Simulation of cDNA microarrays via a parameterized random signal model

cDNA microarrays provide simultaneous expression measurements for thousands of genes that are the result of processing images to recover the average signal intensity from a spot composed of pixels covering the area upon which the cDNA detector has been put down. The accuracy of the signal measurement depends on using an appropriate algorithm to process the images. This includes determining spot locations and processing the data in such a way as to take into account spot geometry, background noise, and various kinds of noise that degrade the signal. This paper presents a stochastic model for microarray images. There are over 20 model parameters, each governed by a probability distribution, that control the signal intensity, spot geometry, spot drift, background effects, and the many kinds of noise that affect microarray images owing to the manner in which they are formed. The model can be used to analyze the performance of image algorithms designed to measure the true signal intensity because the ground truth (signal intensity) for each spot is known. The levels of foreground noise, background noise, and spot distortion can be set, and algorithms can be evaluated under varying conditions.     

Reverse engineering in CAD model reconstruction of customized artificial joint

In order to meet the requirements of customized artificial joint design, and to reduce the production cycle and cost, we present a method to generate the complex surface of an artificial knee joint by co-ordinate measuring machine (CMM) from the normative prosthesis, and form the model data base. First, this paper describes how to plan the measure method to get the better data points and how to deal with the point cloud data. Then, the free-form surfaces are constructed from the point cloud data using the reverse engineering software-Surfacer. Lastly, the solid CAD model of the artificial knee joint is created from the surfaces by extension, intersection and so on. These models formed the data base of the prosthesis, in which we can select a suitable kind of artificial knee joint model to customize for the patient. That is, we only need to change the local data of the corresponding CAD model to meet the different requirements of the patient.     

Three-dimensional reconstruction of joint surfaces using a microcomputer

A microcomputer was used to analyse the surface characteristics and geometry of articulating joints. Both hardware configuration and software organisation were described. Data used in this analysis were obtained by sequential resection of entire joints (elbows, metatarsophalangeal joints and knees) secured in an embedding medium. The exposed joint profile after each resection in a bone milling machine was recorded photographically. Each record of freshly cut profile was manually digitised and automatically processed with a desktop microcomputer. The complete structure of these articulating surfaces was reconstructed in three dimensions to be displayed in any desired orientation as a series of parallel, consecutive and uniformly spaced sections. These data have been used to derive information on cartilage thickness, underlying bone structure, orientation and anatomical shape of the joint surfaces. The stored surface geometry may be retrieved at any time for related studies of joint kinematics, joint sizing and prosthetic joint design.     

Direct cone-beam cardiac reconstruction algorithm with cardiac banding artifact correction

Multislice helical computed tomography (CT) is a promising noninvasive technique for coronary artery imaging. Various factors can cause inconsistencies in cardiac CT data, which can result in degraded image quality. These inconsistencies may be the result of the patient physiology (e.g., heart rate variations), the nature of the data (e.g., cone-angle), or the reconstruction algorithm itself. An algorithm which provides the best temporal resolution for each slice, for example, often provides suboptimal image quality for the entire volume since the cardiac temporal resolution (TRc) changes from slice to slice. Such variations in TRc can generate strong banding artifacts in multiplanar reconstruction images or three-dimensional images. Discontinuous heart walls and coronary arteries may compromise the accuracy of the diagnosis. A beta-blocker is often used to reduce and stabilize patients' heart rate but cannot eliminate the variation. In order to obtain robust and optimal image quality, a software solution that increases the temporal resolution and decreases the effect of heart rate is highly desirable. This paper proposes an ECG-correlated direct cone-beam reconstruction algorithm (TCOT-EGR) with cardiac banding artifact correction (CBC) and disconnected projections redundancy compensation technique (DIRECT). First the theory and analytical model of the cardiac temporal resolution is outlined. Next, the performance of the proposed algorithms is evaluated by using computer simulations as well as patient data. It will be shown that the proposed algorithms enhance the robustness of the image quality against inconsistencies by guaranteeing smooth transition of heart cycles used in reconstruction.     

早期关节活动对前交叉韧带重建后腱骨愈合的影响

背景：异体移植物可作为前交叉韧带重建翻修以及膝关节复合损伤修复的选择。 目的：通过建立异体韧带移植重建前交叉韧带的动物模型,观察早期活动对异体植入物止点腱骨愈合的组织形态以及关节活动功能恢复的影响。 方法：健康成年新西兰兔9只,随机取3只兔双侧跟腱作为供体,取6只兔切断一侧膝关节前交叉韧带,固定重建前交叉韧带。动物随机数字表法均分运动组和制动组,6周后观察关节活动功能、腱骨愈合大体观察以及组织学观察。 结果与结论：术侧肢体活动情况基本正常,所有动物前交叉韧带上下止点愈合情况均良好。前交叉韧带周围滑膜均可见明显增生。活动组可见较多Sharpey纤维,腱骨间接连接形成,而制动组未见明显Sharpey纤维。说明术后6周异体重建物止点已有腱骨愈合,早期活动对重建物的腱骨愈合并无明显不良影响,可能还更有利。     

Left ventricular motion reconstruction with a prolate spheroidal B-spline model

Tagged cardiac magnetic resonance (MR) imaging can non-invasively image deformation of the left ventricular (LV) wall. Three-dimensional (3D) analysis of tag data requires fitting a deformation model to tag lines in the image data. In this paper, we present a 3D myocardial displacement and strain reconstruction method based on a B-spline deformation model defined in prolate spheroidal coordinates, which more closely matches the shape of the LV wall than existing Cartesian or cylindrical coordinate models. The prolate spheroidal B-spline (PSB) deformation model also enforces smoothness across and can compute strain at the apex. The PSB reconstruction algorithm was evaluated on a previously published data set to allow head-to-head comparison of the PSB model with existing LV deformation reconstruction methods. We conclude that the PSB method can accurately reconstruct deformation and strain in the LV wall from tagged MR images and has several advantages relative to existing techniques.     

Comparison of conventional MRI and 3D reconstruction model for evaluation of temporomandibular joint

The aim of this work was to define the diagnostic value of a method for 3D reconstruction of MRI images for the assessment of temporomandibular joint. Sixty subjects, 42 diagnosed with unilateral temporomandibular disorders (TMD) with disc displacement and 18 without signs or symptoms of TMD (control group) were included. All subjects had both temporomandibular joints scanned by MRI. Three-dimensional imaging reconstructions of temporomandibular joint were generated by segmentation software, allowing visualization of the components of temporomandibular joint (articular disc, condyle and temporal bone) on arbitrary planes. Disc displacement was observed in 83% of 3D reconstruction and 81% of conventional MRI. The agreement between 3D diagnosis and MRI findings was significant and high. The present analysis suggested that 3D reconstruction is a useful and accurate method for the assessment of the temporomandibular joint in TMD ID.     

Intraoperative 3D reconstruction of prostate brachytherapy implants with automatic pose correction

The success of prostate brachytherapy critically depends on delivering adequate dose to the prostate gland, and the capability of intraoperatively localizing implanted seeds provides potential for dose evaluation and optimization during therapy. REDMAPS is a recently reported algorithm that carries out seed localization by detecting, matching and reconstructing seeds in only a few seconds from three acquired x-ray images (Lee et al 2011 IEEE Trans. Med. Imaging 29 38-51). In this paper, we present an automatic pose correction (APC) process that is combined with REDMAPS to allow for both more accurate seed reconstruction and the use of images with relatively large pose errors. APC uses a set of reconstructed seeds as a fiducial and corrects the image pose by minimizing the overall projection error. The seed matching and APC are iteratively computed until a stopping condition is met. Simulations and clinical studies show that APC significantly improves the reconstructions with an overall average matching rate of ?99.4%, reconstruction error of ?0.5 mm, and the matching solution optimality of ?99.8%.     

Analytical fan-beam and cone-beam reconstruction algorithms with uniform attenuation correction for SPECT

In this paper, we developed an analytical fan-beam reconstruction algorithm that compensates for uniform attenuation in SPECT. The new fan-beam algorithm is in the form of backprojection first, then filtering, and is mathematically exact. The algorithm is based on three components. The first one is the established generalized central-slice theorem, which relates the 1D Fourier transform of a set of arbitrary data and the 2D Fourier transform of the backprojected image. The second one is the fact that the backprojection of the fan-beam measurements is identical to the backprojection of the parallel measurements of the same object with the same attenuator. The third one is the stable analytical reconstruction algorithm for uniformly attenuated Radon data, developed by Metz and Pan. The fan-beam algorithm is then extended into a cone-beam reconstruction algorithm, where the orbit of the focal point of the cone-beam imaging geometry is a circle. This orbit geometry does not satisfy Tuy's condition and the obtained cone-beam algorithm is an approximation. In the cone-beam algorithm, the cone-beam data are first backprojected into the 3D image volume; then a slice-by-slice filtering is performed. This slice-by-slice filtering procedure is identical to that of the fan-beam algorithm. Both the fan-beam and cone-beam algorithms are efficient, and computer simulations are presented. The new cone-beam algorithm is compared with Bronnikov's cone-beam algorithm, and it is shown to have better performance with noisy projections.     

兔膝骨关节炎合并骨质疏松症动物模型的建立

背景：临床发现同时患有骨质疏松症和骨关节炎患者占相当大的比例,而且目前对骨质疏松与骨关节炎相互关系的认识不一致。 目的：建立骨关节炎合并骨质疏松症的动物模型。 方法：将14只新西兰大白兔随机等分为模型组和正常组。模型组新西兰大白兔行双侧卵巢切除,正常组新西兰大白兔不作任何处理。 结果与结论：去除卵巢10周后,模型组大白兔关节软骨出现明显的退变,血清雌二醇、股骨骨密度水平较正常组显著下降(P < 0.01),而关节软骨Mankin评分比正常组显著增高(P < 0.01);且软骨Mankin评分与骨密度和血清雌二醇呈负相关,而骨密度与血清雌二醇水平呈正相关,表明实验成功建立了兔膝骨关节炎合并骨质疏松症动物模型。     

Computer assisted anatomical reconstruction: a prostate model

Summary We report a computer assisted three dimensional reconstruction technique using serial sections. This reconstruction was achieved by means of a common microcomputer. The organ analyzed in this study was the common European rabbit prostate.

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Reconstruction anatomique assistée par ordinateur: l'exemple de la prostate

Résumé Les auterurs rapportent une technique de reconstruction tridimensionnelle assistée par ordinateur en utilisant les informations de coupes sériées. Cette reconstruction a été faite avec un micro-ordinateur courant. Cette technique a été appliquée à la reconstruction d'une prostate de lapin commun européen.

     

Implementation of a cone-beam reconstruction algorithm for the single-circle source orbit with embedded misalignment correction using homogeneous coordinates.

We present an efficient implementation of an approximate cone-beam image reconstruction algorithm for application in tomography, which accounts for scanner mechanical misalignment. The implementation is based on the algorithm proposed by Feldkamp et al. and is directed at circular scan paths. The algorithm has been developed for the purpose of reconstructing volume data from projections acquired in an experimental x-ray micro-tomography (microCT) scanner. To mathematically model misalignment we use matrix notation with homogeneous coordinates to describe the scanner geometry, its misalignment, and the acquisition process. For convenience analysis is carried out for x-ray CT scanners, but it is applicable to any tomographic modality, where two-dimensional projection acquisition in cone beam geometry takes place, e.g., single photon emission computerized tomography. We derive an algorithm assuming misalignment errors to be small enough to weight and filter original projections and to embed compensation for misalignment in the backprojection. We verify the algorithm on simulations of virtual phantoms and scans of a physical multidisk (Defrise) phantom.     

膝关节前交叉韧带重建兔模型的建立

背景：传统前交叉韧带重建造模腱骨界面愈合缓慢,造模时间较长。   目的：通过在腱骨界面注入以纤维蛋白胶为载体的重组人骨形态发生蛋白2复合物,建立造模周期更短、更完善的兔膝关节前交叉韧带重建动物模型。 方法：取成年新西兰兔同侧半腱肌肌腱作为自体移植材料,建立双侧前交叉韧带重建动物模型,建模后随机分为模型组、纤维蛋白胶组,空白对照组和正常组。模型组在移植腱骨隧道界面注射填充以纤维蛋白胶作为载体的重组人骨形态发生蛋白2,纤维蛋白胶组在重建术后腱骨界面仅填充纤维蛋白胶,空白对照组在重建术后腱骨界面不作任何填充,正常组则不予手术,保留正常的前交叉韧带。各组分别于术后第4和8周取材,进行生物力学检测。 结果与结论：模型组最大载荷和刚度在术后4和8周与纤维蛋白胶组和空白对照组相比均增强(P < 0.01)。由此可见,实验成功建立了双侧前交叉韧带重建动物模型,以纤维蛋白胶作为载体的重组人骨形态发生蛋白2可以在术后早期提高腱骨界面的最大载荷和刚度,促进了腱骨界面的愈合,缩短了重建动物模型的实验周期。     

锁骨钩钢板并喙锁韧带修补治疗重度肩锁关节脱位

肩锁关节脱位在临床上较为常见，占全身关节脱位的4．4％，非手术治疗因固定困难，多致治疗失败。Ⅲ度肩锁关节脱位是手术治疗的指征。我院自2003年6月至2007年12月采用锁骨钩钢板并缘锁韧带修补治疗Ⅲ度肩锁关节脱位21例，疗效满意，现报告如下。     

CT重建人上胫腓骨关节面坡度测量方法及意义

背景：测量上胫腓关节坡度不仅可研究国人上胫腓关节解剖结构与类型,还具有评价上胫腓关节稳定性的作用。 目的：通过测量双侧上胫腓关节面X射线平片坡度与利用64排螺旋CT重建后的关节面坡度进行比较,探讨测量方法的优良及关节坡度的临床意义。 方法：选取正常成年男女各50名志愿者,年龄18~90岁,分别行双膝关节内旋30°或45°或60°摄片及64排螺旋CT扫描并重建胫腓骨全长(包括膝关节)。选用角尺测量上胫腓关节面与腓骨干纵轴的夹角和上胫腓骨关节面与水平线的夹角。 结果与结论：X射线及螺旋CT对同一上胫腓骨关节测量数据差别较大。由于X线受摄片位置影响,且关节面倾斜度的确定比较粗略,因此64排螺旋CT重建后的测量方法准确,方便,对于鉴别上胫腓骨关节脱位和关节不稳提供帮助,减少临床误诊。     

以关节不稳建立的大鼠骨关节炎模型

背景：骨性关节炎是一种复杂的多病因退变性关节疾病。早期进行骨性关节炎的防治尤其重要。但获取足量的适合研究的早期骨性关节炎的人类骨标本十分困难。 目的：观察关节不稳方法建立骨关节炎模型大鼠的关节软骨组织学变化。 方法：10周龄雄性SD大鼠随机分为2组：实验组切除右膝内侧半月板及内侧副韧带,对照组仅切开关节囊。于术后1,2,4,6,8周取右膝关节标本,行病理组织学检查分析大鼠骨关节炎病程的变化情况。 结果与结论：①术后2,4,6,8周,实验组关节软骨退变程度呈现轻度糜烂、溃疡磨损、严重磨损、骨赘形成等病理变化。②术后1,2,4,6,8周,实验组关节软骨评分均明显高于对照组(P < 0.05)。结果显示该实验采用内侧副韧带切断+内侧半月板切除方法成功建立了大鼠膝关节骨关节炎模型,且造模后4周内的病理、形态学改变类似于人类早期膝关节骨关节炎表现,是研究早期骨关节炎的理想模型。     

数字化下颌骨的计算机重建

背景：随着计算机技术与医学相结合及医学与工科相结合的发展,越来越多的方法被用于下颌骨的重建。 目的：分析计算机三维重建技术在下颌骨缺损中的应用及意义。 方法：应用计算机检索万方数据库、维普数据库和PubMed数据库中1999-01/2011-10关于下颌骨数字化三维重建的文章,在标题和摘要中以“下颌骨;数字化;三维重建;计算机技术”或“CAD/CAM;mandible;3D mandible model”为检索词进行检索。 结果与结论：下颌骨缺损类型众多,不同个体间下颌骨形态差异也较大,简单应用下颌骨正常均值来代替个体下颌骨进行修复是不合适的,因而在进行下颌骨修复重建之前行个体化设计至关重要。随着数字化技术医学领域广泛应用,计算机辅助设计和计算机辅助制造较好的解决了此类问题,在计算机上设计出理想下颌骨形态以及它与上颌骨的解剖关系,通过快速原型技术复制出实体模型,便于体外精确测量分析并进行手术设计,而骨组织工程方法可以在计算机辅助下构建出一个与缺损区形态一致的三维、个体化骨组织,使得下颌骨在形态及功能的精确修复成为可能。 关键词：下颌骨;数字化;三维重建;计算机技术;数字化医学 doi:10.3969/j.issn.1673-8225.2012.09.037