Atlas-based automatic mouse brain image segmentation revisited: model complexity vs. image registration

Although many atlas-based segmentation methods have been developed and validated for the human brain, limited work has been done for the mouse brain. This paper investigated roles of image registration and segmentation model complexity in the mouse brain segmentation. We employed four segmentation models [single atlas, multiatlas, simultaneous truth and performance level estimation (STAPLE) and Markov random field (MRF) via four different image registration algorithms (affine, B-spline free-form deformation (FFD), Demons and large deformation diffeomorphic metric mapping (LDDMM)] for delineating 19 structures from in vivo magnetic resonance microscopy images. We validated their accuracies against manual segmentation. Our results revealed that LDDMM outperformed Demons, FFD and affine in any of the segmentation models. Under the same registration, increasing segmentation model complexity from single atlas to multiatlas, STAPLE or MRF significantly improved the segmentation accuracy. Interestingly, the multiatlas-based segmentation using nonlinear registrations (FFD, Demons and LDDMM) had similar performance to their STAPLE counterparts, while they both outperformed their MRF counterparts. Furthermore, when the single-atlas affine segmentation was used as reference, the improvement due to nonlinear registrations (FFD, Demons and LDDMM) in the single-atlas segmentation model was greater than that due to increasing model complexity (multiatlas, STAPLE and MRF affine segmentation). Hence, we concluded that image registration plays a more crucial role in the atlas-based automatic mouse brain segmentation as compared to model complexity. Multiple atlases with LDDMM can best improve the segmentation accuracy in the mouse brain among all segmentation models tested in this study.     

基于COLLATE融合多图谱的心脏电影MRI右心室分割

右心室分割对肺动脉高压等疾病的心功能分析具有重要的临床意义.然而，右心室心肌薄、易变且不规则，其传统的医学图像分割方法仍然未能取得突破性进展.本文提出基于COLLATE（Consensus Level，Labeler Accuracy and Truth Estimation）的多图谱分割方法，首先以归一化互信息为相似测度对目标图像和图谱集进行B样条配准以获取粗分割结果；然后利用COLLATE对粗分割结果进行融合；最后采用基于形状约束的区域生长算法修正出现错误的数据.10例临床心脏磁共振短轴电影图像被用于算法验证.本文还将使用基于COLLATE的多图谱分割方法得到的结果与深度学习算法及手动分割进行了比较.结果显示与深度学习算法比较，使用本文算法得到的射血分数（Ejection Fraction，EF）与手动分割更加一致和相关，表明该算法的分割结果有望辅助临床心脏功能诊断.     

Acoustic cues to lexical segmentation: a study of resynthesized speech

It has been posited that the role of prosody in lexical segmentation is elevated when the speech signal is degraded or unreliable. Using predictions from Cutler and Norris' [J. Exp. Psychol. Hum. Percept. Perform. 14, 113-121 (1988)] metrical segmentation strategy hypothesis as a framework, this investigation examined how individual suprasegmental and segmental cues to syllabic stress contribute differentially to the recognition of strong and weak syllables for the purpose of lexical segmentation. Syllabic contrastivity was reduced in resynthesized phrases by systematically (i) flattening the fundamental frequency (F0) contours, (ii) equalizing vowel durations, (iii) weakening strong vowels, (iv) combining the two suprasegmental cues, i.e., F0 and duration, and (v) combining the manipulation of all cues. Results indicated that, despite similar decrements in overall intelligibility, F0 flattening and the weakening of strong vowels had a greater impact on lexical segmentation than did equalizing vowel duration. Both combined-cue conditions resulted in greater decrements in intelligibility, but with no additional negative impact on lexical segmentation. The results support the notion of F0 variation and vowel quality as primary conduits for stress-based segmentation and suggest that the effectiveness of stress-based segmentation with degraded speech must be investigated relative to the suprasegmental and segmental impoverishments occasioned by each particular degradation.     

Multiple-phase segmentation approach for blood vessel extraction on cervical MRA image sequence

The segmentation of regions is an important first step for a variety of image-related applications such as image analysis, computer vision and visualization tasks. Specifically, the computer algorithm for the delineation of anatomical structures and other regions of interest is an essential component in assisting and automating specific radiological tasks. In this article, we propose a multiple-phase segmentation algorithm for carotid artery (CA) extraction. The seed position was automatically selected on the initially thresholded image by using a priori knowledge of the CA anatomic structure. In consideration of the preserved connectivity between consecutive slice images, the selected seed was maintained within the CA area throughout the entire segmentation process. The average intensity value was adaptively adjusted as a homogeneity criterion for each slice image. In addition, the stack feature should be used to automatically locate the branch, and the duplicated stack was used to save branch detection time for subsequent segmentation processes. This algorithm provided fine segmentation results compared with well-known single-phase segmentation approaches and other combined segmentation methods. This multiple-phase segmentation approach could be applicable to segment tree-like organ structures such as renal artery, coronary artery and airway tree from medical imaging modalities.     

Automated segmentation and quantitative study of retinal pigment epithelium cells for photoacoustic microscopy imaging

We develop an improved region growing method to realize automatic retinal pigment epithelium(RPE) cell segmentation for photoacoustic microscopy(PAM) imaging. The minimum bounding rectangle of the segmented region is used in this method to dynamically update the growing threshold for optimal segmentation. Phantom images and PAM imaging results of normal porcine RPE are applied to demonstrate the effectiveness of the segmentation. The method realizes accurate segmentation of RPE cells and also provides the basis for quantitative analysis of cell features such as cell area and component content, which can have potential applications in studying RPE cell functions for PAM imaging.     

Study of improved Otsu algorithm and its ration evaluation analysis for PCB photoelectric image segmentation

The algorithm of maximum variance between clusters (traditional Otsu algorithm) is discussed, and its advantage is given also. In order to segment the PCB photoelectric image better, on the basis of the traditional Otsu algorithm, considering the different influence of image segmentation about the factors of the distance between target and background as well as each kind of cohesion, an improved Otsu algorithm is proposed, and its basic principle and segmentation advantages are analyzed in detail. In order to evaluate these segmentation results impersonally by using different algorithms, the quantitative criteria of gray-level contrast and district interior uniformity are adopted to evaluate these segmentation results impersonally. Finally, the different segmentation experiment contrasts of PCB photoelectric image between our algorithm and other algorithms is executed, the results of experiment indicate that our algorithm has relatively better segmentation quality.     

Deep Learning-Based Segmentation of Head and Neck Organs-at-Risk with Clinical Partially Labeled Data

Radiotherapy is one of the main treatments for localized head and neck (HN) cancer. To design a personalized treatment with reduced radio-induced toxicity, accurate delineation of organs at risk (OAR) is a crucial step. Manual delineation is time- and labor-consuming, as well as observer-dependent. Deep learning (DL) based segmentation has proven to overcome some of these limitations, but requires large databases of homogeneously contoured image sets for robust training. However, these are not easily obtained from the standard clinical protocols as the OARs delineated may vary depending on the patient’s tumor site and specific treatment plan. This results in incomplete or partially labeled data. This paper presents a solution to train a robust DL-based automated segmentation tool exploiting a clinical partially labeled dataset. We propose a two-step workflow for OAR segmentation: first, we developed longitudinal OAR-specific 3D segmentation models for pseudo-contour generation, completing the missing contours for some patients; with all OAR available, we trained a multi-class 3D convolutional neural network (nnU-Net) for final OAR segmentation. Results obtained in 44 independent datasets showed superior performance of the proposed methodology for the segmentation of fifteen OARs, with an average Dice score coefficient and surface Dice similarity coefficient of 80.59% and 88.74%. We demonstrated that the model can be straightforwardly integrated into the clinical workflow for standard and adaptive radiotherapy.     

基于伪魏格纳分布分解的合成孔径雷达图像目标与阴影分割

在二维魏格纳分布的框架内,针对魏格纳变换的交叉项问题和计算量大的问题,提出了合成孔径雷达图像局部伪魏格纳变换的目标和目标阴影的分割方法.首先,将合成孔径雷达图像进行二维伪魏格纳变换,得到各像素点的二维能量谱图|然后提取各像素点的二维能量谱图对应位置值形成多个不同频段的与原图像同大小的能量谱图|最后,对不同频段的能量谱图采用不同的处理方法后,将各能量谱图相加处理后形成区域标识图像,最终得到原图像的目标和目标阴影分割图像.本文利用该方法对MSTAR切片图像进行了分割试验,并对分割图像与频谱最大值距离或方位分割算法和基于双参量CFAR与隐马尔科夫联合分割算法进行了分割图像对比度对比.实验结果表明,采用本文算法的合成孔径雷达分割图像,对比度明显提高,且保留了目标图像细节.     

A fully automatic three-step liver segmentation method on LDA-based probability maps for multiple contrast MR images

Automatic 3D liver segmentation in magnetic resonance (MR) data sets has proven to be a very challenging task in the domain of medical image analysis. There exist numerous approaches for automatic 3D liver segmentation on computer tomography data sets that have influenced the segmentation of MR images. In contrast to previous approaches to liver segmentation in MR data sets, we use all available MR channel information of different weightings and formulate liver tissue and position probabilities in a probabilistic framework. We apply multiclass linear discriminant analysis as a fast and efficient dimensionality reduction technique and generate probability maps then used for segmentation. We develop a fully automatic three-step 3D segmentation approach based upon a modified region growing approach and a further threshold technique. Finally, we incorporate characteristic prior knowledge to improve the segmentation results. This novel 3D segmentation approach is modularized and can be applied for normal and fat accumulated liver tissue properties.     

Portrait Segmentation Using Ensemble of Heterogeneous Deep-Learning Models

Image segmentation plays a central role in a broad range of applications, such as medical image analysis, autonomous vehicles, video surveillance and augmented reality. Portrait segmentation, which is a subset of semantic image segmentation, is widely used as a preprocessing step in multiple applications such as security systems, entertainment applications, video conferences, etc. A substantial amount of deep learning-based portrait segmentation approaches have been developed, since the performance and accuracy of semantic image segmentation have improved significantly due to the recent introduction of deep learning technology. However, these approaches are limited to a single portrait segmentation model. In this paper, we propose a novel approach using an ensemble method by combining multiple heterogeneous deep-learning based portrait segmentation models to improve the segmentation performance. The Two-Models ensemble and Three-Models ensemble, using a simple soft voting method and weighted soft voting method, were experimented. Intersection over Union (IoU) metric, IoU standard deviation and false prediction rate were used to evaluate the performance. Cost efficiency was calculated to analyze the efficiency of segmentation. The experiment results show that the proposed ensemble approach can perform with higher accuracy and lower errors than single deep-learning-based portrait segmentation models. The results also show that the ensemble of deep-learning models typically increases the use of memory and computing power, although it also shows that the ensemble of deep-learning models can perform more efficiently than a single model with higher accuracy using less memory and less computing power.     

An energy minimization method for MS lesion segmentation from T1-w and FLAIR images

In this paper, we extend the multiplicative intrinsic component optimization (MICO) algorithm to multichannel MR image segmentation, with focus on segmentation of multiple sclerosis (MS) lesions. The MICO algorithm was originally proposed by Li et al. in Ref. [1] for normal brain tissue segmentation and intensity inhomogeneity correction of a single channel MR image, which exhibits desirable advantages over other methods for MR image segmentation and intensity inhomogeneity correction in terms of segmentation accuracy and robustness. In this paper, we extend the MICO algorithm to multi-channel MR image segmentation and enable the segmentation of MS lesions. We assign different weights for different channels to control the impact of each channel. The weighted channels allow the enhancement of the impact of the FLAIR image on the segmentation of MS lesions by assigning a larger weight to the FLAIR image channel than the other channels. With the inherent mechanism of estimation of the bias field, our method is able to deal with the intensity inhomogeneity in the input multi-channel MR images. In the application of our method, we only use T1-w and FLAIR images as the input two channel MR images. Experimental results show promising result of our method.     

Automatic segmentation of cerebral white matter hyperintensities using only 3D FLAIR images

Magnetic Resonance (MR) white matter hyperintensities have been shown to predict an increased risk of developing cognitive decline. However, their actual role in the conversion to dementia is still not fully understood. Automatic segmentation methods can help in the screening and monitoring of Mild Cognitive Impairment patients who take part in large population-based studies. Most existing segmentation approaches use multimodal MR images. However, multiple acquisitions represent a limitation in terms of both patient comfort and computational complexity of the algorithms. In this work, we propose an automatic lesion segmentation method that uses only three-dimensional fluid-attenuation inversion recovery (FLAIR) images. We use a modified context-sensitive Gaussian mixture model to determine voxel class probabilities, followed by correction of FLAIR artifacts. We evaluate the method against the manual segmentation performed by an experienced neuroradiologist and compare the results with other unimodal segmentation approaches. Finally, we apply our method to the segmentation of multiple sclerosis lesions by using a publicly available benchmark dataset. Results show a similar performance to other state-of-the-art multimodal methods, as well as to the human rater.     

Enhanced Slime Mould Algorithm for Multilevel Thresholding Image Segmentation Using Entropy Measures

Image segmentation is a fundamental but essential step in image processing because it dramatically influences posterior image analysis. Multilevel thresholding image segmentation is one of the most popular image segmentation techniques, and many researchers have used meta-heuristic optimization algorithms (MAs) to determine the threshold values. However, MAs have some defects; for example, they are prone to stagnate in local optimal and slow convergence speed. This paper proposes an enhanced slime mould algorithm for global optimization and multilevel thresholding image segmentation, namely ESMA. First, the Levy flight method is used to improve the exploration ability of SMA. Second, quasi opposition-based learning is introduced to enhance the exploitation ability and balance the exploration and exploitation. Then, the superiority of the proposed work ESMA is confirmed concerning the 23 benchmark functions. Afterward, the ESMA is applied in multilevel thresholding image segmentation using minimum cross-entropy as the fitness function. We select eight greyscale images as the benchmark images for testing and compare them with the other classical and state-of-the-art algorithms. Meanwhile, the experimental metrics include the average fitness (mean), standard deviation (Std), peak signal to noise ratio (PSNR), structure similarity index (SSIM), feature similarity index (FSIM), and Wilcoxon rank-sum test, which is utilized to evaluate the quality of segmentation. Experimental results demonstrated that ESMA is superior to other algorithms and can provide higher segmentation accuracy.     

Supervised Domain Adaptation for Automated Semantic Segmentation of the Atrial Cavity

Atrial fibrillation (AF) is the most common cardiac arrhythmia. At present, cardiac ablation is the main treatment procedure for AF. To guide and plan this procedure, it is essential for clinicians to obtain patient-specific 3D geometrical models of the atria. For this, there is an interest in automatic image segmentation algorithms, such as deep learning (DL) methods, as opposed to manual segmentation, an error-prone and time-consuming method. However, to optimize DL algorithms, many annotated examples are required, increasing acquisition costs. The aim of this work is to develop automatic and high-performance computational models for left and right atrium (LA and RA) segmentation from a few labelled MRI volumetric images with a 3D Dual U-Net algorithm. For this, a supervised domain adaptation (SDA) method is introduced to infer knowledge from late gadolinium enhanced (LGE) MRI volumetric training samples (80 LA annotated samples) to a network trained with balanced steady-state free precession (bSSFP) MR images of limited number of annotations (19 RA and LA annotated samples). The resulting knowledge-transferred model SDA outperformed the same network trained from scratch in both RA (Dice equals 0.9160) and LA (Dice equals 0.8813) segmentation tasks.     

基于水平集的闪光照相图像分割算法

针对Chan-Vese(CV)模型局部控制能力差的缺点,将基于区域的CV模型和分割曲线的局部信息结合起来,提出了一种新的水平集图像分割算法。该算法以CV法的分割曲线为初始曲线,以获得全局收敛性,在后继分割中引入分割曲线的局部信息,以提高模型对图像中微弱信号的分割能力。对闪光照相图像的数值实验表明,该算法噪声抵抗能力强,对初始轮廓位置不敏感,能实现对含细长拓扑结构和微小孔洞的弱边界闪光图像的自动分割。     

Spatio-temporal segmentation of moving objects using edge features in infrared videos

In this paper, a novel method is proposed for spatio-temporal segmentation of moving objects using edge features in infrared videos. We define motion saliency of edge (MSoE) to generate the MSoE-map. The seeds of moving objects are extracted from the MSoE-map by using Otsu's method and subsequently compensated by historical data. An improved layer-based region growing method is applied to the seeds to achieve spatial segmentation of moving objects. The region growing method has an adjustable growing threshold. So, one of the focuses of our work is how to determine the best growing threshold. A Markov Random Field (MRF) based criterion with maximum a posterior (MAP) estimation principle is proposed for performance evaluation of moving object segmentation without ground truth (GT) in infrared videos. This criterion can be considered as an object function of threshold determination during global searching. The global optimum is accomplished by using simulated annealing (SA) algorithm to obtain the best growing threshold. The final segmentation mask of moving objects is grown from the seeds with the best growing threshold. Experimental results are provided to illustrate that the proposed method has better performance for moving object segmentation with fewer effects of object-background misclassification in infrared videos.     

Edge linking and image segmentation by combining optical and digital methods

We present a hybrid method for segmentation of intensity images, which combines an optical contouring technique and digital algorithms for linking edge points or image segmentation. In a first stage, the digital image to be processed is displayed in a twisted-nematic liquid-crystal display (LCD), which is placed between a polarizer–analyzer pair at 45 deg (instead of 90 deg as occurs in standard LCDs). It is not difficult to demonstrate that the proposed setup produces a resultant image with very pronounced dark contours at middle intensity. After the optical preprocessing, two different digital algorithms are applied: an edge linking algorithm (modified chain code) and a simple thresholding technique for image segmentation. The proposed procedure works well with monochromatic and color images. The method could be useful as a robust technique for segmentation of large images in real-time, which presents potential applications in medical and biological imaging.     

基于水平集的闪光照相图像分割算法

针对Chan-Vese(C-V)模型局部控制能力差的缺点,将基于区域的C-V模型和分割曲线的局部信息结合起来,提出了一种新的水平集图像分割算法。该算法以C-V法的分割曲线为初始曲线,以获得全局收敛性,在后继分割中引入分割曲线的局部信息,以提高模型对图像中微弱信号的分割能力。对闪光照相图像的数值实验表明,该算法噪声抵抗能力强,对初始轮廓位置不敏感,能实现对含细长拓扑结构和微小孔洞的弱边界闪光图像的自动分割。     

Automatic segmentation of white matter lesions on magnetic resonance images of the brain by using an outlier detection strategy

White matter lesions (WMLs) are commonly observed on the magnetic resonance (MR) images of normal elderly in association with vascular risk factors, such as hypertension or stroke. An accurate WML detection provides significant information for disease tracking, therapy evaluation, and normal aging research. In this article, we present an unsupervised WML segmentation method that uses Gaussian mixture model to describe the intensity distribution of the normal brain tissues and detects the WMLs as outliers to the normal brain tissue model based on extreme value theory. The detection of WMLs is performed by comparing the probability distribution function of a one-sided normal distribution and a Gumbel distribution, which is a specific extreme value distribution. The performance of the automatic segmentation is validated on synthetic and clinical MR images with regard to different imaging sequences and lesion loads. Results indicate that the segmentation method has a favorable accuracy competitive with other state-of-the-art WML segmentation methods.