基于改进U-Net网络的腺体细胞图像分割算法

针对腺体图像在自动分割过程中由于多尺度目标和信息丢失影响导致准确率降低的问题,文中采用了一种引入注意力模块的全卷积神经网络模型。该模型遵循编码器-解码器结构,在编码网络中用空洞残差卷积层代替原有的普通卷积层,并添加空洞金字塔池;再在解码网络中加入注意力模块,使模型输出高分辨率特征图,提高对多尺度目标的分割精度。实验结果表明,提出的网络模型参数少分割精度高,对腺体图像的平均分割精度高达89.7%,具有较好的鲁棒性。     

Automatic 3-D segmentation of internal structures of the head in MR images using a combination of similarity and free-form transformations: Part II, validation on severely atrophied brains

Studies aimed at quantifying neuroanatomical differences between populations require the volume measurements of individual brain structures. If the study contains a large number of images, manual segmentation is not practical. This study tests the hypothesis that a fully automatic, atlas-based segmentation method can be used to quantify atrophy indexes derived from the brain and cerebellum volumes in normal subjects and chronic alcoholics. This is accomplished by registering an atlas volume with a subject volume, first using a global transformation, and then improving the registration using a local transformation. Segmented structures in the atlas volume are then mapped to the corresponding structures in the subject volume using the combined global and local transformations. This technique has been applied to seven normal and seven alcoholic subjects. Three magnetic resonance volumes were obtained for each subject and each volume was segmented automatically, using the atlas-based method. Accuracy was assessed by manually segmenting regions and measuring the similarity between corresponding regions obtained automatically. Repeatability was determined by comparing volume measurements of segmented structures from each acquisition of the same subject. Results demonstrate that the method is accurate, that the results are repeatable, and that it can provide a method for automatic quantification of brain atrophy, even when the degree of atrophy is large.     

Multi-Atlas-Based Segmentation With Local Decision Fusion—Application to Cardiac and Aortic Segmentation in CT Scans

A novel atlas-based segmentation approach based on the combination of multiple registrations is presented. Multiple atlases are registered to a target image. To obtain a segmentation of the target, labels of the atlas images are propagated to it. The propagated labels are combined by spatially varying decision fusion weights. These weights are derived from local assessment of the registration success. Furthermore, an atlas selection procedure is proposed that is equivalent to sequential forward selection from statistical pattern recognition theory. The proposed method is compared to three existing atlas-based segmentation approaches, namely 1) single atlas-based segmentation, 2) average-shape atlas-based segmentation, and 3) multi-atlas-based segmentation with averaging as decision fusion. These methods were tested on the segmentation of the heart and the aorta in computed tomography scans of the thorax. The results show that the proposed method outperforms other methods and yields results very close to those of an independent human observer. Moreover, the additional atlas selection step led to a faster segmentation at a comparable performance.      

Method for segmenting chest CT image data using an anatomicalmodel: preliminary results

Presents an automated, knowledge-based method for segmenting chest computed tomography (CT) datasets. Anatomical knowledge including expected volume, shape, relative position, and X-ray attenuation of organs provides feature constraints that guide the segmentation process. Knowledge is represented at a high level using an explicit anatomical model. The model is stored in a frame-based semantic network and anatomical variability is incorporated using fuzzy sets. A blackboard architecture permits the data representation and processing algorithms in the model domain to be independent of those in the image domain. Knowledge-constrained segmentation routines extract contiguous three-dimensional (3-D) sets of voxels, and their feature-space representations are posted on the blackboard. An inference engine uses fuzzy logic to match image to model objects based on the feature constraints. Strict separation of model and image domains allows for systematic extension of the knowledge base. In preliminary experiments, the method has been applied to a small number of thoracic CT datasets. Based on subjective visual assessment by experienced thoracic radiologists, basic anatomic structures such as the lungs, central tracheobronchial tree, chest wall, and mediastinum were successfully segmented. To demonstrate the extensibility of the system, knowledge was added to represent the more complex anatomy of lung lesions in contact with vessels or the chest wall. Visual inspection of these segmented lesions was also favorable. These preliminary results suggest that use of expert knowledge provides an increased level of automation compared with low-level segmentation techniques. Moreover, the knowledge-based approach may better discriminate between structures of similar attenuation and anatomic contiguity. Further validation is required     

Intrathoracic airway trees: segmentation and airway morphology analysis from low-dose CT scans

The segmentation of the human airway tree from volumetric computed tomography (CT) images builds an important step for many clinical applications and for physiological studies. Previously proposed algorithms suffer from one or several problems: leaking into the surrounding lung parenchyma, the need for the user to manually adjust parameters, excessive runtime. Low-dose CT scans are increasingly utilized in lung screening studies, but segmenting them with traditional airway segmentation algorithms often yields less than satisfying results. In this paper, a new airway segmentation method based on fuzzy connectivity is presented. Small adaptive regions of interest are used that follow the airway branches as they are segmented. This has several advantages. It makes it possible to detect leaks early and avoid them, the segmentation algorithm can automatically adapt to changing image parameters, and the computing time is kept within moderate values. The new method is robust in the sense that it works on various types of scans (low-dose and regular dose, normal subjects and diseased subjects) without the need for the user to manually adjust any parameters. Comparison with a commonly used region-grow segmentation algorithm shows that the newly proposed method retrieves a significantly higher count of airway branches. A method that conducts accurate cross-sectional airway measurements on airways is presented as an additional processing step. Measurements are conducted in the original gray-level volume. Validation on a phantom shows that subvoxel accuracy is achieved for all airway sizes and airway orientations.     

Automated 3-D segmentation of lungs with lung cancer in CT data using a novel robust active shape model approach

Segmentation of lungs with (large) lung cancer regions is a nontrivial problem. We present a new fully automated approach for segmentation of lungs with such high-density pathologies. Our method consists of two main processing steps. First, a novel robust active shape model (RASM) matching method is utilized to roughly segment the outline of the lungs. The initial position of the RASM is found by means of a rib cage detection method. Second, an optimal surface finding approach is utilized to further adapt the initial segmentation result to the lung. Left and right lungs are segmented individually. An evaluation on 30 data sets with 40 abnormal (lung cancer) and 20 normal left/right lungs resulted in an average Dice coefficient of 0.975±0.006 and a mean absolute surface distance error of 0.84±0.23 mm, respectively. Experiments on the same 30 data sets showed that our methods delivered statistically significant better segmentation results, compared to two commercially available lung segmentation approaches. In addition, our RASM approach is generally applicable and suitable for large shape models.     

基于3D区域增长法和改进的凸包算法相结合的全肺分割方法

肺实质分割结果的准确性在实际临床应用中具有非常重要的意义。但由于肺结节的位置、大小、形状的不规则性,肺部病变的多样性,以及人体胸部解剖结构的明显差异等,使得各类分割方法不能统一地适用于所有的胸部CT图像,所以对于肺实质分割方法的研究仍具有很大的挑战。该文在国内外研究分析的基础上提出基于3D区域增长法与改进的凸包修补算法相结合的全肺分割方法。在3D区域增长法的粗分割基础上,对分割的结果进行细化工作,通过连通域标记法与形态学方法相结合去除气管和主支气管,得到初步的肺实质掩膜,最后应用改进的凸包算法对肺部轮廓进行修补平滑,最终得到肺部分割结果。通过与凸包算法及滚球法相对比,证明该文所提改进的凸包算法能够有效地修补肺部轮廓凹陷,修补后的结果分割精度较高。     

基于3D全卷积网络的腹部动脉CTA分割算法

目前卷积神经网络已成为腹部动脉血管分割领域的研究热点,但经典的卷积网络存在分割精度低和分割血管不连续的问题。为此,文中提出了基于改进3D全卷积网络的腹部动脉血管分割算法。该方法在网络的编码路径上构造不同尺度的侧输入,并将侧输入卷积后的图像与下采样卷积后的图像进行融合,提取更多的特征信息。同时,网络中嵌入了新的多尺度特征提取模块,该模块将通道注意力与密集扩张卷积进行了融合,有效地捕获了更高层次的特征信息。对腹部动脉血管进行分割的结果表明,与其他分割方法相比,所提方法在直观性和定量性上均有提高,证明了该方法能够提升血管分割精度。     

The boundary shift integral: an accurate and robust measure ofcerebral volume changes from registered repeat MRI

We propose the boundary shift integral (BSI) as a measure of cerebral volume changes derived from registered repeat three-dimensional (3-D) magnetic resonance (MR) [3D MR] scans. The BSI determines the total volume through which the boundaries of a given cerebral structure have moved and, hence, the volume change, directly from voxel intensities. We found brain and ventricular BSI's correlated tightly (r=1.000 and r=0.999) with simulated volumes of change. Applied to 21 control scan pairs and 11 scan pairs from Alzheimer's disease (AD) patients (mean interval 386 days) the BSI yielded mean brain volume loss of 1.8 cc (controls) and 34.7 cc (AD); the control group was tightly bunched (SD=3.8 cc) and there was wide group separation, the group means differing by 8.7 control group standard deviations (SDs). A measure based on the same segmentation used by the BSI yielded similar group means, but wide spread in the control group (SD=13.4 cc) and group overlap, the group means differing by 2.8 control group SDs. The BSI yielded mean ventricular volume losses of 0.4 cc (controls) and 10.1 cc (AD). Good linear correlation (r=0.997) was obtained between the ventricular BSI and the difference in their segmented volumes. We conclude the BSI is an accurate and robust measure of regional and global cerebral volume changes     

Atlas-driven lung lobe segmentation in volumetric X-ray CT images

High-resolution X-ray computed tomography (CT) imaging is routinely used for clinical pulmonary applications. Since lung function varies regionally and because pulmonary disease is usually not uniformly distributed in the lungs, it is useful to study the lungs on a lobe-by-lobe basis. Thus, it is important to segment not only the lungs, but the lobar fissures as well. In this paper, we demonstrate the use of an anatomic pulmonary atlas, encoded with a priori information on the pulmonary anatomy, to automatically segment the oblique lobar fissures. Sixteen volumetric CT scans from 16 subjects are used to construct the pulmonary atlas. A ridgeness measure is applied to the original CT images to enhance the fissure contrast. Fissure detection is accomplished in two stages: an initial fissure search and a final fissure search. A fuzzy reasoning system is used in the fissure search to analyze information from three sources: the image intensity, an anatomic smoothness constraint, and the atlas-based search initialization. Our method has been tested on 22 volumetric thin-slice CT scans from 12 subjects, and the results are compared to manual tracings. Averaged across all 22 data sets, the RMS error between the automatically segmented and manually segmented fissures is 1.96 +/- 0.71 mm and the mean of the similarity indices between the manually defined and computer-defined lobe regions is 0.988. The results indicate a strong agreement between the automatic and manual lobe segmentations.     

一种改进级联U-Net网络的结肠息肉分割算法

结肠镜图像中息肉的精确分割是诊断结肠癌的关键环节,针对目前结肠息肉分割算法存在孔洞、分割粗糙以及分割不完全的问题,提出了一种改进级联U-Net结构的结肠息肉分割算法。运用特征融合思想,设计了多尺度语义嵌入模块和残差模块,充分利用深、浅层特征的语义信息。引入注意力机制,在模型的级联处构建了改进空洞卷积模块,扩大卷积感受野并增强特征捕获能力。改进了卷积层模块和分割损失函数,提升模型的泛化性和鲁棒性。在Kvasir-SEG数据集上进行实验分析,相似系数、平均交并比、召回率和准确率分别达到了90.39%、88.34%、83.62%和95.12%。实验结果表明,该文所提算法改善了分割图像内部孔洞、边缘粗糙及分割不完全的问题,优于其他息肉分割算法。     

改进的全卷积神经网络的脑肿瘤图像分割

针对现有机器学习算法分割脑肿瘤图像精度不高的问题,提出一种基于改进的全卷积神经网络的脑肿瘤图像分割算法。算法首先将FLAIR、T2和T1C三种模态的MR脑肿瘤图像进行灰度归一化,随后利用灰度图像融合技术得到肿瘤信息更加全面的预处理图像;然后采用融合三次脑肿瘤特征信息的改进全卷积神经网络对预处理图像进行粗分割,并且在每个卷积层后加入批量正则化层以加快网络训练的收敛速度,提高训练模型精度;最后融合全连接条件随机场细化粗分割结果中的脑肿瘤边界。实验结果表明,相较于传统的卷积神经网络脑肿瘤图像分割算法,本算法在分割精度和稳定性上有了较大提升,平均Dice可达91.29%,实时性较好,利用训练模型平均1s内可完成单张脑肿瘤图像的分割。      

Left ventricular deformation recovery from cine MRI using an incompressible model

This paper presents a method for 3-D deformation recovery of the left ventricular (LV) wall from anatomical cine magnetic resonance imaging (MRI). The method is based on a deformable model that is incompressible, a desired property since the myocardium has been shown to be nearly incompressible. The LV wall needs to be segmented in an initial frame after which the method automatically determines the deformation everywhere in the LV wall throughout the cardiac cycle. Two studies were conducted to validate the method. In the first study, the deformation recovered from a 3-D anatomical cine MRI of a healthy volunteer was compared against the manual segmentation of the LV wall and against the corresponding 3-D tagged cine MRI. The average volume agreement between the model and the manual segmentation had a false positive rate of 3%, false negative rate of 3%, and true positive rate of 93%. The average distance between the model and manually determined intersections of perpendicular tag planes was 1.6 mm (1.1 pixel). Another set of 3-D anatomical and tagged MRI scans was taken of the same volunteer four months later. The method was applied to the second set and the recovered deformation was very similar to the one obtained from the first set. In the second study, the method was applied to 3-D anatomical cine MRI scans of three patients with ventricular dyssynchrony and three age-matched healthy volunteers. The LV wall deformations recovered for the three normals agreed well and the recovered strains were similar to those reported by other researchers for normal subjects. Strains and displacements of the three patients were clearly smaller than those of the three normals indicating reduced cardiac function. The deformation recovered for the three normals and the three patients was validated against manual segmentation and corresponding tag cine MRI scans and the agreement was similar to that of the first validation study.     

激光夜视图像分型分割算法研究

为解决以往采用关联规则挖掘算法对图像进行分割时,对于夜视图像中灰暗区域中颜色特征以及前景/背景特征的采集能力差,不能有效判定图像的多尺度分型特征,分型分割效果差的问题。研究激光夜视图像分型分割算法。先利用计盒维数估计方法计算激光夜视图像分型维数尺度,通过分型维数尺度获取激光夜视图像的多尺度分型特征值,将利用多尺度分型特征值获取的多尺度分型特征约束与图像颜色约束相结合获取多尺度分型特征数据项,融合该多尺度分型特征数据项与通过图像中相邻区域顶点颜色距离获取的光滑项,并加入自适应比重系数获取能量函数,利用最大流/最小割算法求解能量函数最小值,实现激光夜视图像的分割。实验结果表明,该算法可准确分割激光夜视图像中人物目标特征,分割10幅激光夜视图像准确率以及均匀性测度平均值均在95%以上。     

一种有效融合多尺度特征的图像语义分割方法

卷积神经网络在高级计算机视觉任务中展现出强 大的特征学习能力,已经在图像语义 分割任务 中取得了显著的效果。然而,如何有效地利用多尺度的特征信息一直是个难点。本文提出一 种有效 融合多尺度特征的图像语义分割方法。该方法包含4个基础模块,分别为特征融合模块(feature fusion module,FFM)、空 间信息 模块(spatial information module,SIM)、全局池化模块(global pooling module,GPM)和边界细化模块(boundary refinement module,BRM)。FFM采用了注意力机制和残差结构,以提高 融合多 尺度特征的效率,SIM由卷积和平均池化组成,为模型提供额外的空间细节信息以 辅助定 位对象的边缘信息,GPM提取图像的全局信息,能够显著提高模型的性能,BRM以残差结构为核心,对特征图进行边界细化。本文在全卷积神经网络中添加4个基础模块, 从而有 效地利用多尺度的特征信息。在PASCAL VOC 2012数据集上的实验结 果表明该方法相比全卷积神 经网络的平均交并比提高了8.7%,在同一框架下与其他方法的对比结 果也验证了其性能的有效性。     

Left Ventricle Segmentation Using Model Fitting and Active Surfaces

A method to perform 4D (3D over time) seg mentation of the left ventricle of a mouse heart using a set of B mode cine slices acquired in vivo from a series of short axis scans is described. We incorporate previ ously suggested methods such as temporal propagation, the gradient vector flow active surface, superquadric models, etc. into our proposed 4D segmentation of the left ventricle. The contributions of this paper are incor poration of a novel despeckling method and the use of locally fitted superellipsoid models to provide a better initialization for the active surface segmentation algorithm. Average distances of the improved surface segmentation to a manually segmented surface through out the entire cardiac cycle and cross-sectional contours are provided to demonstrate the improvements pro duced by the proposed 4D segmentation.     

面向多尺度分割的疑似违章建筑提取算法

针对城市中疑似违章建筑物信息提取的问题,提出了一种基于多尺度分割方法提取疑似违章建筑信息的新算法.该算法首先通过设置多尺度分割参数对遥感影像进行分割,然后通过正射校正、辐射定标、大气校正对遥感影像进行预处理,最后通过多尺度分割实验分析各参数对尺度分割效果的影响.研究结果表明分割尺度为150、形状比例系数为0.7、紧致度...     

Weakly supervised semantic segmentation and optimization algorithm based on multi-scale feature model

In order to improve the accuracy of weakly-supervised semantic segmentation method,a segmentation and optimization algorithm that combines multi-scale feature was proposed.The new algorithm firstly constructs a multi-scale feature model based on transfer learning algorithm.In addition,a new classifier was introduced for category prediction to reduce the failure of segmentation due to the prediction of target class information errors.Then the designed multi-scale model was fused with the original transfer learning model by different weights to enhance the generalization performance of the model.Finally,the predictions class credibility was added to adjust the credibility of the corresponding class of pixels in the segmentation map,avoiding false positive segmentation regions.The proposed algorithm was tested on the challenging VOC 2012 dataset,the mean intersection-over-union is 58.8% on validation dataset and 57.5% on test dataset.It outperforms the original transfer-learning algorithm by 12.9% and 12.3%.And it performs favorably against other segmentation methods using weakly-supervised information based on category labels as well.     

Performance-based classifier combination in atlas-based image segmentation using expectation-maximization parameter estimation

It is well known in the pattern recognition community that the accuracy of classifications obtained by combining decisions made by independent classifiers can be substantially higher than the accuracy of the individual classifiers. We have previously shown this to be true for atlas-based segmentation of biomedical images. The conventional method for combining individual classifiers weights each classifier equally (vote or sum rule fusion). In this paper, we propose two methods that estimate the performances of the individual classifiers and combine the individual classifiers by weighting them according to their estimated performance. The two methods are multiclass extensions of an expectation-maximization (EM) algorithm for ground truth estimation of binary classification based on decisions of multiple experts (Warfield et al., 2004). The first method performs parameter estimation independently for each class with a subsequent integration step. The second method considers all classes simultaneously. We demonstrate the efficacy of these performance-based fusion methods by applying them to atlas-based segmentations of three-dimensional confocal microscopy images of bee brains. In atlas-based image segmentation, multiple classifiers arise naturally by applying different registration methods to the same atlas, or the same registration method to different atlases, or both. We perform a validation study designed to quantify the success of classifier combination methods in atlas-based segmentation. By applying random deformations, a given ground truth atlas is transformed into multiple segmentations that could result from imperfect registrations of an image to multiple atlas images. In a second evaluation study, multiple actual atlas-based segmentations are combined and their accuracies computed by comparing them to a manual segmentation. We demonstrate in both evaluation studies that segmentations produced by combining multiple individual registration-based segmentations are more accurate for the two classifier fusion methods we propose, which weight the individual classifiers according to their EM-based performance estimates, than for simple sum rule fusion, which weights each classifier equally.