Analysis of nerve fibers and their distribution in histologic sections of the human brain

The field of quantitative analysis and subsequent mapping of the cerebral cortex has developed rapidly. New powerful tools have been applied to investigate large regions of complex folded gyrencephalic cortices in order to detect structural transition regions that might partition different cortical fields of disjunct neuronal functions. We have developed a new mapping approach based on axoarchitectonics, a method of cortical visualization that previously has been used only indirectly with regard to myeloarchitectonics. Myeloarchitectonic visualization has the disadvantage of producing strong agglomerative effects of closely neighbored nerve fibers. Therefore, single and neurofunctional-relevant parameters such as axonal branchings, axon areas, and axon numbers have not been determinable with satisfying precision. As a result, different staining techniques had to be explored in order to achieve a suitable histologic staining for axon visualization. The best results were obtained after modifying the Naoumenko-Feigin staining for axons. From these contrast-rich stained histologic sections, videomicroscopic digital image tiles were generated and analyzed using a new fiber analysis framework. Finally, the analysis of histologic images provided topologic ordered parameters of axons that were transferred into parameter maps. The axon parameter maps were analyzed further via a recently developed traverse generating algorithm that calculated test lines oriented perpendicular to the cortical surface and white matter border. The gray value coded parameters of the parameter maps were then transferred into profile arrays. These profile arrays were statistically analyzed by a reliable excess mass approach we recently developed. We found that specific axonal parameters are preferentially distributed throughout granular and agranular types of cortex. Furthermore, our new procedure detected transition regions originally defined by changes of cytoarchitectonic layering. Statistically significant inhomogeneities of the distribution of certain axon quantities were shown to indicate a subparcellation of areas 4 and 6. The quantification techniques established here for the analysis of spatial axon distributions within larger regions of the cerebral cortex are suitable to detect inhomogeneities of laminar axon patterns. Hence, these techniques can be recommended for systematic and observer-supported cortical area mapping and parcellation studies.     

A hybrid approach to smooth surface reconstruction from 2-D cross sections

This article presents a hybrid approach to smooth surface reconstruction from serial cross sections, where the number of contours varies from section to section. In a triangular surface-based approach taken in most reconstruction methods, a triangular surface is constructed by stitching triangular patches over a triangular net generated from the compiled contours. In the proposed approach, the resulting surface is a G¹ composite surface consisting of three kinds of surfaces: skinned, branched, and capped surfaces. Each skinned surface is first represented by a B-spline surface approximating the serial contours of the skinned region and then is transformed into a mesh of rectangular Bezier patches. On branched and capped regions, triangular G¹ surfaces are constructed such that the connections between the triangular surfaces and their neighbouring surfaces are G¹ continuous. Because each skinned region is represented by an approximated rectangular C² surface instead of an interpolated triangular G¹ surface, the proposed approach can provide more visually pleasing surfaces and realize more efficient data reduction than the triangular surface-based approach. Some experimental results demonstrate its usefulness and quality.     

线激光-立体视觉三维数据获取系统研究

通过将三目立体视觉和线激光扫描传感器两种物体表面三维数据获取设备集成到三坐标测量机(CMM),形成一种新型的反求工程中的数据获取系统,其中由三目立体视觉来获得物体的边界或轮廓信息、线激光扫描传感器获得物体表面的三维数据,利用多传感器的信息融合技术对三维数据进行分割,提取被测物体的几何特征,并在此基础上构建物体模型.采用这种多传感器集成坐标测量系统避免了单一传感器的局限性,从而为非接触测量系统在反求工程中的应用开辟了新的途径.     

基于锥束CT切片图像的复杂零件三维表面重构

根据锥束CT切片图像的特点，提出了一种面向复杂零件的三维表面重构新方法：首先采用3D亚体素边缘检测算法提取序列切片图像的高精度封闭轮廓，并重构出切片轮廓的拓扑信息，然后采用一种改进的基于截面属性的轮廓分割算法得到若干组局部结构轮廓集，最后对这些轮廓集进行叠加与拼合，形成零件的整个三维表面。实验结果表明，该方法分割轮廓准确，稳定性好，对具有复杂内外结构的零件，可确保其重构结果的拓扑正确性。     

FEATURE EXTRACTION OF BONES AND SKIN BASED ON ULTRASONIC SCANNING

In the prosthetic socket design,aimed at the high cost and radiation deficiency caused by CT scanning which is a routine technique to obtain the cross-sectional image of the residual limb,a new ultrasonic scanning method is developed to acquire the bones and skin contours of the residual limb.Using a pig fore-leg as the scanning object,an overlapping algorithm is designed to reconstruct the 2D cross-sectional image,the contours of the bone and skin are extracted using edge detection algorithm and the 3D model of the pig fore-leg is reconstructed by using reverse engineering technology.The results of checking the accuracy of the image by scanning a cylinder work pieces show that the extracted contours of the cylinder are quite close to the standard circumference.So it is feasible to get the contours of bones and skin by ultrasonic scanning.The ultrasonic scanning system featuring no radiation and low cost is a kind of new means of cross section scanning for medical images.     

A quantitative approach to cytoarchitectonics: Analysis of structural inhomogeneities in nervous tissue using an image analyser

Cytoarchitectonic investigations are based on the analysis of structural inhomogeneities in the neuronal composition of nervous tissue. Boundaries of brain regions are established at locations where local structural properties, such as density, shape, orientation or arrangement of the nerve cells, change. A quantitative approach requires a complete scanning of histological sections and the measurement of at least one of these properties using an automatic device. In contrast to recently developed stereological methods which result in unbiased estimates of parameters and which are based on efficient sampling procedures, measurements with automatic devices are biased due to section thickness and problems in the segmentation of nerve cell bodies. Automatic measurements are necessary, however, if a complete scanning of histological sections is required in order to localize areal or laminar boundaries. In this approach, the grey level index (GLI) is measured with a TV-based image analysing system from routine histological sections. Using Nissl-staining, this parameter is a biased estimate of the local volume density of Nissl-positive structures (cell bodies). The histological section is digitized into a GLI image by a scanning procedure. The GLI image is processed by image enhancement procedures in order to visualize the laminar pattern. Areal boundaries are localized at positions where this laminar pattern changes. GLI statistics of single brain regions can easily be evaluated by delineating these regions with a cursor in the GLI images of the sections. Information from a series of sections is compiled by specific application programs.     

Combining quantitative 2D and 3D image analysis in the serial block face SEM: application to secretory organelles of pancreatic islet cells

A combination of two‐dimensional (2D) and three‐dimensional (3D) analyses of tissue volume ultrastructure acquired by serial block face scanning electron microscopy can greatly shorten the time required to obtain quantitative information from big data sets that contain many billions of voxels. Thus, to analyse the number of organelles of a specific type, or the total volume enclosed by a population of organelles within a cell, it is possible to estimate the number density or volume fraction of that organelle using a stereological approach to analyse randomly selected 2D block face views through the cells, and to combine such estimates with precise measurement of 3D cell volumes by delineating the plasma membrane in successive block face images. The validity of such an approach can be easily tested since the entire 3D tissue volume is available in the serial block face scanning electron microscopy data set. We have applied this hybrid 3D/2D technique to determine the number of secretory granules in the endocrine α and β cells of mouse pancreatic islets of Langerhans, and have been able to estimate the total insulin content of a β cell.     

An application of numerical taxonomy to the study of the cerebral cortex of Natrix maura (L)

The separate cellular regions of the reptilian cerebral cortex were studied using Numerical Taxonomy. Three parameters were employed: a) The area occupied by each region at the several levels studied. b) The total area of the cell nuclei present in each level. c) The average are of these nuclei. Numerical Taxonomy resolves the problem by means of a dendrogram which represents the normalised distances, which indicate levels of similarity on absciassas. The elements studies are on the ordinate axis. The dendrogram shows the different levels of similarity existing between each one of the chosen populations. Depending upon the degree of similarity one may deduce the similarities or differences existing between these populations, and also the characteristics of each cellular population throughout the length of its presence in the cerebral cortex and the variations between the regions. These results, in the first place, relate to the four cortical regions: medialis cortex, dorsomedialis cortex, dorsalis cortex, and lateralis cortex, and in the second place, to each one of the regions within the entire telencephalic cortex.     

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.     

基于锥束CT图像的数字样品建模方法研究

提出了一种同时包含物体内部材料分布和表面几何信息的数字样品概念,研究并实现了基于锥束CT图像的数字样品建模方法。在材料建模方面,根据材料识别提出了一种计算材料相分布的方法;在几何建模方面,针对锥束CT图像的特点,提出并实现了一种局部结构重构和整体拓扑重构相结合的三维物体表面重构新方法。实验表明,该研究为三维物体内部结构和表面信息的测量重构提供了一种可行的新建模方法和实现技术。     

由基于轮廓重建的表面模型构建实体几何模型

基于工业CT(ICT)图象进行反求是逆向工程的重要内容 ,由ICT图象提取轮廓并进行轮廓重建的模型为表面模型 ,只包含表面几何信息 ,而实体几何模型具有完备的几何和拓扑信息。本文论述了由轮廓重建表面模型的方法和步骤 ,提出了一种由表面模型构建实体几何模型的方法。文中还对存在分叉轮廓、内轮廓的情况提出了具体处理方法。用轮廓重建生成表面模型 ,再转成实体模型的方法可作为三维CAD系统的一种造型手段     

Analysis of local orientation gradients in deformed single crystals

Grain fragmentation and local orientation gradients in deformed single crystals are characterized using electron backscatter diffraction (EBSD) to obtain statistically reliable information. Interrogation of the dislocation substructure is accomplished by extracting information gleaned from small point-to-point misorientations as measured by EBSD. Along with an estimate of the geometrically necessary dislocation (GND) content, the point-to-point deviation from an average grain orientation is described by an orientation difference vector defined in Rodrigues space. Mapping of parameters such as GND, and divergence and gradient fields created from analysis of the difference vectors provide an alternative approach to obtain quantitative information and images from EBSD data.     

A new parametric control method for freeform mesh models

Parametric modeling technology is difficult to apply to freeform mesh models since there is no efficient way to impose geometric constraints. In this paper, we propose a novel method to control freeform mesh models parametrically. Our approach is to construct a control mesh that surrounds an object model and then impose constraints on it. The control mesh is parametrically controlled and the shape of the object model is modified by using an existing freeform deformation method. This paper is mainly concerned with automated construction of a control mesh and treatment of geometric constraints. Procedures for creating a control mesh are as follows: 1) determine the optimal orientation of the model, 2) project the model along three axes and extract contours, 3) create 2D control polygons for the contours, and 4) construct the 3D control mesh from the 2D control polygons. Geometric constraints are imposed on the edges and faces of a control mesh. Types of constraints are given by either a relative relationship between elements or an absolute displacement. A new control mesh is calculated by solving these constraints and the original model is modified accordingly. We tested our algorithms for two freeform models.     

混合型柔性铰链构型设计与柔度建模

通过将对称型柔性铰链进行分段和命名,提出一种基于柔性铰链基段和镜像段串联组合的混合型柔性铰链构型设计方法。基于卡式第二定理,将基段柔度建模转化成与其槽口形状函数有关的定积分问题。推导得到镜像段与其基段间的柔度映射和多段基段的柔度矩阵,进而构建出形式统一的两段混合型柔性铰链通用柔度和精度模型。选取圆锥曲线、矩形梁和棱台型基段类型,基于组合设计共获得96种新型混合型柔性铰链。结合具体算例和借助有限元验证理论模型的正确性,并对所设计和现有的柔性铰链构型性能统一进行评价分析。研究工作可为柔性铰链构型优选和特性评价提供理论指导。     

Shack-Hartmann wave front measurements in cortical tissue for deconvolution of large three-dimensional mosaic transmitted light brightfield micrographs

We present a novel approach for deconvolution of 3D image stacks of cortical tissue taken by mosaic/optical‐sectioning technology, using a transmitted light brightfield microscope. Mosaic/optical‐sectioning offers the possibility of imaging large volumes (e.g. from cortical sections) on a millimetre scale at sub‐micrometre resolution. However, a blurred contribution from out‐of‐focus light results in an image quality that usually prohibits 3D quantitative analysis. Such quantitative analysis is only possible after deblurring by deconvolution. The resulting image quality is strongly dependent on how accurate the point spread function used for deconvolution resembles the properties of the imaging system. Since direct measurement of the true point spread function is laborious and modelled point spread functions usually deviate from measured ones, we present a method of optimizing the microscope until it meets almost ideal imaging conditions. These conditions are validated by measuring the aberration function of the microscope and tissue using a Shack‐Hartmann sensor. The analysis shows that cortical tissue from rat brains embedded in Mowiol and imaged by an oil‐immersion objective can be regarded as having a homogeneous index of refraction. In addition, the amount of spherical aberration that is caused by the optics or the specimen is relatively low. Consequently the image formation is simplified to refraction between the embedding and immersion medium and to 3D diffraction at the finite entrance pupil of the objective. The resulting model point spread function is applied to the image stacks by linear or iterative deconvolution algorithms. For the presented dataset of large 3D images the linear approach proves to be superior. The linear deconvolution yields a significant improvement in signal‐to‐noise ratio and resolution. This novel approach allows a quantitative analysis of the cortical image stacks such as the reconstruction of biocytin‐stained neuronal dendrites and axons.     

Use of atomic force microscopy (AFM) for microfabric study of cohesive soils

Microfabric reflects the imprints of the geologic and stress history of the soil deposit, the depositional environment and weathering history. Many investigators have been concerned with the fundamental problem of how the engineering properties of clay depend on the microfabric, which can be defined as geometric arrangement of particles within the soil mass. It is believed that scanning electron microscopy (SEM) and transmission electron microscopy (TEM) are the only techniques that can reveal particle arrangements of clayey soils directly; however, current research introduces a novel and more advanced technique, atomic force microscopy, to evaluate the microfabric of cohesive materials. The atomic force microscopy has several advantages over SEM/TEM for characterizing cohesive particles at the sub‐micrometre range by providing 3D images and 2D images with Z‐information used in quantitative measurements of soil microfabric using SPIP software, and having the capability of obtaining images in all environments (ambient air, liquids and vacuums). This paper focuses on the use of atomic force microscopy technique to quantify the microfabric of clayey soils by developing the criteria for average and maximum values of angle of particle orientation within the soil mass using proposed empirical equations for intermediate and extreme microfabrics (dispersed, flocculated).     

An automated slide scanning system for membrane filter imaging in diagnosis of urogenital schistosomiasis

Traditionally, automated slide scanning involves capturing a rectangular grid of field-of-view (FoV) images which can be stitched together to create whole slide images, while the autofocusing algorithm captures a focal stack of images to determine the best in-focus image. However, these methods can be time-consuming due to the need for X-, Y- and Z-axis movements of the digital microscope while capturing multiple FoV images. In this paper, we propose a solution to minimise these redundancies by presenting an optimal procedure for automated slide scanning of circular membrane filters on a glass slide. We achieve this by following an optimal path in the sample plane, ensuring that only FoVs overlapping the filter membrane are captured. To capture the best in-focus FoV image, we utilise a hill-climbing approach that tracks the peak of the mean of Gaussian gradient of the captured FoVs images along the Z-axis. We implemented this procedure to optimise the efficiency of the Schistoscope, an automated digital microscope developed to diagnose urogenital schistosomiasis by imaging Schistosoma haematobium eggs on 13 or 25 mm membrane filters. Our improved method reduces the automated slide scanning time by 63.18% and 72.52% for the respective filter sizes. This advancement greatly supports the practicality of the Schistoscope in large-scale schistosomiasis monitoring and evaluation programs in endemic regions. This will save time, resources and also accelerate generation of data that is critical in achieving the targets for schistosomiasis elimination.     

Contour-based algorithms for generating 3D CAD models from medical images

This paper concerns contour-based algorithms for generating a 3D CAD model from medical images. The 3D model generated by contour-based algorithms can be used to generate CAM data for fabrication where the accuracy is of most concern. The overall procedure includes: (1) contour data extraction from medical images, (2) smoothing of the extracted contours, and (3) creation of a surface model from contours. For this, various methods should be applied to generate a high-quality surface model. The main contribution of this paper is to propose a new contour smoothing method, called bi-directional smoothing. The basic idea behind the proposed bi-directional smoothing method is to refine contours along both (u, v) parametric directions. Compared to conventional smoothing methods, the recontouring that comprises the first part of the method can prevent the shape of a contour from shrinking with a large number of iterations. Along with recontouring, a vertical connectivity estimation and a vertical smoothing method are also proposed. The overall procedure for this approach is demonstrated with an application example using CT images of a femur.     

The use of local entropy measures in edge detection for cytological image analysis

Accurate edge detection is a fundamental problem in the areas of image processing and pattern recognition/classification. The lack of effective edge detection methods has slowed the application of image processing to many areas, in particular diagnostic cytology, and is a major factor in the lack of acceptance of image processing in service orientated pathology. In this paper, we present a two-step procedure which detects edges. Since most images are corrupted by noise and often contain artefacts, the first step is to clean up the image. Our approach is to use a median filter to reduce noise and background artefacts. The second operation is to locate image pixels which are ‘information rich’ by using local statistics. This step locates the regions of the image most likely to contain edges. The application of a threshold can then pin-point those pixels forming the edge of structures of interest. The procedure has been tested on routine cytologic specimens.