Photon Factory

Glow in the dark: Ultra compact, high efficient, low cost UV spectrometer for molecular fluorescence detection

Supervisor

Alex Risos

Discipline

Photon Factory; Physics

Project code: SCI099

When molecules are excited with a high energetic electromagnetic wave, they can undergo electronic excitation and emit wonderful light by the process called fluorescence. This signal is often red shifted by a few nm from our UV-C excitation wavelength. This wavelength poses a unique opportunity to develop an optimised spectrometer for highly accurate identification of contaminants in waters. The student will learn hands on experience with optics, lasers to detect spectral radiation using CCD detectors and optical gratings. Your guide will be Alex Risos within the remarkable Photon Factory at the department of physics!

To the other dimension: GPU accelerated phase unwrapping of holographic images for real time volumetric imaging

Supervisor

Alex Risos

Discipline

Photon Factory; Physics

Project code: SCI103

Reconstructing 3D scenes from recorded holograms is a well applied technique but suffers from true precision volumetric imaging in real time. Using latest Tensor core accelerated hardware, we will enable true volumetric imaging in real time using NVidia’s hardware platforms. The opportunity of applying and further developing efficient phase unwrapping enables the student to earn hands on experience in translating algebraic syntax to computer code using python or C++. Your guide will be Alex Risos within the remarkable Photon Factory at the department of physics!

Photonic device for real-time measurement of tissue margins in prostate cancer surgery

Supervisor

Dr Claude Aguergaray
Susanne V. Breugel

Discipline

Photon Factory, Physics Dept

Project code: SCI110

Project description:
This project focuses on assessing the performance of our photonic probes in animal prostate tissue. The project includes experimental work (design experiment, data collection) and data processing with a range of software we have developed (chemometrics techniques).

The fibre-based photonic probe uses Raman spectroscopy to identify healthy and malignant tissue. More specifically, the probe is based on a technique called Spatially Offset Raman Spectroscopy (SORS) which enables measurements on the surface and in the depth of the tissue. However, each probe design has its limitations (i.e. how deep can it measure).
This project will help understanding the maximum measurement depth in a range of biological samples.

Background:
The current standard treatment for patients with prostate cancer is removal of the prostate gland (prostatectomy). Evaluation of surgical margins during these radical prostatectomy procedures remains a significant challenge. Too often (up to 38% of cases) malignant tissue is left behind leading to cancer spreading again and thus significantly lowering the chances of surviving the disease.
We are developing a photonic probe capable of detecting prostate cancer in real-time. This probe will help surgeons during prostatectomy procedures to decide if they need to remove more tissue. Thus, the probe has the potential to significantly change current medical practice.

Key words:
Biosensing, Photonics, Laser, Raman spectroscopy, Fibre laser, Chemometrics, Data analysis.

Note: The project can be extended to a Master project.

Multimodal hyperspectral imaging techniques to solve fundamental biochemistry problems

Supervisor

Dr Hannah Holtkamp

Discipline

Photon Factory, School of Chemical Sciences

Project code: SCI111

Hyperspectral imaging is an emerging technique that can be applied for various medical applications especially disease diagnosis. By generating a 3D dataset or “hypercube” it is possible to carry out spatially resolved spectral imaging. Various techniques can be used in combination including mass spectrometry, and Raman/IR spectroscopy and it is possible to gain highly detailed information about tissue biochemistry, morphology and composition. Currently, areas of research application include skin disease pathogenesis (immune, cancer etc), and eye biochemistry (presbyopia and cataracts).

Areas can focus on either data analysis techniques (e.g. Matlab), or experimental data collection.

Imaging mass cytometry of discoid lupus erythematosus skin samples

Supervisor

Dr Hannah Holtkamp

Discipline

Photon Factory, School of Chemical Sciences

Project code: SCI112

Discoid lupus erythematosus is a chronic disfiguring skin condition with a high prevalence in Māori and Pacific populations. The traditional means of diagnosis are not sensitive enough to detect early molecular events let alone between types of lupus. Using a combination of mass spectrometry and spectroscopy imaging techniques key biochemical changes have been identified which now need to be linked to changes in the immune system using imaging mass cytometry. This is a recent technological development which conjugates distinct metal isotopes (c.f. traditional fluorescent reporters) to specific antibodies. The advantage of this unique approach is that it can detect upwards of 40 markers at the same time with subcellular resolution.

YOLO3D: Development of a high speed neural network detecting particles using 3D data (x, y, z)

Supervisor

Alex Risos

Discipline

Photon Factory, SCS/Physics

Project code: SCI113

YOLO is a sophisticated neural net to detect 2D (P(x,y)) objects. Yet, there is a lack of sufficient neural nets for detecting 3D data. P(x; y; z).The addition of another dimension enables the simultaneous observation and detection of stacked objects using volumetric 3D holographic data. The student will study neural networks and propose a method suitable to efficiently infer 3D volumetric objects. Your guide will be Alex Risos within the remarkable Photon Factory!.

Using Raman hyperspectral imaging and X-Ray powder diffraction to investigate bilateral asymmetry in otoliths of the greenback horse mackerel Trachurus declivis.

Supervisor

Dr Michel Nieuwoudt  
Ms. Hannah Matthews
Dr. Laith Jawad

Discipline

Photon Factory, School of Chemical Sciences

Project code: SCI114

Fish have no external ears to receive sound waves. Instead they receive sound waves travelling through water via a lateral line found on their sides. This line is composed of scales that have small holes rich in nerve endings which transfer sound to otoliths in each inner ear and from there to the brain. Otoliths are composed of the aragonite polymorph of calcium carbonate (CaCO3). Vaterite, another (and rarer) CaCO3 polymorph has been proposed as an unusual addition in the otolith structure, resulting in dissimilar weights in the left and right otoliths of the fish. This results in a bilateral asymmetry which adversely affects the ability of the fish to accurately identify sounds such as advancing predators, thus becoming easy prey. It also affects their ability to navigate, with the result that the fish end up in foreign territory.

In this project you will determine the distribution and amount of vaterite in otolith samples of the greenback horse mackerel Trachurus declivis, using Raman hyperspectral imaging and X-ray powder diffraction.

Optimization of analytical techniques to determine provenance of precious artworks

Supervisor

Dr Michel Nieuwoudt 
Dr Hannah Holtkamp

Discipline

Photon Factory, School of Chemical Sciences

Project code: SCI115

Art works have been collectible for thousands of years, and determining where a piece comes from can increase its value by orders of magnitude. Historically this is often a complex work of historical study and documentation, but the use of spectroscopic techniques has redefined this process. By using techniques such as Raman, infrared and x-ray fluorescence spectroscopy it is possible to perform in situ analyses of artworks simply, and non-destructively. Working together with Auckland Art Gallery Toi o Tāmaki specialised experimental protocols will be developed that can determine the provenance of special pieces that the gallery has in their collection suspected to be from Bruegel, Goldie and Rembrandt.