A survey on deep learning in medical image analysis

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

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)

A reproducible evaluation of ANTs similarity metric performance in brain image registration.

http://www.eecs.qmul.ac.uk/~sgg/papers/ShanGongMcOwan_IVC09.pdf

Facial expression recognition based on Local Binary Patterns: A comprehensive study

This paper proposes a novel approach to extract image features for texture classification. The proposed features are robust to image rotation, less sensitive to histogram equalization and noise. It comprises of two sets of features: dominant local binary patterns (DLBP) in a texture image and the supplementary features extracted by using the circularly symmetric Gabor filter responses. The dominant local binary pattern method makes use of the most frequently occurred patterns to capture descriptive textural information, while the Gabor-based features aim at supplying additional global textural information to the DLBP features. Through experiments, the proposed approach has been intensively evaluated by applying a large number of classification tests to histogram-equalized, randomly rotated and noise corrupted images in Outex, Brodatz, Meastex, and CUReT texture image databases. Our method has also been compared with six published texture features in the experiments. It is experimentally demonstrated that the proposed method achieves the highest classification accuracy in various texture databases and image conditions.

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Dominant Local Binary Patterns for Texture Classification

This paper proposes a novel curvilinear structure detector, called Optimally Oriented Flux (OOF). OOF finds an optimal axis on which image gradients are projected in order to compute the image gradient flux. The computation of OOF is localized at the boundaries of local spherical regions. It avoids considering closely located adjacent structures. The main advantage of OOF is its robustness against the disturbance induced by closely located adjacent objects. Moreover, the analytical formulation of OOF introduces no additional computation load as compared to the calculation of the Hessian matrix which is widely used for curvilinear structure detection. It is experimentally demonstrated that OOF delivers accurate and stable curvilinear structure detection responses under the interference of closely located adjacent structures as well as image noise.

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Three Dimensional Curvilinear Structure Detection Using Optimally Oriented Flux

This paper proposes a novel facial expression recognition approach based on two sets of features extracted from the face images: texture features and global appearance features. The first set is obtained by using the extended local binary patterns in both intensity and gradient maps and computing the Tsallis entropy of the Gabor filtered responses. The second set of features is obtained by performing null-space based linear discriminant analysis on the training face images. The proposed method is evaluated by extensive experiments on the JAFFE database, and compared with two widely used facial expression recognition approaches. Experimental results show that the proposed approach maintains high recognition rate in a wide range of resolution levels and outperforms the other alternative methods.

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Facial Expression Recognition using Advanced Local Binary Patterns, Tsallis Entropies and Global Appearance Features

Diffeomorphic deformable image registration is crucial in many medical image studies, as it offers unique, special features including topology preservation and invertibility of the transformation. Recent deep learning-based deformable image registration methods achieve fast image registration by leveraging a convolutional neural network (CNN) to learn the spatial transformation from the synthetic ground truth or the similarity metric. However, these approaches often ignore the topology preservation of the transformation and the smoothness of the transformation which is enforced by a global smoothing energy function alone. Moreover, deep learning-based approaches often estimate the displacement field directly, which cannot guarantee the existence of the inverse transformation. In this paper, we present a novel, efficient unsupervised symmetric image registration method which maximizes the similarity between images within the space of diffeomorphic maps and estimates both forward and inverse transformations simultaneously. We evaluate our method on 3D image registration with a large scale brain image dataset. Our method achieves state-of-the-art registration accuracy and running time while maintaining desirable diffeomorphic properties.

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Fast Symmetric Diffeomorphic Image Registration with Convolutional Neural Networks

Deep learning-based methods have recently demonstrated promising results in deformable image registration for a wide range of medical image analysis tasks. However, existing deep learning-based methods are usually limited to small deformation settings, and desirable properties of the transformation including bijective mapping and topology preservation are often being ignored by these approaches. In this paper, we propose a deep Laplacian Pyramid Image Registration Network, which can solve the image registration optimization problem in a coarse-to-fine fashion within the space of diffeomorphic maps. Extensive quantitative and qualitative evaluations on two MR brain scan datasets show that our method outperforms the existing methods by a significant margin while maintaining desirable diffeomorphic properties and promising registration speed.

Albert C. S. Chung

Papers

Dominant Local Binary Patterns for Texture Classification

Three Dimensional Curvilinear Structure Detection Using Optimally Oriented Flux

Facial Expression Recognition using Advanced Local Binary Patterns, Tsallis Entropies and Global Appearance Features

Fast Symmetric Diffeomorphic Image Registration with Convolutional Neural Networks

Large Deformation Diffeomorphic Image Registration with Laplacian Pyramid Networks