Automated atlas-based segmentation of NISSL-stained mouse brain sections using supervised learning

The problem of segmentation of mouse brain images into anatomical structures is an important stage of practically every analytical procedure for these images. The present study suggests a new approach to automated segmentation of anatomical structures in the images of NISSL-stained histological sections of mouse brain. The segmentation algorithm is based on the method of supervised learning using the existing anatomical labeling of the corresponding sections from a specialized mouse brain atlas. A mouse brain section to be segmented into anatomical structures is preliminarily associated with a section from the mouse brain atlas displaying the maximum similarity. The image of this section is then preprocessed in order to enhance its quality and to make it as close to the corresponding atlas image as possible. An efficient algorithm of luminance equalization, an extension of the well-known Retinex algorithm is proposed. A random forest is trained on pixel feature vectors constructed based on the atlas section images and the corresponding class labels associated with anatomical structures extracted from the atlas anatomical labeling. The trained classifier is then applied to classify pixels of an experimental section into anatomical structures. A new combination of features based on superpixels and location priors is suggested. Accuracy of the obtained result is increased by using Markov random field. Procedures of luminance equalization and subsequent segmentation into anatomical structures have been tested on real experimental sections.     

Spatially Constrained Student’s <Emphasis Type="Italic">t</Emphasis>-Distribution Based Mixture Model for Robust Image Segmentation

The finite Gaussian mixture model is one of the most popular frameworks to model classes for probabilistic model-based image segmentation. However, the tails of the Gaussian distribution are often shorter than that required to model an image class. Also, the estimates of the class parameters in this model are affected by the pixels that are atypical of the components of the fitted Gaussian mixture model. In this regard, the paper presents a novel way to model the image as a mixture of finite number of Student’s t-distributions for image segmentation problem. The Student’s t-distribution provides a longer tailed alternative to the Gaussian distribution and gives reduced weight to the outlier observations during the parameter estimation step in finite mixture model. Incorporating the merits of Student’s t-distribution into the hidden Markov random field framework, a novel image segmentation algorithm is proposed for robust and automatic image segmentation, and the performance is demonstrated on a set of HEp-2 cell and natural images. Integrating the bias field correction step within the proposed framework, a novel simultaneous segmentation and bias field correction algorithm has also been proposed for segmentation of magnetic resonance (MR) images. The efficacy of the proposed approach, along with a comparison with related algorithms, is demonstrated on a set of real and simulated brain MR images both qualitatively and quantitatively.     

A Modified Fuzzy C-Means Algorithm for Brain MR Image Segmentation and Bias Field Correction

In quantitative brain image analysis, accurate brain tissue segmentation from brain magnetic resonance image (MRI) is a critical step. It is considered to be the most important and difficult issue in the field of medical image processing. The quality of MR images is influenced by partial volume effect, noise, and intensity inhomogeneity, which render the segmentation task extremely challenging. We present a novel fuzzy c-means algorithm (RCLFCM) for segmentation and bias field correction of brain MR images. We employ a new gray-difference coefficient and design a new impact factor to measure the effect of neighbor pixels, so that the robustness of anti-noise can be enhanced. Moreover, we redefine the objective function of FCM (fuzzy c-means) by adding the bias field estimation model to overcome the intensity inhomogeneity in the image and segment the brain MR images simultaneously. We also construct a new spatial function by combining pixel gray value dissimilarity with its membership, and make full use of the space information between pixels to update the membership. Compared with other state-of-the-art approaches by using similarity accuracy on synthetic MR images with different levels of noise and intensity inhomogeneity, the proposed algorithm generates the results with high accuracy and robustness to noise.     

Novel segmentation algorithm in segmenting medical images

The aim of this paper is to develop an effective fuzzy c-means (FCM) technique for segmentation of Magnetic Resonance Images (MRI) which is seriously affected by intensity inhomogeneities that are created by radio-frequency coils. The weighted bias field information is employed in this work to deal the intensity inhomogeneities during the segmentation of MRI. In order to segment the general shaped MRI dataset which is corrupted by intensity inhomogeneities and other artifacts, the effective objective function of fuzzy c-means is constructed by replacing the Euclidean distance with kernel-induced distance. In this paper, the initial cluster centers are assigned using the proposed center initialization algorithm for executing the effective FCM iteratively. To assess the performance of proposed method in comparison with other existed methods, experiments are performed on synthetic image, real breast and brain MRIs. The clustering results are validated using Silhouette accuracy index. The experimental results demonstrate that our proposed method is a promising technique for effective segmentation of medical images.     

局部高斯分布拟合的脑MR图像分割及有偏场校正

为实现对灰度不均匀脑核磁共振(MR)图像分割的同时进行有偏场估计并校正,提出一种基于局部高斯分布拟合(LGDF)模型的多相水平集方法.通过分析图像有偏场模型的局部特性,将有偏场乘性因子引入到图像局部灰度均值的表达中,从而使有偏场乘性因子成为新的能量函数的变量.能量函数的迭代最小化既实现了目标组织分割,又有效估计了有偏场.合成图像和仿真脑MR图像实验结果表明,本文方法比现有多种方法分割性能更好,且利用本文方法估计的有偏场校正后的图像有更好的视觉效果.     

A non-local fuzzy segmentation method: Application to brain MRI

The Fuzzy C-Means (FCM) algorithm is a widely used and flexible approach to automated image segmentation, especially in the field of brain tissue segmentation from 3D MRI, where it addresses the problem of partial volume effects. In order to improve its robustness to classical image deterioration, namely noise and bias field artifacts, which arise in the MRI acquisition process, we propose to integrate into the FCM segmentation methodology concepts inspired by the non-local (NL) framework, initially defined and considered in the context of image restoration. The key algorithmic contributions of this article are the definition of an NL data term and an NL regularisation term to efficiently handle intensity inhomogeneities and noise in the data. The resulting new energy formulation is then built into an NL-FCM brain tissue segmentation algorithm. Experiments performed on both synthetic and real MRI data, leading to the classification of brain tissues into grey matter, white matter and cerebrospinal fluid, indicate a significant improvement in performance in the case of higher noise levels, when compared to a range of standard algorithms.     

多描述子活动轮廓模型的医学图像分割

目的 医学图像分割结果可帮助医生进行预测、诊断及制定治疗方案。医学图像在采集过程中受多种因素影响,同一组织往往具有不同灰度,且伴有强噪声。现有的针对医学图像的分割方法,对图像的灰度分布描述不够充分,不足以为精确的分割图像信息,且抗噪性较差。为实现医学图像的精确分割,提出一种多描述子的活动轮廓（MDAC）模型。方法 首先,引入图像的熵,结合图像的局部均值和方差共同描述图像的灰度分布。其次,在贝叶斯框架下,引入灰度偏移因子,建立活动轮廓模型的能量泛函。最后,利用梯度下降流法得到水平集演化公式,演化的最后在完成分割的同时实现偏移场的矫正。结果 利用合成图像和心脏、血管和脑等医学图像进行了仿真实验。利用MDAC模型对加噪的灰度不均图像进行分割,结果显示,在完成精确分割的同时实现了纠偏。通过对比分割前后图像的灰度直方图,纠偏图像只包含对应两相的两个峰,且界限更加清晰;与经典分割算法进行对比,MDAC在视觉效果和定量分析中,分割效果最好,比LIC的分割精度提高了30%多。结论 实验结果表明,利用均值、方差和局部熵共同描述图像灰度分布,保证了算法的精度。局部熵的引入,在保证算法精度的同时,提高了算法的抗噪性。能泛中嵌入偏移因子,保证算法精确分割的同时实现偏移场纠正,进一步提高分割精度。     

基于隶属度光滑约束的模糊C均值聚类算法

传统的FCM聚类算法未利用图像的空间信息,在分割叠加了噪声的MR图像时分割效果不理想。本文考虑到脑部MR图像真实的灰度值具有分片为常数的特性,按照合理利用图像空间信息的原则,对传统的FCM聚类算法进行了改进,增加了使隶属度趋向于分片光滑的约束项,得到了新的聚类算法。通过对模拟脑部MR图像和临床脑部MR图像的分割实验结果表明,本文提出的新算法比传统的FCM算法等多种图像分割算法有更精确的图像分割能力,并且运算简单、运算速度快、稳健性好。     

基于局部区域拟合模型的磁共振图像分割与偏移估计算法

磁共振(MR)图像的灰度通常是不均匀的,这种不均匀性是由于成像设备的缺陷导致产生了一种光滑的偏移场.一般的基于灰度统计特性的分割算法都是假设目标区域和背景区域图像的灰度分别是一致的,因此该类算法不能很好地应用于磁共振图像的分割.提出一种基于局部拟合模型的磁共振图像分割与偏移估计算法:利用图像的局部区域的灰度特性建立恢复...     

A two-stage fuzzy multi-objective framework for segmentation of 3D MRI brain image data

Segmentation of Magnetic Resonance Imaging (MRI) brain image data has a significant impact on the computer guided medical image diagnosis and analysis. However, due to limitation of image acquisition devices and other related factors, MRI images are severely affected by the noise and inhomogeneity artefacts which lead to blurry edges in the intersection of the intra-organ soft tissue regions, making the segmentation process more difficult and challenging. This paper presents a novel two-stage fuzzy multi-objective framework (2sFMoF) for segmenting 3D MRI brain image data. In the first stage, a 3D spatial fuzzy c-means (3DSpFCM) algorithm is introduced by incorporating the 3D spatial neighbourhood information of the volume data to define a new local membership function along with the global membership function for each voxel. In particular, the membership functions actually define the underlying relationship between the voxels of a close cubic neighbourhood and image data in 3D image space. The cluster prototypes thus obtained are fed into a 3D modified fuzzy c-means (3DMFCM) algorithm, which further incorporates local voxel information to generate the final prototypes. The proposed framework addresses the shortcomings of the traditional FCM algorithm, which is highly sensitive to noise and may stuck into a local minima. The method is validated on a synthetic image volume and several simulated and in-vivo 3D MRI brain image volumes and found to be effective even in noisy data. The empirical results show the supremacy of the proposed method over the other FCM based algorithms and other related methods devised in the recent past.     

A framework with modified fast FCM for brain MR images segmentation

Intensity inhomogeneity, noise and partial volume (PV) effect render a challenging task for segmentation of brain magnetic resonance (MR) images. Most of the current MR image segmentation methods focus on only one or two of the effects listed above. In this paper, a framework with modified fast fuzzy c-means for brain MR images segmentation is proposed to take all these effects into account simultaneously and improve the accuracy of image segmentations. Firstly, we propose a new automated method to determine the initial values of the centroids. Secondly, an adaptive method to incorporate the local spatial continuity is proposed to overcome the noise effectively and prevent the edge from blurring. The intensity inhomogeneity is estimated by a linear combination of a set of basis functions. Meanwhile, a regularization term is added to reduce the iteration steps and accelerate the algorithm. The weights of the regularization terms are all automatically computed to avoid the manually tuned parameter. Synthetic and real MR images are used to test the proposed framework. Improved performance of the proposed algorithm is observed where the intensity inhomogeneity, noise and PV effect are commonly encountered. The experimental results show that the proposed method has stronger anti-noise property and higher segmentation precision than other reported FCM-based techniques.     

Image registration and atlas-based segmentation of cardiac outflow velocity profiles

Cardiovascular disease is the leading cause of death worldwide and for this reason computer-based diagnosis of cardiac diseases is a very important task. In this article, a method for segmentation of aortic outflow velocity profiles from cardiac Doppler ultrasound images is presented. The proposed method is based on the statistical image atlas derived from ultrasound images of healthy volunteers. The ultrasound image segmentation is done by registration of the input image to the atlas, followed by a propagation of the segmentation result from the atlas onto the input image. In the registration process, the normalized mutual information is used as an image similarity measure, while optimization is performed using a multiresolution gradient ascent method. The registration method is evaluated using an in-silico phantom, real data from 30 volunteers, and an inverse consistency test. The segmentation method is evaluated using 59 images from healthy volunteers and 89 images from patients, and using cardiac parameters extracted from the segmented image. Experimental validation is conducted using a set of healthy volunteers and patients and has shown excellent results. Cardiac parameter segmentation evaluation showed that the variability of the automated segmentation relative to the manual is comparable to the intra-observer variability. The proposed method is useful for computer aided diagnosis and extraction of cardiac parameters.     

基于边缘竞争模糊水平集的脑部磁共振图像自动分割

针对脑部磁共振(MR)图像分割时容易出现的受噪声影响大和边缘定位模糊问题,提出一种以基于核函数的增强模糊C均值(RFCMK)算法结果为先验知识的边缘竞争水平集自动分割方法。首先采用RFCMK算法对图像进行预分割;然后对预分割后的各子类图像进行阈值化处理,并将其边缘作为水平集演化的初始轮廓;最后采用引入竞争机制的边缘指示器对各部分边缘进行演化。该方法对模拟图像不同层切面的分割实验表明,基于面积和基于边缘的评估统计值范围分别为[0.91,0.95]和[0.05,0.22]。对噪声图像的实验结果表明该方法能够有效地抑制噪声对分割结果的影响。     

Optimal segmentation of brain MRI based on adaptive bacterial foraging algorithm

Segmentation of brain magnetic resonance images (MRIs) can be used to identify various neural disorders. The MRI segmentation facilitates in extracting different brain tissues such as white matter, gray matter and cerebrospinal fluids. Segmentation of these tissues helps in determining the volume of the tissues in three-dimensional brain MRI, which yields in analyzing many neural disorders such as epilepsy and Alzheimer disease. In this article, multilevel thresholding based on adaptive bacterial foraging (ABF) algorithm is presented for brain MRI segmentation. The proposed ABF algorithm employs an adaptive step size to improve both exploration and exploitation capability of the BF algorithm. Maximization of the measure of separability on the basis of the entropy (Kapur) method and the between-class variance (Otsu) method, which are the two popular thresholding techniques, are employed to evaluate the performance of the proposed method. Application results to axial, T2-weighted brain MRI slices are provided to show the performance of the proposed segmentation approach. These results are compared with bacterial foraging (BF) algorithm, particle swarm optimization (PSO) algorithm and genetic algorithm (GA) in terms of solution quality, robustness and computational efficiency.     

Improved spatial fuzzy c-means clustering for image segmentation using PSO initialization,Mahalanobis distance and post-segmentation correction

In this paper, we propose an improvement method for image segmentation using the fuzzy c-means clustering algorithm (FCM). This algorithm is widely experimented in the field of image segmentation with very successful results. In this work, we suggest further improving these results by acting at three different levels. The first is related to the fuzzy c-means algorithm itself by improving the initialization step using a metaheuristic optimization. The second level is concerned with the integration of the spatial gray-level information of the image in the clustering segmentation process and the use of Mahalanobis distance to reduce the influence of the geometrical shape of the different classes. The final level corresponds to refining the segmentation results by correcting the errors of clustering by reallocating the potentially misclassified pixels. The proposed method, named improved spatial fuzzy c-means IFCMS, was evaluated on several test images including both synthetic images and simulated brain MRI images from the McConnell Brain Imaging Center (BrainWeb) database. This method is compared to the most used FCM-based algorithms of the literature. The results demonstrate the efficiency of the ideas presented.     

自适应最小误差阈值分割算法

对二维最小误差法进行三维推广, 并结合三维直方图重建和降维思想提出了一种鲁 棒的最小误差阈值分割算法. 但该方法为全局算法, 仅适用于分割均匀光照图像. 为 提高其自适应性, 本文采用Water flow模型对非均匀光照图像进行背景估计, 以此获 得原始图像与背景图像的差值图像, 达到降低非均匀光照对图像分割造成干扰的目的. 为进 一步提高分割性能, 本文对差值图像采用γ 矫正进行增强, 然后采用鲁棒最小误差 法进行全局分割, 从而完成目标提取. 最后本文对均匀光照下以及非均匀光照下图像进行了 实验, 并与一维最小误差法、二维最小误差法、三维直方图重建和降维的Otsu阈值分割 算法、灰度波动变换自适应阈值方法以及一种改进的FCM方法在错误分割率和运行时间上进 行了对比. 实验结果表明, 相对于以上方法, 本算法的分割性能均有明显提升.     

Strong fuzzy c-means in medical image data analysis

This paper presents a robust fuzzy c-means (FCM) for an automatic effective segmentation of breast and brain magnetic resonance images (MRI). This paper obtains novel objective functions for proposed robust fuzzy c-means by replacing original Euclidean distance with properties of kernel function on feature space and using Tsallis entropy. By minimizing the proposed effective objective functions, this paper gets membership partition matrices and equations for successive prototypes. In order to reduce the computational complexity and running time, center initialization algorithm is introduced for initializing the initial cluster center. The initial experimental works have done on synthetic image and benchmark dataset to investigate the effectiveness of proposed, and then the proposed method has been implemented to differentiate the different region of real breast and brain magnetic resonance images. In order to identify the validity of proposed fuzzy c-means methods, segmentation accuracy is computed by using silhouette method. The experimental results show that the proposed method is more capable in segmentation of medical images than existed methods.     

稀疏形状先验的脑肿瘤图像分割

目的 在脑部肿瘤图像的分析过程中,准确分割出肿瘤区域对于计算机辅助脑部肿瘤疾病的诊断及治疗过程具有重要意义。然而,由于脑部图像常存在结构复杂、边界模糊、灰度不均以及肿瘤内部存在明暗区域的问题,使得肿瘤图像分割工作面临严峻挑战。为了克服上述困难,更好地实现脑部肿瘤图像分割,提出一种基于稀疏形状先验的脑肿瘤图像分割算法。方法 首先,研究脑部肿瘤图像的配准与形状描述,并以此为基础构建脑部肿瘤的稀疏形状先验约束模型;继而,将该稀疏形状先验约束模型与区域能量描述方法相结合,构建基于稀疏形状先验的能量函数;最后,对能量函数进行优化及迭代,输出脑部肿瘤区域分割结果。结果 本文使用脑胶质瘤公开数据集BraTS2017进行算法测试,本文算法的分割结果与真实数据之间的平均相似度达到93.97%,灵敏度达到91.3%,阳性预测率达到95.9%。本文算法的实验准确度较高,误判率较低,鲁棒性较强。结论 本文算法能够结合水平集方法在拓扑结构描述和稀疏表达方法在复杂形状表达方面的优势,同时由于加入了形状约束,能够有效削弱肿瘤内部明暗区域对分割结果造成的影响,从而更准确和稳定地实现脑部肿瘤图像分割。     

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.     

Multi-objective evolutionary for synthetic aperture radar image segmentation with non-local means denoising

Synthetic aperture radar (SAR) image segmentation is an important problem of the realm of image segmentation. In this study, a novel SAR image segmentation algorithm using a multi-objective evolutionary algorithm based on decomposition with non-local means denoising (MISD) is proposed. The novelty of MISD lies in the following issues: (1) an effective multi-objective method with decomposition to solve SAR image segmentation; (2) in order to denoise the SAR images and retain the details, we employ non-local means to remove the noise. The multi-objective decomposition method makes MISD have lower computational complexity. In order to evaluate the performance of the new method, we compared the results with three other popular segmentation approaches on four simulated and two real SAR images. In our experiments, the new method can always find better results, which means MISD is a promising SAR image segmentation method.