208 research outputs found
Automated segmentation on the entire cardiac cycle using a deep learning work-flow
The segmentation of the left ventricle (LV) from CINE MRI images is essential
to infer important clinical parameters. Typically, machine learning algorithms
for automated LV segmentation use annotated contours from only two cardiac
phases, diastole, and systole. In this work, we present an analysis work-flow
for fully-automated LV segmentation that learns from images acquired through
the cardiac cycle. The workflow consists of three components: first, for each
image in the sequence, we perform an automated localization and subsequent
cropping of the bounding box containing the cardiac silhouette. Second, we
identify the LV contours using a Temporal Fully Convolutional Neural Network
(T-FCNN), which extends Fully Convolutional Neural Networks (FCNN) through a
recurrent mechanism enforcing temporal coherence across consecutive frames.
Finally, we further defined the boundaries using either one of two components:
fully-connected Conditional Random Fields (CRFs) with Gaussian edge potentials
and Semantic Flow. Our initial experiments suggest that significant improvement
in performance can potentially be achieved by using a recurrent neural network
component that explicitly learns cardiac motion patterns whilst performing LV
segmentation.Comment: 6 pages, 2 figures, published on IEEE Xplor
Mass Displacement Networks
Despite the large improvements in performance attained by using deep learning
in computer vision, one can often further improve results with some additional
post-processing that exploits the geometric nature of the underlying task. This
commonly involves displacing the posterior distribution of a CNN in a way that
makes it more appropriate for the task at hand, e.g. better aligned with local
image features, or more compact. In this work we integrate this geometric
post-processing within a deep architecture, introducing a differentiable and
probabilistically sound counterpart to the common geometric voting technique
used for evidence accumulation in vision. We refer to the resulting neural
models as Mass Displacement Networks (MDNs), and apply them to human pose
estimation in two distinct setups: (a) landmark localization, where we collapse
a distribution to a point, allowing for precise localization of body keypoints
and (b) communication across body parts, where we transfer evidence from one
part to the other, allowing for a globally consistent pose estimate. We
evaluate on large-scale pose estimation benchmarks, such as MPII Human Pose and
COCO datasets, and report systematic improvements when compared to strong
baselines.Comment: 12 pages, 4 figure
Hyper-Convolution Networks for Biomedical Image Segmentation
The convolution operation is a central building block of neural network
architectures widely used in computer vision. The size of the convolution
kernels determines both the expressiveness of convolutional neural networks
(CNN), as well as the number of learnable parameters. Increasing the network
capacity to capture rich pixel relationships requires increasing the number of
learnable parameters, often leading to overfitting and/or lack of robustness.
In this paper, we propose a powerful novel building block, the
hyper-convolution, which implicitly represents the convolution kernel as a
function of kernel coordinates. Hyper-convolutions enable decoupling the kernel
size, and hence its receptive field, from the number of learnable parameters.
In our experiments, focused on challenging biomedical image segmentation tasks,
we demonstrate that replacing regular convolutions with hyper-convolutions
leads to more efficient architectures that achieve improved accuracy. Our
analysis also shows that learned hyper-convolutions are naturally regularized,
which can offer better generalization performance. We believe that
hyper-convolutions can be a powerful building block in future neural network
architectures for computer vision tasks. We provide all of our code here:
https://github.com/tym002/Hyper-ConvolutionComment: WACV 202
Incorporating Cardiac Substructures Into Radiation Therapy For Improved Cardiac Sparing
Growing evidence suggests that radiation therapy (RT) doses to the heart and cardiac substructures (CS) are strongly linked to cardiac toxicities, though only the heart is considered clinically. This work aimed to utilize the superior soft-tissue contrast of magnetic resonance (MR) to segment CS, quantify uncertainties in their position, assess their effect on treatment planning and an MR-guided environment.
Automatic substructure segmentation of 12 CS was completed using a novel hybrid MR/computed tomography (CT) atlas method and was improved upon using a 3-dimensional neural network (U-Net) from deep learning. Intra-fraction motion due to respiration was then quantified. The inter-fraction setup uncertainties utilizing a novel MR-linear accelerator were also quantified. Treatment planning comparisons were performed with and without substructure inclusions and methods to reduce radiation dose to sensitive CS were evaluated. Lastly, these described technologies (deep learning U-Net) were translated to an MR-linear accelerator and a segmentation pipeline was created.
Automatic segmentations from the hybrid MR/CT atlas was able to generate accurate segmentations for the chambers and great vessels (Dice similarity coefficient (DSC) \u3e 0.75) but coronary artery segmentations were unsuccessful (DSC\u3c0.3). After implementing deep learning, DSC for the chambers and great vessels was ≥0.85 along with an improvement in the coronary arteries (DSC\u3e0.5). Similar accuracy was achieved when implementing deep learning for MR-guided RT. On average, automatic segmentations required ~10 minutes to generate per patient and deep learning only required 14 seconds. The inclusion of CS in the treatment planning process did not yield statistically significant changes in plan complexity, PTV, or OAR dose.
Automatic segmentation results from deep learning pose major efficiency and accuracy gains for CS segmentation offering high potential for rapid implementation into radiation therapy planning for improved cardiac sparing. Introducing CS into RT planning for MR-guided RT presented an opportunity for more effective sparing with limited increase in plan complexity
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