Vox2Vox: 3D-GAN for Brain Tumour Segmentation

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histological sub-regions, i.e., peritumoral edema, necrotic core, enhancing and non-enhancing tumour core. Although brain tumours can easily be detected using multi-modal MRI, accurate tumor segmentation is a challenging task. Hence, using the data provided by the BraTS Challenge 2020, we propose a 3D volume-to-volume Generative Adversarial Network for segmentation of brain tumours. The model, called Vox2Vox, generates realistic segmentation outputs from multi-channel 3D MR images, segmenting the whole, core and enhancing tumor with mean values of 87.20%, 81.14%, and 78.67% as dice scores and 6.44mm, 24.36mm, and 18.95mm for Hausdorff distance 95 percentile for the BraTS testing set after ensembling 10 Vox2Vox models obtained with a 10-fold cross-validation

Brain Tumor Area Segmentation of MRI Images

Accurate and timely detection of the brain tumor area has a great impact on the choice of treatment, its success rate, and following the disease process during treatment. The existing algorithms for brain tumor diagnosis have problems in terms of good performance on various brain images with different qualities, low sensitivity of the results to the parameters introduced in the algorithm, and also reliable diagnosis of tumors in the early stages of formation. In this study, a two-stage segmentation method for accurate detection of the tumor area in magnetic resonance imaging of the brain is presented. In the first stage, after performing the necessary preprocessing on the image, the location of the tumor is located using a threshold-based segmentation method, and in the second stage, it is used as an indicator in a pond segmentation method based on the marker used. Placed. Given that in the first stage there is not much emphasis on accurate detection of the tumor area, the selection of threshold values over a large range of values will not affect the final results. In the second stage, the use of the marker-based pond segmentation method will lead to accurate detection of the tumor area. The results of the implementations show that the proposed method for accurate detection of the tumor area in a large range of changes in input parameters has the same and accurate results

Prototype-Driven and Multi-Expert Integrated Multi-Modal MR Brain Tumor Image Segmentation

For multi-modal magnetic resonance (MR) brain tumor image segmentation, current methods usually directly extract the discriminative features from input images for tumor sub-region category determination and localization. However, the impact of information aliasing caused by the mutual inclusion of tumor sub-regions is often ignored. Moreover, existing methods usually do not take tailored efforts to highlight the single tumor sub-region features. To this end, a multi-modal MR brain tumor segmentation method with tumor prototype-driven and multi-expert integration is proposed. It could highlight the features of each tumor sub-region under the guidance of tumor prototypes. Specifically, to obtain the prototypes with complete information, we propose a mutual transmission mechanism to transfer different modal features to each other to address the issues raised by insufficient information on single-modal features. Furthermore, we devise a prototype-driven feature representation and fusion method with the learned prototypes, which implants the prototypes into tumor features and generates corresponding activation maps. With the activation maps, the sub-region features consistent with the prototype category can be highlighted. A key information enhancement and fusion strategy with multi-expert integration is designed to further improve the segmentation performance. The strategy can integrate the features from different layers of the extra feature extraction network and the features highlighted by the prototypes. Experimental results on three competition brain tumor segmentation datasets prove the superiority of the proposed method

An attention residual u-net with differential preprocessing and geometric postprocessing: Learning how to segment vasculature including intracranial aneurysms

Objective Intracranial aneurysms (IA) are lethal, with high morbidity and mortality rates. Reliable, rapid, and accurate segmentation of IAs and their adjacent vasculature from medical imaging data is important to improve the clinical management of patients with IAs. However, due to the blurred boundaries and complex structure of IAs and overlapping with brain tissue or other cerebral arteries, image segmentation of IAs remains challenging. This study aimed to develop an attention residual U-Net (ARU-Net) architecture with differential preprocessing and geometric postprocessing for automatic segmentation of IAs and their adjacent arteries in conjunction with 3D rotational angiography (3DRA) images. Methods The proposed ARU-Net followed the classic U-Net framework with the following key enhancements. First, we preprocessed the 3DRA images based on boundary enhancement to capture more contour information and enhance the presence of small vessels. Second, we introduced the long skip connections of the attention gate at each layer of the fully convolutional decoder-encoder structure to emphasize the field of view (FOV) for IAs. Third, residual-based short skip connections were also embedded in each layer to implement in-depth supervision to help the network converge. Fourth, we devised a multiscale supervision strategy for independent prediction at different levels of the decoding path, integrating multiscale semantic information to facilitate the segmentation of small vessels. Fifth, the 3D conditional random field (3DCRF) and 3D connected component optimization (3DCCO) were exploited as postprocessing to optimize the segmentation results. Results Comprehensive experimental assessments validated the effectiveness of our ARU-Net. The proposed ARU-Net model achieved comparable or superior performance to the state-of-the-art methods through quantitative and qualitative evaluations. Notably, we found that ARU-Net improved the identification of arteries connecting to an IA, including small arteries that were hard to recognize by other methods. Consequently, IA geometries segmented by the proposed ARU-Net model yielded superior performance during subsequent computational hemodynamic studies (also known as patient-specific computational fluid dynamics [CFD] simulations). Furthermore, in an ablation study, the five key enhancements mentioned above were confirmed. Conclusions The proposed ARU-Net model can automatically segment the IAs in 3DRA images with relatively high accuracy and potentially has significant value for clinical computational hemodynamic analysis

U-Net and its variants for medical image segmentation: theory and applications

U-net is an image segmentation technique developed primarily for medical image analysis that can precisely segment images using a scarce amount of training data. These traits provide U-net with a very high utility within the medical imaging community and have resulted in extensive adoption of U-net as the primary tool for segmentation tasks in medical imaging. The success of U-net is evident in its widespread use in all major image modalities from CT scans and MRI to X-rays and microscopy. Furthermore, while U-net is largely a segmentation tool, there have been instances of the use of U-net in other applications. As the potential of U-net is still increasing, in this review we look at the various developments that have been made in the U-net architecture and provide observations on recent trends. We examine the various innovations that have been made in deep learning and discuss how these tools facilitate U-net. Furthermore, we look at image modalities and application areas where U-net has been applied.Comment: 42 pages, in IEEE Acces