基于空间频域滤波高动态光学投影层析的斑马鱼三维成像研究

本文提出了一种基于空间频率滤波的多曝光融合的高动态投影层析三维成像方法,实现了活体斑马鱼（17 mm × 4 mm,最大厚度为2.33 mm,最小厚度为0.29 mm）的三维结构成像. 通过相机采用不同曝光时间记录系列吸收图像,将每张图像取变换到频域去除低频后,将各张滤波后叠加并逆傅里叶变换回空域,对变换后的图像进行归一化处理,最终获得高动态图像. 在每个投影角度获得这种高动态吸收投影图像,进行滤波反投影算法重建,获得高动态的整条斑马鱼三维结构信息. 实验成像结果表明,这种空间频率滤波多曝光融合的高动态光学投影层析三维成像研究,可以获得复杂结构更丰富的空间信息,对斑马鱼等模式生物早期胚胎生长发育进程进行监测和定量评估有一定的应用前景.     

利用归一化互相关算法去除吸收强度涨落调制血管造影图像模糊

吸收强度涨落调制成像（AIFM）方法是基于血红细胞和背景组织对低相干光照明的吸收差异,通过在频域分离动态的血红细胞信号和静态的背景信号,实现对近透明活体生物样本全场无标记的光学血管造影成像. 但此成像方法需采集较长的原始图像序列,系统漂移或生物抖动会造成图像模糊,难以实现对某些特定区域的血管造影成像. 本文提出一种结合AIFM成像和归一化互相关算法的新方法来提升血管造影图像的质量：原始的图像序列被分成若干短时序列,每个短时序列先利用AIFM成像算法重构得到全场的血管造影图像;再利用归一化的互相关算法将所有的短时重构图像与第一帧重构图像相匹配,并融合得到最终的血管造影片. 我们以活体鸡蛋胚胎为样品,通过实验验证了利用短时归一化互相关AIFM成像方法,能够消除鸡胚胎心跳引起的图像模糊,从而获得高分辨率和信噪比的心血管造影片,对研究活体动物心脑血管疾病具有重要应用价值.     

高动态光学血管造影成像

我们提出一种高动态光学血管造影成像(HDOA)方法来实现活体生物样本血管造影成像.该方法通过设置高动态范围曝光时间,依据动态积分效应和吸收效应以实现高动态积分时间调制.通过该方法,不仅能够同时获得各级血管清晰的造影图像,还能消除样品厚度不均、吸收系数不同对成像造成的影响.论文以仿体和活体金鱼为样品,通过实验验证了HDOA方法根据动态积分调制效应和吸收效应,能有效实现各级血管同时成像.     

高动态光学血管造影成像（英文）

我们提出一种高动态光学血管造影成像(HDOA)方法来实现活体生物样本血管造影成像.该方法通过设置高动态范围曝光时间,依据动态积分效应和吸收效应以实现高动态积分时间调制.通过该方法,不仅能够同时获得各级血管清晰的造影图像,还能消除样品厚度不均、吸收系数不同对成像造成的影响.论文以仿体和活体金鱼为样品,通过实验验证了HDOA方法根据动态积分调制效应和吸收效应,能有效实现各级血管同时成像.     

基于样品及点源光声信号逆卷积的光声成像方法

光声成像是一种新的生物组织成像方法,在目前的光声成像中,都是通过样品光声信号和超声探测器的脉冲响应来计算样品光吸收的投影,但是由于无法获得超声探测器较准确的脉冲响应,影响重建图像质量。提出一种新的计算样品光吸收投影的方法,从理论上给出了样品光吸收投影和样品及点源光声信号的关系,由样品及点源光声信号的逆卷积可直接计算样品光吸收的投影,点源光声信号通过聚焦入射激光直接测得。试验结果显示,重建图像和样品的相对位置、形状及尺寸完全吻合,成像系统空间分辨率达到0．3mm,证明这是一种有效的光声成像方法。     

初级视皮层神经元集群对拓扑特征响应的可视化表征

神经元集群响应的高维特性是脑机制研究面临的主要困难之一.拓扑特征是图像的基本特征之一,为了有效表征高维的神经元集群响应的拓扑特征特性,提出了一种基于三维自组织映射网络采用RGB颜色特征表征神经元集群响应的动态可视化方法,分析多通道微电极阵列采集的大鼠初级视觉皮层(V1区)神经元集群信号,进而研究了V1区神经元集群对图形拓扑特征的响应特性.通过与主成分分析(PCA)方法进行对比发现:该方法能够有效表征V1区神经元集群对拓扑结构的时序动态响应特征,表征方式形象直观,具有一定的优越性.     

七甲川菁近红外荧光染料对胃癌原位移植模型的靶向识别

目的研究七甲川菁近红外荧光(NIRF)染料在胃癌原位移植模型活体成像中的应用效果。方法将标记荧光酶素的人胃癌细胞系Hep G2原位移植裸鼠建立肿瘤模型,同时诱发制备胃溃疡模型;对上述模型分别采用生物发光成像和NIRF成像,观察胃癌组织对近红外荧光染料的吸收;探索缺氧和阴离子转运肽(OATP)对胃癌组织吸收NIRF染料的影响,明确NIRF染料靶向识别肿瘤细胞的特异性。结果 NIRF信号与生物发光信号在胃癌原位移植模型活体成像中具有较好的相关性。胃癌组织部位可获得较强的NIRF荧光信号,而胃溃疡部位未检测到荧光信号。缺氧能够增强胃癌细胞对NIRF染料的吸收,而阴离子转运肽特异性抑制剂磺溴酞钠(BSP)能够显著降低肿瘤细胞对NIRF染料的吸收。结论七甲川菁近红外荧光染料能够靶向识别胃癌原位移植模型。     

两种微体化石三维无损成像技术的对比

近年来,各种X射线三维无损成像技术在古生物学领域的应用越来越广泛。但是,不同的X射线三维无损成像技术针对不同保存类型和尺寸的化石标本在成像效果上各有利弊。本文以埃迪卡拉纪陡山沱组磷酸盐化的动物胚胎化石为研究对象,将目前应用最广的两种X射线三维无损成像方法,即基于实验室X光源的吸收衬度显微断层成像技术和基于同步辐射光源的相位衬度显微断层成像技术进行了对比分析。通过对两种技术的原理、效率、空间分辨率和图像衬度的对比,认为基于同步辐射光源的相位衬度显微断层成像技术是目前对于均一矿化的微体化石最佳的三维无损成像解决方案。     

自发光学信号成像系统在生物成像中的发展与应用

自发光学信号成像系统是近年来比较新颖的一项用于活体生物的基因或细胞活动的微观检测的光学技术,具有直观、操作简便以及分辨率高的特点。该技术主要分为生物发光成像技术和荧光成像技术,目前主要用于测定活体动物体内的细胞以及分子的活动或变化情况。由于该技术能够对动物体内的微观形态的变化进行精确的捕捉,对于癌症、基因表达、肿瘤以及其他病变均具有较好的监测作用。在本文中,将就自发光学信号成像系统在生物成像中的发展与应用进行详细的阐述。     

基于阵列式换能器的光声成像系统的实现

目的:本文设计了一套光声成像(photoacoustic imaging,PAI)系统,由脉冲激光、阵列换能器、临床超声(ultrasound,US)主机、软件平台以及成像样品组成。系统的图像质量、最大成像深度等重要参数需通过实验进行确定。方法:使用本系统对黑色头发丝横截面进行成像,比较、分析光声(photoacoustic,PA)信号幅值的半极大处全宽度以量化图像分辨率。此外,使用系统对特定的光吸收体和鸡胸肉组织进行成像,确定系统的成像深度。结果:实验结果证明了PAI系统的实现,其PA图像的平均轴向和横向分辨率分别约为0.18 mm和1.44mm,系统的最大成像深度达到4.6 cm。结论:本PAI系统PA图像分辨率优于US主机获得的US图像分辨率,系统最大成像深度与其他国际研究组的系统成像深度的数量级一致。通过进一步优化与活体组织实验的开展,本PAI系统将有望实现临床成像诊断。     

Development of a 3D optical scanner for evaluating patient-specific dose distributions

PurposeThis paper describes the hardware and software characteristics of a 3D optical scanner (P3DS) developed in-house. The P3DS consists of an LED light source, diffuse screen, step motor, CCD camera, and scanner management software with 3D reconstructed software.Materials and methodWe performed optical simulation, 2D and 3D reconstruction image testing, and pre-clinical testing for the P3DS. We developed the optical scanner with three key characteristics in mind. First, we developed a continuous scanning method to expand possible clinical applications. Second, we manufactured a collimator to improve image quality by reducing scattering from the light source. Third, we developed an optical scanner with changeable camera positioning to enable acquisition of optimal images according to the size of the gel dosimeter.ResultsWe confirmed ray-tracing in P3DS with optic simulation and found that 2D projection and 3D reconstructed images were qualitatively similar to the phantom images. For pre-clinical tests, the dose distribution and profile showed good agreement among RTP, optical CT, and external beam radiotherapy film data for the axial and coronal views. The P3DS has shown that it can scan and reconstruct for evaluation of the gel dosimeter within 1 min. We confirmed that the P3DS system is a useful tool for the measurement of 3D dose distributions for 3D radiation therapy QA. Further experiments are needed to investigate quantitative analysis for 3D dose distribution.     

Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images

We present the codimensional principal component analysis (PCA), a novel and straightforward method for resolving sample heterogeneity within a set of cryo-EM 2D projection images of macromolecular assemblies. The method employs PCA of resampled 3D structures computed using subsets of 2D data obtained with a novel hypergeometric sampling scheme. PCA provides us with a small subset of dominating "eigenvolumes" of the system, whose reprojections are compared with experimental projection data to yield their factorial coordinates constructed in a common framework of the 3D space of the macromolecule. Codimensional PCA is unique in the dramatic reduction of dimensionality of the problem, which facilitates rapid determination of both the plausible number of conformers in the sample and their 3D structures. We applied the codimensional PCA to a complex data set of Thermus thermophilus 70S ribosome, and we identified four major conformational states and visualized high mobility of the stalk base region.     

Automated Confocal Laser Scanning Microscopy and Semiautomated Image Processing for Analysis of Biofilms

The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study, Pseudomonas fluorescens or a green fluorescent protein-expressing Escherichia coli strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.     

Statistical learning methods as a preprocessing step for survival analysis: evaluation of concept using lung cancer data

Background

Despite its superb lateral resolution, flat-panel-detector (FPD) based tomosynthesis suffers from low contrast and inter-plane artifacts caused by incomplete cancellation of the projection components stemming from outside the focal plane. The incomplete cancellation of the projection components, mostly due to the limited scan angle in the conventional tomosynthesis scan geometry, often makes the image contrast too low to differentiate the malignant tissues from the background tissues with confidence.

Methods

In this paper, we propose a new method to suppress the inter-plane artifacts in FPD-based tomosynthesis. If 3D whole volume CT images are available before the tomosynthesis scan, the CT image data can be incorporated into the tomosynthesis image reconstruction to suppress the inter-plane artifacts, hence, improving the image contrast. In the proposed technique, the projection components stemming from outside the region-of-interest (ROI) are subtracted from the measured tomosynthesis projection data to suppress the inter-plane artifacts. The projection components stemming from outside the ROI are calculated from the 3D whole volume CT images which usually have lower lateral resolution than the tomosynthesis images. The tomosynthesis images are reconstructed from the subtracted projection data which account for the x-ray attenuation through the ROI. After verifying the proposed method by simulation, we have performed both CT scan and tomosynthesis scan on a phantom and a sacrificed rat using a FPD-based micro-CT.

Results

We have measured contrast-to-noise ratio (CNR) from the tomosynthesis images which is an indicator of the residual inter-plane artifacts on the focal-plane image. In both cases of the simulation and experimental imaging studies of the contrast evaluating phantom, CNRs have been significantly improved by the proposed method. In the rat imaging also, we have observed better visual contrast from the tomosynthesis images reconstructed by the proposed method.

Conclusions

The proposed tomosynthesis technique can improve image contrast with aids of 3D whole volume CT images. Even though local tomosynthesis needs extra 3D CT scanning, it may find clinical applications in special situations in which extra 3D CT scan is already available or allowed.     

Set-up error validation with EPID images: Measurements vs Egs_cbct simulation

AimIn this study, the egs_cbct code’s ability to replicate an electronic portal imaging device (EPID) is explored.BackgroundWe have investigated head and neck (H&N) setup verification on an Elekta Precise linear accelerator. It is equipped with an electronic portal imaging device (EPID) that can capture a set of projection images over different gantry angles.Methods and materialsCone-beam computed tomography (CBCT) images were reconstructed from projection images of two different setup scenarios. Projections of an Anthropomorphic Rando head phantom were also simulated by using the egs_cbct Monte Carlo code for comparison with the measured projections.Afterwards, CBCT images were reconstructed from this data. Image quality was evaluated against a metric defined as the image acquisition interval (IAI). It determines the number of projection images to be used for CBCT image reconstruction.ResultsFrom this results it was established that phantom shifts could be determined within 2 mm and rotations within one degree accuracy using only 20 projection images (IAI = 10 degrees). Similar results were obtained with the simulated data.ConclusionIn this study it is demonstrated that a head and neck setup can be verified using substantially fewer projection images. Bony landmarks and air cavities could still be observed in the reconstructed Rando head phantom. The egs_cbct code can be used as a tool to investigate setup errors without tedious measurements with an EPID system.     

Multispectral/hyperspectral image enhancement for biological cell analysis.

BACKGROUND: Microscopes form projected images from illuminated objects, such as cellular tissue, which are recorded at a distance through the optical system's field of view. A telescope on a satellite or airplane also forms images with a similar optical projection of objects on the ground. Typical visible illuminations form a displayed set of three-color channels (Red Green Blue [RGB]) that are combined from three image sensor arrays (e.g., focal plane arrays) into a single pixel coding for each color present in the image. Analysis of these RGB color images develops a qualitative image representation of the objects. METHODS: Independent component analysis (ICA) is used for analysis and enhancement of multispectral images, and compared with the similar and widely used principal component analysis. RESULTS: The data examples indicate that the ICA enhancement, and the resulting RGB image combination display, can be useful in processing datacubes of cellular data where isolation of unknown subtle image elements representing objects is desired. CONCLUSIONS: ICA image enhancement can aid processing of datacubes of cellular data by clarifying subtle image elements. These parallelizable algorithms can be implemented for real-time, online analysis.     

基于主成分特征投影法建立利用16S rRNA基因序列进行物种分类方法的研究

提出一种有别于系统发育树的根据16S rRNA基因序列进行物种分类的新方法。首先将基因的碱基字母形式转换成数字形式,构建多维向量。然后根据主成分分析方法将该向量向数据分布最大方向投影,将原数据用几个“主成分”线性表出,而不丢失原数据的信息,采用主成分的显示功能作出三维主成分特征投影视图,达到分类的目的。在双歧杆菌和肠球菌的分类识别中得到较好的应用。     

Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images

BackgroundAtomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial.MethodWe aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image.ResultsThe algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations.ConclusionsThe proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail.General significanceHigh-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.     

A Stock Market Forecasting Model Combining Two-Directional Two-Dimensional Principal Component Analysis and Radial Basis Function Neural Network

In this paper, we propose and implement a hybrid model combining two-directional two-dimensional principal component analysis ((2D)²PCA) and a Radial Basis Function Neural Network (RBFNN) to forecast stock market behavior. First, 36 stock market technical variables are selected as the input features, and a sliding window is used to obtain the input data of the model. Next, (2D)²PCA is utilized to reduce the dimension of the data and extract its intrinsic features. Finally, an RBFNN accepts the data processed by (2D)²PCA to forecast the next day''s stock price or movement. The proposed model is used on the Shanghai stock market index, and the experiments show that the model achieves a good level of fitness. The proposed model is then compared with one that uses the traditional dimension reduction method principal component analysis (PCA) and independent component analysis (ICA). The empirical results show that the proposed model outperforms the PCA-based model, as well as alternative models based on ICA and on the multilayer perceptron.     

Image quality assessment of an iterative reconstruction algorithm applied to abdominal CT imaging

PurposeTo compare the noise and accuracy on images of the whole porcine liver acquired with iterative reconstruction (IMR, Philips Healthcare, Cleveland, OH, USA) and filtered back projection (FBP) methods.Materials and methodsWe used non-enhanced porcine liver to simulate the human liver and acquired it 100 times to obtain the average FBP value as the ground-truth. The mean and the standard deviation (“inter-scan SD”) of the pixel values on the 100 image acquisitions were calculated for FBP and for three levels of IMR (L1, L2, and L3). We also calculated the noise power spectrum (NPS) and the normalized NPS for the 100 image acquisitions.ResultsThe spatial SD for the porcine liver parenchyma on these slices was 9.92, 4.37, 3.63, and 2.30 Hounsfield units with FBP, IMR-L1, IMR-L2, and IMR-L3, respectively. The detectability of small faint features was better on single IMR than single FBP images. The inter-scan SD value for IMR-L3 images was 53% larger at the liver edges than at the liver parenchyma; it was only 10% larger on FBP images. Assessment of the normalized NPS showed that the noise on IMR images was comprised primarily of low-frequency components.ConclusionIMR images yield the same structure informations as FBP images and image accuracy is maintained. On level 3 IMR images the image noise is more strongly suppressed than on IMR images of the other levels and on FBP images.