ALUMNI

Past staff and students of the University of Auckland Biophotonics Group

 

STAFF

Yaqub Jonmohamadi (2015-2016)

​Yaqub obtained a PhD from department of Medicine, University of Otago in brain imaging via EEG and MRI (2014), a master's degree in Electrical engineering, from Linnaeus University, Sweden (2009) and a bachelor's degree in Electronic engineering from Iran (2007). Shortly after graduation in 2014 he did an internship in the industry for 4 months in a robotic research team at Crown Equipments. He started his first research fellowship at the University of Auckland was in the Department of Physics with Dr Frederique Vanholsbeeck in biomedical imaging.  He worked on several light-based data acquisition setups as well as image processing techniques for real-time sensing. 

Currently Yaqub is undertaking his second research fellowship with Dr Suresh Muthukumaraswamy at the Department of Pharmacology, with focus on development and application of data fusion techniques for EEG-fMRI recordings.

His research interests are signal and image processing, biomedical imaging (EEG and MRI), light and laser based imaging techniques, and machine learning.

 

STUDENTS

PhD

 
Bastian Brauer  (2013-2017)

During my time in the Biophotonics Group led by Dr. Vanholsbeeck I was working on optical coherence tomography (OCT).  OCT is a non-invasive and real-time imaging technique used in various applications - the most important applications are in ophthalmology and tissue imaging.

In the four years of my PhD studies, I developed laser sources for OCT and their use in dispersion mapping of the eye. Dispersion is an optical effect describing the phenomenon that different wavelengths travel at different speeds in the medium due to a change in refractive index.


Knowing that, we can detect micrometer differences in material thicknesses using different wavelengths for imaging. After that, we can calculate the dispersion coefficient for that material and can see if it is water or oil based.  Future plans include detecting subtle changes in healthy and unhealthy eyes to see if there are changes in the dispersion coefficients.

I also performed smaller projects such as helping to build a second harmonic generation microscope and detecting bacteria and  I was a tutor/mentor in the Tuākana programme, an University-wide learning community to enhance the academic success of  Māori and Pacific students. 
I now work for International Earth Sciences Ltd (IESE), an Auckland-based company specialising in earth sciences and seismic sensing (www.metry.co.nz). 

Rui Ming Yong  (2016)

After graduating from the Medical Physics and Imaging Technology (BTech MPIT), I found a deep passion for how different aspects of science can work together and bridging gaps between fields of research. I had a heart for physics, and thoroughly enjoyed the experimental aspects of my honours project which was on the Dosimetry of Ruthenium-106. 

Because of my expertise in exploring how different sciences can work together, I later joined the FoodSafe project team in the middle of 2015 to explore Microfluidics for a Real-Time Bacteria Counting Device. I was able to successfully combine different fabrication techniques for microfluidic devices, and ultimately bacteria enumeration.

I now work as an intern at Auckland Evangelical Church.

Rachel Guo (2015-2016)

As a student excited by mathematics and human biology, the Medical Physics and Imaging Technology (BTech in MPIT) at the University of Auckland was a fitting degree and also opened my eyes to physics all around us.

 

After graduating, I worked at Orion Health for two years where I was exposed to ideas and evidence of creative software solutions to healthcare and other industries.

 

After hearing about the Food Safe project led by Dr Frédérique Vanholsbeeck, who was the MPIT course supervisor, I returned to UoA for a year and joined the FoodSafe project team in 2015.

 

My research explored the potential of an alternative dye for the detection of bacteria (link to news - Acridine orange in Adelaide), the results of which will be reported in a scientific paper.

 

I now work at Orion Health as a software test engineer.

Norman Lippok, PhD (2009-2013)

Novel polarisation and dispersion concepts for optical coherence tomography

My interests are focused on the development of coherent imaging schemes, primarily for Optical Coherence Tomography (OCT). My work was directed to study dispersion and polarization in scenarios that may permit new solutions for structural and functional imaging. I have a strong interest in signal processing methods that attack problems involving dispersion, polarization and complex conjugate ambiguity.

I have been a exchange student in 2007-2008 and worked on Development of an efficient full-field optical coherence tomography system using polarisation dynamics. Then I started an MSc entitled "Highly efficient polarisation sensitive all fibre Fourier domain OCT for in-vivo polarisation and deformation measurements of skin" in 2008 and converted to a PhD entitled "Novel polarisation and dispersion concepts for optical coherence tomography" that I defended brilliantly in February 2014.

I am now a Research Fellow at the Wellman Centre for Photomedicine at Massachusetts General Hospital, USA.   This is the world’s largest academic research facility dedicated to investigating the effects of light on human biology and to the development oflight-mediated, minimally invasive diagnostic and therapeutic technologies. A pioneer in light-based biomedical research, the Center has been the source of many of the most successful transfers of this research to clinical applications.

Sairam Iyer, PhD (2007-2011)

Optical Coherence Tomography: Dispersion Compensation & Parametric Imaging

 

I completed an MSc in nonlinear fiber optics, where I got to study the dynamics of certain energy exchanges occurring at various frequencies in optical fibers. This was exciting, but I couldn’t answer the question, “what would it be used for?”
Applied research began to interest me more as I wanted to see the light at the end of the tunnel, that is, where my work would ultimately be useful. I opted to do a PhD in the field of biophotonics. My PhD involved building an imaging system known as optical coherence tomography, which uses light to image microscopic biological tissues, non-invasively. Utilizing my strong background in fiber optics we set about trying to make an all-fiber system that would be compact, portable and cost-effective.
‪Since graduating I have worked as an Optical Engineer for number of companies in NZ and USA. Currently I am working for Apple and based in San Francisco.

Andy Chen, PhD (2006-2011)

Novel polarisation and dispersion concepts for optical coherence tomography

 

Since competing my PhD, I have worked as an Optical systems engineer at Trimble Navigation Ltd based  in Christchurch, New Zealand. 
The is a major subsidiary  of a global company developing solutions focused on applications requiring position or location—including surveying, construction, agriculture, forestry, fleet and asset management, public safety and mapping. In addition to utilising positioning technologies, such as GPS, lasers and optics, Trimble solutions may include software-content specific to the needs of the user. 

In this role I am responsible for the research and development of new or improved positioning technology using optical techniques. This includes products such as electronic distance meters (EDMs) to measure distance, stereo cameras to generate point cloud, and devices that can track the movement of an object with 6DOF (for example, the blade of a bulldozer).

Masters

 
Micheal Cheng , MSc (2013)

In situ monitoring of microorganisms using fiber optics

 

 

Sean Liew, MSc (2013)

Preliminary design of a scanning laser SHG microscope for collagen imaging

 

I joined the Biophotonics Team as a visiting researcher pursuing my MSc in Medical Physics. My project involves building a scanning laser second harmonic generation microscope to perform functional imaging of collagenous tissues to detect anomalies indicating the presence of cancerous cells.
During the course of my project, I've discovered my passion in software programming, where I thoroughly enjoyed building the SHG microscope which still resides within the microscopy lab within the Physics Department. 
I am currently working in a technology consulting firm in Melbourne, engaging in large projects for various clients across different industries.

Isha Sharma, MSc (2012-2013)

Spectral domain Doppler optical coherence tomography for vibrometry Applications

 

Since graduating, Isha has been working as an Associate Implementation Consultant at Orion Health.

Kaidi Liang, MSc (2011-2012)

Development of an all-fibre interferometric dosimeter

Arti Patel, MSc (2012)

Optimisation of an all-fibre spectroscopic system for in situ bacteria monitoring

 

My BTech - MPIT did not just provide subject knowledge and background but also enhanced my analytical and practical skills required to ease the transition from university life into corporate world.
‪I have worked as an Optics Engineer at Cubic Defense NZ Ltd since 2013. 
‪CDNZ works with a range of state-of-the-art technologies to develop advanced “laser-strike” type training systems used by defence and security forces around the world.  I work on optical calibration, test and validation of new products and prototyping of new products. My job at CDNZ goes far beyond sitting in an office. During the process of prototyping, I frequently go on field tests to ensure our final product will meet customer requirements. Another important part of my role is to ensure eye safety of laser-dependent products to ensure that our products are designed to meet eye safety requirements according to international safety standards.
 

Ivy Au, MSc (2012)

Development of a second harmonic microscope

Jason Kuo, MSc (2011)

Monte Carlo simulations to optimise the sensitivity of an optrode system

Anna Yang, MSc (2010)

All-fibre dispersion compensation OCT system based on an integrated spectral shaper

I was introduced to many imaging techniques while studying the BTech – Medical Physics and Imaging Technology programme. It was very interesting to learn that OCT, a technique based on interferometry, allowed to achieve near-microscopic resolution without ionising radiation or labelling. These features are particularly significant in biomedical applications and I was motivated to learn more about it theoretically and practically.

For my MSc research in 2010, I developed a 1.5um OCT system using a programmable optical filter in the reference arm, and worked on proof-of-principle experiments to demonstrate the effects of the spcetral filter on the performance and the operation of the OCT system. The three aspects explored were dispersion compensation, spectral shaping and creating time delays in the Fourier-domain OCT systems.

I now work as a Professional Teaching Fellow in the Department of Physics at the University of Auckland. 

Tony P Goldsmith, MSc (2004)

Cancellation of Raman soliton self-frequency shift by cross-phase modulation

Bachelors

 
Victoria Butterworth, BSc (2017)

I'm a third year exchange student from the University of Exeter, UK, working towards a Master of Physics degree. I completed a really enjoyable summer research scholarship in the FoodSafe group in 2017 looking at improving the repeatability of measurements on the flow cytometry analogue set-up.

Fei Wang, BSc (2017)

After completing my Bachelor Degree in Physics, I completed a summer research project with the Biophotonics Group .  I worked on the FoodSafe project using flow to aid enumeration of bacteria and assisted other team members with their experiments.  

 

During this I had the chance to work in microbiology and laser labs and gained valuable lab experience from both. Moreover, I extended my understanding about fluorescence and microbiology.

 

I now work at Auckland University of Technology as a Technician.

Damon Hutley, BE (2017)

Image processing camera module

 

My summer research scholarship with the Biophotonics Group counted towards my work experience as part of my Bachelor of Engineering degree at the University of Canterbury.

 

The scholarship enabled me to work on the FoodSafe project utilised my engineering knowledge and skills.  In particular, I developed an image processing camera module for a microscope using a Raspberry Pi.

 

The camera module could be controlled either directly from the Raspberry Pi, or from a remote computer.

 

Images were processed using a background subtraction algorithm, in order to detect the motion of bacteria passing through the field of view of the microscope.
 

Daniel Huang, BTech MPIT (2016)

Characterising an ophthalmic IPL device

 


The BTech (Hons.) degree in Medical Physics and Imaging Technology has given me a broad range of strengths and interests. My degree enables links to be drawn between multiple disciplines, looking beyond the ‘what’ and more into the ‘how’ and ‘why’.
 
There are numerous options after the completion of a BTech (Hons.) degree. Many go into further research, which is great because our degree allows us to blend in with many other faculties and departments. I have chosen to pursue a different journey, one with the help TeachFirst NZ, leadership and teacher development program. 
 
I am currently a secondary school teacher at Edgewater College, Auckland, where I work with students Years 9 to 13. I am teaching Physics, Mathematics and will most likely teach general science as well in the future.

Nik Kamarolzaman, BTech MPIT (2016)

Nonlinear microscopy using a compact all fiber laser at 1 micron

Josh Monro, BTech MPIT (2016)

Native fluorescence of bacteria

My project with FoodSafe examined the emission spectrum profiles of different species of bacteria under different excitation wavelengths. I did find a unique response in the strand of Salmonella I investigated. However, among the other species of bacteria I looked at, there was not a diverse emission response, so overall I concluded that fluorescence spectroscopy could not be used as an all round bacterial species identifier.

I am now pursuing a Masters in Biomedical Science at the University of Auckland. My project is based on the MRI technique known as Magnetic Resonance Elastography (MRE). This technique applies shear waves to the tissue/ patient being examined accompanied with pulse sequence that allows us to image the waves propagating through the tissue. Image processing techniques allow us to then view the elastic properties of the tissue being examined from which conclusions can be drawn. My focus at the moment is coding an algorithm in Matlab that takes the raw data from the MRE sequence and produces a colour coded image. This image will display information regarding the elastic properties of the phantom or tissue. I then hope to be able to take my algorithm and analyse liver data from volunteer patients.

Alex Spence, BTech MPIT (2016) 

Microfluidic devices for sample preparation

 

As a student that took great interest in physics and human biology, Medical Physics and Imaging Technology (BTech in MPIT) was extremely appealing. MPIT improved my analytical skills and provided great insight to the vast impact physics had in every day life. Throughout MPIT my interest in mathematics and computers grew quickly as I was exposed to various aspects of image analysis and processing.

After graduating from the Medical Physics and Imaging Technology (BTech in MPIT), 
I admired the way that different aspects of science can be integrated. As a consequence 


I have chosen to pursue Computer Science, again at the University of Auckland. 

Neelam Hari, BTech MPIT (2015)

Interactive Playground / Beambox

 

Beambox was all about collaborating with people of other skills to create something beautiful, yet educational. The aim of the project was to build a physical installation which allowed the public to play with physics.  The resulting Beambox installation, sited in Aotea Square, enabled people to explore the characters of the electromagnetic spectrum by moving around interactive cubes around which came to life with colour and sound, passing messages through visible-light communication.   More information here

Mathew Brown, BTech MPIT (2015)

Study of Ostheoarthitis using polarisation sensitive OCT

Guneet Kaur, BTech MPIT (2013)

Studies of Forster resonance energy transfer using an all fibre optical system

Michel Yap, BTech MPIT (2013)

Optical coherence tomography in the assessment of articular cartilage condition

Jennifer Yeh, BTech MPIT (2013)

Ice core layer counting using time-domain OCT

Micheal Cheng, PGDipSc (2012)

Development and studies of dual optical fibre probe sensor for fluorescence measurement

Arti Patel, BTech MPIT (2011)

Bioluminescence measurement using an all-fibre setup

Jason Kuo, BTech MPIT (2010)

Monitoring bacteria tagged with fluorescent proteins by using an optrode

Jenny Lim, BTech MPIT (2010)

Algorithms and method for analysing spectra emitted by bacteria tagged with fluorescent proteins

Hamish Randle, BTech OPTO (2010)

Fabrication and optimisation of fused fibre couplers

Interns

 
Léa Lachaud (2017)

OCT

I am a French 22-year old student in physics who is completing a Master degree at the 
ENS de Lyon, France. My interest in optics and medical applications drove me to go to Auckland on a 3-months internship to focus on Optical Coherence Tomography (OCT).   Personally I had really wanted to go to New Zealand for some time. 
My project, supervised by Dr Sylwia Kolenderska, was to develop a simple, numerical method for dispersion mapping of an object using Fourier domain OCT. I explored both theoretical and practical aspects; characterizing the existing setup in terms of its limitations and performance in the context of the method, trying to improve its characteristics, and begin a study on biological tissue.

Gabrielle Laloy-Borgna (2017)

Foodsafe

I am currently in my fourth year of studies at the Ecole Normale Supérieure de Lyon in France, doing a Master's degree in Physics to become a researcher. I completed my required internship of the end of the year within the University of Auckland Biophotonics Group.  

My project involved modelling the centrifugation of bacteria in order to improve the shape of centrifugal microfluidic devices being developed in the FoodSafe programme. 
 
My time in New Zealand was a lot of fun.  If you are adventurous and want the opportunity to do your internship in New Zealand,  I’d recommend you approach Dr Vanholsbeeck.   Just go for it! 
 

Alizée Mignot (2017)

I am a Masters student studying at the L'Université de Franche-Comté.  I am interested in the application of robotics and software engineering to the medical field. I came all the way from France to complete a research internship the University of Auckland as part of my biomedical engineering curriculum.  It was a really enjoyable experience.
During my three months with the Biophotonics Group I worked on the modelling of a spectrometer system for the OCT setup of Dr Sylwia Kolendreska using Zemax software called Optical studio. My work resulted in a new spectrometer model. I also started implementing a user interface for the processing programmes associated with the OCT setup.  

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