Scar Segmentation Research Articles

Deep learning for quantification of myocardial scar and microvascular obstruction in late gadolinium enhancement cardiovascular magnetic resonance images

Abstract Objectives Detecting and measuring myocardial scar and microvascular obstruction (MVO) accurately following reperfusion therapy is clinically vital for patients with acute myocardial infarction (AMI). Current clinical practice relies on manual delineation of endocardial borders as well as hyper- and hypo-enhanced regions on late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) images for scar and MVO quantification, respectively. However, this approach is subjective, labor-intensive, and time-consuming. The objective of this study is to develop and assess a convolutional neural network (CNN)-based method for the automated quantification of LGE scar and MVO in AMI patients. Methods A total of 1836 LGE images from 252 patients with AMI were analyzed, with the cohort comprising 232 males and an average age of 56±9 years. Our approach, utilizing a combined architecture of cascaded YOLOv8 (You Only Look Once version 8) and nnU-Net, was implemented for the simultaneous segmentation of the left ventricular (LV) myocardium, scar, and MVO in LGE images. Independent datasets for training, validation, and testing were maintained in an 8:1:1 ratio. Performance evaluation was conducted by comparing the results to manual scar and MVO quantification, utilizing metrics such as the Dice similarity coefficient (DSC) and Bland-Altman analysis. Results The automated segmentation process took 0.05 seconds per image. The segmentation accuracy, as assessed by the DSC, yielded values of 0.96±0.04 (per-patient, n=25) and 0.96±0.05 (per-slice, n=184) for scar segmentation, and 0.86±0.17 (per-patient) and 0.89±0.15 (per-slice) for MVO segmentation. In per-patient analysis, the volumes of automatically segmented scar and MVO demonstrated strong agreement with manually derived results, with biases [limits of agreement] of -0.3 [-3.0, 2.4] cm³ and 0.1 [-0.2, 0.3] cm³, respectively. Furthermore, there was strong concordance between automatically and manually derived scar size as a percentage of LV mass (-0.2 [-3.1, 2.7] %) and MVO size as a percentage of scar (1.2 [-5.6, 8.0] %). Conclusions The findings demonstrate excellent agreement between our proposed automated deep-learning solution and clinical expert annotation, suggesting its potential as a predictive tool for prognosis and clinical outcomes in patients with AMI.

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.

Automated DeepLabV3+ based model for left ventricle segmentation on short-axis late gadolinium enhancement-magnetic cardiac resonance imaging images

Accurate segmentation of myocardial scar tissue on late gadolinium enhancement-magnetic cardiac resonance imaging (LGE-CMR) is exceptionally vital for clinical applications, enabling precise diagnosis and effective treatment of various cardiac diseases, such as myocardial infarction and cardiomyopathies. However, the ventricle (LV) variations in the size and shape, artifacts, and image resolution of LGE-CMR has made automatic segmentation of myocardial scar tissue more challenging. While many existing approaches delineate the LV myocardium region using multi-modal segmentation, these models may be computationally complex and suffer from misalignment. Therefore, this study proposed an automatic dual-stage DeepLabV3+ based approach tailored for myocardial scar segmentation on short-axis LGE-MRI exclusively. To segment myocardial scar tissue, the second stage employs the segmented LV chamber from the previous stage. The encoder part of the framework utilizes a MobileNetV2 and ResNet50 backbone for the first and second segmentation, respectively, aiming for optimal resolution of feature maps. Both stages tailor an improved Atrous Spatial Pyramid Pooling module in the DeepLabV3+ model with fine-tuned dilated atrous rates to effectively extract the LV chamber and myocardial scar from the complex LGE-MRI background. Based on the results, the proposed dual-stage network recorded an outstanding segmentation performance, with mean Dice score of 96.02% for LV chamber segmentation and 68.01% for scar tissue extraction.

Improving deep learning based segmentation of scars using multi-view images

The utilization of deep learning for scar segmentation in photographs enables automated and non-contact quantitative analysis of skin scars. Meanwhile, multi-view photographs are commonly employed to capture the 3D information of scars. In this paper, we propose a two-stage deep learning based segmentation framework for delineating scars from surrounding skin, leveraging multi-view images to achieve enhanced segmentation results compared to single-view approaches. In the first stage, a data augmentation method based on 3D reconstruction and view interpolation is proposed. The generated images are used in a semi-supervised setting to train a single-view segmentation network. In the second stage, a multi-view co-segmentation network (MVCSNet) is proposed to exploit the mutual information between views and to further refine the segmentation. The multi-view feature interaction module (MVFI) uses the prior segmentation results from the first stage, computes feature similarities across views, and optimizes the features. The proposed method was evaluated on two multi-view image datasets containing linear scars and patchy scars, respectively. The results show that the proposed data augmentation method can improve the generalization of the model, particularly for the dataset with smaller size. Comparative analyses demonstrate the superior performance of MVCSNet over other deep learning based segmentation or co-segmentation algorithms.

Deep learning for automatic volumetric segmentation of left ventricular myocardium and ischaemic scar from multi-slice late gadolinium enhancement cardiovascular magnetic resonance.

This study details application of deep learning for automatic volumetric segmentation of left ventricular (LV) myocardium and scar and automated quantification of myocardial ischaemic scar burden from late gadolinium enhancement cardiovascular magnetic resonance (LGE-CMR). We included 501 images and manual segmentations of short-axis LGE-CMR from over 20 multinational sites, from which 377 studies were used for training and 124 studies from unique participants for internal validation. A third test set of 52 images was used for external evaluation. Three models, U-Net, Cascaded U-Net, and U-Net++, were trained with a novel adaptive weighted categorical cross-entropy loss function. Model performance was evaluated using concordance correlation coefficients (CCCs) for LV mass and per cent myocardial scar burden. Cascaded U-Net was found to be the best model for the quantification of LV mass and scar percentage. The model exhibited a mean difference of -5 ± 23 g for LV mass, -0.4 ± 11.2 g for scar mass, and -0.8 ± 7% for per cent scar. CCC were 0.87, 0.77, and 0.78 for LV mass, scar mass, and per cent scar burden, respectively, in the internal validation set and 0.75, 0.71, and 0.69, respectively, in the external test set. For segmental scar mass, CCC was 0.74 for apical scar, 0.91 for mid-ventricular scar, and 0.73 for basal scar, demonstrating moderate to strong agreement. We successfully trained a convolutional neural network for volumetric segmentation and analysis of LV scar burden from LGE-CMR images in a large, multinational cohort of participants with ischaemic scar.

Unsupervised unpaired multiple fusion adaptation aided with self-attention generative adversarial network for scar tissues segmentation framework

Late gadolinium enhancement (LGE) is a specialized imaging technique used in cardiovascular magnetic resonance (CMR) imaging to detect and characterize areas of scar tissue or fibrosis within the heart muscle. After a heart attack, the affected region of the heart muscle becomes scarred due to insufficient blood supply. LGE CMR enhances the infarcted myocardium to appear with distinctive brightness compared to healthy tissues. It is primarily used to assess various heart conditions and can identify the extent and location of scar tissue, helping in risk stratification and guiding treatment decisions. Automated myocardium segmentation in LGE CMR poses challenges due to intensity heterogeneity caused by the accumulation of contrast agents in infarcted areas. Furthermore, LGE CMR images with gold standard labels are particularly scarce compared to other sequences, making the task even more demanding. Besides, the heart’s motion involves complex non-rigid deformations, including regional wall thickening, circumferential, and longitudinal ventricular shortening, making it challenging to model. This work presents an unsupervised unpaired domain adaptive scar tissue segmentation framework aided with the self-attention generative adversarial network. Besides, we proposed a novel segmentation architecture based on a parallel transformer for scar segmentation and compared the results with and without style transfer GAN and unpaired style self-supervised attention GAN. Besides, to model longitudinal changes in scare, we used eight days’ time points as a source and 1 month and 12 as a target and applied our proposed attention-generative network to transfer style from one-time point to another time. Experiments on four different LGE MICCAI datasets from 2019 to 2023 achieved significantly better performance than state-of-the-art segmentation methods.

Impact of late gadolinium enhancement image acquisition resolution on neural network based automatic scar segmentation

BackgroundAutomatic myocardial scar segmentation from late gadolinium enhancement (LGE) images using neural networks promises an alternative to time-consuming and observer-dependent semi-automatic approaches. However, alterations in data acquisition, reconstruction as well as post-processing may compromise network performance. The objective of the present work was to systematically assess network performance degradation due to a mismatch of point-spread function between training and testing data. MethodsThirty-six high-resolution (0.7×0.7×2.0 mm3) LGE k-space datasets were acquired post-mortem in porcine models of myocardial infarction. The in-plane point-spread function and hence in-plane resolution Δx was retrospectively degraded using k-space lowpass filtering, while field-of-view and matrix size were kept constant. Manual segmentation of the left ventricle (LV) and healthy remote myocardium was performed to quantify location and area (% of myocardium) of scar by thresholding (≥ SD5 above remote). Three standard U-Nets were trained on training resolutions Δxtrain = 0.7, 1.2 and 1.7 mm to predict endo- and epicardial borders of LV myocardium and scar. The scar prediction of the three networks for varying test resolutions (Δxtest = 0.7 to 1.7 mm) was compared against the reference SD5 thresholding at 0.7 mm. Finally, a fourth network trained on a combination of resolutions (Δxtrain = 0.7 to 1.7 mm) was tested. ResultsThe prediction of relative scar areas showed the highest precision when the resolution of the test data was identical to or close to the resolution used during training. The median fractional scar errors and precisions (IQR) from networks trained and tested on the same resolution were 0.0 percentage points (p.p.) (1.24 - 1.45), and − 0.5 - 0.0 p.p. (2.00 – 3.25) for networks trained and tested on the most differing resolutions, respectively. Deploying the network trained on multiple resolutions resulted in reduced resolution dependency with median scar errors and IQRs of 0.0 p.p. (1.24 – 1.69) for all investigated test resolutions. ConclusionA mismatch of the imaging point-spread function between training and test data can lead to degradation of scar segmentation when using current U-Net architectures as demonstrated on LGE porcine myocardial infarction data. Training networks on multi-resolution data can alleviate the resolution dependency.

The Nottingham Ischaemic Cardiovascular Magnetic Resonance resource (NotIs CMR): a prospective paired clinical and imaging scar database—protocol

IntroductionResearch utilising artificial intelligence (AI) and cardiovascular magnetic resonance (CMR) is rapidly evolving with various objectives, however AI model development, generalisation and performance may be hindered by availability of robust training datasets including contrast enhanced images. MethodsNotIs CMR is a large UK, prospective, multicentre, observational cohort study to guide the development of a biventricular AI scar model. Patients with ischaemic heart disease undergoing clinically indicated contrast-enhanced cardiac magnetic resonance imaging will be recruited at Nottingham University Hospitals NHS Trust and Mid-Yorkshire Hospital NHS Trust. Baseline assessment will include cardiac magnetic resonance imaging, demographic data, medical history, electrocardiographic and serum biomarkers. Participants will undergo monitoring for a minimum of 5 years to document any major cardiovascular adverse events. The main objectives include (1) AI training, validation and testing to improve the performance, applicability and adaptability of an AI biventricular scar segmentation model being developed by the authors and (2) develop a curated, disease-specific imaging database to support future research and collaborations and, (3) to explore associations in clinical outcome for future risk prediction modelling studies. ConclusionNotIs CMR will collect and curate disease-specific, paired imaging and clinical datasets to develop an AI biventricular scar model whilst providing a database to support future research and collaboration in Artificial Intelligence and ischaemic heart disease.

Interpretable machine learning for automated left ventricular scar quantification in hypertrophic cardiomyopathy patients.

Scar quantification on cardiovascular magnetic resonance (CMR) late gadolinium enhancement (LGE) images is important in risk stratifying patients with hypertrophic cardiomyopathy (HCM) due to the importance of scar burden in predicting clinical outcomes. We aimed to develop a machine learning (ML) model that contours left ventricular (LV) endo- and epicardial borders and quantifies CMR LGE images from HCM patients.We retrospectively studied 2557 unprocessed images from 307 HCM patients followed at the University Health Network (Canada) and Tufts Medical Center (USA). LGE images were manually segmented by two experts using two different software packages. Using 6SD LGE intensity cutoff as the gold standard, a 2-dimensional convolutional neural network (CNN) was trained on 80% and tested on the remaining 20% of the data. Model performance was evaluated using the Dice Similarity Coefficient (DSC), Bland-Altman, and Pearson's correlation. The 6SD model DSC scores were good to excellent at 0.91 ± 0.04, 0.83 ± 0.03, and 0.64 ± 0.09 for the LV endocardium, epicardium, and scar segmentation, respectively. The bias and limits of agreement for the percentage of LGE to LV mass were low (-0.53 ± 2.71%), and correlation high (r = 0.92). This fully automated interpretable ML algorithm allows rapid and accurate scar quantification from CMR LGE images. This program does not require manual image pre-processing, and was trained with multiple experts and software, increasing its generalizability.

Automatic development of 3D anatomical models of border zone and core scar regions in the left ventricle.

Patients with myocardial infarction are at elevated risk of sudden cardiac death, and scar tissue arising from infarction is known to play a role. The accurate identification of scars therefore is crucial for risk assessment, quantification and guiding interventions. Typically, core scars and grey peripheral zones are identified by radiologists and clinicians based on cardiac late gadolinium enhancement magnetic resonance images (LGE-MRI). Scar regions from LGE-MRI vary in size, shape, heterogeneity, artifacts, and image resolution. Thus, manual segmentation is time consuming, and influenced by the observer's experience (bias effect). We propose a fully automatic framework that develops 3D anatomical models of the left ventricle with border zone and core scar regions that are free from bias effect. Our myocardium (SOCRATIS), border scar and core scar (BZ-SOCRATIS) segmentation pipelines were evaluated using internal and external validation datasets. The automatic myocardium segmentation framework performed a Dice score of 81.9% and 70.0% in the internal and external validation dataset. The automatic scar segmentation pipeline achieved a Dice score of 60.9% for the core scar segmentation and 43.7% for the border zone scar segmentation in the internal dataset and in the external dataset a Dice score of 44.2% for the core scar segmentation and 54.8% for the border scar segmentation respectively. To the best of our knowledge, this is the first study outlining a fully automatic framework to develop 3D anatomical models of the left ventricle with border zone and core scar regions. Our method exhibits high performance without the need for training or tuning in an unseen cohort (unsupervised).

Improving myocardial pathology segmentation with U-Net++ and EfficientSeg from multi-sequence cardiac magnetic resonance images

Background:Myocardial pathology segmentation plays an utmost role in the diagnosis and treatment of myocardial infarction (MI). However, manual segmentation is time-consuming and labor-intensive, and requires a lot of professional knowledge and clinical experience. Methods:In this work, we develop an automatic and accurate coarse-to-fine myocardial pathology segmentation framework based on the U-Net++ and EfficientSeg model. The U-Net++ network with deep supervision is first applied to delineate the cardiac structures from the multi-sequence cardiac magnetic resonance (CMR) images to generate a coarse segmentation map. Then the coarse segmentation map together with the three-sequence CMR data is sent to the EfficientSeg-B1 for fine segmentation, that is, further segmentation of myocardial scar and edema areas. In addition, we apply the Focal loss to replace the original cross-entropy term, for the purpose of encouraging the model to pay more attention to the pathological areas. Results:The proposed segmentation approach is tested on the public Myocardial Pathology Segmentation Challenge (MyoPS 2020) dataset. Experimental results demonstrate that our solution achieves an average Dice score of 0.7148 ± 0.2213 for scar, an average Dice score of 0.7439 ± 0.1011 for edema + scar, and the final average score of 0.7294 on the overall 20 testing sets, all of which have outperformed the first place method in the competition. Moreover, extensive ablation experiments are performed, which shows that the two-stage strategy with Focal loss greatly improves the segmentation quality of pathological areas. Conclusion:Given its effectiveness and superiority, our method can further facilitate myocardial pathology segmentation in medical practice.

Optimized automated cardiac MR scar quantification with GAN‐based data augmentation

BackgroundThe clinical utility of late gadolinium enhancement (LGE) cardiac MRI is limited by the lack of standardization, and time-consuming postprocessing. In this work, we tested the hypothesis that a cascaded deep learning pipeline trained with augmentation by synthetically generated data would improve model accuracy and robustness for automated scar quantification. MethodsA cascaded pipeline consisting of three consecutive neural networks is proposed, starting with a bounding box regression network to identify a region of interest around the left ventricular (LV) myocardium. Two further nnU-Net models are then used to segment the myocardium and, if present, scar. The models were trained on the data from the EMIDEC challenge, supplemented with an extensive synthetic dataset generated with a conditional GAN. ResultsThe cascaded pipeline significantly outperformed a single nnU-Net directly segmenting both the myocardium (mean Dice similarity coefficient (DSC) (standard deviation (SD)): 0.84 (0.09) vs 0.63 (0.20), p < 0.01) and scar (DSC: 0.72 (0.34) vs 0.46 (0.39), p < 0.01) on a per-slice level. The inclusion of the synthetic data as data augmentation during training improved the scar segmentation DSC by 0.06 (p < 0.01). The mean DSC per-subject on the challenge test set, for the cascaded pipeline augmented by synthetic generated data, was 0.86 (0.03) and 0.67 (0.29) for myocardium and scar, respectively. ConclusionA cascaded deep learning-based pipeline trained with augmentation by synthetically generated data leads to myocardium and scar segmentations that are similar to the manual operator, and outperforms direct segmentation without the synthetic images.

Skin scar segmentation based on saliency detection

Skin scar segmentation based on saliency detection

Cascaded Triplanar Autoencoder M-Net for Fully Automatic Segmentation of Left Ventricle Myocardial Scar From Three-Dimensional Late Gadolinium-Enhanced MR Images.

While three-dimensional (3D) late gadolinium-enhanced (LGE) magnetic resonance (MR) imaging provides good conspicuity of small myocardial lesions with short acquisition time, it poses a challenge for image analysis as a large number of axial images are required to be segmented. We developed a fully automatic convolutional neural network (CNN) called cascaded triplanar autoencoder M-Net (CTAEM-Net) to segment myocardial scar from 3D LGE MRI. Two sub-networks were cascaded to segment the left ventricle (LV) myocardium and then the scar within the pre-segmented LV myocardium. Each sub-network contains three autoencoder M-Nets (AEM-Nets) segmenting the axial, sagittal and coronal slices of the 3D LGE MR image, with the final segmentation determined by voting. The AEM-Net integrates three features: (1) multi-scale inputs, (2) deep supervision and (3) multi-tasking. The multi-scale inputs allow consideration of the global and local features in segmentation. Deep supervision provides direct supervision to deeper layers and facilitates CNN convergence. Multi-task learning reduces segmentation overfitting by acquiring additional information from autoencoder reconstruction, a task closely related to segmentation. The framework provides an accuracy of 86.43% and 90.18% for LV myocardium and scar segmentation, respectively, which are the highest among existing methods to our knowledge. The time required for CTAEM-Net to segment LV myocardium and the scar was 49.72 ± 9.69s and 120.25 ± 23.18s per MR volume, respectively. The accuracy and efficiency afforded by CTAEM-Net will make possible future large population studies. The generalizability of the framework was also demonstrated by its competitive performance in two publicly available datasets of different imaging modalities.

Radiomics and Machine Learning for Detecting Scar Tissue on CT Delayed Enhancement Imaging.

BackgroundDelayed enhancement CT (CT-DE) has been evaluated as a tool for the detection of myocardial scar and compares well to the gold standard of MRI with late gadolinium enhancement (MRI-LGE). Prior work has established that high performance can be achieved with manual reading; however, few studies have looked at quantitative measures to differentiate scar and healthy myocardium on CT-DE or automated analysis.MethodsEighteen patients with clinically indicated MRI-LGE were recruited for CT-DE at multiple 80 and 100 kV post contrast imaging. Left ventricle segmentation was performed on both imaging modalities, along with scar segmentation on MRI-LGE. Segmentations were registered together and scar regions were estimated on CT-DE. 93 radiomic features were calculated and analysed for their ability to differentiate between scarred and non-scarred myocardium regions. Machine learning (ML) classifiers were trained using the strongest set of radiomic features to classify segments containing scar on CT-DE. Features and classifiers were compared across both tube voltages and combined-energy images.ResultsThere were 59 and 51 statistically significant features in the 80 and 100 kV images respectively. Combined-energy imaging increased this to 63 with more features having area under the curve (AUC) above 0.9. The 10 highest AUC features for each image were used in the ML classifiers. The 100 kV images produced the best ML classifier, a support vector machine with an AUC of 0.88 (95% CI 0.87–0.90). Comparable performance was achieved with both the 80 kV and combined-energy images.ConclusionsCT-DE can be quantitatively analyzed using radiomic feature calculations. These features may be suitable for ML classification techniques to prospectively identify AHA segments with performance comparable to previously reported manual reading. Future work on larger CT-DE datasets is warranted to establish optimum imaging parameters and features.

An Improved 3D Deep Learning-Based Segmentation of Left Ventricular Myocardial Diseases from Delayed-Enhancement MRI with Inclusion and Classification Prior Information U-Net (ICPIU-Net).

Accurate segmentation of the myocardial scar may supply relevant advancements in predicting and controlling deadly ventricular arrhythmias in subjects with cardiovascular disease. In this paper, we propose the architecture of inclusion and classification of prior information U-Net (ICPIU-Net) to efficiently segment the left ventricle (LV) myocardium, myocardial infarction (MI), and microvascular-obstructed (MVO) tissues from late gadolinium enhancement magnetic resonance (LGE-MR) images. Our approach was developed using two subnets cascaded to first segment the LV cavity and myocardium. Then, we used inclusion and classification constraint networks to improve the resulting segmentation of the diseased regions within the pre-segmented LV myocardium. This network incorporates the inclusion and classification information of the LGE-MRI to maintain topological constraints of pathological areas. In the testing stage, the outputs of each segmentation network obtained with specific estimated parameters from training were fused using the majority voting technique for the final label prediction of each voxel in the LGE-MR image. The proposed method was validated by comparing its results to manual drawings by experts from 50 LGE-MR images. Importantly, compared to various deep learning-based methods participating in the EMIDEC challenge, the results of our approach have a more significant agreement with manual contouring in segmenting myocardial diseases.

AtrialJSQnet: A New framework for joint segmentation and quantification of left atrium and scars incorporating spatial and shape information.

Left atrial (LA) and atrial scar segmentation from late gadolinium enhanced magnetic resonance imaging (LGE MRI) is an important task in clinical practice. The automatic segmentation is however still challenging due to the poor image quality, the various LA shapes, the thin wall, and the surrounding enhanced regions. Previous methods normally solved the two tasks independently and ignored the intrinsic spatial relationship between LA and scars. In this work, we develop a new framework, namely AtrialJSQnet, where LA segmentation, scar projection onto the LA surface, and scar quantification are performed simultaneously in an end-to-end style. We propose a mechanism of shape attention (SA) via an implicit surface projection to utilize the inherent correlation between LA cavity and scars. In specific, the SA scheme is embedded into a multi-task architecture to perform joint LA segmentation and scar quantification. Besides, a spatial encoding (SE) loss is introduced to incorporate continuous spatial information of the target in order to reduce noisy patches in the predicted segmentation. We evaluated the proposed framework on 60 post-ablation LGE MRIs from the MICCAI2018 Atrial Segmentation Challenge. Moreover, we explored the domain generalization ability of the proposed AtrialJSQnet on 40 pre-ablation LGE MRIs from this challenge and 30 post-ablation multi-center LGE MRIs from another challenge (ISBI2012 Left Atrium Fibrosis and Scar Segmentation Challenge). Extensive experiments on public datasets demonstrated the effect of the proposed AtrialJSQnet, which achieved competitive performance over the state-of-the-art. The relatedness between LA segmentation and scar quantification was explicitly explored and has shown significant performance improvements for both tasks. The code has been released via https://zmiclab.github.io/projects.html.

Anatomically informed deep learning on contrast-enhanced cardiac magnetic resonance imaging for scar segmentation and clinical feature extraction

BackgroundVisualizing fibrosis on cardiac magnetic resonance (CMR) imaging with contrast enhancement (late gadolinium enhancement; LGE) is paramount in characterizing disease progression and identifying arrhythmia substrates. Segmentation and fibrosis quantification from LGE-CMR is intensive, manual, and prone to interobserver variability. There is an unmet need for automated LGE-CMR image segmentation that ensures anatomical accuracy and seamless extraction of clinical features.ObjectiveThis study aimed to develop a novel deep learning solution for analysis of contrast-enhanced CMR images that produces anatomically accurate myocardium and scar/fibrosis segmentations and uses these to calculate features of clinical interest.MethodsData sources were 155 2-dimensional LGE-CMR patient scans (1124 slices) and 246 synthetic “LGE-like” scans (1360 slices) obtained from cine CMR using a novel style-transfer algorithm. We trained and tested a 3-stage neural network that identified the left ventricle (LV) region of interest (ROI), segmented ROI into viable myocardium and regions of enhancement, and postprocessed the segmentation results to enforce conforming to anatomical constraints. The segmentations were used to directly compute clinical features, such as LV volume and scar burden.ResultsPredicted LV and scar segmentations achieved 96% and 75% balanced accuracy, respectively, and 0.93 and 0.57 Dice coefficient when compared to trained expert segmentations. The mean scar burden difference between manual and predicted segmentations was 2%.ConclusionWe developed and validated a deep neural network for automatic, anatomically accurate expert-level LGE- CMR myocardium and scar/fibrosis segmentation, allowing direct calculation of clinical measures. Given the training set heterogeneity, our approach could be extended to multiple imaging modalities and patient pathologies.

MA-SOCRATIS: An automatic pipeline for robust segmentation of the left ventricle and scar

Multi-atlas segmentation of cardiac regions and total infarct scar (MA-SOCRATIS) is an unsupervised automatic pipeline to segment left ventricular myocardium and scar from late gadolinium enhanced MR images (LGE-MRI) of the heart.We implement two different pipelines for myocardial and scar segmentation from short axis LGE-MRI. Myocardial segmentation has two steps; initial segmentation and re-estimation. The initial segmentation step makes a first estimate of myocardium boundaries by using multi-atlas segmentation techniques. The re-estimation step refines the myocardial segmentation by a combination of k-means clustering and a geometric median shape variation technique. An active contour technique determines the unhealthy and healthy myocardial wall. The scar segmentation pipeline is a combination of a Rician–Gaussian mixture model and full width at half maximum (FWHM) thresholding, to determine the intensity pixels in scar regions. Following this step a watershed method with an automatic seed-points framework segments the final scar region.MA-SOCRATIS was evaluated using two different datasets. In both datasets ground truths were based on manual segmentation of short axis images from LGE-MRI scans. The first dataset included 40 patients from the MS-CMRSeg 2019 challenge dataset (STACOM at MICCAI 2019). The second is a collection of 20 patients with scar regions that are challenging to segment. MA-SOCRATIS achieved robust and accurate performance in automatic segmentation of myocardium and scar regions without the need of training or tuning in both cohorts, compared with state-of-the-art techniques (intra-observer and inter observer myocardium segmentation: 81.9% and 70% average Dice value, and scar (intra-observer and inter observer segmentation: 70.5% and 70.5% average Dice value).

Myocardial Infarction Quantification from Late Gadolinium Enhancement MRI Using Top-Hat Transforms and Neural Networks

Late gadolinium enhancement (LGE) MRI is the gold standard technique for myocardial viability assessment. Although the technique accurately reflects the damaged tissue, there is no clinical standard to quantify myocardial infarction (MI). Moreover, commercial software used in clinical practice are mostly semi-automatic, and hence require direct intervention of experts. In this work, a new automatic method for MI quantification from LGE-MRI is proposed. Our novel segmentation approach is devised for accurately detecting not only hyper-enhanced lesions, but also microvascular obstruction areas. Moreover, it includes a myocardial disease detection step which extends the algorithm for working under healthy scans. The method is based on a cascade approach where firstly, diseased slices are identified by a convolutional neural network (CNN). Secondly, by means of morphological operations a fast coarse scar segmentation is obtained. Thirdly, the segmentation is refined by a boundary-voxel reclassification strategy using an ensemble of very light CNNs. We tested the method on a LGE-MRI database with healthy (n = 20) and diseased (n = 80) cases following a 5-fold cross-validation scheme. Our approach segmented myocardial scars with an average Dice coefficient of 77.22 ± 14.3% and with a volumetric error of 1.0 ± 6.9 cm3. In a comparison against nine reference algorithms, the proposed method achieved the highest agreement in volumetric scar quantification with the expert delineations (p&lt; 0.001 when compared to the other approaches). Moreover, it was able to reproduce the scar segmentation intra- and inter-rater variability. Our approach was shown to be a good first attempt towards automatic and accurate myocardial scar segmentation, although validation over larger LGE-MRI databases is needed.