Category: The Team
Published on Thursday, 27 October 2011 13:24
Written by Super User
EPSRC Advanced Research Fellow
Martin Booth studied Engineering Science as an undergraduate at the University of Oxford before completing his doctorate in optical microscopy, also in Oxford. Since then he has been pursuing research into new optical methods for a range of applications from biology to physics.
You are an engineer, so how did you end up working in a centre for biological research?
The whole point of being an engineer is to take scientific concepts and turn them into something useful. For example, physicists make amazing discoveries of new phenomena, which lead to better understanding of how the universe works—clearly a very important task. However, these phenomena only become useful to society once engineers get hold of them. For engineers to be effective, they must bridge the gap between fundamental science and end-users. Being based in the CNCB means that I am exposed to the needs of the scientists and will be able to see very quickly where new technology could be applied. This is far more effective than working separately.
What do you work on at the CNCB?
My work at the CNCB is to try and extend the sensitivity and range of measuring techniques used to record signals in neural circuits.
My background is in electronic and optical engineering. I work on developing new technologies based around optics, such as lasers, lenses, mirrors, optical fibres and so on. These technologies range from optical microscopes to laser manufacturing systems. A major area of my work involves improving optical microscopes for use in biological research, for example by aiming for better resolution, making them faster, easier to use or cheaper. There are many challenges in this work. We often start with theoretical ideas, then develop them into prototype systems, before turning them into robust tools that can be used in biological labs. This work usually involves developing optical, electrical, mechanical and software components.
At the CNCB we need to be able to look inside the fly brain to see what is happening in individual cells. Optical microscopes are one of the essential tools that enable us to do this.
Can you describe some of the optical techniques used at the CNCB and the challenges you face in attempting to improve them?
Optical microscopes are central to the research at the CNCB. Most people are familiar with traditional microscopes—the type one looks through with eyepieces and that has been around for hundreds of years. However, there have been huge advances in this technology over the last thirty years or so. One big step was the development of the confocal microscope. Unlike a traditional microscope, where you see all of the image at once, this microscope scans a laser through the specimen to build up an image in a point-by-point manner in a computer. The real strength of this microscope is that it gives us three-dimensional images instead of the traditional two-dimensional images. This is essential if we are trying to look at the 3D structure of neurons in the brain. At the CNCB we use the confocal microscope—and its cousin, the two-photon microscope—to obtain detailed images of fly brains.
Another essential ingredient is fluorescence. We use fluorescent markers to illuminate only the cells we are interested in. This is done by genetically encoding a fluorescent protein—originally extracted from a jellyfish—into the DNA of the fruit fly. When the fly develops, it creates its own fluorescent label directly inside the cells we have chosen. It is an incredibly powerful tool that enables us to observe exactly those brain processes we are looking for.
What level of detail can you see with these microscopes?
The resolving power of a microscope is limited by the wavelength of visible light, which is about half a micron, and the best resolution that can be got out of the most sophisticated optical microscope is about half of that again, so about a quarter of a micron. A micron is a millionth of a metre. To see deep into the fly’s nervous system we would ideally like to be able to investigate to depths of 300 microns. Currently we can see to depths of around 100, then things start to become more difficult.
The laser gets distorted as it passes through the fly’s body, which blurs the focus, destroying resolution and the quality of the signal. In other words, the image is lost. We could try to improve the images by making the laser brighter, but then we might damage the brain. Alternatively, we could try increasing the number of sensor molecules, but that risks interfering with the inner workings of the neurons under view. Waiting longer to expose the image would not work, as we are trying to observe rapid processes in the brain. But we do have a method that can help—adaptive optics.
What is adaptive optics?
Trying to account for the distortion of the laser beam because of problems inherent in the system itself is called adaptive optics. In adaptive optics, we use a deformable mirror to cancel out the distortions (or aberrations) introduced by the brain tissue. This technique was originally developed for astronomical telescopes, to compensate for the distorting effects of turbulence in the atmosphere. Whether you realise it or not, you probably already have experience of this turbulence, as it causes the twinkling of stars in the night sky. By cancelling the aberrations caused by the brain tissue, we return the performance of the microscope to its optimum and restore image quality. This should mean that we can obtain clearer images from deep within the fly brain.
What are the particular challenges working with flies?
One of the challenges of imaging animals that are alive is that microscopes usually only work well when the specimen is stable. Of course, live flies tend to move so the microscope needs to be able to keep track of the motion of the fly. The question is whether to do this optically (using active optical techniques) or computationally (using image processing); that is, either improve the microscope so that it can track the motion, or take account of the motion later in the computer realisation of the data in image form.
What first attracted you to the CNCB?
I like the open-endedness of the CNCB’s work. Sometimes the technology hasn’t yet been developed to answer the kinds of questions my neuroscientist colleagues are asking. But conversely, improvements in technology make it possible to ask questions they couldn’t have predicted they’d be asking.
As an outsider, what interests you in neuroscience and why?
One of the great, unanswered questions in science is about how intelligence arises from the structures formed by neurons in our brains. Answering this question will require the combined efforts of many people. One big attraction of this work is that, as engineers, we can help neuroscientists tackle these problems by developing new technology designed for purpose. There is also an opportunity to learn about and contribute to a new area of science. It will take some time until I am up to speed, but who knows? Maybe from an engineer’s perspective I will be able to see problems of neuroscience in a new way.
How do you divide your time between your work at the CNCB and elsewhere?
I am based at the CNCB for half of my working week and half in the Engineering department. The half not spent at the CNCB is given over to optical research for other disciplines from physics through to biology. The same optical techniques apply across the board. I make sure I spend a good amount of time in the CNCB building. It makes a huge difference being based there rather than commuting between buildings. I’ve worked closely with biologists on a number of projects in the past, but even being five minutes away changes the culture entirely. I enjoy the strong scientific focus, the small numbers of people involved and the connections that are being made across different disciplines. This is an opportunity for engineers, physicists, chemists, biologists and others to work together. The cross-fertilization is very healthy.
How often will you have to make an instrument from scratch?
For regular biological questions we use commercially available microscopes that are easy to use and have been specially programmed for purpose. Flies are small, but in relation to the resolving power of an optical microscope they are actually large objects. The experimental versions that I construct are usually built from scratch rather than adapted from existing devices. Though I sometimes buy parts off the shelf, like mounts, lenses, specimen holders and the like, often special parts will need to be custom made. My purpose-built microscopes don’t look anything like shop-bought instruments. At first glance you might think you’re looking at a collection of junk lying on a table with a lens stuck at the end of it. But if it is junk, it is organised junk.
What does the immediate future hold?
Part of my work is in laser-based fabrication systems, in which lasers are used to modify some material—turn it into something else—rather than to image it. In conventional laser fabrication systems the light is focussed to a point. However, in the systems we develop we “shape” the light from the laser. Regions of light are used to create complex structures. Such techniques also turn out to be highly useful to stimulate groups of neurons, where you would want to shape light in particular ways to stimulate particular parts of the brain. This is much better than having to isolate some particular neuron to study it. It is science right at the cutting edge.
What about other technologies like electron microscopes and fMRI?
Electron microscopes have much greater resolution power than optical microscopes, but the disadvantage is that they cannot be used with living things. This means that biological specimens need to be dehydrated and fixed in a polymer so that they can be sliced into ultra thin wafers. Electron microscopes have only occasional use in the kind of work being carried out at the CNCB.
Functional magnetic resonance imaging (fMRI) measures change in blood flow as a proxy for neural activity in the brain. It has come to dominate the brain mapping field in humans due to its low invasiveness. In an fMRI scan whole patches of the brain light up. An fMRI scan will tell us where neural activity is taking place but with no detail. Intricate circuitry is invisible. Also, an fMRI measures blood flow over a few seconds. The behaviour we are investigating at the CNCB typically occurs over shorter periods, so fMRI-like methods have limited value for our work.
EEGs measure voltage fluctuations caused by current flows within large groups of neurons in the brain. So conversely, an EEG will tell us when some neural activity is taking place, but with little precision as to where. On the whole EEGs and fMRIs are too broadstroke for our purposes.
What can you do in the future to make optical microscopes even better?
Biologists would be able to understand much more about the function of living matter if they could see more detail. For a long time, we thought that the resolution of optical microscopes was limited to around half a micrometre—the size of the focussed laser spot. This was limited by the physics of light—you simply cannot squeeze the laser beam any more than this. However, in the last ten years or so, there have been some astounding developments in super-resolution microscopes, that can reduce the resolution to around 10 nanometres—equivalent to one millionth of a centimetre. With these microscopes we can reveal details of cells that were previously invisible. We are now working on a project jointly with scientists at Yale and Cambridge Universities to develop new super-resolution microscopes that not only provide high resolution, but will also be engineered for regular use in biological labs.