Reconstructing the microstructure of polyimide–silicalite mixed‐matrix membranes and their particle connectivity using FIB‐SEM tomography

Properties of a composite material made of a continuous matrix and particles often depend on microscopic details, such as contacts between particles. Focusing on processing raw focused‐ion beam scanning electron microscope (FIB‐SEM) tomography data, we reconstructed three mixed‐matrix membrane samples made of 6FDA‐ODA polyimide and silicalite‐1 particles. In the first step of image processing, backscattered electron (BSE) and secondary electron (SE) signals were mixed in a ratio that was expected to obtain a segmented 3D image with a realistic volume fraction of silicalite‐1. Second, after spatial alignment of the stacked FIB‐SEM data, the 3D image was smoothed using adaptive median and anisotropic nonlinear diffusion filters. Third, the image was segmented using the power watershed method coupled with a seeding algorithm based on geodesic reconstruction from the markers. If the resulting volume fraction did not match the target value quantified by chemical analysis of the sample, the BSE and SE signals were mixed in another ratio and the procedure was repeated until the target volume fraction was achieved. Otherwise, the segmented 3D image (replica) was accepted and its microstructure was thoroughly characterized with special attention paid to connectivity of the silicalite phase. In terms of the phase connectivity, Monte Carlo simulations based on the pure‐phase permeability values enabled us to calculate the effective permeability tensor, the main diagonal elements of which were compared with the experimental permeability. In line with the hypothesis proposed in our recent paper (?apek, P. et al. (2014) Comput. Mater. Sci. 89 , 142–156), the results confirmed that the existence of particle clusters was a key microstructural feature determining effective permeability.     

Electron and ion imaging of gland cells using the FIB/SEM system

The FIB/SEM system was satisfactorily used for scanning ion (SIM) and scanning electron microscopy (SEM) of gland epithelial cells of a terrestrial isopod Porcellio scaber (Isopoda, Crustacea). The interior of cells was exposed by site-specific in situ focused ion beam (FIB) milling. Scanning ion (SI) imaging was an adequate substitution for scanning electron (SE) imaging when charging rendered SE imaging impossible. No significant differences in resolution between the SI and SE images were observed. The contrast on both the SI and SE images is a topographic. The consequences of SI imaging are, among others, introduction of Ga⁺ ions on/into the samples and destruction of the imaged surface. These two characteristics of SI imaging can be used advantageously. Introduction of Ga⁺ ions onto the specimen neutralizes the charge effect in the subsequent SE imaging. In addition, the destructive nature of SI imaging can be used as a tool for the gradual removal of the exposed layer of the imaged surface, uncovering the structures lying beneath. Alternative SEM and SIM in combination with site-specific in situ FIB sample sectioning made it possible to image the submicrometre structures of gland epithelium cells with reproducibility, repeatability and in the same range of magnifications as in transmission electron microscopy (TEM). At the present state of technology, ultrastructural elements imaged by the FIB/SEM system cannot be directly identified by comparison with TEM images.     

Sample preparation and microscopical investigation techniques for metal and ceramics containing graphite and graphene‐like layered particles

Scanning electron microscopy (SEM) techniques are widely used in microstructural investigations of materials since it can provide surface morphology, topography, and chemical information. However, it is important to use correct imaging and sample preparation techniques to reveal the microstructures of materials composed of components with different polishing characteristics such as grey cast iron, graphene platelets (GPLs)‐added SiAlON composite, SiC and B₄C ceramics containing graphite or graphene‐like layered particles. In this study, all microstructural details of gray cast iron were successfully revealed by using argon ion beam milling as an alternative to the standard sample preparation method for cast irons, that is, mechanical polishing followed by chemical etching. The in‐lens secondary electron (I‐L‐SE) image was clearly displayed on the surface details of the graphites that could not be revealed by backscattered electron (BSE) and Everhart–Thornley secondary electron (E‐T SE) images. Mechanical polishing leads to pull‐out of GPLs from SiAlON surface, whereas argon ion beam milling preserved the GPLs and resulted in smooth surface. Grain and grain boundaries of polycrystalline SiC and B₄C were easily revealed by using I‐L SE image in the SEM after only mechanical polishing without any etching process. While the BSE and E‐T SE images did not clearly show the residual graphites in the microstructure, their distribution in the B₄C matrix was fully revealed in the I‐L SE image.     

Monte Carlo Simulation of CD‐SEM Images for Linewidth and Critical Dimension Metrology

In semiconductor industry, strict critical dimension control by using a critical dimension scanning electron microscope (CD‐SEM) is an extremely urgent task in near‐term years. A Monte Carlo simulation model for study of CD‐SEM image has been established, which is based on using Mott's cross section for electron elastic scattering and the full Penn dielectric function formalism for electron inelastic scattering and the associated secondary electron (SE) production. In this work, a systematic calculation of CD‐SEM line‐scan profiles and 2D images of trapezoidal Si lines has been performed by taking into account different experimental factors including electron beam condition (primary energy, probe size), line geometry (width, height, foot/corner rounding, sidewall angle, and roughness), material properties, and SE signal detection. The influences of these factors to the critical dimension metrology are investigated, leading to build a future comprehensive model‐based library. SCANNING 35: 127‐139, 2013. © 2012 Wiley Periodicals, Inc.     

High‐performance serial block‐face SEM of nonconductive biological samples enabled by focal gas injection‐based charge compensation

A longstanding limitation of imaging with serial block‐face scanning electron microscopy is specimen surface charging. This charging is largely due to the difficulties in making biological specimens and the resins in which they are embedded sufficiently conductive. Local accumulation of charge on the specimen surface can result in poor image quality and distortions. Even minor charging can lead to misalignments between sequential images of the block‐face due to image jitter. Typically, variable‐pressure SEM is used to reduce specimen charging, but this results in a significant reduction to spatial resolution, signal‐to‐noise ratio and overall image quality. Here we show the development and application of a simple system that effectively mitigates specimen charging by using focal gas injection of nitrogen over the sample block‐face during imaging. A standard gas injection valve is paired with a precisely positioned but retractable application nozzle, which is mechanically coupled to the reciprocating action of the serial block‐face ultramicrotome. This system enables the application of nitrogen gas precisely over the block‐face during imaging while allowing the specimen chamber to be maintained under high vacuum to maximise achievable SEM image resolution. The action of the ultramicrotome drives the nozzle retraction, automatically moving it away from the specimen area during the cutting cycle of the knife. The device described was added to a Gatan 3View system with minimal modifications, allowing high‐resolution block‐face imaging of even the most charge prone of epoxy‐embedded biological samples.     

Signal‐to‐noise ratio enhancement on SEM images using a cubic spline interpolation with Savitzky–Golay filters and weighted least squares error

A new technique based on cubic spline interpolation with Savitzky–Golay smoothing using weighted least squares error filter is enhanced for scanning electron microscope (SEM) images. A diversity of sample images is captured and the performance is found to be better when compared with the moving average and the standard median filters, with respect to eliminating noise. This technique can be implemented efficiently on real‐time SEM images, with all mandatory data for processing obtained from a single image. Noise in images, and particularly in SEM images, are undesirable. A new noise reduction technique, based on cubic spline interpolation with Savitzky–Golay and weighted least squares error method, is developed. We apply the combined technique to single image signal‐to‐noise ratio estimation and noise reduction for SEM imaging system. This autocorrelation‐based technique requires image details to be correlated over a few pixels, whereas the noise is assumed to be uncorrelated from pixel to pixel. The noise component is derived from the difference between the image autocorrelation at zero offset, and the estimation of the corresponding original autocorrelation. In the few test cases involving different images, the efficiency of the developed noise reduction filter is proved to be significantly better than those obtained from the other methods. Noise can be reduced efficiently with appropriate choice of scan rate from real‐time SEM images, without generating corruption or increasing scanning time.     

A comparison of conventional Everhart-Thornley style and in-lens secondary electron detectors: a further variable in scanning electron microscopy

The secondary electron (SE) imaging of several samples across a range of scanning electron microscopes (SEM) and SE detectors under matched operating conditions has generated a highly variable image data set. Using microanalytical conditions (10-15?kV), images from in-column SE detectors reveal the presence of surface films and contaminants that are invisible to conventional Everhart-Thornley SE detectors under the same conditions. Data from studying the effects of working distance, the image resolution derived through contrast transfer function analysis and electrostatic mirror imaging of the SE detectors in operation combine with other studies to suggest that the classically defined SE1 component can be separated from other SE components. SE images obtained by tailored mechanical design and energy-filtering will provide SE images with probe-sized resolution and dominated by surface detail currently only seen in low-voltage SEM, potentially even from thermionic-sourced columns.     

Improved Zernike‐type phase contrast for transmission electron microscopy

Zernike phase contrast has been recognized as a means of recording high‐resolution images with high contrast using a transmission electron microscope. This imaging mode can be used to image typical phase objects such as unstained biological molecules or cryosections of biological tissue. According to the original proposal discussed in Danev and Nagayama (2001) and references therein, the Zernike phase plate applies a phase shift of π/2 to all scattered electron beams outside a given scattering angle and an image is recorded at Gaussian focus or slight underfocus (below Scherzer defocus). Alternatively, a phase shift of ‐π/2 is applied to the central beam using the Boersch phase plate. The resulting image will have an almost perfect contrast transfer function (close to 1) from a given lowest spatial frequency up to a maximum resolution determined by the wave length, the amount of defocus and the spherical aberration of the microscope. In this paper, I present theory and simulations showing that this maximum spatial frequency can be increased considerably without loss of contrast by using a Zernike or Boersch phase plate that leads to a phase shift between scattered and unscattered electrons of only π /4, and recording images at Scherzer defocus. The maximum resolution can be improved even more by imaging at extended Scherzer defocus, though at the cost of contrast loss at lower spatial frequencies.     

Registration of phase‐contrast images in propagation‐based X‐ray phase tomography

X‐ray phase tomography aims at reconstructing the 3D electron density distribution of an object. It offers enhanced sensitivity compared to attenuation‐based X‐ray absorption tomography. In propagation‐based methods, phase contrast is achieved by letting the beam propagate after interaction with the object. The phase shift is then retrieved at each projection angle, and subsequently used in tomographic reconstruction to obtain the refractive index decrement distribution, which is proportional to the electron density. Accurate phase retrieval is achieved by combining images at different propagation distances. For reconstructions of good quality, the phase‐contrast images recorded at different distances need to be accurately aligned. In this work, we characterise the artefacts related to misalignment of the phase‐contrast images, and investigate the use of different registration algorithms for aligning in‐line phase‐contrast images. The characterisation of artefacts is done by a simulation study and comparison with experimental data. Loss in resolution due to vibrations is found to be comparable to attenuation‐based computed tomography. Further, it is shown that registration of phase‐contrast images is nontrivial due to the difference in contrast between the different images, and the often periodical artefacts present in the phase‐contrast images if multilayer X‐ray optics are used. To address this, we compared two registration algorithms for aligning phase‐contrast images acquired by magnified X‐ray nanotomography: one based on cross‐correlation and one based on mutual information. We found that the mutual information‐based registration algorithm was more robust than a correlation‐based method.     

Three‐dimensional imaging of whole mouse models: comparing nondestructive X‐ray phase‐contrast micro‐CT with cryotome‐based planar epi‐illumination imaging

In this study, we compare two evolving techniques for obtaining high‐resolution 3D anatomical data of a mouse specimen. On the one hand, we investigate cryotome‐based planar epi‐illumination imaging (cryo‐imaging). On the other hand, we examine X‐ray phase‐contrast micro‐computed tomography (micro‐CT) using synchrotron radiation. Cryo‐imaging is a technique in which an electron multiplying charge coupled camera takes images of a cryo‐frozen specimen during the sectioning process. Subsequent image alignment and virtual stacking result in volumetric data. X‐ray phase‐contrast imaging is based on the minute refraction of X‐rays inside the specimen and features higher soft‐tissue contrast than conventional, attenuation‐based micro‐CT. To explore the potential of both techniques for studying whole mouse disease models, one mouse specimen was imaged using both techniques. Obtained data are compared visually and quantitatively, specifically with regard to the visibility of fine anatomical details. Internal structure of the mouse specimen is visible in great detail with both techniques and the study shows in particular that soft‐tissue contrast is strongly enhanced in the X‐ray phase images compared to the attenuation‐based images. This identifies phase‐contrast micro‐CT as a powerful tool for the study of small animal disease models.     

Correlation of two‐photon in vivo imaging and FIB/SEM microscopy

Advances in the understanding of brain functions are closely linked to the technical developments in microscopy. In this study, we describe a correlative microscopy technique that offers a possibility of combining two‐photon in vivo imaging with focus ion beam/scanning electron microscope (FIB/SEM) techniques. Long‐term two‐photon in vivo imaging allows the visualization of functional interactions within the brain of a living organism over the time, and therefore, is emerging as a new tool for studying the dynamics of neurodegenerative diseases, such as Alzheimer's disease. However, light microscopy has important limitations in revealing alterations occurring at the synaptic level and when this is required, electron microscopy is mandatory. FIB/SEM microscopy is a novel tool for three‐dimensional high‐resolution reconstructions, since it acquires automated serial images at ultrastructural level. Using FIB/SEM imaging, we observed, at 10 nm isotropic resolution, the same dendrites that were imaged in vivo over 9 days. Thus, we analyzed their ultrastructure and monitored the dynamics of the neuropil around them. We found that stable spines (present during the 9 days of imaging) formed typical asymmetric contacts with axons, whereas transient spines (present only during one day of imaging) did not form a synaptic contact. Our data suggest that the morphological classification that was assigned to a dendritic spine according to the in vivo images did not fit with its ultrastructural morphology. The correlative technique described herein is likely to open opportunities for unravelling the earlier unrecognized complexity of the nervous system.     

Three‐dimensional microstructure characterisation of thermoplastic polyolefin blends

The size, shape and distribution of different phases in thermoplastic polyolefin (TPO) blends and composites are critical to the properties of the materials, but can be difficult to characterise. Here we report the combination of heavy metal staining and focused ion beam – scanning electron microscopy (FIB‐SEM) to reveal the three‐dimensional (3D) structure of an elastomer‐modified poly(propylene) and a talc filled elastomer‐modified poly(propylene). High‐quality, high‐resolution serial images were collected and the 3D structures were characterised quantitatively.     

Morphological segmentation of FIB‐SEM data of highly porous media

Nanoporous materials play an important role in modern batteries as well as fuel cells. The materials microstructure needs to be analyzed as it determines the electrochemical properties. However, the microstructure is too fine to be resolved by microcomputed tomography. The method of choice to analyze the microstructure is focused ion beam nanotomography (FIB‐SEM). However, the reconstruction of the porous 3D microstructure from FIB‐SEM image data in general has been an unsolved problem so far. In this paper, we present a new method using morphological operations. First, features are extracted from the data. Subsequently, these features are combined to an initial segmentation, that is then refined by a constrained watershed transformation. We evaluate our method with synthetic data, generated by a simulation of the FIB‐SEM imaging process. We compare the ground truth in the simulated data to the segmentation result. The new method is found to produce a much smaller error than existing techniques.     

Characterization of the μ and P phase precipitates in the CMSX‐4 single crystal superalloy

A combination of scanning electron microscopy (SEM), transmission electron microscopy (TEM) and scanning‐transmission electron microscopy (STEM) using high‐angle annular‐dark‐field (HAADF) imaging, focussed ion beam‐ scanning electron microscopy (FIB‐SEM) tomography, selected area electron diffraction with beam precession (PED), as well as spatially resolved energy‐dispersive X‐ray spectroscopy (EDS) and electron energy loss spectroscopy (EELS), was used to investigate topologically close‐packed (TCP) phases, occurring in the CMSX‐4 superalloy subjected to high temperature annealing and creep deformation. Structural and chemical analyses were performed to identify the TCP phases and provide information concerning the compositional partitioning of elements between them. The results of SEM and FIB‐SEM tomography revealed the presence of merged TCP particles, which were identified by TEM and PED analysis as coprecipitates of the μ and P phases. Inside the TCP particles that were several micrometres in size, platelets of alternating μ and P phases of nanometric width were found. The combination of STEM‐HAADF imaging with spatially resolved EDS and EELS microanalysis allowed determination of the significant partitioning of the constituent elements between the μ and P phases.     

On the role of electron–ion recombination in low vacuum scanning electron microscopy

Here we demonstrate the effects of electron–ion recombination on imaging signals utilized in low vacuum scanning electron microscopes (SEMs). The presented results show that, under normal operating conditions, recombination of ionized gas molecules with secondary electrons (SEs) suppresses a significant fraction of emitted electrons. If the ion flux (and hence the spatial dependence of the SE–ion recombination rate) is laterally inhomogeneous across the imaged region of a specimen, contrast in SE images can be influenced and in some cases (under conditions of high detector field strength and long ionic mean free path) dominated by variations in the recombination rate. Consequently, SE images of features such as topographic asperities can exhibit edge‐darkening, leading to inversion of some topographic contrast. Recognition of the extent and nature of electron–ion recombination is required for a correct understanding of processes occurring in variable pressure SEMs and, subsequently, for models of image formation.     

Interpretation of secondary electron images obtained using a low vacuum SEM

Charging of insulators in a variable pressure environment was investigated in the context of secondary electron (SE) image formation. Sample charging and ionized gas molecules present in a low vacuum specimen chamber can give rise to SE image contrast. "Charge-induced" SE contrast reflects lateral variations in the charge state of a sample caused by electron irradiation during and prior to image acquisition. This contrast corresponds to SE emission current alterations produced by sub-surface charge deposited by the electron beam. "Ion-induced" contrast results from spatial inhomogeneities in the extent of SE signal inhibition caused by ions in the gaseous environment of a low vacuum scanning electron microscope (SEM). The inhomogeneities are caused by ion focusing onto regions of a sample that correspond to local minima in the magnitude of the surface potential (generated by sub-surface trapped charge), or topographic asperities. The two types of contrast exhibit characteristic dependencies on microscope operating parameters such as scan speed, beam current, gas pressure, detector bias and working distance. These dependencies, explained in terms of the behavior of the gaseous environment and sample charging, can serve as a basis for a correct interpretation of SE images obtained using a low vacuum SEM.     

Automated in‐chamber specimen coating for serial block‐face electron microscopy

When imaging insulating specimens in a scanning electron microscope, negative charge accumulates locally (‘sample charging’). The resulting electric fields distort signal amplitude, focus and image geometry, which can be avoided by coating the specimen with a conductive film prior to introducing it into the microscope chamber. This, however, is incompatible with serial block‐face electron microscopy (SBEM), where imaging and surface removal cycles (by diamond knife or focused ion beam) alternate, with the sample remaining in place. Here we show that coating the sample after each cutting cycle with a 1–2 nm metallic film, using an electron beam evaporator that is integrated into the microscope chamber, eliminates charging effects for both backscattered (BSE) and secondary electron (SE) imaging. The reduction in signal‐to‐noise ratio (SNR) caused by the film is smaller than that caused by the widely used low‐vacuum method. Sample surfaces as large as 12 mm across were coated and imaged without charging effects at beam currents as high as 25 nA. The coatings also enabled the use of beam deceleration for non‐conducting samples, leading to substantial SNR gains for BSE contrast. We modified and automated the evaporator to enable the acquisition of SBEM stacks, and demonstrated the acquisition of stacks of over 1000 successive cut/coat/image cycles and of stacks using beam deceleration or SE contrast.     

Focused ion beam scanning electron microscopy in biology

Since the end of the last millennium, the focused ion beam scanning electron microscopy (FIB‐SEM) has progressively found use in biological research. This instrument is a scanning electron microscope (SEM) with an attached gallium ion column and the 2 beams, electrons and ions (FIB) are focused on one coincident point. The main application is the acquisition of three‐dimensional data, FIB‐SEM tomography. With the ion beam, some nanometres of the surface are removed and the remaining block‐face is imaged with the electron beam in a repetitive manner. The instrument can also be used to cut open biological structures to get access to internal structures or to prepare thin lamella for imaging by (cryo‐) transmission electron microscopy. Here, we will present an overview of the development of FIB‐SEM and discuss a few points about sample preparation and imaging.     

Post‐thinning using Ar ion‐milling system for transmission electron microscopy specimens prepared by focused ion beam system

We investigate Ar ion‐milling rates and Ga‐ion induced damage on sample surfaces of Si and GaAs single crystals prepared by focused ion beam (FIB) method for transmission electron microscopy observation. The convergent beam electron diffraction technique with Bloch simulation is used to measure the thickness of the Ar‐ion milled samples to calculate the milling rates of Si and GaAs single crystals. The measurement shows that an amorphous layer is formed on the sample surface and can be removed by further Ar‐ion milling. In addition, the local symmetry breaking induced by FIB is investigated using quantitative symmetry measurement. The FIBed‐GaAs sample shows local symmetry breaking after FIB milling, although the FIBed‐Si sample has no considerable symmetry breaking.