Semi-supervised discriminative classification with application to tumorous tissues segmentation of MR brain images

Due to the large data size of 3D MR brain images and the blurry boundary of the pathological tissues, tumor segmentation work is difficult. This paper introduces a discriminative classification algorithm for semi-automated segmentation of brain tumorous tissues. The classifier uses interactive hints to obtain models to classify normal and tumor tissues. A non-parametric Bayesian Gaussian random field in the semi-supervised mode is implemented. Our approach uses both labeled data and a subset of unlabeled data sampling from 2D/3D images for training the model. Fast algorithm is also developed. Experiments show that our approach produces satisfactory segmentation results comparing to the manually labeled results by experts.

Robust spatially constrained fuzzy c-means algorithm for brain MR image segmentation

Objective

Accurate brain tissue segmentation from magnetic resonance (MR) images is an essential step in quantitative brain image analysis, and hence has attracted extensive research attention. However, due to the existence of noise and intensity inhomogeneity in brain MR images, many segmentation algorithms suffer from limited robustness to outliers, over-smoothness for segmentations and limited segmentation accuracy for image details. To further improve the accuracy for brain MR image segmentation, a robust spatially constrained fuzzy c-means (RSCFCM) algorithm is proposed in this paper.

Method

Firstly, a novel spatial factor is proposed to overcome the impact of noise in the images. By incorporating the spatial information amongst neighborhood pixels, the proposed spatial factor is constructed based on the posterior probabilities and prior probabilities, and takes the spatial direction into account. It plays a role as linear filters for smoothing and restoring images corrupted by noise. Therefore, the proposed spatial factor is fast and easy to implement, and can preserve more details. Secondly, the negative log-posterior is utilized as dissimilarity function by taking the prior probabilities into account, which can further improve the ability to identify the class for each pixel. Finally, to overcome the impact of intensity inhomogeneity, we approximate the bias field at the pixel-by-pixel level by using a linear combination of orthogonal polynomials. The fuzzy objective function is then integrated with the bias field estimation model to overcome the intensity inhomogeneity in the image and segment the brain MR images simultaneously.

Results

To demonstrate the performances of the proposed algorithm for the images with/without skull stripping, the first group of experiments is carried out in clinical 3T-weighted brain MR images which contain quite serious intensity inhomogeneity and noise. Then we quantitatively compare our algorithm to state-of-the-art segmentation approaches by using Jaccard similarity on benchmark images obtained from IBSR and BrainWeb with different level of noise and intensity inhomogeneity. The comparison results demonstrate that the proposed algorithm can produce higher accuracy segmentation and has stronger ability of denoising, especially in the area with abundant textures and details.

Conclusion

In this paper, the RSCFCM algorithm is proposed by utilizing the negative log-posterior as the dissimilarity function, introducing a novel factor and integrating the bias field estimation model into the fuzzy objective function. This algorithm successfully overcomes the drawbacks of existing FCM-type clustering schemes and EM-type mixture models. Our statistical results (mean and standard deviation of Jaccard similarity for each tissue) on both synthetic and clinical images show that the proposed algorithm can overcome the difficulties caused by noise and bias fields, and is capable of improving over 5% segmentation accuracy comparing with several state-of-the-art algorithms.     

基于模糊马尔可夫场的脑部MR图像分割算法

在传统马尔可夫场模型的基础上,建立了模糊马尔可夫场模型。通过对模型的分析得出图像像素对不同类的隶属度计算公式,提出了一种高效、无监督的图像分割算法,从而实现了对脑部MR图像的精确分割。通过对模拟脑部MR图像和临床脑部MR图像分割实验,表明新算法比传统的基于马尔可夫场的图像分割算法和模糊C-均值等图像分割算法有更精确的图像分割能力。     

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.     

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.     

A multi-plane approach for text segmentation of complex document images

This study presents a new method, namely the multi-plane segmentation approach, for segmenting and extracting textual objects from various real-life complex document images. The proposed multi-plane segmentation approach first decomposes the document image into distinct object planes to extract and separate homogeneous objects including textual regions of interest, non-text objects such as graphics and pictures, and background textures. This process consists of two stages—localized histogram multilevel thresholding and multi-plane region matching and assembling. Then a text extraction procedure is applied on the resultant planes to detect and extract textual objects with different characteristics in the respective planes. The proposed approach processes document images regionally and adaptively according to their respective local features. Hence detailed characteristics of the extracted textual objects, particularly small characters with thin strokes, as well as gradational illuminations of characters, can be well-preserved. Moreover, this way also allows background objects with uneven, gradational, and sharp variations in contrast, illumination, and texture to be handled easily and well. Experimental results on real-life complex document images demonstrate that the proposed approach is effective in extracting textual objects with various illuminations, sizes, and font styles from various types of complex document images.     

Intensity standardization simplifies brain MR image segmentation

Typically, brain MR images present significant intensity variation across patients and scanners. Consequently, training a classifier on a set of images and using it subsequently for brain segmentation may yield poor results. Adaptive iterative methods usually need to be employed to account for the variations of the particular scan. These methods are complicated, difficult to implement and often involve significant computational costs. In this paper, a simple, non-iterative method is proposed for brain MR image segmentation. Two preprocessing techniques, namely intensity-inhomogeneity-correction, and more importantly MR image intensity standardization, used prior to segmentation, play a vital role in making the MR image intensities have a tissue-specific numeric meaning, which leads us to a very simple brain tissue segmentation strategy.Vectorial scale-based fuzzy connectedness and certain morphological operations are utilized first to generate the brain intracranial mask. The fuzzy membership value of each voxel within the intracranial mask for each brain tissue is then estimated. Finally, a maximum likelihood criterion with spatial constraints taken into account is utilized in classifying all voxels in the intracranial mask into different brain tissue groups. A set of inhomogeneity corrected and intensity standardized images is utilized as a training data set. We introduce two methods to estimate fuzzy membership values. In the first method, called SMG (for simple membership based on a gaussian model), the fuzzy membership value is estimated by fitting a multivariate Gaussian model to the intensity distribution of each brain tissue whose mean intensity vector and covariance matrix are estimated and fixed from the training data sets. The second method, called SMH (for simple membership based on a histogram), estimates fuzzy membership value directly via the intensity distribution of each brain tissue obtained from the training data sets. We present several studies to evaluate the performance of these two methods based on 10 clinical MR images of normal subjects and 10 clinical MR images of Multiple Sclerosis (MS) patients. A quantitative comparison indicates that both methods have overall better accuracy than the k-nearest neighbors (kNN) method, and have much better efficiency than the Finite Mixture (FM) model-based Expectation-Maximization (EM) method. Accuracy is similar for our methods and EM method for the normal subject data sets, but much better for our methods for the patient data sets.     

Automatic segmentation of VHR images using type information of local structures acquired by mathematical morphology

The morphological profile (MP) and differential morphological profile (DMP) have been used extensively to acquire spatial information to be used in the segmentation of very high resolution (VHR) remotely sensed images. In most of the previous approaches, the maxima of the MP and DMP were investigated to estimate the best representative scale in the spatial domain for the pixel under consideration. Then, the object type (i.e. dark, bright or flat) was estimated based on the location of the maximum. Finally, the image segmentation was performed using the scale and type information as features. This approach usually causes over-segmentation. In this study, we also investigate the relevance of the DMP and the meaningful object types underlying the pixel of interest, however, instead of the maxima of the DMP, the type information is estimated using the whole DMP which is weighted by a weight function. Thus, the scale is not estimated directly but used indirectly in the estimation of the characteristic type for the object to which the pixel belongs. Then, the pixels are clustered based on their types only. The method has been applied to panchromatic high resolution QuickBird satellite images of the city of Ankara, Turkey. The results of the method were compared with previous studies and the proposed method seems to segment the images more precisely and semantically than the previous approaches.     

White matter hyper-intensities automatic identification and segmentation in magnetic resonance images

A methodology for automatic identification and segmentation of white matter hyper-intensities appearing in magnetic resonance images of brain axial cuts is presented. To this end, a sequence of image processing technics is employed to form an image where the hyper-intensities in white matter differ notoriously from the rest of the objects. This pre-processing stage facilitates the posterior process of identification and segmentation of the hyper-intensity volumes. The proposed methodology was tested on 55 magnetic resonance images from six patients. These images were analysed by the proposed system and the resulted hyper-intensity images were compared with the images manually segmented by experts. The experimental results show the mean rate of true positives of 0.9, the mean rate of false positives of 0.7 and the similarity index of 0.7; it is worth commenting that the false positives are found mostly within the grey matter not causing problems in early diagnosis. The proposed methodology for magnetic resonance image processing and analysis may be useful in the early detection of white matter lesions.     

Combining stationary wavelet transform and self-organizing maps for brain MR image segmentation

This study presents an image segmentation system that automatically segments and labels T1-weighted brain magnetic resonance (MR) images. The method is based on a combination of unsupervised learning algorithm of the self-organizing maps (SOM) and supervised learning vector quantization (LVQ) methods. Stationary wavelet transform (SWT) is applied to the images to obtain multiresolution information for distinguishing different tissues. Statistical information of the different tissues is extracted by applying spatial filtering to the coefficients of SWT. A multidimensional feature vector is formed by combining SWT coefficients and their statistical features. This feature vector is used as input to the SOM. SOM is used to segment images in a competitive unsupervised approach and an LVQ system is used for fine-tuning. Results are evaluated using Tanimoto similarity index and are compared with manually segmented images. Quantitative comparisons of our system with the other methods on real brain MR images using Tanimoto similarity index demonstrate that our system shows better segmentation performance for the gray matter while it gives average results for white matter.     

A new segmentation system for brain MR images based on fuzzy techniques

This work concerns a new method called fuzzy membership C-means (FMCMs) for segmentation of magnetic resonance images (MRI), and an efficient program implementation of it to the segmentation of MRI. Classical unsupervised clustering methods including the FCM by Bezdek, suffer many problems that can be partially treated with a proper rule to construct the initial membership matrix to clusters. This work develops a specific method to construct the initial membership matrix to clusters in order to improve the strength of the clusters. The new FMCM is tested on a set of benchmarks and then the application to the segmentation of MR images is presented and compared with the results obtained using FCM.     

改进的遗传模糊聚类算法对医学图像的分割

利用遗传算法全局随机搜索的特点,可以解决模糊C均值聚类（FCM）算法在医学图像分割中容易陷入局部最优解的问题,但确定遗传算法的初始搜索范围时,需要借助于人的经验。为此,用收敛速度快的硬聚类算法得到的聚类中心作为参考,上下浮动划出一个较小的数据范围,作为遗传算法的初始搜索空间。该方法在避免FCM算法陷入局部最优化的同时,也加速了遗传算法的收敛过程。实验表明,该方法相对于标准的遗传模糊算法,效果要好得多。     

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.     

Topologically controlled segmentation of 3D magnetic resonance images of the head by using morphological operators

This paper proposes a new data-driven segmentation technique of 3D T1-weighted magnetic resonance scans of human head. This technique serves to the construction of individual head models. Several structures of the head are extracted. The morphology-oriented approach combined with an extensive use of topological constraints provides a robust and automatic method requiring minimum user intervention. This new approach is suitable to applications where the topology is one of the main constraints. The originality of the approach lies in the satisfaction of such constraints and in an effort towards robustness.     

基于动态自适应蚁群算法的MRI图像分割

MRI图像分割在医学图像分析中具有极其重要的理论和应用价值.蚁群算法是一种具有离散性、并行性、鲁棒性和模糊聚类能力的进化方法.对目标边界模糊、目标灰度不均匀及目标不连续等情况的图像(如医学图像)分割,蚁群算法是一个比较好的选择.本文针对基本蚁群算法容易出现早熟和停滞现象的特性,提出了一种动态自适应蚁群算法,通过自适应的初始聚类中心调整策略和动态更新局部信息素浓度,使其收敛性和稳定性有一定的提高.实验证明改进的蚁群算法能够有效地分割MRI图像.     

A reinforcement agent for object segmentation in ultrasound images

The principal contribution of this work is to design a general framework for an intelligent system to extract one object of interest from ultrasound images. This system is based on reinforcement learning. The input image is divided into several sub-images, and the proposed system finds the appropriate local values for each of them so that it can extract the object of interest. The agent uses some images and their ground-truth (manually segmented) version to learn from. A reward function is employed to measure the similarities between the output and the manually segmented images, and to provide feedback to the agent. The information obtained can be used as valuable knowledge stored in the Q-matrix. The agent can then use this knowledge for new input images. The experimental results for prostate segmentation in trans-rectal ultrasound images show high potential of this approach in the field of ultrasound image segmentation.     

Fast deformable matching of 3D images over multiscale nested subspaces. Application to atlas-based MRI segmentation

This paper presents a fast method to perform dense deformable matching of 3D images, applied to the registration of inter-subject brain MR images. To recover the complex morphological variations in neuroanatomy, the registration method uses a hierarchy of 3D deformations fields that are estimated, by minimizing a global energy function over a sequence of nested subspaces. The resulting deformable matching method shows low sensitivity to local minima and is able to track large non-linear deformations, with moderate computational load. The performances of the approach are assessed both on simulated 3D transformations and on a real data base of 3D brain MR images from different individuals. An application of the deformable image matching method to 3D atlas-based image segmentation is presented. This atlas-based segmentation is used at Strasbourg Hospital, in daily clinical applications, in order to extract regions of interest from 3D MR images of patients suffering from epilepsy.     

Marginal noise removal of document images

Marginal noise is a common phenomenon in document analysis which results from the scanning of thick documents or skew documents. It usually appears in the front of a large and dark region around the margin of document images. Marginal noise might cover meaningful document objects, such as text, graphics and forms. The overlapping of marginal noise with meaningful objects makes it difficult to perform the task of segmentation and recognition of document objects. This paper proposes a novel approach to remove marginal noise. The proposed approach consists of two steps which are marginal noise detection and marginal noise deletion. Marginal noise detection will reduce an original document image into a smaller image, and then find marginal noise regions according to the shape length and location of the split blocks. After the detection of marginal noise regions, different removal methods are performed. A local thresholding method is proposed for the removal of marginal noise in gray-scale document images, whereas a region growing method is devised for binary document images. Experimenting with a wide variety of test samples reveals the feasibility and effectiveness of our proposed approach in removing marginal noises.     

Brain tissue segmentation based on spatial information fusion by Dempster-Shafer theory

As a result of noise and intensity non-uniformity,automatic segmentation of brain tissue in magnetic resonance imaging (MRI) is a challenging task.In this study a novel brain MRI segmentation approach is presented which employs Dempster-Shafer theory (DST) to perform information fusion.In the proposed method,fuzzy c-mean (FCM) is applied to separate features and then the outputs of FCM are interpreted as basic belief structures.The salient aspect of this paper is the interpretation of each FCM output as a belief structure with particular focal elements.The results of the proposed method are evaluated using Dice similarity and Accuracy indices.Qualitative and quantitative comparisons show that our method performs better and is more robust than the existing method.