Automated anatomical labeling of the bronchial branch and its application to the virtual bronchoscopy system

This paper describes a method for the automated anatomical labeling of the bronchial branch extracted from a three-dimensional (3-D) chest X-ray CT image and its application to a virtual bronchoscopy system (VBS). Automated anatomical labeling is necessary for implementing an advanced computer-aided diagnosis system of 3-D medical images. This method performs the anatomical labeling of the bronchial branch using the knowledge base of the bronchial branch name. The knowledge base holds information on the bronchial branch as a set of rules for its anatomical labeling. A bronchus region is automatically extracted from a given 3-D CT image. A tree structure representing the essential structure of the extracted bronchus is recognized from the bronchus region. Anatomical labeling is performed by comparing this tree structure of the bronchus with the knowledge base. As an application, we implemented the function to automatically present the anatomical names of the branches that are shown in the currently rendered image in real time on the VBS. The result showed that the method could segment about 57% of the branches from CT images and extracted a tree structure of about 91% in branches in the segmented bronchus. The anatomical labeling method could assign the correct branch name to about 93% of the branches in the extracted tree structure. Anatomical names were appropriately displayed in the endoscopic view.     

Computer-aided method for quantification of cartilage thickness and volume changes using MRI: validation study using a synthetic model

The primary objective of this study was to develop a computer-aided method for the quantification of three-dimensional (3-D) cartilage changes over time in knees with osteoarthritis (OA). We introduced a local coordinate system (LCS) for the femoral and tibial cartilage boundaries that provides a standardized representation of cartilage geometry, thickness, and volume. The LCS can be registered in different data sets from the same patient so that results can be directly compared. Cartilage boundaries are segmented from 3-D magnetic resonance (MR) slices with a semi-automated method and transformed into offset-maps, defined by the LCS. Volumes and thickness are computed from these offset-maps. Further anatomical labeling allows focal volumes to be evaluated in predefined subregions. The accuracy of the automated behavior of the method was assessed, without any human intervention, using realistic, synthetic 3-D MR images of a human knee. The error in thickness evaluation is lower than 0.12 mm for the tibia and femur. Cartilage volumes in anatomical subregions show a coefficient of variation ranging from 0.11% to 0.32%. This method improves noninvasive 3-D analysis of cartilage thickness and volume and is well suited for in vivo follow-up clinical studies of OA knees.     

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.     

Rule-based detection of intrathoracic airway trees

New sensitive and reliable methods for assessing alterations in regional lung structure and function are critically important for the investigation and treatment of pulmonary diseases. Accurate identification of the airway tree will provide an assessment of airway structure and will provide a means by which multiple volumetric images of the lung at the same lung volume over time can be used to assess regional parenchymal changes. The authors describe a novel rule-based method for the segmentation of airway trees from three-dimensional (3-D) sets of computed tomography (CT) images, and its validation. The presented method takes advantage of a priori anatomical knowledge about pulmonary airway and vascular trees and their interrelationships. The method is based on a combination of 3-D seeded region growing that is used to identify large airways, rule-based two-dimensional (2-D) segmentation of individual CT slices to identify probable locations of smaller diameter airways, and merging of airway regions across the 3-D set of slices resulting in a tree-like airway structure. The method was validated in 40 3-mm-thick CT sections from five data sets of canine lungs scanned via electron beam CT in vivo with lung volume held at a constant pressure. The method's performance was compared with that of the conventional 3-D region growing method. The method substantially outperformed an existing conventional approach to airway tree detection.     

Tubular surface segmentation for extracting anatomical structures from medical imagery

This work provides a model for tubular structures, and devises an algorithm to automatically extract tubular anatomical structures from medical imagery. Our model fits many anatomical structures in medical imagery, in particular, various fiber bundles in the brain (imaged through diffusion-weighted magnetic resonance (DW-MRI)) such as the cingulum bundle, and blood vessel trees in computed tomography angiograms (CTAs). Extraction of the cingulum bundle is of interest because of possible ties to schizophrenia, and extracting blood vessels is helpful in the diagnosis of cardiovascular diseases. The tubular model we propose has advantages over many existing approaches in literature: fewer degrees-of-freedom over a general deformable surface hence energies defined on such tubes are less sensitive to undesirable local minima, and the tube (in 3-D) can be naturally represented by a 4-D curve (a radius function and centerline), which leads to computationally less costly algorithms and has the advantage that the centerline of the tube is obtained without additional effort. Our model also generalizes to tubular trees, and the extraction algorithm that we design automatically detects and evolves branches of the tree. We demonstrate the performance of our algorithm on 20 datasets of DW-MRI data and 32 datasets of CTA, and quantify the results of our algorithm when expert segmentations are available.     

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%.     

Reconstruction of the human cerebral cortex from magnetic resonanceimages

Reconstructing the geometry of the human cerebral cortex from MR images is an important step in both brain mapping and surgical path planning applications. Difficulties with imaging noise, partial volume averaging, image intensity inhomogeneities, convoluted cortical structures, and the requirement to preserve anatomical topology make the development of accurate automated algorithms particularly challenging. In this paper we address each of these problems and describe a systematic method for obtaining a surface representation of the geometric central layer of the human cerebral cortex. Using fuzzy segmentation, an isosurface algorithm, and a deformable surface model, the method reconstructs the entire cortex with the correct topology, including deep convoluted sulci and gyri. The method is largely automated and its results are robust to imaging noise, partial volume averaging, and image intensity inhomogeneities. The performance of this method is demonstrated, both qualitatively and quantitatively, and the results of its application to six subjects and one simulated MR brain volume are presented.     

Improved implementation of search technique to find spanning trees

The authors have developed a set of algorithms to find the spanning trees, the minimal paths and minimal cutsets of a graph, starting from the incidence matrix of the graph [1,3]. All the above algorithms employ a unique tracing process based on search techniques. The above algorithms have a number of salient features. The arithmetic and logic operations are very simple, which makes it possible to design small desk top calculators capable of handling reasonably large and complex graphs. The major constraint of these equipments is the memory capacity vis à vis their capability of handling larger graphs. The authors designed a microprocessor based system [2] to find spanning trees. The end results were available in the form of code numbers of branches appearing in a spanning tree, which had to be noted down, every time a tree was generated. In the new system the end results are in a more compact form, i.e. the vectors (see definition), one vector for one tree. The user can easily note down the vectors and decode them later to obtain the branches of a tree. In the new system the user can reallocate the available working memory space to suit the problem. The memory requirement in the new approach is also less.     

A supervised patch-based approach for human brain labeling

We propose in this work a patch-based image labeling method relying on a label propagation framework. Based on image intensity similarities between the input image and an anatomy textbook, an original strategy which does not require any nonrigid registration is presented. Following recent developments in nonlocal image denoising, the similarity between images is represented by a weighted graph computed from an intensity-based distance between patches. Experiments on simulated and in vivo magnetic resonance images show that the proposed method is very successful in providing automated human brain labeling.     

Improved labeling of subcortical brain structures in atlas-based segmentation of magnetic resonance images

Precise labeling of subcortical structures plays a key role in functional neurosurgical applications. Labels from an atlas image are propagated to a patient image using atlas-based segmentation. Atlas-based segmentation is highly dependent on the registration framework used to guide the atlas label propagation. This paper focuses on atlas-based segmentation of subcortical brain structures and the effect of different registration methods on the generated subcortical labels. A single-step and three two-step registration methods appearing in the literature based on affine and deformable registration algorithms in the ANTS and FSL algorithms are considered. Experiments are carried out with two atlas databases of IBSR and LPBA40. Six segmentation metrics consisting of Dice overlap, relative volume error, false positive, false negative, surface distance, and spatial extent are used for evaluation. Segmentation results are reported individually and as averages for nine subcortical brain structures. Based on two statistical tests, the results are ranked. In general, among four different registration strategies investigated in this paper, a two-step registration consisting of an initial affine registration followed by a deformable registration applied to subcortical structures provides superior segmentation outcomes. This method can be used to provide an improved labeling of the subcortical brain structures in MRIs for different applications.     

Distributed algorithms for multicast path setup in data networks

Establishing a multicast tree in a point-to-point network of switch nodes, such as a wide-area asynchronous transfer mode (ATM) network, can be modeled as the NP-complete Steiner problem in networks. In this paper, we introduce and evaluate two distributed algorithms for finding multicast trees in point-to-point data networks. These algorithms are based on the centralized Steiner heuristics, the shortest path heuristic (SPH) and the Kruskal-based shortest path heuristic (K-SPH), and have the advantage that only the multicast members and nodes in the neighborhood of the multicast tree need to participate in the execution of the algorithm. We compare our algorithms by simulation against a baseline algorithm, the pruned minimum spanning-tree heuristic that is the basis of many previously published algorithms for finding multicast trees. Our results show that the competitiveness (the ratio of the sum of the heuristic tree's edge weights to that of the best solution found) of both of our algorithms was, on the average, 25% better in comparison to that of the pruned spanning-tree approach. In addition, the competitiveness of our algorithms was, in almost all cases, within 10% of the best solution found by any of the Steiner heuristics considered, including both centralized and distributed algorithms. Limiting the execution of the algorithm to a subset of the nodes in the network results in an increase in convergence time over the pruned spanning-tree approach, but this overhead can be reduced by careful implementation     

Vessel tree reconstruction in thoracic CT scans with application to nodule detection

Vessel tree reconstruction in volumetric data is a necessary prerequisite in various medical imaging applications. Specifically, when considering the application of automated lung nodule detection in thoracic computed tomography (CT) scans, vessel trees can be used to resolve local ambiguities based on global considerations and so improve the performance of nodule detection algorithms. In this study, a novel approach to vessel tree reconstruction and its application to nodule detection in thoracic CT scans was developed by using correlation-based enhancement filters and a fuzzy shape representation of the data. The proposed correlation-based enhancement filters depend on first-order partial derivatives and so are less sensitive to noise compared with Hessian-based filters. Additionally, multiple sets of eigenvalues are used so that a distinction between nodules and vessel junctions becomes possible. The proposed fuzzy shape representation is based on regulated morphological operations that are less sensitive to noise. Consequently, the vessel tree reconstruction algorithm can accommodate vessel bifurcation and discontinuities. A quantitative performance evaluation of the enhancement filters and of the vessel tree reconstruction algorithm was performed. Moreover, the proposed vessel tree reconstruction algorithm reduced the number of false positives generated by an existing nodule detection algorithm by 38%.     

Ensembles of radial basis function networks for spectroscopicdetection of cervical precancer

The mortality related to cervical cancer can be substantially reduced through early detection and treatment. However, current detection techniques, such as Pap smear and colposcopy, fail to achieve a concurrently high sensitivity and specificity. In vivo fluorescence spectroscopy is a technique which quickly, noninvasively and quantitatively probes the biochemical and morphological changes that occur in precancerous tissue. A multivariate statistical algorithm was used to extract clinically useful information from tissue spectra acquired from 361 cervical sites from 95 patients at 337-, 380-, and 460-nm excitation wavelengths. The multivariate statistical analysis was also employed to reduce the number of fluorescence excitation-emission wavelength pairs required to discriminate healthy tissue samples from precancerous tissue samples. The use of connectionist methods such as multilayered perceptrons, radial basis function (RBF) networks, and ensembles of such networks was investigated. RBF ensemble algorithms based on fluorescence spectra potentially provide automated and near real-time implementation of precancer detection in the hands of nonexperts. The results are more reliable, direct, and accurate than those achieved by either human experts or multivariate statistical algorithms     

一种有效降低虚警率的变化检测算法

研究了图像变化检测算法,针对传统的直接比较算法对光照、噪声等变化因素敏感,虚警率较高的问题,提出一种新的变化检测算法加以解决.首先,采用提出的基于二维直方图的最大熵方法对参考图进行分类,然后利用非线性估计方法,对参考图进行估计,并利用分类结果对其进行标注,最后,通过计算测试图像像素点到估计图像对应像素点所在类的马氏距离,来度量测试图像的变化情况.通过实验比较,验证了算法的有效性.     

Automatic Detection of Anatomical Landmarks in Uterine Cervix Images

The work focuses on a unique medical repository of digital cervicographic images (“Cervigrams”) collected by the National Cancer Institute (NCI) in longitudinal multiyear studies. NCI, together with the National Library of Medicine (NLM), is developing a unique web-accessible database of the digitized cervix images to study the evolution of lesions related to cervical cancer. Tools are needed for automated analysis of the cervigram content to support cancer research. We present a multistage scheme for segmenting and labeling regions of anatomical interest within the cervigrams. In particular, we focus on the extraction of the cervix region and fine detection of the cervix boundary; specular reflection is eliminated as an important preprocessing step; in addition, the entrance to the endocervical canal (the “os”), is detected. Segmentation results are evaluated on three image sets of cervigrams that were manually labeled by NCI experts.      

Computerized detection of pulmonary embolism in spiral CT angiography based on volumetric image analysis

A fully automated method for computerized detection of pulmonary embolism in spiral computed tomography angiography was developed based on volumetric image analysis. The detection method is based on segmentation of pulmonary vessels to limit the search space, and analysis of several three-dimensional features inside segmented vessel volume. The features utilized are vascular size, local contrast based on mathematical morphology, degree of curvilinearity based on second derivatives, and geometric features such as volume and length. Detection results were obtained for 19 clinical data sets and the performance of the method was evaluated. Using the number and locations of thrombi diagnosed by radiologists as the gold standard, 100% sensitivity was achieved with 7.7 false positives per case, and 85% sensitivity was obtained with 2.6 false positives. For identification of all the positive cases as positive, i.e., detection of at least one thrombus per positive case, 1.9 false positives per case were obtained. These preliminary results suggest that the method has potential for fully automated detection of pulmonary embolism.     

Development of an automated method for detecting mammographicmasses with a partial loss of region

Recently, we have been developing several automated algorithms for detecting masses on mammograms. For our algorithm, we devised an adaptive thresholding technique for detecting masses, but our system failed to detect masses with a partial loss of region that were located on the edge of the film. This is a common issue in all of the algorithms developed so far by other groups. In order to deal with this problem, we propose a new method in the present study. The partial loss masses are identified by their similarity to a sector-form model in the template matching process. To calculate the similarity, four features are applied: 1) average pixel value; 2) standard deviation of pixel values; 3) standard correlation coefficient defined by the sector-form model; and 4) concentration feature determined from the density gradient. After employing the new method to 335 digitized mammograms, the detection sensitivity for the partial loss masses jumped from 70% to 90% when the number of false positives was kept constant (0.2/image). Moreover, a combination of the existing method and the new method improved the true-positive rate up to 97%. Such results indicate that the new technique may improve the performance of our computer-aided diagnosis system for mammographic masses effectively.     

改进型卷积神经网络焊点缺陷识别算法研究

为了同时对多种焊点缺陷类型进行快速识别,解决现有焊接异常图像识别算法误检率与漏检率偏高的问题,设计了基于改进型卷积神经网络的深度学习算法。利用自组织映射分类技术,提高了卷积神经网络的数据选择自适应性,结合自适应矩估计分析, 约束了焊接异常图像中特征集合的收敛条件。实验中将5种常见焊接异常图像以等比例随机分布的形式放入训练集、验证集和测试集中,再分别用传统识别算法(canny算法和k均值算法)和该算法进行测试。结果表明,对于桥连缺陷,3种方法均无误检、无漏检;对于小球缺陷,3种方法均符合要求,而canny算法的检出能力最优;对于偏球缺陷, 3种算法的误检率分别是12.4%, 7.3%和与1.4%,漏检率分别是13.3%, 6.5%和1.1%;对于虚焊和少锡缺陷,该算法相比传统算法精度高约1个数量级。该算法在对多种焊点缺陷类型识别中具有明显优势。     

Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation

Characterizing the performance of image segmentation approaches has been a persistent challenge. Performance analysis is important since segmentation algorithms often have limited accuracy and precision. Interactive drawing of the desired segmentation by human raters has often been the only acceptable approach, and yet suffers from intra-rater and inter-rater variability. Automated algorithms have been sought in order to remove the variability introduced by raters, but such algorithms must be assessed to ensure they are suitable for the task. The performance of raters (human or algorithmic) generating segmentations of medical images has been difficult to quantify because of the difficulty of obtaining or estimating a known true segmentation for clinical data. Although physical and digital phantoms can be constructed for which ground truth is known or readily estimated, such phantoms do not fully reflect clinical images due to the difficulty of constructing phantoms which reproduce the full range of imaging characteristics and normal and pathological anatomical variability observed in clinical data. Comparison to a collection of segmentations by raters is an attractive alternative since it can be carried out directly on the relevant clinical imaging data. However, the most appropriate measure or set of measures with which to compare such segmentations has not been clarified and several measures are used in practice. We present here an expectation-maximization algorithm for simultaneous truth and performance level estimation (STAPLE). The algorithm considers a collection of segmentations and computes a probabilistic estimate of the true segmentation and a measure of the performance level represented by each segmentation. The source of each segmentation in the collection may be an appropriately trained human rater or raters, or may be an automated segmentation algorithm. The probabilistic estimate of the true segmentation is formed by estimating an optimal combination of the segmentations, weighting each segmentation depending upon the estimated performance level, and incorporating a prior model for the spatial distribution of structures being segmented as well as spatial homogeneity constraints. STAPLE is straightforward to apply to clinical imaging data, it readily enables assessment of the performance of an automated image segmentation algorithm, and enables direct comparison of human rater and algorithm performance.     

Real-time correction of heart interbeat intervals

Heart rate variability (HRV) is traditionally analyzed while a subject is in a controlled environment, such as at rest in a clinic, where it can be used as a medical indicator. This paper concerns analyzing HRV outside of controlled environments, such as on an actively moving person. We describe automated methods for inter-heartbeat interval (IBI) error detection and correction. We collected 124,998 IBIs from 18 subjects, undergoing a variety of active motions, for use in evaluating our methods. Two human graders manually labeled each IBI, evaluating 10% of the IBIs as having an error, which is a far greater error percentage than has been examined in any previous study. Our automated method had a 96% agreement rate with the two human graders when they themselves agreed, with a 49% rate of matching specific error corrections and a 0.01% false alarm rate.