Microscopy Sample Preparation Research Articles

Practical aspects of the use of the X(2) holder for HRTEM-quality TEM sample preparation by FIB.

The X(2) holder enables the effective production of thin, electron transparent samples for high-resolution transmission electron microscopy (HRTEM). Improvements to the X(2) holder for high-quality transmission electron microscopy (TEM) sample preparation are presented in this paper. We discuss the influence of backscattered electrons (BSE) from the sample holder in determining the lamella thickness in situ and demonstrate that a significant improvement in thickness determination can be achieved by comparatively simple means using the relative BSE intensity. We show (using Monte Carlo simulations) that by taking into account the finite collection angle of the electron backscatter detector, an approximately 20% underestimation of the lamella thickness in a silicon sample can be avoided. However, a correct thickness determination for light-element lamellas still remains a problem with the backscatter method; we introduce a more accurate method using the energy dispersive X-ray spectroscopy (EDX) signal for in situ thickness determination. Finally, we demonstrate how to produce a thin lamella with a nearly damage-free surface using the X(2) holder in combination with sub-kV polishing in the Fischione Instruments׳ NanoMill(®) TEM specimen preparation system.

A Multi-Step Transmission Electron Microscopy Sample Preparation Technique for Indented Ceramics having Extensive Sub-Surface Cracking

A Multi-Step Transmission Electron Microscopy Sample Preparation Technique for Indented Ceramics having Extensive Sub-Surface Cracking

Practical Considerations for Single Molecule Localization Microscopy Sample Preparation

Practical Considerations for Single Molecule Localization Microscopy Sample Preparation

3D Atom Probe Microscopy Sample Preparation by Using L-Shape FIB-SEM-Ar Triple Beam

3D Atom Probe Microscopy Sample Preparation by Using L-Shape FIB-SEM-Ar Triple Beam

Volume shrinkage of bone, brain and muscle tissue in sample preparation for micro-CT and light sheet fluorescence microscopy (LSFM).

Two methods are especially suited for tomographic imaging with histological detail of macroscopic samples that consist of multiple tissue types (bone, muscle, nerve or fat): Light sheet (based) fluorescence microscopy (LSFM) and micro-computed tomography (micro-CT). Micro-CT requires staining with heavy chemical elements (and thus fixation and sometimes dehydration) in order to make soft tissue imageable when measured alongside denser structures. LSMF requires fixation, decalcification, dehydration, clearing and staining with a fluorescent dye. The specimen preparation of both imaging methods is prone to shrinkage, which is often not mentioned, let alone quantified. In this paper the presence and degree of shrinkage are quantitatively identified for the selected preparation methods/stains. LSFM delivers a volume shrinkage of 17% for bone, 56% for muscle and 62% for brain tissue. The three most popular micro-CT stains (phosphotungstic acid, iodine with potassium iodide, and iodine in absolute ethanol) deliver a volume shrinkage ranging from 10 to 56% for muscle and 27-66% for brain, while bone does not shrink in micro-CT preparation.

Assessment of photovoltaic junction position using combined focused ion beam and electron beam‐induced current analysis of close space sublimation deposited CdTe solar cells

ABSTRACTA major limitation of the cross‐section electron beam‐induced current method—the use of roughly fractured surfaces to provide the cross‐section—has been overcome with the use of focused ion beam microscope sample preparation. Using this method, it was possible to undertake a study of the relation between junction position and the corresponding external quantum efficiency (EQE) curves. For the case of cadmium telluride (CdTe) cells, it was demonstrated that the EQE curve shape that indicates a buried CdTe homojunction only arises if the junction is buried by more than 0.9 µm from the heterointerface. This highlights the limitations of interpreting EQE curve shape to determine junction position. It was also shown that extended postgrowth annealing degrades the cadmium sulfide by Kirkendall voiding, and this leads to efficiency loss. © 2014 The Authors. Progress in Photovoltaics: Research and Applications published by John Wiley & Sons, Ltd.

The Pore Structure of Compacted and Partly Saturated MX-80 Bentonite at Different Dry Densities

AbstractCompacted MX-80 bentonite is a potential backfill material in radioactive-waste repositories. Pore space in MX-80 has been the subject of considerable debate. 3D reconstructions of the pore space based on tomographic methods could provide new insights into the nature of the pore space of compacted bentonites. To date, few such reconstructions have been done because of problems with the preparation of bentonite samples for electron microscopy. The nanoscale intergranular pore space was investigated here by cryo-Focused Ion Beam nanotomography (FIB-nt) applied to previously high-pressure frozen MX-80 bentonite samples. This approach allowed a tomographic investigation of the in situ microstructure related to different dry densities (1.24, 1.46, and 1.67 g/cm3). The FIB-nt technique is able to resolve intergranular pores with radii >10 nm. With increasing dry density (1.24–1.67 g/cm3) the intergranular porosity (>10 nm) decreased from ~5 vol.% to 0.1 vol.%. At dry densities of 1.24 and 1.46 g/cm3, intergranular pores were filled with clay aggregates, which formed a mesh-like structure, similar to the honeycomb structure observed in diagenetic smectite. Unlike ‘typical’ clay gels, the cores of the honeycomb structure were not filled with pure water, but instead were filled with a less dense material which presumably consists of very fine clay similar to a colloid. In the low-density sample this honeycomb-structured material partly filled the intergranular pore space but some open pores were also present. In the 1.46 g/cm3 sample, the material filled the intergranular pores almost completely. At the highest densities investigated (1.67 g/cm3), the honeycomb-structured material was not present, probably because of the lack of intergranular pores which suppressed the formation of the honeycomb framework or skeleton consisting of clay aggregates.

酸化オスミウム（VIII）を含む電子顕微鏡試料作製廃液の再生に関する研究

酸化オスミウム（VIII）を含む電子顕微鏡試料作製廃液の再生に関する研究

Sample Preparation for Scanning Electron Microscopy: The Surprising Case of Freeze Drying from Tertiary Butanol

Sample Preparation for Scanning Electron Microscopy: The Surprising Case of Freeze Drying from Tertiary Butanol

Rendering graphene supports hydrophilic with non-covalent aromatic functionalization for transmission electron microscopy

Amorphous carbon films have been routinely used to enhance the preparation of frozen-hydrated samples for transmission electron microscopy (TEM), either in retaining protein concentration, providing mechanical stability or dissipating sample charge. However, strong background signal from the amorphous carbon support obstructs that of the sample, and the insulating properties of thin amorphous carbon films preclude any efficiency in dispersing charge. Graphene addresses the limitations of amorphous carbon. Graphene is a crystalline material with virtually no phase or amplitude contrast and unparalleled, high electrical carrier mobility. However, the hydrophobic properties of graphene have prevented its routine application in Cryo-TEM. This Letter reports a method for rendering graphene TEM supports hydrophilic—a convenient approach maintaining graphene's structural and electrical properties based on non-covalent, aromatic functionalization.

The Technology in Sample Preparation for Transmission Electron Microscopy and Ultrastructure Observation of Lung Tissue in Rats with Experimental Silicosis

ts hard to get ideal ultrathin sections because of the adamant SiO2 dust in silicosis, after perfusion fixation methods and strict control of the cutting speed, improving the success rate of the Silicosis tissue TEM sample preparation of ultrathin sections,so we can more clearly and accurately observed ultrastructural changes of silicosis,and it also can offer morphological basis for research the silicosis organizations function histological changes.

Sample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique adopted from single molecule imaging assays which allows adhesion of single virions to glass surfaces with specificity. This preparation is based on grafting the surface of the glass with a mixture of PLL-g-PEG and PLL-g-PEG-Biotin, adding a layer of avidin, and finally creating virion anchors through attachment of biotinylated virus specific antibodies. We have applied this technique across a range of experiments including atomic force microscopy (AFM) and super-resolution fluorescence imaging. This sample preparation method results in a control adhesion of the virions to the surface.

Sample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique adopted from single molecule imaging assays which allows adhesion of single virions to glass surfaces with specificity. This preparation is based on grafting the surface of the glass with a mixture of PLL-g-PEG and PLL-g-PEG-Biotin, adding a layer of avidin, and finally creating virion anchors through attachment of biotinylated virus specific antibodies. We have applied this technique across a range of experiments including atomic force microscopy (AFM) and super-resolution fluorescence imaging. This sample preparation method results in a control adhesion of the virions to the surface.

Focused Ion Beam and Nanomechanical Tests for High Resolution Surface Characterisation: New Resources for Platinum Group Metals Testing

Recently, the increasing importance and scope of nanotechnology has extended the need for high resolution characterisation tools beyond their traditional domains. As a consequence, advanced high-resolution tools at the nanoscale are now increasingly used in research and development (R&D) activities, offering the chance for a better understanding of submicron feature size dependence. This paper gives an overview of the synergic application of two high resolution techniques on the platinum group metals (pgms): focused ion beam (FIB) coupled with electron beam imaging, milling and deposition techniques; and nanoindentation testing. After a brief description of both techniques (architecture, probe-sample interaction basics and operation modes), the effectiveness of this combined approach is demonstrated for microstructural and nanomechanical investigations on very small samples. The advantages are low cost, fast and site-specific sample preparation for transition electron microscopy (TEM) analysis; study of the mechanical hardening effect on microstructure and hardness profile at the micron scale; failure analysis; and understanding of plasticity and elasticity behaviour. Two specific case studies related to a platinum-copper alloy for jewellery use and a platinum-rhodium alloy for sensor manufacturing are presented and discussed.

Chapter 8 - Correlative Cryo-Fluorescence and Cryo-Soft X-Ray Tomography of Adherent Cells at European Synchrotrons

Cryo-soft X-ray tomography (cryo-SXT) is a synchrotron-hosted imaging technique used to analyze the ultrastructure of intact, cryo-prepared cells. Correlation of cryo-fluorescence microscopy and cryo-SXT can be used to localize fluorescent proteins to organelles preserved close to native state. Cryo-correlative light and X-ray microscopy (cryo-CLXM) is particularly useful for the study of organelles that are susceptible to chemical fixation artifacts during sample preparation for electron microscopy. In our recent work, we used cryo-CLXM to characterize GFP-LC3-positive early autophagosomes in nutrient-starved HEK293A cells (Duke et al., 2013). Cup-shaped omegasomes were found to form at "hot-spots" on the endoplasmic reticulum. Furthermore, cryo-SXT image stacks revealed the presence of large complex networks of tubulated mitochondria in the starved cells, which would be challenging to model at this scale and resolution using light or electron microscopy. In this chapter, we detail the cryo-CLXM workflow that we developed and optimized for studying adherent mammalian cells. We show examples of data collected at the three European synchrotrons that currently host cryo-SXT microscopes, and describe how raw cryo-SXT datasets are processed into tomoX stacks, modeled, and correlated with cryo-fluorescence data to identify structures of interest.

The Effect of Hydrophilic Ionic Liquids 1-Ethyl-3-Methylimidazolium Lactate and Choline Lactate on Lipid Vesicle Fusion

Ionic liquids (ILs) are room-temperature molten salts that have applications in both physical sciences and more recently in the purification of proteins and lipids, gene transfection and sample preparation for electron microscopy (EM) studies. Transfection of genes into cells requires membrane fusion between the cell membrane and the transfection reagent, thus, ILs may be induce a membrane fusion event. To clarify the behavior of ILs with cell membranes the effect of ILs on model membranes, i.e., liposomes, were investigated. We used two standard ILs, 1-ethyl-3-methylimidazolium lactate ([EMI][Lac]) and choline lactate ([Ch][Lac]), and focused on whether these ILs can induce lipid vesicle fusion. Fluorescence resonance energy transfer and dynamic light scattering were employed to determine whether the ILs induced vesicle fusion. Vesicle solutions at low IL concentrations showed negligible fusion when compared with the controls in the absence of ILs. At concentrations of 30% (v/v), both types of ILs induced vesicle fusion up to 1.3 and 1.6 times the fluorescence intensity of the control in the presence of [Ch][Lac] and [EMI][Lac], respectively. This is the first demonstration that [EMI][Lac] and [Ch][Lac] induce vesicle fusion at high IL concentrations and this observation should have a significant influence on basic biophysical studies. Conversely, the ability to avoid vesicle fusion at low IL concentrations is clearly advantageous for EM studies of lipid samples and cells. This new information describing IL-lipid membrane interactions should impact EM observations examining cell morphology.

FIB Plan and Side View Cross-Sectional TEM Sample Preparation of Nanostructures

Focused ion beam is a powerful method for cross-sectional transmission electron microscope sample preparation due to being site specific and not limited to certain materials. It has, however, been difficult to apply to many nanostructured materials as they are prone to damage due to extending from the surface. Here we show methods for focused ion beam sample preparation for transmission electron microscopy analysis of such materials, demonstrated on GaAs-GaInP core shell nanowires. We use polymer resin as support and protection and are able to produce cross-sections both perpendicular to and parallel with the substrate surface with minimal damage. Consequently, nanowires grown perpendicular to the substrates could be imaged both in plan and side view, including the nanowire-substrate interface in the latter case. Using the methods presented here we could analyze the faceting and homogeneity of hundreds of adjacent nanowires in a single lamella.

Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM)

Cryo-soft X-ray tomography (cryo-SXT) is a powerful imaging technique that can extract ultrastructural information from whole, unstained mammalian cells as close to the living state as possible. Subcellular organelles including the nucleus, the Golgi apparatus and mitochondria have been identified by morphology alone, due to the similarity in contrast to transmission electron micrographs. In this study, we used cryo-SXT to image endosomes and autophagosomes, organelles that are particularly susceptible to chemical fixation artefacts during sample preparation for electron microscopy. We used two approaches to identify these compartments. For early and recycling endosomes, which are accessible to externally-loaded markers, we used an anti-transferrin receptor antibody conjugated to 10 nm gold particles. For autophagosomes, which are not accessible to externally-applied markers, we developed a correlative cryo-fluorescence and cryo-SXT workflow (cryo-CLXM) to localise GFP-LC3 and RFP-Atg9. We used a stand-alone cryo-fluorescence stage in the home laboratory to localise the cloned fluorophores, followed by cryo-soft X-ray tomography at the synchrotron to analyse cellular ultrastructure. We mapped the 3D ultrastructure of the endocytic and autophagic structures, and discovered clusters of omegasomes arising from ‘hotspots’ on the ER. Thus, immunogold markers and cryo-CLXM can be used to analyse cellular processes that are inaccessible using other imaging modalities.

Starch synthase 4 is essential for coordination of starch granule formation with chloroplast division during Arabidopsis leaf expansion

Arabidopsis thaliana mutants lacking the SS4 isoform of starch synthase have strongly reduced numbers of starch granules per chloroplast, suggesting that SS4 is necessary for the normal generation of starch granules. To establish whether it plays a direct role in this process, we investigated the circumstances in which granules are formed in ss4 mutants.Starch granule numbers and distribution and the accumulation of starch synthase substrates and products were investigated during ss4 leaf development, and in ss4 mutants carrying mutations or transgenes that affect starch turnover or chloroplast volume.We found that immature ss4 leaves have no starch granules, but accumulate high concentrations of the starch synthase substrate ADPglucose. Granule numbers are partially restored by elevating the capacity for glucan synthesis (via expression of bacterial glycogen synthase) or by increasing the volumes of individual chloroplasts (via introduction of arc mutations). However, these granules are abnormal in distribution, size and shape.SS4 is an essential component of a mechanism that coordinates granule formation with chloroplast division during leaf expansion and determines the abundance and the flattened, discoid shape of leaf starch granules.

Preparation of samples for electron microscopy by high osmotic pressure method

Preparation of samples for electron microscopy by high osmotic pressure method