Novel biomedical applications of Cerenkov radiation and radioluminescence imaging

The main goals of this review is to provide an up-to-date account of the different uses of Cerenkov radiation (CR) and radioluminescence imaging for pre-clinical small animal imaging. We will focus on new emerging applications such as the use of Cerenkov imaging for monitoring radionuclide and external radiotherapy in humans. Another novel application that will be described is the monitoring of radiochemical synthesis using microfluidic chips.Several pre-clinical aspects of CR will be discussed such as the development of 3D reconstruction methods for Cerenkov images and the use of CR as excitation source for nanoparticles or for endoscopic imaging.We will also include a discussion on radioluminescence imaging that is a more general method than Cerenkov imaging for the detection using optical methods of alpha and gamma emitters.     

运用CT三维重建测量重度先天性脊柱侧凸Cobb角的临床应用

目的:评价在CT三维重建上测量重度先天性脊柱侧凸Cobb角度的可重复性和可靠性。方法:收集在我院诊治的重度先天性脊柱侧凸病人的CT三维重建和脊柱全长X线片,共计67例。由五名不同测量者对CT三维重建脊柱畸形冠状面主弯Cobb角测量两次,两次间隔在三周以上,并测量脊柱全长X线片脊柱畸形冠状面主弯Cobb角一次,运用组内相关系数分析测量结果之间的可重复性和可靠性。结果:同一测量者两次测量结果之间的差值平均为4.5°。同一测量者两次测量结果之间的组内相关系数为0.969,不同测量者之间测量结果的组内相关系数为0.913。取五名测量者在CT三维重建上第一次测量的Cobb角度,其平均值为(110.5±23.5)°,五名测量者在X线片上测量结果的平均值为(103.1±22.0)°,对两组数据进行Mann-Whitney非参数检验差异有统计学意义(Z=-2.86,P=0.004)。结论:在CT三维重建上测量重度先天性脊柱侧凸的Cobb角,可以减小测量的误差,提高测量的可重复性和可靠性,是一种相对准确的测量方法。     

Molecular imaging of the embryonic heart: Fables and facts on 3D imaging of gene expression patterns

Molecular imaging, which is the three-dimensional (3D) visualization of gene expression patterns, is indispensable for the study of the function of genes in cardiac development. The instrumentation, as well as the development of specific contrast agents for molecular imaging, has shown spectacular advances in the last decade. In this review, the spatial resolutions, contrast agents, and applications of these imaging methods in the field of cardiac embryology are discussed. Apart from 3D reconstructions from histological sections, not many of these methods have been applied in embryological research. This review shows that, for most methods, neither the spatial resolutions nor the specificity and applicability of the contrast agents are adequate for the reliable imaging of specific gene expression at the microscopic resolution required for embryological studies of small organs like the developing heart. Although a 3D reconstruction from sections will always suffer from imperfections, the resulting reconstructions meet the aim of most biological studies, especially since the original microscopic images are linked. With respect to imaging of gene expression, only histological sections and laser scanning microscopy provide the required resolution and specificity at the tissue and cellular level. Episcopic fluorescence image capturing and optical projection tomography are being used for microscopic phenotyping and lineage analysis, and both show potential for detailed molecular imaging. Other methods can be used very efficiently in rapid evaluation of biological experiments and high-throughput screens of large-scale gene expression profiling efforts when high spatial resolution is not required.     

Medical ultrasound imaging

The paper gives an introduction to current medical ultrasound imaging systems. The basics of anatomic and blood flow imaging are described. The properties of medical ultrasound and its focusing are described, and the various methods for two- and three-dimensional imaging of the human anatomy are shown. Systems using both linear and non-linear propagation of ultrasound are described. The blood velocity can also be non-invasively visualized using ultrasound and the basic signal processing for doing this is introduced. Examples for spectral velocity estimation, color flow imaging and the new vector velocity images are presented.     

CT与MRI扫描三维重建在四肢骨关节隐匿性骨折诊断中的应用

摘要 目的：探讨电子计算机断层扫描(Computed Tomography,CT)与磁共振成像(Magnetic resonance imaging,MRI)扫描三维重建在四肢骨关节隐匿性骨折诊断中的应用。方法：2016年9月到2019年10月选择在本院诊治的下拟诊为四肢骨关节隐匿性骨折118例,所有患者都给予CT与MRI扫描三维重建诊断,记录影像学特征与判断诊断价值。结果：在118例患者中,最终确诊为四肢骨关节隐匿性骨折98例,无骨折20例,其中腕关节骨折34例,踝关节骨折22例,膝关节骨折15例,肘关节骨折15例,肩关节骨折8例,髋关节骨折4例。在98例确诊的四肢骨关节隐匿性骨折中,MRI三维重建显示双边征、骨质破坏、充气征、软组织影等比例显著都高于CT (P<0.05)。CT与MRI三维重建诊断四肢骨关节隐匿性骨折的敏感性为89.8 %和99.0 %,特异性为95.0 %和100.0 %,误诊率分别为9.3 %和0.8 %,MRI三维重建诊断的敏感性高于CT ,漏诊率低于CT。结论：CT与MRI扫描三维重建在四肢骨关节隐匿性骨折诊断中的应用都有很好的价值,特别是MRI三维重建能清晰显示骨折特征,具有更高的诊断敏感性,能减少漏诊率,可作为四肢骨关节隐匿性骨折的首选检查方法。     

A high-level 3D visualization API for Java and ImageJ

Background  

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.     

Optimized 3D coordinate reconstruction from paired stereographs using a calibrated phantom

A refinement to a previously described three-dimensional reconstruction algorithm based on point identification in calibrated non-orthogonal radiograms (stereo-pairs) is described. The modification involves a computation of the focal point magnitude of the point in three dimensions, analogous to focusing in two dimensions, as well as the most likely location of the target point in 3-space; the focal point magnitude may be thought of as the precision of the point identification. Multiple observer studies of the same stereopair can be used to estimate three-dimensional reconstruction accuracy by providing an average location and a mean distance from average. Both measures are useful parameters for initial selection of bone landmark references and for error propagation studies.     

树鼩脑三维结构重建的研究 Ⅲ.脑外形立体结构的计算机辅助绘图

作者曾经详细介绍过树鼩脑切片二维结构重建的数据采集、计算机处理数据的算法及图形生成技术。在此基础上,本文介绍树鼩脑三维结构重建的数学模型及其自动生成三维图形的基本技术与计算机绘图的部分结果。     

Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms

Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a “missing wedge” of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.     

Three-dimensional in vivo imaging of green fluorescent protein-expressing T cells in mice with noncontact fluorescence molecular tomography

Given that optical tomography is capable of quantitatively imaging the distribution of several important chromophores and fluorophores in vivo, there has been a great deal of interest in developing optical imaging systems with increased numbers of measurements under optimal experimental conditions. In this article, we present a novel system that enables three-dimensional imaging of fluorescent probes in whole animals using a noncontact setup, in parallel with a three-dimensional surface reconstruction algorithm. This approach is directed toward the in vivo imaging of fluorophore or fluorescent protein concentration in small animals. The system consists of a rotating sample holder and a lens-coupled charge-coupled device camera in combination with a fiber-coupled laser scanning device. By measuring multiple projections, large data sets can be obtained, thus improving the accuracy of the inversion models used for quantitative three-dimensional reconstruction of fluorochrome distribution, as well as facilitating a higher spatial resolution. In this study, the system was applied to determining the distribution of green fluorescent protein (GFP)-expressing T lymphocytes in a transgenic mouse model, thus demonstrating the potential of the system for studying immune system function. The technique was used to image and reconstruct fluorescence originating from 32 x 10(6) T cells in the thymus and 3 x 10(5) T cells in the spleen.     

染色体三维结构重建方法研究

染色体三维结构重构问题是近年生物领域中基因组学的热点研究问题,是以二维交互频率数据为基础来预测其三维空间结构。最新相关实验表明染色质的三维空间结构对于基因表达、调控等方面都具有重要意义。而Hi-c数据能利用染色质交互信息形成二维接触矩阵重构出染色体三维结构。本综述以染色体三维结构重建方法为研究对象,通过对染色体三维结构重建方法进行比较分析,综述了目前基于Hi-c数据在染色体三维结构重建中的经典方法,系统介绍了染色体三维结构重建技术的发展脉络,以促进染色体三维结构重建的进一步研究。     

Looking and listening to light: the evolution of whole-body photonic imaging

Optical imaging of live animals has grown into an important tool in biomedical research as advances in photonic technology and reporter strategies have led to widespread exploration of biological processes in vivo. Although much attention has been paid to microscopy, macroscopic imaging has allowed small-animal imaging with larger fields of view (from several millimeters to several centimeters depending on implementation). Photographic methods have been the mainstay for fluorescence and bioluminescence macroscopy in whole animals, but emphasis is shifting to photonic methods that use tomographic principles to noninvasively image optical contrast at depths of several millimeters to centimeters with high sensitivity and sub-millimeter to millimeter resolution. Recent theoretical and instrumentation advances allow the use of large data sets and multiple projections and offer practical systems for quantitative, three-dimensional whole-body images. For photonic imaging to fully realize its potential, however, further progress will be needed in refining optical inversion methods and data acquisition techniques.     

Three-dimensional velocity field reconstruction

The problem of inter-slice magnetic resonance (MR) image reconstruction is encountered often in medical imaging applications, in such scenarios, there is a need to approximate information not captured in contiguously acquired MR images due to hardware sampling limitations. In the context of velocity field reconstruction, these data are required for visualization and computational analyses of flow fields to be effective. To provide more complete velocity information, a method has been developed for the reconstruction of flow fields based on adaptive control grid interpolation (ACGI). In this study, data for reconstruction were acquired via MRJ from in vitro models of surgically corrected pediatric cardiac vasculatures. Reconstructed velocity fields showed strong qualitative agreement with those obtained via other acquisition techniques. Quantitatively reconstruction was shown to produce data of comparable quality to accepted velocity data acquisition methods. Results indicate that ACGI-based velocity field reconstruction is capable of producing information suitable for a variety of applications demanding three-dimensional in vivo velocity data.     

Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage phi29

A method has been developed for three-dimensional image reconstruction of symmetry-mismatched components in tailed phages. Although the method described here addresses the specific case where differing symmetry axes are coincident, the method is more generally applicable, for instance, to the reconstruction of images of viral particles that deviate from icosahedral symmetry. Particles are initially oriented according to their dominant symmetry, thus reducing the search space for determining the orientation of the less dominant, symmetry-mismatched component. This procedure produced an improved reconstruction of the sixfold-symmetric tail assembly that is attached to the fivefold-symmetric prolate head of phi29, demonstrating that this method is capable of detecting and reconstructing an object that included a symmetry mismatch. A reconstruction of phi29 prohead particles using the methods described here establishes that the pRNA molecule has fivefold symmetry when attached to the prohead, consistent with its proposed role as a component of the stator in the phi29 DNA packaging motor.     

High-Performance Fluorescence Molecular Tomography through Shape-Based Reconstruction Using Spherical Harmonics Parameterization

Fluorescence molecular tomography in the near-infrared region is becoming a powerful modality for mapping the three-dimensional quantitative distributions of fluorochromes in live small animals. However, wider application of fluorescence molecular tomography still requires more accurate and stable reconstruction tools. We propose a shape-based reconstruction method that uses spherical harmonics parameterization, where fluorophores are assumed to be distributed as piecewise constants inside disjointed subdomains and the remaining background. The inverse problem is then formulated as a constrained nonlinear least-squares problem with respect to shape parameters, which decreases ill-posedness because of the significantly reduced number of unknowns. Since different shape parameters contribute differently to the boundary measurements, a two-step and modified block coordinate descent optimization algorithm is introduced to stabilize the reconstruction. We first evaluated our method using numerical simulations under various conditions for the noise level and fluorescent background; it showed significant superiority over conventional voxel-based methods in terms of the spatial resolution, reconstruction accuracy with regard to the morphology and intensity, and robustness against the initial estimated distribution. In our phantom experiment, our method again showed better spatial resolution and more accurate intensity reconstruction. Finally, the results of an in vivo experiment demonstrated its applicability to the imaging of mice.     

基于图像重建的CT三维重建提升腹部增强扫描图像质量的价值

摘要 目的：探讨基于图像重建的电子计算机断层扫描仪器(Computed Tomography,CT)三维成像提升腹部增强扫描图像质量的价值。方法：2019年11月到2020年10月选择在本院进行腹部CT增强扫描的患者76例作为研究对象,采用电脑随机数字法将研究对象分为对照组和重建组各38例,对照组给予常规扫描成像,重建组给予基于自适应统计迭代重建(adaptive statistical iterative reconstruction,ASIR)的CT三维成像,记录两组成像质量与噪声情况。结果：两名医师对重建组的图像主观质量评分都高于对照组(P<0.05)。重建组的图像相对细腻柔和,能清晰显示图像细小血管断面,末梢血管显示良好,血管壁光滑柔和。重建组的动脉期、门静脉期、平衡期的肝脏CT值高于对照组(P<0.05),动脉期、门静脉期、平衡期的肝脏、胰腺对比噪声比(contrast to noise ratio,CNR)值低于对照组(P<0.05)。重建组的容积剂量指数(volume CT dose index,CTDIvol)和剂量长度乘积(Dose-Length product,DLP)、有效剂量(effective dose,ED)值都低于对照组(P<0.05)。结论：基于图像重建的CT三维成像能提升腹部增强扫描主客观图像质量,降低图像噪声,更利于腹部疾病的显示,从而提高正确诊断率。     

Confocal stereology and image analysis: methods for estimating geometrical characteristics of cells and tissues from three-dimensional confocal images

A short review of confocal stereology and three-dimensional image analysis is presented, pointing out the achievements accomplished in this field by the Department of Biomathematics (Institute of Physiology, Prague). One of the methods of confocal stereology, the fakir method for surface area estimation, developed by this laboratory, is described. Methods for automatic measurement of geometrical characteristics of microscopical structures, based on 3-D image processing or surface triangulation, are discussed and compared with interactive stereological methods. Three-dimensional reconstruction programs and software implementation of stereological and digital methods as well as their practical applications are presented. The future trends are discussed.     

Three-dimensional displays and stereo vision

Procedures for three-dimensional image reconstruction that are based on the optical and neural apparatus of human stereoscopic vision have to be designed to work in conjunction with it. The principal methods of implementing stereo displays are described. Properties of the human visual system are outlined as they relate to depth discrimination capabilities and achieving optimal performance in stereo tasks. The concept of depth rendition is introduced to define the change in the parameters of three-dimensional configurations for cases in which the physical disposition of the stereo camera with respect to the viewed object differs from that of the observer's eyes.     

螺旋CT三维重建技术在胫骨平台骨折的诊疗应用分析

目的探讨螺旋CT三维重建在胫骨平台骨折中的临床应用。方法回顾性分析2007-2008年55例胫骨平台骨折病例．手术前均常规行X线摄片,行螺旋CT三维重建并与术中所见对照。结果所有病例螺旋CT三维重建明确地显示了骨折,并在骨折的分型和关节面碎裂情况的描述上较平片优越,与手术中所见一致。结论CT多种成像后处理技术可清晰显示骨折的部位、骨折线的走行方向、骨质碎裂程度和移位的距离以及关节面塌陷情况等,对术前分型、制订手术治疗方案具有重要的参考价值。