Surface damage induced by FIB milling and imaging of biological samples is controllable

Focused ion beam (FIB) techniques are among the most important tools for the nanostructuring of surfaces. We used the FIB/SEM (scanning electron microscope) for milling and imaging of digestive gland cells. The aim of our study was to document the interactions of FIB with the surface of the biological sample during FIB investigation, to identify the classes of artifacts, and to test procedures that could induce the quality of FIB milled sections by reducing the artifacts. The digestive gland cells were prepared for conventional SEM. During FIB/SEM operation we induced and enhanced artifacts. The results show that FIB operation on biological tissue affected the area of the sample where ion beam was rastering. We describe the FIB-induced surface major artifacts as a melting-like effect, sweating-like effect, morphological deformations, and gallium (Ga(+)) implantation. The FIB induced surface artifacts caused by incident Ga(+) ions were reduced by the application of a protective platinum strip on the surface exposed to the beam and by a suitable selection of operation protocol. We recommend the same sample preparation methods, FIB protocol for milling and imaging to be used also for other biological samples.     

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

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

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.     

FIB preparation and SEM investigations for three-dimensional analysis of cell cultures on microneedle arrays

We report the investigation of the interfaces between microneedle arrays and cell cultures in patch-on-chip systems by using Focused Ion Beam (FIB) preparation and Scanning Electron Microscopy (SEM). First, FIB preparations of micro chips are made to determine the size and shape of the designed microneedles. In this essay, we investigate the cell-substrate interaction, especially the cell adhesion, and the microneedle's potential cell penetration. For this purpose, cross-sectional preparation of these hard/soft hybrid structures is performed by the FIB technology. By applying the FIB technology followed by high-resolution imaging with SEM, new insights into the cell-substrate interface can be received. One can clearly distinguish between cells that are only in contact with microneedles and cells that are penetrated by microneedles. A stack of slice images is collected by the application of the slice-and-view setup during FIB preparation and is used for three-dimensional reconstruction of cells and micro-needles.     

Scanning electron microscopic observations on deembedded biological tissue sections: Comparison of different fixatives and embedding materials

Conventional plant histological specimens fixed in formalin-acetic acid-alcohol, chromic acid-acetic acid-formaldehyde, or glutaraldehyde-osmium and embedded in either paraffin or plastic are examined as possible rapid methods for providing an alternative image of cellular structure by using scanning electron microscopy. Using the mitotic figures of actively growing onion root tips as a study specimen, the organization of the nucleus and spindle apparatus is reasonably well preserved as compared with isolated mitotic spindles and studies of mitosis in endosperm tissue. Relief of internal structure in this technique is obtained through the coagulant nature of the fixative. Used judiciously, this technique can reveal aspects of the three-dimensional nature of internal tissue structure that may otherwise be difficult to discern.     

New methods of track membrane treatment in the preparation of samples for further observation with scanning electron microscopy

Track membranes are porous systems consisting of a polymer foil with thin channels (i.e. pores) piercing it from surface to surface. The creation of non‐cylindrical pores in a track membrane is important for the optimization of membrane characteristics, i.e. the highest productivity at the required selectivity. A new method of cleavage preparation (the irradiation of track membrane samples with accelerated electrons) for the observation of channel shapes directly in the membrane cross‐sections is presented. Diagrams showing the tensile and burst strengths as a function of the irradiation dose, and images of surfaces and cleavages of track membrane samples are presented in this work. The changes in the pore sizes and shapes along the channel were clearly seen. These results can be used for the optimization of track membrane production.     

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.     

Comparison of manual and automatic processing of biological samples for electron microscopy

The ultrastructure of a sample can be observed by electron microscopy (EM), which has become an indispensable research tool in morphological studies. However, EM sample preparation techniques are complicated and time‐consuming, with a high labor cost. The current study was conducted to compare the conventional manual and automated methods for sample processing and post‐staining for electron microscopy. Automated sample processing reduces OsO₄ contamination, improves the efficiency of sample preparation and is easy to use. Therefore, the results of their study provide a practical and feasible method for the preparation of biological samples for electron microscopy.     

An investigation of density determination methods for porous materials,small samples and particulates

Three new density measurement techniques have been devised and evaluated for the measurement of non-standard objects, namely porous material samples, small solid samples, powders and particulates. Hydrostatic weighing has traditionally been used to determine the density of solid artefacts. This method is not, however, suitable for porous objects since they will adsorb water making weighing in water unstable and possibly detrimental to the material samples. A method, weighing the artefacts in inert gas, has been developed for this application. The density determination of small solid artefacts cannot be achieved by conventional hydrostatic weighing techniques due to limits on the accuracy with which the weight-in-water can be determined. A density gradient column method for such measurements, delivering very low uncertainties, has been developed and evaluated. A liquid pyknometry method has also been investigated as an alternative to traditional helium and mercury pyknometry. The technique offers improved accuracy and a precise determination of thermal coefficient of the sample under test.     

发光菌急性毒性分析方法的比较和优化

从发光菌急性毒性测试方法的原理出发,分析现行国标方法的缺陷,并深入比较国外主流仪器的优缺点,进而总结出一套可靠性更高的急性毒性测试方法。方法涵盖实验分析、干扰分析、数据处理、质量控制等方面。同时,针对现有方法研究中的不足,提出建立青海弧菌Q67毒性数据库及真和发光菌研发两个方向,为发光菌急性毒性测试方法新国标的修制定提供参考。     

Comparison of hyperspectral classification methods for the analysis of cerium oxide nanoparticles in histological and aqueous samples

Hyperspectral imaging (HSI) and classification are established methods that are being applied in new ways to the analysis of nanoscale materials in a variety of matrices. Typically, enhanced darkfield microscopy (EDFM)‐based HSI data (also known as image datacubes) are collected in the wavelength range of 400–1000 nm for each pixel in a datacube. Utilising different spectral library (SL) creation methods, spectra from pixels in the datacube corresponding to known materials can be collected into reference spectral libraries (RSLs), which can be used to classify materials in datacubes of experimental samples using existing classification algorithms. In this study, EDFM‐HSI was used to visualise and analyse industrial cerium oxide (CeO₂; ceria) nanoparticles (NPs) in rat lung tissues and in aqueous suspension. Rats were exposed to ceria NPs via inhalation, mimicking potential real‐world occupational exposures. The lung tissues were histologically prepared: some tissues were stained with hematoxylin and eosin (H&E) and some were left unstained. The goal of this study was to determine how HSI and classification results for ceria NPs were influenced by (1) the use of different RSL creation and classification methods and (2) the application of those methods to samples in different matrices (stained tissue, unstained tissue, or aqueous solution). Three different RSL creation methods – particle filtering (PF), manual selection, and spectral hourglass wizard (SHW) – were utilised to create the RSLs of known materials in unstained and stained tissue, and aqueous suspensions, which were then used to classify the NPs in the different matrices. Two classification algorithms – spectral angle mapper (SAM) and spectral feature fitting (SFF) – were utilised to determine the presence or absence of ceria NPs in each sample. The results from the classification algorithms were compared to determine how each influenced the classification results for samples in different matrices. The results showed that sample matrix and sample preparation significantly influenced the NP classification thresholds in the complex matrices. Moreover, considerable differences were observed in the classification results when utilising each RSL creation and classification method for each type of sample. Results from this study illustrate the importance of appropriately selecting HSI algorithms based on specific material and matrix characteristics in order to obtain optimal classification results. As HSI is increasingly utilised for NP characterisation for clinical, environmental and health and safety applications, this investigation is important for further refining HSI protocols while ensuring appropriate data collection and analysis.     

Gridded Aclar: preparation methods and use for correlative light and electron microscopy of cell monolayers,by TEM and FIB–SEM

Aclar, a copolymer film with properties very similar to those of tissue culture plastic, is a versatile substrate to grow cells for light (including fluorescence) and electron microscopic applications in combination with both chemical fixation and cryoimmobilization. In this paper, we describe complete procedures to perform correlative light and electron microscopy using Aclar as substrate for the culture of cell monolayers to be finally embedded in plastic. First, we developed straightforward, efficient and flexible ways to mark the surface of the Aclar to create substrates to locate cells first at the light microscopy and then the electron microscopy level. All the methods enable the user to self‐design gridded Aclar pieces, according to the purpose of the experiments, and create a large number of substrates in a short time. Second, we confirmed that marked Aclar supports the normal growth and morphology of cells. Third, we validated the correlative light and electron microscopy procedure using Aclar. This validation was done for the high‐resolution analysis of endothelial cells using transmission electron microscopy and focused ion beam–scanning electron microscopy in combination with the use of fluorescence, phase contrast and/or bright field microscopy to map areas of interest at low resolution. The methods that we present are diverse, easy to implement and highly reproducible, and emphasize the versatility of Aclar as a cell growth substrate for diverse microscopic applications.