Computational approaches to 3D cell imaging using 'Lightgate' microscopy

Rapidly capturing volumetric information of samples for cell counting, biomarker detection and cell sorting are important tasks in cell biology. A new method of imaging developed in our lab named lightgate microscopy seeks, in combination with a microfluidic channel, to rapidly produce 3D volumes of thousands/millions of individual cells at subcellular resolution. Extracting the maximum information from the 2D maps of 3D samples will be an important step in realising the method's full potential in biological research. Multiple digital signal processing methods could be applied for image processing and volume reconstruction, such as inverse filter (deconvolution), Wiener filter, etc. However, established methods often require a large amount of computational power and thus are both time and power consuming. As the technique is capable of operating at 1000s per second, the next important step is to develop new reconstruction methods of greater computational efficiency while preserving high resolution.
This project will develop algorithms for both computational image reconstructions and quantitative evaluation of cellular morphology. We will build a forward imaging model for the new optical system and develop a novel algorithm to overcome the limitation from traditional deblurring methods, which will be tested on both simulation and experimental results to investigate the system performance under both theoretical and real situations. The aim is to ultimately apply this method to answering questions of real biological importance.
This project is a highly interdisciplinary research that will involve photonics and hardware automation and microfluidics as well as knowledge in chemistry from the different fluorescent probes. Also, the background in Fourier optics and coding will be preferred for this project.

The impact of the CDT in Connected Electronic and Photonic Systems is expected to be wide ranging and include both scientific research and industry outcomes. In terms of academia, it is envisaged that there will be a growing range of research activity in this converged field in coming years, and so the research students should not only have opportunities to continue their work as research fellows, but also to increasingly find posts as academics and indeed in policy advice and consulting.

The main area of impact, however, is expected to be industrial manufacturing and service industries. Relevant industries will include those involved in all areas of Information and Communication Technologies (ICT), together with printing, consumer electronics, construction, infrastructure, defence, energy, engineering, security, medicine and indeed systems companies providing information systems, for example for the financial, retail and medical sectors. Such industries will be at the heart of the digital economy, energy, healthcare, security and manufacturing fields. These industries have huge markets, for example the global consumer electronics market is expected to reach $2.97 trillion in 2020. The photonics sector itself represents a huge enterprise. The global photonics market was $510B in 2013 and is expected to grow to $766 billion in 2020. The UK has the fifth largest manufacturing base in electronics in the world, with annual turnover of £78 billion and employing 800,000 people (TechUK 2016). The UK photonics industry is also world leading with annual turnover of over £10.5 billion, employing 70,000 people and showing sustained growth of 6% to 8% per year over the last three decades (Hansard, 25 January 2017 Col. 122WH). As well as involving large companies, such as Airbus, Leonardo and ARM, there are over 10,000 UK SMEs in the electronics and photonics manufacturing sector, according to Innovate UK. Evidence of the entrepreneurial culture that exists and the potential for benefit to the UK economy from establishing the CDT includes the founding of companies such as Smart Holograms, PervasID, Light Blue Optics, Zinwave, Eight19 and Photon Design by staff and our former PhD students. Indeed, over 20 companies have been spun out in the last 10 years from the groups proposing this CDT.

The success of these industries has depended upon the availability of highly skilled researchers to drive innovation and competitive edge. 70% of survey respondents in the Hennik Annual Manufacturing Report 2017 reported difficulty in recruiting suitably skilled workers. Contributing to meeting this acute need will be the primary impact of the CEPS CDT.

Centre research activities will contribute very strongly to research impact in the ICT area (Internet of Things (IoT), data centre interconnects, next generation access technologies, 5G+ network backhaul, converged photonic/electronic integration, quantum information processing etc), underpinning the Information and Communications Technologies (ICT) and Digital Economy themes and contributing strongly to the themes of Energy (low energy lighting, low energy large area photonic/electronics for e-posters and window shading, photovoltaics, energy efficient displays), Manufacturing the Future (integrated photonic and electronic circuits, smart materials processing with photonics, embedded intelligence and interconnects for Industry 4.0), Quantum Technologies (device and systems integration for quantum communications and information processing) Healthcare Technologies (optical coherence tomography, discrete and real time biosensing, personalised healthcare), Global Uncertainties and Living with Environmental Change (resilient converged communications, advanced sensing systems incorporating electronics with photonics).