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.     

Developing 3D SEM in a broad biological context

When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three‐dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze‐fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block‐face, SBF‐SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.     

Focused ion beam manipulation and ultramicroscopy of unprepared cells

The focused ion beam (FIB) technique of nanomachining combined with simultaneous scanning electron microscopy (SEM) was used for submicron manipulation and imaging of unprepared (fresh) cells to demonstrate the potentiality of the FIB/SEM technique for ultramicroscopic studies. Sectioning at the nanoscale level was successfully performed by means of ion beam-driven milling operations that reveal the ultrastructure of fresh yeast cells. The FIB/SEM has many advantages over other ultramicroscopy techniques already applied for unprepared/fresh biological samples.     

A comparison of imaging methodologies for 3D tissue engineering

Imaging of cells in two dimensions is routinely performed within cell biology and tissue engineering laboratories. When biology moves into three dimensions imaging becomes more challenging, especially when multiple cell types are used. This review compares imaging techniques used regularly in our laboratory in the culture of cells in both two and three dimensions. The techniques reviewed include phase contrast microscopy, fluorescent microscopy, confocal laser scanning microscopy, electron microscopy, and optical coherence tomography. We compare these techniques to the current "gold standard" for imaging three-dimensional tissue engineered constructs, histology.     

Tomography of insulating biological and geological materials using focused ion beam (FIB) sectioning and low-kV BSE imaging

Tomography in a focused ion beam (FIB) scanning electron microscope (SEM) is a powerful method for the characterization of three-dimensional micro- and nanostructures. Although this technique can be routinely applied to conducting materials, FIB–SEM tomography of many insulators, including biological, geological and ceramic samples, is often more difficult because of charging effects that disturb the serial sectioning using the ion beam or the imaging using the electron beam. Here, we show that automatic tomography of biological and geological samples can be achieved by serial sectioning with a focused ion beam and block-face imaging using low-kV backscattered electrons. In addition, a new ion milling geometry is used that reduces the effects of intensity gradients that are inherent in conventional geometry used for FIB–SEM tomography.     

Method to deterministically study photonic nanostructures in different experimental instruments

We describe an experimental method to recover a single, deterministically fabricated nanostructure in various experimental instruments without the use of artificially fabricated markers, with the aim to study photonic structures. Therefore, a detailed map of the spatial surroundings of the nanostructure is made during the fabrication of the structure. These maps are made using a series of micrographs with successively decreasing magnifications. The graphs reveal intrinsic and characteristic geometric features that can subsequently be used in different setups to act as markers. As an illustration, we probe surface cavities with radii of 65 nm on a silica opal photonic crystal with various setups: a focused ion beam workstation; a scanning electron microscope (SEM); a wide field optical microscope and a confocal microscope. We use cross-correlation techniques to recover a small area imaged with the SEM in a large area photographed with the optical microscope, which provides a possible avenue to automatic searching. We show how both structural and optical reflectivity data can be obtained from one and the same nanostructure. Since our approach does not use artificial grids or markers, it is of particular interest for samples whose structure is not known a priori , like samples created solely by self-assembly. In addition, our method is not restricted to conducting samples.     

Preparation of site-specific cross-sections of heterogeneous catalysts prepared by focused ion beam milling

Focused ion beam (FIB) milling offers a novel approach to preparation of site‐specific cross‐sections of heterogeneous catalysts for examination in the transmission electron microscope (TEM). Electron‐transparent sections can be obtained without the need to embed or grind the original sample. Because the specimen can be imaged in the FIB with submicrometre resolution before, during and after milling it is possible to select precisely the region from which the section is removed and to control the thickness of the section to within tens of nanometres. The ability to produce sections in this way opens the possibility of studying a range of catalyst systems that have previously been impossible to examine with the TEM.     

Observation of human dentine by focused ion beam and energy-filtering transmission electron microscopy

Molar dentine was sliced into 100 nm ultrathin sections, by means of a focused ion beam, for observation by energy-filtering transmission electron microscopy (EFTEM). Within the matrix, crystals approximately 10 nm wide and 50–100 nm long were clearly observed. When carbon and calcium were mapped in electron spectroscopic images by EFTEM, carbon failed to localize in crystals. However, it was found in other regions, especially those adjacent to crystals. Because carbon localizations were thought to reflect the presence of organic components, carbon concentration in regions near crystals suggested the interaction of crystals and organics, leading to organic control of apatite formation and growth. Ca was present in almost all regions. The majority of Ca localizing in regions other than crystals may be bound to organic substances present in dentine matrix. These substances are thought to both accumulate Ca and act as reservoirs for crystallization of apatite in dentine.     

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.     

Single molecule mapping of the optical field distribution of probes for near-field microscopy

The most difficult task in near-field scanning optical microscopy (NSOM) is to make a high quality subwavelength aperture probe. Recently, we have developed high definition NSOM probes by focused ion beam (FIB) milling. These probes have a higher brightness, better polarization characteristics, better aperture definition and a flatter end face than conventional NSOM probes. We have determined the quality of these probes in four independent ways: by FIB imaging and by shear-force microscopy (both providing geometrical information), by far-field optical measurements (yielding throughput and polarization characteristics), and ultimately by single molecule imaging in the near-field. In this paper, we report on a new method using shear-force microscopy to study the size of the aperture and the end face of the probe (with a roughness smaller than 1.5 nm). More importantly, we demonstrate the use of single molecules to measure the full three-dimensional optical near-field distribution of the probe with molecular spatial resolution. The single molecule images exhibit various intensity patterns, varying from circular and elliptical to double arc and ring structures, which depend on the orientation of the molecules with respect to the probe. The optical resolution in the measurements is not determined by the size of the aperture, but by the high optical field gradients at the rims of the aperture. With a 70 nm aperture probe, we obtain fluorescence field patterns with 45 nm FWHM. Clearly, this unprecedented near-field optical resolution constitutes an order of magnitude improvement over far-field methods like confocal microscopy.     

Fabrication of a versatile substrate for finding samples on the nanometer scale

With increasing interest in nanometer scale studies, a common research issue is the need to use different analytical systems with a universal substrate to relocate objects on the nanometer scale. Our paper addresses this need. Using the delicate milling capability of a focused ion beam (FIB) system, a region of interest (ROI) on a sample is labelled via a milled reference grid. FIB technology allows for milling and deposition of material at the sub 20-nm level, in a similar user environment as a standard scanning electron microscope (SEM). Presently commercially available transmission electron microscope (TEM) grids have spacings on the order 100 μm on average; this technique can extend this dimension down to the submicrometre level. With a grid on the order of a few micrometres optical, FIBs, TEMs, scanning electron microscopes (SEMs), and atomic force microscopes (AFM) are able to image the ROI, without special chemical processes or conductive coatings required. To demonstrate, Au nanoparticles of ∼ 25 nm in size were placed on a commercial Formvar^®- and carbon-coated TEM grid and later milled with a grid pattern. Demonstration of this technique is also extended to bulk glass substrates for the purpose of sample location. This process is explained and demonstrated using all of the aforementioned analytical techniques.     

Observation of the ion-mirror effect during microscopy of insulating materials

Utilizing the ion beam of a focused ion beam (FIB)/scanning electron microscope (SEM) microscope to investigate non‐conductive samples, we observe a mirror image very much similar to the one that is commonly obtained with the electron beam and the same samples. To our knowledge this is the first observation of what can be called ‘Ion‐Mirror Effect’. This effect is produced by a positive charging of the sample obtained by rastering with high‐energy ions (30 kV) and a subsequent imaging with low energy ones (5 kV). The proposed explanation is that first a positive charge is trapped within the sample and eventually the lower energy ions are deflected back by the latter, and hit the surface of the microscope chamber very similar to what happens in the ‘Electron‐Mirror Effect’. The mirror image is produced after detection of the electrons produced by the interaction between ions and the chamber materials.     

Modulus characterization of cells with submicron colloidal probes by atomic force microscope

Colloidal probes have been increasingly demanded for the characterization of cellular modulus in atomic force microscope because of their well-defined geometry and large contact area with cell. In this work, submicron colloidal probes are prepared by scanning electron microscope/focused ion beam and compared with sharp tip and micron colloidal probe, in conjunction with loading velocity and indentation depth on the apparent elastic modulus. NIM and cartilage cells are used as specimens. The results show that modulus value measured by sharp tip changes significantly with loading velocity while remains almost stable by colloidal probes. Also, submicron colloidal probe is superior in characterizing the modulus with increasing indentation depth, which could help reveal the mechanical details of cellular membrane and the modulus of the whole cell. To test the submicron colloidal probe further, the modulus distribution map of cell is scanned with submicron colloidal probe of 50 nm radius during small and large indentation depths with high spatial resolution. The outcome of this work will provide the effective submicron colloidal probe according to the effect of loading velocity and indentation depth, characterizing the mechanical properties of the cells.     

Multiscale imaging and characterization of the effect of mixing temperature on asphalt concrete containing recycled components

When producing asphalt concrete mixture with high amounts of reclaimed asphalt pavement (RAP), the mixing temperature plays a significant role in the resulting spatial distribution of the components as well as on the quality of the resulting mixture, in terms of workability during mixing and compaction as well as in service mechanical properties. Asphalt concrete containing 50% RAP was investigated at mixing temperatures of 140, 160 and 180°C, using a multiscale approach. At the microscale, using energy dispersive X‐ray spectroscopy the RAP binder film thickness was visualized and measured. It was shown that at higher mixing temperatures this film thickness was reduced. The reduction in film thickness can be attributed to the loss of volatiles as well as the mixing of RAP binder with virgin binder at higher temperatures. X‐ray computer tomography was used to characterize statistically the distribution of the RAP and virgin aggregates geometric features: volume, width and shape anisotropy. In addition using X‐ray computer tomography, the packing and spatial distribution of the RAP and virgin aggregates was characterized using the nearest neighbour metric. It was shown that mixing temperature may have a positive effect on the spatial distribution of the aggregates but did not affect the packing. The study shows a tendency for the RAP aggregates to be more likely distributed in clusters at lower mixing temperatures. At higher temperatures, they were more homogeneously distributed. This indicates a higher degree of blending both at microscale (binder film) and macroscale (spatial distribution) between RAP and virgin aggregates as a result of increasing mixing temperatures and the ability to quantify this using various imaging techniques.     

Optical coherence tomography as a tool for characterization of complex biological surfaces

The advent of scanning electron microscopy has facilitated our understanding of the biology in relation to surface microstructure of many invertebrates. In recent years, interest in biomimetics and bio‐inspired materials has further propelled the search for novel microstructures from natural surfaces. As this search widens in diversity to nurture deeper understanding of form and function, the need often arises to examine rare specimens. Unfortunately, most methods for characterization of the microtopography of natural surfaces are sacrificial, and as such, place limiting constraints on research progress in situations where only a few rare specimens are known, such as the rich resources lodged in natural history museum collections. In this paper, we introduce the use of optical coherence tomography (OCT) as a noninvasive tool for bioimaging surface microtopography of crab shells. The technique enables the capture of microstructures down to micron level using low coherence near‐infrared light source. OCT has allowed surface microtopography imaging on crab shells to be carried out rapidly and in a nondestructive manner, compared to the scanning electron microscope technique. The microtopography of four preserved crab specimens from Acanthodromia margarita, Ranina ranina, Conchoecetes intermedius and Dromia dormia imaged using OCT were similar to images obtained from scanning electron microscope, showing that OCT imaging retains the overall morphological form during the scanning process. By comparing the physical lengths of the spinal structures from images obtained from OCT and scanning electron microscope, the results showed that dimensional integrity of the images captured from OCT was also maintained.     

Detection and speciation of brominated flame retardants in high-impact polystyrene (HIPS) polymers

Polymeric materials have been suggested as possible environmental sources of persistent organic pollutants such as flame retardants. In situ, micrometre-scale characterization techniques for polymer matrix containing flame retardants may provide some insight into the dominant environmental transfer mechanism(s) of these brominated compounds. In this work, we demonstrate that micro X-ray fluorescence spectroscopy (μXRF), focused ion beam scanning electron microscopy (FIB-SEM) combined with energy dispersive X-ray spectroscopy (EDS), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are promising techniques for the elemental and chemical identification of brominated fire retardant compounds (such as the deca-congener of polybrominated diphenyl ether, BDE-209) within polymeric materials (e.g. high-impact polystyrene or HIPS). Data from μXRF demonstrated that bromine (Br) inclusions were evenly distributed throughout the HIPS samples, whereas FIB SEM-EDS analysis revealed that small antimony (Sb) and Br inclusions are present, and regionally higher concentrations of Br surround the Sb inclusions (compared to the bulk material). Four prominent mass-to-charge ratio peaks (m/z 485, 487, 489 and 491) that correspond to BDE-209 were identified by ToF-SIMS and can be used to chemically distinguish this molecule on the surface of polymeric materials with respect to other brominated organic molecules. These techniques can be important in any study that investigates the route of entry to the environmental surroundings of BDE-containing materials.     

Focused ion beam/scanning electron microscopy studies of Porcellio scaber (Isopoda, Crustacea) digestive gland epithelium cells

The focused ion beam (FIB) was used to prepare cross sections of precisely selected regions of the digestive gland epithelium of a terrestrial isopod P. scaber (Isopoda, Crustacea) for scanning electron microscopy (SEM). The FIB/SEM system allows ad libitum selection of a region for gross morphologic to ultrastructural investigation, as the repetition of FIB/SEM operations is unrestricted. The milling parameters used in our work proved to be satisfactory to produce serial two-dimensional (2-D) cuts and/or three-dimensional (3-D) shapes on a submicrometer scale. A final, cleaning mill at lower ion currents was employed to minimize the milling artifacts. After cleaning, the milled surface was free of filament- and ridge-like milling artifacts. No other effects of the cleaning mill were observed.     

TEM characterization of precipitates in the segregated regions of a low-carbon, low-manganese, titanium-added steel

A concentric solidification technique has been employed to simulate sulphide precipitation at the centreline of a continuously cast low-carbon, low-manganese, titanium-added steel slab. Selected precipitates were identified using transmission electron microscopy following sample preparation by focused ion beam milling techniques. FeTiS₂ and hexagonal MnS containing iron atoms form in close proximity to each other in super-saturated areas of the concentrically solidified sample. The presence of FeTiS₂ precipitates in low-carbon steel has been verified for the first time, and the crystal structure determined by electron diffraction analysis as a trigonal CdI₂-type with a P 3 m1 space group and lattice parameters of a = 0.341 nm and c = 0.569 nm.     

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.