Interactive Image Selection and Training for Brain Tumor Segmentation Network
Institute of Computing, University of Campinas（坎皮纳斯大学计算研究所）；Hospital de Clínicas, Universidade Federal do Paraná（巴拉那联邦大学临床医院）；Instituto de Neurologia de Curitiba（库里蒂巴神经研究所）
Matheus A. Cerqueira, Flávia Sprenger, Bernardo C. A. Teixeira, Alexandre X. Falcão
医学图像分割是一个重要问题，深度学习是其中的代表性方法。然而，训练大规模模型需要大量完全标注的图像，这一需求可能成为难题，尤其是对于图像呈现高度多样性的应用，例如脑肿瘤，其大小和形状各异。相比之下，一种近期的方法——基于图像标记的特征学习（Feature Learning from Image Markers，FLIM）将专家纳入学习循环中，能够生成只需少量图像即可训练卷积层的小型网络。在本工作中，我们采用一种基于FLIM的交互式图像选择与训练方法，充分利用用户的知识。结果表明，通过我们的方法，可以选择一小组图像来训练U形网络的编码器，获得与人工选择相同的性能，甚至超越了使用反向传播和全部训练图像训练的同一U形网络。
英文摘要：
Medical image segmentation is a relevant problem, with deep learning being an exponent. However, the necessity of a high volume of fully annotated images for training massive models can be a problem, especially for applications whose images present a great diversity, such as brain tumors, which can occur in different sizes and shapes. In contrast, a recent methodology, Feature Learning from Image Markers (FLIM), has involved an expert in the learning loop, producing small networks that require few images to train the convolutional layers. In this work, We employ an interactive method for image selection and training based on FLIM, exploring the user's knowledge. The results demonstrated that with our methodology, we could choose a small set of images to train the encoder of a U-shaped network, obtaining performance equal to manual selection and even surpassing the same U-shaped network trained with backpropagation and all training images.
Data Science Institute, Imperial College London（伦敦帝国理工学院数据科学研究所）；National Heart and Lung Institute, Imperial College London（伦敦帝国理工学院国家心肺研究所）
A major challenge in brain tumor treatment planning and quantitative evaluation is determination of the tumor extent. The noninvasive magnetic resonance imaging (MRI) technique has emerged as a front-line diagnostic tool for brain tumors without ionizing radiation. Manual segmentation of brain tumor extent from 3D MRI volumes is a very time-consuming task and the performance is highly relied on operator's experience. In this context, a reliable fully automatic segmentation method for the brain tumor segmentation is necessary for an efficient measurement of the tumor extent. In this study, we p…
Image segmentation some of the challenging issues on brain magnetic resonance image tumor segmentation caused by the weak correlation between magnetic resonance imaging intensity and anatomical meaning.With the objective of utilizing more meaningful information to improve brain tumor segmentation,an approach which employs bilateral symmetry information as an additional feature for segmentation is proposed.This is motivated by potential performance improvement in the general automatic brain tumor segmentation systems which are important for many medical and scientific applications.Brain Magneti…
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 …
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…
Automated segmentation of brain tumors from 3D magnetic resonance images (MRIs) is necessary for the diagnosis, monitoring, and treatment planning of the disease. Manual delineation practices require anatomical knowledge, are expensive, time consuming and can be inaccurate due to human error. Here, we describe a semantic segmentation network for tumor subregion segmentation from 3D MRIs based on encoder-decoder architecture. Due to a limited training dataset size, a variational auto-encoder branch is added to reconstruct the input image itself in order to regularize the shared decoder and impo…
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 …
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…
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…
Accurate detection of brain tumors could save lots of lives and increasing the accuracy of this binary classification even as much as a few percent has high importance. Neural Gas Networks (NGN) is a fast, unsupervised algorithm that could be used in data clustering, image pattern recognition, and image segmentation. In this research, we used the metaheuristic Firefly Algorithm (FA) for image contrast enhancement as pre-processing and NGN weights for feature extraction and segmentation of Magnetic Resonance Imaging (MRI) data on two brain tumor datasets from the Kaggle platform. Also, tumor cl…
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…
Glioma is one of the most common types of brain tumors; it arises in the glial cells in the human brain and in the spinal cord. In addition to having a high mortality rate, glioma treatment is also very expensive. Hence, automatic and accurate segmentation and measurement from the early stages are critical in order to prolong the survival rates of the patients and to reduce the costs of the treatment. In the present work, we propose a novel end-to-end cascaded network for semantic segmentation that utilizes the hierarchical structure of the tumor sub-regions with ResNet-like blocks and Squeeze…
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…
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…
In this work, we propose a multi-modal Convolutional Neural Network (CNN) approach for brain tumor segmentation. We investigate how to combine different modalities efficiently in the CNN framework.We adapt various fusion methods, which are previously employed on video recognition problem, to the brain tumor segmentation problem,and we investigate their efficiency in terms of memory and performance.Our experiments, which are performed on BRATS dataset, lead us to the conclusion that learning separate representations for each modality and combining them for brain tumor segmentation could increas…
University of California, Los Angeles（加州大学洛杉矶分校）；National University of Singapore（新加坡国立大学）
Brain tumor is a common and fatal form of cancer which affects both adults and children. The classification of brain tumors into different types is hence a crucial task, as it greatly influences the treatment that physicians will prescribe. In light of this, medical imaging techniques, especially those applying deep convolutional networks followed by a classification layer, have been developed to make possible computer-aided classification of brain tumor types. In this paper, we present a novel approach of directly learning deep embeddings for brain tumor types, which can be used for downstrea…
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 …
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…
Kharkevich Institute for Information Transmission Problems（哈尔克维奇信息传输问题研究所）；Moscow Institute of Physics and Technology（莫斯科物理技术学院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Moscow Gamma-Knife Center（莫斯科伽马刀中心）；Burdenko Neurosurgery Institute（布尔坚科神经外科研究所）
Classification-based image retrieval systems are built by training convolutional neural networks (CNNs) on a relevant classification problem and using the distance in the resulting feature space as a similarity metric. However, in practical applications, it is often desirable to have representations which take into account several aspects of the data (e.g., brain tumor type and its localization). In our work, we extend the classification-based approach with multitask learning: we train a CNN on brain MRI scans with heterogeneous labels and implement a corresponding tumor image retrieval system…
King’s College London（伦敦国王学院）；University College London（伦敦大学学院）
Automatic brain tumor segmentation plays an important role for diagnosis, surgical planning and treatment assessment of brain tumors. Deep convolutional neural networks (CNNs) have been widely used for this task. Due to the relatively small data set for training, data augmentation at training time has been commonly used for better performance of CNNs. Recent works also demonstrated the usefulness of using augmentation at test time, in addition to training time, for achieving more robust predictions. We investigate how test-time augmentation can improve CNNs' performance for brain tumor segment…
University of Arkansas（阿肯色大学）；Concordia University（康考迪亚大学）；Carnegie Mellon University（卡内基梅隆大学）
In recent years, deep neural networks have achieved state-of-the-art performance in a variety of recognition and segmentation tasks in medical imaging including brain tumor segmentation. We investigate that segmenting a brain tumor is facing to the imbalanced data problem where the number of pixels belonging to the background class (non tumor pixel) is much larger than the number of pixels belonging to the foreground class (tumor pixel). To address this problem, we propose a multi-task network which is formed as a cascaded structure. Our model consists of two targets, i.e., (i) effectively dif…
Advances in computing technology have allowed researchers across many fields of endeavor to collect and maintain vast amounts of observational statistical data such as clinical data, biological patient data, data regarding access of web sites, financial data, and the like. This paper addresses some of the challenging issues on brain magnetic resonance (MR) image tumor segmentation caused by the weak correlation between magnetic resonance imaging (MRI) intensity and anatomical meaning. With the objective of utilizing more meaningful information to improve brain tumor segmentation, an approach w…
Magnetic Resonance Imaging (MRI) is an important diagnostic tool for precise detection of various pathologies. Magnetic Resonance (MR) is more preferred than Computed Tomography (CT) due to the high resolution in MR images which help in better detection of neurological conditions. Graphical user interface (GUI) aided disease detection has become increasingly useful due to the increasing workload of doctors. In this proposed work, a novel two steps GUI technique for brain tumor segmentation as well as Brodmann area detec-tion of the segmented tumor is proposed. A data set of T2 weighted images …
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…
Variational Level Set (VLS) has been a widely used method in medical segmentation. However, segmentation accuracy in the VLS method dramatically decreases when dealing with intervening factors such as lighting, shadows, colors, etc. Additionally, results are quite sensitive to initial settings and are highly dependent on the number of iterations. In order to address these limitations, the proposed method incorporates VLS into deep learning by defining a novel end-to-end trainable model called as Deep Recurrent Level Set (DRLS). The proposed DRLS consists of three layers, i.e, Convolutional lay…
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…
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）
Brain tumor is considered as one of the deadliest and most common form of cancer both in children and in adults. Consequently, determining the correct type of brain tumor in early stages is of significant importance to devise a precise treatment plan and predict patient's response to the adopted treatment. In this regard, there has been a recent surge of interest in designing Convolutional Neural Networks (CNNs) for the problem of brain tumor type classification. However, CNNs typically require large amount of training data and can not properly handle input transformations. Capsule networks (r…
A cascade of fully convolutional neural networks is proposed to segment multi-modal Magnetic Resonance (MR) images with brain tumor into background and three hierarchical regions: whole tumor, tumor core and enhancing tumor core. The cascade is designed to decompose the multi-class segmentation problem into a sequence of three binary segmentation problems according to the subregion hierarchy. The whole tumor is segmented in the first step and the bounding box of the result is used for the tumor core segmentation in the second step. The enhancing tumor core is then segmented based on the boundi…
Training segmentation networks requires large annotated datasets, but manual annotation is time consuming and costly. We here investigate if the combination of a noise-to-image GAN and an image-to-image GAN can be used to synthesize realistic brain tumor images as well as the corresponding tumor annotations (labels), to substantially increase the number of training images. The noise-to-image GAN is used to synthesize new label images, while the image-to-image GAN generates the corresponding MR image from the label image. Our results indicate that the two GANs can synthesize label images and MR…
Indian Institute of Information Technology Allahabad（印度阿拉哈巴德信息技术学院）
It is essential to classify brain tumors from magnetic resonance imaging (MRI) accurately for better and timely treatment of the patients. In this paper, we propose a hybrid model, using VGG along with Nonlinear-SVM (Soft and Hard) to classify the brain tumors: glioma and pituitary and tumorous and non-tumorous. The VGG-SVM model is trained for two different datasets of two classes; thus, we perform binary classification. The VGG models are trained via the PyTorch python library to obtain the highest testing accuracy of tumor classification. The method is threefold, in the first step, we norma…
UPMAD-Net: A Brain Tumor Segmentation Network with Uncertainty Guidance and Adaptive Multimodal Feature Fusion
School of Computer Science and Technology, Zhengzhou University of Light Industry（郑州轻工业大学计算机与通信工程学院）；Kennesaw State University（肯尼索州立大学）；Michigan Technological University（密歇根理工大学）
University at Buffalo, The State University of New York（纽约州立大学布法罗分校）
Brain Tumor Segmentation from magnetic resonance imaging (MRI) is a critical technique for early diagnosis. However, rather than having complete four modalities as in BraTS dataset, it is common to have missing modalities in clinical scenarios. We design a brain tumor segmentation algorithm that is robust to the absence of any modality. Our network includes a channel-independent encoding path and a feature-fusion decoding path. We use self-supervised training through channel dropout and also propose a novel domain adaptation method on feature maps to recover the information from the missing ch…
Brain Tumor Segmentation with Special Emphasis on the Non-Enhancing Brain Tumor Compartment
CIML Group, Biophysics, University of Regensburg（里堡大学生物物理组）；Department of Neurosurgery , University Hospital Regensburg（里堡大学神经外科部门）；Department of Biomedical Imaging, University Hospital Regensburg（里堡大学生物医学成像部门）；DETI, IEETA, Universidade de Aveiro（阿维罗大学DETI和IEETA）
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…
Department of Neuro-Oncology, Massachusetts General Hospital（麻省总医院神经肿瘤科）；MGH & BWH Center for Clinical Data Science（麻省总医院与布莱根妇女医院临床数据科学中心）；Department of Radiology, Massachusetts General Hospital（麻省总医院放射科）；Massachusetts General Hospital（麻省总医院）；NVIDIA（英伟达）
Deep learning has quickly become the weapon of choice for brain lesion segmentation. However, few existing algorithms pre-configure any biological context of their chosen segmentation tissues, and instead rely on the neural network's optimizer to develop such associations de novo. We present a novel method for applying deep neural networks to the problem of glioma tissue segmentation that takes into account the structured nature of gliomas - edematous tissue surrounding mutually-exclusive regions of enhancing and non-enhancing tumor. We trained multiple deep neural networks with a 3D U-Net arc…
German Cancer Research Center (DKFZ)（德国癌症研究中心（DKFZ））；Heidelberg University Hospital（海德堡大学医院）
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 solve for automatic segmentation methods. In this paper we present our most recent effort on developing a robust segmentation algorithm in the form of a convolutional neural network. Our network architecture was inspired by the popular U-Net and has been carefully modified to maximize brain tumor segmentation performance. We use a dice loss function to cope with class imbalances and use extensive d…
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…
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 …
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 …
This article presents a multiscale patch based convolutional neural network for the automatic segmentation of brain tumors in multi-modality 3D MR images. We use multiscale deep supervision and inputs to train a convolutional network. We evaluate the effectiveness of the proposed approach on the BRATS 2017 segmentation challenge where we obtained dice scores of 0.755, 0.900, 0.782 and 95% Hausdorff distance of 3.63mm, 4.10mm, and 6.81mm for enhanced tumor core, whole tumor and tumor core respectively.
