In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients—manually annotated by up to four raters—and to 65 comparable scans generated using tumor image simulation software Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%–85%), illustrating the difficulty of this task We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource

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The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

Brain tumor segmentation with Deep Neural Networks

MRI-based medical image analysis for brain tumor studies is gaining attention in recent times due to an increased need for efficient and objective evaluation of large amounts of data. While the pioneering approaches applying automated methods for the analysis of brain tumor images date back almost two decades, the current methods are becoming more mature and coming closer to routine clinical application. This review aims to provide a comprehensive overview by giving a brief introduction to brain tumors and imaging of brain tumors first. Then, we review the state of the art in segmentation, registration and modeling related to tumor-bearing brain images with a focus on gliomas. The objective in the segmentation is outlining the tumor including its sub-compartments and surrounding tissues, while the main challenge in registration and modeling is the handling of morphological changes caused by the tumor. The qualities of different approaches are discussed with a focus on methods that can be applied on standard clinical imaging protocols. Finally, a critical assessment of the current state is performed and future developments and trends are addressed, giving special attention to recent developments in radiological tumor assessment guidelines.

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A survey of MRI-based medical image analysis for brain tumor studies

A deep learning model integrating FCNNs and CRFs for brain tumor segmentation.

Radiomics is an emerging translational field of research aiming to extract mineable high-dimensional data from clinical images. The radiomic process can be divided into distinct steps with definable inputs and outputs, such as image acquisition and reconstruction, image segmentation, features extraction and qualification, analysis, and model building. Each step needs careful evaluation for the construction of robust and reliable models to be transferred into clinical practice for the purposes of prognosis, non-invasive disease tracking, and evaluation of disease response to treatment. After the definition of texture parameters (shape features; first-, second-, and higher-order features), we briefly discuss the origin of the term radiomics and the methods for selecting the parameters useful for a radiomic approach, including cluster analysis, principal component analysis, random forest, neural network, linear/logistic regression, and other. Reproducibility and clinical value of parameters should be firstly tested with internal cross-validation and then validated on independent external cohorts. This article summarises the major issues regarding this multi-step process, focussing in particular on challenges of the extraction of radiomic features from data sets provided by computed tomography, positron emission tomography, and magnetic resonance imaging.

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Radiomics: the facts and the challenges of image analysis

We consider the problem of conducting frame rate dependent video quality assessment (VQA) on videos of diverse frame rates, including high frame rate (HFR) videos. More generally, we study how perceptual quality is affected by frame rate, and how frame rate and compression combine to affect perceived quality. We devise an objective VQA model called Space-Time GeneRalized Entropic Difference (GREED) which analyzes the statistics of spatial and temporal band-pass video coefficients. A generalized Gaussian distribution (GGD) is used to model band-pass responses, while entropy variations between reference and distorted videos under the GGD model are used to capture video quality variations arising from frame rate changes. The entropic differences are calculated across multiple temporal and spatial subbands, and merged using a learned regressor. We show through extensive experiments that GREED achieves state-of-the-art performance on the LIVE-YT-HFR Database when compared with existing VQA models. The features used in GREED are highly generalizable and obtain competitive performance even on standard, non-HFR VQA databases. The implementation of GREED has been made available online: this https URL

ST-GREED: Space-Time Generalized Entropic Differences for Frame Rate Dependent Video Quality Prediction

Video quality assessment for User Generated Content (UGC) is an important topic in both industry and academia. Most existing methods only focus on one aspect of the perceptual quality assessment, such as technical quality or compression artifacts. In this paper, we create a large scale dataset to comprehensively investigate characteristics of generic UGC video quality. Besides the subjective ratings and content labels of the dataset, we also propose a DNN-based framework to thoroughly analyze importance of content, technical quality, and compression level in perceptual quality. Our model is able to provide quality scores as well as human-friendly quality indicators, to bridge the gap between low level video signals to human perceptual quality. Experimental results show that our model achieves state-of-the-art correlation with Mean Opinion Scores (MOS).

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Rich features for perceptual quality assessment of UGC videos

Over the past decade, the online video industry has greatly expanded the volume of visual data that is streamed and shared over the Internet. Moreover, because of the increasing ease of video capture, many millions of consumers create and upload large volumes of User-Generated-Content (UGC) videos. Unlike streaming television or cinematic content produced by professional videographers and cinemagraphers, UGC videos are most commonly captured by naive users having limited skills and imperfect technique, and often are afflicted by highly diverse and mixed in-capture distortions. These UGC videos are then often uploaded for sharing onto cloud servers, where they further compressed for storage and transmission. Our paper tackles the highly practical problem of predicting the quality of compressed videos (perhaps during the process of compression, to help guide it), with only (possibly severely) distorted UGC videos as references. To address this problem, we have developed a novel Video Quality Assessment (VQA) framework that we call 1stepVQA (to distinguish it from two-step methods that we discuss). 1stepVQA overcomes limitations of Full-Reference, Reduced-Reference and No-Reference VQA models by exploiting the statistical regularities of both natural videos and distorted videos. We show that 1stepVQA is able to more accurately predict the quality of compressed videos, given imperfect reference videos. We also describe a new dedicated video database which includes (typically distorted) UGC reference videos, and a large number of compressed versions of them. We show that the 1stepVQA model outperforms other VQA models in this scenario. We are providing the dedicated new database free of charge at this https URL

Predicting the Quality of Compressed Videos with Pre-Existing Distortions

In this paper we propose a method to adapt the quantization tables of typical block-based transform codecs when the input to the encoder is a panoramic image resulting from equirectangular projection of a spherical image. When the visual content is projected from the panorama to the viewport, a frequency shift is occurring. The quantization can be adapted accordingly: the quantization step sizes that would be optimal to quantize the transform coefficients of the viewport image block, can be used to quantize the coefficients of the panoramic block. As a proof of concept, the proposed quantization strategy has been used in JPEG compression. Results show that a rate reduction up to 2.99% can be achieved for the same perceptual quality of the spherical signal with respect to a standard quantization.

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Geometry-driven quantization for omnidirectional image coding

Patient-specific orthopedic knee surgery planning requires precisely segmenting from 3D CT images multiple knee bones, namely femur, tibia, fibula, and patella, around the knee joint with severe pathologies. In this work, we propose a fully automated, highly precise, and computationally efficient segmentation approach for multiple bones. First, each bone is initially segmented using a model-based marginal space learning framework for pose estimation followed by non-rigid boundary deformation. To recover shape details, we then refine the bone segmentation using graph cut that incorporates the shape priors derived from the initial segmentation. Finally we remove overlap between neighboring bones using multi-layer graph partition. In experiments, we achieve simultaneous segmentation of femur, tibia, patella, and fibula with an overall accuracy of less than 1mm surface-to-surface error in less than 90s on hundreds of 3D CT scans with pathological knee joints.

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Neil Birkbeck

Papers

ST-GREED: Space-Time Generalized Entropic Differences for Frame Rate Dependent Video Quality Prediction

Rich features for perceptual quality assessment of UGC videos

Predicting the Quality of Compressed Videos with Pre-Existing Distortions

Geometry-driven quantization for omnidirectional image coding

Segmentation of multiple knee bones from CT for orthopedic knee surgery planning.