Automatic segmentation of brain glioma from multimodal MRI scans plays a key role in clinical trials and practice. Unfortunately, manual segmentation is very challenging, time-consuming, costly, and often inaccurate despite human expertise due to the high variance and high uncertainty in the human annotations. In the present work, we develop an end-to-end deep-learning-based segmentation method using a multi-decoder architecture by jointly learning three separate sub-problems using a partly shared encoder. We also propose to apply smoothing methods to the input images to generate denoised versions as additional inputs to the network. The validation performance indicate an improvement when using the proposed method. The proposed method was ranked 2nd in the task of Quantification of Uncertainty in Segmentation in the Brain Tumors in Multimodal Magnetic Resonance Imaging Challenge 2020.
Fingerprint image denoising is a very important step in fingerprint identification. to improve the denoising effect of fingerprint image,we have designs a fingerprint denoising algorithm based on deep encoder-decoder network,which encoder subnet to learn the fingerprint features of noisy images.the decoder subnet reconstructs the original fingerprint image based on the features to achieve denoising, while using the dilated convolution in the network to increase the receptor field without increasing the complexity and improve the network inference speed. In addition, feature fusion at different…
Pancreatic Tumor Segmentation as Anomaly Detection in CT Images Using Denoising Diffusion Models
School of Electrical and Computer Engineering, University of Oklahoma（俄克拉荷马大学电气与计算机工程学院）；University of Oklahoma Health Sciences Center（俄克拉荷马大学健康科学中心）；School of Computer Science, University of Oklahoma（俄克拉荷马大学计算机科学学院）
Accurate visualization of liver tumors and their surrounding blood vessels is essential for noninvasive diagnosis and prognosis prediction of tumors. In medical image segmentation, there is still a lack of in-depth research on the simultaneous segmentation of liver tumors and peritumoral blood vessels. To this end, we collect the first liver tumor, and vessel segmentation benchmark datasets containing 52 portal vein phase computed tomography images with liver, liver tumor, and vessel annotations. In this case, we propose a 3D U-shaped Cross-Attention Network (UCA-Net) that utilizes a tailored …
Huazhong University of Science and Technology（华中科技大学）；Shenzhen University（深圳大学）
Deep convolutional neural network (CNN) achieves remarkable performance for medical image analysis. UNet is the primary source in the performance of 3D CNN architectures for medical imaging tasks, including brain tumor segmentation. The skip connection in the UNet architecture concatenates features from both encoder and decoder paths to extract multi-contextual information from image data. The multi-scaled features play an essential role in brain tumor segmentation. However, the limited use of features can degrade the performance of the UNet approach for segmentation. In this paper, we propose…
In computer-aided diagnosis (CAD) focused on microscopy, denoising improves the quality of image analysis. In general, the accuracy of this process may depend both on the experience of the microscopist and on the equipment sensitivity and specificity. A medical image could be corrupted by both intrinsic noise, due to the device limitations, and, by extrinsic signal perturbations during image acquisition. Nowadays, CAD deep learning applications pre-process images with image denoising models to reinforce learning and prediction. In this work, an innovative and lightweight deep multiscale convol…
Low dose computed tomography is a mainstream for clinical applications. How-ever, compared to normal dose CT, in the low dose CT (LDCT) images, there are stronger noise and more artifacts which are obstacles for practical applications. In the last few years, convolution-based end-to-end deep learning methods have been widely used for LDCT image denoising. Recently, transformer has shown superior performance over convolution with more feature interactions. Yet its ap-plications in LDCT denoising have not been fully cultivated. Here, we propose a convolution-free T2T vision transformer-based Enc…
Convolutional Neural Networks (CNNs) have demonstrated state-of-the-art performance in medical image segmentation tasks. A common feature in most top-performing CNNs is an encoder-decoder architecture inspired by the U-Net. For multi-region brain tumor segmentation, 3D U-Net architecture and its variants provide the most competitive segmentation performances. In this work, we propose an interesting extension of the standard 3D U-Net architecture, specialized for brain tumor segmentation. The proposed network, called E1D3 U-Net, is a one-encoder, three-decoder fully-convolutional neural network…
Glioma, the malignant brain tumor, requires immediate treatment to improve the survival of patients. Gliomas heterogeneous nature makes the segmentation difficult, especially for sub-regions like necrosis, enhancing tumor, non-enhancing tumor, and Edema. Deep neural networks like full convolution neural networks and ensemble of fully convolution neural networks are successful for Glioma segmentation. The paper demonstrates the use of a 3D fully convolution neural network with a three layer encoder decoder approach for layer arrangement. The encoder blocks include the dense modules, and decoder…
Kidney structures segmentation is a crucial yet challenging task in the computer-aided diagnosis of surgery-based renal cancer. Although numerous deep learning models have achieved remarkable success in many medical image segmentation tasks, accurate segmentation of kidney structures on computed tomography angiography (CTA) images remains challenging, due to the variable sizes of kidney tumors and the ambiguous boundaries between kidney structures and their surroundings. In this paper, we propose a boundary-aware network (BA-Net) to segment kidneys, kidney tumors, arteries, and veins on CTA sc…
XLSTM-HVED: Cross-Modal Brain Tumor Segmentation and MRI Reconstruction Method Using Vision XLSTM and Heteromodal Variational Encoder-Decoder
Hangzhou Dianzi University（杭州电子科技大学）；Shenzhen Research Institute of Big Data（深圳大数据研究院）；Children's Hospital, Zhejiang University School of Medicine（浙江大学医学院附属儿童医院）；Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province（浙江省中芬儿童健康人工智能联合实验室）
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Tencent（腾讯）；University of California, Los Angeles（加州大学洛杉矶分校）；Lenovo Research（联想研究院）
Accurate brain tumor segmentation from Magnetic Resonance Imaging (MRI) is desirable to joint learning of multimodal images. However, in clinical practice, it is not always possible to acquire a complete set of MRIs, and the problem of missing modalities causes severe performance degradation in existing multimodal segmentation methods. In this work, we present the first attempt to exploit the Transformer for multimodal brain tumor segmentation that is robust to any combinatorial subset of available modalities. Concretely, we propose a novel multimodal Medical Transformer (mmFormer) for incompl…
Prototype Learning Guided Hybrid Network for Breast Tumor Segmentation in DCE-MRI
School of Health Science and Engineering, University of Shanghai for Science and Technology（上海理工大学健康科学与工程学院）；School of Biomedical Engineering, ShanghaiTech University（上海科技大学生物医学工程学院）；School of Computer Science and Engineering, Nanjing University of Science and Technology（南京理工大学计算机科学与工程学院）；Ruijin Hospital, Shanghai Jiaotong University School of Medicine（上海交通大学医学院附属瑞金医院）；Shanghai General Hospital（上海交通大学附属第一人民医院）
Indian Institute of Information Technology Allahabad（印度阿拉哈巴德信息技术学院）
Brain tumor is the most common and deadliest disease that can be found in all age groups. Generally, MRI modality is adopted for identifying and diagnosing tumors by the radiologists. The correct identification of tumor regions and its type can aid to diagnose tumors with the followup treatment plans. However, for any radiologist analysing such scans is a complex and time-consuming task. Motivated by the deep learning based computer-aided-diagnosis systems, this paper proposes multi-task attention guided encoder-decoder network (MAG-Net) to classify and segment the brain tumor regions using MR…
multiPI-TransBTS: A Multi-Path Learning Framework for Brain Tumor Image Segmentation Based on Multi-Physical Information
Chongqing University of Posts and Telecommunications（重庆邮电大学）；Chongqing Engineering Research Center of Software Quality Assurance, Testing and Assessment（重庆市软件质量保证与测评工程技术研究中心）
Another year of the multimodal brain tumor segmentation challenge (BraTS) 2021 provides an even larger dataset to facilitate collaboration and research of brain tumor segmentation methods, which are necessary for disease analysis and treatment planning. A large dataset size of BraTS 2021 and the advent of modern GPUs provide a better opportunity for deep-learning based approaches to learn tumor representation from the data. In this work, we maintained an encoder-decoder based segmentation network, but focused on a modification of network training process that minimizes redundancy under perturb…
Zhejiang Chinese Medical University（浙江中医药大学）；Royal Brompton Hospital（皇家布朗普顿医院）；Imperial College London（帝国理工学院）；University of California at Los Angeles（加州大学洛杉矶分校）
Glioma is the most common and aggressive brain tumor. Magnetic resonance imaging (MRI) plays a vital role to evaluate tumors for the arrangement of tumor surgery and the treatment of subsequent procedures. However, the manual segmentation of the MRI image is strenuous, which limits its clinical application. With the development of deep learning, a large number of automatic segmentation methods have been developed, but most of them stay in 2D images, which leads to subpar performance. Moreover, the serious voxel imbalance between the brain tumor and the background as well as the different sizes…
We propose a Transformer architecture for volumetric segmentation, a challenging task that requires keeping a complex balance in encoding local and global spatial cues, and preserving information along all axes of the volume. Encoder of the proposed design benefits from self-attention mechanism to simultaneously encode local and global cues, while the decoder employs a parallel self and cross attention formulation to capture fine details for boundary refinement. Empirically, we show that the proposed design choices result in a computationally efficient model, with competitive and promising res…
Canon Medical Research Europe（佳能医疗欧洲研究中心）；University of Glasgow（格拉斯哥大学）；University of Edinburgh（爱丁堡大学）；The Alan Turing Institute（艾伦·图灵研究所）
Pathological brain lesions exhibit diverse appearance in brain images, in terms of intensity, texture, shape, size, and location. Comprehensive sets of data and annotations are difficult to acquire. Therefore, unsupervised anomaly detection approaches have been proposed using only normal data for training, with the aim of detecting outlier anomalous voxels at test time. Denoising methods, for instance classical denoising autoencoders (DAEs) and more recently emerging diffusion models, are a promising approach, however naive application of pixelwise noise leads to poor anomaly detection perform…
Automatic segmentation of brain tumors is an essential but challenging step for extracting quantitative imaging biomarkers for accurate tumor detection, diagnosis, prognosis, treatment planning and assessment. Multimodal Brain Tumor Segmentation Challenge 2020 (BraTS 2020) provides a common platform for comparing different automatic algorithms on multi-parametric Magnetic Resonance Imaging (mpMRI) in tasks of 1) Brain tumor segmentation MRI scans; 2) Prediction of patient overall survival (OS) from pre-operative MRI scans; 3) Distinction of true tumor recurrence from treatment related effects …
Korea Advanced Institute of Science and Technology（韩国科学技术院）
Brain tumor segmentation is essential for the diagnosis and prognosis of patients with gliomas. The brain tumor segmentation challenge has continued to provide a great source of data to develop automatic algorithms to perform the task. This paper describes our contribution to the 2021 competition. We developed our methods based on nn-UNet, the winning entry of last year competition. We experimented with several modifications, including using a larger network, replacing batch normalization with group normalization, and utilizing axial attention in the decoder. Internal 5-fold cross validation a…
Multimodal brain tumor segmentation challenge (BraTS) brings together researchers to improve automated methods for 3D MRI brain tumor segmentation. Tumor segmentation is one of the fundamental vision tasks necessary for diagnosis and treatment planning of the disease. Previous years winning methods were all deep-learning based, thanks to the advent of modern GPUs, which allow fast optimization of deep convolutional neural network architectures. In this work, we explore best practices of 3D semantic segmentation, including conventional encoder-decoder architecture, as well combined loss functio…
NUS Graduate School for Integrative Sciences and Engineering, NUS（新加坡国立大学综合科学与工程研究生院）；National University of Singapore（新加坡国立大学）；NIT, Tiruchirappalli（蒂鲁吉拉伯利国立理工学院）；University of Moratuwa（莫拉图瓦大学）；Punjab Engineering College（旁遮普工程学院）
In this work, we develop an attention convolutional neural network (CNN) to segment brain tumors from Magnetic Resonance Images (MRI). Further, we predict the survival rate using various machine learning methods. We adopt a 3D UNet architecture and integrate channel and spatial attention with the decoder network to perform segmentation. For survival prediction, we extract some novel radiomic features based on geometry, location, the shape of the segmented tumor and combine them with clinical information to estimate the survival duration for each patient. We also perform extensive experiments t…
DiffKAN-Inpainting: KAN-based Diffusion model for brain tumor inpainting
School of Biomedical Engineering, ShanghaiTech University（上海科技大学生物医学工程学院）；The Alan Turing Institute（阿兰·图灵研究所）；School of Engineering, University of Birmingham（伯明翰大学工程学院）；College of Engineering and Physical Sciences, University of Birmingham（伯明翰大学工程与物理科学学院）
We propose an optimized U-Net architecture for a brain tumor segmentation task in the BraTS21 challenge. To find the optimal model architecture and the learning schedule, we have run an extensive ablation study to test: deep supervision loss, Focal loss, decoder attention, drop block, and residual connections. Additionally, we have searched for the optimal depth of the U-Net encoder, number of convolutional channels and post-processing strategy. Our method won the validation phase and took third place in the test phase. We have open-sourced the code to reproduce our BraTS21 submission at the N…
Fully convolutional neural networks have made promising progress in joint liver and liver tumor segmentation. Instead of following the debates over 2D versus 3D networks (for example, pursuing the balance between large-scale 2D pretraining and 3D context), in this paper, we novelly identify the wide variation in the ratio between intra- and inter-slice resolutions as a crucial obstacle to the performance. To tackle the mismatch between the intra- and inter-slice information, we propose a slice-aware 2.5D network that emphasizes extracting discriminative features utilizing not only in-plane sem…
Negligible effect of brain MRI data preprocessing for tumor segmentation
Artificial Intelligence Research Institute (AIRI)（人工智能研究院（AIRI））；Skolkovo Institute of Science and Technology（斯科尔科沃科技学院）；National Medical Research Center for Neurosurgery（国家神经外科医学研究中心）
NVIDIA（英伟达）；University of California, Los Angeles（加州大学洛杉矶分校）
Automated segmentation of kidneys and kidney tumors is an important step in quantifying the tumor's morphometrical details to monitor the progression of the disease and accurately compare decisions regarding the kidney tumor treatment. Manual delineation techniques are often tedious, error-prone and require expert knowledge for creating unambiguous representation of kidneys and kidney tumors segmentation. In this work, we propose an end-to-end boundary aware fully Convolutional Neural Networks (CNNs) for reliable kidney and kidney tumor semantic segmentation from arterial phase abdominal 3D CT…
The performance of a computer-aided automated diagnosis system of lung cancer from Computed Tomography (CT) volumetric images greatly depends on the accurate detection and segmentation of tumor regions. In this paper, we present Recurrent 3D-DenseUNet, a novel deep learning based architecture for volumetric lung tumor segmentation from CT scans. The proposed architecture consists of a 3D encoder block that learns to extract fine-grained spatial and coarse-grained temporal features, a recurrent block of multiple Convolutional Long Short-Term Memory (ConvLSTM) layers to extract fine-grained spat…
VRVis Zentrum für Virtual Reality und Visualisierung Forschungs-GmbH（VRVis虚拟现实与可视化研究有限公司）；Center for Medical Physics and Biomedical Engineering, Medical University of Vienna（维也纳医科大学医学物理与生物医学工程中心）；Center for Nuclear Medicine, Clinical Center of Serbia（塞尔维亚临床中心核医学中心）
Tumor segmentation in multimodal medical images has seen a growing trend towards deep learning based methods. Typically, studies dealing with this topic fuse multimodal image data to improve the tumor segmentation contour for a single imaging modality. However, they do not take into account that tumor characteristics are emphasized differently by each modality, which affects the tumor delineation. Thus, the tumor segmentation is modality- and task-dependent. This is especially the case for soft tissue sarcomas, where, due to necrotic tumor tissue, the segmentation differs vastly. Closing this …
Automatic MRI brain tumor segmentation is of vital importance for the disease diagnosis, monitoring, and treatment planning. In this paper, we propose a two-stage encoder-decoder based model for brain tumor subregional segmentation. Variational autoencoder regularization is utilized in both stages to prevent the overfitting issue. The second-stage network adopts attention gates and is trained additionally using an expanded dataset formed by the first-stage outputs. On the BraTS 2020 validation dataset, the proposed method achieves the mean Dice score of 0.9041, 0.8350, and 0.7958, and Hausdorf…
Lung cancer has emerged as a severe disease that threatens human life and health. The precise segmentation of lung regions is a crucial prerequisite for localizing tumors, which can provide accurate information for lung image analysis. In this work, we first propose a lung image segmentation model using the NASNet-Large as an encoder and then followed by a decoder architecture, which is one of the most commonly used architectures in deep learning for image segmentation. The proposed NASNet-Large-decoder architecture can extract high-level information and expand the feature map to recover the s…
Multi-Modal Brain Tumor Segmentation via 3D Multi-Scale Self-attention and Cross-attention
University of Electronic Science and Technology of China（电子科技大学）；School of Computer Science and Engineering, University of Electronic Science and Technology of China（电子科技大学计算机科学与工程学院）；School of Information and Software Engineering, University of Electronic Science and Technology of China（电子科技大学信息与软件工程学院）
Adaptive Semantic-Enhanced Denoising Diffusion Probabilistic Model for Remote Sensing Image Super-Resolution
School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳）理工学院）；School of Information Science and Engineering, Wuhan University of Science and Technology（武汉科技大学信息科学与工程学院）；College of Urban and Environment Sciences, Central China Normal University（华中师范大学城市与环境科学学院）
Automatic brain tumor segmentation from Magnetic Resonance Imaging (MRI) data plays an important role in assessing tumor response to therapy and personalized treatment stratification.Manual segmentation is tedious and subjective.Deep-learning-based algorithms for brain tumor segmentation have the potential to provide objective and fast tumor segmentation.However, the training of such algorithms requires large datasets which are not always available. Data augmentation techniques may reduce the need for large datasets.However current approaches are mostly parametric and may result in suboptimal …
Couger Inc（库格公司）；Sethu Institute of Technology（塞图理工学院）；Thiagarajar college of Engineering（蒂亚加拉贾工程学院）
KiTs19 challenge paves the way to haste the improvement of solid kidney tumor semantic segmentation methodologies. Accurate segmentation of kidney tumor in computer tomography (CT) images is a challenging task due to the non-uniform motion, similar appearance and various shape. Inspired by this fact, in this manuscript, we present a novel kidney tumor segmentation method using deep learning network termed as Hyper vision Net model. All the existing U-net models are using a modified version of U-net to segment the kidney tumor region. In the proposed architecture, we introduced supervision laye…
UNC Chapel Hill（北卡罗来纳大学教堂山分校）；University of Pennsylvania（宾夕法尼亚大学）
Registration of images with pathologies is challenging due to tissue appearance changes and missing correspondences caused by the pathologies. Moreover, mass effects as observed for brain tumors may displace tissue, creating larger deformations over time than what is observed in a healthy brain. Deep learning models have successfully been applied to image registration to offer dramatic speed up and to use surrogate information (e.g., segmentations) during training. However, existing approaches focus on learning registration models using images from healthy patients. They are therefore not desi…
Universitat Politècnica de Catalunya. BarcelonaTech（加泰罗尼亚理工大学）
Automation of brain tumors in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. Moreover, most methods do not include uncertainty information, which is specially critical in medical diagnosis. This work proposes a 3D encoder-decoder architecture, based on V-Net \cite{vnet} which is trained with patching techniques to reduce memory consumption and decrease the effect of unbalanced data. We a…
Previous works have shown that convolutional neural networks can achieve good performance in image denoising tasks. However, limited by the local rigid convolutional operation, these methods lead to oversmoothing artifacts. A deeper network structure could alleviate these problems, but more computational overhead is needed. In this paper, we propose a novel spatial-adaptive denoising network (SADNet) for efficient single image blind noise removal. To adapt to changes in spatial textures and edges, we design a residual spatial-adaptive block. Deformable convolution is introduced to sample the s…
The paper demonstrates the use of the fully convolutional neural network for glioma segmentation on the BraTS 2019 dataset. Three-layers deep encoder-decoder architecture is used along with dense connection at encoder part to propagate the information from coarse layer to deep layers. This architecture is used to train three tumor sub-components separately. Subcomponent training weights are initialized with whole tumor weights to get the localization of the tumor within the brain. At the end, three segmentation results were merged to get the entire tumor segmentation. Dice Similarity of traini…
Re-DiffiNet: Modeling discrepancies in tumor segmentation using diffusion models
University of Washington（华盛顿大学）；Paul G. Allen School of Computer Science, University of Washington（华盛顿大学保罗·G·艾伦计算机科学学院）；Department of Neurological Surgery, University of Washington（华盛顿大学神经外科系）
Tianjin University（天津大学）；The University of Hong Kong（香港大学）；Huanhu Hospital（环湖医院）；The Hong Kong University of Science and Technology (Guangzhou)（香港科技大学（广州））；The Hong Kong University of Science and Technology（香港科技大学）
Multi-modal MR imaging is routinely used in clinical practice to diagnose and investigate brain tumors by providing rich complementary information. Previous multi-modal MRI segmentation methods usually perform modal fusion by concatenating multi-modal MRIs at an early/middle stage of the network, which hardly explores non-linear dependencies between modalities. In this work, we propose a novel Nested Modality-Aware Transformer (NestedFormer) to explicitly explore the intra-modality and inter-modality relationships of multi-modal MRIs for brain tumor segmentation. Built on the transformer-based…
South China University of Technology（华南理工大学）；Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences（广东省人民医院，广东省医学科学院）
Brain tumor segmentation (BTS) in magnetic resonance image (MRI) is crucial for brain tumor diagnosis, cancer management and research purposes. With the great success of the ten-year BraTS challenges as well as the advances of CNN and Transformer algorithms, a lot of outstanding BTS models have been proposed to tackle the difficulties of BTS in different technical aspects. However, existing studies hardly consider how to fuse the multi-modality images in a reasonable manner. In this paper, we leverage the clinical knowledge of how radiologists diagnose brain tumors from multiple MRI modalities…
Reutlingen University（罗伊特林根大学）；Menoufia University（米努夫大学）；University of Ulm（乌尔姆大学）
Purpose: Gliomas are the most common and aggressive type of brain tumors due to their infiltrative nature and rapid progression. The process of distinguishing tumor boundaries from healthy cells is still a challenging task in the clinical routine. Fluid-Attenuated Inversion Recovery (FLAIR) MRI modality can provide the physician with information about tumor infiltration. Therefore, this paper proposes a new generic deep learning architecture; namely DeepSeg for fully automated detection and segmentation of the brain lesion using FLAIR MRI data. Methods: The developed DeepSeg is a modular decou…
Automated and accurate 3D medical image segmentation plays an essential role in assisting medical professionals to evaluate disease progresses and make fast therapeutic schedules. Although deep convolutional neural networks (DCNNs) have widely applied to this task, the accuracy of these models still need to be further improved mainly due to their limited ability to 3D context perception. In this paper, we propose the 3D context residual network (ConResNet) for the accurate segmentation of 3D medical images. This model consists of an encoder, a segmentation decoder, and a context residual decod…
Cycle-Constrained Adversarial Denoising Convolutional Network for PET Image Denoising: Multi-Dimensional Validation on Large Datasets with Reader Study and Real Low-Dose Data
