A fully automated left atrium segmentation approach from late gadolinium enhanced magnetic resonance imaging based on a convolutional neural network

Edge and dense attention U-net for atrial scar segmentation in LGE-MRI

The segmentation of atrial scars in LGE-MRI images has huge potential value for clinical diagnosis and subsequent treatment. In clinical practice, atrial scars are usually manually calibrated by experienced experts, which is time-consuming and prone to errors. However, automatic segmentation also faces difficulties due to myocardial scars' small size and variable shape. The present study introduces a dual branch network, incorporating edge attention, and deep supervision strategy. Edge attention is introduced to fully utilize the spatial relationship between the scar and the atrium. Besides, dense attention is embedded in bottom layer to solve feature disappearance. At the same time, deep supervision accelerates the convergence of the model and improves segmentation accuracy. The experiments were conducted on the 2022 atrial and scar segmentation challenge dataset. The results demonstrate that the proposed method has achieved superior performance.

Driving cell response through deep learning, a study in simulated 3D cell cultures

Computational simulations are becoming increasingly relevant in biomedical research, providing strategies to reproduce experimental results, improve the resolution of in-vitro experiments, and predict the system's behavior in untested conditions. Their use to determine the features associated with an extensive response to treatment and optimize treatment schedules has, however received little attention. To bridge this gap, we propose a deep learning framework capable of reliably classifying simulated time series data and identifying class-defining features. This information will be shown to be useful for the determination of which changes in treatment schedule elicit a more extensive cellular response. This analysis pipeline will be initially tested on a synthetic dataset created ad-hoc to identify its accuracy in identifying the most relevant portion of the signals. Successively this method will be applied to simulations describing the behaviors of populations of cancer cells treated with either one or two drugs in different concentrations. The proposed method will be shown to be effective in identifying which changes in the treatment protocol lead to a more extensive response to treatment. While lacking direct experimental validation, this result holds great potential for the integration of in-silico and in-vitro analyses and the effective optimization of experimental conditions in complex experimental setups.

RAS Dataset: A 3D Cardiac LGE-MRI Dataset for Segmentation of Right Atrial Cavity

The current challenge in effectively treating atrial fibrillation (AF) stems from a limited understanding of the intricate structure of the human atria. The objective and quantitative interpretation of the right atrium (RA) in late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) scans relies heavily on its precise segmentation. Leveraging the potential of artificial intelligence (AI) for RA segmentation presents a promising solution. However, the successful implementation of AI in this context necessitates access to a substantial volume of annotated LGE-MRI images for model training. In this paper, we present a comprehensive 3D cardiac dataset comprising 50 high-resolution LGE-MRI scans, each meticulously annotated at the pixel level. The annotation process underwent rigorous standardization through crowdsourcing among a panel of medical experts, ensuring the accuracy and consistency of the annotations. Our dataset represents a significant contribution to the field, providing a valuable resource for advancing RA segmentation methods.

Artificial Intelligence in the Image-Guided Care of Atrial Fibrillation

Atrial fibrillation arises mainly due to abnormalities in the cardiac conduction system and is associated with anatomical remodeling of the atria and the pulmonary veins. Cardiovascular imaging techniques, such as echocardiography, computed tomography, and magnetic resonance imaging, are crucial in the management of atrial fibrillation, as they not only provide anatomical context to evaluate structural alterations but also help in determining treatment strategies. However, interpreting these images requires significant human expertise. The potential of artificial intelligence in analyzing these images has been repeatedly suggested due to its ability to automate the process with precision comparable to human experts. This review summarizes the benefits of artificial intelligence in enhancing the clinical care of patients with atrial fibrillation through cardiovascular image analysis. It provides a detailed overview of the two most critical steps in image-guided AF management, namely, segmentation and classification. For segmentation, the state-of-the-art artificial intelligence methodologies and the factors influencing the segmentation performance are discussed. For classification, the applications of artificial intelligence in the diagnosis and prognosis of atrial fibrillation are provided. Finally, this review also scrutinizes the current challenges hindering the clinical applicability of these methods, with the aim of guiding future research toward more effective integration into clinical practice.

Automatic Segmentation of the Left Atrium from Computed Tomography Angiography Images

The left atrial appendage (LAA) causes 91% of thrombi in atrial fibrillation patients, a potential harbinger of stroke. Leveraging computed tomography angiography (CTA) images, radiologists interpret the left atrium (LA) and LAA geometries to stratify stroke risk. Nevertheless, accurate LA segmentation remains a time-consuming task with high inter-observer variability. Binary masks of the LA and their corresponding CTA images were used to train and test a 3D U-Net to automate LA segmentation. One model was trained using the entire unified-image-volume while a second model was trained on regional patch-volumes which were run for inference and then assimilated back into the full volume. The unified-image-volume U-Net achieved median DSCs of 0.92 and 0.88 for the train and test sets, respectively; the patch-volume U-Net achieved median DSCs of 0.90 and 0.89 for the train and test sets, respectively. This indicates that the unified-image-volume and patch-volume U-Net models captured up to 88 and 89% of the LA/LAA boundary's regional complexity, respectively. Additionally, the results indicate that the LA/LAA were fully captured in most of the predicted segmentations. By automating the segmentation process, our deep learning model can expedite LA/LAA shape, informing stratification of stroke risk.

Segmentation of left atrium using CT images and a deep learning model

The left atrium (LA) is one of the cardiac cavities with the most complex anatomical structures. Its role in the clinical diagnosis and patient's management is critical, as it is responsible for the atrial fibrillation, a condition that promotes the thrombogenesis inside the left atrial appendage. The development of an automated approach for LA segmentation is a demanding task mainly due to its anatomical complexity and the variation of its shape among patients. In this study, we focus to develop an unbiased pipeline capable to segment the atrial cavity from CT images. For evaluation purposes state-of-the-art metrics were used to assess the segmentation results. Particularly, the results indicated the mean values of the dice score 80%, the hausdorff distance 11.78mm, the average surface distance 2.24mm and the rand error index 0.2.

Medical image analysis on left atrial LGE MRI for atrial fibrillation studies: A review

Late gadolinium enhancement magnetic resonance imaging (LGE MRI) is commonly used to visualize and quantify left atrial (LA) scars. The position and extent of LA scars provide important information on the pathophysiology and progression of atrial fibrillation (AF). Hence, LA LGE MRI computing and analysis are essential for computer-assisted diagnosis and treatment stratification of AF patients. Since manual delineations can be time-consuming and subject to intra- and inter-expert variability, automating this computing is highly desired, which nevertheless is still challenging and under-researched. This paper aims to provide a systematic review on computing methods for LA cavity, wall, scar, and ablation gap segmentation and quantification from LGE MRI, and the related literature for AF studies. Specifically, we first summarize AF-related imaging techniques, particularly LGE MRI. Then, we review the methodologies of the four computing tasks in detail and summarize the validation strategies applied in each task as well as state-of-the-art results on public datasets. Finally, the possible future developments are outlined, with a brief survey on the potential clinical applications of the aforementioned methods. The review indicates that the research into this topic is still in the early stages. Although several methods have been proposed, especially for the LA cavity segmentation, there is still a large scope for further algorithmic developments due to performance issues related to the high variability of enhancement appearance and differences in image acquisition.

Semi-automatic quantitative analysis of the pelvic bony structures on apparent diffusion coefficient maps based on deep learning: establishment of reference ranges

BACKGROUND

Apparent diffusion coefficient (ADC) maps provide quantitative information on both normal and abnormal tissues. However, it is difficult to distinguish between these tissues unless consistent and precise ADC values can be obtained from normal tissues. For this study we developed a deep learning-based convolutional neural network (CNN) for pelvic bony structure segmentation and established the reference ranges of ADC parameters for normal pelvic bony structures.

METHODS

We retrospectively enrolled 767 prostate cancer (PCa) patients for quantitative ADC analyses of normal pelvic bony structures. A subset of 288 patients who did not receive treatment for PCa (S1) were used to develop a CNN model for the segmentation of 8 pelvic bony structures (lumbar vertebra, sacrococcyx, ilium, acetabulum, femoral head, femoral neck, ischium, and pubis). The proposed CNN was used for the automated segmentation of these pelvic bony structures from a subset of 405 patients who did not receive treatment (S2) and 74 patients who received treatment [radiotherapy (S3) or endocrine therapy (S4)]. The 95% confidence interval (CI) was used to establish reference ranges for the ADC values from the normal pelvic bony structures of S1 and S2.

RESULTS

The Dice scores (Sørensen-Dice coefficient) for the CNN segmentation of the 8 pelvic bones on the ADC maps ranged from 0.90±0.02 (ilium) to 0.95±0.03 (femoral head) in the S1 testing set. In the S2 data set, the Dice scores showed no significant difference among the different scanners (P>0.05), and no significant differences were found among the S2, S3, and S4 data sets. The correlation analysis revealed that the b value and field strength were significantly correlated with ADC values (all P<0.001), while age and treatment were not significant variables (all P>0.05). The ADC reference ranges (95% CI) were as follows: lumbar vertebra, 1.11 (0.90-1.54); sacrococcyx, 0.82 (0.61-1.15); ilium, 0.57 (0.45-0.62); acetabulum, 0.59 (0.40-0.69); femoral head, 0.46 (0.25-0.58); femoral neck, 0.43 (0.25-0.48); ischium, 0.45 (0.26-0.55); and pubis, 0.57 (0.45-0.65).

CONCLUSIONS

This study preliminarily established reference ranges for the ADC values of normal pelvic bony structures. The image acquisition parameters had an influence on the ADC values.

Recent Advances in Fibrosis and Scar Segmentation From Cardiac MRI: A State-of-the-Art Review and Future Perspectives

Segmentation of cardiac fibrosis and scars is essential for clinical diagnosis and can provide invaluable guidance for the treatment of cardiac diseases. Late Gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) has been successful in guiding the clinical diagnosis and treatment reliably. For LGE CMR, many methods have demonstrated success in accurately segmenting scarring regions. Co-registration with other non-contrast-agent (non-CA) modalities [e.g., balanced steady-state free precession (bSSFP) cine magnetic resonance imaging (MRI)] can further enhance the efficacy of automated segmentation of cardiac anatomies. Many conventional methods have been proposed to provide automated or semi-automated segmentation of scars. With the development of deep learning in recent years, we can also see more advanced methods that are more efficient in providing more accurate segmentations. This paper conducts a state-of-the-art review of conventional and current state-of-the-art approaches utilizing different modalities for accurate cardiac fibrosis and scar segmentation.

Bayesian Estimation of Geometric Morphometric Landmarks for Simultaneous Localization of Multiple Anatomies in Cardiac CT Images

We propose a robust method to simultaneously localize multiple objects in cardiac computed tomography angiography (CTA) images. The relative prior distributions of the multiple objects in the three-dimensional (3D) space can be obtained through integrating the geometric morphological relationship of each target object to some reference objects. In cardiac CTA images, the cross-sections of ascending and descending aorta can play the role of the reference objects. We employed the maximum a posteriori (MAP) estimator that utilizes anatomic prior knowledge to address this problem of localizing multiple objects. We propose a new feature for each pixel using the relative distances, which can define any objects that have unclear boundaries. Our experimental results targeting four pulmonary veins (PVs) and the left atrial appendage (LAA) in cardiac CTA images demonstrate the robustness of the proposed method. The method could also be extended to localize other multiple objects in different applications.