of the lens anatomy.

In this project, we aim to examine how a range of different geometrical landmarks of the crystalline lens influence its fluid flow. The geometrical landmarks of interest are:

  1. Lens capsule
  2. Inner cortex barrier region
  3. Star sutures

Specific Aims

  1. To build upon the candidates’ understanding of lens anatomy and basic principle of CAD and CFD modelling.
  2. To examine how the addition of lens capsule would affect fluid flow in the lens.
  3. To examine how the alteration of the inner cortex barrier region affect fluid flow in the lens.
  4. To examine different profiles of the star sutures and how they influence fluid flow in the lens.
  5. Report on all findings with an appropriate form of documentation.

Skills

By the end of the project, the candidate will have a clearer understanding on the anatomy of the crystalline lens, the ability to design and create a 3D CAD model, as well as basic Computational Fluid Dynamics modelling principles.

Timeline

  • The candidate should consolidate their understanding of crystalline lens anatomy, basic principle of CAD modelling and Computational Fluid Dynamics in the first 3 weeks.
  • The candidate can then build on top of an existing CAD crystalline lens model by altering the geometry by adding firstly a lens capsule (5 weeks), the inner cortex barrier region (6 weeks), and finally examining different profiles of the star sutures (8 weeks) to see how each geometrical landmark influences fluid flow in the lens using the CFD model.
  • Any documentation to be completed in the last 2 weeks of the internship.

Laser ray tracing for measurement of ocular lens gradient refractive index


Laser ray tracing for measurement of ocular lens gradient refractive index

Project code:  MHS044

Department

Optometry and Vision Science

Location

Auckland

Supervisor

Ehsan Vaghefi

In a series of previous experiments utilizing Magnetic Resonance Imaging the Molecular Vision Lab (MVL) has shown that the optics of the lens is actively maintained by a circulating flux of ions and water that is generated by its unique cellular physiology. In order to get a better understanding of the connection between lens physiology and optics, we need to first accurately measure such optical changes when the physiology is pharmacologically altered. In order to achieve this, the MVL has setup a custom built laser ray tracing (LRT) system that allows us to reconstruct the gradient index (GRIN) of the lens. However, this system can be improved in several ways, which are the aims of this summer studentship

1.       Further development of our newly built LRT by improving the accuracy in the extraction of data, introducing more sophisticated retrieval algorithms and streamlining overall experimental protocols

2.       Physiological challenge the lens and then measure their optical properties

3.       Improve image processing of LRT images

4.       Develop new MATLAB code for improved GRIN reconstruction

Skills

The student should have a sound knowledge of programming in MATLAB, and interested in the lab work aspect of the project as well. The ultimate goal of this research is to have an improved understanding of how changes in the ocular lens physiology will influence the optics (i.e. GRIN) of the lens.

Beat the leak: A new device designed for pelvic floor muscle training


Beat the leak: A new device designed for pelvic floor muscle training


Project code:  SCI244

Department

Statistics

We are developing a smart novel device, designed to assist women with their pelvic floor muscle exercises. The FemFit is an intra-vaginal pressure sensor which is ‘wearable’ and capable of measuring pressures from the abdomen and the pelvic floor during exercise and activities of daily living. The FemFit consists of an array of eight pressure sensors which transmit pressure signals via Bluetooth to an android device. Each sensor samples pressure at ~100Hz. We are at the point of testing the repeatability and reliability of the FemFit in a population of healthy women.

A student is required to undertake analysis of the data from the sensors, with a particular emphasis on the repeatability of the measurements.

This is a combined project with the Auckland Bioengineering Institute and would be of interest to a student who is capable of dealing with large data sets, and with a genuine interest in clinical research. This is a great opportunity to experience being involved at an early stage in research, and to contribute to the development of the FemFit. A knowledge of physiology to help interpret the in-vivo data would be helpful, as would experience in Matlab.

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