Publications
275 results found
Huang NF, Yang G, Karaca E, et al., 2018, Nanofibrillar Scaffolds Modulate Endothelial Cell Survival and Function in a Mouse Model of Peripheral Arterial Disease, Publisher: LIPPINCOTT WILLIAMS & WILKINS, ISSN: 0009-7322
Yang G, Chen J, Gao Z, et al., 2018, Multiview sequential learning and dilated residual learning for a fully automatic delineation of the left atrium and pulmonary veins from late gadolinium-enhanced cardiac MRI images, 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Publisher: IEEE, Pages: 1123-1127, ISSN: 1557-170X
Accurate delineation of heart substructures is a prerequisite for abnormality detection, for making quantitative and functional measurements, and for computer-aided diagnosis and treatment planning. Late Gadolinium-Enhanced Cardiac MRI (LGE-CMRI) is an emerging imaging technology for myocardial infarction or scar detection based on the differences in the volume of residual gadolinium distribution between scar and healthy tissues. While LGE-CMRI is a well-established non-invasive tool for detecting myocardial scar tissues in the ventricles, its application to left atrium (LA) imaging is more challenging due to its very thin wall of the LA and poor quality images, which may be produced because of motion artefacts and low signal-to-noise ratio. As the LGE-CMRI scan is designed to highlight scar tissues by altering the gadolinium kinetics, the anatomy among different heart substructures has less distinguishable boundaries. An accurate, robust and reproducible method for LA segmentation is highly in demand because it can not only provide valuable information of the heart function but also be helpful for the further delineation of scar tissue and measuring the scar percentage. In this study, we proposed a novel deep learning framework working on LGE-CMRI images directly by combining sequential learning and dilated residual learning to delineate LA and pulmonary veins fully automatically. The achieved results showed accurate segmentation results compared to the state-of-the-art methods. The proposed framework leads to an automatic generation of a patient-specific model that can potentially enable an objective atrial scarring assessment for the atrial fibrillation patients.
Schlemper J, Yang G, Ferreira P, et al., 2018, Stochastic deep compressive sensing for the reconstruction of diffusion tensor cardiac MRI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol: 11070 LNCS, Pages: 295-303, ISSN: 0302-9743
© Springer Nature Switzerland AG 2018. Understanding the structure of the heart at the microscopic scale of cardiomyocytes and their aggregates provides new insights into the mechanisms of heart disease and enables the investigation of effective therapeutics. Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) is a unique non-invasive technique that can resolve the microscopic structure, organisation, and integrity of the myocardium without the need for exogenous contrast agents. However, this technique suffers from relatively low signal-to-noise ratio (SNR) and frequent signal loss due to respiratory and cardiac motion. Current DT-CMR techniques rely on acquiring and averaging multiple signal acquisitions to improve the SNR. Moreover, in order to mitigate the influence of respiratory movement, patients are required to perform many breath holds which results in prolonged acquisition durations (e.g., ~ 30 min using the existing technology). In this study, we propose a novel cascaded Convolutional Neural Networks (CNN) based compressive sensing (CS) technique and explore its applicability to improve DT-CMR acquisitions. Our simulation based studies have achieved high reconstruction fidelity and good agreement between DT-CMR parameters obtained with the proposed reconstruction and fully sampled ground truth. When compared to other state-of-the-art methods, our proposed deep cascaded CNN method and its stochastic variation demonstrated significant improvements. To the best of our knowledge, this is the first study using deep CNN based CS for the DT-CMR reconstruction. In addition, with relatively straightforward modifications to the acquisition scheme, our method can easily be translated into a method for online, at-the-scanner reconstruction enabling the deployment of accelerated DT-CMR in various clinical applications.
Chen J, Yang G, Gao Z, et al., 2018, Multiview two-task recursive attention model for left atrium and atrial scars segmentation, Medical Image Computing and Computer Assisted Intervention – MICCAI 2018, Publisher: Springer, Pages: 455-463, ISSN: 0302-9743
Late Gadolinium Enhanced Cardiac MRI (LGE-CMRI) for detecting atrial scars in atrial fibrillation (AF) patients has recently emerged as a promising technique to stratify patients, guide ablation therapy and predict treatment success. Visualisation and quantification of scar tissues require a segmentation of both the left atrium (LA) and the high intensity scar regions from LGE-CMRI images. These two segmentation tasks are challenging due to the cancelling of healthy tissue signal, low signal-to-noise ratio and often limited image quality in these patients. Most approaches require manual supervision and/or a second bright-blood MRI acquisition for anatomical segmentation. Segmenting both the LA anatomy and the scar tissues automatically from a single LGE-CMRI acquisition is highly in demand. In this study, we proposed a novel fully automated multiview two-task (MVTT) recursive attention model working directly on LGE-CMRI images that combines a sequential learning and a dilated residual learning to segment the LA (including attached pulmonary veins) and delineate the atrial scars simultaneously via an innovative attention model. Compared to other state-of-the-art methods, the proposed MVTT achieves compelling improvement, enabling to generate a patient-specific anatomical and atrial scar assessment model.
Wu F, Li L, Yang G, et al., 2018, Atrial Fibrosis Quantification Based on Maximum Likelihood Estimator of Multivariate Images, 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2018), Pages: 604-612, ISSN: 0302-9743
© 2018, Springer Nature Switzerland AG. We present a fully-automated segmentation and quantification of the left atrial (LA) fibrosis and scars combining two cardiac MRIs, one is the target late gadolinium-enhanced (LGE) image, and the other is an anatomical MRI from the same acquisition session. We formulate the joint distribution of images using a multivariate mixture model (MvMM), and employ the maximum likelihood estimator (MLE) for texture classification of the images simultaneously. The MvMM can also embed transformations assigned to the images to correct the misregistration. The iterated conditional mode algorithm is adopted for optimization. This method first extracts the anatomical shape of the LA, and then estimates a prior probability map. It projects the resulting segmentation onto the LA surface, for quantification and analysis of scarring. We applied the proposed method to 36 clinical data sets and obtained promising results (Accuracy: 0.809±150, Dice: 0.556±187). We compared the method with the conventional algorithms and showed an evidently and statistically better performance (p < 0.03).
Shi Z, Zeng G, Zhang L, et al., 2018, Bayesian VoxDRN: A Probabilistic Deep Voxelwise Dilated Residual Network for Whole Heart Segmentation from 3D MR Images, 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2018), Pages: 569-577, ISSN: 0302-9743
© 2018, Springer Nature Switzerland AG. In this paper, we propose a probabilistic deep voxelwise dilated residual network, referred as Bayesian VoxDRN, to segment the whole heart from 3D MR images. Bayesian VoxDRN can predict voxelwise class labels with a measure of model uncertainty, which is achieved by a dropout-based Monte Carlo sampling during testing to generate a posterior distribution of the voxel class labels. Our method has three compelling advantages. First, the dropout mechanism encourages the model to learn a distribution of weights with better data-explanation ability and prevents over-fitting. Second, focal loss and Dice loss are well encapsulated into a complementary learning objective to segment both hard and easy classes. Third, an iterative switch training strategy is introduced to alternatively optimize a binary segmentation task and a multi-class segmentation task for a further accuracy improvement. Experiments on the MICCAI 2017 multi-modality whole heart segmentation challenge data corroborate the effectiveness of the proposed method.
Seitzer M, Yang G, Schlemper J, et al., 2018, Adversarial and perceptual refinement for compressed sensing MRI reconstruction, 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2018), Pages: 232-240, ISSN: 0302-9743
© Springer Nature Switzerland AG 2018. Deep learning approaches have shown promising performance for compressed sensing-based Magnetic Resonance Imaging. While deep neural networks trained with mean squared error (MSE) loss functions can achieve high peak signal to noise ratio, the reconstructed images are often blurry and lack sharp details, especially for higher undersampling rates. Recently, adversarial and perceptual loss functions have been shown to achieve more visually appealing results. However, it remains an open question how to (1) optimally combine these loss functions with the MSE loss function and (2) evaluate such a perceptual enhancement. In this work, we propose a hybrid method, in which a visual refinement component is learnt on top of an MSE loss-based reconstruction network. In addition, we introduce a semantic interpretability score, measuring the visibility of the region of interest in both ground truth and reconstructed images, which allows us to objectively quantify the usefulness of the image quality for image post-processing and analysis. Applied on a large cardiac MRI dataset simulated with 8-fold undersampling, we demonstrate significant improvements (p<0.01) over the state-of-the-art in both a human observer study and the semantic interpretability score.
Mo Y, Liu F, McIlwraith D, et al., 2018, The Deep Poincaré Map: A Novel Approach for Left Ventricle Segmentation, 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2018), Pages: 561-568, ISSN: 0302-9743
© 2018, Springer Nature Switzerland AG. Precise segmentation of the left ventricle (LV) within cardiac MRI images is a prerequisite for the quantitative measurement of heart function. However, this task is challenging due to the limited availability of labeled data and motion artifacts from cardiac imaging. In this work, we present an iterative segmentation algorithm for LV delineation. By coupling deep learning with a novel dynamic-based labeling scheme, we present a new methodology where a policy model is learned to guide an agent to travel over the image, tracing out a boundary of the ROI – using the magnitude difference of the Poincaré map as a stopping criterion. Our method is evaluated on two datasets, namely the Sunnybrook Cardiac Dataset (SCD) and data from the STACOM 2011 LV segmentation challenge. Our method outperforms the previous research over many metrics. In order to demonstrate the transferability of our method we present encouraging results over the STACOM 2011 data, when using a model trained on the SCD dataset.
Mo Y, Liu F, McIlwraith D, et al., 2018, The deep Poincare map: A novel approach for left ventricle segmentation, 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 561-568, ISSN: 0302-9743
Precise segmentation of the left ventricle (LV) within cardiac MRI images is a prerequisite for the quantitative measurement of heart function. However, this task is challenging due to the limited availability of labeled data and motion artifacts from cardiac imaging. In this work, we present an iterative segmentation algorithm for LV delineation. By coupling deep learning with a novel dynamic-based labeling scheme, we present a new methodology where a policy model is learned to guide an agent to travel over the image, tracing out a boundary of the ROI – using the magnitude difference of the Poincaré map as a stopping criterion. Our method is evaluated on two datasets, namely the Sunnybrook Cardiac Dataset (SCD) and data from the STACOM 2011 LV segmentation challenge. Our method outperforms the previous research over many metrics. In order to demonstrate the transferability of our method we present encouraging results over the STACOM 2011 data, when using a model trained on the SCD dataset.
Lin J, Wang B, Yang G, et al., 2018, Indoor Localization Based on Weighted Surfacing from Crowdsourced Samples, SENSORS, Vol: 18
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- Citations: 8
Grujic O, Menafoglio A, Yang G, et al., 2018, Cokriging for multivariate Hilbert space valued random fields: application to multi-fidelity computer code emulation, STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT, Vol: 32, Pages: 1955-1971, ISSN: 1436-3240
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- Citations: 8
Yang G, Yu S, Hao D, et al., 2018, DAGAN: deep de-aliasing generative adversarial networks for fast compressed sensing MRI reconstruction, IEEE Transactions on Medical Imaging, Vol: 37, Pages: 1310-1321, ISSN: 0278-0062
Compressed Sensing Magnetic Resonance Imaging (CS-MRI) enables fast acquisition, which is highly desirable for numerous clinical applications. This can not only reduce the scanning cost and ease patient burden, but also potentially reduce motion artefacts and the effect of contrast washout, thus yielding better image quality. Different from parallel imaging based fast MRI, which utilises multiple coils to simultaneously receive MR signals, CS-MRI breaks the Nyquist-Shannon sampling barrier to reconstruct MRI images with much less required raw data. This paper provides a deep learning based strategy for reconstruction of CS-MRI, and bridges a substantial gap between conventional non-learning methods working only on data from a single image, and prior knowledge from large training datasets. In particular, a novel conditional Generative Adversarial Networks-based model (DAGAN) is proposed to reconstruct CS-MRI. In our DAGAN architecture, we have designed a refinement learning method to stabilise our U-Net based generator, which provides an endto-end network to reduce aliasing artefacts. To better preserve texture and edges in the reconstruction, we have coupled the adversarial loss with an innovative content loss. In addition, we incorporate frequency domain information to enforce similarity in both the image and frequency domains. We have performed comprehensive comparison studies with both conventional CSMRI reconstruction methods and newly investigated deep learning approaches. Compared to these methods, our DAGAN method provides superior reconstruction with preserved perceptual image details. Furthermore, each image is reconstructed in about 5 ms, which is suitable for real-time processing.
Yang G, Wanjare M, Nakayama K, et al., 2018, Biophysical Properties of Nanofibrillar Scaffolds Modulate Endothelial Cell Survival in the Ischemic Hind Limb, Scientific Sessions of the American-Heart-Association on Vascular Discovery - From Genes to Medicine, Publisher: LIPPINCOTT WILLIAMS & WILKINS, ISSN: 1079-5642
Yang G, Eishi Y, Raza A, et al., 2018, <i>Propionibacterium acnes</i>-associated neurosarcoidosis: A case report with review of the literature, NEUROPATHOLOGY, Vol: 38, Pages: 159-164, ISSN: 0919-6544
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- Citations: 9
Yang G, Zhuang X, Khan H, et al., 2018, Fully automatic segmentation and objective assessment of atrial scars for long-standing persistent atrial fibrillation patients using late gadolinium-enhanced MRI., Med Phys, Vol: 45, Pages: 1562-1576
PURPOSE: Atrial fibrillation (AF) is the most common heart rhythm disorder and causes considerable morbidity and mortality, resulting in a large public health burden that is increasing as the population ages. It is associated with atrial fibrosis, the amount and distribution of which can be used to stratify patients and to guide subsequent electrophysiology ablation treatment. Atrial fibrosis may be assessed noninvasively using late gadolinium-enhanced (LGE) magnetic resonance imaging (MRI) where scar tissue is visualized as a region of signal enhancement. However, manual segmentation of the heart chambers and of the atrial scar tissue is time consuming and subject to interoperator variability, particularly as image quality in AF is often poor. In this study, we propose a novel fully automatic pipeline to achieve accurate and objective segmentation of the heart (from MRI Roadmap data) and of scar tissue within the heart (from LGE MRI data) acquired in patients with AF. METHODS: Our fully automatic pipeline uniquely combines: (a) a multiatlas-based whole heart segmentation (MA-WHS) to determine the cardiac anatomy from an MRI Roadmap acquisition which is then mapped to LGE MRI, and (b) a super-pixel and supervised learning based approach to delineate the distribution and extent of atrial scarring in LGE MRI. We compared the accuracy of the automatic analysis to manual ground truth segmentations in 37 patients with persistent long-standing AF. RESULTS: Both our MA-WHS and atrial scarring segmentations showed accurate delineations of cardiac anatomy (mean Dice = 89%) and atrial scarring (mean Dice = 79%), respectively, compared to the established ground truth from manual segmentation. In addition, compared to the ground truth, we obtained 88% segmentation accuracy, with 90% sensitivity and 79% specificity. Receiver operating characteristic analysis achieved an average area under the curve of 0.91. CONCLUSION: Compared with previously studied methods with manual interve
Soltaninejad M, Yang G, Lambrou T, et al., 2018, Supervised learning based multimodal MRI brain tumour segmentation using texture features from supervoxels, Computer Methods and Programs in Biomedicine, Vol: 157, Pages: 69-84, ISSN: 0169-2607
Background:Accurate segmentation of brain tumour in magnetic resonance images (MRI) is a difficult task due to various tumour types. Using information and features from multimodal MRI including structural MRI and isotropic (p) and anisotropic (q) components derived from the diffusion tensor imaging (DTI) may result in a more accurate analysis of brain images.Methods:We propose a novel 3D supervoxel based learning method for segmentation of tumour in multimodal MRI brain images (conventional MRI and DTI). Supervoxels are generated using the information across the multimodal MRI dataset. For each supervoxel, a variety of features including histograms of texton descriptor, calculated using a set of Gabor filters with different sizes and orientations, and first order intensity statistical features are extracted. Those features are fed into a random forests (RF) classifier to classify each supervoxel into tumour core, oedema or healthy brain tissue.Results:The method is evaluated on two datasets: 1) Our clinical dataset: 11 multimodal images of patients and 2) BRATS 2013 clinical dataset: 30 multimodal images. For our clinical dataset, the average detection sensitivity of tumour (including tumour core and oedema) using multimodal MRI is 86% with balanced error rate (BER) 7%; while the Dice score for automatic tumour segmentation against ground truth is 0.84. The corresponding results of the BRATS 2013 dataset are 96%, 2% and 0.89, respectively.Conclusion:The method demonstrates promising results in the segmentation of brain tumour. Adding eatures from multimodal MRI images can largely increase the segmentation accuracy. The method provides a close match to expert delineation across all tumour grades, leading to a faster and more reproducible method of brain tumour detection and delineation to aid patient management.
Pop M, Sermesant M, Jodoin PM, et al., 2018, Preface, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol: 10663 LNCS, Pages: v-vii, ISSN: 0302-9743
Olliverre N, Yang G, Slabaugh G, et al., 2018, Generating Magnetic Resonance Spectroscopy Imaging Data of Brain Tumours from Linear, Non-linear and Deep Learning Models, Publisher: SPRINGER INTERNATIONAL PUBLISHING AG
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- Citations: 5
Vilhelmsen TN, Maher K, Da Silva C, et al., 2018, Quantifying Uncertainty in Subsurface Systems, QUANTIFYING UNCERTAINTY IN SUBSURFACE SYSTEMS, Publisher: AMER GEOPHYSICAL UNION, Pages: 217-262
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- Citations: 2
Soltaninejad M, Zhang L, Lambrou T, et al., 2018, MRI Brain Tumor Segmentation and Patient Survival Prediction Using Random Forests and Fully Convolutional Networks, 3rd International Workshop on Brain-Lesion (BrainLes) held jointly at the Conference on Medical Image Computing for Computer Assisted Intervention (MICCAI), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 204-215, ISSN: 0302-9743
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- Citations: 40
Vilhelmsen TN, Maher K, Da Silva C, et al., 2018, The Earth Resources Challenge, QUANTIFYING UNCERTAINTY IN SUBSURFACE SYSTEMS, Publisher: AMER GEOPHYSICAL UNION, Pages: 1-27
Eli Y, Yang G, Inoue A, et al., 2017, Increased Dipeptidyl Peptidase-4 Accelerates Diet-Related Vascular Aging and Atherosclerosis in ApoE-Deficient Mice under Chronic Stress, Scientific Sessions of the American-Heart-Association / Resuscitation Science Symposium, Publisher: LIPPINCOTT WILLIAMS & WILKINS, ISSN: 0009-7322
Yang G, Zhuang X, Khan H, et al., 2017, Segmenting atrial fibrosis from late gadolinium-enhanced cardiac MRI by deep-learned features with stacked sparse auto-encoders, MIUA 2017, Publisher: Springer, Pages: 195-206, ISSN: 1865-0929
The late gadolinium-enhanced (LGE) MRI technique is a well-validated method for fibrosis detection in the myocardium. With this technique, the altered wash-in and wash-out contrast agent kinetics in fibrotic and healthy myocardium results in scar tissue being seen with high or enhanced signal relative to normal tissue which is ‘nulled’. Recently, great progress on LGE MRI has resulted in improved visualization of fibrosis in the left atrium (LA). This provides valuable information for treatment planning, image-based procedure guidance and clinical management in patients with atrial fibrillation (AF). Nevertheless, precise and objective atrial fibrosis segmentation (AFS) is required for accurate assessment of AF patients using LGE MRI. This is a very challenging task, not only because of the limited quality and resolution of the LGE MRI images acquired in AF but also due to the thinner wall and unpredictable morphology of the LA. Accurate and reliable segmentation of the anatomical structure of the LA myocardium is a prerequisite for accurate AFS. Most current studies rely on manual segmentation of the anatomical structures, which is very labor-intensive and subject to inter- and intra-observer variability. The subsequent AFS is normally based on unsupervised learning methods, e.g., using thresholding, histogram analysis, clustering and graph-cut based approaches, which have variable accuracy. In this study, we present a fully-automated multi-atlas propagation based whole heart segmentation method to derive the anatomical structure of the LA myocardium and pulmonary veins. This is followed by a supervised deep learning method for AFS. Twenty clinical LGE MRI scans from longstanding persistent AF patients were entered into this study retrospectively. We have demonstrated that our fully automatic method can achieve accurate and reliable AFS compared to manual delineated ground truth.
Yang G, Zhuang X, Khan H, et al., 2017, A fully automatic deep learning method for atrial scarring segmentation from late gadolinium-enhanced MRI images, 2017 IEEE 14th International Symposium on Biomedical Imaging, Publisher: IEEE, Pages: 844-848, ISSN: 1945-7928
Precise and objective segmentation of atrial scarring (SAS) is a prerequisite for quantitative assessment of atrial fibrillation using non-invasive late gadolinium-enhanced (LGE) MRI. This also requires accurate delineation of the left atrium (LA) and pulmonary veins (PVs) geometry. Most previous studies have relied on manual segmentation of LA wall and PVs, which is a tedious and error-prone procedure with limited reproducibility. There are many attempts on automatic SAS using simple thresholding, histogram analysis, clustering and graph-cut based approaches; however, in general, these methods are considered as unsupervised learning thus subject to limited segmentation accuracy. In this study, we present a fully-automated multi-atlas based whole heart segmentation method to derive the LA and PVs geometry objectively that is followed by a fully automatic deep learning method for SAS. Our deep learning method consists of a feature extraction step via super-pixel over-segmentation and a supervised classification step via stacked sparse auto-encoders. We demonstrate the efficacy of our method on 20 clinical LGE MRI scans acquired from a longstanding persistent atrial fibrillation cohort. Both quantitative and qualitative results show that our fully automatic method obtained accurate segmentation results compared to the manual segmentation based ground truths.
Sun Z, Wang X, Ling M, et al., 2017, Acceleration of tendon-bone healing of anterior cruciate ligament graft using intermittent negative pressure in rabbits, JOURNAL OF ORTHOPAEDIC SURGERY AND RESEARCH, Vol: 12, ISSN: 1749-799X
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- Citations: 5
Yang G, Deisch J, Tavares M, et al., 2017, Primary B-Cell Lymphoma of the Uterine Cervix: Presentation in Pap-Test Slide and Cervical Biopsy, DIAGNOSTIC CYTOPATHOLOGY, Vol: 45, Pages: 235-238, ISSN: 8755-1039
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- Citations: 3
Olliverre N, Asad M, Yang G, et al., 2017, Pairwise Mixture Model for Unmixing Partial Volume Effect in Multi-voxel MR Spectroscopy of Brain Tumour Patients
Dong H, Yang G, Liu F, et al., 2017, Automatic Brain Tumor Detection and Segmentation Using U-Net Based Fully Convolutional Networks, 21st Annual Conference on Medical Image Understanding and Analysis (MIUA), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 506-517, ISSN: 1865-0929
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- Citations: 358
Yang G, Zhuang X, Khan H, et al., 2017, Multi-atlas Propagation based Left Atrium Segmentation Coupled with Super-voxel based Pulmonary Veins Delineation in Late Gadolinium-enhanced Cardiac MRI
Meng H-T, Shen C-M, Zhang Y-D, et al., 2017, Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons, ANNALS OF HUMAN BIOLOGY, Vol: 44, Pages: 546-553, ISSN: 0301-4460
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- Citations: 10
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