Online Super-Resolution For Fibre-Bundle-Based Confocal Laser Endomicroscopy

Probe-based Confocal Laser Endomicroscopy (pCLE) produces microscopic images enabling real-time in vivo optical biopsy. However, the miniaturisation of the optical hardware, specifically the reliance on an optical fibre bundle as an imaging guide, fundamentally limits image quality by producing artefacts, noise, and relatively low contrast and resolution. The reconstruction approaches in clinical pCLE products do not fully alleviate these problems. Consequently, image quality remains a barrier that curbs the full potential of pCLE. Enhancing the image quality of pCLE in real-time remains a challenge. The research in this thesis is a response to this need. I have developed dedicated online super-resolution methods that account for the physics of the image acquisition process. These methods have the potential to replace existing reconstruction algorithms without interfering with the fibre design or the hardware of the device. In this thesis, novel processing pipelines are proposed for enhancing the image quality of pCLE. First, I explored a learning-based super-resolution method that relies on mapping from the low to the high-resolution space. Due to the lack of high-resolution pCLE, I proposed to simulate high-resolution data and use it as a ground truth model that is based on the pCLE acquisition physics. However, pCLE images are reconstructed from irregularly distributed fibre signals, and grid-based Convolutional Neural Networks are not designed to take irregular data as input. To alleviate this problem, I designed a new trainable layer that embeds Nadaraya- Watson regression. Finally, I proposed a novel blind super-resolution approach by deploying unsupervised zero-shot learning accompanied by a down-sampling kernel crafted for pCLE. I evaluated these new methods in two ways: a robust image quality assessment and a perceptual quality test assessed by clinical experts. The results demonstrate that the proposed super-resolution pipelines are superior to the current reconstruction algorithm in terms of image quality and clinician preference

Machine Learning/Deep Learning in Medical Image Processing

Many recent studies on medical image processing have involved the use of machine learning (ML) and deep learning (DL). This special issue, “Machine Learning/Deep Learning in Medical Image Processing”, has been launched to provide an opportunity for researchers in the area of medical image processing to highlight recent developments made in their fields with ML/DL. Seven excellent papers that cover a wide variety of medical/clinical aspects are selected in this special issue

3D Face Modelling, Analysis and Synthesis

Human faces have always been of a special interest to researchers in the computer vision and graphics areas. There has been an explosion in the number of studies around accurately modelling, analysing and synthesising realistic faces for various applications. The importance of human faces emerges from the fact that they are invaluable means of effective communication, recognition, behaviour analysis, conveying emotions, etc. Therefore, addressing the automatic visual perception of human faces efficiently could open up many influential applications in various domains, e.g. virtual/augmented reality, computer-aided surgeries, security and surveillance, entertainment, and many more. However, the vast variability associated with the geometry and appearance of human faces captured in unconstrained videos and images renders their automatic analysis and understanding very challenging even today. The primary objective of this thesis is to develop novel methodologies of 3D computer vision for human faces that go beyond the state of the art and achieve unprecedented quality and robustness. In more detail, this thesis advances the state of the art in 3D facial shape reconstruction and tracking, fine-grained 3D facial motion estimation, expression recognition and facial synthesis with the aid of 3D face modelling. We give a special attention to the case where the input comes from monocular imagery data captured under uncontrolled settings, a.k.a. \textit{in-the-wild} data. This kind of data are available in abundance nowadays on the internet. Analysing these data pushes the boundaries of currently available computer vision algorithms and opens up many new crucial applications in the industry. We define the four targeted vision problems (3D facial reconstruction $\&$ tracking, fine-grained 3D facial motion estimation, expression recognition, facial synthesis) in this thesis as the four 3D-based essential systems for the automatic facial behaviour understanding and show how they rely on each other. Finally, to aid the research conducted in this thesis, we collect and annotate a large-scale videos dataset of monocular facial performances. All of our proposed methods demonstarte very promising quantitative and qualitative results when compared to the state-of-the-art methods

An Investigation of the Diagnostic Potential of Autofluorescence Lifetime Spectroscopy and Imaging for Label-Free Contrast of Disease

The work presented in this thesis aimed to study the application of fluorescence lifetime spectroscopy (FLS) and fluorescence lifetime imaging microscopy (FLIM) to investigate their potential for diagnostic contrast of diseased tissue with a particular emphasis on autofluorescence (AF) measurements of gastrointestinal (GI) disease. Initially, an ex vivo study utilising confocal FLIM was undertaken with 420 nm excitation to characterise the fluorescence lifetime (FL) images obtained from 71 GI samples from 35 patients. A significant decrease in FL was observed between normal colon and polyps (p = 0.024), and normal colon and inflammatory bowel disease (IBD) (p = 0.015). Confocal FLIM was also performed on 23 bladder samples. A longer, although not significant, FL for cancer was observed, in paired specimens (n = 5) instilled with a photosensitizer. The first in vivo study was a clinical investigation of skin cancer using a fibre-optic FL spectrofluorometer and involved the interrogation of 27 lesions from 25 patients. A significant decrease in the FL of basal cell carcinomas compared to healthy tissue was observed (p = 0.002) with 445 nm excitation. A novel clinically viable FLS fibre-optic probe was then applied ex vivo to measure 60 samples collected from 23 patients. In a paired analysis of neoplastic polyps and normal colon obtained from the same region of the colon in the same patient (n = 12), a significant decrease in FL was observed (p = 0.021) with 435 nm excitation. In contrast, with 375 nm excitation, the mean FL of IBD specimens (n = 4) was found to be longer than that of normal tissue, although not statistically significant. Finally, the FLS system was applied in vivo in 17 patients, with initial data indicating that 435 nm excitation results in AF lifetimes that are broadly consistent with ex vivo studies, although no diagnostically significant differences were observed in the signals obtained in vivo.Open Acces

Artificial Intelligence Tools for Facial Expression Analysis.

Inner emotions show visibly upon the human face and are understood as a basic guide to an individual’s inner world. It is, therefore, possible to determine a person’s attitudes and the effects of others’ behaviour on their deeper feelings through examining facial expressions. In real world applications, machines that interact with people need strong facial expression recognition. This recognition is seen to hold advantages for varied applications in affective computing, advanced human-computer interaction, security, stress and depression analysis, robotic systems, and machine learning. This thesis starts by proposing a benchmark of dynamic versus static methods for facial Action Unit (AU) detection. AU activation is a set of local individual facial muscle parts that occur in unison constituting a natural facial expression event. Detecting AUs automatically can provide explicit benefits since it considers both static and dynamic facial features. For this research, AU occurrence activation detection was conducted by extracting features (static and dynamic) of both nominal hand-crafted and deep learning representation from each static image of a video. This confirmed the superior ability of a pretrained model that leaps in performance. Next, temporal modelling was investigated to detect the underlying temporal variation phases using supervised and unsupervised methods from dynamic sequences. During these processes, the importance of stacking dynamic on top of static was discovered in encoding deep features for learning temporal information when combining the spatial and temporal schemes simultaneously. Also, this study found that fusing both temporal and temporal features will give more long term temporal pattern information. Moreover, we hypothesised that using an unsupervised method would enable the leaching of invariant information from dynamic textures. Recently, fresh cutting-edge developments have been created by approaches based on Generative Adversarial Networks (GANs). In the second section of this thesis, we propose a model based on the adoption of an unsupervised DCGAN for the facial features’ extraction and classification to achieve the following: the creation of facial expression images under different arbitrary poses (frontal, multi-view, and in the wild), and the recognition of emotion categories and AUs, in an attempt to resolve the problem of recognising the static seven classes of emotion in the wild. Thorough experimentation with the proposed cross-database performance demonstrates that this approach can improve the generalization results. Additionally, we showed that the features learnt by the DCGAN process are poorly suited to encoding facial expressions when observed under multiple views, or when trained from a limited number of positive examples. Finally, this research focuses on disentangling identity from expression for facial expression recognition. A novel technique was implemented for emotion recognition from a single monocular image. A large-scale dataset (Face vid) was created from facial image videos which were rich in variations and distribution of facial dynamics, appearance, identities, expressions, and 3D poses. This dataset was used to train a DCNN (ResNet) to regress the expression parameters from a 3D Morphable Model jointly with a back-end classifier

Towards PACE-CAD Systems

Despite phenomenal advancements in the availability of medical image datasets and the development of modern classification algorithms, Computer-Aided Diagnosis (CAD) has had limited practical exposure in the real-world clinical workflow. This is primarily because of the inherently demanding and sensitive nature of medical diagnosis that can have far-reaching and serious repercussions in case of misdiagnosis. In this work, a paradigm called PACE (Pragmatic, Accurate, Confident, & Explainable) is presented as a set of some of must-have features for any CAD. Diagnosis of glaucoma using Retinal Fundus Images (RFIs) is taken as the primary use case for development of various methods that may enrich an ordinary CAD system with PACE. However, depending on specific requirements for different methods, other application areas in ophthalmology and dermatology have also been explored. Pragmatic CAD systems refer to a solution that can perform reliably in day-to-day clinical setup. In this research two, of possibly many, aspects of a pragmatic CAD are addressed. Firstly, observing that the existing medical image datasets are small and not representative of images taken in the real-world, a large RFI dataset for glaucoma detection is curated and published. Secondly, realising that a salient attribute of a reliable and pragmatic CAD is its ability to perform in a range of clinically relevant scenarios, classification of 622 unique cutaneous diseases in one of the largest publicly available datasets of skin lesions is successfully performed. Accuracy is one of the most essential metrics of any CAD system's performance. Domain knowledge relevant to three types of diseases, namely glaucoma, Diabetic Retinopathy (DR), and skin lesions, is industriously utilised in an attempt to improve the accuracy. For glaucoma, a two-stage framework for automatic Optic Disc (OD) localisation and glaucoma detection is developed, which marked new state-of-the-art for glaucoma detection and OD localisation. To identify DR, a model is proposed that combines coarse-grained classifiers with fine-grained classifiers and grades the disease in four stages with respect to severity. Lastly, different methods of modelling and incorporating metadata are also examined and their effect on a model's classification performance is studied. Confidence in diagnosing a disease is equally important as the diagnosis itself. One of the biggest reasons hampering the successful deployment of CAD in the real-world is that medical diagnosis cannot be readily decided based on an algorithm's output. Therefore, a hybrid CNN architecture is proposed with the convolutional feature extractor trained using point estimates and a dense classifier trained using Bayesian estimates. Evaluation on 13 publicly available datasets shows the superiority of this method in terms of classification accuracy and also provides an estimate of uncertainty for every prediction. Explainability of AI-driven algorithms has become a legal requirement after Europe’s General Data Protection Regulations came into effect. This research presents a framework for easy-to-understand textual explanations of skin lesion diagnosis. The framework is called ExAID (Explainable AI for Dermatology) and relies upon two fundamental modules. The first module uses any deep skin lesion classifier and performs detailed analysis on its latent space to map human-understandable disease-related concepts to the latent representation learnt by the deep model. The second module proposes Concept Localisation Maps, which extend Concept Activation Vectors by locating significant regions corresponding to a learned concept in the latent space of a trained image classifier. This thesis probes many viable solutions to equip a CAD system with PACE. However, it is noted that some of these methods require specific attributes in datasets and, therefore, not all methods may be applied on a single dataset. Regardless, this work anticipates that consolidating PACE into a CAD system can not only increase the confidence of medical practitioners in such tools but also serve as a stepping stone for the further development of AI-driven technologies in healthcare