3 September 2020
… cool tech that helps us to see more clearly through 3D biological tissue samples and into the Universe
To find out more we talk to Benjamin (Ben) Gore – who is just about to complete his 4-year Engineering Doctorate (EngD). Graduates who want to explore a career in industry often opt to do an EngD, as an alternative to the traditional PhD. Ben’s EngD has been a collaboration with the Advanced Microscopy Group at the Centre for Doctoral Training (CDT) at Heriot Watt University, and the applied optics engineering group at the UK Astronomy Technology Centre (UK ATC), part of the Science and Technology Facilities Council (STFC).
Ben shares with us not only the outputs of his ground-breaking research, but how this partnership between industry and academia, has enabled the sharing of knowledge between disciplines – driving advances in both astronomy and microscopy, and giving the next generation of scientists and engineers the kind of world-class skills that are in high demand by employers.
Tell us about your research Ben?
“Essentially, I am investigating how to improve the quality of the image we see when looking at a 3D biological tissue sample through a microscope.
“As the microscope begins to focus deeper into the sample, more and more aberrations (or distortions) occur. Using a high-tech solution called ‘adaptive optics’– which is used extensively in astronomy – we can correct for these optical aberrations, and see better through the sample.”
That’s really exciting. So you’re using tech developed for astronomy and applying it in microscopy! How does it work?
“In astronomy, turbulence in the Earth’s atmosphere blurs a telescope’s view of space. Adaptive Optics (AO) is the tech solution to fix that problem. Essentially, how it works is that AO measures the distortion, and then sophisticated, deformable mirrors which are controlled by computers, in real-time, correct the distortion – enabling the world’s telescopes to bring the Universe into focus. In fact, here’s a really good digest of AO in astronomy by my supervisor at UK ATC, Dr Noah Schwartz. He breaks the area down into 8 cool AO astrofacts.
“The main difference however, between AO in astronomy and AO in microscopy is that in astronomy you have what’s called a wavefront sensor. This is a camera combined with a special set of optics and software that measures the distortion of the incoming light, taken from a ‘guide star’. The guide star is a light source bright enough and close enough to what the astronomer wants to observe, that acts as a reference point. A guide star is often created using a laser. If you’ve seen cool photos of huge telescopes with laser beams shooting from them… that’s AO in action!
“We usually don’t have the benefit of a guide star or a wavefront sensor in microscopy, but we have the advantage that these aberrations are changing very slowly, so we can generally view them as being static. This means we can correct for aberrations in a sample using a software algorithm that calculates the distortion from a small number of camera images, and then correct for it using the deformable mirror. My work has focused on the use of a technique called multifocal plane microscopy (MUM) where a section of the sample being imaged is acquired in a single camera frame. In my EngD I have been investigating what improvements can be made to the image quality of a 3D biological tissue sample captured through MUM, using AO systems. Here is an example of the results I have got, applying AO for microscopy with a tissue sample.
AO corrected image of a tissue
(Credit: B. Gore)
“If you would like more technical detail, here is conference paper, called ‘Adaptive optics for multifocal plane microscopy’ that I wrote with my supervisors both at UK ATC and at Heriot Watt University.“
Has being at UK ATC informed your research methodology?
“The UK ATC provided me with a bespoke software package – the Object-Oriented Matlab Adaptive Optics (OOMAO) package, which has been invaluable for me in simulating AO systems. Although this software package was developed for astronomy, I’ve been able to modify it to use in microscopy.”
How has the relationship between the Centre for Doctoral Training at Heriot Watt, and UK ATC worked?
“For my project I have two supervisors, Dr Noah Schwartz at UK ATC and Dr Paul Dalgarno from Heriot Watt University. I’m in regular contact with both, as my project lies between their areas of expertise. It’s also opened up an informal communications channel, which means that ideas for future collaborations can be discussed, and everyone is kept up-to-date about the work happening at each of these centres – so that knowledge and expertise can be shared.”
Ben’s EngD supervisor at Heriot Watt, Dr Paul Dalgarno, says of the collaboration:
“It has been a pleasure working with Ben and the UK ATC on this novel research programme – to take cutting-edge astronomy technologies and push the limits of what is possible in diffraction limited and sub-diffraction limited practical biological microscopy.
“Typically we adapt microscopy to AO, but here we have been uniquely placed to translate world-leading expertise in astronomy-based AO and apply it to the breadth of knowledge we have about the practical application of frontline biological imaging for microscopy.
“The results are significant. We have been able to cast practical AO for microscopy in light of what is actually viable for end user biological systems.”
What knowledge/expertise of UK ATC staff has been most valuable to you?
“The most valuable part of working with the optical engineers at UK ATC has definitely been the AO expertise provided by my supervisor and the rest of the staff. As I’ve been involved with the applied optics group I’ve had a range of experienced engineering staff to ask questions of, and draw inspiration from. It’s great to have this level of knowledge at my fingertips.”
What is the outcome of your research?
“In my project I’ve been able to push the sensorless adaptive optics techniques commonly used in microscopy to their limits. I’ve established the range of conditions for which they can be effective and directly compared them to the approaches used in astronomy.
“This has also helped to identify areas in astronomy where these techniques may be valid, and these techniques are now being considered for the calibration of a CubeSat system which has been developed at UK ATC. This work, which I collaborated on with the UK ATC optical engineering team is written up as a paper here – Laboratory Demonstration of an Active Optics System for High-Resolution Deployable CubeSat.
“I’ve also identified some technical limits which can arise from using commonly used correction devices to different applications. For example the shape of the deformable mirror can drift over time – something we call ‘DM creep’. This isn’t usually an issue in astronomy because the shape of the deformable mirror is constantly changing as there are changes in the atmosphere. For microscopy, however, we need to apply repeatable deformable mirror shapes so we can work out which aberrations are present. The DM creep makes this much more difficult.
“We’ve been able to provide AO correction to a number of biological samples in Heriot Watt’s lab, resulting in higher quality imaging capabilities.”
Knowledge transfer between disciplines is key to a thriving scientific community. How do you think this has been achieved in this particular collaboration?
“This project would not have been possible at either of these institutions separately. The range of imaging facilities at Heriot Watt combined with the AO expertise, simulation package and equipment provided by UK ATC has allowed the unprecedented sharing of knowledge between these two disciplines.
“Both institutions have gained new knowledge, enabling new research and new ground-breaking outputs in both fields. Didn’t Aristotle advocate “The whole is greater than the sum of the parts” to explain the importance of synergy. It’s really been a privilege to build my knowledge and skills base for the benefit of both industry and academia through this particular relationship between UK ATC as the industrial partner, and Heriot Watt, as the academic collaborator.”
Ben’s EngD supervisor at UK ATC, Dr Noah Schwartz says:
“The UK ATC has been working with Heriot Watt’s CDT in Applied Photonics for a number of years. The EngD students we have worked with and trained have found jobs in industry almost immediately – demonstrating the high-demand from employers for the type of world-class skills developed through a multi-disciplinary collaboration, such as this.
“Working with Ben and Paul we were able to tap into a wide-ranging set of skills available at Heriot Watt that would been unavailable to us otherwise. We are now bringing this new knowledge back to applications that are closer to the UK ATC’s core business, and fostering new collaboration in space instrumentation.
“We are developing new CubeSat technology that is benefiting from the expertise in adaptive optics algorithms developed during Ben’s EngD.”
You’re just about to complete your 4-year EngD, Ben. What do you want to do next?
“I’ve been trying to keep as many doors open as possible for life after my EngD. I have the option to continue working in academia, but a path to a career in industry is also open to me. Whereas PhD students do extra-curriculums such as teaching or outreach, EngD students undertake part time MBA level business courses alongside their research. I’ve completed courses in Accounting, Project management and marketing, which I feel has really helped me to expand my options.”
Last updated: 04 September 2020