UCL MEDICAL PHYSICS
AND BIOMEDICAL ENGINEERING
Medical Physics and
Biomedical Engineering
Annual Newsletter 2015
TRANSFORMING TECHNOLOGY INTO HEALTHCARE
1
2 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Welcome
WELCOME TO THE 2015 EDITION OF THE ANNUAL
NEWSLETTER OF THE UCL DEPARTMENT OF MEDICAL
PHYSICS AND BIOMEDICAL ENGINEERING.
The past year has been a period of unprecedented growth
and change for the department, including recruitment of
several new academic staff, major changes to the departmental
professional services team (including a new Department
Manager), the launch of a new undergraduate programme,
the creation of new research groups and new research facilities,
and a change to the name of the department! There have also
been considerable successes, including excellent outcomes to
the REF2014 research assessment exercise and the National
Student Survey. Once again our Newsletter features some
of the new and exciting research activity in the department,
and includes miscellaneous news items which we hope will
be of particular interest to former students and staff. In this
issue we report on research into medical imaging, therapy
and biomedical engineering, and on teaching and other
developments.
We hope you enjoy our Newsletter. If you have any questions
or comments, we would be delighted to hear from you, via
medphys.newsletter@ucl.ac.uk.
Jeremy C. Hebden | Head of Department
CONTACTS
Department of Medical Physics and Biomedical Engineering
University College London, Gower Street, London WC1E 6BT
Web: www.ucl.ac.uk/medphys
Tel: 020 7679 0200
Email: medphys.newsletter@ucl.ac.uk
Twitter: @UCLMedphys
3
Departmental news
REF 2014
Results of the recent assessment of the quality of UK
Universities’ research (Research Excellence Framework,
REF 2014) found that UCL is the top-rated university in the
UK for research strength, by a measure of average research score
multiplied by staff numbers submitted. Academic members of
staff in our department were evaluated under one of two units
of assessment – Biomedical Engineering and Computer Science,
which achieved the 4th and 2nd highest average research
scores respectively out of 36 submitted units at UCL. (The
Research Excellence Framework does not have an official unit of
assessment called Biomedical Engineering, so these researchers
were submitted under a unit entitled General Engineering).
The Dean of Engineering, Prof Anthony Finkelstein, noted that
the result for Biomedical Engineering was remarkable given
that it was the first time that UCL had submitted as a single
unit under this category. This submission included 55 academic
research staff (53.7 FTE) drawn from seven different UCL
departments and institutes, most of whom were drawn from
just three: the UCL Department of Medical Engineering (13
staff), the UCL Institute of Orthopaedics & Musculoskeletal
Science (20), and our own Department of Medical Physics and
Biomedical Engineering (16), making us the largest group of
biomedical engineers in the UK. Overall, 95% of the submission
was rated as either 3*(internationally excellent) or 4* (worldleading). Three of our department’s academics were submitted
with those from the UCL Department of Computer Science in a
unit which achieved a 96% overall rating at 3* or 4*.
Overall, REF 2014 was tremendous news for the UCL Faculty
of Engineering, with three of its units ranked in the top four
of all those submitted by UCL. More information about the
outcome of REF2014 is available at http://www.ucl.ac.uk/
ref2014/ref2014-results
NEW DEGREE PROGRAMMES IN
BIOMEDICAL ENGINEERING
We have launched our new BEng and MEng degrees in
Biomedical Engineering, with an initial intake of 13 students.
The students have studied modules on mathematical modelling,
professional skills, cardiac engineering, materials and mechanics,
electronics, and physics of the human body. One of the biggest
changes has been the introduction of scenarios, during which
formal teaching is suspended for a week whilst students carry
out an intensive group project. We have an article on scenarios
later in the Newsletter.
NATIONAL STUDENT SURVEY
We were delighted to be one of only four departments in UCL
to receive 100% overall satisfaction in the National Student
Survey. Prof Anthony Smith, UCL Vice-Provost (Education
& Student Affairs), said: “The overall increase in student
satisfaction in this year’s NSS results is very welcome news and
something that the UCL community should take pride in”.
CHANGE OF NAME
In September 2014 we began teaching new undergraduate
degree programmes in Biomedical Engineering in addition
to those we already offer in Medical Physics. To address the
obvious incongruity between the name of this programme
and the “Bioengineering” which appeared in the name of our
department, we made a subtle change to the department’s name,
replacing “Bioengineering” with “Biomedical Engineering”.
This avoids confusion among some of our incoming students,
and also underlines the uniquely strong medical focus of most
of the department’s research. The name change was approved by
UCL Academic Board and UCL Council, and came into effect
on August 1st 2014.
4 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Departmental news
NEW APPOINTMENTS
PROMOTIONS
Jorge Cardoso – Lecturer.
Matt Clarkson – Lecturer.
Vikki Crowe – Office Administrator.
Lynsey Duffell – Lecturer.
Allen Goodship – Professor of Orthopaedic Surgery.
Eve Hatten – Teaching Laboratory Technician.
Joy Hirsch – Professor of Neuroscience.
Marc Modat – Lecturer.
Jamie McClelland – Lecturer.
Peter Munro – Royal Society University Research Fellow.
Andy O’Reilly – Departmental Manager.
Tracy Pearmain – Executive Assistant to the HoD
and Staffing Officer.
Jo Pearson – Senior Teaching & Learning Administrator.
Hab Salik – Research and Finance Administrator.
Bradley Treeby – EPSRC Early Career Fellow.
Ilias Tachtsidis – Wellcome Trust Research Fellow.
Vasileios Vavourakis – Marie Curie Research Fellow.
Dean Barratt – Reader in Medical Image Computing.
Adam Gibson – Professor of Medical Physics.
STAFF LEAVING
The Phase II award will fund longitudinal studies in the
Gambia and the UK, to investigate markers of typical
and atypical brain function in infants from birth to 18
months of age. More information about this project can
be found at www.globalfnirs.org and @globalfnirs
Karen Cardy – Karen retired in February 2015 after
thirteen years of loyal service to the department as
Departmental Manager.
NEW FUNDING AWARD
Prof Clare Elwell and her Globalfnirs team have secured
prestigious Phase II Grand Challenges Exploration funding
from the Bill & Melinda Gates Foundation to extend
their work on delivering novel biomarkers of nutrition
related cognitive development in Africa and beyond.
Grand Challenges Explorations funds scientists, researchers
and entrepreneurs worldwide to explore innovative solutions
to persistent global health and development challenges.
Phase I funding resulted in the first functional brain imaging of
African infants. Data was acquired using a portable near infrared
spectroscopy (NIRS) brain imaging system which was built in
the department and transported to a rural village in the Gambia.
Lucy Braddick – Lucy left the department in February 2015
to take up a position with the Royal Academy of Engineering.
Image above: Clare Elwell describing the Globalfnirs
project to Bill Gates at a Grand Challenges
Conference in Seattle in October 2014.
Research highlights
6 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
GIFT-Surg: Guided Instrumentation
for Fetal Therapy and Surgery
WWW.GIFT-SURG.AC.UK
In July 2014 we were delighted to begin a £10million,
seven-year grant from the Wellcome Trust and the
EPSRC, under the ‘Innovative Engineering for Health’
Initiative, to revolutionise the field of fetal therapy
and surgery.
GIFT-Surg is led by Prof Sebastien Ourselin, Director of the
Translational Imaging Group. The project consists of a large
collaborative team of engineers, clinicians, computer scientists,
chemists and physicists from UCL, UCLH, Great Ormond
Street Hospital, KU Leuven and UZ Leuven. Over 41 staff and
students in two countries are working towards the common goal
of developing safe and minimally invasive tools and therapies
for the unborn child. The project is closely managed in line with
the Wellcome Trust and EPSRC, who form part of a Research
Steering Committee measuring progress at key developmental
stages through nine different Work Packages.
Combining expertise from such a breadth of research areas
allows our project objectives to be ambitious. Our aims
currently include the development of advanced miniature
surgical instrumentation, novel photoacoustic imaging probes,
surgical planning and visualisation software suites, and active
intraoperative guidance, brought together under an
integrated platform.
Advances in prenatal treatment of congenital malformations
will have a major impact on clinical practice, potentially
targeting a third of all paediatric hospital admissions and
providing greatly improved outcomes for the child.
Central to the project’s aims is the development of a self-aware
synergetic stabiliser and highly dexterous multi-arm instrument.
This will support the minimally invasive surgical techniques at a
single entry point, used both for operative needs and to deliver
advanced therapies such as stem cell patches. These objectives
are currently out of the reach of surgeons, who need to rely on
existing rigid instruments or invasive open surgery.
Advanced control approaches which rely on image guidance and
visual servoing will be explored to intelligently assist the surgeon
during the minimally invasive procedure. The design will enable
access to areas that cannot presently be treated with the current
rigid instruments, help lessen tremors in the surgeon’s hand, and
allow for bigger or more fine-grained manipulation by scaling
down the surgeon’s gestures.
Image above: Stabiliser designed for ophthalmological
micro-surgery, KUL technology made available for GIFTSurg.
Image above: A dual-segment fluidic-actuated instrument.
The compliant nature of this actuator is well suited to
operating in a fragile environment.
Engineers on the project are currently testing early prototypes
of the devices using a lab testbed (made up of a layer of artificial
tissue with adaptable tension and stiffness, mounted on a
force sensitive plate), which provides realistic feedback of the
equipment through a simulated surgical task and will link to
eventual surgical training.
7
Image above: Anatomical information extracted from MR (blue) is propagated into US to guide segmentation.
Another key objective currently in development is a novel
intraoperative endoscopic imaging platform based on
photoacoustic (PA) imaging and laser generated ultrasound
(US), for visualising fetal and maternal anatomy and function.
Current external intraoperative imaging is insufficient in
providing the high resolution imaging of the delicate organs
of interest to the surgeon, notably because of the large distance
between these organs and the maternal skin. PA imaging
provides absorption-based optical contrast making it well
suited to visualising vascular architectures, while endoscopic
ultrasound can provide complementary high resolution
structural information based on mechanical contrast. The broad
objective is to develop a multimodal platform that will provide
co-registered 3D PA-US images over two different spatial scales.
To complement the work on the PA and US systems, we are
currently performing tests using human placentas collected
from consenting patients to gain a better understanding of their
optical and structural characteristics, as well as the capabilities
of the endoscopic probes in development. Furthermore, a
complementary method called laser speckle contrast imaging
is also being developed for obtaining accurate mapping of
blood flow in placental vessels. These novel intraoperative
imaging tools will provide an unprecedented view into fetal
and placental anatomy and help overcome many of the
current challenges in fetal surgery.
Along with the hardware developments, algorithmic design,
software design and implementation form a large part of the
current work on the project. Despite, or perhaps because of,
the complexity of fetal surgery, there currently exists no surgical
planning tool to help the surgeon prepare for the operation.
At GIFT-Surg, we will take advantage of all the pre-operative
imaging available to develop such a surgical planning systemnotably to assist in optimal surgical port placement, which
guarantees improved access of probes and instruments during
the operation. For this purpose, novel image segmentation
and modelling techniques to extract the fetal and maternal
anatomy are currently being developed, and an early prototype
for the localization of the placenta is currently being evaluated.
Modelling of the fetal and maternal anatomy is also required
for surgical risk analysis and outcome prediction, in addition
to guidance and data fusion during the procedure. As such, the
developed models will support intraoperative updates through
biomechanical model changes and fusion with real-time
modalities, which provide information about changes in the
anatomical structures observed pre-operatively.
Within this work package, novel image analysis techniques are
also being developed which can notably generate 3D models
of internal areas of operation from a series of limited field of
view 2D fetoscopic images, allowing for more efficient surgical
planning and navigation whilst minimising risk of error.
Finally, the full development of a GIFT-Surg Software Platform
will bring the advances in all aspects of the project’s research
together into an easy to use system for clinicians and staff.
Our aim is to provide a state-of-the-art clinical application
suite for pre-operative surgical planning, and image-guided
intervention for aiding surgeons in fetal surgery, which currently
does not exist. Furthermore a data-sharing platform called
GIFT-Cloud will facilitate secure information exchange between
collaborating institutions allowing for large numbers of datasets,
multiple modalities, and annotations with back-up, security,
and support for open data.
8 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
The software will also allow researchers to develop new
algorithms for image processing, which will allow them to
rapidly prototype their ideas with accurate validation from real
anonymised data from GIFT-Cloud, allowing for development
of new image mosaicking and vessel tracking algorithms.
Image above: Insertion of a balloon into the trachea to
increase intrapulmonary pressure and encourage lung
development Surgeon defines green region: safe for trocar
insertion, yellow region: optimal for trocar insertion.
Strokes Our Method Using MRI for accurate surgical planning (below)
Segmentation of the placenta from fetal MRI is critical for fetal
surgical planning. It is however made difficult by poor image
quality due to sparse acquisition, inter-slice motion, and the
widely varying position and orientation of the placenta between
pregnant women. We are developing a minimally interactive
method to obtain accurate placenta segmentations from MRI.
The clinician loads an MRI and selects one of the central slices.
After creating a few strokes inside and outside the placenta, the
algorithm learns the appearance of the placenta and creates a
complete segmentation in the 3D volume.
GeoS Graph Cut
9
A Brilliant Coincidence?
AUTHORS: ANNA ZAMIR AND STEFFI MENDES
Anna
Steffi
As a current PhD student at the Medical Physics and Biomedical
Engineering department, I was exposed to the opportunity to
get involved with the Brilliant Club. As their official website
states, the Brilliant Club aims to widen access to highly selective
universities by placing PhD students in schools serving low
participation communities to deliver university-style teaching to
high performing pupils. As well as deeply believing in this cause,
I was excited by the opportunity to show secondary school
students how the basic scientific principles they were learning
about could be practically used to solve real-world problems.
I designed a six lecture course about medical imaging, covering
the basics of MRI, Ultrasound, X-ray and CT imaging, and
even included a lecture covering my own research about PhaseContrast X-ray imaging. With the aid of the Brilliant Club,
I gained experience in designing lectures, presenting, setting
and marking effective course work.
Currently as an A-Level student I study Maths, Physics and
Chemistry at Lampton School, situated in West London in the
Borough of Hounslow. Of all my lessons at AS, it was physics
that I thoroughly enjoyed and looked forward to the most.
Consequently, this led me to participate in The Brilliant Club in
which I had Anna Zamir, a current PhD student at UCL, as my
mentor. It was a great experience as we were taught about a wide
range of medical imaging techniques, as well as their advances,
and those that are still being developed. The greatest impact the
Brilliant Club had on me was that it not only helped me decide
what I wanted to study at university, but also where I wanted
to spend the next few years as a student. I am now delighted to
say that I hold a conditional offer to study on the undergraduate
Medical Physics degree at UCL, and am waiting for my exam
results in the summer so I can start at UCL, which is exciting.
Finally, I was grateful for having Anna as my mentor because she
made sure we made the most of this experience and gave us the
best possible help to finish our final projects.
I was assigned to teach eight high performing pupils in Lampton
School. The students were all very bright and engaged in the
course. One of these students was Steffi Mendes, whose final
assignment about X-ray imaging was marked as a first and
received a distinction. At the end of the course Steffi told me
she’d decided she wanted to study Medical Physics, and I was
thrilled to see the influence the course had.
A few months later, since I was previously an undergraduate
student in our department, I was asked to meet prospective
students on their open day and give them a tour of the campus.
To my surprise, I saw Steffi in the crowd of students! I was
so happy to see she followed through with her wish to study
Medical Physics, and to find out that she applied and got a
conditional offer from my department. It was a true testament
to the influence of public engagement.
10 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Cranioplasty – Repairing Holes in the Head
AUTHOR: DENZIL BOOTH
Medical Physics at UCLH is a small team, made up
of a Scientist and three Mechanical Engineers, who
manufacture skull implants out of titanium for UCLH
and other hospitals within the UK. In most cases these
are for trauma or tumours, though some are cosmetic.
There are four procedures in completing the manufacture of
titanium plates for use on patients. First of all, we use specific
software to create a computer assisted design of a repair template
from a patient’s CT scan. We are able to make a repair over the
hole using a mirror technique, which is then fed to either a 3D
printer, or CNC Milling Machine- where a defect and repair
model will be made from a single point tapered tool using a
hard foam type material. Using surgical plaster on the repair
model, we are able to build a mould from another plaster called
Dentstone. The mould is then invested in a pot and placed in a
Hydraulic Press, with a piece of 0.7mm titanium sheet placed
on top of the mould. The main component of the Press is a hard
rubber diaphragm which is steadily pressured to 2400 psi.
By doing this the titanium forms into the mould.
The formed sheet of titanium is removed and cut using various
hand tools to the required size and shape. Once this is done,
all edges are smoothed off using a rubber wheel on a rotary
hand tool. Fixing holes and holes for the release of fluid are
drilled through the titanium plate. A unique patient number
is engraved onto the plate. The plate is polished with various
rubber silicone wheels.
The plate is left to be cleaned in an etching solution, made up
of distilled water, nitric and hydrofluoric acid. It’s left in this
solution for about 20 minutes, making sure it is turned over
to etch all surfaces. This is then thoroughly cleaned with cold
running water. To anodise the plate an electrical charge is
put through it whilst it is being dipped into a solution of
distilled water, sulphuric acid and orthophoshoric acid.
The finished Cranioplasty Plate is then autoclaved, before
being implanted onto the patient’s skull.
Images above (top): Unilateral defect. From left to right –
CT Scan / Defect / Mirror / Repair.
Image above: Bilateral defect.
Cranioplasty
Cranioplasty illustrates the importance of medical
physicists and biomedical engineers working closely
with clinicians. In this multidisciplinary collaboration,
engineers work with surgeons to develop new materials
and techniques for repairing damage to the skull.
UCLH’s cranioplasty unit was the first in the UK to
use computer assisted design technology and now
provides support for cranioplasty across the UK.
11
Images above (left and right): Repair and defect models.
Image above: Hydraulic press.
Images above: Finished plate.
12 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
X-ray phase contrast computed tomography:
Improving soft tissue contrast for
biomedical applications
AUTHOR: CHARLOTTE HAGEN ON BEHALF OF THE UCL PHASE CONTRAST GROUP
Poor soft tissue contrast is one of the major limitations
of conventional radiography and computed tomography
(CT). It stems from a lack of attenuation differences
of adjacent soft tissue types and affects many
areas of diagnostic medicine- mammography, for
example. X-ray phase contrast imaging (XPCi) offers
a revolutionary approach to solving this problem:
instead of measuring x-ray attenuation (the contrast
mechanism in conventional radiography and CT), it
exploits the small (micro-radian) directional changes
x-rays suffer when they travel through matter, an effect
known as phase shift, or refraction. Refraction can be
several orders of magnitude stronger than attenuation,
meaning that improved contrast can be obtained also
when attenuation differences between tissues are weak.
XPCi has originally been developed at specialized synchrotron
radiation facilities, but recent advances have transferred the
technology into standard research labs. This has been a very
important step: the technology has become easily accessible
to researchers from various biomedical disciplines.
The UCL Phase Contrast group, led by Prof Alessandro
Olivo, is one of the world leading groups in developing
lab-based XPCi technology. The technology developed
by the group, called edge illumination XPCi, is highly
sensitive to refraction, even though it is based on a robust
experimental setup. While there are other groups that are
trying to achieve something similar, technical limitations in
their approaches mean they are delivering very high doses of
radiation, which is completely impractical for both clinical
and pre-clinical applications. Edge illumination XPCi solves
this problem, and delivers doses which are even lower than
those currently used, for example, in preclinical imaging. The
method has already been exploited for several biomedical
applications, including mammography and imaging cartilage.
Recently, edge illumination XPCi has been further developed
such that computed tomography (CT) scans can be performed.
A CT scan involves rotating the sample over an angular range
of at least 180 degrees and taking images at multiple view
angles. From this data, a three-dimensional representation
of the sample and the internal structure can be recovered
via mathematical methods. The ability to perform CT scans
with edge illumination XPCi combines three-dimensional
imaging with improved soft tissue contrast. The first CT images
acquired with the UCL method, which were published in the
journal Medical Physics, showed a very high image quality.
Moreover, and most importantly, they were obtained entirely
with commercially available x-ray equipment and with low
doses of radiation. This led to the article being the “Editor’s
Pick” and the images appearing on the front cover of the
journal (see Hagen et al., Med. Phys. 41(7): 070701, 2014).
The capability to improve soft tissue contrast, alongside the
high spatial resolution achievable with x-rays and the robustness
of the method, means that edge illumination XPCi could
be applied to a wide range of biomedical applications in the
future. Current areas that are under investigation include
small animal imaging, atherosclerosis and osteoarthritis
research, and regenerative medicine. The UCL Phase Contrast
group welcomes collaborations, especially across biomedical
disciplines where non-destructive imaging using conventional
radiographic techniques is considered challenging.
What is edge illumination XPCi?
Edge illumination XPCi has been developed at UCL
in order to measure x-ray refraction. The fundamental
idea is to use two x-ray masks: the first one splits
the x-ray beam into small beamlets, and the second
one creates “edges” in between the pixels of an x-ray
detector. By positioning the first mask in such a way
that each beamlet falls half onto a detector pixel and
half onto an absorbing edge, sensitivity to refraction is
created. When the x-rays are refracted towards a pixel,
the measured intensity is higher. Conversely, when
the x-rays are refracted towards an edge, the measured
intensity is lower. This generates contrast in the image.
XPCi
13
Edge illumination
Mask
Mask
Sample
X-ray tube
Refracted x-rays
CT scan
Refraction contrast
Pixelated detector
Image above: Schematic of the UCL x-ray phase contrast CT scanner.
Image below: Three-dimensional image of a beetle, acquired with edge illumination XPCi CT.
The zoom reveals the hairs on the beetle’s leg.
14 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Susceptibility Mapping: from MRI to tissue
magnetic susceptibility and beyond
AUTHORS: EMMA BIONDETTI AND EMMA DIXON
Susceptibility Mapping (SM) is a technique that
uses Magnetic Resonance Imaging (MRI) to produce
a map of the magnetic susceptibility in the brain or
body. An MRI scan actually outputs two independent
images: a magnitude image- the one we are most used
to seeing- and a phase image, which has often been
discarded in the past. The phase image in gradient
echo MRI is proportional to the local magnetic field
which is determined by the magnetic susceptibilities of
surrounding structures. This means that a map of the
tissue magnetic susceptibility can be calculated from
the phase image.
Arteriovenous Malformations (AVM) in the brain. This work is
in collaboration with the group of Prof Rolf Jäger at the UCL
Institute of Neurology.
So why do we need to go a step further and develop
susceptibility mapping? Firstly, the contrast we observe in
phase images is non-local, influenced by surrounding tissues
of different magnetic susceptibility. Moreover, the phase
depends on the orientation of the tissue with respect to the
scanner’s main magnetic field. These two problems affect phase
images as well as SWI, and have led researchers to develop SM,
which overcomes these problems and directly represents the
underlying tissue susceptibility.
Many different constituents, from calcium to deoxyhaemoglobin
and beyond, can change the susceptibility of tissue; so
susceptibility mapping has the potential to reveal a wide
variety of pathologies or tissue changes. Please do contact us at
k.shmueli@ucl.ac.uk if you think tissue magnetic susceptibility
mapping might be useful in your research.
The susceptibility of blood changes dramatically depends on its
oxygenation. Anita Karsa is using this as the basis for optimising
susceptibility mapping to reveal the oxygenation levels inside
head and neck tumours. Measuring tumour oxygenation is
clinically important because low oxygenation leads tumours to
respond poorly to radiotherapy. Susceptibility mapping may
provide a powerful non-invasive biomarker to predict tumour
responses to radiotherapy.
What is magnetic susceptibility?
The MRI group, led by Dr Karin Shmueli, is currently
developing SM techniques and optimising them for a variety
of clinical applications.
Emma Dixon is a PhD student working with SM to reveal
the location of bone and air in the head, something which is
difficult to do with MRI due to the lack of signal in bone and
air in conventional magnitude MR images. As the information
in phase images is non-local, susceptibility maps calculated
from them give us information about the susceptibility in the
regions of bone and air that are not usually MRI-visible.
This method for visualising bone and air may allow MRI-based
maps to be used to correct Positron Emission Tomography
(PET) images for attenuation by bone, particularly in
combined PET-MRI scanners.
Venous vasculature appears bright in susceptibility maps
because it contains paramagnetic deoxyhaemoglobin. In
her PhD research, Emma Biondetti plans to exploit this
strong vascular contrast with the aim of using SM to image
Magnetic susceptibility is a property of a material which
determines how it will behave in a magnetic field: will
it be magnetised in alignment with the field or opposite
to it, and how strong will this magnetisation be?
Susceptibility mapping (SM) is not the first technique to
exploit the phase of the MRI signal. Another approach,
known as Susceptibility Weighted Imaging (SWI), was
developed before SM. SWI enhances the contrast of
paramagnetic or diamagnetic structures, such as microbleeds or calcifications, by multiplying the magnitude
image by a mask derived from the phase image.
SWI entered clinical practice a few years ago: many MRI
scanner manufacturers now provide sequences for creating
SWI maps, and clinicians are beginning to appreciate the
additional information provided by this method.
MRI
15
Image above: MRI Susceptibility Maps Reveal Iron-Rich Deep-Brain Structures
The arrows point to two iron-rich deep-brain structures: red nuclei (red arrows) and substantia nigra (black arrow).
These structures are not visible in the magnitude image, whereas they can be seen really well in both the phase image
and the susceptibility map. However, the phase contrast of these structures is non-local and spreads outside the
structure. This problem has been overcome in the susceptibility map: here the iron-rich deep-brain structures have
local contrast and are clearly visible as they have higher magnetic susceptibility than the surrounding tissues. These
images of a healthy volunteer were acquired at UCL on a 3 Tesla MRI scanner with a gradient echo sequence.
16 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
An ‘Appt’ start to the
Biomedical Engineering degree
AUTHOR: REBECCA YERWORTH
The first of these scenarios ran 9–13 February 2015, and
challenged students to design a smartphone app capable of
determining pulse rate, using the built in camera and LED
light. Students were given example codes to perform certain
tasks, e.g. switching on the LED, accessing the RGB values
of an image pixel captured by the camera, and calculating the
frequency using Fourier Transform. In the first three days they
familiarised themselves with these subroutines by developing
an app to send Morse codes via the LED, and another app to
decode them using the camera. In the last two days students
had to put these different subroutines together to form a
pulse rate app. They also had to design a user interface for the
app based on design principles learned from the Design and
Professional Skills module in the first term. In the afternoon of
the fifth day they tested the apps on each other, and compared
the results against readings recorded by a pulse oximeter.
Some students found the scenario a challenging task, but were
rewarded by their success when their apps began to work! One
creative pair applied their knowledge of physiological responses
to add a novel, though tongue-in-cheek, twist to their app –
styling it as a ‘Love detector’.
What is scenario based learning?
Scenario
Last September the department launched a new
undergraduate Biomedical Engineering degree, which
is based around innovative, research-focused approaches
to teaching and learning approaches. As part of this,
students will take part in six ‘scenarios’ – intensive week
long group projects aimed at developing their previously
taught technical and professional skills.
Scenarios require students to apply previously taught
theoretical knowledge (e.g. circuit design), and
professional skills (e.g. team working and use of the
‘design cycle’), to a real life problem. Different scenarios
focus on different areas of the design cycle (e.g. the 2nd
scenario will focus on the ‘modelling and testing’ phase),
and other professional skills (e.g. one scenario will prompt
students to think about implications of preparing a device
for market, and yet another on communication with
people outside of biomedical engineering – interacting
with medical staff or disabled clients, understanding their
need, making a device to meet that need and explaining
to them how to use it).
We believe that these scenarios will motivate students to
• learn at a deeper level – you only really understand
the theory when you try to apply it,
• use their initiative and creativity
• ‘make connections across subjects and out into the world’
• see the importance of developing the non-technical skills
that are rightly valued by employers
17
18 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
ASPIRE CREATe – a new centre of excellence in
rehabilitation engineering and assistive technologies
AUTHOR: ANNE VANHOESTENBERGHE
To bring academic research ever closer to the patients
and medical teams, the Department of Medical Physics
and Biomedical Engineering is taking part in a new joint
research venture between the ASPIRE Charity, UCL,
and the Royal National Orthopaedic Hospital (RNOH):
the ASPIRE Centre for Rehabilitation Engineering
and Assistive Technology (or CREATe). Based at UCL’s
Stanmore campus, on the grounds of the RNOH in leafy
north London, the centre was established in early 2014
to develop translational research to improve the quality
of life of people with spinal cord injuries (SCI) and
other neurological conditions.
Our links with the department are strong; indeed one of the
founding members, Dr Anne Vanhoestenberghe, spent the
first 10 years of her career in the department before moving
to the Institute of Orthopaedics and Musculoskeletal Science
to found CREATe. She remains a close collaborator of Prof
Donaldson’s Implanted Devices Group. Building on this
excellent experience, the departments Dr Lynsey Duffell
joined the team in March this year.
As the name might suggest, at the Centre for Rehabilitation
Engineering and Assistive Technology, we blend assistive
technology with advanced rehabilitation devices and novel
interventions to actively promote neuroplasticity and support
the restoration of function. The biomedical engineering
techniques we develop are often applicable to related areas
of interest, such as stroke and muscular dystrophy, and the
demands of amputees and an ageing population.
Whole body rehabilitation
A key principle of our work is the idea of Whole Body
Rehabilitation; enhancing a patient’s own plasticity with
interventions such as electrical stimulation and acute
intermittent hypoxia, combined with novel engineered
solutions and physical therapy (assisted locomotor training or
cycling for example), to improve the patient’s quality of life.
This holistic approach is especially crucial for patients with
complex disabilities such as spinal cord injuries, brain injuries
and musculoskeletal disorders. Instead of considering each
intervention in isolation, our integrated approach to a patient’s
needs and abilities combines evidence-based medicine with
state-of-the-art engineering solutions to deliver long-standing
improvements in function.
Image above: Sensewheel – an instrumented pushrim
for improving propulsion efficiency.
Practical examples of our work
Our work integrates components such as electrophysiological
signal processing and wearable environmental sensing with
robotic and haptic systems. We also explore the importance
of the environment (in the home and community as well as in
a virtual space) on social integration and rehabilitation.
Turning new ideas and untried concepts into workable
interventions is a core strength of the centre. Currently we
are instrumenting a wheelchair and an exoskeleton, so that
they can automatically acquire information about their
surroundings to assist the users driving them with the finer
details of manoeuvring in a crowded environment, depending
on the cognitive load they experience. This method is known
as adaptive shared control. Another stream of work is focused
around the development of devices that actively suppress
essential tremor, along with others that address phantom
limb pain, to assist in reach and grasp rehabilitation for stroke
patients and promote social and collaborative skill development
for adults with brain injuries and children with autism. These
advances are integrated in a single unit called the ROBIN
(Rehabilitation of Brain Injuries) system, a highly configurable
19
setup that promotes the restoration of upper limb function
through a combination of electrical stimulation, haptic
tasks and virtual reality.
We are also developing fully implantable devices that monitor
and record nerve and muscle activity that can then be used in
control algorithms to drive prosthetic limbs or control artificial
organs. Our work on implantable devices also includes the
instrumentation of orthopaedic implants to measure the
forces acting on them in situ within the patient (e.g. tibia,
elbow, shoulder).
Some of our more translational work includes our ongoing
collaboration with the London Spinal Cord Injury Research
Centre at the RNOH to develop neuromodulators that reduce
spasticity and control the bladder and bowel after spinal cord
injury. These devices send small electrical impulses to the
nerves via disposable adhesive electrodes applied on the skin,
which allows control of both organs and muscle contractions.
The centre is currently home to five academics; Dr Tom
Carlson, Dr Lynsey Duffell, Dr Rui Loureiro, Dr Stephen
Taylor and Dr Anne Vanhoestenberghe, along with their
research teams. We have strong links with several departments
in the faculty of Engineering- including of course Medical
Physics and Biomedical Engineering- as well as with the John
Scales Centre for Biomedical Engineering lead by Prof Blunn,
and the Biomedical Instrumentation Group led by
Dr Holloway at the PAMELA facility.
As well as the skills and experience found at the RNOH,
ASPIRE and UCL, the ASPIRE CREATe team draws upon the
expertise of their collaborators at Imperial College London, the
University of Reading and Middlesex University here in the
UK, the Swiss Federal Institute of Technology, the University
of Freiburg in Germany, the Université libre de Bruxelles in
Belgium, Ritsumeikan University in Japan and the University
of New South Wales in Australia. The centre has also forged
links with the world-renowned Rehabilitation Institute of
Chicago and the Toronto Rehabilitation Institute.
Learning with ASPIRE CREATe
Central to our vision for the future is the development of
world-class teaching, which will itself help shape future
academics and clinicians who will then go on to contribute to
our mission. With this in mind, we will, in September 2015,
start a brand new MSc in Rehabilitation Engineering and
Assistive Technologies, which will be taught on the
Royal National Orthopaedic Hospital site to promote
strong interactions with our medical collaborators.
Image above: Working with an exoskeleton: a person
with spinal cord injury carrying out robotic gait training
on the lokomat®.
Image below: Functional Electrical Stimulation can
allow people to cycle, providing mobility and exercise.
20 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Schools, shows and pubs
AUTHORS: ADAM GIBSON AND CLARE ELWELL
This has been a particularly successful year for
those members of the Department involved in
public engagement and outreach. Medical Physics
and Biomedical Engineering are ideal for engaging
young people and the public as they allow concepts
in science and engineering to be related to everyday
activities which people may already be familiar with.
Over the last year, we have led public engagement and
outreach activities which have reached over 3000 people.
Activities which are aimed at adults are generally referred to
as public engagement, while those aimed at school students
come under outreach, though in practice there are overlaps.
Probably the biggest set piece public engagement activity last
year was the Biomedical Optics Research Group’s contribution
to a UCL/Wellcome “On Light” festival, led by Prof Clare
Elwell. We persuaded members of the public to exercise on
an arm ergometer (basically an exercise bike for the arms)
while we measured the oxygenation of blood in their arms
with near infrared spectroscopy (NIRS). As well as generating
lots of noise and interest this demo gave us the chance to
explain how our optical monitoring and imaging is being
used in a wide range of clinical and research projects. We
also demonstrated how a video camera can be adapted to
measure pulse rate just by looking at the changes in colour
of the hand as capillaries fill and empty with the pulse cycle.
Image above: Laura Dempsey, Sabrina Brigadoi,
Thomas Dowrick and Pilar Garcia Souto at the SET
for Britain competition in Parliament.
Image below (left): Danial Chitnis with a demonstration of
colour mixing at the UCL/Wellcome On Light exhibition.
Perhaps the bravest examples of public engagement have
been Gemma Bale’s forays into science comedy through Pint
of Science, Science Showoff and a Bright Club performance
to a packed Bloomsbury Theatre. Her Science Showoff and
Bright Club stand-up routines included dreadful puns and
making a model of the brain out of beer, gin, Baileys and
grenadine which she shone light through and then drank!
Gemma has also been involved Brilliant Club and various
schools activities from primary to A-level. Unsurprisingly,
given the range and excellence of her commitment to public
engagement and outreach, she was awarded first prize in
the 2015 Provost’s Engineering Engagement Awards.
Dr Jo Brunker and Dr Jenny Griffiths (of the Institute of
Biomedical Engineering) were also recognised at the Provost’s
Engineering Engagement Awards for their contribution
to outreach at a range of schools and other events. Among
other events, Jo has been a STEM volunteer at the Big Bang
UK Young Scientists and Engineers Fairs, and Jenny led a
Royal Institution Engineering Masterclass. Along with Prof
Clare Elwell and Dr Karin Shmueli, Jo and Jenny have also
contributed to wide range of Women in STEM activities.
21
In October 2014 Prof Clare Elwell won Inspirational Teacher
at the Inspiration Awards for Women and Dr Karin Shmueli
won the UCL Top Teacher award as voted by the UCL medical
students. Between June and December 2014 Dr Dean Barratt
organised a public exhibition in the UCL Octagon Gallery
which explored the impact of advances in technology on the
diagnosis and treatment of prostate cancer and perceptions
of ill-health in men. The exhibition contained historical art
and objects, dating as far back as Ancient Egypt, as well as
contemporary objects illustrating state-of-the-art medical
imaging and surgical technologies.
The Department has frequently been heavily represented at
SET for Britain, an event where scientists and engineers present
posters explaining their research to MPs in the House of
Commons. This year, seven out of UCL’s 17 contributors were
from Medical Physics and Biomedical Engineering, covering
the whole diversity of our work from imaging to radiotherapy.
Many members of the Department take part in schools
outreach events, and we have open days, masterclasses and
workshops for A level students based in the Department.
One highlight was at Henry Maynard Primary School who
invited us in to support their Science Week. One morning,
Laura Dempsey, Dr Jenny Griffiths, Dr Thomas Allen and
Dr Charlotte Hagen held workshops for Years 3 and 4 on
light, biomedical engineering, ultrasound and x-rays which
included hands-on experience with an ultrasound scanner,
pulse oximeters and quizzes.. At the same time, Prof Adam
Gibson led assemblies and explained the science behind
Frankenstein by demonstrating electrical stimulation of
his leg. Prof Alan Cottenden took our outreach activities
continental when he spoke with a group of 7 and 8 year olds
at the European School of The Hague in the Netherlands.
Outreach and public engagement have been highlights of the
Department’s work for many years, but the breadth of activities
this year has been striking. We firmly believe that Medical
Physics and Biomedical Engineering provide accessible routes
into science for people who are not specialists because the
science and engineering are clearly used to solve real-world
problems which can have a direct impact on people’s lives.
Image top: Laura Dempsey and Sabrina Brigadoi
explaining oxygenation changes during exercise measured
with Near Infrared Spectroscopy at the UCL/Wellcome
On Light exhibition.
Image above: Pupils from Henry Maynard Primary School
examining a hip implant.
22 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
4D Treatment Planning Workshop
AUTHOR: JAMIE MCCLELLAND
On the 28th and 29th November 2014, the 4D
Treatment Planning Workshop was held at Moorhall
conference centre in Cookham, just outside London.
This was jointly organised by Dr Jamie McClelland from
UCL and Dr Antje Knopf from the Institute of Cancer
Research. This is the sixth time the workshop has taken
place, but the first time it has been in the UK.
The workshop covered all aspects of planning and delivering
Radiotherapy treatments to moving targets, including
Proton Therapy (which is due to be available at UCH and
the Christie Hospital in Manchester from 2018) and other
Particle Therapies, as well as conventional Photon Therapy. The
workshop featured twelve invited talks by world leading experts
in the field, as well as an extensive poster session where other
participants could present their work.
The aim – as with previous workshops – was to bring together
senior and more junior researches in an informal atmosphere,
to promote plenty of discussion covering the unsolved problems
and challenges facing the field, and the future directions that
the work should take.
The workshop was attended by almost sixty participants,
including some from the US (even though it was Thanksgiving
weekend!) and Japan. The workshop was a great success and
lots of positive feedback has been received. Slides from most
of the invited talks, together with the abstracts for all poster
presentation, can be found on the workshop website at:
http://4d-treatment-planning-workshop-2014.cs.ucl.ac.uk
(look under workshop program).
There is an article on medicalphysicsweb about the workshop,
focussing on the talks on MR guidance and Ultrasound
guidance for Radiotherapy, which can be found here:
http://medicalphysicsweb.org/cws/article/opinion/59650.
As in previous years a report from the workshop is being
written, which will be published in the coming months.
2015’s workshop will be held in Dresden, Germany, with the
plan for the workshop to return to the UK in 2016. If you
would like to be added to the email list to receive news about
the future workshops please email j.mcclelland@ucl.ac.uk.
23
Image gallery
Images of the department at work. All images copyright ©Getty Images 2015. All rights reserved.
24 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Selected grants 2014 –15
Sponsor
Project Title
Total
award
Investigator
EPSRC
Model-based treatment planning for focused ultrasound energy
£870,656
Dr Bradley Treeby
IoE/UCL
Introduction and assessment of a new robust peer-assessment
in Engineering
£3,750
Dr Pilar Garcia
Souto
Integrated
Technologies Ltd
Development of a nasal blockage analyser using acoustic sensors
£33,933
Dr Terence Leung
Bill and Melinda
Gates Foundation
Developing brain function-for-age curves using novel
biomarkers of Gambian and UK infants
£399,963
Prof Clare Elwell
European
Commission FP7
The simulation of breast surgical lumpectomy and surgery
planning through an isogeometric numerical analysis approach
£173,462
Prof David Hawkes
NIHR
Clinical translation of novel imaging methods for assessing
moving structures in inflammatory diseases of the bowel or lung
validation and clinical translation of novel imaging biomarkers
of cancer heterogeneity
£20,000
Prof David Hawkes
Glaxosmithkline Research
and Development Ltd
GSK pilot study
£195,289
Prof David Holder
Blackrock Microsystems
Electrical Impedance Tomography of fast neural activity in the
brain dring epilepsy or evoked activity
£66,113
Prof David Holder
European
Commission FP7
Improving physical dosimetry and developing biologicallyrelevant metrology for spot-scanned proton therapy beams
£187,181
Prof Gary Royle
Mauna Kea Technologies
Online Super-resolution for fiber-bundle based video
acquisition medical devices
£94,888
Dr Tom Vercauteren
Wellcome Trust
Controlling abnormal network dynamics with pptogenetics
(CANDO)
£887,921
Prof Nick Donaldson
Glaxosmithkline Research
and Development Ltd
Innovation challenge fund
£70,656
Prof Nick Donaldson
Innovate UK
Project composite aircraft NDE (Project CAN)
£334,226
Prof Robert Speller
STFC
Prompt gamma Compton camera for proton therapy
£117,196
Prof Robert Speller
Nikon Corporation
Evaluation of X-Ray phase contrast imaging (XPCI) technology
£49,648
Prof Sandro Olivo
The Home Office
Detecting explosives and weapons via high-throughput
multi-modal X-Ray imaging
£366,970
Prof Sandro Olivo
MRC
The UK GENetic Frontotemporal dementia Initiative
(UK GENFI)
£471,455
Prof Sebastien
Ourselin
National Institute For
Health Research
Centre for doctoral training in medical imaging PhD
studentship
£94,880
Prof Sebastien
Ourselin
Wellcome Trust
The fusion of optical and magnetic resonance spectroscopy
technologies to deliver novel multimodal methods to
investigate brain injury in adults and neonates
£528,436
Dr Ilias Tachtsidis
25
PhD award successes
Pankaj Daga (28/10/14)
Towards Efficient Neurosurgery: Image Analysis for
Interventional MRI
Stefano Pedemonte (28/06/14)
4-D Tomographic Inference: Application to SPECT and
MR-driven PET
Sabrina Falloon (28/12/14)
An Experimental Study of Friction Between Wet and Dry
Human Skin and Nonwoven Fabrics
Teedah Saratoon (28/10/14)
Gradient-Based Methods for Quantitative Photoacoustic
Tomography
Uran Ferizi (28/11/14)
Compartment Models and Model Selection for In-Vivo
Diffusion-MRI of Human Brain White Matter
Harikrishn Varu (28/09/14)
The optical modelling and design of Fabry Perot Interferometer
sensors for ultrasound detection
Valentin Hamy (28/07/14)
Improving Accuracy of Information Extraction from
Quantitative Magnetic Resonance Imaging
Johann Wanek (28/07/14)
Direct Action of Radiation on Mummified Cells: Modelling
of Computed Tomography by Monte Carlo Algorithms
Vanessa La Rosa (28/08/14)
Proton-Induced X-ray Emissions from Metal Markers for
Range Verification in Eye Proton Therapy
26 | UCL Medical Physics and Biomedical Engineering | Newsletter 2015
Prizes
INSPIRATIONAL TEACHING AWARD
PHD SHOWCASE
Many congratulations to Prof Clare Elwell who was the
winner of the Inspirational Teaching Award, part of the
Inspiration Awards for Women 2014.
The annual Medical Physics & Biomedical Engineering PhD
Showcase was held on the 24th April 2015 where all third year
PhD students gave a short and accessible ‘snapshot’ of their
key research goals using just five PowerPoint slides to give a
greater awareness of the breadth of research activity within the
department. Prizes were awarded in three categories and the
winners were as follows:
These Inspiration Awards for Women are run by the
Breakthrough Breast Cancer charity and celebrate the
achievements of remarkable women who inspire those around
them either through the media or through their astounding
achievements in their everyday lives.
TOP TEACHER AWARD
Congratulations to Dr Karin Shmueli who won a top teacher
award for Year 3 IBSc. Throughout the course of the year, UCL
Medical School students are given the opportunity to nominate
teachers who were particularly helpful or inspiring to them
during their studies. In 2013–14 students cast over 1000
votes, from which there are 65 award winners.
UCL ENGINEERING/ROYAL ACADEMY
OF ENGINEERING TECHNICAL
COMMUNICATION AWARDS
The prize for Best Overall Communicator went to
Edward James, a first year MEng Biomedical
Engineering student.
THE ANNUAL STUDENT PRIZE AWARD
CEREMONY
Samuel Searles-Bryant: John Clifton Prize for Best
performance by a non-final-year undergraduate.
Phong Thanh Phan: Sidney Russ Prize for Best performance
by a final-year undergraduate.
Kehao Wang: Joseph Rotblat Prize for Best performance
by an MSc student.
James Breen-Norris: IPEM Prize for Best MSc project.
Gemma Bale: Medical Physics & Biomedical Engineering
PhD Prize.
Gemma Bale: Presentation Style
Andrada Ianus: Enthusiasm and Engagement
Markus Jehl: Communication of Ideas
PROVOST’S ENGINEERING
ENGAGEMENT AWARDS
The Provost’s Engineering Engagement awards were announced
on Monday 11th May. Congratulations to Jo Brunker, Gemma
Bale and Jenny Griffiths, who were recognised for their
excellence in engaging young people in engineering.
27
Prize Winners Gallery
Image top: Student Prize Award Winners, clockwise from top left: Samuel Searles-Bryant, James Breen-Norris, Kehao Wang,
Gemma Bale and Phong Thanh Phan. Image above (left): Gemma Bale winning the Provost’s Engineering Engagement Award.
Image above (right): Jo Brunker receiving her Provost’s Engineering Award certificate from Prof Michael Arthur, Provost,
and Prof Anthony Finkelstein, Dean of Engineering.
Cover Image: Scintillation of a therapeutic proton beam
Adam Gibson and Mansour Almurayshid
Protons travel through tissue, depositing energy as they go, but deliver most of the energy at a fixed distance into tissue.
Here, we show a proton beam entering a scintillating liquid from the top of the page. The blue glow gets brighter as the protons travel
further into the liquid, reaching a peak at a depth of a few centimetres. The challenge of proton therapy is to steer the direction and
energy of the beam to “paint” the tumour with the bright part, ensuring the tumour gets sufficient radiation dose to destroy it while
minimising the dose elsewhere. This image was taken using a standard SLR camera looking at a beam of protons entering a tank
of tonic water, which scintillates when irradiated. The small bright spots occur when other types of radiation hit the detector
of the camera. This work was carried out at the Douglas Cyclotron at Clatterbridge Cancer Centre with the support of our
2015 Joel Lecturer, Dr Andrzej Kacperek.
CONTACTS
Department of Medical Physics and Biomedical Engineering
University College London
Gower Street
London WC1E 6BT
Web: www.ucl.ac.uk/medphys
Tel: 020 7679 0200
Email: medphys.newsletter@ucl.ac.uk
Twitter: @UCLMedphys