Brain Tumor Segmentation with Deep Neural Networks

In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we've found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test dataset reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster

Effective Brain Tumor Classification Using Deep Residual Network-Based Transfer Learning

Brain tumor classification is an essential task in medical image processing that provides assistance to doctors for accurate diagnoses and treatment plans. A Deep Residual Network based Transfer Learning to a fully convoluted Convolutional Neural Network (CNN) is proposed to perform brain tumor classification of Magnetic Resonance Images (MRI) from the BRATS 2020 dataset. The dataset consists of a variety of pre-operative MRI scans to segment integrally varied brain tumors in appearance, shape, and histology, namely gliomas. A Deep Residual Network (ResNet-50) to a fully convoluted CNN is proposed to perform tumor classification from MRI of the BRATS dataset. The 50-layered residual network deeply convolutes the multi-category of tumor images in classification tasks using convolution block and identity block. Limitations such as Limited accuracy and complexity of algorithms in CNN-based ME-Net, and classification issues in YOLOv2 inceptions are resolved by the proposed model in this work. The trained CNN learns boundary and region tasks and extracts successful contextual information from MRI scans with minimal computation cost. The tumor segmentation and classification are performed in one step using a U-Net architecture, which helps retain spatial features of the image. The multimodality fusion is implemented to perform classification and regression tasks by integrating dataset information. The dice scores of the proposed model for Enhanced Tumor (ET), Whole Tumor (WT), and Tumor Core (TC) are 0.88, 0.97, and 0.90 on the BRATS 2020 dataset, and also resulted in 99.94% accuracy, 98.92% sensitivity, 98.63% specificity, and 99.94% precision

Longitudinal Brain Tumor Tracking, Tumor Grading, and Patient Survival Prediction Using MRI

This work aims to develop novel methods for brain tumor classification, longitudinal brain tumor tracking, and patient survival prediction. Consequently, this dissertation proposes three tasks. First, we develop a framework for brain tumor segmentation prediction in longitudinal multimodal magnetic resonance imaging (mMRI) scans, comprising two methods: feature fusion and joint label fusion (JLF). The first method fuses stochastic multi-resolution texture features with tumor cell density features, in order to obtain tumor segmentation predictions in follow-up scans from a baseline pre-operative timepoint. The second method utilizes JLF to combine segmentation labels obtained from (i) the stochastic texture feature-based and Random Forest (RF)-based tumor segmentation method; and (ii) another state-of-the-art tumor growth and segmentation method known as boosted Glioma Image Segmentation and Registration (GLISTRboost, or GB). With the advantages of feature fusion and label fusion, we achieve state-of-the-art brain tumor segmentation prediction. Second, we propose a deep neural network (DNN) learning-based method for brain tumor type and subtype grading using phenotypic and genotypic data, following the World Health Organization (WHO) criteria. In addition, the classification method integrates a cellularity feature which is derived from the morphology of a pathology image to improve classification performance. The proposed method achieves state-of-the-art performance for tumor grading following the new CNS tumor grading criteria. Finally, we investigate brain tumor volume segmentation, tumor subtype classification, and overall patient survival prediction, and then we propose a new context- aware deep learning method, known as the Context Aware Convolutional Neural Network (CANet). Using the proposed method, we participated in the Multimodal Brain Tumor Segmentation Challenge 2019 (BraTS 2019) for brain tumor volume segmentation and overall survival prediction tasks. In addition, we also participated in the Radiology-Pathology Challenge 2019 (CPM-RadPath 2019) for Brain Tumor Subtype Classification, organized by the Medical Image Computing & Computer Assisted Intervention (MICCAI) Society. The online evaluation results show that the proposed methods offer competitive performance from their use of state-of-the-art methods in tumor volume segmentation, promising performance on overall survival prediction, and state-of-the-art performance on tumor subtype classification. Moreover, our result was ranked second place in the testing phase of the CPM-RadPath 2019

Deep learning based Brain Tumour Classification based on Recursive Sigmoid Neural Network based on Multi-Scale Neural Segmentation

Brain tumours are malignant tissues in which cells replicate rapidly and indefinitely, and tumours grow out of control. Deep learning has the potential to overcome challenges associated with brain tumour diagnosis and intervention. It is well known that segmentation methods can be used to remove abnormal tumour areas in the brain. It is one of the advanced technology classification and detection tools. Can effectively achieve early diagnosis of the disease or brain tumours through reliable and advanced neural network classification algorithms. Previous algorithm has some drawbacks, an automatic and reliable method for segmentation is needed. However, the large spatial and structural heterogeneity between brain tumors makes automated segmentation a challenging problem. Image tumors have irregular shapes and are spatially located in any part of the brain, making their segmentation is inaccurate for clinical purposes a challenging task. In this work, propose a method Recursive SigmoidNeural Network based on Multi-scale Neural Segmentation (RSN2-MSNS) for image proper segmentation. Initially collets the image dataset from standard repository for brain tumour classification.  Next, pre-processing method that targets only a small part of an image rather than the entire image. This approach reduces computational time and overcomes the over complication. Second stage, segmenting the images based on the Enhanced Deep Clustering U-net (EDCU-net) for estimating the boundary points in the brain tumour images. This method can successfully colour histogram values are evaluating segment complex images that contain both textured and non-textured regions. Third stage, Feature extraction for extracts the features from segmenting images using Convolution Deep Feature Spectral Similarity (CDFS2) scaled the values from images extracting the relevant weights based on its threshold limits. Then selecting the features from extracting stage, this selection is based on the relational weights. And finally classified the features based on the Recursive Sigmoid Neural Network based on Multi-scale Neural Segmentation (RSN2-MSNS) for evaluating the proposed brain tumour classification model consists of 1500 trainable images and the proposed method achieves 97.0% accuracy. The sensitivity, specificity, detection accuracy and F1 measures were 96.4%, 952%, and 95.9%, respectively

3D Convolution Neural Networks for Medical Imaging; Classification and Segmentation : A Doctor’s Third Eye

Master's thesis in Information- and communication technology (IKT591)In this thesis, we studied and developed 3D classification and segmentation models for medical imaging. The classification is done for Alzheimer’s Disease and segmentation is for brain tumor sub-regions. For the medical imaging classification task we worked towards developing a novel deep architecture which can accomplish the complex task of classifying Alzheimer’s Disease volumetrically from the MRI scans without the need of any transfer learning. The experiments were performed for both binary classification of Alzheimer’s Disease (AD) from Normal Cognitive (NC), as well as multi class classification between the three stages of Alzheimer’s called NC, AD and Mild cognitive impairment (MCI). We tested our model on the ADNI dataset and achieved mean accuracy of 94.17% and 89.14% for binary classification and multiclass classification respectively. In the second part of this thesis which is segmentation of tumors sub-regions in brain MRI images we studied some popular architecture for segmentation of medical imaging and inspired from them, proposed our architecture of end-to-end trainable fully convolutional neural net-work which uses attention block to learn the localization of different features of the multiple sub-regions of tumor. Also experiments were done to see the effect of weighted cross-entropy loss function and dice loss function on the performance of the model and the quality of the output segmented labels. The results of evaluation of our model are received through BraTS’19 dataset challenge. The model is able to achieve a dice score of 0.80 for the segmentation of whole tumor, and a dice scores of 0.639 and 0.536 for other two sub-regions within the tumor on validation data. In this thesis we successfully applied computer vision techniques for medical imaging analysis. We show the huge potential and numerous benefits of deep learning to combat and detect diseases opens up more avenues for research and application for automating medical imaging analysis