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Fibreless Diffuse Optical Tomography summer internship

Adam PGibson31 October 2018

by Aman Ganglani

Over the summer I was lucky enough to be given a leading role in an 11 week research project working with Dr. Robert Cooper, Dr. Hubin Zhao and Dr. Sabrina Brigadoi on a fibreless Diffuse Optical Tomography (DOT) system.

DOT is a novel imaging technique that has a wide variety of applications in neuroscience and clinical research. Specifically, using DOT to investigate neonatal brain development is a very important focus. Cerebral haemodynamic patterns in brain injured neonates is not well understood. Complications at this vital stage of development can result in critical danger to the patient and long-term disabilities. Further investigation into these complex haemodynamic signals is necessary to better understand the underlying physiology and to develop DOT into a novel imaging tool that could help diagnose and treat compromised infants [1].

Current DOT technology is limited by bulky fibres which limit comfort, movement and ease of use. Transforming the current DOT systems into wearable, fibreless devices is a vital step in the development of DOT technology [2]. This advance will enable long term clinical application of DOT, improve data quality and make the instruments viable in a wider range of applications. However, transforming the bulky wearable DOT modules into a fibreless wearable comes with challenges. This investigation aimed to minimize motion artifacts with fibreless systems. While there are post processing methods of tackling motion artifacts [3], they alone are not enough for fibreless systems. Our novel approach has been to develop the application of motion sensors specifically for this type of movement and add them to the current fibreless systems to build the world’s first dataset of fibreless DOT and 9 axis (3x accelerometer, 3x gyroscope and 3x magnetometer) motion data.

Testing the motion sensors

Testing the motion sensors

We decided to focus our investigation on the effect of forced induced movement on DOT data. We introduced two 9 axis motion sensors along with 2 DOT fibreless modules each containing a 9 axis motion sensor. Our experiment paradigm consisted of controlled head, eyebrow and full body movements.

After many considerations, we purchased two Razor 9DoF motion sensors containing the MPU_9250 Invensense chip which is the same sensor used on the DOT modules. I was able to match the operating conditions of the chip with the DOT chip by writing my own code in the Arduino IDE and MATLAB. This would ensure data acquired from both sensors could be accurately compared.

Due to the DOT modules being standalone devices, I also had to figure out a way of mounting everything (the two DOT modules and the two motion sensors) in a comfortable way. After a lot of experimentation and time in the Institute of Making, I managed to build my own headgear system which kept all the sensors completely independent of each other. The DOT modules were secured using separate sewn velcro and rubber band straps while the motion sensors used adhesive tape placed directly on the scalp.

Design of the headgear system

Design of the headgear system

Finally, all this preparation was for the experiment paradigm itself. We eventually decided we wanted to investigate the effects of eyebrow movement (this has not been explored and previous pilot studies showed large eyebrow related artifacts), the effect of scalp movement compared to head movement and induced head movement along with walking and designed a paradigm accordingly.

Within each block, chirp noises of decreasing lengths were used. When the subject hears the chirp, they must move their head throughout the chirp, this way we can control the speed of movements. Varying the speed of these movements is useful because is allows us to look at relationships between the sizes of motion artifacts and the speed of movement. The speaking section was done with words of varying syllables for the same reason. The timing of eyebrow movement was controlled by a simple tone sound rather than a chirp, because it is difficult for people to control the speed of eyebrow raises.

Dr. Cooper just before a pilot study

Dr. Cooper just before a pilot study

Additionally, I created a MATLAB script which would efficiently run everything with one press of a button using parallel computing. This massive streamlining of the whole experimental procedure will make studies synchronised and far easier to run. Our aim in the first term is to use my experiment to run multiple studies on a variety of healthy adult volunteers.

Our initial conclusions show that more investigation into 9 axis data with fibreless systems is clearly justified. I was able to help publish a poster which was presented at the fNIRS 2018 conference in Japan titled ‘Investigating the Benefits of Integrated Motion Sensing and Wearable, Modular High Density Diffuse Optical Tomography’, of which I was an author.

This has been an incredible experience. In 11 short weeks, we have managed to build and execute an experiment paradigm which has never been done before. I have been exposed to real research and have obtained a publication under my name by having my work presented at a conference. I will continue to work with the team throughout the first term.

I would like to thank Dr. Zhao, Dr. Brigadoi and Dr. Cooper for their never-ending patience and commitment. They have exposed me to world-leading research and have given me an excellent insight into the life of an academic.

Our poster at fNIRS 2018 in Tokyo

Our poster at fNIRS 2018 in Tokyo

1 Cooper RJ, et al. Transient haemodynamic events in neurologically compromised infants: a simultaneous EEG and diffuse optical imaging study. Neuroimage (2011).
2 Danial Chitnis, et al. Functional imaging of the human brain using a modular, fibre-less, high-density diffuse optical tomography system. Biomed Opt Express. 10 (2016)
3 Cooper, R. J. et al. A Systematic Comparison of Motion Artifact Correction Techniques for Functional Near-Infrared Spectroscopy. Front. Neurosci. 6, (2012)

A breath of fresh air

Adam PGibson14 March 2018

By Rebecca Yerworth

How do you let steam out of you kitchen if the only window is behind the kitchen sink and, as an octogenarian you can no longer climb on the work-surface to reach the handle? We gave our second year biomedical engineers one week to find a solution.

At first it seemed trivial – just put a hook on a stick… but then they met the 87-year old client and realised that wielding anything much heavier than a cup of tea was going to be a problem, and she would like to be able to store the aid on the kitchen work surface.  … and don’t forget the screw on the bottom bracket which is needed to stop the open window flapping about in the breeze.

By Friday afternoon all the student teams had a device which they could use to open the window, and were waiting in trepidation for the client to test them out.  “Bit heavy”, “nicely finished”, “easy to use”, were some of the comments heard. Different solutions were found to the issue of weight, from using intrinsically light bamboo to strategically shaping wooden planks to reduce their weight, to not using a pole at all – just use pulleys. Seven different ideas from seven teams.

Window Opener being tested

Window Opener being tested

During the week students put into practice skills they had learnt in other modules – included user-centered design, and the practical implications of material choice. They also learnt new skills as they made good use of the tools in the biomedical engineering teaching laboratory and in UCL’s MakeSpace.

This project is inspired by the work of REMAP, a national charity specialising in custom making aids for elderly and disabled people, where no suitable aid is commercially available. UCL staff and students have recently set up a REMAP-affiliated group Impactive. Volunteers from both organisations gave an inspiring talk to the students at the beginning of the week, and it sounds like they have gained some new volunteers: Biomedical Engineering students putting their skills to good use even before they graduate – well done and keep it up.

Visiting the Stanmore Royal National Orthopaedic Hospital

Adam PGibson1 March 2017

by Madeline Lok, Emma Ponting and Sarita Meekul

On Friday 27th of January, our 2nd year Biomedical Engineering class got the opportunity to visit the Stanmore Royal National Orthopaedic Hospital. The purpose of the trip was for us to gain an understanding of how the clinical environment works and how devices we may help to create in the future fit into real people’s lives.

rhoh3The day began early with a long journey on the tube to Stanmore, on the outskirts of London where the class met. After a short taxi ride to the hospital, we were met by Professor Hart at the London Implant Retrieval Centre (LIRC). Prof Hart is the director of research and development at LIRC and a consultant orthopaedic surgeon at the hospital. He gave us a warm welcome and introduced us to some of the PhD students working there. At LIRC they recover and study knee and hip replacement implants that have been removed from patients to better understand why they failed. We were shown the processes these implants go through once they arrive, from cleaning to being scanned for wear and deformation and got to hold some actual implants. It was very interesting to see how something that we learn about in lectures actually looks and feels in real life.

rnoh1Then the lovely people of LIRC kindly provided us with lunch with their team. This was a good chance to chat to the people who work in the hospital and get a better insight into the kind of jobs available that we might be interested in once we graduate.

After lunch, we were split into smaller groups; some went to watch the surgeries while other went to sit-in with the doctors and their patients for real consultations. We swapped after 1.5 hours.rnoh4

We were brought to the surgery area to be able to see a real operation taking place. Before entering the operation theatres, we changed into scrubs. We were then separated into pairs and entered different theatres. Among all of us, we saw a range of operations including hip replacements, knee replacements and one ankle-foot correction surgery. We were told that the ankle-foot surgery is one of the most complicated and delicate procedures. The doctor that took us in even made a joke about how he avoided it. They used x-rays during that operation so we had to wear a lead apron to protect ourselves from the radiation. Some others of us saw the removal of implants, which was completely opposite of what the others saw. It was interesting to be able to discuss our different experiences at the end of the day when everyone was together.

Within the operating theatre, the surgeons explained to us what and how they were performing this surgery. Most of us were surprised by the atmosphere in the operating room. It was very relaxed with music playing in the background. The anaesthetist was reading his Kindle; the surgeons were even able to have a conversation and joke about their family while operating on the patient. It was surprising to see how calm and confident they were. Due to the time constraints, none of us were in there for the whole process which was a pity because we all really enjoyed it.

rnoh2The consultation sessions were an eye-opening experience too. We had the opportunity to sit through a few consultations with an orthopaedic specialist doctor, and see how they interact with their patients. All patients had very different reasons to be there, so we got to see various cases, the medical images used, and procedure followed. After sitting through the consultations, we now have a better understanding of what doctors go through when seeing patients and it definitely is a very difficult job. It’s not all smiles, hellos, reassurance and prescribing treatments as some people would think. In reality, they are potentially the ones who would be telling you how you would live out the next 10-20 years of your life (in our case, with hip/knee replacements, constant rehab, medication and so on). They have to always maintain professionalism and courtesy no matter how their patients react to whatever they tell them; even answer questions about their other concerns whether or not it is related to the real reason they came in for the consultation in the first place. The most important take-away I had from the session was that the doctors should let the patients leave with the best reassurance they can provide.

We all had a great day and learnt a lot about working in a clinical setting and working with patients. We would like to say a massive thank you to a ll of the people at Stanmore hospital who helped in making this day happen! What a day and what an experience!

Peer assessment in group work

Adam PGibson13 May 2016

By Pilar Garcia Souto

UCL Engineering trains students to use engineering knowledge within extended group practical activities to better prepare them for their careers after graduation. However, despite the substantial educational benefits of getting students to work in teams, students express and experience concerns that significantly decrease the student satisfaction.

We decided to look deeper into this matter and organized student focus groups across the Engineering Faculty, and spoke with various members of staff that use and assess group work. The message is clear: an element of “individual contribution” is needed, possible set by peers and tutor moderated, which improves the group dynamics and penalize the “passengers”. Otherwise students frequently express dissatisfaction if all members of a team are given the same mark regardless of the individual effort.

The concept is simple. At the end of a group work students rate the contribution of each team member, and this is used by the tutor to generate an individual mark. This encourages self-reflection, increase student satisfaction and reduce student’s complaints. The only major drawback is that the peer assessment of individual contribution is mainly collected using pen and paper, hence very staff consuming, as current e-learning tools are inadequate. From our research, this tool should be online, anonymous, preferable within Moodle and flexible so staff can adapt it and ask or value different aspects (e.g. reliability, punctuality, contribution to ideas, etc.).

This is an ongoing project. We presented some results at the UCL Teaching and Learning conference in April 2016, which attracted a lot of interest. It is clear that individual contribution assessment is something that staff from across UCL want to implement, and yet we lack the appropriate system. We decided to take the lead on establishing a consortium with those interested, and seek for some funding to develop an appropriate system within Moodle that would allow us to efficiently incorporate this practice into our teaching. If you are interested on participating and/or hearing more of our results, please contact p.garciasouto@ucl.ac.uk.

Our thanks to ELDG 2015 who partially funded this project.

Pitching UCL Biomedical Engineering Inventions To A Panel Of Dragons

Adam PGibson11 April 2016

By Jenny Griffiths

We made an unusual homework demand on our second year Biomedical Engineers over the Christmas vacation: they had to watch TV.

The students were asked to use UCL’s subscription to Box of Broadcasts to watch episodes of BBC’s Dragon’s Den in order to prepare for their first week back when they would be asked to spend a few days applying knowledge and understanding of enterprise, ethics, and regulations to medical devices.

On the first day of term, groups of students were each given a UCL Biomedical Engineering invention and told that they were to present a written portfolio and give a pitch to a panel of expert ‘Dragons’ on Friday afternoon.  They then went off, made contact with the UCL inventors of the devices, and with the help of a Teaching Assistant with a background in Medical Device Innovation, researched:

  • the devices’ capabilities
  • the market for the invention
  • routes to that market
  • ethical implications and requirements
  • medical device regulations for the device

All this information – key to bringing an engineering concept from lab to public use –  needed to be at their fingertips for the Friday presentations.

The full assignment marks for the work were split between the presentation, a written group portfolio and individual contributions to the team. We also upped the competitive element by awarding a prize for the best pitch, judged entirely subjectively by the Dragons and unlinked to any summative assessment marks.

dragons den presentation

This year’s devices were an optical ultrasound transcatheter imaging system (Dr Adrien Desjardins), a percutaneous heart valve delivery system (Dr Gaetano Burriesci) and SenseWheel – a force sensing wheelchair wheel to measure biomechanics (Dr Catherine Holloway).

On Friday afternoon, each group had five minutes to present their device to a panel of experts consisting of:

  • an academic medical devices expert
  • a Royal Academy of Engineering Enterprise Fellow
  • an academic who has commercialised a medical device through a spin-out
  • an external marketing and communications expert with no expert medical device knowledge.

The presentations were held in the appropriately intimidating Executive Education Suite, where the panel sat in high backed chairs and asked probing questions after each presentation. The students responded professionally and gave excellent pitches, selling devices that they had not know about just five days before!

Our highly sought after prize of copies of Eric Ries’ ‘The Lean Start up’ and (chocolate) money was won by team SenseWheel.

dragons den prize

In future years we aim to encourage more external Dragons to take part and will link the prize giving to an industrial careers and networking event for the students. If you are an employer who would like to be a part of this fun and valuable event, the department would love to hear from you.

Pebble in the Pond

Adam PGibson2 December 2015

By Alan Cottenden

Congratulations to the victorious Biomedical Engineering team who managed to transport their pebble the length of the assault course they had designed and built – involving a catapult, a lift, numerous slides and prodigious quantities of string and sticky tape – and deposit it in a bucket at the finishing line with fewer “interventions” (that is, manual interferences to help it on its way!) per meter of travel than either of their two rival teams. The pictures show the creators of the assault course’s four sections admiring their handiwork while savouring the taste of victory!

pebble_in_the_pond_winning_team_1

Team Catapult

pebble_in_the_pond_winning_team_2

Team Vertical

pebble_in_the_pond_winning_team_3

Team Cup

pebble_in_the_pond_winning_team_4

Team Balloon

Clinical engineering visit to Royal National Orthopaedic Hospital

Adam PGibson13 November 2015

By Nishat Ahmed and Bindia Venugopal

On Wednesday the 11th of November, we were up at the crack of dawn, pumped and ready to go to the Royal National Orthopaedic Hospital in Stanmore. After missing trains due to tube closures and our taxi rides arriving a half hour late, we finally managed to reach the hospital in time to attend the Multi-Disciplinary Team meeting.

We found the meeting very interesting, watching the consultant surgeons and nurses discuss real case studies of patients. They collaborated well to work out the best way to rehabilitate patients, whether this was through further surgery or simply giving them advice and support.

Later on we headed to the operation theatres, adhering to hospital dress code we threw on our scrubs, hair nets and masks beforehand! Since we were only allowed three students at a time in the theatres, we split into groups and then went off to watch various operations taking place. The first surgery we watched involved attaching a metal plate to a fractured tibia bone to aid its healing process in a way that was ingenious! It was fascinating watching the surgeon screw the bone together and then brace the join with a metal plate. The screws held the fracture under compression, this meant it was forced to combine together rather than slide apart, and the metal plate stopped it from twisting.

The second surgery we went to was an extremely rare case where the surgeons ended up dislocating the hip bone in order to remove a benign tumour from inside the bone. They sawed the hip bone in half as bone-to-bone healing worked best compared to tendon-to-bone healing. The challenge was in trying to avoid damaging the femoral head to get to the tumour.

After this we had a little tea break and then made way to our next surgery! This was a spinal surgery where the patient had a twisted spine due to being paralysed for 10 years. They operated with a diathermy machine which uses electricity to cut through the skin and muscles as this reduces blood loss. Although we only saw the surgery for 10 minutes we learnt how vital it was to keep the fluids in the patient regulated. This job was monitored by the anaesthetist, who informed us about the patient and the precautions which needed to be taken. Two neurophysiologists were monitoring electrical activity in the spinal cord to ensure that it wasn’t damaged by the surgery.

Scrubbed up

After an insane experience watching all the surgeries, we went to have lunch which was provided by the lovely team at Stanmore. In the afternoon we got a tour around the BME department at the hospital and learnt about all the weird and wonderful things they collect and experiments they run! In fact, we found out that they have over 6000 failed hip replacements from 25 different countries in their labs to study and analyse. They conduct experiments to research why implant failure happens in some patients the way it does, especially those with metal on metal implants. They use tools for metrology which measures the exact size of the ball and socket implants with crazy precision! This information is then used to work out the amount of corrosion that happened in the body when the implants were inserted.

Overall, we had an amazing and truly valuable experience. The entire team were extremely friendly and helpful! We loved that we could ask questions and interact with the staff so well. It was remarkable to see the transition from a real-life patient problem to actually seeing the solution executed in the surgeries. It was also encouraging to see how the hospital carries out their own research which can then be implemented to the surgery procedures in only a few years’ time.

On behalf of our whole BME department, we thank you for this experience Professor Hart and RNOH!

“Oh God this is so cool! Do we really have to stick to our budget?!”

Adam PGibson9 November 2015

By Jenny Griffiths

Scenarios are a highlight of our new biomedical engineering programme. In a scenario, all lectures stop and students spend the whole week working on a group project where they solve a biomedical engineering problem. Last week, our second year students worked with Jenny Griffiths to build articles of smart clothing. Their brief was to design and build an item of clothing to monitor a marathon runner’s wellbeing and give an alert to inform the runner and all those around them to prevent injury. Students were encouraged to be creative and develop their own solutions as long as their device met the design brief and was safe.DSC00656

Jenny provided the students with a range of components, mainly centered around the Adafruit Flora wearable arduino. We gave them sensors including temperature and pressure sensors, accelerometers, GPS, UV and light sensors and stretchy conductive rubber. Outputs included buzzers, vibration motors, Bluetooth connectivity and programmable RGB LEDs, but they were only allowed to use up to £40 for materials. The task built upon electronics modules which students took last year, and a clinical engineering module which includes lectures on transducers which the students are taking at the moment.

We put the students into random groups and let them loose!

shoesTwo groups chose to design their own sensors from scratch to monitor electrolyte concentration in sweat. They quickly learnt how challenging it is to build a robust sensor! They sewed their home-made sensors into running shirts with conductive thread and used the arduino to control LEDs based on the resisitivity of the sensor. Another group built an arm band to monitor skin temperature. They learnt that packing 10 LEDs, a microcontroller, batteries and an temperature sensor into a package the size of a iphone can lead to wiring complexities. The winning group instrumented a running shoe with pressure-sensitive pads to measure gait continuously during the running cycle. They sewed their Flora onto the shoe and daisy-chained LEDs around the shoe with conductive thread. They went shopping to find low-cost trainers which fitted a team member and also gave them something additional to write about in their sustainability analysis.

 

Range of smart clothing

Students enjoyed the scenario, some saying this was the first time they’d ever worked as a team under pressure. They were ambitious and undaunted by such an open-ended task. Despite one team doing a complete redesign at the beginning of Day 4 out of 5, project management and budgeting were good even when students were tempted to go over budget (see  title of post!). All worked hard and Jenny had fun leading it, with great support from Eve, the lab technician. All enjoyed the occasional punctuations from smoking components and whoops of success. There’s now competing demand for the clothing, with students wanting to take them home to show family and friends and us wanting to hang onto them to entice prospective students in UCAS visits to join us next year.