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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)

Investigating neurovascular coupling in infants with seizures using EEG and DOT

Adam PGibson19 October 2017

By Aman Ganglani

Over the summer I was lucky enough to undertake an eight-week research project in the Biomedical Optics Research Lab (BORL) with the research group focusing on diffuse optical tomography.

Using data acquired from simultaneous electroencephalography (EEG) and diffuse optical tomography (DOT) measurements from the NTS system (developed by Gowerlabs), we looked at the relationship between cerebral blood flow and seizures in neonatal infants with hypoxic ischemic encephalopathy (HIE).  This work follows a previous investigation by the group titled ‘Mapping cortical haemodynamics during neonatal seizures using diffuse optical tomography: A case study’ [1]. The data analysed in this study is from the same patient as the previous investigation.

Figure 1 - The GowerLabs NTS system

Figure 1 – The GowerLabs NTS system

Most of my work was done in Matlab. By employing various statistical tests and by creating my own scripts with the help of the department I further understood the relationship between neonatal seizures and cerebral haemodynamics. Through my own investigation and discussions with the DOT team in formal weekly meetings, I was able uncover patterns and identify further research topics.

A lot of my work was concentrated on the relationship between oxy/deoxy haemoglobin (HbO and HbR respectively) and the spikes on the EEG which indicated seizure like activity. I was able to demonstrate the HbO signal leading the EEG signal through cross correlation tests and visual inspection. I was also able to show evidence of the ‘initial dip’ phenomenon and understood why it remains to be controversial given how it was not seen in every seizure (the ‘initial dip’ phenomenon is observed when there is a dip in HbO prior to a seizure). We also found other time correlations with HbR which warrants further investigation. I ran various other statistical tests such as t-tests to validate my results. Along with this, I also looked at the derivative to investigate if a sudden change in the EEG correlates to a sudden change in haemoglobin levels. Given how I previously found a time lag between the haemoglobin signals and the EEG signal, it came as no surprise that there was no direct correlation without a time lag. I also identified further research topics such as investigating the phase difference between the HbR and HbO signal along with further statistical tests that could be employed on more datasets. All of my code was commented on to specifically allow for other people to continue my work.

Along with the analysis work I was also able to visit the Evelyn Perinatal Imaging Centre at Rosie hospital in Cambridge. This was where the patients were scanned with EEG and DOT, and I could see how the devices built in the university were tailored to a hospital environment. By then attending meetings with neoLAB. I understood some of the challenges faced by engineers to connect their products with hospital staff. I was also able to do some brief work on image reconstruction which gave me an exciting scope to the future of DOT imaging.

I would like to thank the Engineering department for this amazing opportunity to be a part of this phenomenal project. Everyone at BORL has been incredibly friendly and approachable. A special thanks to Ms Dempsey, Dr Cooper and Dr Hebden for their never-ending support. This opportunity has given me a fantastic insight into the world of research and I look forward to being a part of it.

Figure 2 - Laura Dempsey and me with the NTS kit.

Figure 2 – Laura Dempsey and me with the NTS kit.

[1] H.Singh, R.Cooper, C.Lee, L.Dempsey, A.Edwards, S.Brigadoi, D.Airantzis, N.Everdell, A.Michell, D.Holder, J.Hebden, T.Austin. (2014). Mapping cortical haemodynamics during neonatal seizures using diffuse optical tomography: A case study. NeuroImage: Clinical. 5

The Laidlaw Leadership and Research Programme

Adam PGibson6 October 2017

By Lorenzo Molinari

During one of my study sessions in the IoE library, I came across a banner promoting “The Laidlaw Leadership and Research Programme”. Curious to know more about the scheme, I googled it and I started reading more. It took me two minutes to fall in love with it: two summer research-projects fully funded, a series of training workshops of the theme of leadership and ambassadorial work in different universities across the UK. It was undoubtedly a fantastic opportunity for first years and I didn’t think twice before apply!

The project I was involved with during my first summer is called  “Brain Detectives: Design Experimental Task Design”, organised and hosted by the Centre for Research in Autism and Education (CRAE). During the course of six weeks, I took part in so many activities and here I’ll describe a few:

I went to special schools to help other researches run an Autism Diagnostic Observation Schedule test (ADOS), which is the standardised measure for assessing autism. Having nev er been in contact with autistic people in my life, this experience was fundamental for me to see with my own eyes who I was working for and to elucidate what the ultimate aim was: to improve the quality of life of autistic people. I also had the chance to talk to teachers and discuss more about the advantages of being in a special school, where each child is thoroughly followed and sustained during their learning process.

The picture shows the setting of an ADOS: participants were asked to play with different toys and their responses were noted down and later assessed by an ADOS-trained expert.

The picture shows the setting of an ADOS: participants were asked to play with different toys and their responses were noted down and later assessed by an ADOS-trained expert.

I contributed to the organisation, planning and running of CRAE’s research initiative and public engagement science workshops; Brain Detectives. Brain Detectives invites children and young people to take part in half-day workshops within the research lab where they engage in fun, interactive activities, designed to help them explore how the mind and brain work, whilst also participating in real psychological research. The event ran for six days, with two four-hour sessions (morning or afternoon) scheduled per day. During these sessions, I was responsible for leading the collection of my own research project data, to investigate whether autistic and non-autistic young people who took part possessed an enhanced perceptual load capacity by running a specially designed research task. Essential to the success of the workshops, is a team work ethos and I also contributed to many other aspects of the sessions, including meeting families, helping other researchers run their tests, and co-creating and delivering workshop presentations and activities.

This is me (!) next to the fantastic Brain Detectives banner. Please, note the wooden badge on my t-shirt - directly from the Institute of Making!

This is me (!) next to the fantastic Brain Detectives banner. Please, note the wooden badge on my t-shirt – directly from the Institute of Making!

I secured and electronically stored all the data that I collected, to then perform statistical data analysis to confirm the hypothesis raised in the research question. In order to do so, I have been trained on how to use the statistical software SPSS-Statistics to run correlation, regression and normality tests. Owing to the success of my project, I agreed with my supervisor to write a final report of approximately 5000 words, following the format Introduction, Methods, Results and Conclusion. I was able to write a literary review for the Introduction and the Methods of the experiments even before the beginning of our testing, but I had to wait until the end of our testing sessions to write up the Results and Conclusion.

The experience I had at CRAE is simply invaluable: researchers were very supportive and able to help me whenever I struggled, the environment was always very professional and motivated me to work harder and harder and, last but not least, I had so much fun with my colleagues outside working hours.

If you are interested in a career in academia or if you are looking for a research experience in early stages of your academic career, the Laidlaw scheme is definitely what you are looking for. Personally, I am now even more convinced that what I want to do in my future is pursuing an academic career.