Exploring a frequency-domain attention-guided cascade U-Net: Towards spatially tunable segmentation of vasculature.

Developing fully automatic and highly accurate medical image segmentation methods is critically important for vascular disease diagnosis and treatment planning. Although advances in convolutional neural networks (CNNs) have spawned an array of automatic segmentation models converging to saturated high performance, none have explored whether CNNs can achieve (spatially) tunable segmentation. As a result, we propose multiple attention modules from a frequency-domain perspective to construct a unified CNN architecture for segmenting vasculature with desired (spatial) scales. The proposed CNN architecture is named frequency-domain attention-guided cascaded U-Net (FACU-Net). Specifically, FACU-Net contains two innovative components: (1) a frequency-domain-based channel attention module that adaptively tunes channel-wise feature responses and (2) a frequency-domain-based spatial attention module that enables the deep network to concentrate on foreground regions of interest (ROIs) effectively. Furthermore, we devised a novel frequency-domain-based content attention module to enhance or weaken the high (spatial) frequency information, allowing us to strengthen or eliminate vessels of interest. Extensive experiments using clinical data from patients with intracranial aneurysms (IA) and abdominal aortic aneurysms (AAA) demonstrated that the proposed FACU-Net met its design goal. In addition, we further investigated the association between varying (spatial) frequency components and the desirable vessel size/scale attributes. In summary, our preliminary findings are encouraging, and further developments may lead to deployable image segmentation models that are spatially tunable for clinical applications.

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.

Deep-learning-based image segmentation for image-based computational hemodynamic analysis of abdominal aortic aneurysms: a comparison study.

Computational hemodynamics is increasingly being used to quantify hemodynamic characteristics in and around abdominal aortic aneurysms (AAA) in a patient-specific fashion. However, the time-consuming manual annotation hinders the clinical translation of computational hemodynamic analysis. Thus, we investigate the feasibility of using deep-learning-based image segmentation methods to reduce the time required for manual segmentation. Two of the latest deep-learning-based image segmentation methods, ARU-Net and CACU-Net, were used to test the feasibility of automated computer model creation for computational hemodynamic analysis. Morphological features and hemodynamic metrics of 30 computed tomography angiography (CTA) scans were compared between pre-dictions and manual models. The DICE score for both networks was 0.916, and the correlation value was above 0.95, indicating their ability to generate models comparable to human segmentation. The Bland-Altman analysis shows a good agreement between deep learning and manual segmentation results. Compared with manual (computational hemodynamics) model recreation, the time for automated computer model generation was significantly reduced (from ∼2 h to ∼10 min). Automated image segmentation can significantly reduce time expenses on the recreation of patient-specific AAA models. Moreover, our study showed that both CACU-Net and ARU-Net could accomplish AAA segmentation, and CACU-Net outperformed ARU-Net in terms of accuracy and time-saving.

Characterization of small abdominal aortic aneurysms' growth status using spatial pattern analysis of aneurismal hemodynamics.

Aneurysm hemodynamics is known for its crucial role in the natural history of abdominal aortic aneurysms (AAA). However, there is a lack of well-developed quantitative assessments for disturbed aneurysmal flow. Therefore, we aimed to develop innovative metrics for quantifying disturbed aneurysm hemodynamics and evaluate their effectiveness in predicting the growth status of AAAs, specifically distinguishing between fast-growing and slowly-growing aneurysms. The growth status of aneurysms was classified as fast (≥ 5 mm/year) or slow (< 5 mm/year) based on serial imaging over time. We conducted computational fluid dynamics (CFD) simulations on 70 patients with computed tomography (CT) angiography findings. By converting hemodynamics data (wall shear stress and velocity) located on unstructured meshes into image-like data, we enabled spatial pattern analysis using Radiomics methods, referred to as "Hemodynamics-informatics" (i.e., using informatics techniques to analyze hemodynamic data). Our best model achieved an AUROC of 0.93 and an accuracy of 87.83%, correctly identifying 82.00% of fast-growing and 90.75% of slowly-growing AAAs. Compared with six classification methods, the models incorporating hemodynamics-informatics exhibited an average improvement of 8.40% in AUROC and 7.95% in total accuracy. These preliminary results indicate that hemodynamics-informatics correlates with AAAs' growth status and aids in assessing their progression.

Radiomic-based Textural Analysis of Intraluminal Thrombus in Aortic Abdominal Aneurysms: A Demonstration of Automated Workflow.

Our main objective is to investigate how the structural information of intraluminal thrombus (ILT) can be used to predict abdominal aortic aneurysms (AAA) growth status through an automated workflow. Fifty-four human subjects with ILT in their AAAs were identified from our database; those AAAs were categorized as slowly- (< 5 mm/year) or fast-growing (≥ 5 mm/year) AAAs. In-house deep-learning image segmentation models were used to generate 3D geometrical AAA models, followed by automated analysis. All features were fed into a support vector machine classifier to predict AAA's growth status.The most accurate prediction model was achieved through four geometrical parameters measuring the extent of ILT, two parameters quantifying the constitution of ILT, antihypertensive medication, and the presence of co-existing coronary artery disease. The predictive model achieved an AUROC of 0.89 and a total accuracy of 83%. When ILT was not considered, our prediction's AUROC decreased to 0.75 (P-value < 0.001).

Automatic segmentation of abdominal aortic aneurysms from CT angiography using a context-aware cascaded U-Net.

We delineate abdominal aortic aneurysms, including lumen and intraluminal thrombosis (ILT), from contrast-enhanced computed tomography angiography (CTA) data in 70 patients with complete automation. A novel context-aware cascaded U-Net configuration enables automated image segmentation. Notably, auto-context structure, in conjunction with dilated convolutions, anisotropic context module, hierarchical supervision, and a multi-class loss function, are proposed to improve the delineation of ILT in an unbalanced, low-contrast multi-class labeling problem. A quantitative analysis shows that the automated image segmentation produces comparable results with trained human users (e.g., DICE scores of 0.945 and 0.804 for lumen and ILT, respectively). Resultant morphological metrics (e.g., volume, surface area, etc.) are highly correlated to those parameters generated by trained human users. In conclusion, the proposed automated multi-class image segmentation tool has the potential to be further developed as a translational software tool that can be used to improve the clinical management of AAAs.

Computerized Differentiation of Growth Status for Abdominal Aortic Aneurysms: A Feasibility Study.

Fast-growing abdominal aortic aneurysms (AAA) have a high rupture risk and poor outcomes if not promptly identified and treated. Our primary objective is to improve the differentiation of small AAAs' growth status (fast versus slow-growing) through a combination of patient health information, computational hemodynamics, geometric analysis, and artificial intelligence. 3D computed tomography angiography (CTA) data available for 70 patients diagnosed with AAAs with known growth status were used to conduct geometric and hemodynamic analyses. Differences among ten metrics (out of ninety metrics) were statistically significant discriminators between fast and slow-growing groups. Using a support vector machine (SVM) classifier, the area under receiving operating curve (AUROC) and total accuracy of our best predictive model for differentiation of AAAs' growth status were 0.86 and 77.50%, respectively. In summary, the proposed analytics has the potential to differentiate fast from slow-growing AAAs, helping guide resource allocation for the management of patients with AAAs.

An attention residual u-net with differential preprocessing and geometric postprocessing: Learning how to segment vasculature including intracranial aneurysms.

OBJECTIVE: Intracranial aneurysms (IA) are lethal, with high morbidity and mortality rates. Reliable, rapid, and accurate segmentation of IAs and their adjacent vasculature from medical imaging data is important to improve the clinical management of patients with IAs. However, due to the blurred boundaries and complex structure of IAs and overlapping with brain tissue or other cerebral arteries, image segmentation of IAs remains challenging. This study aimed to develop an attention residual U-Net (ARU-Net) architecture with differential preprocessing and geometric postprocessing for automatic segmentation of IAs and their adjacent arteries in conjunction with 3D rotational angiography (3DRA) images. METHODS: The proposed ARU-Net followed the classic U-Net framework with the following key enhancements. First, we preprocessed the 3DRA images based on boundary enhancement to capture more contour information and enhance the presence of small vessels. Second, we introduced the long skip connections of the attention gate at each layer of the fully convolutional decoder-encoder structure to emphasize the field of view (FOV) for IAs. Third, residual-based short skip connections were also embedded in each layer to implement in-depth supervision to help the network converge. Fourth, we devised a multiscale supervision strategy for independent prediction at different levels of the decoding path, integrating multiscale semantic information to facilitate the segmentation of small vessels. Fifth, the 3D conditional random field (3DCRF) and 3D connected component optimization (3DCCO) were exploited as postprocessing to optimize the segmentation results. RESULTS: Comprehensive experimental assessments validated the effectiveness of our ARU-Net. The proposed ARU-Net model achieved comparable or superior performance to the state-of-the-art methods through quantitative and qualitative evaluations. Notably, we found that ARU-Net improved the identification of arteries connecting to an IA, including small arteries that were hard to recognize by other methods. Consequently, IA geometries segmented by the proposed ARU-Net model yielded superior performance during subsequent computational hemodynamic studies (also known as "patient-specific" computational fluid dynamics [CFD] simulations). Furthermore, in an ablation study, the five key enhancements mentioned above were confirmed. CONCLUSIONS: The proposed ARU-Net model can automatically segment the IAs in 3DRA images with relatively high accuracy and potentially has significant value for clinical computational hemodynamic analysis.

USING CONVOLUTIONAL NEURAL NETWORK-BASED SEGMENTATION FOR IMAGE-BASED COMPUTATIONAL FLUID DYNAMICS SIMULATIONS OF BRAIN ANEURYSMS: INITIAL EXPERIENCE IN AUTOMATED MODEL CREATION.

"Image-based" computational fluid dynamics (CFD) simulations provide insights into each patient's hemodynamic environment. However, current standard procedures for creating CFD models start with manual segmentation and are time-consuming, hindering the clinical translation of image-based CFD simulations. This feasibility study adopts deep-learning-based image segmentation (hereafter referred to as Artificial Intelligence (AI) segmentation) to replace manual segmentation to accelerate CFD model creation. Two published convolutional neural network-based AI methods (MIScnn and DeepMedic) were selected to perform CFD model extraction from three-dimensional (3D) rotational angiography data containing intracranial aneurysms. In this study, aneurysm morphological and hemodynamic results using models generated by AI segmentation methods were compared with those obtained by two human users for the same data. Interclass coefficients (ICC), Bland-Altman plots, and Pearson's correlation coefficients (PCC) were combined to assess how well AI-generated CFD models were performed. We found that almost perfect agreement was obtained between the human and AI results for all eleven morphological and five out of eight hemodynamic parameters, while a moderate agreement was obtained from the remaining three hemodynamic parameters. Given this level of agreement, using AI segmentation to create CFD models is feasible, given more developments.