Auckland Bioengineering Institute summer research projects

Browse the range of summer research projects on offer in the Auckland Bioengineering Institute.

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MicroCT imaging for liver tissues


Supervisor

Dr Harvey Ho
Dr Shawn Means

Discipline

Auckland Bioengineering Institute

Project code: ABI001

The liver environment is intrinsically spatially heterogeneous, where hepatic lobe structure is divided per oxygen- and nutrient-rich zones according to proximity with the portal triad. In silico modeling of hepatic drug perfusion further demonstrates a subtle impact of spatial distributions for hepatocyte steatosis (fatty liver). These variant physical and spatial components are being investigated in Auckland Bioengineering Institute (ABI) in multi-scale mathematical models. The aim of this study is to establish the imaging protocols of microCT, including the tissue preparation methods (fixation and staining) and imaging processing techniques, to visualise the 3D spatial heterogeneity of liver tissues at the lobular level. We will use the microCT scanner in ABI which has a high resolution (sub-micrometre) and can yield subtle micro-structures of the liver. This project suits a student with a science or engineering background.

3D printed muscle actuators


Supervisor

Andrew Taberner

Discipline

Auckland Bioengineering Institute

Project code: ABI002

Isolated cardiac myocytes are self contained biological actuators that can readily be isolated from the tissues of the heart. In this project, we plan to use existing techniques for isolated cardiac myocytes and to explore ideas for reusing the myocytes in functional 2D and 3D structures.

Project aims

  • Implement techniques for myocyte isolation and handling, using tissues provided by ABI cardiac team.
  • Explore techniques for encapsulating and patterning the myocytes in 2D structures.
  • Implement existing techniques for testing the contractile performance of these structures. 

Jet-tissue interaction in needle-free jet injection


Supervisor

Andrew Taberner

Discipline

Auckland Bioengineering Institute

Project code: ABI003

Jet injection is a well-established technique for achieving subcutaneous and intramuscular drug delivery without requiring the use of needles. During injection, the liquid jet creates a pathway through the skin into the underlying tissues. What effect does this process have on the tissues at the cellular (~1 µm) scale? Is it possible to develop techniques for imaging the disruption to the tissues surrounding the jet path?

Project aims

 Work with ABI imaging experts to develop a technique for obtaining high-resolution MicroCT images of tissue structure in post-mortem pig skin.

  • Use an existing jet injection system to perform shallow injections into skin samples
  • Repeat tissue imaging, post-injection, and the examine changes in tissue morphology
  • Explore the use of other destructive post-injection imaging techniques for imaging tissue damage

Tissue cutting with a jet injector


Supervisor

Andrew Taberner

Discipline

Auckland Bioengineering Institute

Project code: ABI004

A water jet cutter is a device that uses a narrow, high pressure liquid jet to slice through materials such as wood, rubber, and other soft materials. The addition of abrasive powder to the liquid allows cutting of harder materials such metal and stone. A needle-free jet injector can be thought of as a stationary water jet cutter. What might happen if we deliberately move an injector across the surface of biological tissue, while jet-injecting liquid? Can we use such an approach to engrave shallow incisions in the surface of skin, or cut sections from other biological tissues?

Project aims

  • Control an existing two-axis stepper motor system for moving a sample of post-mortem tissue
  • Synchronise the motors with a controllable jet injector
  • Perform jet injections into skin or through pericardium, while translating the tissue
  • Image and analyse the resulting incisions. 

Curation and annotation of mathematical models and simulation experiments


Supervisor

David Nickerson
Peter Hunter

Discipline

Auckland Bioengineering Institute

Project code: ABI005

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 best 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. Leading up to the launch in August, we 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 adding descriptions of the simulation experiments in the standard SED-ML format to supplement the models and make them truly reproducible. Given the large number of models, the variety of physiological systems being modelled, and the refining of our approaches, this is an ongoing project at the ABI.

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.

Modelling microbial biofilms on open wounds


Supervisor

Jagir Hussan

Discipline

Auckland Bioengineering Institute

Project code: ABI006

The interaction between the microbial population and the skin resident immune system is important for normal skin function and this interaction plays a critical role when wound healing occurs.

We have developed a large scale agent based modelling framework to model microbial interactions.

In this project we will apply this framework to modelling the dynamics of known microbial population on open wounds.  Specifically, develop a model where the agents generate biofilms based on the molecular and biomechanical interactions.

This system has been widely studied and has a rich literature base that can be used to validate and measure the effectiveness of our model and the modelling framework. Experiences from applying the modelling framework to such systems will also feed into the future feature development goals for the framework.

An ideal candidate would be someone who is interested in computer modelling of biological systems with the acuity to analyse complex systems. 

Robust segmentation of contrast enhanced MRIs using machine learning


Supervisor

Dr. Jichao Zhao
Dr. Martin Stiles

Discipline

Auckland Bioengineering Institute

Project code: ABI007

Atrial fibrillation (AF) is the most common arrhythmia, and current treatment is suboptimal. Accurate representation of the 3D atrial anatomy and its underlying structure from medical images (CT/MRI) provides an effective, patient-specific approach for clinical diagnosis of atrial scar and targeted treatment for patients with AF. The automatic segmentation of the atria to visualize its geometry in 3D is a challenging task.

A gadolinium-enhanced (GE)-MRI dataset (N=60), with a spatial resolution of 0.625x0.625x1.25 mm³ for patients with AF (provided by the University of Utah), will be used to develop a deep convolutional neural network to recognize features specific to atrial and non-atrial tissue, and to segment atria in 3D. The student is expected to further develop the machine learning approach for segmentation.

This project will be suitable for students interested in programming and analysis using a computer software, such as python 3 or Matlab.

Better representation and understanding of atrial myofibre structure


Supervisor

Dr. Jichao Zhao

Discipline

Auckland Bioengineering Institute

Project code: ABI008

Analysing cardiac myofibre structure can improve our understanding of preferential electrical pathways under normal and diseased conditions. Potentially it can be used to explain why some regions of the heart are prone to trigger or sustain arrhythmias than other regions.

This study aims to further develop computational tools to facilitate analysis of cardiac myofibres using the gradient-based structure tensor approach developed in our lab. The structure tensor method utilizes the colour intensity variation of the original images and 3D eigen-analysis to estimate 3D fibre orientations by modelling the local fibre alignment as the orientation with the least signal variation. Particularly, the student is expected to develop a robust clustering tool to group myofibre orientations across atrial chambers into different groups. Also the student is expected to conduct high resolution diffusion tensor and micro Xray computed tomography imaging (DTI and micro-CT) of the same large animal heart (such as sheep) for validation purpose.

This project will be suitable for students interested in programming and analysis using a computer software, such as C or Matlab.

Simultaneous measurement of gut contractions and electrophysiology


Supervisor

Niranchan Paskaranandavadivel
Thiranja Prasad Babarenda Gamage
Greg O’Grady
Leo K Cheng

Discipline

Auckland Bioengineering Institute

Project code: ABI009

The objective of this study is to understand the dynamics between the gastrointestinal (GI) bio-electrical activity and contractions (or motility) in an in vivo animal setup. There are two main types of GI bio-electrical activity: slow waves and spike activity. Slow waves are responsible for coordinating motility, while spike potentials are known to play a major role in eliciting contraction of the smooth muscles in the gut. However, to date the spatiotemporal dynamics of these waves are not fully understood. We will use stereoscopic imaging and electrical mapping techniques to investigate the underlying dynamics.

The objectives of the study are to:

  1. Develop an experimental framework to simultaneously record motility from the stomach and small intestine. This will involve:
    • incorporating existing equipment and electrical mapping techniques developed by the GI group at ABI for measuring electrical activity in the gut
    • designing and implementing a stereoscopic optical imaging system for tracking tissue motion during gut contractions; and 
    • implementing an approach for synchronizing the electrical and optical measurements
  2. Record in slow waves and spike activity in sparse and high resolutions during motility measurements in the gut.
  3. Analyse the measurements and define a relationship between slow waves, spikes, and motility.

The student would ideally have an interest in signal/image processing, electrophysiology and will be interested in developing their programming skills in Matlab, Python and Labview. There will be an opportunity to participate in animal-based experimental studies

Design of Electrode Arrays for Recovery Mapping of Gastric Slow Waves


Supervisor

Niranchan Paskaranandavadivel
Saeed Alighaleh
Greg O’Grady
Leo Cheng

Discipline

Auckland Bioengineering Institute

Project code: ABI010

Stomach contractions are governed by an underlying bio-electrical event known as slow wave activity. Slow wave dysrhythmias have been linked to a number of major digestive disorders. The recent development and application of high-resolution electrical mapping techniques has enabled critical advances in understanding normal and dysrhythmic patterns of gastric slow wave activity.

A key hypothesis developed from these studies was that the refractory phase of gastric slow wave activity could be a significant factor in the initiation and maintenance of dysrhythmic patterns. This project will aim to develop a new generation of high-resolution mapping techniques for studying the refractory phase of slow wave activity in the stomach.

The main objective of the study is to develop and validate a novel suction electrode array in an experimental setup. This will involve

  1. Designing and/or improving the existing electrode array
  2. Building the prototype using the 3D printer or other tools present at the Auckland Bioengineering Institute 
  3. Bench top and animal experiments to validate the recordings using the novel array to standard surface contact recordings.

The student should ideally have an interest in device development, electrophysiology and have interest in developing their programming skills in Matlab, Python and Labview. There will be an opportunity to participate in animal-based experimental studies.

Experimental designs for identifying mechanical properties of skin


Supervisor

Dr Thiranja Prasad Babarenda Gamage
Prof. Martyn Nash
Prof. Poul Nielsen

Discipline

Auckland Bioengineering Institute

Project code: ABI011

3-axis force sensitive micro-robot indenter
Figure 1. A 3-axis force sensitive micro-robot indenter developed at ABI for applying controlled deformations to skin. A stereoscopic camera system is used to track the resulting skin surface deformations.

Simulating the mechanical behaviour of skin using biomechanical models is useful for a wide range of applications from simulating surgical interventions to helping to create more realistic models of the face for the animation industry.  Existing biomechanical models of skin require many parameters to describe the complex mechanical behaviour observed in real skin. Attempting to identify these parameters using ad-hoc experimentation protocols often results in non-unique parameter estimates. This situation arises because of difficulties in predicting whether the experimental protocols being applied can provide sufficiently rich information for robustly identifying the model parameters. A model-based design of experiments framework has recently been developed at ABI to help address these issue by determining experimental protocols that maximise the identifiability of the mechanical parameters. 

The main aim of this project is to conduct experiments to validate our model-based design of experiments framework and apply it to computational models of skin. The framework will first be validated by performing experiments on silicone gel phantoms. The framework will then be applied to determine optimal indentation protocols for identifying mechanical properties of skin using existing computational models and a novel micro-robot indenter developed at ABI for applying controlled deformation to skin (Figure 1).

The student would ideally be keen on computer modelling and will develop skills in finite element modelling, design of experiments techniques, nonlinear parameter optimisation, and code development using python and Matlab.

Project aims

1.      Validate the design of experiments framework by performing a series of indentation and gravity loading experiments on phantoms made of silicone gel.

2.      Apply the design of experiments framework to existing biomechanical models of skin to determine the optimal indentation trajectories that maximise the identifiability of the mechanical parameters in the model.

3.      Perform the optimal indentation protocol on the forearm skin of an individual using the micro-robot (as shown in Figure 1) and identify their individual-specific mechanical parameters using an existing numerical optimisation algorithm.

Investigating the frequency content and spatiotemporal distribution of ‘waxing and waning’ in high-resolution bioelectrical recordings from the small intestine


Supervisor

Supervisor: Dr Tim Angeli
Co-Supervisors: Dr Nira Paskaranandavadivel, A/Prof Leo Cheng

Discipline

Auckland Bioengineering Institute

Project code: ABI012

Contractions of the gastrointestinal (GI) tract are controlled by rhythmic, propagating electrical events, termed ‘slow waves’, which thereby serve as a key regulatory mechanism of digestion. In the small intestinal, slow waves have been observed to occasionally exhibit a ‘waxing and waning’ phenomenon where the slow wave amplitude periodically increases and decreases in time. This phenomenon was originally observed by Diamant and Bortoff in 1969 and subsequently expanded by Suzuki et al. in 1986.1,2 It was hypothesized that waxing and waning is caused by competing pacemakers operating in and out of phase, although technology did not exist at the time to conclusive prove that hypothesis.2 Interest in the waxing and waning phenomenon has more recently been re-invigorated by Huizinga et al., who have now hypothesized that it is an effect of phase-amplitude coupling of two separate bioelectrical rhythms: a low and high-frequency activity.3

In vivo high-resolution GI slow wave mapping has employed simultaneous recordings across arrays of 128-256 electrodes to map the spatial propagation patterns of small intestine slow wave activity in high spatiotemporal detail,4,5 and the opportunity now exists to:

1.    investigate the spatial distribution of waxing and waning activity in the small intestine, to determine if it is a spatial effect of competing pacemakers.

2.    determine the frequency content of in vivo waxing and waning recordings, combined with the spatial distribution, to investigate potential phase-amplitude coupling of multiple dominant frequencies.

The student should ideally have a strong interest and background in experimental electrophysiology, data analysis and processing, and computational development.

Specific Aims

  1. Review the literature on waxing and waning of small intestine slow wave signals, and the underlying cause / significance of this phenomenon.
  2. Generate synthetic waxing and waning signals and use them to validate and/or revise an existing algorithm for identifying periods of waxing and waning.
  3. Using the existing database of high-resolution recordings of in vivo small intestine slow wave activity, identify periods of waxing and waning, and:

            i.       perform frequency content analysis (e.g., FFT) on the identified signals that display waxing and waning and assess the possibility of this phenomenon being the result of phase-amplitude coupling of activity naturally occurring at two different frequencies, as proposed by Huizinga et al.3

           ii.       determine the spatial location of waxing and waning in relation to surrounding slow wave propagation dynamics.

          iii.       quantify the occurrence and electrophysiological parameters of waxing and waning versus normal activity, from the existing database of in vivo high-resolution mapping data.

References

1.   Diamant NE, Bortoff A. Nature of the intestinal slow-wave frequency gradient. Am J Physiol. 1969;216(2):301–7.

2.   Suzuki N, Prosser CL, DeVos W. Waxing and waning of slow waves in intestinal musculature. Am J Physiol. 1986;250(1 Pt 1):G28-34.

3.   Huizinga JD, Chen J, Zhu YF, Pawelka A, Mcginn RJ, Bardakjian BL, et al. The origin of segmentation motor activity in the intestine. Nat Commun. 2014;5:3326.

4.   Angeli TR, O’Grady G, Paskaranandavadivel N, Erickson JC, Du P, Pullan AJ, et al. Experimental and automated analysis techniques for high-resolution electrical mapping of small intestine slow wave activity. J Neurogastroenterol Motil. 2013;19(2):179–91.

5.   Angeli TR, O’Grady G, Du P, Paskaranandavadivel N, Pullan AJ, Bissett IP, et al. Circumferential and functional re-entry of in vivo slow-wave activity in the porcine small intestine. Neurogastroenterol Motil. 2013;25(5):e304-314.

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