263 research outputs found
Automatic Segmentation of the Left Ventricle in Cardiac CT Angiography Using Convolutional Neural Network
Accurate delineation of the left ventricle (LV) is an important step in
evaluation of cardiac function. In this paper, we present an automatic method
for segmentation of the LV in cardiac CT angiography (CCTA) scans. Segmentation
is performed in two stages. First, a bounding box around the LV is detected
using a combination of three convolutional neural networks (CNNs).
Subsequently, to obtain the segmentation of the LV, voxel classification is
performed within the defined bounding box using a CNN. The study included CCTA
scans of sixty patients, fifty scans were used to train the CNNs for the LV
localization, five scans were used to train LV segmentation and the remaining
five scans were used for testing the method. Automatic segmentation resulted in
the average Dice coefficient of 0.85 and mean absolute surface distance of 1.1
mm. The results demonstrate that automatic segmentation of the LV in CCTA scans
using voxel classification with convolutional neural networks is feasible.Comment: This work has been published as: Zreik, M., Leiner, T., de Vos, B.
D., van Hamersvelt, R. W., Viergever, M. A., I\v{s}gum, I. (2016, April).
Automatic segmentation of the left ventricle in cardiac CT angiography using
convolutional neural networks. In Biomedical Imaging (ISBI), 2016 IEEE 13th
International Symposium on (pp. 40-43). IEE
Medical Image Segmentation Combining Level Set Method and Deep Belief Networks
Medical image segmentation is an important step in medical image analysis, where the main goal is the precise delineation of organs and tumours from medical images. For instance there is evidence in the field that shows a positive correlation between the precision of these segmentations and the accuracy observed in classification systems that use these segmentations as their inputs. Over the last decades, a vast number of medical image segmentation models have been introduced, where these models can be divided into five main groups: 1) image-based approaches, 2) active contour methods, 3) machine learning techniques, 4) atlas-guided segmentation and registration and 5) hybrid models. Image-based approaches use only intensity value or texture for segmenting (i.e., thresholding technique) and they usually do not produce precise segmentation. Active contour methods can use an explicit representation (i.e., snakes) with the goal of minimizing an energy function that forces the contour to move towards strong edges and maintains the contour smoothness. The use of implicit representation in active contour methods (i.e., level set method) embeds the contour as zero level set of a higher dimensional surface (i.e., the curve representing the contour does not need to be parameterized as in the Snakes model). Although successful, the main issue with active contour methods is the fact that the energy function must contain terms describing all possible shape and appearance variations, which is a complicated task given that it is hard to design by hand all these terms. Also, this type of active contour methods may get stuck at image regions that do not belong to the object of interest. Machine learning techniques address this issue by automatically learning shape and appearance models using annotated training images. Nevertheless, in order to meet the high accuracy requirements of medical image analysis applications, machine learning methods usually need large and rich training sets and also face the complexity of the inference process. Atlas-guided segmentation and registration use an atlas image, which is constructed based on manually segmentation images. The new image is segmented by registering it with the atlas image. These techniques have been applied successfully in many applications, but they still face some issues, such as their ability to represent the variability of anatomical structure and scale in medical image, and the complexity of the registration algorithms. In this work, we propose a new hybrid segmentation approach by combining a level set method with a machine learning approach (deep belief network). Our main objective with this approach is to achieve segmentation accuracy results that are either comparable or better than the ones produced with machine learning methods, but using relatively smaller training sets. These weaker requirements on the size of training sets is compensated by the hand designed segmentation terms present in typical level set methods, that are used as prior information on the anatomy to be segmented (e.g., smooth contours, strong edges, etc.). In addition, we choose a machine learning methodology that typically requires smaller annotated training sets, compared to other methods proposed in this field. Specifically, we use deep belief networks, with training sets consisting to a large extent of un-annotated training images. In general, our hybrid segmentation approach uses the result produced by the deep belief network as a prior in the level set evolution. We validate this method on the Medical Image Computing and Computer Assisted Intervention (MICCAI) 2009 left ventricle segmentation challenge database and on the Japanese Society of Radiological Technology (JSRT) lung segmentation dataset. The experiments show that our approach produces competitive results in the field in terms of segmentation accuracy. More specifically, we show that the use of our proposed methodology in a semi-automated segmentation system (i.e., using a manual initialization) produces the best result in the field in both databases above, and in the case of a fully automated system, our method shows results competitive with the current state of the art.Thesis (Ph.D.) -- University of Adelaide, School of Computer Science, 201
Deep Learning Analysis of Cardiac MRI in Legacy Datasets:Multi-Ethnic Study of Atherosclerosis
The shape and motion of the heart provide essential clues to understanding
the mechanisms of cardiovascular disease. With the advent of large-scale
cardiac imaging data, statistical atlases become a powerful tool to provide
automated and precise quantification of the status of patient-specific heart
geometry with respect to reference populations. The Multi-Ethnic Study of
Atherosclerosis (MESA), begun in 2000, was the first large cohort study to
incorporate cardiovascular MRI in over 5000 participants, and there is now a
wealth of follow-up data over 20 years. Building a machine learning based
automated analysis is necessary to extract the additional imaging information
necessary for expanding original manual analyses. However, machine learning
tools trained on MRI datasets with different pulse sequences fail on such
legacy datasets. Here, we describe an automated atlas construction pipeline
using deep learning methods applied to the legacy cardiac MRI data in MESA. For
detection of anatomical cardiac landmark points, a modified VGGNet
convolutional neural network architecture was used in conjunction with a
transfer learning sequence between two-chamber, four-chamber, and short-axis
MRI views. A U-Net architecture was used for detection of the endocardial and
epicardial boundaries in short axis images. Both network architectures resulted
in good segmentation and landmark detection accuracies compared with
inter-observer variations. Statistical relationships with common risk factors
were similar between atlases derived from automated vs manual annotations. The
automated atlas can be employed in future studies to examine the relationships
between cardiac morphology and future events
Image Quality Assessment for Population Cardiac MRI: From Detection to Synthesis
Cardiac magnetic resonance (CMR) images play a growing role in diagnostic imaging of cardiovascular diseases. Left Ventricular (LV) cardiac anatomy and function are widely used for diagnosis and monitoring disease progression in cardiology and to assess the patient's response to cardiac surgery and interventional procedures. For population imaging studies, CMR is arguably the most comprehensive imaging modality for non-invasive and non-ionising imaging of the heart and great vessels and, hence, most suited for population imaging cohorts. Due to insufficient radiographer's experience in planning a scan, natural cardiac muscle contraction, breathing motion, and imperfect triggering, CMR can display incomplete LV coverage, which hampers quantitative LV characterization and diagnostic accuracy.
To tackle this limitation and enhance the accuracy and robustness of the automated cardiac volume and functional assessment, this thesis focuses on the development and application of state-of-the-art deep learning (DL) techniques in cardiac imaging. Specifically, we propose new image feature representation types that are learnt with DL models and aimed at highlighting the CMR image quality cross-dataset. These representations are also intended to estimate the CMR image quality for better interpretation and analysis. Moreover, we investigate how quantitative analysis can benefit when these learnt image representations are used in image synthesis.
Specifically, a 3D fisher discriminative representation is introduced to identify CMR image quality in the UK Biobank cardiac data. Additionally, a novel adversarial learning (AL) framework is introduced for the cross-dataset CMR image quality assessment and we show that the common representations learnt by AL can be useful and informative for cross-dataset CMR image analysis. Moreover, we utilize the dataset invariance (DI) representations for CMR volumes interpolation by introducing a novel generative adversarial nets (GANs) based image synthesis framework, which enhance the CMR image quality cross-dataset
Segmentation of heart chambers in 2-D heart ultrasounds with deep learning
Echocardiography is a non-invasive image diagnosis technique where ultrasound waves are used to obtain an image or sequence of the structure and function of the heart. The segmentation of the heart chambers on ultrasound images is a task usually performed by experienced cardiologists, in which they delineate and extract the shape of both atriums and ventricles to obtain important indexes of a patient’s heart condition. However, this task is usually hard to perform accurately due to the poor image quality caused by the equipment and techniques used and due to the variability across different patients and pathologies. Therefore, medical image processing is needed in this particular case to avoid inaccuracy and obtain proper results. Over the last decade, several studies have proved that deep learning techniques are a possible solution to this problem, obtaining good results in automatic segmentation. The major problem with deep learning techniques in medical image processing is the lack of available data to train and test these architectures. In this work we have trained, validated, and tested a convolutional neural network based on the architecture of U-Net for 2D echocardiogram chamber segmentation. The data used for the training of the convolutional neural network was the B-Mode 4-chamber apical view Echogan dataset with data augmentation techniques applied. The novelty of this work is the hyperparameter and architecture optimizations to reduce the computation time while obtaining significant training and testing accuraciesObjectius de Desenvolupament Sostenible::3 - Salut i Benesta
3D/2D Registration with Superabundant Vessel Reconstruction for Cardiac Resynchronization Therapy
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Automated segmentation of normal and diseased coronary arteries – The ASOCA challenge
Cardiovascular disease is a major cause of death worldwide. Computed Tomography Coronary Angiography (CTCA) is a non-invasive method used to evaluate coronary artery disease, as well as evaluating and reconstructing heart and coronary vessel structures. Reconstructed models have a wide array of for educational, training and research applications such as the study of diseased and non-diseased coronary anatomy, machine learning based disease risk prediction and in-silico and in-vitro testing of medical devices. However, coronary arteries are difficult to image due to their small size, location, and movement, causing poor resolution and artefacts. Segmentation of coronary arteries has traditionally focused on semi-automatic methods where a human expert guides the algorithm and corrects errors, which severely limits large-scale applications and integration within clinical systems. International challenges aiming to overcome this barrier have focussed on specific tasks such as centreline extraction, stenosis quantification, and segmentation of specific artery segments only. Here we present the results of the first challenge to develop fully automatic segmentation methods of full coronary artery trees and establish the first large standardized dataset of normal and diseased arteries. This forms a new automated segmentation benchmark allowing the automated processing of CTCAs directly relevant for large-scale and personalized clinical applications
4D Cardiac MRI Segmentation
Realitzat en col·laboració amb el centre o empresa: Northeastern Universit
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