Design and performance of a combined secondary ion mass spectrometry-scanning probe microscopy instrument for high sensitivity and high-resolution elemental three-dimensional analysis

State-of-the-art secondary ion mass spectrometry (SIMS) instruments allow producing 3D chemical mappings with excellent sensitivity and spatial resolution. Several important artifacts however arise from the fact that SIMS 3D mapping does not take into account the surface topography of the sample. In order to correct these artifacts, we have integrated a specially developed scanning probe microscopy (SPM) system into a commercial Cameca NanoSIMS 50 instrument. This new SPM module, which was designed as a DN200CF flange-mounted bolt-on accessory, includes a new high-precision sample stage, a scanner with a range of 100 μm in x and y direction, and a dedicated SPM head which can be operated in the atomic force microscopy (AFM) and Kelvin probe force microscopy modes. Topographical information gained from AFM measurements taken before, during, and after SIMS analysis as well as the SIMS data are automatically compiled into an accurate 3D reconstruction using the software program "SARINA," which was developed for this first combined SIMS-SPM instrument. The achievable lateral resolutions are 6 nm in the SPM mode and 45 nm in the SIMS mode. Elemental 3D images obtained with our integrated SIMS-SPM instrument on Al/Cu and polystyrene/poly(methyl methacrylate) samples demonstrate the advantages of the combined SIMS-SPM approach.     

Scanning ion microprobe analysis of composite materials

Applications of scanning ion imaging with high lateral resolution in the microchemical investigation of metal – and ceramic-matrix composites are described. The technique, which combines a scanning ion microprobe with secondary ion mass spectrometry (SIMS), is ideally suited to the study of complex, multicomponent composite structures. Most elements can be detected with good sensitivity, enabling the determination of spatial distributions for major and minor elements. Analytical images obtained with this technique reveal unprecedented chemical information about interfacial segregation and interdiffusion phenomena. As examples, the characterization of both ceramic–matrix (Al borate–SiC) and metal–matrix (Ni alloy–Al₂O₃) composite materials is described.     

X-ray microanalysis of freeze-dried and frozen-hydrated cryosections

The elemental composition and the ultrastructure of biological cells were studied by scanning transmission electron microscopy (STEM) combined with energy dispersive X-ray microanalysis. The preparation technique involves cryofixation, cryoultramicrotomy, cryotransfer, and freeze-drying of samples. Freeze-dried cryosections 100-nm thick appeared to be appropriate for measuring the distribution of diffusible elements and water in different compartments of the cells. The lateral analytical resolution was less than 50 nm, depending on ice crystal damage and section thickness. The detection limit was in the range of 10 mmol/kg dry weight for all elements with an atomic number higher than 12; for sodium and magnesium the detection limits were about 30 and 20 mmol/kg dry weight, respectively. The darkfield intensity in STEM is linearly related to the mass thickness. Thus, it becomes possible to measure the water content in intracellular compartments by using the darkfield signal of the dry mass remaining after freeze-drying. By combining the X-ray microanalytical data expressed as dry weight concentrations with the measurements of the water content, physiologically more meaningful wet weight concentrations of elements were determined. In comparison to freeze-dried cryosections frozen-hydrated sections showed poor contrast and were very sensitive against radiation damage, resulting in mass loss. The high electron exposure required for recording X-ray spectra made reproducible microanalysis of ultrathin (about 100-nm thick) frozen-hydrated sections impossible. The mass loss could be reduced by carbon coating; however, the improvement achieved thus far is still insufficient for applications in X-ray microanalysis. Therefore, at present only bulk specimens or at least 1-μm thick sections can be used for X-ray microanalysis of frozen-hydrated biological samples.     

Biological microanalysis by secondary ion mass spectrometry: status and prospects

Secondary ion mass spectrometric (SIMS) analysis of biological problems is an evolving technique. Lateral resolution of currently available commercial instrumentation estimated from actual samples is 0.5 micron, and subcellular organelles can be distinguished. The interrelationship of lateral resolution, elemental concentration and ionizability are, however, important in controlling the actual lateral resolution achievable. Although depth resolutions of 5 nm have been measured in other systems, no test of depth resolution in biological systems has been done, and this parameter is also concentration and ionization dependent. The development of liquid metal ion sources in combination with scanning ion microprobes has a potential lateral resolution of as little as 20 nm, but initial studies with this instrumentation show that tissue preservation at the submicron level becomes an important issue. The current development of a cold-transfer stage for SIMS instruments may obviate the problem of submicron localization of diffusible elements, and initial studies indicate that much more needs to be understood about the ionization process in hydrated samples. Quantitation of diffusible elements using external standards has been achieved over a 30 micron diameter analyzed area. Strategies for analysis of areas limited to 1 micron or less has been suggested using image processing techniques, which take advantage of the lateral resolution inherent in the ion optical system. Matrix effects in biological tissues have been reported and constitute a serious problem for analysis of biologicals which must be addressed for each question. However, development of laser ionization of sputtered particles may both increase the sensitivity of analysis and decrease the importance of ionizability of elements. Chemical analysis of organic molecules is another use of SIMS, but, at present, at the cost of losing localized information. SIMS analysis of biological samples is being systematically evaluated and requires increased accessibility of this instrumentation to the end-user for full development of its role in physiological problems.     

Elemental and molecular imaging of human hair using secondary ion mass spectrometry.

Secondary ion mass spectrometry (SIMS) is used to image the spatial distribution of elemental and molecular species on the surface and in cross sections of doped human hair using a magnetic sector SIMS instrument operated as an ion microprobe. Analysis of electrically insulating, non-planar hair samples requires one of two different methods of charge compensation to be used depending on the polarity of the sputtered secondary ions. For detection of positive secondary ions, the hair is imaged using a approximately 0.5 micron diameter, 19.5 keV impact energy, O- microbeam with no auxiliary electron bombardment. For detection of negative secondary ions, a approximately 0.2 micron diameter, 14.5 keV impact energy Cs+ microbeam is used in conjunction with normal incidence, low-energy electron bombardment. Both of these methods allow submicrometer spatial resolution elemental and molecular secondary ion images to be obtained from hair samples without metallic coating of the sample surface prior to analysis. Several examples are presented that reflect potential application areas for these analytical methods.     

Studies of cell division (mitosis and cytokinesis) by dynamic secondary ion mass spectrometry ion microscopy: LLC-PK1 epithelial cells as a model for subcellular isotopic imaging

The feasibility of the renal epithelial LLC-PK₁ cell line as a model for cell division studies with secondary ion mass spectrometry (SIMS) was tested. In this cell line, cells undergoing all stages of mitosis and cytokinesis remained firmly attached to the substrate and could be cryogenically prepared. Fractured freeze-dried mitotic cells showed well-preserved organelles as revealed by fluorescence imaging of rhodamine-123 and C₆-NBD-ceramide by confocal laser scanning microscopy. Secondary electron microscopy analysis of fractured freeze-dried dividing cells revealed minimal surface topography that does not interfere in isotopic imaging of both positive (³⁹K, ²³Na, ²⁴Mg, ⁴⁰Ca, etc.) and negative (³¹P, ³⁵Cl, etc.) secondaries with a CAMECA IMS-3f ion microscope. Mitotic cells revealed well-preserved intracellular ionic composition of even the most diffusible ions (total concentrations of ³⁹K⁺ and ²³Na⁺) as revealed by K : Na ratios of approximately 10. Structurally damaged mitotic cells could be identified by their reduced K : Na ratios and an excessive loading of calcium. Quantitative three-dimensional SIMS analysis was required for studying subcellular calcium distribution in dividing cells. The LLC-PK₁ model also allowed SIMS studies of M-phase arrested cells with mitosis-arresting drugs (taxol, monastrol and nocodazole). This study opens new avenues of cell division research related to ion fluxes and chemical composition with SIMS.     

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.     

The cutting of ultrathin sections with the thickness less than 20 nm from biological specimens embedded in resin blocks

Low voltage electron microscopes working in transmission mode, like LVEM5 (Delong Instruments, Czech Republic) working at accelerating voltage 5 kV or scanning electron microscope working in transmission mode with accelerating voltage below 1 kV, require ultrathin sections with the thickness below 20 nm. Decreasing of the primary electron energy leads to enhancement of image contrast, which is especially useful in the case of biological samples composed of elements with low atomic numbers. As a result treatments with heavy metals, like post‐fixation with osmium tetroxide or ultrathin section staining, can by omitted. The disadvantage is reduced penetration ability of incident electrons influencing the usable thickness of the specimen resulting in the need of ultrathin sections of under 20 nm thickness. In this study we want to answer basic questions concerning the cutting of extremely ultrathin sections: Is it possible routinely and reproducibly to cut extremely thin sections of biological specimens embedded in commonly used resins with contemporary ultramicrotome techniques and under what conditions? Microsc. Res. Tech. 79:512–517, 2016. © 2016 Wiley Periodicals, Inc.     

Sephadex globules placed as landmarks in combined stereo microscopy,scanning and transmission electron microscopy

Regions of specific interest in tissue blocks were localized in a stereo microscope and landmarked with Sephadex spheres (10–40 μm in diameter). This procedure made it possible to recognize these regions easily and quickly in the scanning electron microscope. When the tissue was later embedded in Epon the spheres facilitated orientation when sectioning. Thus it was possible with great certainty to determine the level at which ultrathin sections should be cut for transmission electron microscopy to attain an exact correspondence between scanning and transmission electron microscopic observations. The procedure is described and an example of its application is shown in a study of experimental hypertensive endothelial changes.     

Transmission electron microscopy applied to the study of works of art: sample preparation methodology and possible techniques

Technical examination of a work of art is a necessary preliminary stage both for proper conservation/restoration of the work and for purposes of dating and/or authentication. There is a wide variety of methods and procedures, and of these a particularly valuable technique is stratigraphic analysis in view of the data that it furnishes on the composition of the pictorial layers of which a painting is composed. The techniques utilized in this type of analysis to date have been essentially light microscopy and scanning electron microscopy. Transmission electron microscopy can provide new data for characterization of pictorial layers, thanks to the possibility of individually using ultrathin sections of paint sample. This study provides morphological analysis and microanalysis by X-ray energy dispersion, with determination of the crystalline structure of each particle by electron diffraction. The sample preparation method for producing thin sections from the pictorial layers for examination in the TEM is described. This allows the stratigraphic section to be preserved exactly as applied by the artist. The first results from the examination of three microsamples from actual old works of art are presented. The individual components of each strata were successfully identified in all cases.     

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.     

Quantitative subcellular imaging of boron compounds in individual mitotic and interphase human glioblastoma cells with imaging secondary ion mass spectrometry (SIMS)

Boron measurements at subcellular scale are essential in boron neutron capture therapy (BNCT) of cancer as the nuclear localization of boron‐10 atoms can enhance the effectiveness of killing individual tumour cells. Since tumours contain a heterogeneous population of cells in interphase as well as in the M phase (mitotic division) of the cell cycle, it is important to evaluate the subcellular distribution of boron in both phases. In this work, the secondary ion mass spectrometry (SIMS) based imaging technique of ion microscopy was used to quantitatively image boron from two BNCT agents, clinically used p‐boronophenylalanine (BPA) and 3‐[4‐(o‐carboran‐1‐yl)butyl]thymidine (N4), in mitotic metaphase and interphase human glioblastoma T98G cells. N4 belongs to a class of experimental BNCT agents, designated 3‐carboranyl thymidine analogues (3CTAs), which presumably accumulate selectively in cancer cells due to a process referred to as kinase‐mediated trapping (KMT). The cells were exposed to BPA for 1 h and N4 for 2 h. A CAMECA IMS‐3f SIMS ion microscope instrument capable of producing isotopic images with 500 nm spatial resolution was used in the study. Observations were made in cryogenically prepared fast frozen, and freeze‐fractured, freeze‐dried cells. Three discernible subcellular regions were studied: the nucleus, a characteristic mitochondria‐rich perinuclear cytoplasmic region, and the remaining cytoplasm in interphase T98G cells. In metaphase cells, the chromosomes and the cytoplasm were studied for boron localization. Intracellular concentrations of potassium and sodium also were measured in each cell in which the subcellular boron concentrations were imaged. Since the healthy cells maintain a K/Na ratio of approximately 10 due to the presence of Na‐K‐ATPase in the plasma membrane of mammalian cells, these measurements provided validation for cryogenic sample preparation and indicated the analysis healthy, well preserved cells. The BPA‐treated interphase cells revealed significantly lower concentrations of boron in the perinuclear mitochondria‐rich cytoplasmic region as compared to the remaining cytoplasm and the nucleus, which were not significantly different from each other. In contrast, the BPA‐treated metaphase cells revealed significantly lower concentration of boron in their chromosomes than cytoplasm. In addition, the cytoplasm of metaphase cells contained significantly less boron than the cytoplasm of interphase cells. These observations provide valuable information on the reduced uptake of boron from BPA in mitotic cells for BPA‐mediated BNCT. SIMS observations on N4 revealed that boron was distributed throughout the interphase and mitotic cells, including the chromosomes. The presence of boron in chromosomes of metaphase cells treated with N4 is indicative of a possible incorporation of this thymidine analogue into DNA. The 3‐D SIMS imaging approach for the analysis of mitotic cells shown in this work should be equally feasible to the evaluation of other BNCT agents.     

Quasicrystalline Materials

SIMS matrix effects (mass interferences, sputter yield variations and practical ion yield variations) were evaluated in freeze-fractured, freeze-dried cultured cells at the ～0.5 μm spatial resolution of the Cameca IMS-3f ion microscope. Cell lines studied include normal rat kidney (NRK), 3T3 mouse fibroblast, L6 rat myoblast, chinese hamster ovary (CHO) and rat kangaroo kidney (PtK2) cells. High mass resolution studies indicated that the secondary ion signals of H^—, C^—, O^—, Na⁺, Mg⁺, CN^—, P^—, S^—, Cl^—, K⁺ and Ca⁺ were free from major mass interferences. However, a large mass interference was observed for nitrogen at mass 14. No significant sputtering yield difference between the nuclear and cytoplasmic compartments of the cells studied was observed. The subcellular distributions of the major (H, C, N and O) and minor (P, S, K, Cl, Na, Mg and Ca) matrix elements were found to be largely homogeneous with the exception of Ca, which was observed mainly in the cell cytoplasm. Practical ion yield variations were compared by three different approaches: (i) by the use of cells doped with known electrolyte concentrations, (ii) by quantitative ion implantation, and (iii) by analysis of the same cell with both electron probe and ion microscope. Each approach indicated an absence of significant practical ion yield differences between the nuclear and cytoplasmic regions of these specimens. These observations indicate that secondary ion signals in this type of sample are not significantly affected by local matrix effect variations. Hence, qualitative imaging of such specimens provides a true representation of subcellular elemental distribtions. These observations should allow the development of quantitative ion imaging methodologies and enhance the applicability of ion microscopy to biomedical problems.     

Transformation of 20Х13 steel structure during intensive friction interactions

The results of an investigation of the influence of intensive friction interactions upon the transformation of a 20Х13 steel structure using optic metallography, scanning electron microscopy, and X-ray microanalysis have been described. It has been stated that, at a depth of 3 mm, structural changes connected with heating and intensive plastic deformation processes take place. Diagrams of chemical elements distribution show changes in the steel chemical composition in the surface layer up to 20 μm depth. An increase in microhardness to 5000 MPa has been observed at certain sections.     

3D correlative morphological and elemental characterization of materials at the deep submicrometre scale

This paper shows how X‐ray computed nanotomography (CNT) can be correlated with focused ion beam time‐of‐flight secondary ion mass spectrometry (FIB‐TOF‐SIMS) tomography on the same sample to investigate both the morphological and elemental structure. This methodology is applicable to relatively large specimens with dimensions of several tens of microns whilst maintaining a high spatial resolution of the order of 100 nm. However, combining X‐ray CNT and FIB‐TOF‐SIMS tomography requires innovative sample preparation protocols to allow both experiments to be conducted on exactly the same sample without chemically or structurally modifying the sample between measurements. Moreover, dedicated algorithms have been developed for effective data fusion that is biased with nine degrees of freedom. This methodology has been tested using a porous and heterogeneous solid oxide fuel cell (SOFC) that has features varying in size by three orders of magnitude – from hundreds of nanometre large pores and grains to tens of micron wide functional layers.     

Neuronal imaging with colloidal gold

Colloidal gold is easily prepared, and readily adsorbs to a number of immunoreagents and other proteins for a wide variety of uses for neuronal visualization. Gold probes serve a role as immunolabels for both light and electron microscopy. As an ultrastructural immunocytochemical marker for detection of proteins, peptides or amino acids, gold can be used for immunostaining thick or thin sections prior to embedding, or for immunostaining ultrathin sections after embedding tissue in conventional or unusual embedding matrices. By virtue of its particulate nature, gold as an immunolabel facilitates a semi-quantitative analysis of relative antigen densities on ultrathin sections. Various combinations of different size gold particles or dual immunolabelling with enzymatic immunolabels together with colloidal gold or silver-intensified gold serve well for ultrastructural immunocytochemical localization of two antigens in the same tissue section. Colloidal gold can be detected with light microscopy, transmission and scanning electron microscopy, and with confocal laser microscopy. Silver intensification allows detection of gold at both the light and electron microscope level, and increases the sensitivity of immunogold procedures. Colloidal gold is useful as a tracer for physiological studies of transport and internalization in neurons in vivo and in vitro; computer-assisted video imaging techniques allow detection and tracking of single gold particles in living cells.     

A tridimensional view of the organization of actin filaments in the central nervous system by use of fluorescent photooxidation

Cellular and subcellular organization and distribution of actin filaments have been studied with various techniques. The use of fluorescence photo-oxidation combined with phalloidin conjugates with eosin has allowed the examination of the precise cellular and subcellular location of F-actin. Correlative fluorescence light microscopy and transmission electron microscopy studies of F-actin distribution are facilitated with this method for morphological and physiological studies. Because phalloidin-eosin is smaller than other markers, this method allows the analysis of the three-dimensional location of F-actin with high-resolution light microscopy, three-d serial sections reconstructions, and electron tomography. The combination of selective staining and three-dimensional reconstructions provide a valuable tool for revealing aspects of the synaptic morphology that are not available when conventional electron microscopy is used. By applying this selective staining technique and three-dimensional imaging, we uncovered the structural organization of actin in the postsynaptic densities in physiological and pathological conditions.     

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.     

Probing the role of C+ ion energy,thickness and graded structure on the functional and microstructural characteristics of ultrathin carbon films (<2 nm)

We report a comprehensive study on the protective, functional and microstructural properties of filtered cathodic vacuum arc (FCVA) deposited ultrathin carbon overcoats (COCs), which are being considered as potential candidates for future media recording technology such as heat-assisted magnetic recording (HAMR). Specifically, the influence of the C⁺ ion energy (50–345 eV) and the film thickness (0.5–3.2 nm) on these properties were investigated and supported with Raman and X-ray photoelectron spectroscopy (XPS). Finally, an optimized deposition recipe has been proposed to develop an ultrathin (≤2.0 nm) yet continuous COC with improved wear and corrosion resistance compared to thicker conventional COCs (~2.7 nm).     

High resolution polar Kerr magnetometer for nanomagnetism and nanospintronics

A new high resolution polar magneto-optical (MO) Kerr magnetometer, devoted to the study of nanometer sized elements with perpendicular magnetic anisotropy, is described. The unique performances of this setup in terms of sensitivity (1.2x10(-15) emu), stability (lateral drift +/-35 nm over 3 h), and resolution (laser spot full width at half maximum down to 470 nm) are demonstrated, and illustrated by Kerr hysteresis loop measurements on a unique ultrathin magnetic nanodot, and over small segments of ultranarrow magnetic tracks. Large scanning MO Kerr microscopy images were also obtained with the same performances.