Full anatomical labeling of magnetic resonance images of human brain by registration with multiple atlases

The problem of automatic segmentation of magnetic resonance (MR) images of human brain into anatomical structures is considered. Currently, the most popular segmentation algorithms are based on the registration (matching) of the input image with (to) an atlas—an image for which an expert labeling is known. Segmentation on the basis of registration with multiple atlases allows one to better take into account anatomical variability and thereby to compensate, to some extent, for the errors of matching to each individual atlas. In this work, a more efficient (in speed and memory) implementation is proposed of one of the best multiatlas label fusion algorithms in order to obtain a labeling of the input image. The algorithm is applied to the problem of segmentation of brain MR images into 43 anatomical regions with the use of the publicly available IBSR database, in contrast to the original work, where the authors provide test results for the problem of extraction of a single anatomical structure, the hippocampus.     

Adaptive pixon represented segmentation (APRS) for 3D MR brain images based on mean shift and Markov random fields

In this paper, we proposed an adaptive pixon represented segmentation (APRS) algorithm for 3D magnetic resonance (MR) brain images. Different from traditional method, an adaptive mean shift algorithm was adopted to adaptively smooth the query image and create a pixon-based image representation. Then K-means algorithm was employed to provide an initial segmentation by classifying the pixons in image into a predefined number of tissue classes. By using this segmentation as initialization, expectation-maximization (EM) iterations composed of bias correction, a priori digital brain atlas information, and Markov random field (MRF) segmentation were processed. Pixons were assigned with final labels when the algorithm converges. The adoption of bias correction and brain atlas made the current method more suitable for brain image segmentation than the previous pixon based segmentation algorithm. The proposed method was validated on both simulated normal brain images from BrainWeb and real brain images from the IBSR public dataset. Compared with some other popular MRI segmentation methods, the proposed method exhibited a higher degree of accuracy in segmenting both simulated and real 3D MRI brain data. The experimental results were numerically assessed using Dice and Tanimoto coefficients.     

基于阈值和B样条插值的MR图像增强算法

提出了利用双门限分割灰度级后再进行三次B样条插值非线性变换的MR图像增强算法,将图像灰度级按两个灰度阈值分割为目标区、过渡区、背景区,对这三个不同的区域采用不同的灰度变换方法。在徐军等提出的对比度和目标细节评价标准基础上,提出了一个新的图像质量客观评价标准来评价图像质量。该客观标准可以动态调节对比度和细节的权重参数!,具有交互性。通过寻求该标准最优时的三次B样条插值非线性变换来增强MR图像。实验表明,和目前主要的灰度图像增强算法相比,用该算法增强后的图像不仅提高了图像对比度,也加强了目标的细节,而且具有交互性,特别适合于MR图像处理。     

3D anatomical shape atlas construction using mesh quality preserved deformable models

3D anatomical shape atlas construction has been extensively studied in medical image analysis research, owing to its importance in model-based image segmentation, longitudinal studies and populational statistical analysis, etc. Among multiple steps of 3D shape atlas construction, establishing anatomical correspondences across subjects, i.e., surface registration, is probably the most critical but challenging one. Adaptive focus deformable model (AFDM) [1] was proposed to tackle this problem by exploiting cross-scale geometry characteristics of 3D anatomy surfaces. Although the effectiveness of AFDM has been proved in various studies, its performance is highly dependent on the quality of 3D surface meshes, which often degrades along with the iterations of deformable surface registration (the process of correspondence matching). In this paper, we propose a new framework for 3D anatomical shape atlas construction. Our method aims to robustly establish correspondences across different subjects and simultaneously generate high-quality surface meshes without removing shape details. Mathematically, a new energy term is embedded into the original energy function of AFDM to preserve surface mesh qualities during deformable surface matching. More specifically, we employ the Laplacian representation to encode shape details and smoothness constraints. An expectation–maximization style algorithm is designed to optimize multiple energy terms alternatively until convergence. We demonstrate the performance of our method via a set of diverse applications, including a population of sparse cardiac MRI slices with 2D labels, 3D high resolution CT cardiac images and rodent brain MRIs with multiple structures. The constructed shape atlases exhibit good mesh qualities and preserve fine shape details. The constructed shape atlases can further benefit other research topics such as segmentation and statistical analysis.     

基于脑图谱和模糊聚类的磁共振图像分割标注

利用TT Atlas中丰富的结构信息,文章提出了一种自动分割脑MRI(magnetic resonance image)图像的方法.这种方法可分为两步.首先,将MRI图像和TT Atlas配准,通过图像和医学图谱的匹配,利用图谱中结构信息的先验知识,就可以对图像作初步的分割标注.然后,利用这个预分割的模板对MRI图像进行模糊聚类分割,从而提高分割的精度.为了自动地将预模板中的结构信息用于分割,文章还提出了一种引入形状因子的FCM聚类算法.除了在匹配时需要手工定出一些点之外,该方法基本上是自动的.     

胎儿脑磁共振图像分割研究进展

医学影像是产前筛查、诊断、治疗引导和评估的重要工具,能有效避免胎儿脑的发育异常。近年来,磁共振成像在产前诊断中愈加重要,而实现自动、定量、精确地分析胎儿脑磁共振图像依赖于可靠的图像分割。因此,胎儿脑磁共振图像分割具有十分重要的临床意义与研究价值。由于胎儿图像中存在组织器官多、图像质量差及结构变化快等问题,胎儿脑磁共振图像的分割面临着巨大的困难与挑战。目前,尚未有文献对该领域的方法进行系统性的总结和分析,尤其是基于深度学习的方法。本文针对胎儿脑磁共振图像分割方法进行综述,首先,对胎儿脑磁共振图像的主要公开图谱/数据集进行详细说明;接着,对脑实质提取、组织分割和病灶分割方法进行全面的分类与分析;最后,对胎儿脑磁共振图像分割面临的挑战及未来的研究方向进行总结与展望。     

舌图像自动分割方法

提出了一种基于亮度信息和形态特征的舌图像自动分割方法。该方法首先利用大津法在亮度范围内自动选取阈值，进行二值化，然后通过对图像的像素进行标记，剔除非目标区域。最后利用数学形态学的方法获得最终的分割结果。试验结果表明，本方法具有令人满意的分割性能。     

A review of atlas-based segmentation for magnetic resonance brain images

Normal and abnormal brains can be segmented by registering the target image with an atlas. Here, an atlas is defined as the combination of an intensity image (template) and its segmented image (the atlas labels). After registering the atlas template and the target image, the atlas labels are propagated to the target image. We define this process as atlas-based segmentation. In recent years, researchers have investigated registration algorithms to match atlases to query subjects and also strategies for atlas construction. In this paper we present a review of the automated approaches for atlas-based segmentation of magnetic resonance brain images. We aim to point out the strengths and weaknesses of atlas-based methods and suggest new research directions. We use two different criteria to present the methods. First, we refer to the algorithms according to their atlas-based strategy: label propagation, multi-atlas methods, and probabilistic techniques. Subsequently, we classify the methods according to their medical target: the brain and its internal structures, tissue segmentation in healthy subjects, tissue segmentation in fetus, neonates and elderly subjects, and segmentation of damaged brains. A quantitative comparison of the results reported in the literature is also presented.     

一种特征约束的有限元人脑图像配准方法

提出了一种结合图像的解剖标记点和自适应有限元网格进行人脑图像的精确配准方法.首先利用Forstner算子提取对应图像的解剖标记点,并作初始的图像刚性变换.为了使有限元网格能更加准确地刻画图像解剖结构分布特征,本文利用图像的梯度分布建立了自适应的有限元网格剖分,结合标记点作为有限元的形变约束,使得配准的精度和有限元的计算效率得到提高.人脑图像配准的实验结果表明,该方法能有效地解决图像弹性配准问题.     

Unsupervised scene segmentation using sparse coding context

This paper presents an approach to image understanding on the aspect of unsupervised scene segmentation. With the goal of image understanding in mind, we consider ‘unsupervised scene segmentation’ a task of dividing a given image into semantically meaningful regions without using annotation or other human-labeled information. We seek to investigate how well an algorithm can achieve at partitioning an image with limited human-involved learning procedures. Specifically, we are interested in developing an unsupervised segmentation algorithm that only relies on the contextual prior learned from a set of images. Our algorithm incorporates a small set of images that are similar to the input image in their scene structures. We use the sparse coding technique to analyze the appearance of this set of images; the effectiveness of sparse coding allows us to derive a priori the context of the scene from the set of images. Gaussian mixture models can then be constructed for different parts of the input image based on the sparse-coding contextual prior, and can be combined into an Markov-random-field-based segmentation process. The experimental results show that our unsupervised segmentation algorithm is able to partition an image into semantic regions, such as buildings, roads, trees, and skies, without using human-annotated information. The semantic regions generated by our algorithm can be useful, as pre-processed inputs for subsequent classification-based labeling algorithms, in achieving automatic scene annotation and scene parsing.     

基于图像片马尔科夫随机场的脑MR图像分割算法

传统的高斯混合模型（Gaussian mixture model,GMM）算法在图像分割中未考虑像素的空间信息,导致其对于噪声十分敏感.马尔科 夫随机场（Markov random field,MRF）模型通过像素类别标记的Gibbs分布先验概率引入了图像的空间信息,能较好地分割含有噪声的图 像,然而MRF模型的分割结果容易出现过平滑现象.为了解决上述缺陷,提出了一种新的基于图像片权重方法的马 尔科夫随机场图像分割模型,对邻域内的不同图像片根据相似度赋予不同的权重,使其在克服噪声影响的同时能 保持图像细节信息.同时,采用KL距离引入先验概率与后验概率关于熵的惩罚项,并对该惩罚项进行平滑,得到 最终的分割结果.实验结果表明,算法具有较强的自适应性,能够有效克服噪声对于分割结果的影响,并获得较高的分割精度.     

一种基于K均值分类稀疏表示的灰度图像颜色重建方法

本文充分利用参考图像与待处理灰度图像的关联关系,运用稀疏表示理论和字典学习的方法,提出一种基于K均值分类和残差补偿的稀疏表示的方法来对灰度图像进行颜色重建。首先根据K均值算法将参考图像分成K类,利用K阶奇异值分解（K-SVD）算法训练各类的亮度—特征—颜色的联合字典;其次,根据最小形心距离将待处理灰度图像自适应地分成K类,利用其亮度和特征信息根据正交匹配追踪（OMP）算法得到各类的稀疏系数;然后利用各类的字典和稀疏系数重建初始的彩色图像;最后用残差补偿对重建结果进行修正。实验结果表明,该算法相比于经典算法及其他改进算法对灰度图像进行颜色重建时取得了更好的效果,重建的图像看起来更自然、平滑并且在客观评价标准方面也优于对比算法。     

An approach to segmentation of mouse brain images via intermodal registration

One way to perform a segmentation of the images of mouse brain sections is to register them to some reference images with known segmentation. We designed a new registration algorithm for this task. It is based on hierarchical mutual information maximizationand draws on several recent methods. Besides combining them in a novel way, we identify their weak spots and propose new ways to overcome them, resulting in a more robust performance.     

基于编解码结构的多特征融合眼底图像分割

为解决现有眼底图像分割方法对于细微血管存在低分割精度和低准确率的问题,提出一种基于编解码结构的U-Net改进网络模型。首先对数据进行预处理与扩充,提取绿色通道图像,并将其通过对比度限制直方图均衡化和伽马变换以增强对比度;其次训练集被输入到用于分割的神经网络中,在编码过程加入残差模块,用短跳跃连接将高、低特征信息融合,并利用空洞卷积增加感受野,解码模块加入注意力机制增加对细微血管分割精度;最后利用训练完成的分割模型进行预测得出视网膜血管分割结果。在DRIVE和CHASE-DB1眼底图像数据集上进行对比实验,模型算法的平均准确率、特异性和灵敏度分别达到96.77%和97.22%、98.74%和98.40%、80.93%和81.12%。实验结果表明该算法能够改善微细血管分割准确率及效率不高的问题,对视网膜血管可以进行更准确的分割。     

Segmentation through variable-order surface fitting

The solution of the segmentation problem requires a mechanism for partitioning the image array into low-level entities based on a model of the underlying image structure. A piecewise-smooth surface model for image data that possesses surface coherence properties is used to develop an algorithm that simultaneously segments a large class of images into regions of arbitrary shape and approximates image data with bivariate functions so that it is possible to compute a complete, noiseless image reconstruction based on the extracted functions and regions. Surface curvature sign labeling provides an initial coarse image segmentation, which is refined by an iterative region-growing method based on variable-order surface fitting. Experimental results show the algorithm's performance on six range images and three intensity images     

基于改进粗糙集概率模型的鲁棒医学图像分割算法*

基于参数化模型的图像分割算法对复杂的医学图像分割精度较低,对此提出一种基于改进粗糙集概率模型的鲁棒医学图像分割算法。首先,将粗糙集的上下逼近与概率边界区引入最大期望算法中,表征每个类簇;然后,将图像的灰度分布建模为一个有限数量的混合粗糙集概率分布;最终,通过马尔可夫随机场引入图像的空间信息,提高图像分割算法的鲁棒性。基于合成脑部MR(核磁共振)图像库与真实脑部MR图像库的分割实验结果显示,本算法的分割精度与鲁棒性均优于其他参数化模型的分割算法及其他专门的脑部MR图像分割算法。     

Brain image segmentation using semi-supervised clustering

The objective of brain image segmentation is to partition the brain images into different non-overlapping homogeneous regions representing the different anatomical structures. Magnetic resonance brain image segmentation has large number of applications in diagnosis of neurological disorders like Alzheimer diseases, Parkinson related syndrome etc. But automatically segmenting the MR brain image is not an easy task. To solve this problem, several unsupervised and supervised based classification techniques have been developed in the literature. But supervised classification techniques are more time consuming and cost-sensitive due to the requirement of sufficient labeled data. In contrast, unsupervised classification techniques work without using any prior information but it suffers from the local trap problems. So, to overcome the problems associated with unsupervised and supervised classification techniques, we have proposed a new semi-supervised clustering technique using the concepts of multiobjective optimization and applied this technique for automatic segmentation of MR brain images in the intensity space. Multiple centers are used to encode a cluster in the form of a string. The proposed clustering technique utilizes intensity values of the brain pixels as the features. Additionally it also assumes that the actual class label information of 10% points of a particular image data set is also known. Three cluster validity indices are utilized as the objective functions, which are simultaneously optimized using AMOSA, a modern multiobjective optimization technique based on the concepts of simulated annealing. First two cluster validity indices are symmetry distance based Sym-index and Euclidean distance based I-index, which are based on unsupervised properties. Last one is a supervised information based cluster validity index, Minkowski Index. The effectiveness of this proposed semi-supervised clustering technique is demonstrated on several simulated MR normal brain images and MR brain images having some multiple sclerosis lesions. The performance of the proposed semi-supervised clustering technique is compared with some other popular image segmentation techniques like Fuzzy C-means, Expectation Maximization and some recent image clustering techniques like multi-objective based MCMOClust technique, and Fuzzy-VGAPS clustering techniques.     

一种基于多层次MRF的多源图象融合算法

图象融合技术的主要目的是将多种图象传感器数据中的互补信息组合起来 ,使形成的新图象更适合于计算机处理 (如分割、特征提取和目标识别 )等 .在多层次 MRF模型的基础上 ,提出了一种应用于多源图象分类的图象融合算法 .该融合算法将定义在多层次图结构上的非线性因果 Markov模型与贝叶斯 SMAP(sequential m axi-mum a posteriori)最优化准则结合起来 ,克服了 MAP(maximum a posteriori)准则在多层次图结构上计算不合理的缺陷 .该算法可应用于多源遥感图象中的信息融合 ,使像素分类更精确 ,并解决多源海量数据的富集表示 .另外还利用合成图象与自然图象分别针对多层次 MRF模型的改进及算法中可最优化准则的不同进行了对比实验 ,结果表明 ,该算法具有许多优越性     

基于C-V模型和MRF的脑部MRI分割

为准确分割脑部磁共振图像(MRI)的灰质、白质和背景,提出一种基于C-V模型和马尔可夫随机场的全自动分割方法。采用C-V模型与形态学相结合的方法对脑MRI进行预处理,去除多余脑组织,获得待分割图像。引入灰度场局部熵的思想对惩罚因子进行估计,利用马尔可夫随机场模型建模实现脑灰白质的分割,并运用形态学方法获得最终分割结果。对96幅IBSR图像和46幅临床图像进行实验,结果表明,该方法能够实现脑部MRI灰白质的全自动分割,且具有较好的分割精度和较快的处理速度。