Combining Ar ion milling with FIB lift-out techniques to prepare high quality site-specific TEM samples

Focused ion beam (FIB) techniques can prepare site‐specific transmission electron microscopy (TEM) cross‐section samples very quickly but they suffer from beam damage by the high energy Ga⁺ ion beam. An amorphous layer about 20–30 nm thick on each side of the TEM lamella and the supporting carbon film makes FIB‐prepared samples inferior to the traditional Ar⁺ thinned samples for some investigations such as high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). We have developed techniques to combine broad argon ion milling with focused ion beam lift‐out methods to prepare high‐quality site‐specific TEM cross‐section samples. Site‐specific TEM cross‐sections were prepared by FIB and lifted out using a Narishige micromanipulator onto a half copper‐grid coated with carbon film. Pt deposition by FIB was used to bond the lamellae to the Cu grid, then the coating carbon film was removed and the sample on the bare Cu grid was polished by the usual broad beam Ar⁺ milling. By doing so, the thickness of the surface amorphous layers is reduced substantially and the sample quality for TEM observation is as good as the traditional Ar⁺ milled samples.     

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.     

Controlling FIB‐SBEM slice thickness by monitoring the transmitted ion beam

Serial block‐face electron microscopy with focused ion beam cutting suffers from cutting artefacts caused by changes in the relative position of beam and sample, which are, for example, inevitable when reconditioning the ion gun. The latter has to be done periodically, which limits the continuous stack‐acquisition time to several days. Here, we describe a method for controlling the ion‐beam position that is based on detecting that part of the ion beam that passes the sample (transmitted beam). We find that the transmitted‐beam current decreases monotonically as the beam approaches the sample and can be used to determine the relative position of beam and sample to an accuracy of around one nanometre. By controlling the beam approach using this current as the feedback parameter, it is possible to ion‐mill consecutive 5 nm slices without detectable variations in thickness even in the presence of substantial temperature fluctuations and to restart the acquisition of a stack seamlessly. In addition, the use of a silicon junction detector instead of the in‐column detector is explored.     

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.     

Spin‐coated epoxy resin embedding technique enables facile SEM/FIB thickness determination of porous metal oxide ultra‐thin films

A facile nonsubjective method was designed to measure porous nonconductive iron oxide film thickness using a combination of a focused ion beam (FIB) and scanning electron microscopy. Iron oxide films are inherently nonconductive and porous, therefore the objective of this investigation was to optimize a methodology that would increase the conductivity of the film to facilitate high resolution imaging with a scanning electron microscopy and to preserve the porous nature of the film that could potentially be damaged by the energy of the FIB. Sputter coating the sample with a thin layer of iridium before creating the cross section with the FIB decreased sample charging and drifting, but differentiating the iron layer from the iridium coating with backscattered electron imaging was not definitive, making accurate assumptions of the delineation between the two metals difficult. Moreover, the porous nature of the film was lost due to beam damage following the FIB process. A thin layer plastication technique was therefore used to embed the porous film in epoxy resin that would provide support for the film during the FIB process. However, the thickness of the resin created using conventional thin layer plastication processing varied across the sample, making the measuring process only possible in areas where the resin layer was at its thinnest. Such variation required navigating the area for ideal milling areas, which increased the subjectivity of the process. We present a method to create uniform thin resin layers, of controlled thickness, that are ideal for quantifying the thickness of porous nonconductive films with FIB/scanning electron microscopy.     

Particle‐induced x‐ray analysis using focused ion beams

In addition to the production of secondary electrons and secondary ions, characteristic x‐ray emission may also result from ion/solid interactions and is the basis for the well‐known analysis technique referred to as particle‐induced x‐ray emission. Characteristic x‐rays may be emitted by either bombardment by MeV protons or heavy ions of a few keV. The advantage to heavy ions is that the x‐ray yield is confined to the region near the surface defined by the collision cascade. An advantage of heavy ion‐induced x‐ray emission over electron‐induced x‐ray emission is that the Bremsstrahlung is potentially orders of magnitude lower. Thus, ion‐induced x‐ray spectra may provide for superior peak‐to‐noise ratios, and there‐fore, offers trace element sensitivity compared with elec‐tron‐induced x‐ray emission. In addition, the near surface ion/solid interactions also allow for the possibility of surface analysis or depth profiling. A Dual Beam instrument was used to collect focused ion beam‐induced x‐ray (FIBIX) spectra. The acquisition of characteristic x‐rays from targets via FIBIX is demonstrated and compared with scanning electron microscopy‐induced x‐ray energy dispersive spectroscopy spectra and is consistent with the theory described above.     

3D elemental and structural analysis of biological specimens using electrons and ions

We demonstrate the utility of focused ion beam scanning electron microscopy combined with energy dispersive x-ray spectrometry for 3D morphological and elemental correlative analysis of subcellular features. Although recent advances in super-resolution light microscopy techniques and traditional transmission electron microscopy methods can provide cellular imaging at a wide range of length scales, simultaneous 3D morphological and elemental imaging of cellular features at nanometre scale can only be achieved with techniques such as focused ion beam scanning electron microscopy with energy dispersive x-ray spectrometry capability. We demonstrate the technique by analysing the 3D silicon cell wall structure of a marine diatom, Thalassiosira pseudonana. This study also highlights the limitations of the technique in its current state and suggests several possible improvements needed for the routine use of the technique for biological specimens.     

Combining FIB milling and conventional Argon ion milling techniques to prepare high‐quality site‐specific TEM samples for quantitative EELS analysis of oxygen in molten iron

This paper reports a procedure to combine the focused ion beam micro‐sampling method with conventional Ar‐milling to prepare high‐quality site‐specific transmission electron microscopy cross‐section samples. The advantage is to enable chemical and structural evaluations of oxygen dissolved in a molten iron sample to be made after quenching and recovery from high‐pressure experiments in a laser‐heated diamond anvil cell. The evaluations were performed by using electron energy‐loss spectroscopy and high‐resolution transmission electron microscopy. The high signal to noise ratios of electron energy‐loss spectroscopy core‐loss spectra from the transmission electron microscopy thin foil, re‐thinned down to 40 nm in thickness by conventional Argon ion milling, provided us with oxygen quantitative analyses of the quenched molten iron phase. In addition, we could obtain lattice‐fringe images using high‐resolution transmission electron microscopy. The electron energy‐loss spectroscopy analysis of oxygen in Fe_0.94O has been carried out with a relative accuracy of 2%, using an analytical procedure proposed for foils thinner than 80 nm. Oxygen K‐edge energy‐loss near‐edge structure also allows us to identify the specific phase that results from quenching and its electronic structure by the technique of fingerprinting of the spectrum with reference spectra in the Fe‐O system.     

Challenges of microtome‐based serial block‐face scanning electron microscopy in neuroscience

Serial block‐face scanning electron microscopy (SBEM) is becoming increasingly popular for a wide range of applications in many disciplines from biology to material sciences. This review focuses on applications for circuit reconstruction in neuroscience, which is one of the major driving forces advancing SBEM. Neuronal circuit reconstruction poses exceptional challenges to volume EM in terms of resolution, field of view, acquisition time and sample preparation. Mapping the connections between neurons in the brain is crucial for understanding information flow and information processing in the brain. However, information on the connectivity between hundreds or even thousands of neurons densely packed in neuronal microcircuits is still largely missing. Volume EM techniques such as serial section TEM, automated tape‐collecting ultramicrotome, focused ion‐beam scanning electron microscopy and SBEM (microtome serial block‐face scanning electron microscopy) are the techniques that provide sufficient resolution to resolve ultrastructural details such as synapses and provides sufficient field of view for dense reconstruction of neuronal circuits. While volume EM techniques are advancing, they are generating large data sets on the terabyte scale that require new image processing workflows and analysis tools. In this review, we present the recent advances in SBEM for circuit reconstruction in neuroscience and an overview of existing image processing and analysis pipelines.     

The assessment of microscopic charging effects induced by focused electron and ion beam irradiation of dielectrics

Energetic beams of electrons and ions are widely used to probe the microscopic properties of materials. Irradiation with charged beams in scanning electron microscopes (SEM) and focused ion beam (FIB) systems may result in the trapping of charge at irradiation induced or pre-existing defects within the implanted microvolume of the dielectric material. The significant perturbing influence on dielectric materials of both electron and (Ga(+)) ion beam irradiation is assessed using scanning probe microscopy (SPM) techniques. Kelvin Probe Microscopy (KPM) is an advanced SPM technique in which long-range Coulomb forces between a conductive atomic force probe and the silicon dioxide specimen enable the potential at the specimen surface to be characterized with high spatial resolution. KPM reveals characteristic significant localized potentials in both electron and ion implanted dielectrics. The potentials are observed despite charge mitigation strategies including prior coating of the dielectric specimen with a layer of thin grounded conductive material. Both electron- and ion-induced charging effects are influenced by a delicate balance of a number of different dynamic processes including charge-trapping and secondary electron emission. In the case of ion beam induced charging, the additional influence of ion implantation and nonstoichiometric sputtering from compounds is also important. The presence of a localized potential will result in the electromigration of mobile charged defect species within the irradiated volume of the dielectric specimen. This electromigration may result in local modification of the chemical composition of the irradiated dielectric. The implications of charging induced effects must be considered during the microanalysis and processing of dielectric materials using electron and ion beam techniques.     

Ultra‐thin resin embedding method for scanning electron microscopy of individual cells on high and low aspect ratio 3D nanostructures

The preparation of biological cells for either scanning or transmission electron microscopy requires a complex process of fixation, dehydration and drying. Critical point drying is commonly used for samples investigated with a scanning electron beam, whereas resin‐infiltration is typically used for transmission electron microscopy. Critical point drying may cause cracks at the cellular surface and a sponge‐like morphology of nondistinguishable intracellular compartments. Resin‐infiltrated biological samples result in a solid block of resin, which can be further processed by mechanical sectioning, however that does not allow a top view examination of small cell–cell and cell–surface contacts. Here, we propose a method for removing resin excess on biological samples before effective polymerization. In this way the cells result to be embedded in an ultra‐thin layer of epoxy resin. This novel method highlights in contrast to standard methods the imaging of individual cells not only on nanostructured planar surfaces but also on topologically challenging substrates with high aspect ratio three‐dimensional features by scanning electron microscopy.     

Metrological challenges for reconstruction of 3‐D microstructures by focused ion beam tomography methods

The development of combined focused ion beam and scanning electron microscopes has enabled significant advances in the characterization of the 3‐D structure of materials. The repeated removal of thin layers or slices with an ion beam and imaging or mapping the chemical or crystallographic structure of each slice enables a 3‐D reconstruction from the images or maps. The accuracy of the reconstruction thus depends on the accuracy with which the slice thickness is measured and maintained throughout the process, and the alignment accuracy of the slices achieved during acquisition or by postacquisition corrections. A survey of papers published in this field suggests that the reconstruction accuracy is not often considered or reported. Using examples from examination of the 3‐D structure of hardmetals, issues affecting the accuracy of slice thicknesses and image realignments are examined and illustrated and potential errors quantified by the use of fiducial markers and the expected isotropy of the hardmetal structure itself.     

TEM foil preparation of sub-micrometre sized individual grains by focused ion beam technique

Analysis of presolar silicate grains provides new knowledge on interstellar and circumstellar environments and can be used to test models of the Galactic chemical evolution. However, structural information of these grains is rare because sample preparation for transmission electron microscopy is very difficult due to the small dimensions of these grains (<0.5 μm). With the use of the focused ion beam technique thin foils from these grains for transmission electron microscopy analysis can be prepared. Nevertheless, reaching the required precision of some tens of nanometres for the preparation of the transmission electron microscopy foil in the place of interest is not trivial. Furthermore, in the current samples, the grain of interest can only be identified by its different isotopic composition; i.e. there is no contrast difference in scanning electron microscopy or transmission electron microscopy images which allow the identification of the grain. Therefore, the grain has to be marked in some way before preparing the transmission electron microscopy foil. In the present paper, a method for transmission electron microscopy foil preparation of grains about 200 to 400 nm in diameter is presented. The method utilizes marking of the grain by Pt deposition and milling of holes to aid in the exact orientation of the transmission electron microscopy foil with respect to the grain. The proposed method will be explained in detail by using an example grain.     

Read-out of soft X-ray contact microscopy microradiographs by focused ion beam/scanning electron microscope

A novel focused ion beam-based technique is presented for the read-out of microradiographs of Caenorhabditis elegans nematodes generated by soft x-ray contact microscopy (SXCM). In previous studies, the read-out was performed by atomic force microscopy (AFM), but in our work SXCM microradiographs were imaged by scanning ion microscopy (SIM) in a focused ion beam/scanning electron microscope (FIB/SEM). It allows an ad libitum selection of a sample region for gross morphologic to nanometric investigations, with a sequence of imaging and cutting. The FIB/SEM is less sensitive to height variation of the relief, and sectioning makes it possible to analyse the sample further. The SXCM can be coupled to SIM in a more efficient and faster way than to AFM. Scanning ion microscopy is the method of choice for the read-out of microradiographs of small multicellular organisms.     

Focused ion beam characterization of plasma-assisted deposition on polymer films at the nanoscale

In this paper, a novel technique is presented for the characterization at the nanoscale of plasma-assisted deposit on polyethylene-terephthalate (PET) polymer films. In previous studies, some microcharacterization and morphology analyses of plasma-assisted deposition were performed by atomic force microscopy (AFM). In the work presented here, we analysed the thickness and homogeneity of plasma-assisted deposits by focused ion beam (FIB). This technique with 5-7 nm resolution requires no sample preparation and relies on a sequence of operations on a relatively fast time scale, so that it is easy to make thorough investigations of the sample. We performed electron and ion imaging of the surface of the material, and a subsequent ionic cutting allowed the study of the morphology of the same sample. We developed a novel approach to the edge detection techniques (EDT) in images for a fast evaluation and monitoring of the deposited layer.     

Using the FIB to characterize nanoparticle materials

In the 1–100‐nm size regime, the properties of materials can differ significantly from those of their bulk counterparts. The present study applies the focused ion beam (FIB) tool to the characterization of nanoscale structures for scanning and transmission electron microscopy. The strength of this method is its ability to manufacture samples that cannot be produced using traditional means. The films of nanoparticles examined here are examples of such systems; the films are found to be not fully dense, composed of chemically heterogeneous areas and mechanically different from the substrate. Distinct advantages of the application of the FIB for characterization of nanoscale structures are highlighted for several nanoparticle structures. This successful application of FIB techniques provides a pathway to integrate the study of nanoscale production techniques and their resulting structure–property relationships.     

Towards the imaging of Weibel–Palade body biogenesis by serial block face‐scanning electron microscopy

Electron microscopy is used in biological research to study the ultrastructure at high resolution to obtain information on specific cellular processes. Serial block face‐scanning electron microscopy is a relatively novel electron microscopy imaging technique that allows three‐dimensional characterization of the ultrastructure in both tissues and cells by measuring volumes of thousands of cubic micrometres yet at nanometre‐scale resolution. In the scanning electron microscope, repeatedly an image is acquired followed by the removal of a thin layer resin embedded biological material by either a microtome or a focused ion beam. In this way, each recorded image contains novel structural information which can be used for three‐dimensional analysis. Here, we explore focused ion beam facilitated serial block face‐scanning electron microscopy to study the endothelial cell–specific storage organelles, the Weibel–Palade bodies, during their biogenesis at the Golgi apparatus. Weibel–Palade bodies predominantly contain the coagulation protein Von Willebrand factor which is secreted by the cell upon vascular damage. Using focused ion beam facilitated serial block face‐scanning electron microscopy we show that the technique has the sensitivity to clearly reveal subcellular details like mitochondrial cristae and small vesicles with a diameter of about 50 nm. Also, we reveal numerous associations between Weibel–Palade bodies and Golgi stacks which became conceivable in large‐scale three‐dimensional data. We demonstrate that serial block face‐scanning electron microscopy is a promising tool that offers an alternative for electron tomography to study subcellular organelle interactions in the context of a complete cell.     

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.     

Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy

In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV‐pulsed mature human dendritic cells.     

Characterization of dentine structure in three dimensions using FIB-SEM

All biological tissues are three dimensional and contain structures that span a range of length scales from nanometres through to hundreds of millimetres. These are not ideally suited to current three-dimensional characterization techniques such as X-ray or transmission electron tomography. Such detailed morphological analysis is critical to understanding the structural features relevant to tissue function and designing therapeutic strategies intended to address structural deficiencies encountered in pathological states. We show that use of focused ion beam milling combined with scanning electron microscopy can provide three-dimensional information at nanometre resolution from biologically relevant volumes of material, in this case dentine.