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。     

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.     

3D Coronary Artery Reconstruction by 2D Motion Compensation Based on Mutual Information

Background

3D reconstruction of the coronary arteries can provide more information in the interventional surgery. Motion compensation is one kind of the 3D reconstruction method.

Influence of Head Motion on the Accuracy of 3D Reconstruction with Cone-Beam CT: Landmark Identification Errors in Maxillofacial Surface Model

PurposeThe purpose of this study was to investigate the influence of head motion on the accuracy of three-dimensional (3D) reconstruction with cone-beam computed tomography (CBCT) scan.ResultsRendered surface models with head motion were similar to the control model in appearance; however, the landmark identification errors showed larger values in models with head motion than in the control. In particular, the Porion in the horizontal rotation models presented statistically significant differences (P < .05). Statistically significant difference in the errors between the right and left side landmark was present in the left side rotation which was opposite direction to the scanner rotation (P < .05).ConclusionsPatient movement during CBCT scan might cause landmark identification errors on the 3D surface model in relation to the direction of the scanner rotation. Clinicians should take this into consideration to prevent patient movement during CBCT scan, particularly horizontal movement.     

Reconstruction for 3D PET Based on Total Variation Constrained Direct Fourier Method

This paper presents a total variation (TV) regularized reconstruction algorithm for 3D positron emission tomography (PET). The proposed method first employs the Fourier rebinning algorithm (FORE), rebinning the 3D data into a stack of ordinary 2D data sets as sinogram data. Then, the resulted 2D sinogram are ready to be reconstructed by conventional 2D reconstruction algorithms. Given the locally piece-wise constant nature of PET images, we introduce the total variation (TV) based reconstruction schemes. More specifically, we formulate the 2D PET reconstruction problem as an optimization problem, whose objective function consists of TV norm of the reconstructed image and the data fidelity term measuring the consistency between the reconstructed image and sinogram. To solve the resulting minimization problem, we apply an efficient methods called the Bregman operator splitting algorithm with variable step size (BOSVS). Experiments based on Monte Carlo simulated data and real data are conducted as validations. The experiment results show that the proposed method produces higher accuracy than conventional direct Fourier (DF) (bias in BOSVS is 70% of ones in DF, variance of BOSVS is 80% of ones in DF).     

植物对环境的响应——定量重建古气候的研究进展

生物演化的本质是生物遗传物质与外部环境的辩证统一。一方面,植物和环境的协调发展推动植物界自身的演化;另一方面,外部环境的改变在植物的形态结构、生理功能、繁衍机理,以至最终在遗传物质上留下痕迹,这就是植物对环境的响应。从长时间尺度上（可以达到上亿年）研究植物界的发生发展,是一个探讨和理解植物起源与演化的生命科学问题,也是从宏观角度认识生物演化和全球变化的相关关系的环境科学问题。目前,国际上对全球环境变化的研究,正在加大研究的时间尺度和提高研究的精确程度,即在距今百万年至数千万年,甚至更长的时间范围内,从定性到定量的研究和理解全球变化的过程、规律和机制,以便更有效地预测气候的未来变化。本文介绍了最近10年里,采用特有种气候分析法、共存分析法、叶相分析法、植物气孔参数与古大气CO2浓度变化的相关性,定量研究古环境和古气候方面所取得的进展。     

植物对环境的响应--定量重建古气候的研究进展

生物演化的本质是生物遗传物质与外部环境的辩证统一。一方面,植物和环境的协调发展推动植物界自身的演化;另一方面,外部环境的改变在植物的形态结构、生理功能、繁衍机理,以至最终在遗传物质上留下痕迹,这就是植物对环境的响应。从长时间尺度上(可以达到上亿年)研究植物界的发生发展,是一个探讨和理解植物起源与演化的生命科学问题,也是从宏观角度认识生物演化和全球变化的相关关系的环境科学问题。目前,国际上对全球环境变化的研究,正在加大研究的时间尺度和提高研究的精确程度,即在距今百万年至数千万年,甚至更长的时间范围内,从定性到定量的研究和理解全球变化的过程、规律和机制,以便更有效地预测气候的未来变化。本文介绍了最近10年里,采用特有种气候分析法、共存分析法、叶相分析法、植物气孔参数与古大气CO2浓度变化的相关性,定量研究古环境和古气候方面所取得的进展。     

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。     

The Validity of a New Low-Dose Stereoradiography System to Perform 2D and 3D Knee Prosthetic Alignment Measurements

Introduction

The EOS stereoradiography system has shown to provide reliable varus/valgus (VV) measurements of the lower limb in 2D (VV2D) and 3D (VV3D) after total knee arthroplasty (TKA). Validity of these measurements has not been investigated yet, therefore the purpose of this study was to determine validity of EOS VV2D and VV3D.

Methods

EOS images were made of a lower limb phantom containing a knee prosthesis, while varying VV angle from 15° varus to 15° valgus and flexion angle from 0° to 20°, and changing rotation from 20° internal to 20° external rotation. Differences between the actual VV position of the lower limb phantom and its position as measured on EOS 2D and 3D images were investigated.

Results

Rotation, flexion or VV angle alone had no major impact on VV2D or VV3D. Combination of VV angle and rotation with full extension did not show major differences in VV2D measurements either. Combination of flexion and rotation with a neutral VV angle showed variation of up to 7.4° for VV2D; maximum variation for VV3D was only 1.5°. A combination of the three variables showed an even greater distortion of VV2D, while VV3D stayed relatively constant. Maximum measurement difference between preset VV angle and VV2D was 9.8°, while the difference with VV3D was only 1.9°. The largest differences between the preset VV angle and VV2D were found when installing the leg in extreme angles, for example 15° valgus, 20° flexion and 20° internal rotation.

Conclusions

After TKA, EOS VV3D were more valid than VV2D, indicating that 3D measurements compensate for malpositioning during acquisition. Caution is warranted when measuring VV angle on a conventional radiograph of a knee with a flexion contracture, varus or valgus angle and/or rotation of the knee joint during acquisition.     

Accuracy Analysis with Special Reference to the Prediction of Grassland Yield

In this paper techniques are presented which allow the evaluation of accuracy of prediction methods, with special reference to the prediction of grassland yield. The more prominent methods of predicting grassland yield are discussed. Two coefficients, which are normalizations of the mean-squared-error, are proposed as measures of accuracy. It is shown that the mean-squared-error partitions into the sum of three meaningful components of error. The distribution of the components is discussed under the assumption that the actual and predicted yields have a bivariate normal distribution. The problem of accuracy analysis is addressed when one is only interested in ranking the yields of grassland areas. The ratio of the mean-squared-error for two competing prediction methods is investigated. Finally, a multiplicative model is studied which allows predicting ability to differ over time or over regions.     

基于VTK和MFC的医学图像三维重建研究与实现

VTK是医学可视化领域的主流工具,MFC是Windows平台下的应用程序框架。尝试将两者进行结合编程,以实现二维医学图像的三维重建。实现医学图像三维重建的主要方法是面绘制和体绘制。将利用多组医学图像数据进行三维重建研究,其中面绘制用移动立方体法,体绘制用光线投射法、最大密度投影法和合成体绘制法实现。最后比较两种绘制技术的结果并讨论了它们的特点。结果表明,VTK作为一种图像处理和三维可视化工具其功能是十分强大的。     

Evaluation and Validation of Reference Genes for Normalization of Quantitative Real-Time PCR Based Gene Expression Studies in Peanut

The quantitative real-time PCR (qPCR) based techniques have become essential for gene expression studies and high-throughput molecular characterization of transgenic events. Normalizing to reference gene in relative quantification make results from qPCR more reliable when compared to absolute quantification, but requires robust reference genes. Since, ideal reference gene should be species specific, no single internal control gene is universal for use as a reference gene across various plant developmental stages and diverse growth conditions. Here, we present validation studies of multiple stably expressed reference genes in cultivated peanut with minimal variations in temporal and spatial expression when subjected to various biotic and abiotic stresses. Stability in the expression of eight candidate reference genes including ADH3, ACT11, ATPsyn, CYP2, ELF1B, G6PD, LEC and UBC1 was compared in diverse peanut plant samples. The samples were categorized into distinct experimental sets to check the suitability of candidate genes for accurate and reliable normalization of gene expression using qPCR. Stability in expression of the references genes in eight sets of samples was determined by geNorm and NormFinder methods. While three candidate reference genes including ADH3, G6PD and ELF1B were identified to be stably expressed across experiments, LEC was observed to be the least stable, and hence must be avoided for gene expression studies in peanut. Inclusion of the former two genes gave sufficiently reliable results; nonetheless, the addition of the third reference gene ELF1B may be potentially better in a diverse set of tissue samples of peanut.     

基于无人机三维重建现状模型的风景园林设计研究与教学探索

随着无人机技术在风景园林规划设计中发挥越来越重要的作用,将无人机技术引入风景园林设计和教学已经成为可能。本文通过阐述无人机三维重建技术的概念、技术流程和技术优势、该技术在风景园林设计中的应用以及该技术与风景园林设计教学的结合方式,展示了以无人机三维重建现状模型为结合点,风景园林设计、教学与前沿科学技术的融合。     

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments.     

A 3D Interactive Model and Atlas of the Jaw Musculature of Alligator mississippiensis

Modern imaging and dissemination methods enable morphologists to share complex, three-dimensional (3D) data in ways not previously possible. Here we present a 3D interactive model of the jaw musculature of the American Alligator (Alligator mississippiensis). Alligator and crocodylian jaw musculature is notoriously challenging to inspect and interpret because of the derived nature of the feeding apparatus. Using Iodine-contrast enhanced microCT imaging, a segmented model of jaw muscles, trigeminal nerve, brain and skull are presented as a cross-sectional atlas and 3D, interactive pdf of the rendered model. Modern 3D dissemination methods like this 3D Alligator hold great potential for morphologists to share anatomical information to scientists, educators, and the public in an easily downloadable format.     

Autophagy Correlates with the Therapeutic Responsiveness of Malignant Pleural Mesothelioma in 3D Models

Malignant pleural mesothelioma is a highly chemoresistant solid tumor. We have studied this apoptotic resistance using in vitro and ex vivo three-dimensional models, which acquire a high level of chemoresistance that can be reduced by PI3K/mTOR inhibitors. Here, we investigate the activity of GDC-0980, a novel dual PI3K/mTOR inhibitor, which has been proposed to be effective in mesothelioma. In this work, we aimed to identify mechanisms and markers of efficacy for GDC-0980 by utilizing 3D models of mesothelioma, both in vitro multicellular spheroids and ex vivo tumor fragment spheroids grown from patient tumor samples. We found that a subset of mesothelioma spheroids is sensitive to GDC-0980 alone and to its combination with chemotherapy. Unexpectedly, this sensitivity did not correlate with the activation of the Akt/mTOR pathway. Instead, sensitivity to GDC-0980 correlated with the presence of constitutive ATG13 puncta, a feature of autophagy, a cellular program that supports cells under stress. In tumor fragment spheroids grown from 21 tumors, we also found a subset (n = 11) that was sensitive to GDC-0980, a sensitivity that also correlated with the presence of ATG13 puncta. Interference with autophagy by siRNA of ATG7, an essential autophagic protein, increased the response to chemotherapy, but only in the sensitive multicellular spheroids. In the spheroids resistant to GDC-0980, autophagy appeared to play no role. In summary, we show that GDC-0980 is effective in mesothelioma 3D models that display ATG13 puncta, and that blockade of autophagy increases their response to chemotherapy. For the first time, we show a role for autophagy in the response to chemotherapy of 3D models of mesothelioma and propose ATG13 as a potential biomarker of the therapeutic responsiveness of mesothelioma.     

Understanding the Impact of 2D and 3D Fibroblast Cultures on In Vitro Breast Cancer Models

The utilization of 3D, physiologically relevant in vitro cancer models to investigate complex interactions between tumor and stroma has been increasing. Prior work has generally focused on the cancer cells and, the role of fibroblast culture conditions on tumor-stromal cell interactions is still largely unknown. Here, we focus on the stroma by comparing functional behaviors of human mammary fibroblasts (HMFs) cultured in 2D and 3D and their effects on the invasive progression of breast cancer cells (MCF10DCIS.com). We identified increased levels of several paracrine factors from HMFs cultured in 3D conditions that drive the invasive transition. Using a microscale co-culture model with improved compartmentalization and sensitivity, we demonstrated that HMFs cultured in 3D intensify the promotion of the invasive progression through the HGF/c-Met interaction. This study highlights the importance of the 3D stromal microenvironment in the development of multiple cell type in vitro cancer models.