A Computational Geometry Approach to Automated Pulmonary Fissure Segmentation in CT Examinations

Identification of pulmonary fissures, which form the boundaries between the lobes in the lungs, may be useful during clinical interpretation of computed tomography (CT) examinations to assess the early presence and characterization of manifestation of several lung diseases. Motivated by the unique nature of the surface shape of pulmonary fissures in 3-D space, we developed a new automated scheme using computational geometry methods to detect and segment fissures depicted on CT images. After a geometric modeling of the lung volume using the marching cubes algorithm, Laplacian smoothing is applied iteratively to enhance pulmonary fissures by depressing nonfissure structures while smoothing the surfaces of lung fissures. Next, an extended Gaussian image based procedure is used to locate the fissures in a statistical manner that approximates the fissures using a set of plane ldquopatchesrdquo. This approach has several advantages such as independence of anatomic knowledge of the lung structure except the surface shape of fissures, limited sensitivity to other lung structures, and ease of implementation. The scheme performance was evaluated by two experienced thoracic radiologists using a set of 100 images (slices) randomly selected from 10 screening CT examinations. In this preliminary evaluation 98.7% and 94.9% of scheme segmented fissure voxels are within 2 mm of the fissures marked independently by two radiologists in the testing image dataset. Using the scheme detected fissures as reference, 89.4% and 90.1% of manually marked fissure points have distance les2 mm to the reference suggesting a possible under-segmentation of the scheme. The case-based root mean square (rms) distances (ldquoerrorsrdquo) between our scheme and the radiologist ranged from 1.48plusmn0.92 to 2.04plusmn3.88 mm. The discrepancy of fissure detection results between the automated scheme and either radiologist is smaller in this dataset than the interreader variability.     

Anatomy-Guided Lung Lobe Segmentation in X-Ray CT Images

The human lungs are divided into five distinct anatomic compartments called the lobes, which are separated by the pulmonary fissures. The accurate identification of the fissures is of increasing importance in the early detection of pathologies, and in the regional functional analysis of the lungs. We have developed an automatic method for the segmentation and analysis of the fissures, based on the information provided by the segmentation and analysis of the airway and vascular trees. This information is used to provide a close initial approximation to the fissures, using a watershed transform on a distance map of the vasculature. In a further refinement step, this estimate is used to construct a region of interest (ROI) encompassing the fissures. The ROI is enhanced using a ridgeness measure, which is followed by a 3-D graph search to find the optimal surface within the ROI. We have also developed an automatic method to detect incomplete fissures, using a fast-marching based segmentation of a projection of the optimal surface. The detected incomplete fissure is used to extrapolate and smoothly complete the fissure. We evaluate the method by testing on data sets from normal subjects and subjects with mild to moderate emphysema.      

Segmentation of Lung Lobes in High-Resolution Isotropic CT Images

Modern multislice computed tomography (CT) scanners produce isotropic CT images with a thickness of 0.6 mm. These CT images offer detailed information of lung cavities, which could be used for better surgical planning of treating lung cancer. The major challenge for developing a surgical planning system is the automatic segmentation of lung lobes by identifying the lobar fissures. This paper presents a lobe segmentation algorithm that uses a two-stage approach: 1) adaptive fissure sweeping to find fissure regions and 2) wavelet transform to identify the fissure locations and curvatures within these regions. Tested on isotropic CT image stacks from nine anonymous patients with pathological lungs, the algorithm yielded an accuracy of 76.7%–94.8% with strict evaluation criteria. In comparison, surgeons obtain an accuracy of 80% for localizing the fissure regions in clinical CT images with a thickness of 2.5–7.0 mm. As well, this paper describes a procedure for visualizing lung lobes in three dimensions using software—amira—and the segmentation algorithm. The procedure, including the segmentation, needed about 5 min for each patient. These results provide promising potential for developing an automatic algorithm to segment lung lobes for surgical planning of treating lung cancer.      

一种全自动的肺裂分割方法

CT（Computer Tomography）图像中自动分割肺裂是很困难的,肺裂往往存在不完整、形变、断裂和附裂等现象.本文提出一种融合肺部解剖结构特征来实现自动分割肺裂的方法.首先结合肺部气管和动脉血管信息定位肺裂感兴趣区域.然后利用肺裂方向信息增强肺裂,并利用多剖面滤波器滤除噪声从而对肺裂进行预分割.最后融合已定位的肺裂感兴趣区域和肺裂预分割结果来自动分割肺裂.与人工参考对比,提出的算法在人体左肺和右肺中分割的肺裂的F₁-score中值分别为0.881和0.878.     

Automatic lung segmentation for accurate quantitation of volumetricX-ray CT images

Segmentation of pulmonary X-ray computed tomography (CT) images is a precursor to most pulmonary image analysis applications. This paper presents a fully automatic method for identifying the lungs in three-dimensional (3-D) pulmonary X-ray CT images. The method has three main steps. First, the lung region is extracted from the CT images by gray-level thresholding. Then, the left and right lungs are separated by identifying the anterior and posterior junctions by dynamic programming. Finally, a sequence of morphological operations is used to smooth the irregular boundary along the mediastinum in order to obtain results consistent with those obtained by manual analysis, in which only the most central pulmonary arteries are excluded from the lung region. The method has been tested by processing 3-D CT data sets from eight normal subjects, each imaged three times at biweekly intervals with lungs at 90% vital capacity. We present results by comparing our automatic method to manually traced borders from two image analysts. Averaged over all volumes, the root mean square difference between the computer and human analysis is 0.8 pixels (0.54 mm). The mean intrasubject change in tissue content over the three scans was 2.75% +/- 2.29% (mean +/- standard deviation).     

Construction of an abdominal probabilistic atlas and its application in segmentation

There have been significant efforts to build a probabilistic atlas of the brain and to use it for many common applications, such as segmentation and registration. Though the work related to brain atlases can be applied to nonbrain organs, less attention has been paid to actually building an atlas for organs other than the brain. Motivated by the automatic identification of normal organs for applications in radiation therapy treatment planning, we present a method to construct a probabilistic atlas of an abdomen consisting of four organs (i.e., liver, kidneys, and spinal cord). Using 32 noncontrast abdominal computed tomography (CT) scans, 31 were mapped onto one individual scan using thin plate spline as the warping transform and mutual information (MI) as the similarity measure. Except for an initial coarse placement of four control points by the operators, the MI-based registration was automatic. Additionally, the four organs in each of the 32 CT data sets were manually segmented. The manual segmentations were warped onto the "standard" patient space using the same transform computed from their gray scale CT data set and a probabilistic atlas was calculated. Then, the atlas was used to aid the segmentation of low-contrast organs in an additional 20 CT data sets not included in the atlas. By incorporating the atlas information into the Bayesian framework, segmentation results clearly showed improvements over a standard unsupervised segmentation method.     

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.     

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.     

Automatic 3-D segmentation of internal structures of the head in MR images using a combination of similarity and free-form transformations: Part I, Methodology and validation on normal subjects

The study presented in this paper tests the hypothesis that the combination of a global similarity transformation and local free-form deformations can be used for the accurate segmentation of internal structures in MR images of the brain. To quantitatively evaluate our approach, the entire brain, the cerebellum, and the head of the caudate have been segmented manually by two raters on one of the volumes (the reference volume) and mapped back onto all the other volumes, using the computed transformations. The contours so obtained have been compared to contours drawn manually around the structures of interest in each individual brain. Manual delineation was performed twice by the same two raters to test inter- and intrarater variability. For the brain and the cerebellum, results indicate that for each rater, contours obtained manually and contours obtained automatically by deforming his own atlas are virtually indistinguishable. Furthermore, contours obtained manually by one rater and contours obtained automatically by deforming this rater's own atlas are more similar than contours obtained manually by two raters. For the caudate, manual intra- and interrater similarity indexes remain slightly better than manual versus automatic indexes, mainly because of the spatial resolution of the images used in this study. Qualitative results also suggest that this method can be used for the segmentation of more complex structures, such as the hippocampus.     

Segmentation and analysis of the human airway tree from three-dimensional X-ray CT images

The lungs exchange air with the external environment via the pulmonary airways. Computed tomography (CT) scanning can be used to obtain detailed images of the pulmonary anatomy, including the airways. These images have been used to measure airway geometry, study airway reactivity, and guide surgical interventions. Prior to these applications, airway segmentation can be used to identify the airway lumen in the CT images. Airway tree segmentation can be performed manually by an image analyst, but the complexity of the tree makes manual segmentation tedious and extremely time-consuming. We describe a fully automatic technique for segmenting the airway tree in three-dimensional (3-D) CT images of the thorax. We use grayscale morphological reconstruction to identify candidate airways on CT slices and then reconstruct a connected 3-D airway tree. After segmentation, we estimate airway branchpoints based on connectivity changes in the reconstructed tree. Compared to manual analysis on 3-mm-thick electron-beam CT images, the automatic approach has an overall airway branch detection sensitivity of approximately 73%.     

Supervised enhancement filters: application to fissure detection in chest CT scans

In medical image processing, many filters have been developed to enhance certain structures in 3-D data. In this paper, we propose to use pattern recognition techniques to design more optimal filters. The essential difference with previous approaches is that we provide a system with examples of what it should enhance and suppress. This training data is used to construct a classifier that determines the probability that a voxel in an unseen image belongs to the target structure(s). The output of a rich set of basis filters serves as input to the classifier. In a feature selection process, this set is reduced to a compact, efficient subset. We show that the output of the system can be reused to extract new features, using the same filters, that can be processed by a new classifier. Such a multistage approach further improves performance. While the approach is generally applicable, in this work the focus is on enhancing pulmonary fissures in 3-D computed tomography (CT) chest scans. A supervised fissure enhancement filter is evaluated on two data sets, one of scans with a normal clinical dose and one of ultra-low dose scans. Results are compared with those of a recently proposed conventional fissure enhancement filter. It is demonstrated that both methods are able to enhance fissures, but the supervised approach shows better performance; the areas under the receiver operating characteristic (ROC) curve are 0.98 versus 0.90, for the normal dose data and 0.97 versus 0.87 for the ultra low dose data, respectively.     

Toward automated segmentation of the pathological lung in CT

Conventional methods of lung segmentation rely on a large gray value contrast between lung fields and surrounding tissues. These methods fail on scans with lungs that contain dense pathologies, and such scans occur frequently in clinical practice. We propose a segmentation-by-registration scheme in which a scan with normal lungs is elastically registered to a scan containing pathology. When the resulting transformation is applied to a mask of the normal lungs, a segmentation is found for the pathological lungs. As a mask of the normal lungs, a probabilistic segmentation built up out of the segmentations of 15 registered normal scans is used. To refine the segmentation, voxel classification is applied to a certain volume around the borders of the transformed probabilistic mask. Performance of this scheme is compared to that of three other algorithms: a conventional, a user-interactive and a voxel classification method. The algorithms are tested on 10 three-dimensional thin-slice computed tomography volumes containing high-density pathology. The resulting segmentations are evaluated by comparing them to manual segmentations in terms of volumetric overlap and border positioning measures. The conventional and user-interactive methods that start off with thresholding techniques fail to segment the pathologies and are outperformed by both voxel classification and the refined segmentation-by-registration. The refined registration scheme enjoys the additional benefit that it does not require pathological (hand-segmented) training data.     

Pulmonary Lobe Segmentation in CT Examinations Using Implicit Surface Fitting

Lobe identification in computed tomography (CT) examinations is often an important consideration during the diagnostic process as well as during treatment planning because of their relative independence of each other in terms of anatomy and function. In this paper, we present a new automated scheme for segmenting lung lobes depicted on 3-D CT examinations. The unique characteristic of this scheme is the representation of fissures in the form of implicit functions using Radial Basis Functions (RBFs), capable of seamlessly interpolating “holes” in the detected fissures and smoothly extrapolating the fissure surfaces to the lung boundaries resulting in a “natural” segmentation of lung lobes. A previously developed statistically based approach is used to detect pulmonary fissures and the constraint points for implicit surface fitting are selected from detected fissure surfaces in a greedy manner to improve fitting efficiency. In a preliminary assessment study, lobe segmentation results of 65 chest CT examinations, five of which were reconstructed with three section thicknesses of 0.625 mm, 1.25 mm, and 2.5 mm, were subjectively and independently evaluated by two experienced chest radiologists using a five category rating scale (i.e., excellent, good, fair, poor, and unacceptable). Thirty-three of 65 examinations (50.8%) with a section thickness of 0.625 mm were rated as either “excellent” or “good” by both radiologists and only one case (1.5%) was rated by both radiologists as “poor” or “unacceptable.” Comparable performance was obtained with a slice thickness of 1.25 mm, but substantial performance deterioration occurred in examinations with a section thickness of 2.5 mm. The advantages of this scheme are its full automation, relative insensitivity to fissure completeness, and ease of implementation.      

Automatic segmentation of newborns’ skull and fontanel from CT data using model-based variational level set

The newborn’s cranium is composed of flat cranial bone and fontanels forming together the envelope of the cerebral cavity. The fontanels are relatively flexible since they consist of fibrous membrane that ossifies during maturation becoming flat cranial bone as well. Fontanels give less contrast in computerized tomography (CT) images; they can be identified as gaps between the cranial bones. In this paper, we propose an automatic model-based method using variational level set to segment the skull and fontanels from CT images. In this approach, firstly a skull model consisting of cranial bones and fontanels is created and then used as constraint for level set evolution. Then, by removing the cranial bones from the segmented skulls, the fontanels are obtained. To verify the validity of the achieved results, automatically segmented skull and fontanels have been compared with the ones manually segmented by an expert using Dice similarity and Hausdorff dissimilarity measures, which show the good agreement between them. Furthermore, the surface areas of cranium and fontanel have been determined for these segmentations. The results for both, manual and automatic segmentation, are in good agreement.     

一种全新的两步自动化医学图像分割方案

针对现有图像分割方法存在需要手动分割,以及精确度较低的问题。采用一种全新的两步图像分割方案。该方案。以基于人工神经网络的模式识别技术,即人工神经网络的大规模培训的方法,通过对肺区不同子区域内结构进行分割处理,利用训练好的大规模人工神经网络对标准胸片中的肋骨、锁骨等骨质结构进行抑制,结合以基于区域的活动轮廓模型,即Snake模型,正确分割亮度不均匀的图像。文中选择与医护人员人工分割的图像进行对比,通过放射科医生采用等级法打分,原图的平均分为20分,而通过文中改进的分割方法平均分高达34分。     

Precise segmentation of the lateral ventricles and caudate nucleusin MR brain images using anatomically driven histograms

This paper demonstrates a time-saving, automated method that helps to segment the lateral ventricles and caudate nucleus in T1-weighted coronal magnetic resonance (MR) brain images of normal control subjects. The method involves choosing intensity thresholds by using anatomical information and by locating peaks in histograms. To validate the method, the lateral ventricles and caudate nucleus were segmented in three brain scans by four experts, first using an established method involving isointensity contours and manual editing, and second using automatically generated intensity thresholds as an aid to the established method. The results demonstrate both time savings and increased reliability     

Automated Pulmonary Fibrosis Segmentation Using a 3D Multi-Scale Convolutional Encoder-Decoder Approach in Thoracic CT for the Rhesus Macaque with Radiation-Induced Lung Damage

To develop an automated pulmonary fibrosis (PF) segmentation methodology using a 3D multi-scale convolutional encoder-decoder approach following the robust atlas-based active volume model in thoracic CT for Rhesus Macaques with radiation-induced lung damage. 152 thoracic computed tomography scans of Rhesus Macaques with radiation-induced lung damage were collected. The 3D input data are randomly augmented with the Gaussian blurring when applying the 3D multi-scale convolutional encoder-decoder (3D MSCED) segmentation method.PF in each scan was manually segmented in which 70% scans were used as training data, 20% scans were used as validation data, and 10% scans were used as testing data. The performance of the method is assessed based on a10-fold cross validation method. The workflow of the proposed method has two parts. First, the compromised lung volume with acute radiation-induced PF was segmented using a robust atlas-based active volume model. Next, a 3D multi-scale convolutional encoder-decoder segmentation method was developed which merged the higher spatial information from low-level features with the high-level object knowledge encoded in upper network layers. It included a bottom-up feed-forward convolutional neural network and a top-down learning mask refinement process. The quantitative results of our segmentation method achieved mean Dice score of (0.769, 0.853), mean accuracy of (0.996, 0.999), and mean relative error of (0.302, 0.512) with 95% confidence interval. The qualitative and quantitative comparisons show that our proposed method can achieve better segmentation accuracy with less variance in testing data. This method was extensively validated in NHP datasets. The results demonstrated that the approach is more robust relative to PF than other methods. It is a general framework which can easily be applied to segmentation other lung lesions.

     

A model-based, semi-global segmentation approach for automatic 3-D point landmark localization in neuroimages

The existing differential approaches for localization of 3-D anatomic point landmarks in 3-D images are sensitive to noise and usually extract numerous spurious landmarks. The parametric model-based approaches are not practically usable for localization of landmarks that can not be modeled by simple parametric forms. Some dedicated methods using anatomic knowledge to identify particular landmarks are not general enough to cope with other landmarks. In this paper, we propose a model-based, semi-global segmentation approach to automatically localize 3-D point landmarks in neuroimages. To localize a landmark, the semi-global segmentation (meaning the segmentation of a part of the studied structure in a certain neighborhood of the landmark) is first achieved by an active surface model, and then the landmark is localized by analyzing the segmented part only. The joint use of global model-to-image registration, semi-global structure registration, active surface-based segmentation, and point-anchored surface registration makes our method robust to noise and shape variation. To evaluate the method, we apply it to the localization of ventricular landmarks including curvature extrema, centerline intersections, and terminal points. Experiments with 48 clinical and 18 simulated magnetic resonance (MR) volumetric images show that the proposed approach is able to localize these landmarks with an average accuracy of 1 mm (i.e., at the level of image resolution). We also illustrate the use of the proposed approach to cortical landmark identification and discuss its potential applications ranging from computer-aided radiology and surgery to atlas registration with scans.      

Three-dimensional anatomical model-based segmentation of MR brainimages through principal axes registration

Model-based segmentation and analysis of brain images depends on anatomical knowledge which may be derived from conventional atlases. Classical anatomical atlases are based on the rigid spatial distribution provided by a single cadaver. Their use to segment internal anatomical brain structures in a high-resolution MR brain image does not provide any knowledge about the subject variability, and therefore they are not very efficient in analysis. The authors present a method to develop three-dimensional computerized composite models of brain structures to build a computerized anatomical atlas. The composite models are developed using the real MR brain images of human subjects which are registered through the principal axes transformation. The composite models provide probabilistic spatial distributions, which represent the variability of brain structures and can be easily updated for additional subjects. The authors demonstrate the use of such a composite model of ventricular structure to help segmentation of the ventricles and cerebrospinal fluid of MR brain images. Here, a composite model of ventricles using a set of 22 human subjects is developed and used in a model-based segmentation of ventricles, sulci, and white matter lesions. To illustrate the clinical usefulness, automatic volumetric measurements on ventricular size and cortical atrophy for an additional eight alcoholics and 10 normal subjects were made. The volumetric quantitative results indicated regional brain atrophy in chronic alcoholics     

TTS语音单元边界的自动切分

语音单元边界的准确切分对基于波形拼接的语音合成系统至关重要。文章采用了两步切分方法，第一步中先由基于HMM模型的强制对齐方法得到初始的边界．在第二步中提出用基于前后音素的边界模型来修正初始边界。为解决训练数据不足的问题，提出用分类与衰退树将前后因素发音相近的边界模型进行聚类。这样可以根据训练数据的多少，动态调节边界模型的数目，以保证模型训练的可靠性。在对中文语音库的实验中，自动切分的准确度由78．7％提高到91．5％。