29,408 research outputs found
Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach
Deep learning approaches have achieved state-of-the-art performance in
cardiac magnetic resonance (CMR) image segmentation. However, most approaches
have focused on learning image intensity features for segmentation, whereas the
incorporation of anatomical shape priors has received less attention. In this
paper, we combine a multi-task deep learning approach with atlas propagation to
develop a shape-constrained bi-ventricular segmentation pipeline for short-axis
CMR volumetric images. The pipeline first employs a fully convolutional network
(FCN) that learns segmentation and landmark localisation tasks simultaneously.
The architecture of the proposed FCN uses a 2.5D representation, thus combining
the computational advantage of 2D FCNs networks and the capability of
addressing 3D spatial consistency without compromising segmentation accuracy.
Moreover, the refinement step is designed to explicitly enforce a shape
constraint and improve segmentation quality. This step is effective for
overcoming image artefacts (e.g. due to different breath-hold positions and
large slice thickness), which preclude the creation of anatomically meaningful
3D cardiac shapes. The proposed pipeline is fully automated, due to network's
ability to infer landmarks, which are then used downstream in the pipeline to
initialise atlas propagation. We validate the pipeline on 1831 healthy subjects
and 649 subjects with pulmonary hypertension. Extensive numerical experiments
on the two datasets demonstrate that our proposed method is robust and capable
of producing accurate, high-resolution and anatomically smooth bi-ventricular
3D models, despite the artefacts in input CMR volumes
Scalable multimodal convolutional networks for brain tumour segmentation
Brain tumour segmentation plays a key role in computer-assisted surgery. Deep
neural networks have increased the accuracy of automatic segmentation
significantly, however these models tend to generalise poorly to different
imaging modalities than those for which they have been designed, thereby
limiting their applications. For example, a network architecture initially
designed for brain parcellation of monomodal T1 MRI can not be easily
translated into an efficient tumour segmentation network that jointly utilises
T1, T1c, Flair and T2 MRI. To tackle this, we propose a novel scalable
multimodal deep learning architecture using new nested structures that
explicitly leverage deep features within or across modalities. This aims at
making the early layers of the architecture structured and sparse so that the
final architecture becomes scalable to the number of modalities. We evaluate
the scalable architecture for brain tumour segmentation and give evidence of
its regularisation effect compared to the conventional concatenation approach.Comment: Paper accepted at MICCAI 201
Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates
The study of cerebral anatomy in developing neonates is of great importance for
the understanding of brain development during the early period of life. This
dissertation therefore focuses on three challenges in the modelling of cerebral
anatomy in neonates during brain development. The methods that have been
developed all use Magnetic Resonance Images (MRI) as source data.
To facilitate study of vascular development in the neonatal period, a set of image
analysis algorithms are developed to automatically extract and model cerebral
vessel trees. The whole process consists of cerebral vessel tracking from
automatically placed seed points, vessel tree generation, and vasculature
registration and matching. These algorithms have been tested on clinical Time-of-
Flight (TOF) MR angiographic datasets.
To facilitate study of the neonatal cortex a complete cerebral cortex segmentation
and reconstruction pipeline has been developed. Segmentation of the neonatal
cortex is not effectively done by existing algorithms designed for the adult brain
because the contrast between grey and white matter is reversed. This causes pixels
containing tissue mixtures to be incorrectly labelled by conventional methods. The
neonatal cortical segmentation method that has been developed is based on a novel
expectation-maximization (EM) method with explicit correction for mislabelled
partial volume voxels. Based on the resulting cortical segmentation, an implicit
surface evolution technique is adopted for the reconstruction of the cortex in
neonates. The performance of the method is investigated by performing a detailed
landmark study.
To facilitate study of cortical development, a cortical surface registration algorithm
for aligning the cortical surface is developed. The method first inflates extracted
cortical surfaces and then performs a non-rigid surface registration using free-form
deformations (FFDs) to remove residual alignment. Validation experiments using
data labelled by an expert observer demonstrate that the method can capture local
changes and follow the growth of specific sulcus
Medical imaging analysis with artificial neural networks
Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging
Factorised spatial representation learning: application in semi-supervised myocardial segmentation
The success and generalisation of deep learning algorithms heavily depend on
learning good feature representations. In medical imaging this entails
representing anatomical information, as well as properties related to the
specific imaging setting. Anatomical information is required to perform further
analysis, whereas imaging information is key to disentangle scanner variability
and potential artefacts. The ability to factorise these would allow for
training algorithms only on the relevant information according to the task. To
date, such factorisation has not been attempted. In this paper, we propose a
methodology of latent space factorisation relying on the cycle-consistency
principle. As an example application, we consider cardiac MR segmentation,
where we separate information related to the myocardium from other features
related to imaging and surrounding substructures. We demonstrate the proposed
method's utility in a semi-supervised setting: we use very few labelled images
together with many unlabelled images to train a myocardium segmentation neural
network. Specifically, we achieve comparable performance to fully supervised
networks using a fraction of labelled images in experiments on ACDC and a
dataset from Edinburgh Imaging Facility QMRI. Code will be made available at
https://github.com/agis85/spatial_factorisation.Comment: Accepted in MICCAI 201
Histopathological image analysis : a review
Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe
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