基于VTK的医学图像三维可视化系统

医学图像的三维可视化可以通过可视化工具包（VTK）提供的API实现。VTK是医学图像可视化的开法工具包,它把可视化的算法封装起来,利用简单的代码生成所需图形。基于VTK的医学图像三维可视化系统阐述了如何借助VTKAPI读入二维医学图像序列、操作二维图像、重建三维图像以及进行三维图像可视化的全套方案,为临床医生的诊断、治疗提供了有益的途径。     

基于VT K 的D IC OM 医学图像三维重建研究

医学图像三维重建技术利用二维医学图像序列重建出三维模型,为医生提供直观、全面、准确的病灶和正常组织信息．是当今医学影像领域研究的热点之一。VTK是国际上广泛应用的可视化工具包,具有优秀的架构和运行机制。本文研究了DICOM3．0标准,提出了正确解读DICOM医学图像的方法;深入VTK内部机制,解决了VTK和DICOM医学图像读取模块间的数据接口问题;在三维重建过程中,为解决数据量巨大、成像时间漫长、阶梯效应、交互性不强等问题,重点剖析了VTK的数据处理机制。并给出相关优化方法。实验结果表明本文提出的解决方案和优化方法实用可靠,为进一步开发医学三雏图形系统打下了基础。     

冷冻电镜密度图可视化软件VAT4M

基于冷冻电镜三维密度图的特征分析,研究开发了冷冻电镜密度图可视化软件VAT4M(Visual Analysis Tools for Macro-Molecule Map and Model),实现了对三维冷冻电镜密度图的可视化分析,其主要功能包括密度图和分子模型的可视化、密度图的分割和晶体结构在密度图中的匹配。在可视化方面,在实现等值面可视化方法的同时还实现了体绘制可视化模式。对于结构分析,VAT4M提供了自动分割工具,和所见即所得的分割浏览器。同时,VAT4M还提供了极值吸收法与梯度法相结合的自动匹配方法,而且,对于具有对称性的密度图,可根据一个亚基的匹配结果,迅速得到其准原子模型。最后给出了若干应用实例。实验表明,本平台对冷冻电镜密度数据具有良好的可视与分析功能。     

基于光学相干层析图像的离体牙三维重建

利用shear-warp算法对离体牙的光学相干层析图像进行三维重建,通过不透明度传递函数的合理设置及光照模型的引入实现牙齿内部组织结构的可视化,便于医生在早期龋齿诊断中定位病变.介绍了shear-warp算法的原理、用于龋齿检测的全光纤光学相干层析成像系统及其二维层析图,以及利用离体牙牙冠的二维层析图重建获得三维结构图.     

磁共振肿瘤矩特征信息研究

目的:采用MR脑肿瘤图像分割与矩方法进行结合,以获取特定器官及组织的轮廓。方法:对MR脑肿瘤图像进行分割,并对分割的结果进行矩描述。通过分析当前常用的医学图像分割方法,采用了一种基于形变模型的医学图像分割方法,并按照相应的理论算法模型和实现步骤对医学图像进行了处理,最后用Visual C 6.0编程,并对MR脑肿瘤图像进行分割实验。结果:从切割的图形中可以看出,本分割方法分割边界清晰,总体不确定性较小,利用矩技术所提取的图像特征在基于内容的图像检索中是有效的。结论:本分割方法切实可行,分割效果较好,为进一步的MR脑肿瘤图像分析和研究提供了一种有效工具。     

脑室系统可视化研究在医学影像学教学培训中的应用

脑室系统疾病的诊断主要有赖于CT、MRI检查,掌握脑室系统的断层解剖学知识是认识正常和进行疾病诊断的基础.本文利用中国可视化人体中颅脑薄层连续断层图像,运用虚拟断层切割技术和三维重建技术,建立了脑室系统三维可视化模型.脑室系统可视化模型将断层解剖学与整体解剖相衔接,将横断、矢状与冠状位图像相结合,有助于培养学生的空间思维能力及建立脑室系统结构的三维立体概念,在临床医学影像学教学培训中取得了良好的教学效果.     

Java AWT和JAI技术在生物数据库图像显示上的应用

利用Java AWT和JAI技术绘制生物图像的方法可以使在实验室中得到的生物实验数据自动转化为需要的图谱,并且图像的精确度高。绘制成的图像既可以保存在本地硬盘中,也可以在浏览器中以网页的形式展示出来供研究人员分析使用。该方法目前已在上海生物信息技术研究中心开发的可视化工具MapViewer和主题数据库H2H,SRA中得到应用。     

生物投影片绘制技法

生物投影片的绘制是教师必备的基本技能之一。生物投影片配合课堂教学具有直观性 ,教师根据教学需要 ,自己绘制投影片 ,能丰富教学内容 ,增强教学效果。下面介绍几种绘制投影片的绘制方法。1　黑白画法投影胶片有 2种 ,一种是胶片上敷着一层药膜 ,这种胶片适合画着颜色的投影片。另一种是光面胶片 ,这种胶片适合画黑白投影片。黑白投影片绘画一般先在纸上打好草稿 ,再把胶片按在纸上描线 ,如画蝗虫身体外部形态 ,画时要掌握好蝗虫各部分比例关系 ,准确反映蝗虫的特征 ,先画出大体结构 :头部、胸部、腹部、前翅、后翅、前足和后足 ,最后画各…     

三维超声心脏图像的模糊聚类分割

采用三维超声心动图对小儿先天性心脏病进行诊断与治疗能达到比传统二维超声心动图更直观的效果。然而由于超声图像质量较差,三维超声心动图的可视化效果往往无法达到医生的要求。本文对三维超声心脏图像进行分割,以改进超声图像的可视化效果,并为参数提取等提供基础。首先采用快速的模糊c均值聚类得到初始分割结果;然后利用图像多分辨率技术进行修正;接着结合图像的对比度进行进一步的分割;最后,把处理后的图像用绘制的方法显示出来。本文的结果对超声图像的可视化效果有一定的改善.     

一个可用于复杂大群体的可视化系谱绘制和分析软件

对于在遗传研究和家系研究中大的系谱结构图还很难分析。系谱的绘制通常是遗传性状的分析研究的第一步。系图可以反映整个群体的结构、每个个体之间的相互关系以及基因流的走向,便于理解遗传性状的本质。因为所用家系数目的增大和复杂性的增加,绘制1个清晰的系谱有时变得十分困难。因此开发了1种名为Pedigraph软件,可以解决这个问题。Pedigraph能够完成对于大的复杂的群体的系谱绘制工作,并能进行相应的系谱分析。初步的测试表明这个软件在研究动植物的遗传育种中是1个有用的工具,同时它也可以用于人类的群体和历史等方面的研究。     

A precise and non-destructive method to calculate the surface area in living scleractinian corals using X-ray computed tomography and 3D modeling

The surface area of corals represents a major reference parameter for the standardization of flux rates, for coral growth investigations, and for investigations of coral metabolism. The methods currently used to determine the surface area of corals are rather approximate approaches lacking accuracy, or are invasive and often destructive methods that are inapplicable for experiments involving living corals. This study introduces a novel precise and non-destructive technique to quantify surface area in living coral colonies by applying computed tomography (CT) and subsequent 3D reconstruction. Living coral colonies of different taxa were scanned by conventional medical CT either in air or in sea water. Resulting data volumes were processed by 3D modeling software providing realistic 3D coral skeleton surface reconstructions, thus enabling surface area measurements. Comparisons of CT datasets obtained from calibration bodies and coral colonies proved the accuracy of the surface area determination. Surface area quantifications derived from two different surface rendering techniques applied for scanning living coral colonies showed congruent results (mean deviation ranging from 1.32 to 2.03%). The validity of surface area measurement was verified by repeated measurements of the same coral colonies by three test persons. No significant differences between all test persons in all coral genera and in both surface rendering techniques were found (independent sample t-test: all n.s.). Data analysis of a single coral colony required approximately 15 to 30 min for a trained user using the isosurface technique regardless of the complexity and growth form of the latter, rendering the method presented in this study as a time-saving and accurate method to quantify surface areas in both living coral colonies and bare coral skeletons. Communicated by Biology Editor Dr Michael Lesser     

Three-dimensional surface reconstruction software system for IBM personal computers

Surface and volumetric three-dimensional imaging methods have found application in fields as diverse as diagnostic medical imaging and paleontological research. The acquisition, modeling, classification, and computer graphics rendering of discrete image volumes will be introduced. Applications in diagnosis (craniofacial, orthopedic, cardiovascular, and others) as well as reconstruction methods for generic serial sections will be described. C language software for three-dimensional reconstruction which operates on an IBM PC/AT clone is described.     

三维DSA在颅内动脉瘤中的应用

目的探讨三维数字减影血管造影(3D DSA)在颅内动脉瘤中的应用价值。方法使用GE Innova 3100平板血管造影机对40例疑似颅内动脉瘤患者行双侧颈内、外动脉和双侧椎动脉正、侧位2D DSA,进一步对感兴趣血管行3D DSA,通过容积再现(VR)进行颅内血管重建。结果 3D DSA检出39例动脉瘤患者,47枚动脉瘤,2D DSA检出31例动脉瘤患者,35枚动脉瘤,二者检出动脉瘤的长、短径无统计学差异(P>0.05),图像质量有统计学差异(P<0.05)。2D DSA出现假阳性动脉瘤3枚,假阴性动脉瘤15枚,评估颅内动脉瘤的灵敏度为78.9%,特异性为85.2%;3D DSA没有出现假阳性、假阴性动脉瘤,评估颅内动脉瘤的灵敏度为100%,特异性为100%。在动脉瘤形态、瘤颈尺寸及与相邻血管间的关系的显示上,3D DSA明显优于2D DSA。结论 3D DSA作为脑动脉造影中2D DSA的进一步补充,对颅内动脉瘤的诊断与治疗具有重要价值。     

3D打印肺段模型在胸外科解剖教学中的应用

目的:探讨3D打印肺段模型在胸外科解剖教学中的应用效果。方法:60名医学新生随机分为3D打印组和三维重建图像组,每组30人。经相关知识介绍后,参加问卷调查并记录得分,包括理论知识、肺段鉴别、病灶鉴别,共14分。结果:3D打印肺段模型能清晰准确地显示出肺脏结构。3D打印组问卷调查得分显著高于三维重建图像组,差异具有统计学意义(P=0.031)。结论:3D打印肺段模型在医学生肺段解剖教学中的效果优于三维重建图像。     

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Histology volume reconstruction facilitates the study of 3D shape and volume change of an organ at the level of macrostructures made up of cells. It can also be used to investigate and validate novel techniques and algorithms in volumetric medical imaging and therapies. Creating 3D high-resolution atlases of different organs^1,2,3 is another application of histology volume reconstruction. This provides a resource for investigating tissue structures and the spatial relationship between various cellular features. We present an image registration approach for histology volume reconstruction, which uses a set of optical blockface images. The reconstructed histology volume represents a reliable shape of the processed specimen with no propagated post-processing registration error. The Hematoxylin and Eosin (H&E) stained sections of two mouse mammary glands were registered to their corresponding blockface images using boundary points extracted from the edges of the specimen in histology and blockface images. The accuracy of the registration was visually evaluated. The alignment of the macrostructures of the mammary glands was also visually assessed at high resolution.This study delineates the different steps of this image registration pipeline, ranging from excision of the mammary gland through to 3D histology volume reconstruction. While 2D histology images reveal the structural differences between pairs of sections, 3D histology volume provides the ability to visualize the differences in shape and volume of the mammary glands.     

Dental cone beam CT: A review

For the maxillofacial region, there are various indications that cannot be interpreted from 2D images and will benefit from multiplanar viewing. Dental cone beam CT (CBCT) utilises a cone- or pyramid-shaped X-ray beam using mostly flat-panel detectors for 3D image reconstruction with high spatial resolution. The vast increase in availability and amount of these CBCT devices offers many clinical benefits, and their ongoing development has potential to bring various new clinical applications for medical imaging. Additionally, there is also a need for high quality research and education. European guidelines promote the use of a medical physics expert for advice on radiation protection, patient dose optimisation, and equipment testing. In this review article, we perform a comparison of technical equipment based on manufacturer data, including scanner specific X-ray spectra, and describe issues concerning CBCT image reconstruction and image quality, and also address radiation dose issues, dosimetry, and optimisation. We also discuss clinical needs and what type of education users should have in order to operate CBCT systems safely. We will also take a look into the future and discuss the issues that still need to be solved.     

Three-dimensional bio-printing

Three-dimensional(3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.     

Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions

Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.     

Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms

A three-dimensional (3D) version of the spectral signal-to-noise ratio (SSNR)-based resolution measure is introduced. The measure is defined for a class of 3D reconstruction algorithms that use interpolation in Fourier space. The statistical properties of the SSNR are discussed and related to the properties of another resolution measure, the Fourier shell correlation (FSC). The new measure was tested on 3D structures calculated from a simulated set of quasi-evenly spaced 2D projections using a nearest-neighbor interpolation and a gridding algorithm. In the latter case, the results agree very well with the FSC-based estimate, with the exception of very high SSNR values. The main applicability of the 3D SSNR is tomography, where due to the small number of projections collected, FSC cannot be used. The new measure was applied to three sets of tomographic data. It was demonstrated that the measure is sufficiently sensitive to yield theoretically expected results. Therefore, the 3D SSNR opens up the possibility of evaluating the quality of tomographic reconstructions in an objective manner. The 3D distribution of SSNR is of major interest in single-particle analysis. It is shown that the new measure can be used to evaluate the anisotropy of 3D reconstructions. The distribution of SSNR is characterized by three anisotropy indices derived from principal axes of the 3D inertia covariance matrix of the SSNR. These indices are used to construct a 3D Fourier filter which, when applied to a 3D reconstruction of a macromolecule, maximizes the SNR in real space and minimizes real-space artifacts caused by uneven distribution of 2D projections.     

Ultramicroscopy: 3D reconstruction of large microscopical specimens

Ultramicroscopy is a microscopical technique that allows optical sectioning and 3D reconstruction of biological and medical specimens. While in confocal microscopy specimen size is limited to several hundred micrometers at best, using ultramicroscopy even centimeter sized objects like whole mouse embryos can be reconstructed with micrometer resolution. This is possible by using a combination of a clearing procedure and the principle of lightsheet illumination. We present ultramicroscopic 3D reconstructions of whole immunohistochemically labelled mouse embryos and adult Drosophila, giving detailed insight into their anatomy. Its speed and simplicity makes ultramicroscopy ideally suited for high‐throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)