Brain Tumor Segmentation Using a Patch-Based Convolutional Neural Network: A Big Data Analysis Approach

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Abstract

Early detection of brain tumors is critical to ensure successful treatment, and medical imaging is essential in this process. However, analyzing the large amount of medical data generated from various sources such as magnetic resonance imaging (MRI) has been a challenging task. In this research, we propose a method for early brain tumor segmentation using big data analysis and patch-based convolutional neural networks (PBCNNs). We utilize BraTS 2012–2018 datasets. The data is preprocessed through various steps such as profiling, cleansing, transformation, and enrichment to enhance the quality of the data. The proposed CNN model utilizes a patch-based architecture with global and local layers that allows the model to analyze different parts of the image with varying resolutions. The architecture takes multiple input modalities, such as T1, T2, T2-c, and FLAIR, to improve the accuracy of the segmentation. The performance of the proposed model is evaluated using various metrics, such as accuracy, sensitivity, specificity, Dice similarity coefficient, precision, false positive rate, and true positive rate. Our results indicate that the proposed method outperforms the existing methods and is effective in early brain tumor segmentation. The proposed method can also assist medical professionals in making accurate and timely diagnoses, and thus improve patient outcomes, which is especially critical in the case of brain tumors. This research also emphasizes the importance of big data analysis in medical imaging research and highlights the potential of PBCNN models in this field.

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Brain tumor segmentation with Deep Neural Networks

Mohammad Havaei, Axel Davy, David Warde-Farley … (2017)

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 data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster.

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3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation

Özgün Çiçek, Ahmed Abdulkadir, Soeren Lienkamp … (2016)

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Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation

Konstantinos Kamnitsas, Christian Ledig, Virginia F.J. Newcombe … (2017)

We propose a dual pathway, 11-layers deep, three-dimensional Convolutional Neural Network for the challenging task of brain lesion segmentation. The devised architecture is the result of an in-depth analysis of the limitations of current networks proposed for similar applications. To overcome the computational burden of processing 3D medical scans, we have devised an efficient and effective dense training scheme which joins the processing of adjacent image patches into one pass through the network while automatically adapting to the inherent class imbalance present in the data. Further, we analyze the development of deeper, thus more discriminative 3D CNNs. In order to incorporate both local and larger contextual information, we employ a dual pathway architecture that processes the input images at multiple scales simultaneously. For post-processing of the network's soft segmentation, we use a 3D fully connected Conditional Random Field which effectively removes false positives. Our pipeline is extensively evaluated on three challenging tasks of lesion segmentation in multi-channel MRI patient data with traumatic brain injuries, brain tumours, and ischemic stroke. We improve on the state-of-the-art for all three applications, with top ranking performance on the public benchmarks BRATS 2015 and ISLES 2015. Our method is computationally efficient, which allows its adoption in a variety of research and clinical settings. The source code of our implementation is made publicly available.