Real time uses of color for electron microscopy via a television-rate digital frame store

An on-line television-rate digital frame store device is utilized to provide color representations of a wide range of electron microscope images and image data. Various types of hardware devices in the frame store coupled with software manipulations via the host computer make rapid image acquisition, modification, measurement, and full-color display possible in real time either from micrographs or directly from an electron microscope. Lookup tables used in conjunction with grey-level image memories can be controlled from a menu display to provide a wide range of color-coding schemes and sequencing. It is also possible to use color graphics overlays and alpha numeric displays along with full-color image displays. This paper will describe many of the recent applications of color developed for electron microscopy studies of materials.     

Reduction in acquisition time of scanning electron microscopy image using complex hysteresis smoothing

Complex hysteresis smoothing (CHS), which was developed for noise removal of scanning electron microscopy (SEM) images some years ago, is utilized in acquisition of an SEM image. When using CHS together, recording time can be reduced without problems by about one-third under the condition of SEM signal with a comparatively high signal-to-noise ratio (SNR). We do not recognize artificiality in a CHS-filtered image, because it has some advantages, that is, no degradation of resolution, only one easily chosen processing parameter (this parameter can be fixed and used in this study), and no processing artifacts. This originates in the fact that its criterion for distinguishing noise depends simply on the amplitude of the SEM signal. The automation of reduction in acquisition time is not difficult, because CHS successfully works for almost all varieties of SEM images with a fairly high SNR.     

Practical method for noise removal in scanning electron microscopy

A new smoothing filter has been developed for noise removal of scanning electron microscopy (SEM) images. We call this the complex hysteresis smoothing (CHS) filter. It is much easier to use for SEM operators than any other conventional smoothing filter, and it rarely produces processing artifacts because it does not utilize a definite mask (which usually has processing parameters of size, shape, weight, and the number of iterations) like a common averaging filter or a complicated filter shape in the Fourier domain. Its criterion for distinguishing noise depends simply on the amplitude of the SEM signal. When applied to several images with different characteristics, it is shown that the present method has a high performance with some original advantages.     

The detection quantum efficiency of electronic image recording systems

The principles in design and operation of TV electron-image recording systems are elucidated. Using the ‘detection quantum efficiency’ (DQE) as a figure of merit, the influence of various parameters is discussed, such as single electron response, read-out noise and saturation of the camera tubes as well as the properties of digital frame stores. The analogue signal processing mode gives a DQE of about 0·8 and can be adapted to a wide range of operating conditions. Counting of normalized electron signals in digital storages allows an almost ideal image detection, which can, however, at best only be applied with a current density below 10^?13 A cm^?2. Compared to photographic recording, electronic systems offer real-time response, compatibility with computers and great flexibility of stored information. Their DQE is similar in the analogue mode but superior in the counting mode. The storage capacity, on the other hand—particularly the number of pixels—is presently still inferior to the photoplate.     

Future trends in microscopy

Recent progress and current trends in microscopy are examined with particular reference to possible future developments. The scope for systematic improvement of the traditional optical or electron designs and procedures seems far from exhausted. However the introduction of novel, lens-free microscopes which, like the scanning tunnelling microscope, produce magnification using an electronic lever arm, could expand the boundaries of the subject most dramatically. The future microscopist may find himself displaced from the more routine tasks of focusing, alignment, image recording and even simple interpretation by the electronic robot. On the other hand, he will gain access to a wider and more sophisticated range of physical and chemical phenomena governing the interaction between the specimen and the radiations he uses to probe its microscopic structure and properties.     

Low-energy electron microscopy (LEEM) and mirror electron microscopy (MEM) of biological specimens: Preliminary results with a novel beam separating system

Low-energy electron microscopy (LEEM) and mirror electron microscopy (MEM) utilize a parallel beam of slow-moving electrons backscattered from the specimen surface to form an image. If the electrons strike the surface an LEEM image is produced and if they are turned back just before reaching the surface an MEM image results. The applications thus far have been in surface physics. In the present study, applications of LEEM and MEM in the biological sciences are discussed. The preliminary results demonstrate the feasibility of forming images of uncoated cultured cells and cellular components using electrons in the threshold region (i.e. 0–10 V). The results also constitute a successful test of a novel beam-separating system for LEEM and MEM.     

A statistical model of signal-noise in scanning electron microscopy

A statistical model describing signal-noise generation and development along the signal formation process in a standard scanning electron microscope (SEM) using an Everhart-Thornley secondary electron detector is derived. Noise in the detector signal is modeled to originate from a cascade of five signal conversion stages. Based on the derived model, general conclusions are drawn concerning the total signal-to-noise ratio (SNR) at each stage, and the influence of each stage on the total SNR of the detector signal. The model is furthermore applied to a real-world SEM, and verified by experimental data.     

The use of helium gas to reduce beam scattering in high vapour pressure scanning electron microscopy applications

Both image quality and the accuracy of x-ray analysis invariable pressure scanning electron microscopes (VPSEMs) are often limited by the spread of the primary electronbeam due to scattering by the introduced gas. The degree of electron scattering depends partly on the atomic number Z of the gas, and the use of a low Z gas such as helium should reduce beam scattering and enhance image quality. Using anuncoated test sample of copper iron sulphide inclusions in calcium fluorite, we show that the reduction in beam scatter produced by helium is more than sufficient to compensate for its reduced efficiency of charge neutralisation. The relative insensitivity to pressure of x-ray measurements in a helium atmosphere compared with air, and the consequent ability to work over a wider range of working distances, pressures, and voltages, make helium potentially the gas of choice for many routine VPSEM applications.     

Quantitative microscopy reveals 3D organization and kinetics of endocytosis in rat hepatocytes

In order to demonstrate the power of quantitative microscopy, the endocytic apparatus of rat hepatocytes was reexamined using in situ liver and short term cultured hepatocyte couplets that were allowed to internalize endocytic markers for various time intervals. Correlative confocal light and electron microscopy demonstrate a tubulovesicular reticulum representing the endocytic apparatus. Volume and membrane area account for 2% of cell volume and 30% plasma membrane surface. Colocalization analysis demonstrated that pathway-specific ligands and fluid-phase markers enter EEA1-positive vesicles, the early endosomal compartment, immediately after internalization. These vesicles are translocated rapidly from basolateral to perinuclear and apical locations. Ligands are sorted within 5 min to their respective pathways. Sequential colocalization of an asialoglycoprotein-pulse with rab7 and lamp3 demonstrates that early endosomes change into or fuse with late endosomes and lysosomes. Alternatively, markers are sequestered into the common endosome consisting of rab11-positive, long tubules that originate from early endosomes and show an affinity for the transcytotic marker pIgA and its receptor. This compartment mediates transcytosis by delivering the receptor-ligand complex to the subapical compartment, a set of apical, rab11-positive vesicles, which are connected to the tubular reticulum. We conclude that vesicular traffic between preexisting compartments, maturation or fusion of endocytic organelles, and transport in tubules act in concert and together mediate transport between compartments of a tubulovesicular endocytic apparatus. In addition, we show that quantitative microscopy using high resolution data sets can detect and characterize kinetics of various parameters thus adding a dynamic component to 3D information.     

A simple method for the handling and orientation of small specimens for electron microscopy

Cyanoacrylic glue (Eastman 910) was used to affix small pieces of nasal scrapings to lens paper immediately before fixation in the glutaraldehyde. The lens paper not only served to hold specimens together so that they were not lost during tissue processing, but also functioned as a ‘landmark’ for the specimens, so that specimens could be oriented in a specific manner during embedding and subsequent sectioning.     

Representation of three-dimensionally reconstructed objects in electron microscopy by surfaces of equal density

A surface representation algorithm has been developed to visualize the results of three-dimensional reconstructions from projections in electron microscopy. It produces an easily recognizable image of the reconstructed particle and facilitates comprehension of the three-dimensional structure. Thus building of physical models can be avoided in many cases. If such a model is needed the algorithm can be used to establish the correct particle boundary in advance. Some further effort has been made to represent long fibres and visualize inner structures of objects, which are obscured by outer high-density regions. Shading may be used to enhance the depth perception from single views.     

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.     

A method for personal expertise-independent evaluation of image resolution in scanning electron microscopy

The two conventional methods currently employed for the evaluation of image resolution in scanning electron microscopy are the gap method and a fast Fourier transform (FFT) method. These can be highly dependent on personal expertise on the distinction between signal information and noise contained in a micrograph. Hence, the present paper proposes an alternative method (referred to as a contrast-to-gradient (CG) method) that can determine the image resolution of a micrograph without requiring personal expertise on the judgment of noise. The image resolution in the CG method is defined as a weighted harmonic mean of the local resolution, which is proportional to the quotient of the threshold contrast divided by the local gradient. The local gradient is calculated from the quadratic function that best fits the local pixel intensities over 5 x 5 pixels. It has been shown that the CG method, compared with the FFT method, has a broader range of applications for various types of images, such as low-contrast, noise-containing, filter-processed, highly directional, and quasi-periodic feature images.     

Imaging an optical disc by the combined use of scanning tunnelling microscopy and scanning electron microscopy

We present the data obtained by scanning tunnelling microscopy combined with scanning electron microscopy of the digitally encoded structure on a stamper used to fabricate optical discs. The combination allows us to focus the STM tip on a preselected spot with a precision of ?0·3 μm. The data show the superiority of STM for a more detailed characterization of shape, width, length, height and fine structure appearing on the sample. We also show the influence of tip shape on STM resolution. Simultaneous use of both microscopes is possible but high electron doses produce an insulating layer of contaminants thick enough to make STM operation impossible.     

A new algorithm to reduce noise in microscopy images implemented with a simple program in python

All microscopical images contain noise, increasing when (e.g., transmission electron microscope or light microscope) approaching the resolution limit. Many methods are available to reduce noise. One of the most commonly used is image averaging. We propose here to use the mode of pixel values. Simple Python programs process a given number of images, recorded consecutively from the same subject. The programs calculate the mode of the pixel values in a given position (a, b). The result is a new image containing in (a, b) the mode of the values. Therefore, the final pixel value corresponds to that read in at least two of the pixels in position (a, b). The application of the program on a set of images obtained by applying salt and pepper noise and GIMP hurl noise with 10-90% standard deviation showed that the mode performs better than averaging with three-eight images. The data suggest that the mode would be more efficient (in the sense of a lower number of recorded images to process to reduce noise below a given limit) for lower number of total noisy pixels and high standard deviation (as impulse noise and salt and pepper noise), while averaging would be more efficient when the number of varying pixels is high, and the standard deviation is low, as in many cases of Gaussian noise affected images. The two methods may be used serially.     

Assessment and correction of geometric distortions in low-magnification scanning electron microscopy images

A method is introduced to assess and correct the geometric distortions which frequently occur in low-magnification scanning electron microscopy (SEM) images. Such images typically exhibit a complex pattern of varying deviations from orthogonality which cannot be adequately corrected by simple geometric transformations such as shifting, scaling, rotation, or shearing. A suitable approach to rectify low-magnification SEM images is polynomial warping, a correction procedure which also accomplishes rubber sheet transformation. To demonstrate the approach, a reference grid for low magnifications has been scanned at 40- and 55-fold magnifications by means of a microanalyzer. Calculated geometric distortions range from 1.5 to 3.5% of the image dimensions; applying polynomial warping, distortions could be reduced to approximately 0.1% of the image dimensions. Because of its easy application and the widespread availability in image processing packages, polynomial warping can be recommended as a routine procedure for rectifying low-magnification SEM images.     

Resolution in low voltage scanning electron microscopy

As the energy of an electron beam is reduced, the range falls and the secondary electron yield rises. A low voltage scanning electron microscope can therefore, in principle, examine without damage or charging samples such as insulators, dielectrics or beam sensitive materials. This paper investigates the way in which the choice of beam energy affects the spatial resolution of a secondary electron image. It is shown that for samples which are thin compared to the electron range, the edge resolution and contrast in the image improve with increasing beam energy. In samples that are thicker than the electron range, the resolution can be optimized at either high or low energies, but low energy operation will produce images of higher contrast. At an energy of 2 keV or less beam interaction limited resolutions of the order of 3 nm should be possible.     

Compression of fluorescence microscopy images based on the signal-to-noise estimation

Modern microscopic techniques like high-content screening (HCS), high-throughput screening, 4D imaging, and multispectral imaging may involve collection of thousands of images per experiment. Efficient image-compression techniques are indispensable to manage these vast amounts of data. This goal is frequently achieved using lossy compression algorithms such as JPEG and JPEG2000. However, these algorithms are optimized to preserve visual quality but not necessarily the integrity of the scientific data, which are often analyzed in an automated manner. Here, we propose three observer-independent compression algorithms, designed to preserve information contained in the images. These algorithms were constructed using signal-to-noise ratio (SNR) computed from a single image as a quality measure to establish which image components may be discarded. The compression efficiency was measured as a function of image brightness and SNR. The alterations introduced by compression in biological images were estimated using brightness histograms (earth's mover distance (EMD) algorithm) and textures (Haralick parameters). Furthermore, a microscope test pattern was used to assess the effect of compression on the effective resolution of microscope images.