Brain Tumor Segmentation in MRI Images with 3D U-Net and Contextual Transformer
University of Information Technology（信息科技大学）；Vietnam National University（越南国家大学）；College of Technology and Design, University of Economics Ho Chi Minh City（胡志明市经济大学技术与设计学院）；Ho Chi Minh City Open University（胡志明市开放大学）
Thien-Qua T. Nguyen, Hieu-Nghia Nguyen, Thanh-Hieu Bui, Thien B. Nguyen-Tat, Vuong M. Ngo
This research presents an enhanced approach for precise segmentation of brain tumor masses in magnetic resonance imaging (MRI) using an advanced 3D-UNet model combined with a Context Transformer (CoT). By architectural expansion CoT, the proposed model extends its architecture to a 3D format, integrates it smoothly with the base model to utilize the complex contextual information found in MRI scans, emphasizing how elements rely on each other across an extended spatial range. The proposed model synchronizes tumor mass characteristics from CoT, mutually reinforcing feature extraction, facilitating the precise capture of detailed tumor mass structures, including location, size, and boundaries. Several experimental results present the outstanding segmentation performance of the proposed method in comparison to current state-of-the-art approaches, achieving Dice score of 82.0%, 81.5%, 89.0% for Enhancing Tumor, Tumor Core and Whole Tumor, respectively, on BraTS2019.
University of Minho（米尼奥大学）；University Hospital Inselspital（因塞尔施皮塔尔大学医院）；University of Bern（伯尔尼大学）
Glioblastoma Multiforme is a high grade, very aggressive, brain tumor, with patients having a poor prognosis. Lower grade gliomas are less aggressive, but they can evolve into higher grade tumors over time. Patient management and treatment can vary considerably with tumor grade, ranging from tumor resection followed by a combined radio- and chemotherapy to a "wait and see" approach. Hence, tumor grading is important for adequate treatment planning and monitoring. The gold standard for tumor grading relies on histopathological diagnosis of biopsy specimens. However, this procedure is invasive, …
Towards Label-Free Brain Tumor Segmentation: Unsupervised Learning with Multimodal MRI
Universitat Politècnica de Catalunya (UPC)（西班牙巴塞罗那理工大学）；University College Dublin (UCD)（都柏林大学）；Dublin City University (DCU)（都柏林城市大学）；Insight Research Ireland Center For Data Analytics（爱尔兰数据分析研究中心）
University of Calcutta（加尔各答大学）；West Bengal University of Technology（西孟加拉技术大学）
Tumor segmentation from magnetic resonance imaging (MRI) data is an important but time consuming manual task performed by medical experts. Automating this process is a challenging task because of the high diversity in the appearance of tumor tissues among different patients and in many cases similarity with the normal tissues. MRI is an advanced medical imaging technique providing rich information about the human soft-tissue anatomy. There are different brain tumor detection and segmentation methods to detect and segment a brain tumor from MRI images. These detection and segmentation approache…
Background: Glioma is the most common brain malignant tumor, with a high morbidity rate and a mortality rate of more than three percent, which seriously endangers human health. The main method of acquiring brain tumors in the clinic is MRI. Segmentation of brain tumor regions from multi-modal MRI scan images is helpful for treatment inspection, post-diagnosis monitoring, and effect evaluation of patients. However, the common operation in clinical brain tumor segmentation is still manual segmentation, lead to its time-consuming and large performance difference between different operators, a con…
The brain tumor segmentation on MRI images is a very difficult and important task which is used in surgical and medical planning and assessments. If experts do the segmentation manually with their own medical knowledge, it will be time-consuming. Therefore, researchers propose methods and systems which can do the segmentation automatically and without any interference. In this article, an unsupervised automatic method for brain tumor segmentation on MRI images is presented. In this method, at first in the pre-processing level, the extra parts which are outside the skull and don't have any help…
Partial Information Decomposition as a Multi-Contrast 3D MRI Selection Strategy for Resource-Constrained Deep Neural Network Training in Brain Tumor Segmentation
Beijing-Dublin International College（北京-都柏林国际学院）；University College Dublin（都柏林大学）
This technical report presents a comparative analysis of existing deep learning (DL) based approaches for brain tumor segmentation with missing MRI modalities. Approaches evaluated include the Adversarial Co-training Network (ACN) and a combination of mmGAN and DeepMedic. A more stable and easy-to-use version of mmGAN is also open-sourced at a GitHub repository. Using the BraTS2018 dataset, this work demonstrates that the state-of-the-art ACN performs better especially when T1c is missing. While a simple combination of mmGAN and DeepMedic also shows strong potentials when only one MRI modality…
Technical University of Munich（慕尼黑工业大学）；LMU Hospital Grosshadern（路德维希-马克西米利安-慕尼黑大学格罗斯哈德恩医院）
Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input …
School of Computer Science, University of Lincoln（林肯大学计算机科学学院）；National Heart & Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）
In this paper, we propose a novel learning based method for automated segmentation of brain tumor in multimodal MRI images, which incorporates two sets of machine -learned and hand crafted features. Fully convolutional networks (FCN) forms the machine learned features and texton based features are considered as hand-crafted features. Random forest (RF) is used to classify the MRI image voxels into normal brain tissues and different parts of tumors, i.e. edema, necrosis and enhancing tumor. The method was evaluated on BRATS 2017 challenge dataset. The results show that the proposed method provi…
Massachusetts General Hospital（麻省总医院）；Harvard University（哈佛大学）；General Electric Healthcare（通用电气医疗集团）；Indian Institute of Science（印度科学学院）
Gliomas are one of the most frequent brain tumors and are classified into high grade and low grade gliomas. The segmentation of various regions such as tumor core, enhancing tumor etc. plays an important role in determining severity and prognosis. Here, we have developed a multi-threshold model based on attention U-Net for identification of various regions of the tumor in magnetic resonance imaging (MRI). We propose a multi-path segmentation and built three separate models for the different regions of interest. The proposed model achieved mean Dice Coefficient of 0.59, 0.72, and 0.61 for enhan…
In this paper, we propose a novel learning based method for automated segmenta-tion of brain tumor in multimodal MRI images. The machine learned features from fully convolutional neural network (FCN) and hand-designed texton fea-tures are used to classify the MRI image voxels. The score map with pixel-wise predictions is used as a feature map which is learned from multimodal MRI train-ing dataset using the FCN. The learned features are then applied to random for-ests to classify each MRI image voxel into normal brain tissues and different parts of tumor. The method was evaluated on BRATS 2013 …
Medical Resonance Imaging or MRI is a medical image processing technique that used radio waves to scan the body. It is a tomographic imaging technique, principally used in the field of radiology. With the advantage of being a painless diagnostic procedure, MRI allows medical personnel to illustrate clear pictures of the anatomy and the physiological processes occurring in the body, thus allowing early detection and treatment of diseases. These images, combined with image processing techniques may be used in the detection of tumors, difficult to identify with the naked eye. This digital assignm…
Shandong Normal University（山东师范大学）；Western University（韦仕敦大学）
Simultaneous segmentation and detection of liver tumors (hemangioma and hepatocellular carcinoma (HCC)) by using multi-modality non-contrast magnetic resonance imaging (NCMRI) are crucial for the clinical diagnosis. However, it is still a challenging task due to: (1) the HCC information on NCMRI is invisible or insufficient makes extraction of liver tumors feature difficult; (2) diverse imaging characteristics in multi-modality NCMRI causes feature fusion and selection difficult; (3) no specific information between hemangioma and HCC on NCMRI cause liver tumors detection difficult. In this stu…
One of the most important tasks in medical image processing is the brain's whole tumor segmentation. It assists in quicker clinical assessment and early detection of brain tumors, which is crucial for lifesaving treatment procedures of patients. Because, brain tumors often can be malignant or benign, if they are detected at an early stage. A brain tumor is a collection or a mass of abnormal cells in the brain. The human skull encloses the brain very rigidly and any growth inside this restricted place can cause severe health issues. The detection of brain tumors requires careful and intricate a…
Vingroup Big Data Institute (VinBigdata)（越南 VinBigdata 大数据研究院）；Hanoi University of Science and Technology (HUST)（河内科技大学）；University of Engineering and Technology (UET), VNU（越南国立大学工程技术大学）
Brain tumor segmentation plays an essential role in medical image analysis. In recent studies, deep convolution neural networks (DCNNs) are extremely powerful to tackle tumor segmentation tasks. We propose in this paper a novel training method that enhances the segmentation results by adding an additional classification branch to the network. The whole network was trained end-to-end on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 training dataset. On the BraTS's validation set, it achieved an average Dice score of 78.43%, 89.99%, and 84.22% respectively for the enhancing tumo…
Convolutional neural networks (CNNs) have achieved remarkable success in automatically segmenting organs or lesions on 3D medical images. Recently, vision transformer networks have exhibited exceptional performance in 2D image classification tasks. Compared with CNNs, transformer networks have an appealing advantage of extracting long-range features due to their self-attention algorithm. Therefore, we propose a CNN-Transformer combined model, called BiTr-Unet, with specific modifications for brain tumor segmentation on multi-modal MRI scans. Our BiTr-Unet achieves good performance on the BraTS…
Segmentation of images holds an important position in the area of image processing. It becomes more important whi le typically dealing with medical images where presurgery and post surgery decisions are required for the purpose of initiating and speeding up the recovery process. Segmentation of 3-D tumor structures from magnetic resonance images (MRI) is a very challenging problem due to the variability of tumor geometry and intensity patterns. Level set evolution combining global smoothness with the flexibility of topology changes offers significant advantages over the conventional statistica…
Treatment-aware Diffusion Probabilistic Model for Longitudinal MRI Generation and Diffuse Glioma Growth Prediction
Oslo University Hospital（奥斯陆大学医院）；Universitat Politècnica de València（瓦伦西亚理工大学）；Instituto Universitario de Tecnologías de la Información y Comunicaciones（信息技术与通信大学学院）
Concordia Institute for Information Systems Engineering, Concordia University（康考迪亚大学康考迪亚信息系统工程研究所）；University of Toronto（多伦多大学）
According to official statistics, cancer is considered as the second leading cause of human fatalities. Among different types of cancer, brain tumor is seen as one of the deadliest forms due to its aggressive nature, heterogeneous characteristics, and low relative survival rate. Determining the type of brain tumor has significant impact on the treatment choice and patient's survival. Human-centered diagnosis is typically error-prone and unreliable resulting in a recent surge of interest to automatize this process using convolutional neural networks (CNNs). CNNs, however, fail to fully utilize …
University College Dublin（都柏林大学学院）；Université Paris-Est Créteil Val de Marne - Université Paris 12（巴黎东-马恩拉瓦莱大学（巴黎第十二大学））；ADAPT SFI Research Centre（ADAPT SFI研究中心）
Magnetic Resonance Imaging (MRI) is the most commonly used non-intrusive technique for medical image acquisition. Brain tumor segmentation is the process of algorithmically identifying tumors in brain MRI scans. While many approaches have been proposed in the literature for brain tumor segmentation, this paper proposes a lightweight implementation of U-Net. Apart from providing real-time segmentation of MRI scans, the proposed architecture does not need large amount of data to train the proposed lightweight U-Net. Moreover, no additional data augmentation step is required. The lightweight U-Ne…
Exploiting Test-Time Augmentation in Federated Learning for Brain Tumor MRI Classification
Institute of Exact and Technological Sciences, Federal University of Viçosa - UFV, Rio Paranaíba-MG, Brazil（精确与技术科学研究所，弗拉维亚联邦大学-UFV，里奥帕拉纳伊巴-MG，巴西）；Department of Computing, Federal University of São Carlos, São Carlos-SP, Brazil（计算系，萨o卡洛斯联邦大学，萨o卡洛斯-SP，巴西）
Automatic image segmentation becomes very crucial for tumor detection in medical image processing.In general, manual and semi automatic segmentation techniques require more time and knowledge. However these drawbacks had overcome by automatic segmentation still there needs to develop more appropriate techniques for medical image segmentation. Therefore, we proposed hybrid approach based image segmentation using the combined features of region growing and threshold based segmentation techniques. It is followed by pre-processing stage to provide an accurate brain tumor extraction by the help of …
Brain Tumor Classification from MRI Scans via Transfer Learning and Enhanced Feature Representation
Department of CSE, Netrokona University（计算机科学与工程系，Netrokona大学）；Department of CSE, The University of Rajshahi（计算机科学与工程系，拉贾沙希大学）；Department of Information Technology, Allen E. Paulson College of Engineering and Computing, Georgia Southern University（信息技术系，乔治亚南方大学）；Centre for Image and Vision Computing (CIVC), COE for Artificial Intelligence, Faculty of Artificial Intelligence and Engineering (FAIE), Multimedia University（图像与视觉计算中心（CIVC），人工智能学院，人工智能与工程学院，多媒体大学）
This paper presents an efficient architecture for various image filtering algorithms and tumor characterization using Xilinx System Generator (XSG). This architecture offers an alternative through a graphical user interface that combines MATLAB, Simulink and XSG and explores important aspects concerned to hardware implementation. Performance of this architecture implemented in SPARTAN-3E Starter kit (XC3S500E-FG320) exceeds those of similar or greater resources architectures. The proposed architecture reduces the resources available on target device by 50%.
Tumor Location-weighted MRI-Report Contrastive Learning: A Framework for Improving the Explainability of Pediatric Brain Tumor Diagnosis
The Hospital for Sick Children（病童医院）；University of Toronto（多伦多大学）；Vector Institute for Artificial Intelligence（矢量人工智能研究所）；University Hospital Augsburg（奥格斯堡大学医院）
TumorFlow: Physics-Guided Longitudinal MRI Synthesis of Glioblastoma Growth
Technical University of Munich (TUM), Germany（慕尼黑技术大学（TUM））；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心）；AI for Image-Guided Diagnosis and Therapy（图像引导诊断与治疗的AI）；Chair for AI in Healthcare and Medicine, TUM and TUM University Hospital, Munich, Germany（医疗与医学中的AI主任，慕尼黑技术大学及慕尼黑大学医院）
Segmenting a MRI images into homogeneous texture regions representing disparate tissue types is often a useful preprocessing step in the computer-assisted detection of breast cancer. That is why we proposed new algorithm to detect cancer in mammogram breast cancer images. In this paper we proposed segmentation using vector quantization technique. Here we used Linde Buzo-Gray algorithm (LBG) for segmentation of MRI images. Initially a codebook of size 128 was generated for MRI images. These code vectors were further clustered in 8 clusters using same LBG algorithm. These 8 images were displayed…
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…
University of North Carolina at Charlotte（北卡罗来纳大学夏洛特分校）；University of Science and Technology Beijing（北京科技大学）；Scoop Medical
Brain tumor segmentation plays a pivotal role in medical image processing. In this work, we aim to segment brain MRI volumes. 3D convolution neural networks (CNN) such as 3D U-Net and V-Net employing 3D convolutions to capture the correlation between adjacent slices have achieved impressive segmentation results. However, these 3D CNN architectures come with high computational overheads due to multiple layers of 3D convolutions, which may make these models prohibitive for practical large-scale applications. To this end, we propose a highly efficient 3D CNN to achieve real-time dense volumetric …
The most common primary brain tumors are gliomas, evolving from the cerebral supportive cells. For clinical follow-up, the evaluation of the preoperative tumor volume is essential. Volumetric assessment of tumor volume with manual segmentation of its outlines is a time-consuming process that can be overcome with the help of computerized segmentation methods. In this contribution, two methods for World Health Organization (WHO) grade IV glioma segmentation in the human brain are compared using magnetic resonance imaging (MRI) patient data from the clinical routine. One method uses balloon infla…
