Development of registration methods for cardiovascular anatomy and function using advanced 3T MRI, 320-slice CT and PET imaging

Different medical imaging modalities provide complementary anatomical and functional information. One increasingly important use of such information is in the clinical management of cardiovascular disease. Multi-modality data is helping improve diagnosis accuracy, and individualize treatment. The Clinical Research Imaging Centre at the University of Edinburgh, has been involved in a number of cardiovascular clinical trials using longitudinal computed tomography (CT) and multi-parametric magnetic resonance (MR) imaging. The critical image processing technique that combines the information from all these different datasets is known as image registration, which is the topic of this thesis. Image registration, especially multi-modality and multi-parametric registration, remains a challenging field in medical image analysis. The new registration methods described in this work were all developed in response to genuine challenges in on-going clinical studies. These methods have been evaluated using data from these studies. In order to gain an insight into the building blocks of image registration methods, the thesis begins with a comprehensive literature review of state-of-the-art algorithms. This is followed by a description of the first registration method I developed to help track inflammation in aortic abdominal aneurysms. It registers multi-modality and multi-parametric images, with new contrast agents. The registration framework uses a semi-automatically generated region of interest around the aorta. The aorta is aligned based on a combination of the centres of the regions of interest and intensity matching. The method achieved sub-voxel accuracy. The second clinical study involved cardiac data. The first framework failed to register many of these datasets, because the cardiac data suffers from a common artefact of magnetic resonance images, namely intensity inhomogeneity. Thus I developed a new preprocessing technique that is able to correct the artefacts in the functional data using data from the anatomical scans. The registration framework, with this preprocessing step and new particle swarm optimizer, achieved significantly improved registration results on the cardiac data, and was validated quantitatively using neuro images from a clinical study of neonates. Although on average the new framework achieved accurate results, when processing data corrupted by severe artefacts and noise, premature convergence of the optimizer is still a common problem. To overcome this, I invented a new optimization method, that achieves more robust convergence by encoding prior knowledge of registration. The registration results from this new registration-oriented optimizer are more accurate than other general-purpose particle swarm optimization methods commonly applied to registration problems. In summary, this thesis describes a series of novel developments to an image registration framework, aimed to improve accuracy, robustness and speed. The resulting registration framework was applied to, and validated by, different types of images taken from several ongoing clinical trials. In the future, this framework could be extended to include more diverse transformation models, aided by new machine learning techniques. It may also be applied to the registration of other types and modalities of imaging data

Learning to synthesise the ageing brain without longitudinal data

How will my face look when I get older? Or, for a more challenging question: How will my brain look when I get older? To answer this question one must devise (and learn from data) a multivariate auto-regressive function which given an image and a desired target age generates an output image. While collecting data for faces may be easier, collecting longitudinal brain data is not trivial. We propose a deep learning-based method that learns to simulate subject-specific brain ageing trajectories without relying on longitudinal data. Our method synthesises images conditioned on two factors: age (a continuous variable), and status of Alzheimer's Disease (AD, an ordinal variable). With an adversarial formulation we learn the joint distribution of brain appearance, age and AD status, and define reconstruction losses to address the challenging problem of preserving subject identity. We compare with several benchmarks using two widely used datasets. We evaluate the quality and realism of synthesised images using ground-truth longitudinal data and a pre-trained age predictor. We show that, despite the use of cross-sectional data, our model learns patterns of gray matter atrophy in the middle temporal gyrus in patients with AD. To demonstrate generalisation ability, we train on one dataset and evaluate predictions on the other. In conclusion, our model shows an ability to separate age, disease influence and anatomy using only 2D cross-sectional data that should be useful in large studies into neurodegenerative disease, that aim to combine several data sources. To facilitate such future studies by the community at large our code is made available at https://github.com/xiat0616/BrainAgeing

Is attention all you need in medical image analysis? A review

Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated

SaliencyGAN: Deep Learning Semisupervised Salient Object Detection in the Fog of IoT

In modern Internet of Things (IoT), visual analysis and predictions are often performed by deep learning models. Salient object detection (SOD) is a fundamental preprocessing for these applications. Executing SOD on the fog devices is a challenging task due to the diversity of data and fog devices. To adopt convolutional neural networks (CNN) on fog-cloud infrastructures for SOD-based applications, we introduce a semisupervised adversarial learning method in this article. The proposed model, named as SaliencyGAN, is empowered by a novel concatenated generative adversarial network (GAN) framework with partially shared parameters. The backbone CNN can be chosen flexibly based on the specific devices and applications. In the meanwhile, our method uses both the labeled and unlabeled data from different problem domains for training. Using multiple popular benchmark datasets, we compared state-of-the-art baseline methods to our SaliencyGAN obtained with 10-100% labeled training data. SaliencyGAN gained performance comparable to the supervised baselines when the percentage of labeled data reached 30%, and outperformed the weakly supervised and unsupervised baselines. Furthermore, our ablation study shows that SaliencyGAN were more robust to the common “mode missing” (or “mode collapse”) issue compared to the selected popular GAN models. The visualized ablation results have proved that SaliencyGAN learned a better estimation of data distributions. To the best of our knowledge, this is the first IoT-oriented semisupervised SOD method

Industrial Cyber-Physical Systems-based Cloud IoT Edge for Federated Heterogeneous Distillation.

Deep convoloutional networks have achieved remarkable performance in a wide range of vision-based tasks in modern internet of things (IoT). Due to privacy issue and transmission cost, mannually annotated data for training the deep learning models are usually stored in different sites with fog and edge devices of various computing capacity. It has been proved that knowledge distillation technique can effectively compress well trained neural networks into light-weight models suitable to particular devices. However, different fog and edge devices may perform different sub-tasks, and simplely performing model compression on powerful cloud servers failed to make use of the private data sotred at different sites. To overcome these obstacles, we propose an novel knowledge distillation method for object recognition in real-world IoT sencarios. Our method enables flexible bidirectional online training of heterogeneous models distributed datasets with a new ``brain storming'' mechanism and optimizable temperature parameters. In our comparison experiments, this heterogeneous brain storming method were compared to multiple state-of-the-art single-model compression methods, as well as the newest heterogeneous and homogeneous multi-teacher knowledge distillation methods. Our methods outperformed the state of the arts in both conventional and heterogeneous tasks. Further analysis of the ablation expxeriment results shows that introducing the trainable temperature parameters into the conventional knowledge distillation loss can effectively ease the learning process of student networks in different methods. To the best of our knowledge, this is the IoT-oriented method that allows asynchronous bidirectional heterogeneous knowledge distillation in deep networks