The automatic segmentation of cardiac computed tomography (CT) and magnetic resonance imaging (MRI) plays a pivotal role in the prevention and treatment of cardiovascular diseases. In this study, we propose an efficient network based on the multi-scale, multi-head self-attention (MSMHSA) mechanism. The incorporation of this mechanism enables us to achieve larger receptive fields, facilitating the accurate segmentation of whole heart structures in both CT and MRI images. Within this network, features extracted from the shallow feature extraction network undergo a MHSA mechanism that closely aligns with human vision, resulting in the extraction of contextual semantic information more comprehensively and accurately. To improve the precision of cardiac substructure segmentation across varying sizes, our proposed method introduces three MHSA networks at distinct scales. This approach allows for fine-tuning the accuracy of micro-object segmentation by adapting the size of the segmented images. The efficacy of our method is rigorously validated on the Multi-Modality Whole Heart Segmentation (MM-WHS) Challenge 2017 dataset, demonstrating competitive results and the accurate segmentation of seven cardiac substructures in both cardiac CT and MRI images. Through comparative experiments with advanced transformer-based models, our study provides compelling evidence that despite the remarkable achievements of transformer-based models, the fusion of CNN models and self-attention remains a simple yet highly effective approach for dual-modality whole heart segmentation.

OBJECTIVE: Transformer, which is notable for its ability of global context modeling, has been used to remedy the shortcomings of Convolutional neural networks (CNN) and break its dominance in medical image segmentation. However, the self-attention module is both memory and computational inefficient, so many methods have to build their Transformer branch upon largely downsampled feature maps or adopt the tokenized image patches to fit their model into accessible GPUs. This patch-wise operation restricts the network in extracting pixel-level intrinsic structural or dependencies inside each patch, hurting the performance of pixel-level classification tasks.
METHODS: To tackle these issues, we propose a memory- and computation-efficient self-attention module to enable reasoning on relatively high-resolution features, promoting the efficiency of learning global information while effective grasping fine spatial details. Furthermore, we design a novel Multi-Branch Transformer (MultiTrans) architecture to provide hierarchical features for handling objects with variable shapes and sizes in medical images. By building four parallel Transformer branches on different levels of CNN, our hybrid network aggregates both multi-scale global contexts and multi-scale local features.
RESULTS: MultiTrans achieves the highest segmentation accuracy on three medical image datasets with different modalities: Synapse, ACDC and M&Ms. Compared to the Standard Self-Attention (SSA), the proposed Efficient Self-Attention (ESA) can largely reduce the training memory and computational complexity while even slightly improve the accuracy. Specifically, the training memory cost, FLOPs and Params of our ESA are 18.77%, 20.68% and 74.07% of the SSA.
CONCLUSIONS: Experiments on three medical image datasets demonstrate the generality and robustness of the designed network. The ablation study shows the efficiency and effectiveness of our proposed ESA. Code is available at: https://github.com/Yanhua-Zhang/MultiTrans-extension.

Objectives. In this work, we proposed a deep-learning segmentation algorithm for cardiac magnetic resonance imaging to aid in contouring of the left ventricle, right ventricle, and Myocardium (Myo).Approach.We proposed a shifted window multilayer perceptron (Swin-MLP) mixer network which is built upon a 3D U-shaped symmetric encoder-decoder structure. We evaluated our proposed network using public data from 100 individuals. The network performance was quantitatively evaluated using 3D volume similarity between the ground truth contours and the predictions using Dice score coefficient, sensitivity, and precision as well as 2D surface similarity using Hausdorff distance (HD), mean surface distance (MSD) and residual mean square distance (RMSD). We benchmarked the performance against two other current leading edge networks known as Dynamic UNet and Swin-UNetr on the same public dataset.Results.The proposed network achieved the following volume similarity metrics when averaged over three cardiac segments: Dice = 0.952 ± 0.017, precision = 0.948 ± 0.016, sensitivity = 0.956 ± 0.022. The average surface similarities were HD = 1.521 ± 0.121 mm, MSD = 0.266 ± 0.075 mm, and RMSD = 0.668 ± 0.288 mm. The network shows statistically significant improvement in comparison to the Dynamic UNet and Swin-UNetr algorithms for most volumetric and surface metrics withp-value less than 0.05. Overall, the proposed Swin-MLP mixer network demonstrates better or comparable performance than competing methods.Significance.The proposed Swin-MLP mixer network demonstrates more accurate segmentation performance compared to current leading edge methods. This robust method demonstrates the potential to streamline clinical workflows for multiple applications.

OBJECTIVE: This study investigated the additional prognostic value of epicardial adipose tissue (EAT) volume for major adverse cardiovascular events (MACE) in patients undergoing stress cardiac magnetic resonance (CMR) imaging.
METHODS: 730 consecutive patients [mean age: 63 ± 10 years; 616 men] who underwent stress CMR for known or suspected coronary artery disease were randomly divided into derivation (n = 365) and validation (n = 365) cohorts. MACE was defined as non-fatal myocardial infarction and cardiac deaths. A deep learning algorithm was developed and trained to quantify EAT volume from CMR. EAT volume was adjusted for height (EAT volume index). A composite CMR-based risk score by Cox analysis of the risk of MACE was created.
RESULTS: In the derivation cohort, 32 patients (8.7 %) developed MACE during a follow-up of 2103 days. Left ventricular ejection fraction (LVEF) < 35 % (HR 4.407 [95 % CI 1.903-10.202]; p<0.001), stress perfusion defect (HR 3.550 [95 % CI 1.765-7.138]; p<0.001), late gadolinium enhancement (LGE) (HR 4.428 [95%CI 1.822-10.759]; p = 0.001) and EAT volume index (HR 1.082 [95 % CI 1.045-1.120]; p<0.001) were independent predictors of MACE. In a multivariate Cox regression analysis, adding EAT volume index to a composite risk score including LVEF, stress perfusion defect and LGE provided additional value in MACE prediction, with a net reclassification improvement of 0.683 (95%CI, 0.336-1.03; p<0.001). The combined evaluation of risk score and EAT volume index showed a higher Harrel C statistic as compared to risk score (0.85 vs. 0.76; p<0.001) and EAT volume index alone (0.85 vs.0.74; p<0.001). These findings were confirmed in the validation cohort.
CONCLUSIONS: In patients with clinically indicated stress CMR, fully automated EAT volume measured by deep learning can provide additional prognostic information on top of standard clinical and imaging parameters.

OBJECTIVE: Insight into the three-dimensional (3D) anatomy of the equine heart is essential in veterinary education and to develop minimally invasive intracardiac procedures. The aim was to create a 3D computer model simulating the in vivo anatomy of the adult equine heart.
METHODS: Ten horses and five ponies.
METHODS: Ten horses, euthanized for non-cardiovascular reasons, were used for in situ cardiac casting with polyurethane foam and subsequent computed tomography (CT) of the excised heart. In five anaesthetized ponies, a contrast-enhanced electrocardiogram-gated CT protocol was optimized to image the entire heart. Dedicated image processing software was used to create 3D models of all CT scans derived from both methods. Resulting models were compared regarding relative proportions, detail and ease of segmentation.
RESULTS: The casting protocol produced high detail, but compliant structures such as the pulmonary trunk were disproportionally expanded by the foam. Optimization of the contrast-enhanced CT protocol, especially adding a delayed phase for visualization of the cardiac veins, resulted in sufficiently detailed CT images to create an anatomically correct 3D model of the pony heart. Rescaling was needed to obtain a horse-sized model.
CONCLUSIONS: Three-dimensional computer models based on contrast-enhanced CT images appeared superior to those based on casted hearts to represent the in vivo situation and are preferred to obtain an anatomically correct heart model useful for education, client communication and research purposes. Scaling was, however, necessary to obtain an approximation of an adult horse heart as cardiac CT imaging is restricted by thoracic size.

UNASSIGNED: Artificial intelligence (AI) techniques have been proposed for automating analysis of short-axis (SAX) cine cardiac magnetic resonance (CMR), but no CMR analysis tool exists to automatically analyse large (unstructured) clinical CMR datasets. We develop and validate a robust AI tool for start-to-end automatic quantification of cardiac function from SAX cine CMR in large clinical databases.
UNASSIGNED: Our pipeline for processing and analysing CMR databases includes automated steps to identify the correct data, robust image pre-processing, an AI algorithm for biventricular segmentation of SAX CMR and estimation of functional biomarkers, and automated post-analysis quality control to detect and correct errors. The segmentation algorithm was trained on 2793 CMR scans from two NHS hospitals and validated on additional cases from this dataset (n = 414) and five external datasets (n = 6888), including scans of patients with a range of diseases acquired at 12 different centres using CMR scanners from all major vendors. Median absolute errors in cardiac biomarkers were within the range of inter-observer variability: <8.4 mL (left ventricle volume), <9.2 mL (right ventricle volume), <13.3 g (left ventricular mass), and <5.9% (ejection fraction) across all datasets. Stratification of cases according to phenotypes of cardiac disease and scanner vendors showed good performance across all groups.
UNASSIGNED: We show that our proposed tool, which combines image pre-processing steps, a domain-generalizable AI algorithm trained on a large-scale multi-domain CMR dataset and quality control steps, allows robust analysis of (clinical or research) databases from multiple centres, vendors, and cardiac diseases. This enables translation of our tool for use in fully automated processing of large multi-centre databases.

Automatic segmentation of the cardiac left ventricle with scars remains a challenging and clinically significant task, as it is essential for patient diagnosis and treatment pathways. This study aimed to develop a novel framework and cost function to achieve optimal automatic segmentation of the left ventricle with scars using LGE-MRI images. To ensure the generalization of the framework, an unbiased validation protocol was established using out-of-distribution (OOD) internal and external validation cohorts, and intra-observation and inter-observer variability ground truths. The framework employs a combination of traditional computer vision techniques and deep learning, to achieve optimal segmentation results. The traditional approach uses multi-atlas techniques, active contours, and k-means methods, while the deep learning approach utilizes various deep learning techniques and networks. The study found that the traditional computer vision technique delivered more accurate results than deep learning, except in cases where there was breath misalignment error. The optimal solution of the framework achieved robust and generalized results with Dice scores of 82.8 ± 6.4% and 72.1 ± 4.6% in the internal and external OOD cohorts, respectively. The developed framework offers a high-performance solution for automatic segmentation of the left ventricle with scars using LGE-MRI. Unlike existing state-of-the-art approaches, it achieves unbiased results across different hospitals and vendors without the need for training or tuning in hospital cohorts. This framework offers a valuable tool for experts to accomplish the task of fully automatic segmentation of the left ventricle with scars based on a single-modality cardiac scan.

Deep learning models can achieve high accuracy when trained on large amounts of labeled data. However, real-world scenarios often involve several challenges: Training data may become available in installments, may originate from multiple different domains, and may not contain labels for training. Certain settings, for instance medical applications, often involve further restrictions that prohibit retention of previously seen data due to privacy regulations. In this work, to address such challenges, we study unsupervised segmentation in continual learning scenarios that involve domain shift. To that end, we introduce GarDA (Generative Appearance Replay for continual Domain Adaptation), a generative-replay based approach that can adapt a segmentation model sequentially to new domains with unlabeled data. In contrast to single-step unsupervised domain adaptation (UDA), continual adaptation to a sequence of domains enables leveraging and consolidation of information from multiple domains. Unlike previous approaches in incremental UDA, our method does not require access to previously seen data, making it applicable in many practical scenarios. We evaluate GarDA on three datasets with different organs and modalities, where it substantially outperforms existing techniques. Our code is available at: https://github.com/histocartography/generative-appearance-replay.

UNASSIGNED: Structural and functional heart abnormalities can be examined non-invasively with cardiac magnetic resonance imaging (CMR). Thanks to the development of MR devices, diagnostic scans can capture more and more relevant information about possible heart diseases. T1 and T2 mapping are such novel technology, providing tissue specific information even without the administration of contrast material. Artificial intelligence solutions based on deep learning have demonstrated state-of-the-art results in many application areas, including medical imaging. More specifically, automated tools applied at cine sequences have revolutionized volumetric CMR reporting in the past five years. Applying deep learning models to T1 and T2 mapping images can similarly improve the efficiency of post-processing pipelines and consequently facilitate diagnostic processes.
UNASSIGNED: In this paper, we introduce a deep learning model for myocardium segmentation trained on over 7,000 raw CMR images from 262 subjects of heterogeneous disease etiology. The data were labeled by three experts. As part of the evaluation, Dice score and Hausdorff distance among experts is calculated, and the expert consensus is compared with the model\'s predictions.
UNASSIGNED: Our deep learning method achieves 86% mean Dice score, while contours provided by three experts on the same data show 90% mean Dice score. The method\'s accuracy is consistent across epicardial and endocardial contours, and on basal, midventricular slices, with only 5% lower results on apical slices, which are often challenging even for experts.
UNASSIGNED: We trained and evaluated a deep learning based segmentation model on 262 heterogeneous CMR cases. Applying deep neural networks to T1 and T2 mapping could similarly improve diagnostic practices. Using the fine details of T1 and T2 mapping images and high-quality labels, the objective of this research is to approach human segmentation accuracy with deep learning.

OBJECTIVE: The sheer volume of data generated by population imaging studies is unparalleled by current capabilities to extract objective and quantitative cardiac phenotypes; subjective and time-consuming manual image analysis remains the gold standard. Automated image analytics to compute quantitative imaging biomarkers of cardiac function are desperately needed. Data volumes and their variability pose a challenge to most state-of-the-art methods for endo- and epicardial contours, which lack robustness when applied to very large datasets. Our aim is to develop an analysis pipeline for the automatic quantification of cardiac function from cine magnetic resonance imaging data.
METHODS: This work adopt 4,638 cardiac MRI cases coming from UK Biobank with ground truth available for left and RV contours. A hybrid and robust algorithm is proposed to improve the accuracy of automatic left and right ventricle segmentation by harnessing the localization accuracy of deep learning and the morphological accuracy of 3D-ASM (three-dimensional active shape models). The contributions of this paper are three-fold. First, a fully automatic method is proposed for left and right ventricle initialization and cardiac MRI segmentation by taking full advantage of spatiotemporal constraint. Second, a deeply supervised network is introduced to train and segment the heart. Third, the 3D-ASM image search procedure is improved by combining image intensity models with convolutional neural network (CNN) derived distance maps improving endo- and epicardial edge localization.
RESULTS: The proposed architecture outperformed the state of the art for cardiac MRI segmentation from UK Biobank. The statistics of RV landmarks detection errors for Triscuspid valve and RV apex are 4.17 mm and 5.58 mm separately. The overlap metric, mean contour distance, Hausdorff distance and cardiac functional parameters are calculated for the LV (Left Ventricle) and RV (Right Ventricle) contour segmentation. Bland-Altman analysis for clinical parameters shows that the results from our automated image analysis pipelines are in good agreement with results from expert manual analysis.
CONCLUSIONS: Our hybrid scheme combines deep learning and statistical shape modeling for automatic segmentation of the LV/RV from cardiac MRI datasets is effective and robust and can compute cardiac functional indexes from population imaging.