The conversion of a field-emission scanning electron microscope to a high-resolution,high-performance scanning transmission electron microscope,while maintaining original functions

Recently, the reliability of field-emission electron guns has increased. In addition, the cost of computer systems for on-line processing has dropped. Hence, we should now consider the use of scanning transmission electron microscopy (STEM) for routine work, especially, in the field of biology where one may expect to utilize digital image processing techniques. An STEM has been constructed, without disturbing the original functions, by converting a commercial scanning electron microscope equipped with a fieldemission gun. The STEM is generally operated at accelerating voltage 30 kV, focal length 7.5 mm, and beam current 1?2 × 10^?10 A. Several improvements have been incorporated for removing the effects of vibration, contamination, and stray magnetic fields. Also, an adjustable detector aperture was utilized. The modified instrument was connected to an on-line digital image processing system for utilizing the information obtained from STEM images. The advantages of the modified system were studied from various viewpoints.     

Seamless stitching of tile scan microscope images

For diagnostic purposes, optical imaging techniques need to obtain high‐resolution images of extended biological specimens in reasonable time. The field of view of an objective lens, however, is often smaller than the sample size. To image the whole sample, laser scanning microscopes acquire tile scans that are stitched into larger mosaics. The appearance of such image mosaics is affected by visible edge artefacts that arise from various optical aberrations which manifest in grey level jumps across tile boundaries. In this contribution, a technique for stitching tiles into a seamless mosaic is presented. The stitching algorithm operates by equilibrating neighbouring edges and forcing the brightness at corners to a common value. The corrected image mosaics appear to be free from stitching artefacts and are, therefore, suited for further image analysis procedures. The contribution presents a novel method to seamlessly stitch tiles captured by a laser scanning microscope into a large mosaic. The motivation for the work is the failure of currently existing methods for stitching nonlinear, multimodal images captured by our microscopic setups. Our method eliminates the visible edge artefacts that appear between neighbouring tiles by taking into account the overall illumination differences among tiles in such mosaics. The algorithm first corrects the nonuniform brightness that exists within each of the tiles. It then compensates for grey level differences across tile boundaries by equilibrating neighbouring edges and forcing the brightness at the corners to a common value. After these artefacts have been removed further image analysis procedures can be applied on the microscopic images. Even though the solution presented here is tailored for the aforementioned specific case, it could be easily adapted to other contexts where image tiles are assembled into mosaics such as in astronomical or satellite photos.     

Feature evaluation of complex hysteresis smoothing and its practical applications to noisy SEM images

Quality of a scanning electron microscopy (SEM) image is strongly influenced by noise. This is a fundamental drawback of the SEM instrument. Complex hysteresis smoothing (CHS) has been previously developed for noise removal of SEM images. This noise removal is performed by monitoring and processing properly the amplitude of the SEM signal. As it stands now, CHS may not be so utilized, though it has several advantages for SEM. For example, the resolution of image processed by CHS is basically equal to that of the original image. In order to find wide application of the CHS method in microscopy, the feature of CHS, which has not been so clarified until now is evaluated correctly. As the application of the result obtained by the feature evaluation, cursor width (CW), which is the sole processing parameter of CHS, is determined more properly using standard deviation of noise Nσ. In addition, disadvantage that CHS cannot remove the noise with excessively large amplitude is improved by a certain postprocessing. CHS is successfully applicable to SEM images with various noise amplitudes. SCANNING 35:292‐301, 2013. © 2012 Wiley Periodicals, Inc     

Application of the Laplacian filter to high-resolution enhancement of SEM images

Certain digital image-processing methods, which are useful for nonperiodic structural images, have been applied to high-resolution SEM images for the improvement of resolution. Samples utilized in the present study consisted of magnetic tape coated with gold, T4 phage coated with gold-palladium, and uncoated specimens of Prolamellar body (PLB) in Cucurbita moschata. These images were blurred and otherwise disturbed by electronic noise, though the images were taken at the limit of efficiency of intrinsic instrument. The major image-processing tool was the Laplacian filter, which subtracts the Laplacian from the original image. Noise, which is a serious problem in digital processing of high-resolution SEM images, was suppressed by the nonlinear type smoothing method. Also, the noise was evaluated by an autocorrelation function and a power spectrum of the image. By using these methods of “deblurring” and noise removal, we achieved better resolution, and structural details of our biological specimens were revealed.     

Digital image acquisition in in vivo confocal microscopy

A flexible system for the real-time acquisition of in vivo images has been developed. Images are generated using a tandem scanning confocal microscope interfaced to a low-light-level camera. The video signal from the camera is digitized and stored using a Gould image processing system with a real-time digital disk (RTDD). The RTDD can store up to 3200 512 times 512 pixel images at video rates (30 images s^?1). Images can be input directly from the camera during the study, or off-line from a Super VHS video recorder. Once a segment of experimental interest is digitized onto the RTDD, the user can interactively step through the images, average stable sequences, and identify candidates for further processing and analysis. Examples of how this system can be used to study the physiology of various organ systems in vivo are presented.     

Three-dimensional visualization methods for confocal microscopy

Three-dimensional images of microscopic objects can be obtained by confocal scanning laser microscopy (CSLM). The imaging process in a CSLM consists of sampling a specific volume in the object and storing the result in a three-dimensional memory array of a digital computer. Methods are needed to visualize these images. In this paper three methods are discussed, each suitable in a specific area of application. For purposes where realistic rendering of solid or semi-transparent objects is required, an algorithm based on simulation of a fluorescence process is most suitable. When speed is essential, as for interactive purposes, a simple procedure to generate anaglyphs can be used. Both methods have in common that they require no previous interpretation or analysis of the image. When the study of an object imaged by CSLM involves analysis in terms of a geometrical model, sophisticated graphics techniques can be used to display the results of the analysis.     

The Use of Macros in Atomic Force Microscopy Image Analysis and Image Processing

The public domain image analysis program NIH Image (http://rsb.info.nih.gov/nih-image) has been modified and extended to produce Image SXM (http://reg.ssci.liv.ac.uk), a program that supports many of the image file formats used by various scanning probe microscope manufacturers. This article discusses the different approaches to software customization and describes the use of two sets of macros in the analysis and processing of atomic force microscopy images.     

Strategies for optimum use of superposition diffractogram in scanning electron microscopy

Characteristics of the superposition diffractogram used for precisely estimating scanning electron microscopy (SEM) resolution are investigated. It is shown that the choice of pixel density to satisfy the sampling theorem, the direction of scanning, the choice of image shift direction, the properties of the specimen, the effect of external disturbances such as vibration and stray magnetic fields, and the effect of the window function required in the Fourier transform, are all factors which must be considered in order to make the superposition diffractogram a practical technique. An additional important improvement required to exploit fully the ability of the superposition diffractogram, which potentially is very high, is a special scanning mode which employs a digital scan generator, and digital image processing technology with autocorrelation functions.     

Mechanical scanning of the specimen in the scanning electron microscope

A scanning electron microscope (SEM) system equipped with a motor drive specimen stage fully controlled with a personal computer (PC) has been utilized for obtaining ultralow magnification SEM images. This modem motor drive stage works as a mechanical scanning device. To produce ultra-low magnification SEM images, we use a successful combination of the mechanical scanning, electronic scanning, and digital image processing techniques. This new method is extremely labor and time saving for ultra-low magnification and wide-area observation. The option of ultra-low magnification observation (while maintaining the original SEM functions and performance) is important during a scanning electron microscopy session.     

一种便携式工业视频内窥镜的开发

在介绍了通用工业内窥镜的结构及原理的基础上,推出了一种用于检查内径20mm以下零件较深部位的内表面的便携式内窥镜,该装置由照明系统、光学系统、CCD摄像机、显示系统四部分组成,相对于普通内窥镜而言具有体积小(80×20×20mm³),重量轻(约50g),结构简单,方便携带,成本低的优点,实验结果表明经图像处理后成像质量较高,小口径零件内表面微小缺陷的检测可达mm级精度.     

New generation scanning electron microscopy technology based on the concept of active image processing

A new generation of scanning electron microscopy (SEM) technology is proposed based on the concept of “active image processing.” In order to collect sufficient data for a purpose which is defined in the utilization of active image processing, we may need more devices from among a variety of useful hardware, for example, a digital scan generator with meaningful parameters and an analog-to-digital converter for ultrahigh density recording. After the data acquisition, the application of some digital image processing techniques is certainly effective, because the method in question is specially designed so that the property of obtained data will be suitable for the application of these techniques. The present technology should produce a variety of attractive options in the field of SEM.     

阶梯轴尺寸及形位误差的机器视觉检测

介绍了基于数字图像处理技术的阶梯轴机器视觉检测方法。对原始数字图像经滤波、二值化、边缘检测及细化等处理后得到轴轮廓图像。通过对轮廓分析,自动测出阶梯轴的长度、直径、圆度误差、同轴度误差,并给出测量后的尺寸结果,分析误差产生的原因。     

Progress in electron microscopic diagnostics: semi-quantitative determination of precipitable calcium in different cell types of the organ of Corti in the guinea-pig

Potassium antimonate was used to precipitate calcium in the cochlea of the guinea-pig. The distribution of the calcium antimonate precipitates was analysed by electron microscopy. The precipitate density was determined in different cell types in the organ of Corti by counting the number of calcium binding sites in a 10-μm² area. The size of the precipitates varied considerably, and thus the relative amount of the precipitable calcium was estimated only semi-quantitatively. As the prominent carbon signal is superimposed over the nearby small Ca²⁺ -edge signals, the combined signal of the antimony M_4,5-edge and the oxygen K-edge of the calcium antimonate salt formed was chosen for the semi-quantitative estimation. Images of the inelastically scattered electrons of the precipitates at ΔE = 570 eV were recorded by electron spectroscopic imaging. The area covered by the calcium precipitates within a given cell type was determined in different ultrathin sections of the same organ of Corti by an image processing system.     

Digital image processing as a tool to monitor biomass growth in Aspergillus niger 3T5B8 solid-state fermentation: preliminary results

The estimation of biomass is an essential parameter for controlling fermentation processes. However, monitoring biomass growth in filamentous fungi solid‐state fermentation is laborious. The aim of this study was to provide a better insight into the monitoring of biomass growth in Aspergillus niger 3T5B8 solid‐state fermentation using a digital image‐processing technique. The images were acquired with a stereomicroscope and a digital camera, and processed using KS400 software. Growth was evaluated every 24 h for 5 days, and quantified as the total area occupied by the hyphae. The correlation between the results of the proposed methodology and the polygalacturonase data was greater than 0.9, showing that a direct and linear relationship can be expected among these parameters. This work indicates that the digital processing technique can be used for indirect biomass estimation in a solid‐state fermentation process.     

The projection of a negatively-stained filamentous object down its central axis as revealed by image reconstruction from tilt series

Helical reconstructions of negatively stained biological objects contain distortions arising from filament flattening and the non-cylindrical profile of the stain envelope. Current methods of estimating flattening do not make full use of the information available in electron micrographs. We have applied the more rigorous approach of reconstructing the density profile from tilt series using digital image processing techniques. Tilt series were collected for tobacco mosaic viruses (TMV) and seven independent reconstructions were calculated using equatorial data out as far as ～1/9·3 nm^—1. They indicated that the filaments were flattened with an axial ratio of about 2·4:1, which was probably closer to 3:1 in the original specimen, because the limited resolution caused flattening to be underestimated. The stain envelope around TMV and some indication of the underlying carbon substrate were also observed. This information could enable correction factors for flattening to be developed, which could be useful when calculating helical reconstructions or indexing helical diffraction patterns. This method could also be extended to non-equatorial layer planes, which would provide three-dimensional information on a wide range of macromolecules that possess a one-dimensional repeat.     

PIV as a method for quantifying root cell growth and particle displacement in confocal images

Particle image velocimetry (PIV) quantifies displacement of patches of pixels between successive images. We evaluated PIV as a tool for microscopists by measuring displacements of cells and of a surrounding granular medium in confocal laser scanning microscopy images of Arabidopsis thaliana roots labeled with cell‐membrane targeted green fluorescent protein. Excellent accuracy (e.g., displacement standard deviation <0.006 pixels) was obtained for root images that had undergone rigid digital translations of up to 40 pixels. Analysis of zoomed images showed that magnifications of up to 5% maintained good linear relations between PIV‐predicted and actual displacements (r² > 0.83). Root mean squared error for these distorted images was 0.4–1.1 pixels, increasing at higher magnification factors. Cell growth and rhizosphere deformation were tracked with good temporal (e.g., 1‐min interval) and spatial resolution, with PIV patches located on recognizable cell features being tracked more successfully. Appropriate choice of GFP‐label was important to decrease small‐scale biological noise due to intracellular motion. PIV of roots grown in stiff 2% versus 0.7% agar showed patterns of cell expansion consistent with physically impeded roots of other species. Roots in glass ballotini underwent rapid changes in growth direction on a timescale of minutes, associated with localized arching of ballotini. By tracking cell vertices, we monitored automatically cell length, width, and area every minute for 0.5 h for cells in different stages of development. In conclusion, PIV measured displacements successfully in images of living root cells and the external granular medium, revealing much potential for use by microscopists. Microsc. Res. Tech., 2009. © 2009 Wiley‐Liss, Inc.     

Extended depth from focus reconstruction using NIH ImageJ plugins: Quality and resolution of elevation maps

In this work, NIH ImageJ plugins for extended depth‐from‐focus reconstructions (EDFR) based on spatial domain operations were compared and tested for usage optimization. Also, some preprocessing solutions for light microscopy image stacks were evaluated, suggesting a general routine for the ImageJ user to get reliable elevation maps from grayscale image stacks. Two reflected light microscope image stacks were used to test the EDFR plugins: one bright‐field image stack for the fracture of carbon‐epoxy composite and its darkfield corresponding stack at same (x,y,z) spatial coordinates. Image quality analysis consisted of the comparison of signal‐to‐noise ratio and resolution parameters with the consistence of elevation maps, based on roughness and fractal measurements. Darkfield illumination contributed to enhance the homogeneity of images in stack and resulting height maps, reducing the influence of digital image processing choices on the dispersion of topographic measurements. The subtract background filter, as a preprocessing tool, contributed to produce sharper focused images. In general, the increasing of kernel size for EDFR spatial domain‐based solutions will produce smooth height maps. Finally, this work has the main objective to establish suitable guidelines to generate elevation maps by light microscopy. Microsc. Res. Tech. 2012. © 2012 Wiley Periodicals, Inc.     

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.     

Automatic quantification of viability in epithelial cell cultures by texture analysis

Quantification of live cells in phase contrast microscopy images allows in vivo assessment of the viability of cultured cells. An automatic screening procedure seems advisable because of the large number of cells that must be counted to achieve reasonable accuracy. This paper presents a method that quantifies necrosis in cell cultures by texture analysis of microscope images. The image is divided into regions of equal size that are classified by means of a segmentation algorithm based on texture analysis into three categories: live cells, necrotic cells and background. The classification uses three discriminant functions, built from parameters derived from the histogram and the co‐occurrence matrix and calculated by performing an initial stepwise discriminant analysis on 21 sample images from a training set. The areas occupied by live and necrotic cells and number of live cells have been obtained for primary cellular cultures in intervals of 48 h during 2 weeks. The results have been compared with those obtained by an experienced observer, showing a very good correlation (Pearson's coefficient 0.95, kappa 0.87, N= 1600). A method has been developed that provides an accuracy similar to that provided by an expert, while allowing a much higher number of fields to be counted.     

Video microscopic image processing facilitates the evaluation of light microscopic autoradiography at high magnification

Light microscopic autoradiographs of H-thymidine labelled unstained semithin sections of Xenopus laevis embryonic nuclei were examined with conventional Nomarski differential interference contrast, phase-contrast and video microscopy. Whereas at low magnification it was possible to obtain a photograph of the nuclear structure and the silver grains in one focal plain, at high magnification, with small depths of focus, a satisfactory image was not attainable. Therefore, we stored the images of the two different focus levels with a digital image processing system and combined both images by an arithmetic operation. This video microscopic technique allows the use of high magnification light microscopy with oil immersion objectives and the application of additional electronic contrast enhancing methods for an adequate and rapid analysis of light microscopic autoradiographs.