Using U-Net Network for Efficient Brain Tumor Segmentation in MRI Images
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）
Jason Walsh, Alice Othmani, Mayank Jain, Soumyabrata Dev
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-Net shows very promising results on BITE dataset and it achieves a mean intersection-over-union (IoU) of 89% while outperforming the standard benchmark algorithms. Additionally, this work demonstrates an effective use of the three perspective planes, instead of the original three-dimensional volumetric images, for simplified brain tumor segmentation.
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…
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）
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…
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）
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…
Objective: Magnetic resonance imaging (MRI) has been widely used for the analysis and diagnosis of brain diseases. Accurate and automatic brain tumor segmentation is of paramount importance for radiation treatment. However, low tissue contrast in tumor regions makes it a challenging task.Approach: We propose a novel segmentation network named Category Guided Attention U-Net (CGA U-Net). In this model, we design a Supervised Attention Module (SAM) based on the attention mechanism, which can capture more accurate and stable long-range dependency in feature maps without introducing much computati…
Mohamed Bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Glioblastoma is a common brain malignancy that tends to occur in older adults and is almost always lethal. The effectiveness of chemotherapy, being the standard treatment for most cancer types, can be improved if a particular genetic sequence in the tumor known as MGMT promoter is methylated. However, to identify the state of the MGMT promoter, the conventional approach is to perform a biopsy for genetic analysis, which is time and effort consuming. A couple of recent publications proposed a connection between the MGMT promoter state and the MRI scans of the tumor and hence suggested the use o…
Isfahan University of Technology（伊斯法罕理工大学）；Seattle University（西雅图大学）；McMaster University（麦克马斯特大学）
According to the World Health Organization (WHO), cancer is the second leading cause of death worldwide, responsible for over 9.5 million deaths in 2018 alone. Brain tumors count for one out of every four cancer deaths. Therefore, accurate and timely diagnosis of brain tumors will lead to more effective treatments. Physicians classify brain tumors only with biopsy operation by brain surgery, and after diagnosing the type of tumor, a treatment plan is considered for the patient. Automatic systems based on machine learning algorithms can allow physicians to diagnose brain tumors with noninvasive…
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 …
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…
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…
Indian Statistical Institute（印度统计研究所）；University of Calcutta（加尔各答大学）；University of Genova（热那亚大学）
Glioma constitutes 80% of malignant primary brain tumors and is usually classified as HGG and LGG. The LGG tumors are less aggressive, with slower growth rate as compared to HGG, and are responsive to therapy. Tumor biopsy being challenging for brain tumor patients, noninvasive imaging techniques like Magnetic Resonance Imaging (MRI) have been extensively employed in diagnosing brain tumors. Therefore automated systems for the detection and prediction of the grade of tumors based on MRI data becomes necessary for assisting doctors in the framework of augmented intelligence. In this paper, we t…
University of Electronic Science and Technology of China（电子科技大学）；New Jersey Institute of Technology（新泽西理工学院）
Past few years have witnessed the prevalence of deep learning in many application scenarios, among which is medical image processing. Diagnosis and treatment of brain tumors requires an accurate and reliable segmentation of brain tumors as a prerequisite. However, such work conventionally requires brain surgeons significant amount of time. Computer vision techniques could provide surgeons a relief from the tedious marking procedure. In this paper, a 3D U-net based deep learning model has been trained with the help of brain-wise normalization and patching strategies for the brain tumor segmenta…
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…
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…
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…
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…
Glioma is a common type of brain tumor, and accurate detection of it plays a vital role in the diagnosis and treatment process. Despite advances in medical image analyzing, accurate tumor segmentation in brain magnetic resonance (MR) images remains a challenge due to variations in tumor texture, position, and shape. In this paper, we propose a fast, automated method, with light computational complexity, to find the smallest bounding box around the tumor region. This region-of-interest can be used as a preprocessing step in training networks for subregion tumor segmentation. By adopting the out…
The Segment Anything foundation model achieves favorable brain tumor autosegmentation accuracy on MRI to support radiotherapy treatment planning
Universitätsklinikum Erlangen（埃尔兰根大学医院）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希·亚历山大大学）；Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN)（埃尔兰根-欧洲分子神经科学网络综合癌症中心）
BrainNormalizer: Anatomy-Informed Pseudo-Healthy Brain Reconstruction from Tumor MRI via Edge-Guided ControlNet
University of Pittsburgh（匹兹堡大学）；Georgia Institute of Technology（佐治亚理工学院）；University of Texas at Austin（德克萨斯大学奥斯汀分校）；Cedars-Sinai Medical Center（西德萨斯医疗中心）；Mayo Clinic Arizona（梅奥诊所亚利桑那分部）
Glioma Multimodal MRI Analysis System for Tumor Layered Diagnosis via Multi-task Semi-supervised Learning
Cancer Research Institute, Central South University（中南大学肿瘤研究所）；School of Physics & Electronic Science, Changsha University of Science & Technology（长沙理工大学物理与电子科学学院）；IFLYTEK Research（iFlytek研究院）；School of Life Sciences, Central South University（中南大学生命科学学院）；Department of Radiology, Xiangya Hospital, Central South University（中南大学湘雅医院放射科）；School of Computer Science and Engineering, Central South University（中南大学计算机科学与工程学院）；Department of Neurosurgery, Xiangya Hospital, Central South University（中南大学湘雅医院神经外科）
The Institute of Medical Robotics, Shanghai Jiao Tong University（上海交通大学医疗机器人研究所）；The Hamlyn Centre for Robotic Surgery, Imperial College London（帝国理工学院哈姆林机器人手术中心）；Queen Mary University of London（伦敦玛丽女王大学）；Hangzhou Dianzi University（杭州电子科技大学）
Segmentation of brain tumors and their subregions remains a challenging task due to their weak features and deformable shapes. In this paper, three patterns (cross-skip, skip-1 and skip-2) of distributed dense connections (DDCs) are proposed to enhance feature reuse and propagation of CNNs by constructing tunnels between key layers of the network. For better detecting and segmenting brain tumors from multi-modal 3D MR images, CNN-based models embedded with DDCs (DDU-Nets) are trained efficiently from pixel to pixel with a limited number of parameters. Postprocessing is then applied to refine t…
Pakistan Institute of Engineering and Applied Sciences（巴基斯坦工程与应用科学学院）
Brain tumors analysis is important in timely diagnosis and effective treatment to cure patients. Tumor analysis is challenging because of tumor morphology like size, location, texture, and heteromorphic appearance in the medical images. In this regard, a novel two-phase deep learning-based framework is proposed to detect and categorize brain tumors in magnetic resonance images (MRIs). In the first phase, a novel deep boosted features and ensemble classifiers (DBF-EC) scheme is proposed to detect tumor MRI images from healthy individuals effectively. The deep boosted feature space is achieved t…
Comparative Evaluation of Transfer Learning for Classification of Brain Tumor Using MRI
Florida Institute of Technology（佛罗里达理工学院）；Daffodil International University（达福德国际大学）；University of North Texas（北德克萨斯大学）；The University of Alabama at Birmingham（阿拉巴马大学伯明翰分校）
Pakistan Institute of Engineering and Applied Sciences (PIEAS)（巴基斯坦工程与应用科学学院）；Ibadat International University（伊巴达特国际大学）；University of Engineering and Applied Science (UEAS)（工程与应用科学大学）
Brain tumor classification is crucial for clinical analysis and an effective treatment plan to cure patients. Deep learning models help radiologists to accurately and efficiently analyze tumors without manual intervention. However, brain tumor analysis is challenging because of its complex structure, texture, size, location, and appearance. Therefore, a novel deep residual and regional-based Res-BRNet Convolutional Neural Network (CNN) is developed for effective brain tumor (Magnetic Resonance Imaging) MRI classification. The developed Res-BRNet employed Regional and boundary-based operations …
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…
University of Hyogo（兵库大学）；Vanderbilt University（范德堡大学）；BRAC University（BRAC大学）
Diagnosing Brain Tumor with the aid of Magnetic Resonance Imaging (MRI) has gained enormous prominence over the years, primarily in the field of medical science. Detection and/or partitioning of brain tumors solely with the aid of MR imaging is achieved at the cost of immense time and effort and demands a lot of expertise from engaged personnel. This substantiates the necessity of fabricating an autonomous model brain tumor diagnosis. Our work involves implementing a deep convolutional neural network (DCNN) for diagnosing brain tumors from MR images. The dataset used in this paper consists of …
We explore encoding brain symmetry into a neural network for a brain tumor segmentation task. A healthy human brain is symmetric at a high level of abstraction, and the high-level asymmetric parts are more likely to be tumor regions. Paying more attention to asymmetries has the potential to boost the performance in brain tumor segmentation. We propose a method to encode brain symmetry into existing neural networks and apply the method to a state-of-the-art neural network for medical imaging segmentation. We evaluate our symmetry-encoded network on the dataset from a brain tumor segmentation ch…
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…
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…
Polytechnique Montreal（蒙特利尔理工学院）；Mila, Quebec AI Institute（米拉魁北克人工智能研究所）；Beijing Tiantan Hospital, Capital Medical University（首都医科大学附属北京天坛医院）；Université de Montréal（蒙特利尔大学）
Spinal cord tumors lead to neurological morbidity and mortality. Being able to obtain morphometric quantification (size, location, growth rate) of the tumor, edema, and cavity can result in improved monitoring and treatment planning. Such quantification requires the segmentation of these structures into three separate classes. However, manual segmentation of 3-dimensional structures is time-consuming and tedious, motivating the development of automated methods. Here, we tailor a model adapted to the spinal cord tumor segmentation task. Data were obtained from 343 patients using gadolinium-enha…
National University of Computer and Emerging Sciences（国立计算机与新兴科学大学）；MD ANDERSON Cancer Center, The University of Texas（德克萨斯大学MD安德森癌症中心）；Hamad Bin Khalifa University（哈马德·本·哈利法大学）
Generative models have been very successful over the years and have received significant attention for synthetic data generation. As deep learning models are getting more and more complex, they require large amounts of data to perform accurately. In medical image analysis, such generative models play a crucial role as the available data is limited due to challenges related to data privacy, lack of data diversity, or uneven data distributions. In this paper, we present a method to generate brain tumor MRI images using generative adversarial networks. We have utilized StyleGAN2 with ADA methodol…
Brain tumor segmentation is a challenging problem in medical image analysis. The endpoint is to generate the salient masks that accurately identify brain tumor regions in an fMRI screening. In this paper, we propose a novel attention gate (AG model) for brain tumor segmentation that utilizes both the edge detecting unit and the attention gated network to highlight and segment the salient regions from fMRI images. This feature enables us to eliminate the necessity of having to explicitly point towards the damaged area(external tissue localization) and classify(classification) as per classical c…
Hybrid Multihead Attentive Unet-3D for Brain Tumor Segmentation
University of Engineering and Technology, Lahore（拉合尔工程技术大学）；School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology（国家科技大学跨学科工程与科学学院）
Brain Tumor Classification in MRI Images: A Computationally Efficient Convolutional Neural Network
Department of Computer Science and Engineering, University of North Texas, USA（北卡罗来纳州立大学计算机科学与工程系）；Department of Electrical and Electronic Engineering, International Islamic University Chittagong, Bangladesh（伊斯兰国际大学查塔格昂分校电子与电气工程系）
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%.
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, …
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…
