Purpose: Echocardiography is the most commonly used modality for assessing the heart in clinical practice. In an echocardiographic exam, an ultrasound probe samples the heart from different orientations and positions, thereby creating different viewpoints for assessing the cardiac function. The determination of the probe viewpoint forms an essential step in automatic echocardiographic image analysis.
Approach: In this study, convolutional neural networks are used for the automated identification of 14 different anatomical echocardiographic views (larger than any previous study) in a dataset of 8732 videos acquired from 374 patients. Differentiable architecture search approach was utilized to design small neural network architectures for rapid inference while maintaining high accuracy. The impact of the image quality and resolution, size of the training dataset, and number of echocardiographic view classes on the efficacy of the models were also investigated.
Results: In contrast to the deeper classification architectures, the proposed models had significantly lower number of trainable parameters (up to 99.9% reduction), achieved comparable classification performance (accuracy 88.4% to 96%, precision 87.8% to 95.2%, recall 87.1% to 95.1%) and real-time performance with inference time per image of 3.6 to 12.6 ms.
Conclusion: Compared with the standard classification neural network architectures, the proposed models are faster and achieve comparable classification performance. They also require less training data. Such models can be used for real-time detection of the standard views.
Segmentation of skin lesions is an important step in computer-aided diagnosis of melanoma; it is also a very challenging task due to fuzzy lesion boundaries and heterogeneous lesion textures. We present a fully automatic method for skin lesion segmentation based on deep fully convolutional networks (FCNs). We investigate a shallow encoding network to model clinically valuable prior knowledge, in which spatial filters simulating simple cell receptive fields function in the primary visual cortex (V1) is considered. An effective fusing strategy using skip connections and convolution operators is then leveraged to couple prior knowledge encoded via shallow network with hierarchical data-driven features learned from the FCNs for detailed segmentation of the skin lesions. To our best knowledge, this is the first time the domain-specific hand craft features have been built into a deep network trained in an end-to-end manner for skin lesion segmentation. The method has been evaluated on both ISBI 2016 and ISBI 2017 skin lesion challenge datasets. We provide comparative evidence to demonstrate that our newly designed network can gain accuracy for lesion segmentation by coupling the prior knowledge encoded by the shallow network with the deep FCNs. Our method is robust without the need for data augmentation or comprehensive parameter tuning, and the experimental results show great promise of the method with effective model generalization compared to other state-of-the-art-methods.
Barrett’s esophagus (BE) is a premalignant condition that has an increased risk to turn into esophageal adenocarcinoma. Classification and staging of the different changes (BE in particular) in the esophageal mucosa are challenging since they have a very similar appearance. Confocal laser endomicroscopy (CLE) is one of the newest endoscopy tools that is commonly used to identify the pathology type of the suspected area of the esophageal mucosa. However, it requires a well-trained physician to classify the image obtained from CLE. An automatic stage classification of esophageal mucosa is presented. The proposed model enhances the internal features of CLE images using an image filter that combines fractional integration with differentiation. Various features are then extracted on a multiscale level, to classify the mucosal tissue into one of its four types: normal squamous (NS), gastric metaplasia (GM), intestinal metaplasia (IM or BE), and neoplasia. These sets of features are used to train two conventional classifiers: support vector machine (SVM) and random forest. The proposed method was evaluated on a dataset of 96 patients with 557 images of different histopathology types. The SVM classifier achieved the best performance with 96.05% accuracy based on a leave-one-patient-out cross-validation. Additionally, the dataset was divided into 60% training and 40% testing; the model achieved an accuracy of 93.72% for the testing data using the SVM. The presented model showed superior performance when compared with four state-of-the-art methods. Accurate classification is essential for the intestinal metaplasia grade, which most likely develops into esophageal cancer. Not only does our method come to the aid of physicians for more accurate diagnosis by acting as a second opinion, but it also acts as a training method for junior physicians who need practice in using CLE. Consequently, this work contributes to an automatic classification that facilitates early intervention and decreases samples of required biopsy.
Owing to the inconsistent image quality existing in routine obstetric ultrasound (US) scans that leads to a large intraobserver and interobserver variability, the aim of this study is to develop a quality-assured, fully automated US fetal head measurement system. A texton-based fetal head segmentation is used as a prerequisite step to obtain the head region. Textons are calculated using a filter bank designed specific for US fetal head structure. Both shape- and anatomic-based features calculated from the segmented head region are then fed into a random forest classifier to determine the quality of the image (e.g., whether the image is acquired from a correct imaging plane), from which fetal head measurements [biparietal diameter (BPD), occipital–frontal diameter (OFD), and head circumference (HC)] are derived. The experimental results show a good performance of our method for US quality assessment and fetal head measurements. The overall precision for automatic image quality assessment is 95.24% with 87.5% sensitivity and 100% specificity, while segmentation performance shows 99.27% (±0.26) of accuracy, 97.07% (±2.3) of sensitivity, 2.23 mm (±0.74) of the maximum symmetric contour distance, and 0.84 mm (±0.28) of the average symmetric contour distance. The statistical analysis results using paired t-test and Bland–Altman plots analysis indicate that the 95% limits of agreement for inter observer variability between the automated measurements and the senior expert measurements are 2.7 mm of BPD, 5.8 mm of OFD, and 10.4 mm of HC, whereas the mean differences are −0.038±1.38 mm, −0.20±2.98 mm, and −0.72±5.36 mm, respectively. These narrow 95% limits of agreements indicate a good level of consistency between the automated and the senior expert’s measurements.
Guang Yang, Xiahai Zhuang, Habib Khan, Shouvik Haldar, Eva Nyktari, Lei Li, Xujiong Ye, Greg Slabaugh, Tom Wong, Raad Mohiaddin, Jennifer Keegan, David Firmin
Late Gadolinium-Enhanced Cardiac MRI (LGE CMRI) is an emerging non-invasive technique to image and quantify preablation native and post-ablation atrial scarring. Previous studies have reported that enhanced image intensities of the atrial scarring in the LGE CMRI inversely correlate with the left atrial endocardial voltage invasively obtained by electro-anatomical mapping. However, the reported reproducibility of using LGE CMRI to identify and quantify atrial scarring is variable. This may be due to two reasons: first, delineation of the left atrium (LA) and pulmonary veins (PVs) anatomy generally relies on manual operation that is highly subjective, and this could substantially affect the subsequent atrial scarring segmentation; second, simple intensity based image features may not be good enough to detect subtle changes in atrial scarring. In this study, we hypothesized that texture analysis can provide reliable image features for the LGE CMRI images subject to accurate and objective delineation of the heart anatomy based on a fully-automated whole heart segmentation (WHS) method. We tested the extracted texture features to differentiate between pre-ablation and post-ablation LGE CMRI studies in longstanding persistent atrial fibrillation patients. These patients often have extensive native scarring and differentiation from post-ablation scarring can be difficult. Quantification results showed that our method is capable of solving this classification task, and we can envisage further deployment of this texture analysis based method for other clinical problems using LGE CMRI.
Barretts Esophagus (BE) is a precancerous condition that affects the esophagus tube and has the risk of developing esophageal adenocarcinoma. BE is the process of developing metaplastic intestinal epithelium and replacing the normal cells in the esophageal area. The detection of BE is considered difficult due to its appearance and properties. The diagnosis is usually done through both endoscopy and biopsy. Recently, Computer Aided Diagnosis systems have been developed to support physicians opinion when facing difficulty in detection/classification in different types of diseases. In this paper, an automatic classification of Barretts Esophagus condition is introduced. The presented method enhances the internal features of a Confocal Laser Endomicroscopy (CLE) image by utilizing a proposed enhancement filter. This filter depends on fractional differentiation and integration that improve the features in the discrete wavelet transform of an image. Later on, various features are extracted from each enhanced image on different levels for the multi-classification process. Our approach is validated on a dataset that consists of a group of 32 patients with 262 images with different histology grades. The experimental results demonstrated the efficiency of the proposed technique. Our method helps clinicians for more accurate classification. This potentially helps to reduce the need for biopsies needed for diagnosis, facilitate the regular monitoring of treatment/development of the patients case and can help train doctors with the new endoscopy technology. The accurate automatic classification is particularly important for the Intestinal Metaplasia (IM) type, which could turn into deadly cancerous. Hence, this work contributes to automatic classification that facilitates early intervention/treatment and decreasing biopsy samples needed.
Guang Yang, Xiahai Zhuang, Habib Khan, Shouvik Haldar, Eva Nyktari, Lei Li, Xujiong Ye, Greg Slabaugh, Tom Wong, Raad Mohiaddin, Jennifer Keegan, David Firmin
KEYWORDS: Image segmentation, Cardiovascular magnetic resonance imaging, Visualization, Veins, Heart, Electrocardiography, Medical imaging, 3D image processing, Lithium, Medical research
Late Gadolinium-Enhanced Cardiac MRI (LGE CMRI) is a non-invasive technique, which has shown promise in detecting native and post-ablation atrial scarring. To visualize the scarring, a precise segmentation of the left atrium (LA) and pulmonary veins (PVs) anatomy is performed as a first step—usually from an ECG gated CMRI roadmap acquisition—and the enhanced scar regions from the LGE CMRI images are superimposed. The anatomy of the LA and PVs in particular is highly variable and manual segmentation is labor intensive and highly subjective. In this paper, we developed a multi-atlas propagation based whole heart segmentation (WHS) to delineate the LA and PVs from ECG gated CMRI roadmap scans. While this captures the anatomy of the atrium well, the PVs anatomy is less easily visualized. The process is therefore augmented by semi-automated manual strokes for PVs identification in the registered LGE CMRI data. This allows us to extract more accurate anatomy than the fully automated WHS. Both qualitative visualization and quantitative assessment with respect to manual segmented ground truth showed that our method is efficient and effective with an overall mean Dice score of 0.91.
In this paper, we propose a novel self-learning based single-image super-resolution (SR) method, which is coupled with dual-tree complex wavelet transform (DTCWT) based denoising to better recover high-resolution (HR) medical images. Unlike previous methods, this self-learning based SR approach enables us to reconstruct HR medical images from a single low-resolution (LR) image without extra training on HR image datasets in advance. The relationships between the given image and its scaled down versions are modeled using support vector regression with sparse coding and dictionary learning, without explicitly assuming reoccurrence or self-similarity across image scales. In addition, we perform DTCWT based denoising to initialize the HR images at each scale instead of simple bicubic interpolation. We evaluate our method on a variety of medical images. Both quantitative and qualitative results show that the proposed approach outperforms bicubic interpolation and state-of-the-art single-image SR methods while effectively removing noise.
Automatic segmentation of medical images is a challenging problem due to the complexity and variability of human
anatomy, poor contrast of the object being segmented, and noise resulting from the image acquisition process. This
paper presents a novel feature-guided method for the segmentation of 3D medical lesions. The proposed algorithm
combines 1) a volumetric shape feature (shape index) based on high-order partial derivatives; 2) mean shift clustering in
a joint spatial-intensity-shape (JSIS) feature space; and 3) a modified expectation-maximization (MEM) algorithm on
the mean shift mode map to merge the neighboring regions (modes). In such a scenario, the volumetric shape feature is
integrated into the process of the segmentation algorithm. The joint spatial-intensity-shape features provide rich
information for the segmentation of the anatomic structures or lesions (tumors). The proposed method has been
evaluated on a clinical dataset of thoracic CT scans that contains 68 nodules. A volume overlap ratio between each
segmented nodule and the ground truth annotation is calculated. Using the proposed method, the mean overlap ratio
over all the nodules is 0.80. On visual inspection and using a quantitative evaluation, the experimental results
demonstrate the potential of the proposed method. It can properly segment a variety of nodules including juxta-vascular
and juxta-pleural nodules, which are challenging for conventional methods due to the high similarity of intensities
between the nodules and their adjacent tissues. This approach could also be applied to lesion segmentation in other
anatomies, such as polyps in the colon.
Computer-aided detection (CAD) is a computerized procedure in medical science that supports the medical team's interpretations and decisions. CAD often uses information from a medical imaging modality such as Computed Tomography to detect suspicious lesions. Algorithms to detect these lesions are based on geometric models which can describe the local structures and thus provide potential region candidates. Geometrical descriptive models are very dependent on the data quality which may affect the false positive rates in CAD. In this paper we propose an efficient adaptive diffusion technique that adaptively controls the diffusion flux of the local structures in the data using robust statistics. The proposed method acts isotropically in the homogeneous regions and anisotropically in the vicinity of jump discontinuities. This method structurally enhances the data and makes the geometrical descriptive models robust. For the iterative solver, we use an efficient gradient descent flow solver based on a PDE formulation of the problem. The whole proposed strategy, which makes use of adaptive diffusion filter coupled with gradient descent flows has been developed and evaluated on clinical data in the application to colonic polyp detection in Computed Tomography Colonography.
Multidetector row CT, multiphase CT in particular, has been widely accepted as a sensitive imaging modality in
the detection of liver cancer. Segmentation of liver from CT images is of great importance in terms of accurate
detection of tumours, volume measurement, pre-surgical planning. The segmentation of liver, however, remains
to be an unsolved problem due to the complicated nature of liver CT such as imaging noise, similar intensity to
its adjacent structures and large variations of contrast kinetics and localised geometric features. The purpose
of this paper is to present our newly developed algorithm aiming to tackle this problem. In our method, a CT
image was first smoothed by geometric diffusion method; the smoothed image was segmented by thresholding
operators. In order to gain optimal segmentation, a novel method was developed to choose threshold values
based on both the anatomical knowledge and features of liver CT. Then morphological operators were applied
to fill the holes in the generated binary image and to disconnect the liver from other unwanted adjoining
structures. After this process, a so-called "2.5D region overlapping" filter was introduced to further remove
unwanted regions. The resulting 3D region was regarded as the final segmentation of the liver region. This
method was applied to venous phase CT data of 45 subjects (30 patient and 15 asymptomatic subjects). Our
results show good agreement with the annotations delineated manually by radiologists and the overlapping ratio
of volume is 87.7% on average and the correlation coefficient between them is 98.1%.
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