System for the analysis and visualization of large 3D anatomical trees

Modern micro-CT and multi-detector helical CT scanners can produce high-resolution 3D digital images of various anatomical trees. The large size and complexity of these trees make it essentially impossible to define them interactively. Automatic approaches have been proposed for a few specific problems, but none of these approaches guarantee extracting geometrically accurate multi-generational tree structures. This paper proposes an interactive system for defining and visualizing large anatomical trees and for subsequent quantitative data mining. The system consists of a large number of tools for automatic image analysis, semi-automatic and interactive tree editing, and an assortment of visualization tools. Results are presented for a variety of 3D high-resolution images.     

IVUSAngio Tool: A publicly available software for fast and accurate 3D reconstruction of coronary arteries

There is an ongoing research and clinical interest in the development of reliable and easily accessible software for the 3D reconstruction of coronary arteries. In this work, we present the architecture and validation of IVUSAngio Tool, an application which performs fast and accurate 3D reconstruction of the coronary arteries by using intravascular ultrasound (IVUS) and biplane angiography data. The 3D reconstruction is based on the fusion of the detected arterial boundaries in IVUS images with the 3D IVUS catheter path derived from the biplane angiography. The IVUSAngio Tool suite integrates all the intermediate processing and computational steps and provides a user-friendly interface. It also offers additional functionality, such as automatic selection of the end-diastolic IVUS images, semi-automatic and automatic IVUS segmentation, vascular morphometric measurements, graphical visualization of the 3D model and export in a format compatible with other computer-aided design applications. Our software was applied and validated in 31 human coronary arteries yielding quite promising results. Collectively, the use of IVUSAngio Tool significantly reduces the total processing time for 3D coronary reconstruction. IVUSAngio Tool is distributed as free software, publicly available to download and use.     

冠状动脉的三维运动特征提取

提出一种根据X射线造影图像序列提取冠状动脉血管三维运动特征的方法.首先对由两个角度的造影图像重建得到的三维血管骨架进行运动估计,计算出两个时刻间骨架上各点的三维运动向量.然后结合心脏解剖和运动的先验知识,对血管运动进行定性分析,如位移方向、振幅及运动模式.提取、解释运动信息,并采用符号表达,方便医生进行观察和分析.最后给出了对临床得到的造影图像序列进行实验的结果.     

Development of a model of the coronary arterial tree for the 4D XCAT phantom

A detailed three-dimensional (3D) model of the coronary artery tree with cardiac motion has great potential for applications in a wide variety of medical imaging research areas. In this work, we first developed a computer-generated 3D model of the coronary arterial tree for the heart in the extended cardiac-torso (XCAT) phantom, thereby creating a realistic computer model of the human anatomy. The coronary arterial tree model was based on two datasets: (1) a gated cardiac dual-source computed tomography (CT) angiographic dataset obtained from a normal human subject and (2) statistical morphometric data of porcine hearts. The initial proximal segments of the vasculature and the anatomical details of the boundaries of the ventricles were defined by segmenting the CT data. An iterative rule-based generation method was developed and applied to extend the coronary arterial tree beyond the initial proximal segments. The algorithm was governed by three factors: (1) statistical morphometric measurements of the connectivity, lengths and diameters of the arterial segments; (2) avoidance forces from other vessel segments and the boundaries of the myocardium, and (3) optimality principles which minimize the drag force at the bifurcations of the generated tree. Using this algorithm, the 3D computational model of the largest six orders of the coronary arterial tree was generated, which spread across the myocardium of the left and right ventricles. The 3D coronary arterial tree model was then extended to 4D to simulate different cardiac phases by deforming the original 3D model according to the motion vector map of the 4D cardiac model of the XCAT phantom at the corresponding phases. As a result, a detailed and realistic 4D model of the coronary arterial tree was developed for the XCAT phantom by imposing constraints of anatomical and physiological characteristics of the coronary vasculature. This new 4D coronary artery tree model provides a unique simulation tool that can be used in the development and evaluation of instrumentation and methods for imaging normal and pathological hearts with myocardial perfusion defects.     

High resolution three-dimensional imaging and measurement of lung,heart, liver,and diaphragmatic development in the fetal rat based on micro-computed tomography (micro-CT)

Understanding of normal fetal organ development is crucial for the evaluation of the pathogenesis of congenital anomalies. Various techniques have been used to generate imaging of fetal rat organogenesis, such as histological dissection with 3-dimensional reconstruction and scanning electron microscopy. However, these techniques did not imply quantitative measurements of developing organs (volumes, surface areas of organs). Furthermore, a partial or total destruction of the embryos prior to analysis was inevitable. Recently, micro-computed tomography (micro-CT) has been established as a novel tool to investigate embryonic development in non-dissected embryos of rodents. In this study, we used the micro-CT technique to generate 4D datasets of rat embryos aged between embryonic day 15–22 and newborns. Lungs, hearts, diaphragms, and livers were digitally segmented in order to measure organ volumes and analyze organ development as well as generate high-resolution 3D images. These data provide objective values compiling a 4D atlas of pulmonary, cardiac, diaphragmatic, and hepatic development in the fetal rat.     

冠脉树三维重建中几何变换矩阵的优化

冠脉造影图像间的几何变换矩阵是实现冠脉树三维重建的关键。本研究分析了优化几何变换矩阵的必要性，提出利用分支点坐标、分支血管方向矢量和分支夹角三类数据优化几何变换矩阵的方法，并给出了kvenberg-Marquardt算法的优化步骤。最后利用两幅未标定的单面冠脉造影图像，实现冠脉树骨架的三维重建。重建的误差统计结果表明，优化方法有效地提高了冠状动脉树三维重建的精度。     

A new approach towards volumetric assessment of left ventricular function with MSCT

Cardiovascular CT is considered the diagnostic standard for establishing the presence of a functional and dynamic imaging system. It is difficult, however, to estimate the ventricular motion and volumes that are processed using hundreds and thousands of CT images, in a few moments.The main concept and design of our work are two fold - the development of effective semi-automatic tools for measuring the sequential left ventricular volumes from the hundreds or thousands of cardiac trans-axial images, and providing a simple interface with an interactive diagnostic tool for the volumetry of left ventricle and valuable cardiac 4D visualisation.We converted ten and more sequential volume data sets of the heart acquired from retrospective ECG-gating helical scan into 3D images by volume rendering. These sequential 3D images could be displayed as a movie (4D cardiac image) file. Furthermore, we developed a method for semi-automatic calculation of ejection fraction (EF) and cardiac cycle (%)-volume (ml) curve for estimation of the motion and the volume of the left ventricle. This method involved the use an interactive selection tool in the region of interest (ROI). All 3D processing methods, such as, cutting objects, segmentation, and image fusion were based on mask processing data. We now describe the software developed for cardiac 4D imaging and the estimation of ventricular volume.     

Coronary extraction and characterization in multi-detector computed tomography

The last technological advances of multi-detector computed tomography (MDCT) have brought significant improvements in image quality and consequently diagnostic performance. It opens, in particular, new perspectives for the coronary artery disease assessment. This paper presents a method for the coronary artery extraction and the lesion quantification. It makes use of a two stage-process. A tracking algorithm of the vascular structure, based on a 3D geometric moment operator, is first applied to estimate the vessel central axis location and its local diameter. It led to the extraction of the overall coronary tree. A deformable model technique, using a modified version of 3D level set technique, is then run on pathological vascular segments to refine the delineation of the wall and parietal calcifications. Parameters such as the narrowing or enlargement ratio of the vascular lumen, the minimum/maximum areas and the percent-area stenosis or aneurysm, are then computed for diagnosis purpose. The first method was submitted to a clinical evaluation on six data sets that showed good sensitivity and specificity performances. The second one was validated by experts, through a visual inspection of 2D cross-sections and volume rendering.     

A Web platform for the interactive visualization and analysis of the 3D fractal dimension of MRI data

This study presents a Web platform (http://3dfd.ujaen.es) for computing and analyzing the 3D fractal dimension (3DFD) from volumetric data in an efficient, visual and interactive way. The Web platform is specially designed for working with magnetic resonance images (MRIs) of the brain. The program estimates the 3DFD by calculating the 3D box-counting of the entire volume of the brain, and also of its 3D skeleton. All of this is done in a graphical, fast and optimized way by using novel technologies like CUDA and WebGL. The usefulness of the Web platform presented is demonstrated by its application in a case study where an analysis and characterization of groups of 3D MR images is performed for three neurodegenerative diseases: Multiple Sclerosis, Intrauterine Growth Restriction and Alzheimer’s disease. To the best of our knowledge, this is the first Web platform that allows the users to calculate, visualize, analyze and compare the 3DFD from MRI images in the cloud.     

基于造影图像的冠脉树中感兴趣血管段最佳视角的研究

在冠心病的临床诊断中，血管的遮盖和投影缩短会引起血管狭窄等的定量分析错误，而血管遮盖与投影缩短与造影角度的选择有关。传统的解决方法是由医生根据临床经验提供同时满足最小投影缩短和最小遮盖的造影角度，这种方法具有很大的主观性。本研究在冠脉树三维重建的基础上，研究了感兴趣血管段最佳视角的计算方法，该方法首先获得满足感兴趣血管段最小投影缩短的造影角度范围，然后在该范围中选取满足最小血管遮盖的造影角度。临床造影图像实验结果表明，在最佳视角下的投影图像中，血管狭窄损伤能够清楚地显示出来。从而可以对血管狭窄进行可靠地诊断。     

An interactive Internet-based system for tracking upper limb motion in home-based rehabilitation

In this paper, we introduce an interactive telecommunication system that supports video/audio signal acquisition, data processing, transmission, and 3D animation for post stroke rehabilitation. It is designed for stroke patients to use in their homes. It records motion exercise data, and immediately transfers this data to hospitals via the internet. A real-time videoconferencing interface is adopted for patients to observe therapy instructions from therapists. The system uses a peer-to-peer network architecture, without the need for a server. This is a potentially effective approach to reducing costs, allowing easy setup and permitting group-rehabilitation sessions. We evaluate this system using the following steps: (1) motion detection in different movement patterns, such as reach, drink, and reach-flexion; (2) online bidirectional visual telecommunication; and (3) 3D rendering using a proposed offline animation package. This evaluation has subjectively been proved to be optimal.     

PC机辅助三维重建在颌面部骨折中的临床应用价值

目的探讨PC机在颌面部外伤中三维（3D）重建的临床应用可行性。方法37例颌面部外伤患者．其中男性23例，女性14例，年龄13-71岁。进行3D重建的颌面部外伤患者采用螺旋方式扫描．扫描完成后在CT机上先进行薄层重建，然后将重建图像传送至PC工作站。应用PC机3D重建软件的适当模板进行容积重建（VR），部分加表面重建（SSD），形成彩色3D图像。结果37例颌面部骨折病例，经PC机上重建后的3D图像与轴位、冠状位扫描后的图像及二维图像进行比较，不仅显示了CT机上3D图像所显示的所有诊断信息．而且更方便、更快捷。结论PC机辅助颌面部3D重建在临床上具有明显的应用价值．     

基于高精度断层图片数据集的大鼠动脉血管重建

目的基于微米级大鼠断层图片数据集,建立高精度的大鼠动脉血管的三维模型,为各种监测鼠血管组织形态变化的试验提供客观依据。方法采用一套高分辨率大鼠断层切片图像数据集,使用半自动交互方法对动脉血管进行分割,使用改进的移动立方体(marching cube,MC)算法,在一台IBM图形工作站上对80 GByte大小的血管图片数据集进行重建。结果建立了完整的高精度大鼠动脉血管的三维表面模型,能显示出0.4mm大小的微细血管。结论该大鼠动脉血管三维模型可以为观测试验鼠血管组织形态变化提供一个立体的空间比较标准。     

Measurement of femoral neck anteversion in 3D. Part 1: 3D imaging method

Femoral neck anteversion is the torsion of the femoral head with reference to the distal femur. Conventional methods that use cross-sectional computed tomography (CT), magnetic resonance or ultrasound images to estimate femoral anteversion have met with several problems owing to the complex, three-dimensional (3D) structure of the femur. These problems include not only the difficulty of defining the direction of the femoral neck axis and condylar line but also the dependency upon patient positioning. In particular, the femoral neck axis, the direction of the femoral head, known as the major source of error, is difficult to determine from either a single or several two-dimensional (2D) cross-sectional images. A new method has been devised for the measurement of femoral anteversion using the 3D imaging technique. 3D reconstructed CT images from the femoral head and trochanter to the distal femur are used to measure the anteversion. It is necessary to remove the soft tissue from the CT images and extract just the bone part. Then, the femoral anteversion is measured from a computer-rendered femur image. The 3D imaging method is compared with both the conventional 2D method and the physical method using 20 dried femurs. For the physical method, which is used as a reference value, a special apparatus is devised. The average difference between the results of the physical method and those of the 2D CT method is 5.33°. The average difference between the results of the physical method and those of the 3D imaging method is 0.45°. Seventy-four patients, who suffer from toe-in-gait disease, are tested to compare the 3D imaging method with the conventional 2D CT method. The average difference between the 2D and 3D methods is 8.6°, and the standard is 7.43°. This method provides a very accurate and reliable measurement of femoral anteversion, as it is virtually equivalent to the direct measurement of bisected dried femur in vitro.     

Rest period duration of the coronary arteries: implications for magnetic resonance coronary angiography

Magnetic resonance (MR) and computed tomography coronary imaging is susceptible to artifacts caused by motion of the heart. The presence of rest periods during the cardiac and respiratory cycles suggests that images free of motion artifacts could be acquired. In this paper, we studied the rest period (RP) duration of the coronary arteries during a cardiac contraction and a tidal respiratory cycle. We also studied whether three MR motion correction methods could be used to increase the respiratory RP duration. Free breathing x-ray coronary angiograms were acquired in ten patients. The three-dimensional (3D) structure of the coronary arteries was reconstructed from a biplane acquisition using stereo reconstruction methods. The 3D motion of the arterial model was then recovered using an automatic motion tracking algorithm. The motion field was then decomposed into separate cardiac and respiratory components using a cardiac respiratory parametric model. For the proximal-to-middle segments of the right coronary artery (RCA), a cardiac RP (<1 mm 3D displacement) of 76+/-34 ms was measured at end systole (ES), and 65+/-42 ms in mid-diastole (MD). The cardiac RP was 80+/-25 ms at ES and 112+/-42 ms at MD for the proximal 5 cm of the left coronary tree. At end expiration, the respiratory RP (in percent of the respiratory period) was 26+/-8% for the RCA and 27+/-17% for the left coronary tree. Left coronary respiratory RP (<0.5 mm 3D displacement) increased with translation (32% of the respiratory period), rigid body (51%), and affine (79%) motion correction. The RCA respiratory RP using translational (27%) and rigid body (33%) motion correction were not statistically different from each other. Measurements of the cardiac and respiratory rest periods will improve our understanding of the temporal and spatial resolution constraints for coronary imaging.     

基于肺部CT序列图像的肺实质三维分割

目的:肺实质分割是基于CT图像的肺结节计算机辅助检测技术必不可少的步骤。结合阈值技术、连通区域标记以及形态学技术,提出了一种简单有效的从CT图像中分割三维肺实质的方法,以期能为后续肺结节计算机辅助检测技术的研究奠定基础。方法:首先,将原图像二值化,并应用三维连通域标记去除背景及细小空洞;然后,经三维区域生长法去除气管;最后,经形态学滤波平滑肺边界得到肺部精确的三维模板,并采用该模板从CT序列图像中分割出肺实质。结果:根据对20组层厚2.0mm、每组约250个切片的肺部CT临床数据实验验证,其肺实质分割的平均正确度为91.55%,处理单组数据平均耗时167.4563s。结论:实验结果表明,本文方法能自动快速地从CT序列图像中分割出肺实质。     

基于血管平行性和拓扑性的冠脉树分割

本研究提出了一种基于血管平行性和拓扑性的冠脉树分割方法。利用冠脉的曲率和平行性，获取冠脉段的边缘；利用冠脉的连通性和拓扑性，获取整个冠脉树的边缘。本方法的优点是，冠脉树的跟踪是从中心初始点到冠脉的末梢点，跟踪冠脉树的拓扑结构与真实冠脉的拓扑结构接近，解决了大冠脉段分支被分成几段的缺点，使冠脉段达到了很好的连续性；利用血管边缘的平行性和连通性，能找出准确冠脉的配对边缘，很好的解决了由三维图像投影为二维图像冠脉之间的部分重叠和遮挡问题。上述方法能获取完整、单连通和单像素的冠脉树边缘。实验结果表明，本研究提出的方法有很好的准确性。     

Validation of Image-Based Method for Extraction of Coronary Morphometry

An accurate analysis of the spatial distribution of blood flow in any organ must be based on detailed morphometry (diameters, lengths, vessel numbers, and branching pattern) of the organ vasculature. Despite the significance of detailed morphometric data, there is relative scarcity of data on 3D vascular anatomy. One of the major reasons is that the process of morphometric data collection is labor intensive. The objective of this study is to validate a novel segmentation algorithm for semi-automation of morphometric data extraction. The utility of the method is demonstrated in porcine coronary arteries imaged by computerized tomography (CT). The coronary arteries of five porcine hearts were injected with a contrast-enhancing polymer. The coronary arterial tree proximal to 1 mm was extracted from the 3D CT images. By determining the centerlines of the extracted vessels, the vessel radii and lengths were identified for various vessel segments. The extraction algorithm described in this paper is based on a topological analysis of a vector field generated by normal vectors of the extracted vessel wall. With this approach, special focus is placed on achieving the highest accuracy of the measured values. To validate the algorithm, the results were compared to optical measurements of the main trunk of the coronary arteries with microscopy. The agreement was found to be excellent with a root mean square deviation between computed vessel diameters and optical measurements of 0.16 mm (<10% of the mean value) and an average deviation of 0.08 mm. The utility and future applications of the proposed method to speed up morphometric measurements of vascular trees are discussed.     

基于投影图像和CT容积图像的三维冠状动脉运动跟踪新方法

目的利用双平面X射线投影图像序列和参考CT容积图像进行冠状动脉的三维运动跟踪建模。方法①提取投影图像序列中的冠状动脉树;②利用多尺度滤波和血管函数提取CT容积图像中的动脉血管;③采用基于B样条配准的方法进行三维运动建模。结果将双投影图像中血管的运动估计结果的三维重建形态与三维运动模型预测出的结果进行了量化比较,调整配准的B样条参数后,两者误差处于有效范围之内。结论由此表明采用投影图像和对应容积图像的联合先验知识进行冠状动脉的三维运动建模是有效的。