A contribution to unobtrusive video-based measurement of respiratory signals

Due to the growing popularity of video-based methods for physiological signal measurement, and taking into account the technological advancements of these type of devices, this work proposes a series of new novel methods to obtain the respiratory signal from a distance, based on video analysis. This thesis aims to improve the state of the art video methods for respiratory measurement, more specifically, by presenting methods that can be used to obtain respiratory variability or perform respiratory rhythm measurements. Moreover, this thesis also aims to present a new implementation of a time-frequency signal processing technique, to improve its computational efficiency when applied to the respiratory signals. In this document a first approach to video-based methods for respiratory signal measurement is performed, to assert the feasibility of using a consumer-grade camera, not only to measure the mean respiratory rate or frequency, but to assert if this hardware could be used to acquire the raw respiratory signal and the respiratory rhythm as well. In this regard a new video-based method was introduced that measures the respiratory signal of a subject at a distance, with the aid of a custom pattern placed on the thorax of the subject. Given the results from the first video-based method, a more broad approach was taken by comparing three different types of video hardware, with the aim to characterise if they could be used for respiratory signal acquisition and respiratory variability measurements. The comparative analysis was performed in terms of instantaneous frequency, as it allowed to characterise the methods in terms of respiratory variability and to compare them in the same terms with the reference method. Subsequently, and due to the previous obtained results, a new method was proposed using a stereo depth camera with the aim to tackle the limitations of the previous study. The proposed method uses an hybrid architecture were the synchronized infrared frame and depth point-cloud from the same camera are acquired. The infrared frame is used to detect the movements of the subject inside the scene, and to recompute on demand a region of interest to obtain the respiratory signal from the depth point-cloud. Furthermore, in this study an opportunistic approach is taken in order to process all the obtained data, as it is also the aim of this study to verify if using a more realistic approach to respiratory signal analysis in real-life conditions, would influence the respiratory rhythm measurement. Even though the depth camera method proved reliable in terms of respiratory rhythm measurement, the opportunistic approach relied on visual inspection of the obtained respiratory signal to properly define each piece. For this reason, a quality indicator had to be proposed that could objectively identify whenever a respiratory signal contained errors. Furthermore, from the idea to characterise the movements of a subject, and by changing the measuring point from a frontal to a lateral perspective to avoid most of the occlusions, a new method based on obtaining the movement of the thoraco-abdominal region using dense optical flow was proposed. This method makes us of the phase of the optical flow to obtain the respiratory signal of the subject, while using the modulus to compute a quality index. Finally, regarding the different signal processing methods used in this thesis to obtain the instantaneous frequency, there were none that could perform in real-time, making the analysis of the respiratory variability not possible in real-life systems where the signals have to be processed in a sample by sample basis. For this reason, as a final chapter a new implementation of the synchrosqueezing transform for time-frequency analysis in real-time is proposed, with the aim to provide a new tool for non-contact methods to obtain the variability of the respiratory signal in real-time.A causa de la creixent popularitat en la mesura de senyals fisiològics amb mètodes de vídeo, i tenint en compte els avenços tecnològics d'aquests dispositius, aquesta tesi proposa una sèrie de nous mètodes per tal d'obtenir la respiració a distància mitjançant l'anàlisi de vídeo. Aquesta tesi té com a objectiu millorar l'estat de l'art referent a la mesura de senyal respiratòria mitjançant els mètodes que en ella es descriuen, així com presentar mètodes que puguin ser usats per obtenir la variabilitat o el ritme respiratori. A més, aquesta tesi té com a objectiu presentar una nova implementació d'un mètode de processat de senyal temps-freqüencial, per tal de millorar-ne l'eficiència computacional quant s’aplica a senyals respiratoris. En aquest document, es realitza una primera aproximació a la mesura de senyal respiratòria mitjançant mètodes de vídeo per tal de verificar si és factible utilitzar una càmera de consum, no només per mesurar el senyal respiratori, sinó verificar si aquest tipus de hardware també pot ser emprat per obtenir el ritme respiratori. En aquest sentit, es presenta en aquest document un nou mètode d'adquisició de senyal respiratòria a distància basat en vídeo, el qual fa ús d'un patró ubicat al tòrax del subjecte per tal d'obtenir-ne la respiració. Un cop obtinguts els resultats del primers resultats, s'han analitzat tres tipus diferents de càmeres, amb la finalitat de caracteritzar-ne la viabilitat d'obtenir el senyal respiratori i la seva variabilitat. L'estudi comparatiu s'ha realitzat en termes de freqüència instantània, donat que permet caracteritzar els mètodes en termes de variabilitat respiratòria i comparar-los, en les mateixes condicions, amb el mètode de referencia. A continuació, s'ha presentat un nou mètode basat en una càmera de profunditat estèreo amb la finalitat de millorar i corregir les limitacions anteriors. El nou mètode proposat es basa en una arquitectura hibrida la qual utilitza els canals de vídeo infraroig i de profunditat de forma sincronitzada. El canal infraroig s'utilitza per detectar els moviments del subjecte dins l'escena i calcular, sota demanda, una regió d'interès que s'utilitza posteriorment en el canal de profunditat per extreure el senyal respiratori. A més a més, en aquest estudi s'ha utilitzat una aproximació oportunista en el processat del senyal respiratori, donat que també és un dels objectius d'aquest estudi, verificar si el fet d'utilitzar una aproximació més realista en l'adquisició de senyal, pot influir en la mesura del ritme respiratori. Tot i que el mètode anterior es mostra fiable en termes de mesura del ritme respiratori, la selecció oportunista del senyal necessita d’inspecció visual per tal de definir correctament cada fragment. Per aquest motiu, era necessari definir un índex de qualitat el qual permetés identificar de forma objectiva cada tram de senyal, així com detectar si el senyal conté errors. Partint de la idea de caracteritzar el moviment del subjecte de l'estudi anterior, i modificant el punt de mesura frontal cap a un de lateral per tal d'evitar oclusions, es proposa un nou mètode basat en l'obtenció del moviment toràcic-abdominal a partir del flux òptic del senyal de vídeo. Aquest mètode recupera el senyal respiratori del subjecte a partir de la fase del flux òptic, tot calculant un índex de qualitat a partir del mòdul. Finalment, i tenint en compte els diferents mètodes de processat utilitzats en aquesta tesi per tal de obtenir la freqüència instantània, es pot apreciar que cap d'ells és capaç de funcionar en temps real, fent inviable l'anàlisi de la variabilitat respiratòria en sistemes reals amb processat mostra a mostra. Per aquest motiu, en el capítol final d'aquesta tesi, s'ha proposat una nova implementació de la transformació "synchrosqueezing" per tal de realitzar l’anàlisi temporal-freqüencial en temps real, i proveir d'una nova eina per tal d'obtenir la variabilitat respiratòria en temps real, amb mètodes sense contacte

Sleep Stage Classification: A Deep Learning Approach

Sleep occupies significant part of human life. The diagnoses of sleep related disorders are of great importance. To record specific physical and electrical activities of the brain and body, a multi-parameter test, called polysomnography (PSG), is normally used. The visual process of sleep stage classification is time consuming, subjective and costly. To improve the accuracy and efficiency of the sleep stage classification, automatic classification algorithms were developed. In this research work, we focused on pre-processing (filtering boundaries and de-noising algorithms) and classification steps of automatic sleep stage classification. The main motivation for this work was to develop a pre-processing and classification framework to clean the input EEG signal without manipulating the original data thus enhancing the learning stage of deep learning classifiers. For pre-processing EEG signals, a lossless adaptive artefact removal method was proposed. Rather than other works that used artificial noise, we used real EEG data contaminated with EOG and EMG for evaluating the proposed method. The proposed adaptive algorithm led to a significant enhancement in the overall classification accuracy. In the classification area, we evaluated the performance of the most common sleep stage classifiers using a comprehensive set of features extracted from PSG signals. Considering the challenges and limitations of conventional methods, we proposed two deep learning-based methods for classification of sleep stages based on Stacked Sparse AutoEncoder (SSAE) and Convolutional Neural Network (CNN). The proposed methods performed more efficiently by eliminating the need for conventional feature selection and feature extraction steps respectively. Moreover, although our systems were trained with lower number of samples compared to the similar studies, they were able to achieve state of art accuracy and higher overall sensitivity

Characterization and processing of novel neck photoplethysmography signals for cardiorespiratory monitoring

Epilepsy is a neurological disorder causing serious brain seizures that severely affect the patients' quality of life. Sudden unexpected death in epilepsy (SUDEP), for which no evident decease reason is found after post-mortem examination, is a common cause of mortality. The mechanisms leading to SUDEP are uncertain, but, centrally mediated apneic respiratory dysfunction, inducing dangerous hypoxemia, plays a key role. Continuous physiological monitoring appears as the only reliable solution for SUDEP prevention. However, current seizure-detection systems do not show enough sensitivity and present a high number of intolerable false alarms. A wearable system capable of measuring several physiological signals from the same body location, could efficiently overcome these limitations. In this framework, a neck wearable apnea detection device (WADD), sensing airflow through tracheal sounds, was designed. Despite the promising performance, it is still necessary to integrate an oximeter sensor into the system, to measure oxygen saturation in blood (SpO2) from neck photoplethysmography (PPG) signals, and hence, support the apnea detection decision. The neck is a novel PPG measurement site that has not yet been thoroughly explored, due to numerous challenges. This research work aims to characterize neck PPG signals, in order to fully exploit this alternative pulse oximetry location, for precise cardiorespiratory biomarkers monitoring. In this thesis, neck PPG signals were recorded, for the first time in literature, in a series of experiments under different artifacts and respiratory conditions. Morphological and spectral characteristics were analyzed in order to identify potential singularities of the signals. The most common neck PPG artifacts critically corrupting the signal quality, and other breathing states of interest, were thoroughly characterized in terms of the most discriminative features. An algorithm was further developed to differentiate artifacts from clean PPG signals. Both, the proposed characterization and classification model can be useful tools for researchers to denoise neck PPG signals and exploit them in a variety of clinical contexts. In addition to that, it was demonstrated that the neck also offered the possibility, unlike other body parts, to extract the Jugular Venous Pulse (JVP) non-invasively. Overall, the thesis showed how the neck could be an optimum location for multi-modal monitoring in the context of diseases affecting respiration, since it not only allows the sensing of airflow related signals, but also, the breathing frequency component of the PPG appeared more prominent than in the standard finger location. In this context, this property enabled the extraction of relevant features to develop a promising algorithm for apnea detection in near-real time. These findings could be of great importance for SUDEP prevention, facilitating the investigation of the mechanisms and risk factors associated to it, and ultimately reduce epilepsy mortality.Open Acces

Combining Synthesis of Cardiorespiratory Signals and Artifacts with Deep Learning for Robust Vital Sign Estimation

Healthcare has been remarkably morphing on the account of Big Data. As Machine Learning (ML) consolidates its place in simpler clinical chores, more complex Deep Learning (DL) algorithms have struggled to keep up, despite their superior capabilities. This is mainly attributed to the need for large amounts of data for training, which the scientific community is unable to satisfy. The number of promising DL algorithms is considerable, although solutions directly targeting the shortage of data lack. Currently, dynamical generative models are the best bet, but focus on single, classical modalities and tend to complicate significantly with the amount of physiological effects they can simulate. This thesis aims at providing and validating a framework, specifically addressing the data deficit in the scope of cardiorespiratory signals. Firstly, a multimodal statistical synthesizer was designed to generate large, annotated artificial signals. By expressing data through coefficients of pre-defined, fitted functions and describing their dependence with Gaussian copulas, inter- and intra-modality associations were learned. Thereafter, new coefficients are sampled to generate artificial, multimodal signals with the original physiological dynamics. Moreover, normal and pathological beats along with artifacts were included by employing Markov models. Secondly, a convolutional neural network (CNN) was conceived with a novel sensor-fusion architecture and trained with synthesized data under real-world experimental conditions to evaluate how its performance is affected. Both the synthesizer and the CNN not only performed at state of the art level but also innovated with multiple types of generated data and detection error improvements, respectively. Cardiorespiratory data augmentation corrected performance drops when not enough data is available, enhanced the CNN’s ability to perform on noisy signals and to carry out new tasks when introduced to, otherwise unavailable, types of data. Ultimately, the framework was successfully validated showing potential to leverage future DL research on Cardiology into clinical standards

Big data analysis of cyclic alternating pattern during sleep using deep learning

Sleep scoring has been of great interest since the invention of the polysomnography method, which enabled the recording of physiological signals overnight. With the surge in wearable devices in recent years, the topic of what is high-quality sleep, how can it be determined and how can it be achieved attracted increasing interest. In the last two decades, cyclic alternating pattern (CAP) was introduced as a scoring alternative to traditional sleep staging. CAP is known as a synonym for sleep microstructure and describes sleep instability. Manual CAP scoring performed by sleep experts is a very exhausting and time-consuming task. Hence, an automatic method would facilitate the processing of sleep data and provide a valuable tool to enhance the understanding of the role of CAP. This thesis aims to expand the knowledge about CAP by developing a high-performance automated CAP scoring system that can reliably detect and classify CAP events in sleep recordings. The automated system is equipped with state-of-the-art signal processing methods and exploits the dynamic, temporal information in brain activity using deep learning. The automated scoring system is validated using large community-based cohort studies and comparing the output to verified values in the literature. Our findings present novel clinical results on the relationship between CAP and age, gender, subjective sleep quality, and sleep disorders demonstrating that automated CAP analysis of large population based studies can lead to new findings on CAP and its subcomponents. Next, we study the relationship between CAP and behavioural, cognitive, and quality-of-life measures and the effect of adenotonsillectomy on CAP in children with obstructive sleep apnoea as the link between CAP and cognitive functioning in children is largely unknown. Finally, we investigate cortical-cardiovascular interactions during CAP to gain novel insights into the causal relationships between cortical and cardiovascular activity that are underpinning the microstructure of sleep. In summary, the research outcomes in this thesis outline the importance of a fully automated end-to-end CAP scoring solution for future studies on sleep microstructure. Furthermore, we present novel critical information for a better understanding of CAP and obtain first evidence on physiological network dynamics between the central nervous system and the cardiovascular system during CAP.Thesis (Ph.D.) -- University of Adelaide, School of Electrical and Electronic Engineering, 202

Wearable and Nearable Biosensors and Systems for Healthcare

Biosensors and systems in the form of wearables and “nearables” (i.e., everyday sensorized objects with transmitting capabilities such as smartphones) are rapidly evolving for use in healthcare. Unlike conventional approaches, these technologies can enable seamless or on-demand physiological monitoring, anytime and anywhere. Such monitoring can help transform healthcare from the current reactive, one-size-fits-all, hospital-centered approach into a future proactive, personalized, decentralized structure. Wearable and nearable biosensors and systems have been made possible through integrated innovations in sensor design, electronics, data transmission, power management, and signal processing. Although much progress has been made in this field, many open challenges for the scientific community remain, especially for those applications requiring high accuracy. This book contains the 12 papers that constituted a recent Special Issue of Sensors sharing the same title. The aim of the initiative was to provide a collection of state-of-the-art investigations on wearables and nearables, in order to stimulate technological advances and the use of the technology to benefit healthcare. The topics covered by the book offer both depth and breadth pertaining to wearable and nearable technology. They include new biosensors and data transmission techniques, studies on accelerometers, signal processing, and cardiovascular monitoring, clinical applications, and validation of commercial devices

Optoelectronics – Devices and Applications

Optoelectronics - Devices and Applications is the second part of an edited anthology on the multifaced areas of optoelectronics by a selected group of authors including promising novices to experts in the field. Photonics and optoelectronics are making an impact multiple times as the semiconductor revolution made on the quality of our life. In telecommunication, entertainment devices, computational techniques, clean energy harvesting, medical instrumentation, materials and device characterization and scores of other areas of R&D the science of optics and electronics get coupled by fine technology advances to make incredibly large strides. The technology of light has advanced to a stage where disciplines sans boundaries are finding it indispensable. New design concepts are fast emerging and being tested and applications developed in an unimaginable pace and speed. The wide spectrum of topics related to optoelectronics and photonics presented here is sure to make this collection of essays extremely useful to students and other stake holders in the field such as researchers and device designers

Digital phenotyping through multimodal, unobtrusive sensing

The growing adoption of multimodal wearable and mobile devices, such as smartphones and wrist-worn watches has generated an increase in the collection of physiological and behavioural data at scale. This digital phenotyping data enables researchers to make inferences regarding users’ physical and mental health at scale, for the first time. However, translating this data into actionable insights requires computational approaches that turn unlabelled, multimodal time-series sensor data into validated measures that can be interpreted at scale. This thesis describes the derivation of novel computational methods that leverage digital phenotyping data from wearable devices in large-scale populations to infer physical behaviours. These methods combine insights from signal processing, data mining and machine learning alongside domain knowledge in physical activity and sleep epidemiology. First, the inference of sleeping windows in free-living conditions through a heart rate sensing approach is explored. This algorithm is particularly valuable in the absence of ground truth or sleep diaries given its simplicity, adaptability and capacity for personalization. I then explore multistage sleep classification through combined movement and cardiac wearable sensing and machine learning. Further, I demonstrate that postural changes detected through wrist accelerometers can inform habitual behaviours and are valuable complements to traditional, intensity-based physical activity metrics. I then leverage the concomitant responses of heart rate to physical activity that can be captured through multimodal wearable sensors through a self-supervised training task. The resulting embeddings from this task are shown to be useful for the downstream classification of demographic factors, BMI, energy expenditure and cardiorespiratory fitness. Finally, I describe a deep learning model for the adaptive inference of cardiorespiratory fitness (VO2max) using wearable data in free living conditions. I demonstrate the robustness of the model in a large UK population and show the models’ adaptability by evaluating its performance in a subset of the population with repeated measures ~6 years after the original recordings. Together, this work increases the potential of multimodal wearable and mobile sensors for physical activity and behavioural inferences in population studies. In particular, this thesis showcases the potential of using wearable devices to make valuable physical activity, sleep and fitness inferences in large cohort studies. Given the nature of the data collected and the fact that most of this data is currently generated by commercial providers and not research institutes, laying the foundations for responsible data governance and ethical use of these technologies will be critical to building trust and enabling the development of the field of digital phenotyping.I was funded by GlaxoSmithKline and the Engineering and Physical Sciences Research Council. I was also supported by the Alan Turing Institute through their Enrichment Scheme