Automatic delineation of the myocardial wall from CT images via shape segmentation and variational region growing

S-Net: a multiple cross aggregation convolutional architecture for automatic segmentation of small/thin structures for cardiovascular applications

With the success of U-Net or its variants in automatic medical image segmentation, building a fully convolutional network (FCN) based on an encoder-decoder structure has become an effective end-to-end learning approach. However, the intrinsic property of FCNs is that as the encoder deepens, higher-level features are learned, and the receptive field size of the network increases, which results in unsatisfactory performance for detecting low-level small/thin structures such as atrial walls and small arteries. To address this issue, we propose to keep the different encoding layer features at their original sizes to constrain the receptive field from increasing as the network goes deeper. Accordingly, we develop a novel S-shaped multiple cross-aggregation segmentation architecture named S-Net, which has two branches in the encoding stage, i.e., a resampling branch to capture low-level fine-grained details and thin/small structures and a downsampling branch to learn high-level discriminative knowledge. In particular, these two branches learn complementary features by residual cross-aggregation; the fusion of the complementary features from different decoding layers can be effectively accomplished through lateral connections. Meanwhile, we perform supervised prediction at all decoding layers to incorporate coarse-level features with high semantic meaning and fine-level features with high localization capability to detect multi-scale structures, especially for small/thin volumes fully. To validate the effectiveness of our S-Net, we conducted extensive experiments on the segmentation of cardiac wall and intracranial aneurysm (IA) vasculature, and quantitative and qualitative evaluations demonstrated the superior performance of our method for predicting small/thin structures in medical images.

Anatomical knowledge based level set segmentation of cardiac ventricles from MRI

This paper represents a novel level set framework for segmentation of cardiac left ventricle (LV) and right ventricle (RV) from magnetic resonance images based on anatomical structures of the heart. We first propose a level set approach to recover the endocardium and epicardium of LV by using a bi-layer level set (BILLS) formulation, in which the endocardium and epicardium are represented by the 0-level set and k-level set of a level set function. Furthermore, the recovery of LV endocardium and epicardium is achieved by a level set evolution process, called convexity preserving bi-layer level set (CP-BILLS). During the CP-BILLS evolution, the 0-level set and k-level set simultaneously evolve and move toward the true endocardium and epicardium under the guidance of image information and the impact of the convexity preserving mechanism as well. To eliminate the manual selection of the k-level, we develop an algorithm for automatic selection of an optimal k-level. As a result, the obtained endocardial and epicardial contours are convex and consistent with the anatomy of cardiac ventricles. For segmentation of the whole ventricle, we extend this method to the segmentation of RV and myocardium of both left and right ventricles by using a convex shape decomposition (CSD) structure of cardiac ventricles based on anatomical knowledge. Experimental results demonstrate promising performance of our method. Compared with some traditional methods, our method exhibits superior performance in terms of segmentation accuracy and algorithm stability. Our method is comparable with the state-of-the-art deep learning-based method in terms of segmentation accuracy and algorithm stability, but our method has no need for training and the manual segmentation of the training data.

Effect of myocardial heterogeneity on ventricular electro-mechanical responses: a computational study

BACKGROUND

The heart wall exhibits three layers of different thicknesses: the outer epicardium, mid-myocardium, and inner endocardium. Among these layers, the mid-myocardium is typically the thickest. As indicated by preliminary studies, heart-wall layers exhibit various characteristics with regard to electrophysiology, pharmacology, and pathology. Construction of an accurate three-dimensional (3D) model of the heart is important for predicting physiological behaviors. However, the wide variability of myocardial shapes and the unclear edges between the epicardium and soft tissues are major challenges in the 3D model segmentation approach for identifying the boundaries of the epicardium, mid-myocardium, and endocardium. Therefore, this results in possible variations in the heterogeneity ratios between the epicardium, mid-myocardium, and endocardium. The objective of this study was to observe the effects of different thickness ratios of the epicardium, mid-myocardium, and endocardium on cardiac arrhythmogenesis, reentry instability, and mechanical responses during arrhythmia.

METHODS

We used a computational method and simulated three heterogeneous ventricular models: Model 1 had the thickest M cell layer and thinnest epicardium and endocardium. Model 2 had intermediate layer thicknesses. Model 3 exhibited the thinnest mid-myocardium and thickest epicardium and endocardium. Electrical and mechanical simulations of the three heterogeneous models were performed under normal sinus rhythm and reentry conditions.

RESULTS

Model 1 exhibited the highest probability of terminating reentrant waves, and Model 3 exhibited to experience greater cardiac arrhythmia. In the reentry simulation, at 8 s, Model 3 generated the largest number of rotors (eight), while Models 1 and 2 produced five and seven rotors, respectively. There was no significant difference in the cardiac output obtained during the sinus rhythm. Under the reentry condition, the highest cardiac output was generated by Model 1 (19 mL/s), followed by Model 2 (9 mL/s) and Model 3 (7 mL/s).

CONCLUSIONS

A thicker mid-myocardium led to improvements in the pumping efficacy and contractility and reduced the probability of cardiac arrhythmia. Conversely, thinner M cell layers generated more unstable reentrant spiral waves and hindered the ventricular pumping.

Integrated 3D Anatomical Model for Automatic Myocardial Segmentation in Cardiac CT Imagery

Segmentation of epicardial and endocardial boundaries is a critical step in diagnosing cardiovascular function in heart patients. The manual tracing of organ contours in Computed Tomography Angiography (CTA) slices is subjective, time-consuming and impractical in clinical setting. We propose a novel multi-dimensional automatic edge detection algorithm based on shape priors and principal component analysis (PCA). We have developed a highly customized parametric model for implicit representations of segmenting curves (3D) for Left Ventricle (LV), Right Ventricle (RV), and Epicardium (Epi) used simultaneously to achieve myocardial segmentation. We have combined these representations in a region-based image modeling framework with high level constraints enabling the modeling of complex cardiac anatomical structures to automatically guide the segmentation of endo/epicardial boundaries. Test results on 30 short-axis CTA datasets show robust segmentation with error (mean ± std mm) of (1.46 ± 0.41), (2.06 ± 0.65), (2.88 ± 0.59) for LV, RV and Epi respectively.

A 3D Hermite-based multiscale local active contour method with elliptical shape constraints for segmentation of cardiac MR and CT volumes

Analysis of cardiac images is a fundamental task to diagnose heart problems. Left ventricle (LV) is one of the most important heart structures used for cardiac evaluation. In this work, we propose a novel 3D hierarchical multiscale segmentation method based on a local active contour (AC) model and the Hermite transform (HT) for LV analysis in cardiac magnetic resonance (MR) and computed tomography (CT) volumes in short axis view. Features such as directional edges, texture, and intensities are analyzed using the multiscale HT space. A local AC model is configured using the HT coefficients and geometrical constraints. The endocardial and epicardial boundaries are used for evaluation. Segmentation of the endocardium is controlled using elliptical shape constraints. The final endocardial shape is used to define the geometrical constraints for segmentation of the epicardium. We follow the assumption that epicardial and endocardial shapes are similar in volumes with short axis view. An initialization scheme based on a fuzzy C-means algorithm and mathematical morphology was designed. The algorithm performance was evaluated using cardiac MR and CT volumes in short axis view demonstrating the feasibility of the proposed method.

An Assessment of Imaging Informatics for Precision Medicine in Cancer

Objectives: Precision medicine requires the measurement, quantification, and cataloging of medical characteristics to identify the most effective medical intervention. However, the amount of available data exceeds our current capacity to extract meaningful information. We examine the informatics needs to achieve precision medicine from the perspective of quantitative imaging and oncology. Methods: The National Cancer Institute (NCI) organized several workshops on the topic of medical imaging and precision medicine. The observations and recommendations are summarized herein. Results: Recommendations include: use of standards in data collection and clinical correlates to promote interoperability; data sharing and validation of imaging tools; clinician's feedback in all phases of research and development; use of open-source architecture to encourage reproducibility and reusability; use of challenges which simulate real-world situations to incentivize innovation; partnership with industry to facilitate commercialization; and education in academic communities regarding the challenges involved with translation of technology from the research domain to clinical utility and the benefits of doing so. Conclusions: This article provides a survey of the role and priorities for imaging informatics to help advance quantitative imaging in the era of precision medicine. While these recommendations were drawn from oncology, they are relevant and applicable to other clinical domains where imaging aids precision medicine.

Dynamic updating atlas for heart segmentation with a nonlinear field-based model

BACKGROUND

Segmentation of cardiac computed tomography (CT) images is an effective method for assessing the dynamic function of the heart and lungs. In the atlas-based heart segmentation approach, the quality of segmentation usually relies upon atlas images, and the selection of those reference images is a key step. The optimal goal in this selection process is to have the reference images as close to the target image as possible.

METHODS

This study proposes an atlas dynamic update algorithm using a scheme of nonlinear deformation field. The proposed method is based on the features among double-source CT (DSCT) slices. The extraction of these features will form a base to construct an average model and the created reference atlas image is updated during the registration process. A nonlinear field-based model was used to effectively implement a 4D cardiac segmentation.

RESULTS

The proposed segmentation framework was validated with 14 4D cardiac CT sequences. The algorithm achieved an acceptable accuracy (1.0-2.8 mm).

CONCLUSION

Our proposed method that combines a nonlinear field-based model and dynamic updating atlas strategies can provide an effective and accurate way for whole heart segmentation. The success of the proposed method largely relies on the effective use of the prior knowledge of the atlas and the similarity explored among the to-be-segmented DSCT sequences.

Hepatic vessel segmentation using variational level set combined with non-local robust statistics

Hepatic vessel segmentation is a challenging step in therapy guided by magnetic resonance imaging (MRI). This paper presents an improved variational level set method, which uses non-local robust statistics to suppress the influence of noise in MR images. The non-local robust statistics, which represent vascular features, are learned adaptively from seeds provided by users. K-means clustering in neighborhoods of seeds is utilized to exclude inappropriate seeds, which are obviously corrupted by noise. The neighborhoods of appropriate seeds are placed in an array to calculate the non-local robust statistics, and the variational level set formulation can be constructed. Bias correction is utilized in the level set formulation to reduce the influence of intensity inhomogeneity of MRI. Experiments were conducted over real MR images, and showed that the proposed method performed better on small hepatic vessel segmentation compared with other segmentation methods.

Prediction models for solitary pulmonary nodules based on curvelet textural features and clinical parameters

Lung cancer, one of the leading causes of cancer-related deaths, usually appears as solitary pulmonary nodules (SPNs) which are hard to diagnose using the naked eye. In this paper, curvelet-based textural features and clinical parameters are used with three prediction models [a multilevel model, a least absolute shrinkage and selection operator (LASSO) regression method, and a support vector machine (SVM)] to improve the diagnosis of benign and malignant SPNs. Dimensionality reduction of the original curvelet-based textural features was achieved using principal component analysis. In addition, non-conditional logistical regression was used to find clinical predictors among demographic parameters and morphological features. The results showed that, combined with 11 clinical predictors, the accuracy rates using 12 principal components were higher than those using the original curvelet-based textural features. To evaluate the models, 10-fold cross validation and back substitution were applied. The results obtained, respectively, were 0.8549 and 0.9221 for the LASSO method, 0.9443 and 0.9831 for SVM, and 0.8722 and 0.9722 for the multilevel model. All in all, it was found that using curvelet-based textural features after dimensionality reduction and using clinical predictors, the highest accuracy rate was achieved with SVM. The method may be used as an auxiliary tool to differentiate between benign and malignant SPNs in CT images.

Automatic detection of left and right ventricles from CTA enables efficient alignment of anatomy with myocardial perfusion data

BACKGROUND

Accurate alignment between cardiac CT angiographic studies (CTA) and nuclear perfusion images is crucial for improved diagnosis of coronary artery disease. This study evaluated in an animal model the accuracy of a CTA fully automated biventricular segmentation algorithm, a necessary step for automatic and thus efficient PET/CT alignment.

METHODS AND RESULTS

Twelve pigs with acute infarcts were imaged using Rb-82 PET and 64-slice CTA. Post-mortem myocardium mass measurements were obtained. Endocardial and epicardial myocardial boundaries were manually and automatically detected on the CTA and both segmentations used to perform PET/CT alignment. To assess the segmentation performance, image-based myocardial masses were compared to experimental data; the hand-traced profiles were used as a reference standard to assess the global and slice-by-slice robustness of the automated algorithm in extracting myocardium, LV, and RV. Mean distances between the automated and the manual 3D segmented surfaces were computed. Finally, differences in rotations and translations between the manual and automatic surfaces were estimated post-PET/CT alignment. The largest, smallest, and median distances between interactive and automatic surfaces averaged 1.2 ± 2.1, 0.2 ± 1.6, and 0.7 ± 1.9 mm. The average angular and translational differences in CT/PET alignments were 0.4°, -0.6°, and -2.3° about x, y, and z axes, and 1.8, -2.1, and 2.0 mm in x, y, and z directions.

CONCLUSIONS

Our automatic myocardial boundary detection algorithm creates surfaces from CTA that are similar in accuracy and provide similar alignments with PET as those obtained from interactive tracing. Specific difficulties in a reliable segmentation of the apex and base regions will require further improvements in the automated technique.