38 research outputs found
Deep learning for fast and robust medical image reconstruction and analysis
Medical imaging is an indispensable component of modern medical research as well as clinical practice. Nevertheless, imaging techniques such as magnetic resonance imaging (MRI) and computational tomography (CT) are costly and are less accessible to the majority of the world. To make medical devices more accessible, affordable and efficient, it is crucial to re-calibrate our current imaging paradigm for smarter imaging. In particular, as medical imaging techniques have highly structured forms in the way they acquire data, they provide us with an opportunity to optimise the imaging techniques holistically by leveraging data. The central theme of this thesis is to explore different opportunities where we can exploit data and deep learning to improve the way we extract information for better, faster and smarter imaging.
This thesis explores three distinct problems. The first problem is the time-consuming nature of dynamic MR data acquisition and reconstruction. We propose deep learning methods for accelerated dynamic MR image reconstruction, resulting in up to 10-fold reduction in imaging time. The second problem is the redundancy in our current imaging pipeline. Traditionally, imaging pipeline treated acquisition, reconstruction and analysis as separate steps. However, we argue that one can approach them holistically and optimise the entire pipeline jointly for a specific target goal. To this end, we propose deep learning approaches for obtaining high fidelity cardiac MR segmentation directly from significantly undersampled data, greatly exceeding the undersampling limit for image reconstruction. The final part of this thesis tackles the problem of interpretability of the deep learning algorithms. We propose attention-models that can implicitly focus on salient regions in an image to improve accuracy for ultrasound scan plane detection and CT segmentation. More crucially, these models can provide explainability, which is a crucial stepping stone for the harmonisation of smart imaging and current clinical practice.Open Acces
Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images
We propose a novel attention gate (AG) model for medical image analysis that
automatically learns to focus on target structures of varying shapes and sizes.
Models trained with AGs implicitly learn to suppress irrelevant regions in an
input image while highlighting salient features useful for a specific task.
This enables us to eliminate the necessity of using explicit external
tissue/organ localisation modules when using convolutional neural networks
(CNNs). AGs can be easily integrated into standard CNN models such as VGG or
U-Net architectures with minimal computational overhead while increasing the
model sensitivity and prediction accuracy. The proposed AG models are evaluated
on a variety of tasks, including medical image classification and segmentation.
For classification, we demonstrate the use case of AGs in scan plane detection
for fetal ultrasound screening. We show that the proposed attention mechanism
can provide efficient object localisation while improving the overall
prediction performance by reducing false positives. For segmentation, the
proposed architecture is evaluated on two large 3D CT abdominal datasets with
manual annotations for multiple organs. Experimental results show that AG
models consistently improve the prediction performance of the base
architectures across different datasets and training sizes while preserving
computational efficiency. Moreover, AGs guide the model activations to be
focused around salient regions, which provides better insights into how model
predictions are made. The source code for the proposed AG models is publicly
available.Comment: Accepted for Medical Image Analysis (Special Issue on Medical Imaging
with Deep Learning). arXiv admin note: substantial text overlap with
arXiv:1804.03999, arXiv:1804.0533
Generalising Deep Learning MRI Reconstruction across Different Domains
We look into robustness of deep learning based MRI reconstruction when tested
on unseen contrasts and organs. We then propose to generalise the network by
training with large publicly-available natural image datasets with synthesised
phase information to achieve high cross-domain reconstruction performance which
is competitive with domain-specific training. To explain its generalisation
mechanism, we have also analysed patch sets for different training datasets.Comment: Accepted for ISBI2019 as a 1-page abstrac
-net: Ensembled Iterative Deep Neural Networks for Accelerated Parallel MR Image Reconstruction
We explore an ensembled -net for fast parallel MR imaging, including
parallel coil networks, which perform implicit coil weighting, and sensitivity
networks, involving explicit sensitivity maps. The networks in -net are
trained in a supervised way, including content and GAN losses, and with various
ways of data consistency, i.e., proximal mappings, gradient descent and
variable splitting. A semi-supervised finetuning scheme allows us to adapt to
the k-space data at test time, which, however, decreases the quantitative
metrics, although generating the visually most textured and sharp images. For
this challenge, we focused on robust and high SSIM scores, which we achieved by
ensembling all models to a -net.Comment: fastMRI challenge submission (team: holykspace
Deep Network Interpolation for Accelerated Parallel MR Image Reconstruction
We present a deep network interpolation strategy for accelerated parallel MR
image reconstruction. In particular, we examine the network interpolation in
parameter space between a source model that is formulated in an unrolled scheme
with L1 and SSIM losses and its counterpart that is trained with an adversarial
loss. We show that by interpolating between the two different models of the
same network structure, the new interpolated network can model a trade-off
between perceptual quality and fidelity.Comment: Presented at 2020 ISMRM Conference & Exhibition (Abstract #4958
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