Segmentation Of Cardiac Magnetic Resonance Images Research Articles

Quality control of cardiac magnetic resonance imaging segmentation, feature tracking, aortic flow and native T1 analysis using automated batch processing in the UK Biobank Study

Abstract Background Automated algorithms are regularly used to analyse cardiac magnetic resonance (CMR) images. Validating data output reliability from this method is crucial for enabling widespread adoption. We outline a visual quality control (QC) process for image analysis using automated batch processing. We assess the performance of automated analysis and the reliability of replacing visual checks with statistical outlier removal approach in UK Biobank CMR scans. Methods We included 1,987 CMR scans from the UK Biobank COVID imaging study. We used batch processing software (Circle Cardiovascular Imaging Inc. - CVI42) to automatically extract chamber volumetric data, strain, native T1, and aortic flow data. The automated analysis outputs (∼62,000 videos and 2,000 images) were visually checked by six experienced clinicians using a standardised approach and a custom-built R Shiny app. Inter-observer variability was assessed. Data from scans passing visual QC was compared with a statistical outlier removal QC method in a subset of healthy individuals (n = 1069). Results Automated segmentation was highly rated, with over 95% of scans passing visual QC. Overall inter-observer agreement was very good (Gwet’s AC2 0.91; 95% confidence interval [0.84,0.94]). No difference in overall data derived from visual QC or statistical outlier removal in healthy individuals was observed. Conclusion Automated image analysis using CVI42 prototypes for UK Biobank CMR scans demonstrated high quality. Larger UK Biobank datasets analysed using these automated algorithms do not require in-depth visual QC. Statistical outlier removal is sufficient as a QC measure, with operator discretion for visual checks based on population or research objectives.

A geometric approach to robust medical image segmentation

Robustness of deep learning segmentation models is crucial for their safe incorporation into clinical practice. However, these models can falter when faced with distributional changes. This challenge is evident in magnetic resonance imaging (MRI) scans due to the diverse acquisition protocols across various domains, leading to differences in image characteristics such as textural appearances. We posit that the restricted anatomical differences between subjects could be harnessed to refine the latent space into a set of shape components. The learned set then aims to encompass the relevant anatomical shape variation found within the patient population.We explore this by utilising multiple MRI sequences to learn texture invariant and shape equivariant features which are used to construct a shape dictionary using vector quantisation. We investigate shape equivariance to a number of different types of groups. We hypothesise and prove that the greater the group order, i.e., the denser the constraint, the better becomes the model robustness. We achieve shape equivariance either with a contrastive based approach or by imposing equivariant constraints on the convolutional kernels. The resulting shape equivariant dictionary is then sampled to compose the segmentation output. Our method achieves state-of-the-art performance for the task of single domain generalisation for prostate and cardiac MRI segmentation. Code is available at https://github.com/AinkaranSanthi/A_Geometric_Perspective_For_Robust_Segmentation.

Bayesian Uncertainty Estimation by Hamiltonian Monte Carlo: Applications to Cardiac MRI Segmentation

Deep learning (DL)-based methods have achieved state-of-the-art performance for many medical image segmentation tasks. Nevertheless, recent studies show that deep neural net- works (DNNs) can be miscalibrated and overconfident, leading to ”silent failures” that are risky for clinical applications. Bayesian DL provides an intuitive approach to DL failure de- tection, based on posterior probability estimation. However, the posterior is intractable for large medical image segmentation DNNs. To tackle this challenge, we propose a Bayesian learning framework using Hamiltonian Monte Carlo (HMC), tempered by cold posterior (CP) to accommodate medical data augmentation, named HMC-CP. For HMC compu- tation, we further propose a cyclical annealing strategy, capturing both local and global geometries of the posterior distribution, enabling highly efficient Bayesian DNN training with the same computational budget as training a single DNN. The resulting Bayesian DNN outputs an ensemble segmentation along with the segmentation uncertainty. We evaluate the proposed HMC-CP extensively on cardiac magnetic resonance image (MRI) segmentation, using in-domain steady-state free precession (SSFP) cine images as well as out-of-domain datasets of quantitative T1 and T2 mapping. Our results show that the proposed method improves both segmentation accuracy and uncertainty estimation for in- and out-of-domain data, compared with well-established baseline methods such as Monte Carlo Dropout and Deep Ensembles. Additionally, we establish a conceptual link between HMC and the commonly known stochastic gradient descent (SGD) and provide general insight into the uncertainty of DL. This uncertainty is implicitly encoded in the training dynamics but often overlooked. With reliable uncertainty estimation, our method provides a promising direction toward trustworthy DL in clinical applications. We release our code in <a href='https://gitlab.tudelft.nl/yidongzhao/hmc_uncertainty'>https://gitlab.tudelft.nl/yidongzhao/hmc_uncertainty</a>

A review of self-supervised, generative, and few-shot deep learning methods for data-limited magnetic resonance imaging segmentation.

Magnetic resonance imaging (MRI) is a ubiquitous medical imaging technology with applications in disease diagnostics, intervention, and treatment planning. Accurate MRI segmentation is critical for diagnosing abnormalities, monitoring diseases, and deciding on a course of treatment. With the advent of advanced deep learning frameworks, fully automated and accurate MRI segmentation is advancing. Traditional supervised deep learning techniques have advanced tremendously, reaching clinical-level accuracy in the field of segmentation. However, these algorithms still require a large amount of annotated data, which is oftentimes unavailable or impractical. One way to circumvent this issue is to utilize algorithms that exploit a limited amount of labeled data. This paper aims to review such state-of-the-art algorithms that use a limited number of annotated samples. We explain the fundamental principles of self-supervised learning, generative models, few-shot learning, and semi-supervised learning and summarize their applications in cardiac, abdomen, and brain MRI segmentation. Throughout this review, we highlight algorithms that can be employed based on the quantity of annotated data available. We also present a comprehensive list of notable publicly available MRI segmentation datasets. To conclude, we discuss possible future directions of the field-including emerging algorithms, such as contrastive language-image pretraining, and potential combinations across the methods discussed-that can further increase the efficacy of image segmentation with limited labels.

ViT-UperNet: a hybrid vision transformer with unified-perceptual-parsing network for medical image segmentation

The existing image semantic segmentation models have low accuracy in detecting tiny targets or multi-targets at overlapping regions. This work proposes a hybrid vision transformer with unified-perceptual-parsing network (ViT-UperNet) for medical image segmentation. A self-attention mechanism is embedded in a vision transformer to extract multi-level features. The image features are extracted hierarchically from low to high dimensions using 4 groups of Transformer blocks with different numbers. Then, it uses a unified-perceptual-parsing network based on a feature pyramid network (FPN) and a pyramid pooling module (PPM) for the fusion of multi-scale contextual features and semantic segmentation. FPN can naturally use hierarchical features, and generate strong semantic information on all scales. PPM can better use the global prior knowledge to understand complex scenes, and extract features with global context information to improve segmentation results. In the training process, a scalable self-supervised learner named masked autoencoder is used for pre-training, which strengthens the visual representation ability and improves the efficiency of the feature learning. Experiments are conducted on cardiac magnetic resonance image segmentation where the left and right atrium and ventricle are selected for segmentation. The pixels accuracy is 93.85%, the Dice coefficient is 92.61% and Hausdorff distance is 11.16, which are improved compared with the other methods. The results show the superiority of Vit-UperNet in medical images segmentation, especially for the low-recognition and serious-occlusion targets.

DAFNet: A dual attention-guided fuzzy network for cardiac MRI segmentation

<abstract> <sec><title>Background</title><p>In clinical diagnostics, magnetic resonance imaging (MRI) technology plays a crucial role in the recognition of cardiac regions, serving as a pivotal tool to assist physicians in diagnosing cardiac diseases. Despite the notable success of convolutional neural networks (CNNs) in cardiac MRI segmentation, it remains a challenge to use existing CNNs-based methods to deal with fuzzy information in cardiac MRI. Therefore, we proposed a novel network architecture named DAFNet to comprehensively address these challenges.</p> </sec> <sec><title>Methods</title><p>The proposed method was used to design a fuzzy convolutional module, which could improve the feature extraction performance of the network by utilizing fuzzy information that was easily ignored in medical images while retaining the advantage of attention mechanism. Then, a multi-scale feature refinement structure was designed in the decoder portion to solve the problem that the decoder structure of the existing network had poor results in obtaining the final segmentation mask. This structure further improved the performance of the network by aggregating segmentation results from multi-scale feature maps. Additionally, we introduced the dynamic convolution theory, which could further increase the pixel segmentation accuracy of the network.</p> </sec> <sec><title>Result</title><p>The effectiveness of DAFNet was extensively validated for three datasets. The results demonstrated that the proposed method achieved DSC metrics of 0.942 and 0.885, and HD metricd of 2.50mm and 3.79mm on the first and second dataset, respectively. The recognition accuracy of left ventricular end-diastolic diameter recognition on the third dataset was 98.42%.</p> </sec> <sec><title>Conclusion</title><p>Compared with the existing CNNs-based methods, the DAFNet achieved state-of-the-art segmentation performance and verified its effectiveness in clinical diagnosis.</p> </sec> </abstract>

Deep Learning Based Parameterization of Diffeomorphic Image Registration for Cardiac Image Segmentation.

Cardiac segmentation from magnetic resonance imaging (MRI) is one of the essential tasks in analyzing the anatomy and function of the heart for the assessment and diagnosis of cardiac diseases. However, cardiac MRI generates hundreds of images per scan, and manual annotation of them is challenging and time-consuming, and therefore processing these images automatically is of interest. This study proposes a novel end-to-end supervised cardiac MRI segmentation framework based on a diffeomorphic deformable registration that can segment cardiac chambers from 2D and 3D images or volumes. To represent actual cardiac deformation, the method parameterizes the transformation using radial and rotational components computed via deep learning, with a set of paired images and segmentation masks used for training. The formulation guarantees transformations that are invertible and prevents mesh folding, which is essential for preserving the topology of the segmentation results. A physically plausible transformation is achieved by employing diffeomorphism in computing the transformations and activation functions that constrain the range of the radial and rotational components. The method was evaluated over three different data sets and showed significant improvements compared to exacting learning and non-learning based methods in terms of the Dice score and Hausdorff distance metrics.

Attention-guided residual W-Net for supervised cardiac magnetic resonance imaging segmentation

ObjectiveWith latest developments in deep learning approaches, automated, accurate, fast, and generalized segmentation model for left atrium, left ventricle, right ventricle, and myocardium from MR images is becoming increasingly desirable. In deep learning-based approaches, model generalizability is an essential concern. The strength of an approach that has proven competent for one dataset, and then executed for other without fine-tuning, started to decline. MethodsIn medical image segmentation, U-Net-based architecture with its skip-connection has attained the highest levels of success. This article, therefore presents a novel Attention-guided Residual W-Net (ARW-Net), a deep learning-based segmentation approach with residual links, attention gates at each feature dimensions, and upgraded deep supervision for cardiac MRI (CMRI) segmentation. As the basic building block, the W-Net, a unique methodology for medical image segmentation (centred on U-Net layout), is used. In a W-Net-based structure, ARW-Net suggests residual connections in encoder and attention gates at each feature dimension in decoder. Combination of Dice and Cross-entropy losses is used for model training. ResultsFour CMRI datasets, (i) ACDC 2017, (ii) 2018 ASC, (iii) M&Ms 2020, and (iv) LAScarQS 2022, which are publicly available, have been utilized to examine effectiveness of ARW-Net. It accomplished improved segmentation results and was among the top two for several metrics. ConclusionNumerous comparisons have demonstrated that ARW-Net is profoundly promising, with several segmentation findings delivering innovative state-of-the-art outcomes on four datasets. SignificanceThe results of experiments demonstrate that ARW-Net is able to effectively segment cardiac MR images, as demonstrated by comparisons with existing algorithms.

Estimating Uncertainty in Neural Networks for Cardiac MRI Segmentation: A Benchmark Study.

Convolutional neural networks (CNNs) have demonstrated promise in automated cardiac magnetic resonance image segmentation. However, when using CNNs in a large real-world dataset, it is important to quantify segmentation uncertainty and identify segmentations which could be problematic. In this work, we performed a systematic study of Bayesian and non-Bayesian methods for estimating uncertainty in segmentation neural networks. We evaluated Bayes by Backprop, Monte Carlo Dropout, Deep Ensembles, and Stochastic Segmentation Networks in terms of segmentation accuracy, probability calibration, uncertainty on out-of-distribution images, and segmentation quality control. We observed that Deep Ensembles outperformed the other methods except for images with heavy noise and blurring distortions. We showed that Bayes by Backprop is more robust to noise distortions while Stochastic Segmentation Networks are more resistant to blurring distortions. For segmentation quality control, we showed that segmentation uncertainty is correlated with segmentation accuracy for all the methods. With the incorporation of uncertainty estimates, we were able to reduce the percentage of poor segmentation to 5% by flagging 31-48% of the most uncertain segmentations for manual review, substantially lower than random review without using neural network uncertainty (reviewing 75-78% of all images). This work provides a comprehensive evaluation of uncertainty estimation methods and showed that Deep Ensembles outperformed other methods in most cases. Neural network uncertainty measures can help identify potentially inaccurate segmentations and alert users for manual review.

Epoch and accuracy based empirical study for cardiac MRI segmentation using deep learning technique.

Cardiac magnetic resonance imaging (CMRI) is a non-invasive imaging technique to analyse the structure and function of the heart. It was enhanced considerably over several years to deliver functional information for diagnosing and managing cardiovascular disease. CMRI image delivers non-invasive, clear access to the heart and great vessels. The segmentation of CMRI provides quantification parameters such as myocardial viability, ejection fraction, cardiac chamber volume, and morphological details. In general, experts interpret the CMR images by delineating the images manually. The manual segmentation process is time-consuming, and it has been observed that the final observation varied with the opinion of the different experts. Convolution neural network is a new-age technology that provides impressive results compared to manual ones. In this study convolution neural network model is used for the segmentation task. The neural network parameters have been optimized to perform on the novel data set for accurate predictions. With other parameters, epochs play an essential role in training the network, as the network should not be under-fitted or over-fitted. The relationship between the hyperparameter epoch and accuracy is established in the model. The model delivers the accuracy of 0.88 in terms of the IoU coefficient.

Dilated convolution network with edge fusion block and directional feature maps for cardiac MRI segmentation.

Cardiac magnetic resonance imaging (MRI) segmentation task refers to the accurate segmentation of ventricle and myocardium, which is a prerequisite for evaluating the soundness of cardiac function. With the development of deep learning in medical imaging, more and more heart segmentation methods based on deep learning have been proposed. Due to the fuzzy boundary and uneven intensity distribution of cardiac MRI, some existing methods do not make full use of multi-scale characteristic information and have the problem of ambiguity between classes. In this paper, we propose a dilated convolution network with edge fusion block and directional feature maps for cardiac MRI segmentation. The network uses feature fusion module to preserve boundary information, and adopts the direction field module to obtain the feature maps to improve the original segmentation features. Firstly, multi-scale feature information is obtained and fused through dilated convolutional layers of different scales while downsampling. Secondly, in the decoding stage, the edge fusion block integrates the edge features into the side output of the encoder and concatenates them with the upsampled features. Finally, the concatenated features utilize the direction field to improve the original segmentation features and generate the final result. Our propose method conducts comprehensive comparative experiments on the automated cardiac diagnosis challenge (ACDC) and myocardial pathological segmentation (MyoPS) datasets. The results show that the proposed cardiac MRI segmentation method has better performance compared to other existing methods.

NVTrans-UNet: Neighborhood vision transformer based U-Net for multi-modal cardiac MR image segmentation.

With the rapid development of artificial intelligence and image processing technology, medical imaging technology has turned into a critical tool for clinical diagnosis and disease treatment. The extraction and segmentation of the regions of interest in cardiac images are crucial to the diagnosis of cardiovascular diseases. Due to the erratically diastolic and systolic cardiac, the boundaries of Magnetic Resonance (MR) images are quite fuzzy. Moreover, it is hard to provide complete information using a single modality due to the complex structure of the cardiac image. Furthermore, conventional CNN-based segmentation methods are weak in feature extraction. To overcome these challenges, we propose a multi-modal method for cardiac image segmentation, called NVTrans-UNet. Firstly, we employ the Neighborhood Vision Transformer (NVT) module, which takes advantage of Neighborhood Attention (NA) and inductive biases. It can better extract the local information of the cardiac image as well as reduce the computational cost. Secondly, we introduce a Multi-modal Gated Fusion (MGF) network, which can automatically adjust the contributions of different modal feature maps and make full use of multi-modal information. Thirdly, the bottleneck layer with Atrous Spatial Pyramid Pooling (ASPP) is proposed to expand the feature receptive field. Finally, the mixed loss is added to the cardiac image to focus the fuzzy boundary and realize accurate segmentation. We evaluated our model on MyoPS 2020 dataset. The Dice score of myocardial infarction (MI) was 0.642±0.171, and the Dice score of myocardial infarction + edema (MI + ME) was 0.574±0.110. Compared with the baseline, the MI increases by 11.2%, and the MI + ME increases by 12.5%. The results show the effectiveness of the proposed NVTrans-UNet in the segmentation of MI and ME.

Cardiac Magnetic Resonance Image Segmentation Method Based on Multi-Scale Feature Fusion and Sequence Relationship Learning.

Accurate segmentation of the left atrial structure using magnetic resonance images provides an important basis for the diagnosis of atrial fibrillation (AF) and its treatment using robotic surgery. In this study, an image segmentation method based on sequence relationship learning and multi-scale feature fusion is proposed for 3D to 2D sequence conversion in cardiac magnetic resonance images and the varying scales of left atrial structures within different slices. Firstly, a convolutional neural network layer with an attention module was designed to extract and fuse contextual information at different scales in the image, to strengthen the target features using the correlation between features in different regions within the image, and to improve the network's ability to distinguish the left atrial structure. Secondly, a recurrent neural network layer oriented to two-dimensional images was designed to capture the correlation of left atrial structures in adjacent slices by simulating the continuous relationship between sequential image slices. Finally, a combined loss function was constructed to reduce the effect of positive and negative sample imbalance and improve model stability. The Dice, IoU, and Hausdorff distance values reached 90.73%, 89.37%, and 4.803 mm, respectively, based on the LASC2013 (left atrial segmentation challenge in 2013) dataset; the corresponding values reached 92.05%, 89.41% and 9.056 mm, respectively, based on the ASC2018 (atrial segmentation challenge at 2018) dataset.

Toward Automated Right Ventricle Segmentation via Edge Feature-Induced Self-Attention Multiscale Feature Aggregation Full Convolution Network

In the field of cardiac magnetic resonance (MR) image analysis, the accurate segmentation of right ventricle (RV) regions plays an important role in the quantitative examination and medical diagnosis of various cardiovascular diseases. However, the automated RV segmentation in cardiac MR images is still challenging, due to its obscure and ill-defined boundaries, variably crescent-shaped structures, and extremely-unbalanced area ratio between the RV region and the background. In this work, an edge feature-induced self-attention multi-scale feature aggregation full convolutional neural network, called EFiSaMsFAFUnet, is proposed, to address the RV segmentation tasks. Specifically, EFiSaMsFAFUnet introduces an edge feature extraction module (EFEM) to mine the crescent-shaped boundary features of the RV area, and a kind of self-attention multi-scale feature expansion block (SaMsFEB) is proposed to mine the internal structure characteristics of the crescent-shaped RV internal regions. In addition, a kind of composite loss function is used to address the problem of model degradation caused by the proportion imbalance between RV region and background. The proposed EFiSaMsFAFUnet was evaluated on the MICCAI2017 Automatic Cardiac Diagnosis Challenge (ACDC) dataset. Extensive confirmatory and comparative experiments show that the EFiSaMsFAFUnet can achieve better segmentation results than the representatively state-of-the-art methods, and it can achieve comparable or the closest segmentation results to the manual segmentation of clinical specialist.

Multiresolution Mutual Assistance Network for Cardiac Magnetic Resonance Images Segmentation.

The automatic segmentation of cardiac magnetic resonance (MR) images is the basis for the diagnosis of cardiac-related diseases. However, the segmentation of cardiac MR images is a challenging task due to the inhomogeneity of MR images intensity distribution and the unclear boundaries between adjacent tissues. In this paper, we propose a novel multiresolution mutual assistance network (MMA-Net) for cardiac MR images segmentation. It is mainly composed of multibranch input module, multiresolution mutual assistance module, and multilabel deep supervision. First, the multibranch input module helps the network to extract local and global features more pertinently. Then, the multiresolution mutual assistance module implements multiresolution feature interaction and progressively improves semantic features to more completely express the information of the tissue. Finally, the multilabel deep supervision is proposed to generate the final segmentation map. We compare with state-of-the-art medical image segmentation methods on the medical image computing and computer-assisted intervention (MICCAI) automated cardiac diagnosis challenge datasets and the MICCAI atrial segmentation challenge datasets. The mean dice scores of our method in the left atrium, right ventricle, myocardium, and left ventricle are 0.919, 0.920, 0.881, and 0.960, respectively. The analysis of evaluation indicators and segmentation results shows that our method achieves the best performance in cardiac magnetic resonance images segmentation.

Cardiac MRI segmentation with sparse annotations: Ensembling deep learning uncertainty and shape priors.

The performance of deep learning for cardiac magnetic resonance imaging (MRI) segmentation is oftentimes degraded when using small datasets and sparse annotations for training or adapting a pre-trained model to previously unseen datasets. Here, we developed and evaluated an approach to addressing some of these issues to facilitate broader use of deep learning for short-axis cardiac MRI segmentation. We developed a globally optimal label fusion (GOLF) algorithm that enforced spatial smoothness to generate consensus segmentation from segmentation predictions provided by a deep learning ensemble algorithm. The GOLF consensus was entered into an uncertainty-guided coupled continuous kernel cut (ugCCKC) algorithm that employed normalized cut, image-grid continuous regularization, and "nesting" and circular shape priors of the left ventricular myocardium (LVM) and cavity (LVC). In addition, the uncertainty measurements derived from the segmentation predictions were used to constrain the similarity of GOLF and final segmentation. We optimized ugCCKC through upper bound relaxation, for which we developed an efficient coupled continuous max-flow algorithm implemented in an iterative manner. We showed that GOLF yielded average symmetric surface distance (ASSD) 0.2-0.8mm lower than an averaging method with higher or similar Dice similarity coefficient (DSC). We also demonstrated that ugCCKC incorporating the shape priors improved DSC by 0.01-0.05 and reduced ASSD by 0.1-0.9mm. In addition, we integrated GOLF and ugCCKC into a deep learning ensemble algorithm by refining the segmentation of an unannotated dataset and using the refined segmentation to update the trained models. With the proposed framework, we demonstrated the capability of using relatively small datasets (5-10 subjects) with sparse (5-25% slices labeled) annotations to train a deep learning algorithm, while achieving DSC of 0.871-0.893 for LVM and 0.933-0.959 for LVC on the LVQuan dataset, and these were 0.844-0.871 for LVM and 0.923-0.931 for LVC on the ACDC dataset. Furthermore, we showed that the proposed approach can be adapted to substantially alleviate the domain shift issue. Moreover, we calculated a number of commonly used LV function measurements using the derived segmentation and observed strong correlations (Pearson r=0.77-1.00, p<0.001) between algorithm and manual LV function analyses. These results suggest that the developed approaches can be used to facilitate broader application of deep learning in research and clinical cardiac MR imaging workflow.

Combining UNet 3+ and Transformer for Left Ventricle Segmentation via Signed Distance and Focal Loss

Left ventricle (LV) segmentation of cardiac magnetic resonance (MR) images is essential for evaluating cardiac function parameters and diagnosing cardiovascular diseases (CVDs). Accurate LV segmentation remains a challenge because of the large differences in cardiac structures in different research subjects. In this work, a network based on an encoder–decoder architecture for automatic LV segmentation of short-axis cardiac MR images is proposed. It combines UNet 3+ and Transformer to jointly predict the segmentation masks and signed distance maps (SDM). UNet 3+ can extract coarse-grained semantics and fine-grained details from full scales, while a Transformer is used to extract global features from cardiac MR images. It solves the problem of low segmentation accuracy caused by blurred LV edge information. Meanwhile, the SDM provides a shape-aware representation for segmentation. The performance of the proposed network is validated on the 2018 MICCAI Left Ventricle Segmentation Challenge dataset. The five-fold cross-validation evaluation was performed on 145 clinical subjects, and the average dice metric, Jaccard coefficient, accuracy, and positive predictive value reached 0.908, 0.834, 0.979, and 0.903, respectively, showing a better performance than that of other mainstream ones.

W-Net: Novel Deep Supervision for Deep Learning-based Cardiac Magnetic Resonance Imaging Segmentation

Cardiac magnetic resonance imaging (CMRI) segmentation transforms cardiac MR images into semantic regions to define the left ventricle cavity, right ventricle cavity, and myocardium. CMRI segmentation provides ventricles’ volume, mass, and ejection fraction, playing a significant role in cardiac disease diagnosis. This paper aims to propose novel deep supervision in U-Net-based architecture to enhance the segmentation performance. It presents a deeply supervised W-Net, which creates another path in parallel with the decoder path in U-Net-based architecture. The output of every upsampling layer in the decoder path is combined with pixel-wise addition for feature reuse, and loss is computed at each feature dimension on the deep supervision layer, which enables gradients to be implanted at a greater depth into the network and enhances the training of all layers in the network. Proposed W-Net applied on single scanner-based ACDC dataset and Multi-Centre, Multi-Vendor & Multi-Disease dataset, making it more robust in model generalization. W-Net significantly outperforms numerous state-of-the-art methods on the two publicly available CMRI datasets, according to experiments conducted. W-Net obtained better segmentation results ranked in the top three for many metrics. It is evident that the proposed W-Net has considerable potential in CMRI segmentation, cardiac assessment, and disease diagnosis.

Deep Neural Network for Cardiac Magnetic Resonance Image Segmentation.

The analysis and interpretation of cardiac magnetic resonance (CMR) images are often time-consuming. The automated segmentation of cardiac structures can reduce the time required for image analysis. Spatial similarities between different CMR image types were leveraged to jointly segment multiple sequences using a segmentation model termed a multi-image type UNet (MI-UNet). This model was developed from 72 exams (46% female, mean age 63 ± 11 years) performed on patients with hypertrophic cardiomyopathy. The MI-UNet for steady-state free precession (SSFP) images achieved a superior Dice similarity coefficient (DSC) of 0.92 ± 0.06 compared to 0.87 ± 0.08 for a single-image type UNet (p < 0.001). The MI-UNet for late gadolinium enhancement (LGE) images also had a superior DSC of 0.86 ± 0.11 compared to 0.78 ± 0.11 for a single-image type UNet (p = 0.001). The difference across image types was most evident for the left ventricular myocardium in SSFP images and for both the left ventricular cavity and the left ventricular myocardium in LGE images. For the right ventricle, there were no differences in DCS when comparing the MI-UNet with single-image type UNets. The joint segmentation of multiple image types increases segmentation accuracy for CMR images of the left ventricle compared to single-image models. In clinical practice, the MI-UNet model may expedite the analysis and interpretation of CMR images of multiple types.

DeU-Net 2.0: Enhanced deformable U-Net for 3D cardiac cine MRI segmentation.

Automatic segmentation of cardiac magnetic resonance imaging (MRI) facilitates efficient and accurate volume measurement in clinical applications. However, due to anisotropic resolution, ambiguous borders and complicated shapes, existing methods suffer from the degradation of accuracy and robustness in cardiac MRI segmentation. In this paper, we propose an enhanced Deformable U-Net (DeU-Net) for 3D cardiac cine MRI segmentation, composed of three modules, namely Temporal Deformable Aggregation Module (TDAM), Enhanced Deformable Attention Network (EDAN), and Probabilistic Noise Correction Module (PNCM). TDAM first takes consecutive cardiac MR slices (including a target slice and its neighboring reference slices) as input, and extracts spatio-temporal information by an offset prediction network to generate fused features of the target slice. Then the fused features are also fed into EDAN that exploits several flexible deformable convolutional layers and generates clear borders of every segmentation map. A Multi-Scale Attention Module (MSAM) in EDAN is proposed to capture long range dependencies between features of different scales. Meanwhile, PNCM treats the fused features as a distribution to quantify uncertainty. Experimental results show that our DeU-Net achieves the state-of-the-art performance in terms of the commonly used evaluation metrics on the Extended ACDC dataset and competitive performance on other two datasets, validating the robustness and generalization of DeU-Net.