Brain tumors are one of the deadliest forms of cancer with a mortality rate of over 80%. A quick and accurate diagnosis is crucial to increase the chance of survival. However, in medical analysis, the manual annotation and segmentation of a brain tumor can be a complicated task. Multiple MRI modalities are typically analyzed as they provide unique information regarding the tumor regions. Although these MRI modalities are helpful for segmenting gliomas, they tend to increase overfitting and computation. This paper proposes a region of interest detection algorithm that is implemented during data preprocessing to locate salient features and remove extraneous MRI data. This decreases the input size, allowing for more aggressive data augmentations and deeper neural networks. Following the preprocessing of the MRI modalities, a fully convolutional autoencoder with soft attention segments the different brain MRIs. When these deep learning algorithms are implemented in practice, analysts and physicians cannot differentiate between accurate and inaccurate predictions. Subsequently, test time augmentations and an energy-based model were used for voxel-based uncertainty predictions. Experimentation was conducted on the BraTS benchmarks and achieved state-of-the-art segmentation performance. Additionally, qualitative results were used to assess the segmentation models and uncertainty predictions.
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, …
Hierarchical Generalized Category Discovery for Brain Tumor Classification in Digital Pathology
Institute of Clinical Epidemiology, Public Health, Health Economics, Medical Statistics and Informatics(临床流行病学、公共卫生、健康经济学、医学统计与信息学研究所);Institute of Neuropathology and Neuromolecular Pathology(神经病理学与神经分子病理学研究所)
Detection and segmentation of Brain tumor is very important because it provides anatomical information of normal and abnormal tissues which helps in treatment planning and patient follow-up. There are number of techniques for image segmentation. Proposed research work uses ANFIS (Artificial Neural Network Fuzzy Inference System) for image classification and then compares the results with FCM (Fuzzy C means) and K-NN (K-nearest neighbor). ANFIS includes benefits of both ANN and the fuzzy logic systems. A comprehensive feature set and fuzzy rules are selected to classify an abnormal image to the…
Automated brain tumor detection in MRI images using CNN and ResNet architectures
Department of Computer Science and Engineering, The National Institute of Engineering, Mysuru, Karnataka, India(计算机科学与工程系,国家工程学院,mysuru,卡纳塔克邦,印度);Department of MCA, The National Institute of Engineering, Mysuru, Karnataka, India(MCA系,国家工程学院,mysuru,卡纳塔克邦,印度);Department of Computer Science and Engineering, Vidyavardhaka College of Engineering, Mysuru, Karnataka, India(计算机科学与工程系,维迪瓦尔达卡学院,mysuru,卡纳塔克邦,印度);Department of ECE, Vidyavardhaka College of Engineering, Mysuru, Karnataka, India(电子工程系,维迪瓦尔达卡学院,mysuru,卡纳塔克邦,印度)
Deep learning methods for brain tumor segmentation are typically trained in an ad hoc fashion on all available data. Brain tumors are tremendously heterogeneous in image appearance and labeled training data is limited. We argue that incorporation of additional prior information, specifically tumor grade, associated with tumor imaging phenotypes during model training can significantly improve segmentation performance. Two strategies for incorporation of tumor grade during model training are proposed and their impact on segmentation performance is demonstrated on the BRATS 2018 dataset.
Non-invasive techniques such as magnetic resonance imaging (MRI) are widely employed in brain tumor diagnostics. However, manual segmentation of brain tumors from 3D MRI volumes is a time-consuming task that requires trained expert radiologists. Due to the subjectivity of manual segmentation, there is low inter-rater reliability which can result in diagnostic discrepancies. As the success of many brain tumor treatments depends on early intervention, early detection is paramount. In this context, a fully automated segmentation method for brain tumor segmentation is necessary as an efficient and…
School of Biomedical Engineering(生物医学工程学院);Universidad Autónoma de Ciudad Juárez(华雷斯自治大学)
The brain is a complex organ controlling cognitive process and physical functions. Tumors in the brain are accelerated cell growths affecting the normal function and processes in the brain. MRI scans provides detailed images of the body being one of the most common tests to diagnose brain tumors. The process of segmentation of brain tumors from magnetic resonance imaging can provide a valuable guide for diagnosis, treatment planning and prediction of results. Here we consider the problem brain tumor segmentation using a Deep learning architecture for use in tumor segmentation. Although the pro…
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…
Shanghai United Imaging Intelligence Co. Ltd(上海联影智能医疗科技有限公司);Southern Medical University(南方医科大学)
In brain tumor diagnosis and surgical planning, segmentation of tumor regions and accurate analysis of surrounding normal tissues are necessary for physicians. Pathological variability often renders difficulty to register a well-labeled normal atlas to such images and to automatic segment/label surrounding normal brain tissues. In this paper, we propose a new registration approach that first segments brain tumor using a U-Net and then simulates missed normal tissues within the tumor region using a partial convolutional network. Then, a standard normal brain atlas image is registered onto such …
Brain tumor segmentation intends to delineate tumor tissues from healthy brain tissues. The tumor tissues include necrosis, peritumoral edema, and active tumor. In contrast, healthy brain tissues include white matter, gray matter, and cerebrospinal fluid. The MRI based brain tumor segmentation research is gaining popularity as; 1. It does not irradiate ionized radiation like X-ray or computed tomography imaging. 2. It produces detailed pictures of internal body structures. The MRI scans are input to deep learning-based approaches which are useful for automatic brain tumor segmentation. The fea…
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…
Beihang University(北京航空航天大学);Massachusetts General Hospital, Harvard Medical School(哈佛医学院麻省总医院);Shanghai Jiao Tong University(上海交通大学);Ruijin Hospital, Shanghai Jiao Tong University School of Medicine(上海交通大学医学院附属瑞金医院)
In the clinical diagnosis and treatment of brain tumors, manual image reading consumes a lot of energy and time. In recent years, the automatic tumor classification technology based on deep learning has entered people's field of vision. Brain tumors can be divided into primary and secondary intracranial tumors according to their source. However, to our best knowledge, most existing research on brain tumors are limited to primary intracranial tumor images and cannot classify the source of the tumor. In order to solve the task of tumor source type classification, we analyze the existing technolo…
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)
Brain tumor analysis in MRI images is a significant and challenging issue because misdiagnosis can lead to death. Diagnosis and evaluation of brain tumors in the early stages increase the probability of successful treatment. However, the complexity and variety of tumors, shapes, and locations make their segmentation and classification complex. In this regard, numerous researchers have proposed brain tumor segmentation and classification methods. This paper presents an approach that simultaneously segments and classifies brain tumors in MRI images using a framework that contains MRI image enhan…
The brain tumor is the most aggressive kind of tumor and can cause low life expectancy if diagnosed at the later stages. Manual identification of brain tumors is tedious and prone to errors. Misdiagnosis can lead to false treatment and thus reduce the chances of survival for the patient. Medical resonance imaging (MRI) is the conventional method used to diagnose brain tumors and their types. This paper attempts to eliminate the manual process from the diagnosis process and use machine learning instead. We proposed the use of pretrained convolutional neural networks (CNN) for the diagnosis and …
Rowan University(罗文大学);University of Alabama at Birmingham(阿拉巴马大学伯明翰分校)
Magnetic resonance imaging (MRI) is routinely used for brain tumor diagnosis, treatment planning, and post-treatment surveillance. Recently, various models based on deep neural networks have been proposed for the pixel-level segmentation of tumors in brain MRIs. However, the structural variations, spatial dissimilarities, and intensity inhomogeneity in MRIs make segmentation a challenging task. We propose a new end-to-end brain tumor segmentation architecture based on U-Net that integrates Inception modules and dilated convolutions into its contracting and expanding paths. This allows us to ex…
Gliomas are among the most aggressive and deadly brain tumors. This paper details the proposed Deep Neural Network architecture for brain tumor segmentation from Magnetic Resonance Images. The architecture consists of a cascade of three Deep Layer Aggregation neural networks, where each stage elaborates the response using the feature maps and the probabilities of the previous stage, and the MRI channels as inputs. The neuroimaging data are part of the publicly available Brain Tumor Segmentation (BraTS) 2020 challenge dataset, where we evaluated our proposal in the BraTS 2020 Validation and Tes…
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…
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…
University of Isfahan(伊斯法罕大学);Geneva University Hospital(日内瓦大学医院)
Brain tumor segmentation is highly contributive in diagnosing and treatment planning. The manual brain tumor delineation is a time-consuming and tedious task and varies depending on the radiologists skill. Automated brain tumor segmentation is of high importance, and does not depend on either inter or intra-observation. The objective of this study is to automate the delineation of brain tumors from the FLAIR, T1 weighted, T2 weighted, and T1 weighted contrast-enhanced MR sequences through a deep learning approach, with a focus on determining which MR sequence alone or which combination thereof…
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…
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…
Shenzhen University(深圳大学);Huazhong University of Science and Technology(华中科技大学)
The brain tumor segmentation task aims to classify tissue into the whole tumor (WT), tumor core (TC), and enhancing tumor (ET) classes using multimodel MRI images. Quantitative analysis of brain tumors is critical for clinical decision making. While manual segmentation is tedious, time-consuming, and subjective, this task is at the same time very challenging to automatic segmentation methods. Thanks to the powerful learning ability, convolutional neural networks (CNNs), mainly fully convolutional networks, have shown promising brain tumor segmentation. This paper further boosts the performance…
University of Leicester(莱斯特大学);University of Lancaster(兰卡斯特大学);Queen Mary, University of London(伦敦大学玛丽女王学院);Xidian University(西安电子科技大学);Bielefeld University(比勒费尔德大学)
Brain tumor segmentation is one of the most challenging problems in medical image analysis. The goal of brain tumor segmentation is to generate accurate delineation of brain tumor regions. In recent years, deep learning methods have shown promising performance in solving various computer vision problems, such as image classification, object detection and semantic segmentation. A number of deep learning based methods have been applied to brain tumor segmentation and achieved promising results. Considering the remarkable breakthroughs made by state-of-the-art technologies, we use this survey to …
In the past few years, deep learning (DL) models have drawn great attention and shown superior performance on brain tumor and subregion segmentation tasks. However, the success is limited to segmentation of adult gliomas, where sufficient data have been collected, manually labeled, and published for training DL models. It is still challenging to segment pediatric tumors, because the appearances are different from adult gliomas. Hence, directly applying a pretained DL model on pediatric data usually generates unacceptable results. Because pediatric data is very limited, both labeled and unlabel…
Kavli Institute for Systems Neuroscience, NTNU(挪威科技大学卡弗里系统神经科学研究所)
Early diagnosis and accurate segmentation of brain tumors are imperative for successful treatment. Unfortunately, manual segmentation is time consuming, costly and despite extensive human expertise often inaccurate. Here, we present an MRI-based tumor segmentation framework using an autoencoder-regularized 3D-convolutional neural network. We trained the model on manually segmented structural T1, T1ce, T2, and Flair MRI images of 335 patients with tumors of variable severity, size and location. We then tested the model using independent data of 125 patients and successfully segmented brain tumo…
In this paper, a convolutional neural network (CNN) was used to classify NMR images of human brains with 4 different types of tumors: meningioma, glioma and pituitary gland tumors. During the training phase of this project, an accuracy of 100% was obtained, meanwhile, in the evaluation phase the precision was 96%.
Shenzhen University(深圳大学);Islamic Azad University(伊斯兰阿扎德大学)
The magnetic resonance (MR) analysis of brain tumors is widely used for diagnosis and examination of tumor subregions. The overlapping area among the intensity distribution of healthy, enhancing, non-enhancing, and edema regions makes the automatic segmentation a challenging task. Here, we show that a convolutional neural network trained on high-contrast images can transform the intensity distribution of brain lesions in its internal subregions. Specifically, a generative adversarial network (GAN) is extended to synthesize high-contrast images. A comparison of these synthetic images and real i…
School of Computer Science and Technology, Harbin Institute of Technology(哈尔滨工业大学计算机科学与技术学院)
Automatic brain tumor segmentation method plays an extremely important role in the whole process of brain tumor diagnosis and treatment. In this paper, we propose a multi-step cascaded network which takes the hierarchical topology of the brain tumor substructures into consideration and segments the substructures from coarse to fine .During segmentation, the result of the former step is utilized as the prior information for the next step to guide the finer segmentation process. The whole network is trained in an end-to-end fashion. Besides, to alleviate the gradient vanishing issue and reduce o…
College of Physics and Information Engineering, Fuzhou University(福州大学物理与信息工程学院);School of Data Science, Fudan University(复旦大学数据科学学院);School of Biomedical Engineering, Shanghai Jiao Tong University(上海交通大学生物医学工程学院);School of Biomedical Engineering and Imaging Sciences, King’s College London(伦敦国王学院生物医学工程与成像科学学院)
Delineating the brain tumor from magnetic resonance (MR) images is critical for the treatment of gliomas. However, automatic delineation is challenging due to the complex appearance and ambiguous outlines of tumors. Considering that multi-modal MR images can reflect different tumor biological properties, we develop a novel multi-modal tumor segmentation network (MMTSN) to robustly segment brain tumors based on multi-modal MR images. The MMTSN is composed of three sub-branches and a main branch. Specifically, the sub-branches are used to capture different tumor features from multi-modal images,…
Today, over 700,000 people are living with brain tumors in the United States. Brain tumors can spread very quickly to other parts of the brain and the spinal cord unless necessary preventive action is taken. Thus, the survival rate for this disease is less than 40% for both men and women. A conclusive and early diagnosis of a brain tumor could be the difference between life and death for some. However, brain tumor detection and segmentation are tedious and time-consuming processes as it can only be done by radiologists and clinical experts. The use of computer vision techniques, such as Mask R…
Brain tumor segmentation from Magnetic Resonance Images (MRIs) is an important task to measure tumor responses to treatments. However, automatic segmentation is very challenging. This paper presents an automatic brain tumor segmentation method based on a Normalized Gaussian Bayesian classification and a new 3D Fluid Vector Flow (FVF) algorithm. In our method, a Normalized Gaussian Mixture Model (NGMM) is proposed and used to model the healthy brain tissues. Gaussian Bayesian Classifier is exploited to acquire a Gaussian Bayesian Brain Map (GBBM) from the test brain MR images. GBBM is further p…
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…
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 …
Federal University of Santa Catarina(圣卡塔琳娜联邦大学);Santa Luzia Hospital(圣卢西亚医院)
State-of-the-art brain tumor segmentation is based on deep learning models applied to multi-modal MRIs. Currently, these models are trained on images after a preprocessing stage that involves registration, interpolation, brain extraction (BE, also known as skull-stripping) and manual correction by an expert. However, for clinical practice, this last step is tedious and time-consuming and, therefore, not always feasible, resulting in skull-stripping faults that can negatively impact the tumor segmentation quality. Still, the extent of this impact has never been measured for any of the many diff…
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…
Research & Development Institute of Northwestern Polytechnical University in Shenzhen(西北工业大学深圳研究院);Northwestern Polytechnical University(西北工业大学);University of Pittsburgh(匹兹堡大学);University of Sydney(悉尼大学);JD Finance America Corporation(京东金融美国公司)
In this paper, we propose a Hybrid High-resolution and Non-local Feature Network (H2NF-Net) to segment brain tumor in multimodal MR images. Our H2NF-Net uses the single and cascaded HNF-Nets to segment different brain tumor sub-regions and combines the predictions together as the final segmentation. We trained and evaluated our model on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 dataset. The results on the test set show that the combination of the single and cascaded models achieved average Dice scores of 0.78751, 0.91290, and 0.85461, as well as Hausdorff distances ($95\%$…
Intracranial tumors are groups of cells that usually grow uncontrollably. One out of four cancer deaths is due to brain tumors. Early detection and evaluation of brain tumors is an essential preventive medical step that is performed by magnetic resonance imaging (MRI). Many segmentation techniques exist for this purpose. Low segmentation accuracy is the main drawback of existing methods. In this paper, we use a deep learning method to boost the accuracy of tumor segmentation in MR images. Cascade approach is used with multiple scales of images to induce both local and global views and help the…
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…
Recently deep learning has been playing a major role in the field of computer vision. One of its applications is the reduction of human judgment in the diagnosis of diseases. Especially, brain tumor diagnosis requires high accuracy, where minute errors in judgment may lead to disaster. For this reason, brain tumor segmentation is an important challenge for medical purposes. Currently several methods exist for tumor segmentation but they all lack high accuracy. Here we present a solution for brain tumor segmenting by using deep learning. In this work, we studied different angles of brain MR ima…
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)
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…
Chittagong University of Engineering and Technology(吉大港工程技术大学)
In recent advancement towards computer based diagnostics system, the classification of brain tumor images is a challenging task. This paper mainly focuses on elevating the classification accuracy of brain tumor images with transfer learning based deep neural network. The classification approach is started with the image augmentation operation including rotation, zoom, hori-zontal flip, width shift, height shift, and shear to increase the diversity in image datasets. Then the general features of the input brain tumor images are extracted based on a pre-trained transfer learning method comprised…
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 …