Focused ion beam milling of vitreous water: prospects for an alternative to cryo-ultramicrotomy of frozen-hydrated biological samples

The feasibility of using a focused ion beam (FIB) for the purpose of thinning vitreously frozen biological specimens for transmission electron microscopy (TEM) was explored. A concern was whether heat transfer beyond the direct ion interaction layer might devitrify the ice. To test this possibility, we milled vitreously frozen water on a standard TEM grid with a 30‐keV Ga⁺ beam, and cryo‐transferred the grid to a TEM for examination. Following FIB milling of the vitreous ice from a thickness of approximately 1200 nm to 200–150 nm, changes characteristic of heat‐induced devitrification were not observed by TEM, in either images or diffraction patterns. Although numerous technical challenges remain, it is anticipated that ‘cryo‐FIB thinning’ of bulk frozen‐hydratred material will be capable of producing specimens for TEM cryo‐tomography with much greater efficiency than cryo‐ultramicrotomy, and without the specimen distortions and handling difficulties of the latter.     

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.     

Argon broad ion beam tomography in a cryogenic scanning electron microscope: a novel tool for the investigation of representative microstructures in sedimentary rocks containing pore fluid

The contribution describes the implementation of a broad ion beam (BIB) polisher into a scanning electron microscope (SEM) functioning at cryogenic temperature (cryo). The whole system (BIB‐cryo‐SEM) provides a first generation of a novel multibeam electron microscope that combines broad ion beam with cryogenic facilities in a conventional SEM to produce large, high‐quality cross‐sections (up to 2 mm²) at cryogenic temperature to be imaged at the state‐of‐the‐art SEM resolution. Cryogenic method allows detecting fluids in their natural environment and preserves samples against desiccation and dehydration, which may damage natural microstructures. The investigation of microstructures in the third dimension is enabled by serial cross‐sectioning, providing broad ion beam tomography with slices down to 350 nm thick. The functionalities of the BIB‐cryo‐SEM are demonstrated by the investigation of rock salts (synthetic coarse‐grained sodium chloride synthesized from halite‐brine mush cold pressed at 150 MPa and 4.5 GPa, and natural rock salt mylonite from a salt glacier at Qom Kuh, central Iran). In addition, results from BIB‐cryo‐SEM on a gas shale and Boom Clay are also presented to show that the instrument is suitable for a large range of sedimentary rocks. For the first time, pore and grain fabrics of preserved host and reservoir rocks can be investigated at nm‐scale range over a representative elementary area. In comparison with the complementary and overlapping performances of the BIB‐SEM method with focused ion beam‐SEM and X‐ray tomography methods, the BIB cross‐sectioning enables detailed insights about morphologies of pores at greater resolution than X‐ray tomography and allows the production of large representative surfaces suitable for FIB‐SEM investigations of a specific representative site within the BIB cross‐section.     

Pros and cons: cryo-electron microscopic evaluation of block faces versus cryo-sections from frozen-hydrated skin specimens prepared by different techniques

Over the last two decades, several different preparative techniques have been developed to investigate frozen‐hydrated biological samples by electron microscopy. In this article, we describe an alternative approach that allows either ultrastructural investigations of frozen human skin at a resolution better than 15 nm or sample throughput that is sufficiently high enough for quantitative morphological analysis. The specimen preparation method we describe is fast, reproducible, does not require much user experience or elaborate equipment. We compare high‐pressure freezing with plunge freezing, and block faces with frozen‐hydrated slices (sections), to study variations in cell thickness upon hydration changes. Plunge freezing is optimal for morphological and stereological investigations of structures with low water content. By contrast, high‐pressure freezing proved optimal for high‐resolution studies and provided the best ultrastructural preservation. A combination of these fast‐freezing techniques with cryo‐ultramicrotomy yielded well‐preserved block faces of the original biological material. Here we show that these block faces did not exhibit any of the artefacts normally associated with cryo‐sections, and – after evaporating a heavy metal and carbon onto the surface – are stable enough in the electron beam to provide high‐resolution images of large surface areas for statistical analysis in a cryo‐SEM (scanning electron microscope). Because the individual preparation steps use only standard equipment and do not require much experience from the experimenter, they are generally more usable, making this approach an interesting alternative to other methods for the ultrastructural investigation of frozen‐hydrated material.     

Making the practically impossible “Merely difficult”—Cryogenic FIB lift‐out for “Damage free” soft matter imaging

The preparation of thinned lamellae from bulk samples for transmission electron microscopy (TEM) analysis has been possible in the focussed ion beam scanning electron microscope (FIB‐SEM) for over 20 years via the in situ lift‐out method. Lift‐out offers a fast and site specific preparation method for TEM analysis, typically in the field of materials science. More recently it has been applied to a low‐water content biological sample (Rubino 2012). This work presents the successful lift‐out of high‐water content lamellae, under cryogenic conditions (cryo‐FIB lift‐out) and using a nanomanipulator retaining its full range of motion, which are advances on the work previously done by Rubino (2012). Strategies are explored for maintaining cryogenic conditions, grid attachment using cryo‐condensation of water and protection of the lamella when transferring to the TEM. Microsc. Res. Tech. 79:298–303, 2016. © 2016 Wiley Periodicals, Inc.     

Focussed ion beam milling at grazing incidence angles

A combined scanning electron microscope and focussed ion beam instrument is suitable for micro- and nanopatterning, cross-sectioning and subsequent imaging, of specimens at room temperature as well as under cryo conditions. In order to reveal internal details, samples are conventionally milled with the ion beam positioned perpendicular to the sample surface. Using this approach certain limitations are frequently encountered, e.g. accumulation of redeposited material, shadowing effects, image distortion and a limited imaging area. Here we show an approach in which samples are pre-trimmed using a microtome to obtain a sample block face that is parallel to the ion beam. This new grazing incidence geometry eliminates the need for removal of bulk material with the ion beam and enables immediate fine polishing of a pre-selected area of interest. Many of the limitations previously described are avoided and in addition milling time is reduced, whilst creating larger cross-sectional areas. Another advantage is that electron imaging can be accomplished by tilting the sample surface perpendicular to the electron beam, providing a geometrically undistorted image. The proposed approach is suitable for materials that can be microtomed, both in ambient and cryogenic conditions, and proves to be of particular benefit for biological and food samples.     

Novel techniques of preparing TEM samples for characterization of irradiation damage

Focus ion beam preparation of transmission electron microscopy (TEM) samples has become increasingly popular due to the relative ease of extraction of TEM foils from specific locations within a larger sample. However the sputtering damage induced by Ga ion bombardment in focus ion beam means that traditional electropolishing may be a preferable method. First, we describe a special electropolishing method for the preparation of irregular TEM samples from ex‐service nuclear reactor components, spring‐shaped spacers. This method has also been used to prepare samples from a nonirradiated component for a TEM in situ heavy ion irradiation study. Because the specimen size is small (0.7 × 0.7 × 3 mm), a sandwich installation is adopted to obtain high quality polishing. Second, we describe some modifications to a conventional TEM cross‐section sample preparation method that employs Ni electroplating. There are limitations to this method when preparing cross‐section samples from either (1) metals which are difficult to activate for electroplating, or (2) a heavy ion irradiated foil with a very shallow damage layer close to the surface, which may be affected by the electroplating process. As a consequence, a novel technique for preparing cross‐section samples was developed and is described.     

Transmission electron microscopy of fluorapatite–gelatine composite particles prepared using focused ion beam milling

In this paper, synthetic fluorapatite–gelatine composite particles are prepared for transmission electron microscopy (TEM) studies using two methods based on focused ion beam (FIB) milling. TEM studies on the FIB‐prepared specimens are compared with TEM observations on samples prepared using an ultramicrotome. The results show that ultramicrotome slicing causes significant cracking of the apatite, whereas the ion beam can be used to make high‐quality, crack‐free specimens with no apparent ion beam‐induced damage. The TEM observations on the FIB‐prepared samples confirm that the fluorapatite composite particles are composed of elongated, preferentially orientated grains and reveal that the grain boundaries contain many small interstices filled with an amorphous phase.     

Revealing local variations in nanoparticle size distributions in supported catalysts: a generic TEM specimen preparation method

The specimen preparation method is crucial for how much information can be gained from transmission electron microscopy (TEM) studies of supported nanoparticle catalysts. The aim of this work is to develop a method that allows for observation of size and location of nanoparticles deposited on a porous oxide support material. A bimetallic Pt‐Pd/Al₂O₃ catalyst in powder form was embedded in acrylic resin and lift‐out specimens were extracted using combined focused ion beam/scanning electron microscopy (FIB/SEM). These specimens allow for a cross‐section view across individual oxide support particles, including the unaltered near surface region of these particles. A site‐dependent size distribution of Pt‐Pd nanoparticles was revealed along the radial direction of the support particles by scanning transmission electron microscopy (STEM) imaging. The developed specimen preparation method enables obtaining information about the spatial distribution of nanoparticles in complex support structures which commonly is a challenge in heterogeneous catalysis.     

Static and dynamic experiments in cryo-electron microscopy: comparative observations using high-vacuum, low-voltage and low-vacuum SEM

We carried out a unique comparative study between three modes of cryo‐scanning electron imaging: high‐vacuum, low‐voltage and low‐vacuum, using ice cream as a model system. Specimens were investigated both with and without a conductive coating (Au/Pd) and at temperatures for which ice either remains fully frozen (< ?110 °C) or undergoes sublimation (?110 to ?90 °C). At high magnification, high‐vacuum imaging of coated specimens gave the best results for ‘static’ specimens (i.e. containing fully frozen ice). Low voltages, such as 1 kV, could be used for imaging uncoated specimens at high vacuum, although slight ‘classical’ charging artefacts remained an issue, and the reduced electron beam penetration tended to decrease the definition between different microstructural features. However, this mode was useful for observing in situ sublimation from uncoated specimens. Low‐vacuum mode, involving small partial pressures of nitrogen gas, was particularly suited to in situ sublimation work: when sublimation was carried out in low vacuum in the absence of an anti‐contaminator plate, sublimation rates were significantly reduced. This is attributed to a small partial pressure of sublimated water vapour remaining near the specimen surface, enhancing thermodynamic stability.     

Ion beam polishing for three‐dimensional electron backscattered diffraction

Serial sectioning by focused ion beam milling for three‐dimensional electron backscatter diffraction (3D‐EBSD) can create surface damage and amorphization in certain materials and consequently reduce the EBSD signal quality. Poor EBSD signal causes longer data acquisition time due to signal averaging and/or poor 3D‐EBSD data quality. In this work a low kV focused ion beam was successfully implemented to automatically polish surfaces during 3D‐EBSD of La‐ and Nb‐doped strontium titanate of volume 12.6 × 12.6 × 3.0 μm. The key to achieving this technique is the combination of a defocused low kV high current ion beam and line scan milling. The line scan was used to restrict polishing to the sample surface and the ion beam was defocused to ensure the beam contacted the complete sample surface. In this study 1 min polishing time per slice increases total acquisition time by approximately 3.3% of normal 3D‐EBSD mapping compared to a significant increase of indexing percentage and pattern quality. The polishing performance in this investigation is discussed, and two potential methods for further improvement are presented.     

Off-axis electron holography of electrostatic potentials in unbiased and reverse biased focused ion beam milled semiconductor devices

Off‐axis electron holography in the transmission electron microscope (TEM) is used to measure two‐dimensional electrostatic potentials in both unbiased and reverse biased silicon specimens that each contain a single p–n junction. All the specimens are prepared for examination in the TEM using focused ion beam (FIB) milling. The in situ electrical biasing experiments make use of a novel specimen geometry, which is based on a combination of cleaving and FIB milling. The design and construction of an electrical biasing holder are described, and the effects of TEM specimen preparation on the electrostatic potential in the specimen, as well as on fringing fields beyond the specimen surface, are assessed.     

Direct observation of liquid crystals using cryo‐TEM: Specimen preparation and low‐dose imaging

Liquid crystals (LCs) represent a challenging group of materials for direct transmission electron microscopy (TEM) studies due to the complications in specimen preparation and the severe radiation damage. In this paper, we summarize a series of specimen preparation methods, including thin film and cryo‐sectioning approaches, as a comprehensive toolset enabling high‐resolution direct cryo‐TEM observation of a broad range of LCs. We also present comparative analysis using cryo‐TEM and replica freeze‐fracture TEM on both thermotropic and lyotropic LCs. In addition to the revisits of previous practices, some new concepts are introduced, e.g., suspended thermotropic LC thin films, combined high‐pressure freezing and cryo‐sectioning of lyotropic LCs, and the complementary applications of direct TEM and indirect replica TEM techniques. The significance of subnanometer resolution cryo‐TEM observation is demonstrated in a few important issues in LC studies, including providing direct evidences for the existence of nanoscale smectic domains in nematic bent‐core thermotropic LCs, comprehensive understanding of the twist‐bend nematic phase, and probing the packing of columnar aggregates in lyotropic chromonic LCs. Direct TEM observation opens ways to a variety of TEM techniques, suggesting that TEM (replica, cryo, and in situ techniques), in general, may be a promising part of the solution to the lack of effective structural probe at the molecular scale in LC studies. Microsc. Res. Tech. 77:754–772, 2014. © 2014 Wiley Periodicals, Inc.     

Electron backscatter diffraction applied to lithium sheets prepared by broad ion beam milling

Due to its very low hardness and atomic number, pure lithium cannot be prepared by conventional methods prior to scanning electron microscopy analysis. Here, we report on the characterization of pure lithium metallic sheets used as base electrodes in the lithium‐ion battery technology using electron backscatter diffraction (EBSD) and X‐ray microanalysis using energy dispersive spectroscopy (EDS) after the sheet surface was polished by broad argon ion milling (IM). No grinding and polishing were necessary to achieve the sufficiently damage free necessary for surface analysis. Based on EDS results the impurities could be characterized and EBSD revealed the microsctructure and microtexture of this material with accuracy. The beam damage and oxidation/hydration resulting from the intensive use of IM and the transfer of the sample into the microscope chamber was estimated to be <50 nm. Despite the fact that the IM process generates an increase of temperature at the specimen surface, it was assumed that the milling parameters were sufficient to minimize the heating effect on the surface temperature. However, a cryo‐stage should be used if available during milling to guaranty a heating artefact free surface after the milling process. Microsc. Res. Tech., 78:30?39, 2015. © 2014 Wiley Periodicals, Inc.     

Dopant profiling of focused ion beam milled semiconductors using off-axis electron holography; reducing artifacts,extending detection limits and reducing the effects of gallium implantation

Focused ion beam (FIB) milling is one of the few specimen preparation techniques that can be used to prepare parallel-sided specimens with nm-scale site specificity for examination using off-axis electron holography in the transmission electron microscope (TEM). However, FIB milling results in the implantation of Ga, the formation of amorphous surface layers and the introduction of defects deep into the specimens. Here we show that these effects can be reduced by lowering the operating voltage of the FIB and by annealing the specimens at low temperature. We also show that the electrically inactive thickness is dependent on both the operating voltage and type of ion used during FIB milling.     

Site-specific structural investigations of oxidized nickel samples modified by plasma erosion processes

A focused ion beam was employed for local target preparation for EBSD analysis. The volume of the ion‐solid interaction is well below 50 nm at glancing incidence for metallic and transition metal oxide samples. Therefore, focused ion beam can successfully be used for electron backscatter diffraction (EBSD) sample preparation. The sample investigated consists of Ni covered with a NiO layer of ～5 μm thickness. Focused ion beam cross‐sectioning of these layers and subsequent electron imaging in addition to EBSD maps shows a bimodal structure of the oxide layer. In order to test the potential of such oxidized samples as electrode materials, single spark erosion experiments were performed. The erosion craters have diameters up to 40 μm and have a depth corresponding to the thickness of the oxide layer. In addition, a deformation zone produced by thermoshock accompanies the formation of the crater. This deformation zone was further investigated by EBSD analysis using a new way of sample preparation employing the focused ion beam technology. This target preparation routine is called Volume of Interest Transfer and has the potential of providing a full three‐dimensional characterization.     

Ex vivo characterization of human atherosclerotic iliac plaque components using cryo‐imaging

We characterized atherosclerotic plaque components with a novel cryo‐imaging system in lieu of standard histological methods commonly used for imaging validation and research endpoints. We aim to accurately identify plaque tissue types from fresh cadaver specimens rapidly (less than 5 h) in three dimensions for large specimens (up to 4 cm vessel segments). A single‐blind validation study was designed to determine sensitivity, specificity and inter‐rater agreement (Fleiss' Kappa) of cryo‐imaging tissue types with histology as the gold standard. Six naïve human raters identified 344 tissue type samples in 36 cryo‐image sets after being trained. Tissue type sensitivities are as follows: greater than 90% for adventitia, media‐related, smooth muscle cell ingrowth, external elastic lamina, internal elastic lamina, fibrosis, dense calcification and haemorrhage; greater than 80% for lipid and light calcification; and greater than 50% for cholesterol clefts. Specificities were greater than 95% for all tissue types. The results demonstrate convincingly that cryo‐imaging can be used to accurately identify most tissue types. If the cryo‐imaging data are entered into visualization software, three‐dimensional renderings of the plaque can be generated to visualize and quantify plaque components.     

Cryogenic‐temperature electron microscopy direct imaging of carbon nanotubes and graphene solutions in superacids

Cryogenic electron microscopy (cryo‐EM) is a powerful tool for imaging liquid and semiliquid systems. While cryogenic transmission electron microscopy (cryo‐TEM) is a standard technique in many fields, cryogenic scanning electron microscopy (cryo‐SEM) is still not that widely used and is far less developed. The vast majority of systems under investigation by cryo‐EM involve either water or organic components. In this paper, we introduce the use of novel cryo‐TEM and cryo‐SEM specimen preparation and imaging methodologies, suitable for highly acidic and very reactive systems. Both preserve the native nanostructure in the system, while not harming the expensive equipment or the user. We present examples of direct imaging of single‐walled, multiwalled carbon nanotubes and graphene, dissolved in chlorosulfonic acid and oleum. Moreover, we demonstrate the ability of these new cryo‐TEM and cryo‐SEM methodologies to follow phase transitions in carbon nanotube (CNT)/superacid systems, starting from dilute solutions up to the concentrated nematic liquid‐crystalline CNT phases, used as the ‘dope’ for all‐carbon‐fibre spinning. Originally developed for direct imaging of CNTs and graphene dissolution and self‐assembly in superacids, these methodologies can be implemented for a variety of highly acidic systems, paving a way for a new field of nonaqueous cryogenic electron microscopy.     

Preparation of (InGa)As/GaAs materials for TEM by one side non-rotation ion beam thinning

A technique is described for the preparation of thin specimens for transmission electron microscopy (TEM) of (InGa)As/GaAs multilayered materials. In this technique, a shielding method is used for selective-area perforation by ion beam thinning. Thin cross-sectional specimen slices are mechanically pre-thinned to about 30 μm and then thinned by ion sputtering from one side of the specimen at a time without rotation of the specimen stage. No direct ion sputtering occurs at the growth surface of the specimen so that a specimen with thin areas containing the desired near-surface structures can be obtained. The recipe for this technique is given in detail. A patterning method for increasing the size of the thin area for TEM investigation is also described. It is shown that a smooth surface can be obtained by sputtering without rotating the stage if obstacles that produce redeposits onto the sputtered surface are removed.     

Use of permanent marker to deposit a protection layer against FIB damage in TEM specimen preparation

Permanent marker deposition (PMD), which creates permanent writing on an object with a permanent marker, was investigated as a method to deposit a protection layer against focused ion beam damage. PMD is a simple, fast and cheap process. Further, PMD is excellent in filling in narrow and deep trenches, enabling damage‐free observation of high aspect ratio structures with atomic resolution in transmission electron microscopy (TEM). The microstructure, composition, gap filling ability and planarization of the PMD layer were studied using dual beam focused ion beam, transmission electron microscopy, energy dispersive X‐ray spectroscopy and electron energy loss spectroscopy. It was found that a PMD layer is basically an amorphous carbon structure, and that such a layer should be at least 65 nm thick to protect a surface against 30 keV focused ion beam damage. We suggest that such a PMD layer can be an excellent protection layer to maintain a pristine sample structure against focused ion beam damage during transmission electron microscopy specimen preparation.