Three-dimensional volume reconstruction of extracellular matrix proteins in uveal melanoma from fluorescent confocal laser scanning microscope images

The distribution of looping patterns of laminin in uveal melanomas and other tumours has been associated with adverse outcome. Moreover, these patterns are generated by highly invasive tumour cells through the process of vasculogenic mimicry and are not therefore blood vessels. Nevertheless, these extravascular matrix patterns conduct plasma. The three‐dimensional (3D) configuration of these laminin‐rich patterns compared with blood vessels has been the subject of speculation and intensive investigation. We have developed a method for the 3D reconstruction of volume for these extravascular matrix proteins from serial paraffin sections cut at 4 µm thicknesses and stained with a fluorescently labelled antibody to laminin ( Maniotis et al., 2002 ). Each section was examined via confocal laser‐scanning focal microscopy (CLSM) and 13 images were recorded in the Z‐dimension for each slide. The input CLSM imagery is composed of a set of 3D subvolumes (stacks of 2D images) acquired at multiple confocal depths, from a sequence of consecutive slides. Steps for automated reconstruction included (1) unsupervised methods for selecting an image frame from a subvolume based on entropy and contrast criteria, (2) a fully automated registration technique for image alignment and (3) an improved histogram equalization method that compensates for spatially varying image intensities in CLSM imagery due to photo‐bleaching. We compared image alignment accuracy of a fully automated method with registration accuracy achieved by human subjects using a manual method. Automated 3D volume reconstruction was found to provide significant improvement in accuracy, consistency of results and performance time for CLSM images acquired from serial paraffin sections.     

Restoration of confocal images for quantitative image analysis

Quantitative studies of three-dimensional (3-D) structure of microscopic objects have been made possible through the introduction of microscopic volume imaging techniques, most notably the confocal fluorescence microscope (CFM). Although the CFM is a true volume imager, its specific imaging properties give rise to distortions in the images and hamper subsequent quantitative analysis. Therefore, it is a prerequisite that confocal images are restored prior to analysis. The distortions can be divided into several categories: attenuation of areas in the image due to self-absorption, bleaching effects, geometrical effects and distortions due to diffraction effects. Of these, absorption and diffraction effects are the most important. This paper describes a method aimed at the correction of diffraction-induced distortions. All the steps necessary in restoring confocal images are discussed, including a novel method to measure instrumental properties on a routine basis. To test the restoration procedure an image of a fluorescent planar object was restored. The results show a considerable improvement in the z-resolution and no ringing artefacts. The relevance of the method for image analysis is demonstrated by a comparison of results of applying 3-D texture analysis to restored and unrestored images of a synthetic object. Furthermore, the method can be successfully applied to noisy fluorescence images of biological objects, such as interphase cell nucei.     

A nondestructive method for three-dimensional reconstruction of luminescence materials: Principles,data acquisition,image processing

In the study presented here we have tried to state the principles and calculate and visualize models of three-dimensional (3-D)-cathodoluminescence reconstruction of luminescence structures by scanning electron microscopy (SEM). The new technique does not destroy the specimen and uses the variable energy of the electron beam to penetrate to different depths in the specimen volume. The SEM in color cathodoluminescence mode (CCL-SEM) detects integrated panchromatic CL-images for different energies of the electron beam. The use of electron scattering theory in solids and theories of cathodoluminescence and color allow the production of problem-oriented software for the routine processing of primary images. Processed images represent the CCL-SEM displays of separated layers (without CL information from other layers) up to the maximum depth penetrated by the beam. The 3-D reconstruction is carried out through algorithms developed using a personal computer, software, and a set of processed two-dimensional (2-D) images. The first experimental work was accomplished using a multilayer SiC mesastructure. The final reconstructed image of SiC material demonstrates separated epitaxial layers of different SiC polytypes and Z sections (YOZ and XOZ sections). The 3-D image represents the space distribution of CL-spectral data in color CL interpretation.     

Compensation of inhomogeneous fluorescence signal distribution in 2D images acquired by confocal microscopy

In images acquired by confocal laser scanning microscopy (CLSM), regions corresponding to the same concentration of fluorophores in the specimen should be mapped to the same grayscale levels. However, in practice, due to multiple distortion effects, CLSM images of even homogeneous specimen regions suffer from irregular brightness variations, e.g., darkening of image edges and lightening of the center. The effects are yet more pronounced in images of real biological specimens. A spatially varying grayscale map complicates image postprocessing, e.g., in alignment of overlapping regions of two images and in 3D reconstructions, since measures of similarity usually assume a spatially independent grayscale map. We present a fast correction method based on estimating a spatially variable illumination gain, and multiplying acquired CLSM images by the inverse of the estimated gain. The method does not require any special calibration of reference images since the gain estimate is extracted from the CLSM image being corrected itself. The proposed approach exploits two types of morphological filters: the median filter and the upper Lipschitz cover. The presented correction method, tested on images of both artificial (homogeneous fluorescent layer) and real biological specimens, namely sections of a rat embryo and a rat brain, proved to be very fast and yielded a significant visual improvement. Microsc. Res. Tech., 2011. © 2010 Wiley‐Liss, Inc.     

Three-dimensional electron microscopy of entire cells

The digital processing of serial electron-microscope sections containing laser-induced topographical references allows a three-dimensional (3-D) reconstruction of entire cells at a depth resolution of 40–60 nm by the use of novel image analysis methods. The images are directly processed by a video-camera placed under the electron microscope in TEM mode or by the electron counting device in STEM mode. The deformations associated with the cutting of embedded cells are back-calculated by new computer algorithms developed for image analysis and treatment. They correct the artefacts caused by serial sectioning and automatically reconstruct the third dimension of the cells. Used in such a way, our data provide definitive information on the 3-D architecture of cells. This computer-assisted 3-D analysis represents a new tool for the documentation and analysis of cell ultrastructure and for morphometric studies. Furthermore, it is now possible for the observer to view the contents of the reconstructed tissue volume in a variety of different ways using computer-aided display techniques.     

Reconstruction and display of curvilinear objects from optical section data using 3-D curve fitting algorithms

Biological objects resembling filaments are often highly elongated while presenting a small cross-sectional area. Examination of such objects requires acquisition of images from regions large enough to contain entire objects, but at sufficiently high resolution to resolve individual filaments. These requirements complicate the application of conventional optical sectioning and volume reconstruction techniques. For example, objective lenses used to acquire images of entire filaments or filament networks may lack sufficient depth ( Z ) resolution to localize filament cross-sections along the optical axis. Because volume reconstruction techniques consider only the information represented by a single volume element (voxel), views of filament networks reconstructed from images obtained at low Z -resolution will not accurately represent filament morphology. A possible solution to these problems is to simultaneously utilize all available information on the path of an object by fitting 3-D curves through data points localized in 2-D images. Here, we present an application of this approach to the reconstruction of microtubule networks from 2-D optical sections obtained using confocal microscopy, and to synthesized curves which have been distorted using a simple mathematical model of optical sectioning artefacts. Our results demonstrate that this strategy can produce high resolution 3-D views of filamentous objects from a small number of optical sections.     

Study of Golgi-impregnated material using the confocal tandem scanning reflected light microscope

The tandem scanning reflected-light microscope (TSM) is a real-time, direct-view confocal microscope. Only those points in the specimen situated in the focal plane contribute information to the image. A Tracor Northern TMS with piezo-electric control of the objective lens was used to generate 3-D images from Golgi-impregnated hamster cerebral cortex. Stereoscopic pairs of images were recorded as 35-mm colour film transparencies by photographing while automatically through-focusing along inclined axes. Transferring the image via a TV camera to the computer, stereo-pairs were obtained by oblique through-focusing and summing, displaying maximum intensity data in each line of sight. Pseudocolour topographic displays were generated by assigning the pixel value in a z map image as the focal depth at which the back-scattered light signal was maximal. The TSM was also modified so that a conventional transmitted-light image with a large depth of field could be obtained simultaneously as the very shallow depth of field confocal back-scattered-light image seen at any focus level. The conventional image is a silhouette of the impregnated neurons: the top surface of the cell is not visible and the relationships of processes that cross over cell bodies cannot be discerned. TSM gives a high-contrast image. The Golgi precipitate over the neuronal surface is resolved as globular or ovoid, coloured particles. The smaller particles also cover the dendritic spines. All the confocal range (extended focus) image display methods satisfactorily demonstrated the 3-D arrangement of cell bodies and processes in the chosen volume.     

基于工业计算机断层成像技术的三维CAD模型重构方法

为解决复杂形状产品的三维计算机辅助设计模型的重构难题,提出了一种基于工业计算机断层成像技术的三维计算机辅助设计模型的重构方法.首先用工业计算机断层成像技术对产品进行扫描,得到产品切片图像,然后通过切片图像获取体数据;在采用高斯滤波对体数据进行预处理后,使用移动立方体算法重建三维表面,并用顶点删除法和二次误差测度算法简化三维表面;在采用Laplacian算法平滑三维表面后,将三维表面模型保存为STL格式的文件;最后,将STL格式的文件导入到UG中,重构出产品的三维计算机辅助设计模型.实际应用验证了该方法的有效性和正确性.     

Modelling and analysis of 3-D arrangements of particles by point processes with examples of application to biological data obtained by confocal scanning light microscopy

Within the concept of point processes, a review is presented of quantities which can be used in studies of three-dimensional (3-D) aggregates of particles. Suitable characteristics and estimators are given for both unmarked and marked point processes. To demonstrate the feasibility of such quantitative approaches, an application in histology, dealing with 3-D arrangements of cell nuclei in rat liver, is described. Using a confocal scanning light microscope, 3-D images are recorded and image analysis used to obtain the coordinates of the centroid, together with the volume and DNA content, of each cell nucleus. Examples of results are given, using both unmarked and marked point processes. In the latter case, cell type, nuclear volume and ploidy group are suitable marks.     

多通道门选通纳秒分幅相机

采用光学分幅技术和多通道门选通法研制了纳秒分幅相机。首次应用八棱锥将图像分为8幅,每幅图像有相等的光学能量并包含与原图像相同的光学信息,每个通道使用独立的带门选通的像增强器和CCD相机,自行开发的近贴门选通像增强器用于增强弱光图像。相机系统可一次获得8幅图像,分幅速率达到1×10⁸ frame/s,最短曝光时间和时间间隔为3 ns和10 ns并分别可调,可记录持续时间为百纳秒到几十微秒的发光现象,动态空间分辨率达到15 lp/mm。该相机已成功应用于电脉冲、等离子发光等现象的试验并获得了有意义的数据,可满足高速摄影机等设备具有高分幅速率,短曝光时间和适当间隔以及在曝光时间内固定时刻记录超快现象过程的要求。     

金字塔光流三维运动估计与深度重建直接方法

针对基于图像序列光流的三维运动估计与深度重建问题,提出一种基于图像金字塔光流的三维运动估计与深度重建直接方法。首先根据光流计算亮度守恒假设和像素点光流与三维空间点运动的对应关系推导出基于图像亮度的三维运动守恒假设;然后借鉴变分原理,通过设计基于L1模型的鲁棒数据项以及图像与运动联合控制的平滑项构造基于变分光流的三维运动估计能量函数;为了应对图像序列中包含的大位移运动及运动遮挡问题,采用图像金字塔分层策略设计三维运动估计模型;最后根据图像三维运动估计结果重建图像中运动物体或场景的深度信息。实验表明,该方法能够较好地应对图像序列中光照变化、多目标大位移运动以及运动遮挡等情况,具有较高的三维运动估计与深度重建精度和较好的鲁棒性。     

A simple method allowing DIC imaging in conjunction with confocal microscopy

Current optical methods to collect Nomarski differential interference contrast (DIC) or phase images with a transmitted light detector (TLD) in conjunction with confocal laser scanning microscopy (CLSM) can be technically challenging and inefficient. We describe for the first time a simple method that combines the use of the commercial product QPm (Iatia, Melbourne Australia) with brightfield images collected with the TLD of a CLSM, generating DIC, phase, Zernike phase, dark-field or Hoffman modulation contrast images. The brightfield images may be collected at the same time as the confocal images. This method also allows the calculation of contrast-enhanced images from archival data. The technique described here allows for the creation of contrast-enhanced images such as DIC or phase, without compromising the intensity or quality of confocal images collected simultaneously. Provided the confocal microscope is equipped with a motorized z-drive and a TLD, no hardware or optical modifications are required. The contrast-enhanced images are calculated with software using the quantitative phase-amplitude microscopy technique ( Barone-Nugent et al., 2002 ). This technique, being far simpler during image collection, allows the microscopist to concentrate on their confocal imaging and experimental procedures. Unlike conventional DIC, this technique may be used to calculate DIC images when cells are imaged through plastic, and without the use of expensive strain-free objective lenses.     

Three-dimensional computer reconstruction of large tissue volumes based on composing series of high-resolution confocal images by GlueMRC and LinkMRC software

Computer-based visualization of large tissue volumes with high resolution based on composing series of high-resolution confocal images is presented. GlueMRC and LinkMRC programs are introduced, implementing composition of overlapping series of optical sections captured by a confocal microscope, registration and subsequent composition of successive confocal stacks. Both programs are using an interactive approach in combination with automatic algorithms for image registration. Further, the method for obtaining surface renderings of microscopical structure under study is described. For this purpose, structure contours visible in the sections are interactively digitized using a Colon plug-in module running in Ellipse environment. Then the coordinates of the contours are processed by special modules in the graphic programming environment IRIS Explorer and the structure surface is rendered. The method is shown on the 3-D reconstruction of the capillary bed of human placental villi and chick embryonic gut and its vascular bed.     

Volume reconstruction of large tissue specimens from serial physical sections using confocal microscopy and correction of cutting deformations by elastic registration

A set of methods leading to volume reconstruction of biological specimens larger than the field of view of a confocal laser scanning microscope (CLSM) is presented. Large tissue specimens are cut into thin physical slices and volume data sets are captured from all studied physical slices by CLSM. Overlapping spatial tiles of the same physical slice are stitched in horizontal direction. Image volumes of successive physical slices are linked in axial direction by applying an elastic registration algorithm to compensate for deformations because of cutting the specimen. We present a method enabling us to keep true object morphology using a priori information about the shape and size of the specimen, available from images of the cutting planes captured by a USB light microscope immediately before cutting the specimen by a microtome. The errors introduced by elastic registration are evaluated using a stereological point counting method and the Procrustes distance. Finally, the images are enhanced to compensate for the effect of the light attenuation with depth and visualized by a hardware accelerated volume rendering. Algorithmic steps of the reconstruction, namely elastic registration, object morphology preservation, image enhancement, and volume visualization, are implemented in a new Rapid3D software package. Because confocal microscopes get more and more frequently used in scientific laboratories, the described volume reconstruction may become an easy‐to‐apply tool to study large biological objects, tissues, and organs in histology, embryology, evolution biology, and developmental biology. In this work, we demonstrate the reconstruction using a postcranial part of a 17‐day‐old laboratory Wistar rat embryo. Microsc. Res. Tech., 2009. © 2008 Wiley‐Liss, Inc.     

联合光度立体视觉和图像校正的磨粒三维形貌重建

分析铁谱技术在机械装备磨损状态检测中发挥了重要作用,但其仅能提供磨粒二维图像,导致磨粒形貌信息不足。为实现磨粒三维形貌的精确重建,联合光度立体视觉和图像校正,为精确重建磨粒的三维形貌,联合光度立体视觉和图像。该方法首先采用大津阈值法由全光源图像识别磨粒与背景区域;然后为消除LED发光强度差异对磨粒形貌重建的影响,结合平面形状和朗伯反射模型确定背景区域的理想成像亮度,并校正各光度图像序列的亮度;最后根据光度立体视觉方法,由校正后光度图像序列重建磨粒的三维形貌。以不同类型的磨粒为测试样本,将所提出的方法的重建结果与激光共聚焦显微镜的测量结果进行对比。结果表明：重建磨粒的形貌参数误差小于15%,表明提出的方法能够精确重建磨粒的三维形貌。     

Methods for compensation of the light attenuation with depth of images captured by a confocal microscope

A confocal laser scanning microscope (CLSM) enables us to capture images from a biological specimen in different depths and obtain a series of precisely registered fluorescent images. However, images captured from deep layers of the specimen may be darker than images from the topmost layers because of light loss distortions. This effect causes difficulties in subsequent analysis of biological objects. We propose a solution using two approaches: either an online method working already during image acquisition or an offline method assisting as a postprocessing step. In the online method, the gain value of a photomultiplier tube of a CLSM is controlled according to the difference of mean image intensities between the reference and currently acquired image. The offline method consists of two stages. In the first stage, a standard histogram maintaining relative frequencies of gray levels and improving brightness and contrast is created from all images in the series. In the second stage, individual image histograms are warped according to this standard histogram. The methods were tested on real confocal image data captured from human placenta and rat skeletal muscle specimens. It was shown that both approaches diminish the light attenuation in images captured from deep layers of the specimen.     

Modelling of three-dimensional fluorescence images of muscle fibres: an application of the three-dimensional optical transfer function

Striated muscle fibres can be modelled by a simple geometry, which has allowed three-dimensional (3-D) images in conventional and confocal microscopes to be calculated. This model is useful for comparing different imaging methods and represents a simple example of an application of the 3-D optical transfer function (OTF) for the system. The rejection of out-of-focus blur is demonstrated, and the effects of fibre thickness and confocal pinhole size on image contrast are investigated. The effects of using a simple filter for image enhancement are studied, elucidating the characteristics of the OTF.     

Application of confocal scanning laser microscopy for an automated nuclear grading of prostate lesions in three dimensions

Confocal scanning laser microscopy provides the opportunity to obtain three-dimensional (3-D) images by piling up consecutive confocal planes. This technique was applied to capture 3-D images from 100-μm-thick tissue blocks from prostate lesions (hyperplasia, dysplasia, adenocarcinomas). Automated methods were implemented to perform a nuclear grading of 3-D cell nuclei from these specimens. Special attention was focused on the development of a new approach to 3-D chromatin texture analysis. This method uses mathematical morphology operations to tessellate the chromatin into homogeneous domains. The nuclear features (volume, shape, texture) were subjected to a discriminant analysis. Using a set of five features, the classification of cell nuclei yielded an accuracy of 963%. The results indicate the potential of 3-D imaging and analysis techniques for an automated nuclear grading of prostate lesions.     

The distribution of caveolin-3 immunofluorescence in skeletal muscle fibre membrane defined by dual channel confocal laser scanning microscopy, fast Fourier transform and image modelling

Membrane domains rich in caveolin‐3 overlie sarcomeric actin in skeletal muscle. The membrane exhibits a regular array of caveolin‐3 immunofluorescence using confocal laser scanning microscopy (CLSM). Fourier analysis of tissue imaged by CLSM accurately defines a repeating intensity with a long‐axis spacing of 1.48 µm confirmed by measurement of direct images. Reverse fast Fourier transform (FFT) and image‐modelling allow reconstruction of the pattern. Mathematical modelling has allowed replication of several features of the FFT, including the second order maxima that confirm the relatively high information content of the original images. Measurements of membrane‐pattern primary long‐axis spacings are consistent with our measurements of the I‐band sarcomere repeat in similarly prepared specimens labelled with fluorescent phalloidin or imaged using differential interference contrast microscopy. Dual‐channel CLSM analysis of the sarcomeric banding pattern of actin and the repeating pattern of muscle fibre membrane caveolin showed that caveolae overlie the I‐band. The anti‐caveolin immunofluorescence is deficient over the Z‐disc and maximal toward each of the I‐band extremities. A mechanism of membrane shape change in which membrane–lipid molecules are interposed between more stable anchored rafts associated with caveolae can be envisaged. Thus, increasing girth and reducing length of the sarcolemma in rapid contraction may be explained.     

Four-dimensional factor analysis of confocal image sequences (4D-FAMIS) to detect and characterize low copy numbers of human papillomavirus DNA by FISH in HeLa and SiHa cells

Visualization and localization of specific DNA sequences were performed by fluorescence in situ hybridization, confocal laser scanning microscopy (CLSM), and four-dimensional factor analysis of biomedical image sequences (4D-FAMIS). HeLa and SiHa cells containing, respectively 20–50 and 1–2 copies per cell of human papillomavirus (HPV) DNA type 18 and 16 integrated in cellular DNA were used as models. HPV-DNA was identified using DNA probes containing the whole genome of HPV-DNA type 18 or 16, and DNA–DNA hybrids were revealed by alkaline phosphatase and Fast Red. Cell nuclei were counterstained with thiazole orange (TO) or TOTO-iodide. 4D image sequences were obtained using successive dynamic or spectral sequences of images on different optical sections from CLSM. The location of fluorescent signals within the preparations was determined by FAMIS. This original method summarizes image sequences into a reduced number of images called factor images, and curves called factors. Factors estimate different individual physical behaviours in the sequence such as extinction velocity, spectral patterns and depth emission profiles. Factor images correspond to spatial distributions of the different factors. We distinguished between Fast Red and nucleus stainings in HPV-DNA hybridization signals by taking into account differences in their extinction velocities (fluorescence decay rate) or spectral patterns, and in their focus (depth emission profiles). In HeLa cells, factor images showed that Fast-Red-stained targets could be distinguished from nucleus stainings, and were located on different focal planes of the nuclei. In SiHa cells, 4D-FAMIS determined as few as 1–2 copies per cell of HPV-DNA type 16 located in continuous focal planes. Therefore, 4D-FAMIS, together with CLSM, made the detection and characterization of low copy numbers of genes in whole cells possible.