A completely automated pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices

Leveraging 3D Atrial Geometry for the Evaluation of Atrial Fibrillation: A Comprehensive Review

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia associated with significant morbidity and mortality. Managing risk of stroke and AF burden are pillars of AF management. Atrial geometry has long been recognized as a useful measure in achieving these goals. However, traditional diagnostic approaches often overlook the complex spatial dynamics of the atria. This review explores the emerging role of three-dimensional (3D) atrial geometry in the evaluation and management of AF. Advancements in imaging technologies and computational modeling have enabled detailed reconstructions of atrial anatomy, providing insights into the pathophysiology of AF that were previously unattainable. We examine current methodologies for interpreting 3D atrial data, including qualitative, basic quantitative, global quantitative, and statistical shape modeling approaches. We discuss their integration into clinical practice, highlighting potential benefits such as personalized treatment strategies, improved outcome prediction, and informed treatment approaches. Additionally, we discuss the challenges and limitations associated with current approaches, including technical constraints and variable interpretations, and propose future directions for research and clinical applications. This comprehensive review underscores the transformative potential of leveraging 3D atrial geometry in the evaluation and management of AF, advocating for its broader adoption in clinical practice.

Toward Enabling Cardiac Digital Twins of Myocardial Infarction Using Deep Computational Models for Inverse Inference

Cardiac digital twins (CDTs) have the potential to offer individualized evaluation of cardiac function in a non-invasive manner, making them a promising approach for personalized diagnosis and treatment planning of myocardial infarction (MI). The inference of accurate myocardial tissue properties is crucial in creating a reliable CDT of MI. In this work, we investigate the feasibility of inferring myocardial tissue properties from the electrocardiogram (ECG) within a CDT platform. The platform integrates multi-modal data, such as cardiac MRI and ECG, to enhance the accuracy and reliability of the inferred tissue properties. We perform a sensitivity analysis based on computer simulations, systematically exploring the effects of infarct location, size, degree of transmurality, and electrical activity alteration on the simulated QRS complex of ECG, to establish the limits of the approach. We subsequently present a novel deep computational model, comprising a dual-branch variational autoencoder and an inference model, to infer infarct location and distribution from the simulated QRS. The proposed model achieves mean Dice scores of 0.457 ±0.317 and 0.302 ±0.273 for the inference of left ventricle scars and border zone, respectively. The sensitivity analysis enhances our understanding of the complex relationship between infarct characteristics and electrophysiological features. The in silico experimental results show that the model can effectively capture the relationship for the inverse inference, with promising potential for clinical application in the future. The code is available at https://github.com/lileitech/MI_inverse_inference.

A Comprehensive Review of Vision-Based 3D Reconstruction Methods

With the rapid development of 3D reconstruction, especially the emergence of algorithms such as NeRF and 3DGS, 3D reconstruction has become a popular research topic in recent years. 3D reconstruction technology provides crucial support for training extensive computer vision models and advancing the development of general artificial intelligence. With the development of deep learning and GPU technology, the demand for high-precision and high-efficiency 3D reconstruction information is increasing, especially in the fields of unmanned systems, human-computer interaction, virtual reality, and medicine. The rapid development of 3D reconstruction is becoming inevitable. This survey categorizes the various methods and technologies used in 3D reconstruction. It explores and classifies them based on three aspects: traditional static, dynamic, and machine learning. Furthermore, it compares and discusses these methods. At the end of the survey, which includes a detailed analysis of the trends and challenges in 3D reconstruction development, we aim to provide a comprehensive introduction for individuals who are currently engaged in or planning to conduct research on 3D reconstruction. Our goal is to help them gain a comprehensive understanding of the relevant knowledge related to 3D reconstruction.

Advancements in artificial intelligence-driven techniques for interventional cardiology

This paper aims to thoroughly discuss the impact of artificial intelligence (AI) on clinical practice in interventional cardiology (IC) with special recognition of its most recent advancements. Thus, recent years have been exceptionally abundant in advancements in computational tools, including the development of AI. The application of AI development is currently in its early stages, nevertheless new technologies have proven to be a promising concept, particularly considering IC showing great impact on patient safety, risk stratification and outcomes during the whole therapeutic process. The primary goal is to achieve the integration of multiple cardiac imaging modalities, establish online decision support systems and platforms based on augmented and/or virtual realities, and finally to create automatic medical systems, providing electronic health data on patients. In a simplified way, two main areas of AI utilization in IC may be distinguished, namely, virtual and physical. Consequently, numerous studies have provided data regarding AI utilization in terms of automated interpretation and analysis from various cardiac modalities, including electrocardiogram, echocardiography, angiography, cardiac magnetic resonance imaging, and computed tomography as well as data collected during robotic-assisted percutaneous coronary intervention procedures. Thus, this paper aims to thoroughly discuss the impact of AI on clinical practice in IC with special recognition of its most recent advancements.

Multi-class point cloud completion networks for 3D cardiac anatomy reconstruction from cine magnetic resonance images

Cine magnetic resonance imaging (MRI) is the current gold standard for the assessment of cardiac anatomy and function. However, it typically only acquires a set of two-dimensional (2D) slices of the underlying three-dimensional (3D) anatomy of the heart, thus limiting the understanding and analysis of both healthy and pathological cardiac morphology and physiology. In this paper, we propose a novel fully automatic surface reconstruction pipeline capable of reconstructing multi-class 3D cardiac anatomy meshes from raw cine MRI acquisitions. Its key component is a multi-class point cloud completion network (PCCN) capable of correcting both the sparsity and misalignment issues of the 3D reconstruction task in a unified model. We first evaluate the PCCN on a large synthetic dataset of biventricular anatomies and observe Chamfer distances between reconstructed and gold standard anatomies below or similar to the underlying image resolution for multiple levels of slice misalignment. Furthermore, we find a reduction in reconstruction error compared to a benchmark 3D U-Net by 32% and 24% in terms of Hausdorff distance and mean surface distance, respectively. We then apply the PCCN as part of our automated reconstruction pipeline to 1000 subjects from the UK Biobank study in a cross-domain transfer setting and demonstrate its ability to reconstruct accurate and topologically plausible biventricular heart meshes with clinical metrics comparable to the previous literature. Finally, we investigate the robustness of our proposed approach and observe its capacity to successfully handle multiple common outlier conditions.

Artificial Intelligence-Based Methods for Precision Cardiovascular Medicine

Precision medicine has the potential to revolutionize the way cardiovascular diseases are diagnosed, predicted, and treated by tailoring treatment strategies to the individual characteristics of each patient. Artificial intelligence (AI) has recently emerged as a promising tool for improving the accuracy and efficiency of precision cardiovascular medicine. In this scoping review, we aimed to identify and summarize the current state of the literature on the use of AI in precision cardiovascular medicine. A comprehensive search of electronic databases, including Scopes, Google Scholar, and PubMed, was conducted to identify relevant studies. After applying inclusion and exclusion criteria, a total of 28 studies were included in the review. We found that AI is being increasingly applied in various areas of cardiovascular medicine, including the diagnosis, prognosis of cardiovascular diseases, risk prediction and stratification, and treatment planning. As a result, most of these studies focused on prediction (50%), followed by diagnosis (21%), phenotyping (14%), and risk stratification (14%). A variety of machine learning models were utilized in these studies, with logistic regression being the most used (36%), followed by random forest (32%), support vector machine (25%), and deep learning models such as neural networks (18%). Other models, such as hierarchical clustering (11%), Cox regression (11%), and natural language processing (4%), were also utilized. The data sources used in these studies included electronic health records (79%), imaging data (43%), and omics data (4%). We found that AI is being increasingly applied in various areas of cardiovascular medicine, including the diagnosis, prognosis of cardiovascular diseases, risk prediction and stratification, and treatment planning. The results of the review showed that AI has the potential to improve the performance of cardiovascular disease diagnosis and prognosis, as well as to identify individuals at high risk of developing cardiovascular diseases. However, further research is needed to fully evaluate the clinical utility and effectiveness of AI-based approaches in precision cardiovascular medicine. Overall, our review provided a comprehensive overview of the current state of knowledge in the field of AI-based methods for precision cardiovascular medicine and offered new insights for researchers interested in this research area.

Enhanced optimization-based method for the generation of patient-specific models of Purkinje networks

Cardiac Purkinje networks are a fundamental part of the conduction system and are known to initiate a variety of cardiac arrhythmias. However, patient-specific modeling of Purkinje networks remains a challenge due to their high morphological complexity. This work presents a novel method based on optimization principles for the generation of Purkinje networks that combines geometric and activation accuracy in branch size, bifurcation angles, and Purkinje-ventricular-junction activation times. Three biventricular meshes with increasing levels of complexity are used to evaluate the performance of our approach. Purkinje-tissue coupled monodomain simulations are executed to evaluate the generated networks in a realistic scenario using the most recent Purkinje/ventricular human cellular models and physiological values for the Purkinje-ventricular-junction characteristic delay. The results demonstrate that the new method can generate patient-specific Purkinje networks with controlled morphological metrics and specified local activation times at the Purkinje-ventricular junctions.

3D Shape-Based Myocardial Infarction Prediction Using Point Cloud Classification Networks

Myocardial infarction (MI) is one of the most prevalent cardiovascular diseases with associated clinical decision-making typically based on single-valued imaging biomarkers. However, such metrics only approximate the complex 3D structure and physiology of the heart and hence hinder a better understanding and prediction of MI outcomes. In this work, we investigate the utility of complete 3D cardiac shapes in the form of point clouds for an improved detection of MI events. To this end, we propose a fully automatic multi-step pipeline consisting of a 3D cardiac surface reconstruction step followed by a point cloud classification network. Our method utilizes recent advances in geometric deep learning on point clouds to enable direct and efficient multi-scale learning on high-resolution surface models of the cardiac anatomy. We evaluate our approach on 1068 UK Biobank subjects for the tasks of prevalent MI detection and incident MI prediction and find improvements of ∼13% and ∼5% respectively over clinical benchmarks. Furthermore, we analyze the role of each ventricle and cardiac phase for 3D shape-based MI detection and conduct a visual analysis of the morphological and physiological patterns typically associated with MI outcomes.Clinical relevance- The presented approach enables the fast and fully automatic pathology-specific analysis of full 3D cardiac shapes. It can thus be employed as a real-time diagnostic tool in clinical practice to discover and visualize more intricate biomarkers than currently used single-valued metrics and improve predictive accuracy of myocardial infarction.

A benchmark study of convolutional neural networks in fully automatic segmentation of aortic root

Recent clinical studies have suggested that introducing 3D patient-specific aortic root models into the pre-operative assessment procedure of transcatheter aortic valve replacement (TAVR) would reduce the incident rate of peri-operative complications. Tradition manual segmentation is labor-intensive and low-efficient, which cannot meet the clinical demands of processing large data volumes. Recent developments in machine learning provided a viable way for accurate and efficient medical image segmentation for 3D patient-specific models automatically. This study quantitively evaluated the auto segmentation quality and efficiency of the four popular segmentation-dedicated three-dimensional (3D) convolutional neural network (CNN) architectures, including 3D UNet, VNet, 3D Res-UNet and SegResNet. All the CNNs were implemented in PyTorch platform, and low-dose CTA image sets of 98 anonymized patients were retrospectively selected from the database for training and testing of the CNNs. The results showed that despite all four 3D CNNs having similar recall, Dice similarity coefficient (DSC), and Jaccard index on the segmentation of the aortic root, the Hausdorff distance (HD) of the segmentation results from 3D Res-UNet is 8.56 ± 2.28, which is only 9.8% higher than that of VNet, but 25.5% and 86.4% lower than that of 3D UNet and SegResNet, respectively. In addition, 3D Res-UNet and VNet also performed better in the 3D deviation location of interest analysis focusing on the aortic valve and the bottom of the aortic root. Although 3D Res-UNet and VNet are evenly matched in the aspect of classical segmentation quality evaluation metrics and 3D deviation location of interest analysis, 3D Res-UNet is the most efficient CNN architecture with an average segmentation time of 0.10 ± 0.04 s, which is 91.2%, 95.3% and 64.3% faster than 3D UNet, VNet and SegResNet, respectively. The results from this study suggested that 3D Res-UNet is a suitable candidate for accurate and fast automatic aortic root segmentation for pre-operative assessment of TAVR.

A deep learning approach for fully automated cardiac shape modeling in tetralogy of Fallot

BACKGROUND

Cardiac shape modeling is a useful computational tool that has provided quantitative insights into the mechanisms underlying dysfunction in heart disease. The manual input and time required to make cardiac shape models, however, limits their clinical utility. Here we present an end-to-end pipeline that uses deep learning for automated view classification, slice selection, phase selection, anatomical landmark localization, and myocardial image segmentation for the automated generation of three-dimensional, biventricular shape models. With this approach, we aim to make cardiac shape modeling a more robust and broadly applicable tool that has processing times consistent with clinical workflows.

METHODS

Cardiovascular magnetic resonance (CMR) images from a cohort of 123 patients with repaired tetralogy of Fallot (rTOF) from two internal sites were used to train and validate each step in the automated pipeline. The complete automated pipeline was tested using CMR images from a cohort of 12 rTOF patients from an internal site and 18 rTOF patients from an external site. Manually and automatically generated shape models from the test set were compared using Euclidean projection distances, global ventricular measurements, and atlas-based shape mode scores.

RESULTS

The mean absolute error (MAE) between manually and automatically generated shape models in the test set was similar to the voxel resolution of the original CMR images for end-diastolic models (MAE = 1.9 ± 0.5 mm) and end-systolic models (MAE = 2.1 ± 0.7 mm). Global ventricular measurements computed from automated models were in good agreement with those computed from manual models. The average mean absolute difference in shape mode Z-score between manually and automatically generated models was 0.5 standard deviations for the first 20 modes of a reference statistical shape atlas.

CONCLUSIONS

Using deep learning, accurate three-dimensional, biventricular shape models can be reliably created. This fully automated end-to-end approach dramatically reduces the manual input required to create shape models, thereby enabling the rapid analysis of large-scale datasets and the potential to deploy statistical atlas-based analyses in point-of-care clinical settings. Training data and networks are available from cardiacatlas.org.

Interpretable cardiac anatomy modeling using variational mesh autoencoders

Cardiac anatomy and function vary considerably across the human population with important implications for clinical diagnosis and treatment planning. Consequently, many computer-based approaches have been developed to capture this variability for a wide range of applications, including explainable cardiac disease detection and prediction, dimensionality reduction, cardiac shape analysis, and the generation of virtual heart populations. In this work, we propose a variational mesh autoencoder (mesh VAE) as a novel geometric deep learning approach to model such population-wide variations in cardiac shapes. It embeds multi-scale graph convolutions and mesh pooling layers in a hierarchical VAE framework to enable direct processing of surface mesh representations of the cardiac anatomy in an efficient manner. The proposed mesh VAE achieves low reconstruction errors on a dataset of 3D cardiac meshes from over 1,000 patients with acute myocardial infarction, with mean surface distances between input and reconstructed meshes below the underlying image resolution. We also find that it outperforms a voxelgrid-based deep learning benchmark in terms of both mean surface distance and Hausdorff distance while requiring considerably less memory. Furthermore, we explore the quality and interpretability of the mesh VAE's latent space and showcase its ability to improve the prediction of major adverse cardiac events over a clinical benchmark. Finally, we investigate the method's ability to generate realistic virtual populations of cardiac anatomies and find good alignment between the synthesized and gold standard mesh populations in terms of multiple clinical metrics.

A novel data-driven method for the analysis and reconstruction of cardiac cine MRI

Cardiac cine magnetic resonance imaging (MRI) can be considered the optimal criterion for measuring cardiac function. This imaging technique can provide us with detailed information about cardiac structure, tissue composition and even blood flow, which makes it highly used in medical science. But due to the image time acquisition and several other factors the MRI sequences can easily get corrupted, causing radiologists to misdiagnose 40 million people worldwide each and every single year. Hence, the urge to decrease these numbers, researchers from different fields have been introducing novel tools and methods in the medical field. Aiming to the same target, we consider in this work the application of the higher order dynamic mode decomposition (HODMD) technique. The HODMD algorithm is a linear method, which was originally introduced in the fluid dynamics domain, for the analysis of complex systems. Nevertheless, the proposed method has extended its applicability to numerous domains, including medicine. In this work, HODMD in used to analyze sets of MR images of a heart, with the ultimate goal of identifying the main patterns and frequencies driving the heart dynamics. Furthermore, a novel interpolation algorithm based on singular value decomposition combined with HODMD is introduced, providing a three-dimensional reconstruction of the heart. This algorithm is applied (i) to reconstruct corrupted or missing images, and (ii) to build a reduced order model of the heart dynamics.

Automated 3D Whole-Heart Mesh Reconstruction From 2D Cine MR Slices Using Statistical Shape Model

Cardiac magnetic resonance (CMR) imaging is the one of the gold standard imaging modalities for the diagnosis and characterization of cardiovascular diseases. The clinical cine protocol of the CMR typically generates high-resolution 2D images of heart tissues in a finite number of separated and independent 2D planes, which are appropriate for the 3D reconstruction of biventricular heart surfaces. However, they are usually inadequate for the whole-heart reconstruction, specifically for both atria. In this regard, the paper presents a novel approach for automated patient-specific 3D whole-heart mesh reconstruction from limited number of 2D cine CMR slices with the help of a statistical shape model (SSM). After extracting the heart contours from 2D cine slices, the SSM is first optimally fitted over the sparse heart contours in 3D space to provide the initial representation of the 3D whole-heart mesh, which is further deformed to minimize the distance from the heart contours for generating the final reconstructed mesh. The reconstruction performance of the proposed approach is evaluated on a cohort of 30 subjects randomly selected from the UK Biobank study, demonstrating the generation of high-quality 3D whole-heart meshes with average contours to surface distance less than the underlying image resolution and the clinical metrics within acceptable ranges reported in previous literature. Clinical Relevance- Automated patient-specific 3D whole-heart mesh reconstruction has numerous applications in car-diac diagnosis and multimodal visualization, including treatment planning, virtual surgery, and biomedical simulations.

A Heart Segmentation Algorithm Based on Dynamic Ultrasound

The heart is one of the most important organs of the human body. The role of the heart is to promote blood flow and provide sufficient blood flow to organs and tissues. The research on the heart has important theoretical and clinical significance. Because of the noninvasive and intuitive display of ultrasound image, it can dynamically obtain the heart state and has become the main means to detect the heart dynamics. We analyze the characteristics of cardiac ultrasound image from the medical point of view and signal processing. The heart movement is periodic and rhythmic. The image signal can be decomposed. Firstly, the image is decomposed into high- and low-frequency signals to highlight different dimensional information. Then, the attention model was introduced, focusing on the heart region. Finally, the multidimensional network carrying model was established to achieve cardiac segmentation. The experimental results show that the AOM of the algorithm proposed in this paper reaches 92%, which has a certain degree of advancement and can assist doctors to make accurate diagnosis.

Multi-Domain Variational Autoencoders for Combined Modeling of MRI-Based Biventricular Anatomy and ECG-Based Cardiac Electrophysiology

Human cardiac function is characterized by a complex interplay of mechanical deformation and electrophysiological conduction. Similar to the underlying cardiac anatomy, these interconnected physiological patterns vary considerably across the human population with important implications for the effectiveness of clinical decision-making and the accuracy of computerized heart models. While many previous works have investigated this variability separately for either cardiac anatomy or physiology, this work aims to combine both aspects in a single data-driven approach and capture their intricate interdependencies in a multi-domain setting. To this end, we propose a novel multi-domain Variational Autoencoder (VAE) network to capture combined Electrocardiogram (ECG) and Magnetic Resonance Imaging (MRI)-based 3D anatomy information in a single model. Each VAE branch is specifically designed to address the particular challenges of the respective input domain, enabling efficient encoding, reconstruction, and synthesis of multi-domain cardiac signals. Our method achieves high reconstruction accuracy on a United Kingdom Biobank dataset, with Chamfer Distances between reconstructed and input anatomies below the underlying image resolution and ECG reconstructions outperforming multiple single-domain benchmarks by a considerable margin. The proposed VAE is capable of generating realistic virtual populations of arbitrary size with good alignment in clinical metrics between the synthesized and gold standard anatomies and Maximum Mean Discrepancy (MMD) scores of generated ECGs below those of comparable single-domain approaches. Furthermore, we observe the latent space of our VAE to be highly interpretable with separate components encoding different aspects of anatomical and ECG variability. Finally, we demonstrate that the combined anatomy and ECG representation improves the performance in a cardiac disease classification task by 3.9% in terms of Area Under the Receiver Operating Characteristic (AUROC) curve over the best corresponding single-domain modeling approach.

Advanced computation in cardiovascular physiology: new challenges and opportunities

Recent developments in computational physiology have successfully exploited advanced signal processing and artificial intelligence tools for predicting or uncovering characteristic features of physiological and pathological states in humans. While these advanced tools have demonstrated excellent diagnostic capabilities, the high complexity of these computational 'black boxes' may severely limit scientific inference, especially in terms of biological insight about both physiology and pathological aberrations. This theme issue highlights current challenges and opportunities of advanced computational tools for processing dynamical data reflecting autonomic nervous system dynamics, with a specific focus on cardiovascular control physiology and pathology. This includes the development and adaptation of complex signal processing methods, multivariate cardiovascular models, multiscale and nonlinear models for central-peripheral dynamics, as well as deep and transfer learning algorithms applied to large datasets. The width of this perspective highlights the issues of specificity in heartbeat-related features and supports the need for an imminent transition from the black-box paradigm to explainable and personalized clinical models in cardiovascular research. This article is part of the theme issue 'Advanced computation in cardiovascular physiology: new challenges and opportunities'.