135 research outputs found
3D High-Resolution Cardiac Segmentation Reconstruction From 2D Views Using Conditional Variational Autoencoders
Accurate segmentation of heart structures imaged by cardiac MR is key for the quantitative analysis of pathology. High-resolution 3D MR sequences enable whole-heart structural imaging but are time-consuming, expensive to acquire and they often require long breath holds that are not suitable for patients. Consequently, multiplanar breath-hold 2D cines sequences are standard practice but are disadvantaged by lack of whole-heart coverage and low through-plane resolution. To address this, we propose a conditional variational autoencoder architecture able to learn a generative model of 3D high-resolution left ventricular (LV) segmentations which is conditioned on three 2D LV segmentations of one short-axis and two long-axis images. By only employing these three 2D segmentations, our model can efficiently reconstruct the 3D high-resolution LV segmentation of a subject. When evaluated on 400 unseen healthy volunteers, our model yielded an average Dice score of 87.92 ± 0.15 and outperformed competing architectures (TL-net, Dice score = 82.60 ± 0.23, p = 2.2 · 10 -16 )
Machine learning approaches to model cardiac shape in large-scale imaging studies
Recent improvements in non-invasive imaging, together with the introduction of fully-automated segmentation algorithms and big data analytics, has paved the way for large-scale population-based imaging studies. These studies promise to increase our understanding of a large number of medical conditions, including cardiovascular diseases. However, analysis of cardiac shape in such studies is often limited to simple morphometric indices, ignoring large part of the information available in medical images. Discovery of new biomarkers by machine learning has recently gained traction, but often lacks interpretability. The research presented in this thesis aimed at developing novel explainable machine learning and computational methods capable of better summarizing shape variability, to better inform association and predictive clinical models in large-scale imaging studies.
A powerful and flexible framework to model the relationship between three-dimensional (3D) cardiac atlases, encoding multiple phenotypic traits, and genetic variables is first presented. The proposed approach enables the detection of regional phenotype-genotype associations that would be otherwise neglected by conventional association analysis. Three learning-based systems based on deep generative models are then proposed. In the first model, I propose a classifier of cardiac shapes which exploits task-specific generative shape features, and it is designed to enable the visualisation of the anatomical effect these features encode in 3D, making the classification task transparent. The second approach models a database of anatomical shapes via a hierarchy of conditional latent variables and it is capable of detecting, quantifying and visualising onto a template shape the most discriminative anatomical features that characterize distinct clinical conditions. Finally, a preliminary analysis of a deep learning system capable of reconstructing 3D high-resolution cardiac segmentations from a sparse set of 2D views segmentations is reported. This thesis demonstrates that machine learning approaches can facilitate high-throughput analysis of normal and pathological anatomy and of its determinants without losing clinical interpretability.Open Acces
Multi-class point cloud completion networks for 3D cardiac anatomy reconstruction from cine magnetic resonance images
Cine magnetic resonance imaging (MRI) is the current gold standard for the
assessment of cardiac anatomy and function. However, it typically only acquires
a set of two-dimensional (2D) slices of the underlying three-dimensional (3D)
anatomy of the heart, thus limiting the understanding and analysis of both
healthy and pathological cardiac morphology and physiology. In this paper, we
propose a novel fully automatic surface reconstruction pipeline capable of
reconstructing multi-class 3D cardiac anatomy meshes from raw cine MRI
acquisitions. Its key component is a multi-class point cloud completion network
(PCCN) capable of correcting both the sparsity and misalignment issues of the
3D reconstruction task in a unified model. We first evaluate the PCCN on a
large synthetic dataset of biventricular anatomies and observe Chamfer
distances between reconstructed and gold standard anatomies below or similar to
the underlying image resolution for multiple levels of slice misalignment.
Furthermore, we find a reduction in reconstruction error compared to a
benchmark 3D U-Net by 32% and 24% in terms of Hausdorff distance and mean
surface distance, respectively. We then apply the PCCN as part of our automated
reconstruction pipeline to 1000 subjects from the UK Biobank study in a
cross-domain transfer setting and demonstrate its ability to reconstruct
accurate and topologically plausible biventricular heart meshes with clinical
metrics comparable to the previous literature. Finally, we investigate the
robustness of our proposed approach and observe its capacity to successfully
handle multiple common outlier conditions
Exploring variability in medical imaging
Although recent successes of deep learning and novel machine learning techniques improved the perfor-
mance of classification and (anomaly) detection in computer vision problems, the application of these
methods in medical imaging pipeline remains a very challenging task. One of the main reasons for this
is the amount of variability that is encountered and encapsulated in human anatomy and subsequently
reflected in medical images. This fundamental factor impacts most stages in modern medical imaging
processing pipelines.
Variability of human anatomy makes it virtually impossible to build large datasets for each disease
with labels and annotation for fully supervised machine learning. An efficient way to cope with this is
to try and learn only from normal samples. Such data is much easier to collect. A case study of such
an automatic anomaly detection system based on normative learning is presented in this work. We
present a framework for detecting fetal cardiac anomalies during ultrasound screening using generative
models, which are trained only utilising normal/healthy subjects.
However, despite the significant improvement in automatic abnormality detection systems, clinical
routine continues to rely exclusively on the contribution of overburdened medical experts to diagnosis
and localise abnormalities. Integrating human expert knowledge into the medical imaging processing
pipeline entails uncertainty which is mainly correlated with inter-observer variability. From the per-
spective of building an automated medical imaging system, it is still an open issue, to what extent
this kind of variability and the resulting uncertainty are introduced during the training of a model
and how it affects the final performance of the task. Consequently, it is very important to explore the
effect of inter-observer variability both, on the reliable estimation of model’s uncertainty, as well as
on the model’s performance in a specific machine learning task. A thorough investigation of this issue
is presented in this work by leveraging automated estimates for machine learning model uncertainty,
inter-observer variability and segmentation task performance in lung CT scan images.
Finally, a presentation of an overview of the existing anomaly detection methods in medical imaging
was attempted. This state-of-the-art survey includes both conventional pattern recognition methods
and deep learning based methods. It is one of the first literature surveys attempted in the specific
research area.Open Acces
Pathology Synthesis of 3D-Consistent Cardiac MR Images using 2D VAEs and GANs
We propose a method for synthesizing cardiac magnetic resonance (MR) images
with plausible heart pathologies and realistic appearances for the purpose of
generating labeled data for the application of supervised deep-learning (DL)
training. The image synthesis consists of label deformation and label-to-image
translation tasks. The former is achieved via latent space interpolation in a
VAE model, while the latter is accomplished via a label-conditional GAN model.
We devise three approaches for label manipulation in the latent space of the
trained VAE model; i) \textbf{intra-subject synthesis} aiming to interpolate
the intermediate slices of a subject to increase the through-plane resolution,
ii) \textbf{inter-subject synthesis} aiming to interpolate the geometry and
appearance of intermediate images between two dissimilar subjects acquired with
different scanner vendors, and iii) \textbf{pathology synthesis} aiming to
synthesize a series of pseudo-pathological synthetic subjects with
characteristics of a desired heart disease. Furthermore, we propose to model
the relationship between 2D slices in the latent space of the VAE prior to
reconstruction for generating 3D-consistent subjects from stacking up 2D
slice-by-slice generations. We demonstrate that such an approach could provide
a solution to diversify and enrich an available database of cardiac MR images
and to pave the way for the development of generalizable DL-based image
analysis algorithms. We quantitatively evaluate the quality of the synthesized
data in an augmentation scenario to achieve generalization and robustness to
multi-vendor and multi-disease data for image segmentation. Our code is
available at https://github.com/sinaamirrajab/CardiacPathologySynthesis.Comment: Accepted for publication at the Journal of Machine Learning for
Biomedical Imaging (MELBA) https://www.melba-journal.org/2023:01
Automated Diagnosis of Cardiovascular Diseases from Cardiac Magnetic Resonance Imaging Using Deep Learning Models: A Review
In recent years, cardiovascular diseases (CVDs) have become one of the
leading causes of mortality globally. CVDs appear with minor symptoms and
progressively get worse. The majority of people experience symptoms such as
exhaustion, shortness of breath, ankle swelling, fluid retention, and other
symptoms when starting CVD. Coronary artery disease (CAD), arrhythmia,
cardiomyopathy, congenital heart defect (CHD), mitral regurgitation, and angina
are the most common CVDs. Clinical methods such as blood tests,
electrocardiography (ECG) signals, and medical imaging are the most effective
methods used for the detection of CVDs. Among the diagnostic methods, cardiac
magnetic resonance imaging (CMR) is increasingly used to diagnose, monitor the
disease, plan treatment and predict CVDs. Coupled with all the advantages of
CMR data, CVDs diagnosis is challenging for physicians due to many slices of
data, low contrast, etc. To address these issues, deep learning (DL) techniques
have been employed to the diagnosis of CVDs using CMR data, and much research
is currently being conducted in this field. This review provides an overview of
the studies performed in CVDs detection using CMR images and DL techniques. The
introduction section examined CVDs types, diagnostic methods, and the most
important medical imaging techniques. In the following, investigations to
detect CVDs using CMR images and the most significant DL methods are presented.
Another section discussed the challenges in diagnosing CVDs from CMR data.
Next, the discussion section discusses the results of this review, and future
work in CVDs diagnosis from CMR images and DL techniques are outlined. The most
important findings of this study are presented in the conclusion section
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
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