Browse
Submit Data
Databases
API
Help

Dataset Information

43 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Monitoring Carbon in Electron and Ion Beam Deposition within FIB-SEM.

ABSTRACT: It is well known that carbon present in scanning electron microscopes (SEM), Focused ion beam (FIB) systems and FIB-SEMs, causes imaging artefacts and influences the quality of TEM lamellae or structures fabricated in FIB-SEMs. The severity of such effects depends not only on the quantity of carbon present but also on its bonding state. Despite this, the presence of carbon and its bonding state is not regularly monitored in FIB-SEMs. Here we demonstrated that Secondary Electron Hyperspectral Imaging (SEHI) can be implemented in different FIB-SEMs (ThermoFisher Helios G4-CXe PFIB and Helios Nanolab G3 UC) and used to observe carbon built up/removal and bonding changes resulting from electron/ion beam exposure. As well as the ability to monitor, this study also showed the capability of Plasma FIB Xe exposure to remove carbon contamination from the surface of a Ti6246 alloy without the requirement of chemical surface treatments.

SUBMITTER: Farr NTH

PROVIDER: S-EPMC8199708 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Monitoring Carbon in Electron and Ion Beam Deposition within FIB-SEM.

Farr Nicholas T H NTH Hughes Gareth M GM Rodenburg Cornelia C

Materials (Basel, Switzerland) 20210602 11

It is well known that carbon present in scanning electron microscopes (SEM), Focused ion beam (FIB) systems and FIB-SEMs, causes imaging artefacts and influences the quality of TEM lamellae or structures fabricated in FIB-SEMs. The severity of such effects depends not only on the quantity of carbon present but also on its bonding state. Despite this, the presence of carbon and its bonding state is not regularly monitored in FIB-SEMs. Here we demonstrated that Secondary Electron Hyperspectral Ima ...[more]

PMID: 34199625

Similar Datasets

Axonal debris accumulates in corneal epithelial cells after intraepithelial corneal nerves are damaged: A focused Ion Beam Scanning Electron Microscopy (FIB-SEM) study.

Project description:The intraepithelial corneal nerves (ICNs) that innervate the corneal epithelium are maintained through interactions with corneal epithelial cells and the extracellular matrix they produce. One to several axons bundle together within the basal cell layer and extend parallel to the ocular surface or branch and extend apically. Here we use 3-dimentional (3D) ultrastructural reconstructions of control and trephine injured mouse corneal epithelium and stroma produced using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) to determine whether corneal epithelial or immune cells resident in the epithelium remove axonal debris and degrade it in their lysosomes after trephine injury to the cornea. We demonstrate that axonal fragments are internalized in the corneal epithelium and accumulate within electron dense structures consistent with lysosomes 3 h after trephine injury in both epithelial and immune cells located among the basal cells of the trephine injured cornea. Confocal imaging showed fewer CD45+ immune cells within the corneal epithelium after trephine injury compared to controls. The resolution obtained using FIB-SEM also allowed us to show that the presence of sensory axons at the basal aspect of the epithelial basal cells close to the anterior aspect of the epithelial basement membrane (EBM) is associated with a focal reduction in EBM thickness. In addition, we show using FIB-SEM and confocal imaging that superficial trephine injuries that do not penetrate the stroma, damage the integrity of anterior stromal nerves. These studies are the first to look at the mouse cornea following nerve injury using FIB-SEM.

| S-EPMC7697722 | biostudies-literature

Preparation of hybrid samples for scanning electron microscopy (SEM) coupled to focused ion beam (FIB) analysis: A new way to study cell adhesion to titanium implant surfaces.

Project description:The study of the intimate connection occurring at the interface between cells and titanium implant surfaces is a major challenge for dental materials scientists. Indeed, several imaging techniques have been developed and optimized in the last decades, but an optimal method has not been described yet. The combination of the scanning electron microscopy (SEM) with a focused ion beam (FIB), represents a pioneering and interesting tool to allow the investigation of the relationship occurring at the interface between cells and biomaterials, including titanium. However, major caveats concerning the nature of the biological structures, which are not conductive materials, and the physico-chemical properties of titanium (i.e. color, surface topography), require a fine and accurate preparation of the sample before its imaging. Hence, the aim of the present work is to provide a suitable protocol for cell-titanium sample preparation before imaging by SEM-FIB. The concepts presented in this paper are also transferrable to other fields of biomaterials research.

| S-EPMC9345346 | biostudies-literature

FIB-SEM imaging of carbon nanotubes in mouse lung tissue.

Project description:Ultrastructural characterisation is important for understanding carbon nanotube (CNT) toxicity and how the CNTs interact with cells and tissues. The standard method for this involves using transmission electron microscopy (TEM). However, in particular, the sample preparation, using a microtome to cut thin sample sections for TEM, can be challenging for investigation of regions with agglomerations of large and stiff CNTs because the CNTs cut with difficulty. As a consequence, the sectioning diamond knife may be damaged and the uncut CNTs are left protruding from the embedded block surface excluding them from TEM analysis. To provide an alternative to ultramicrotomy and subsequent TEM imaging, we studied focused ion beam scanning electron microscopy (FIB-SEM) of CNTs in the lungs of mice, and we evaluated the applicability of the method compared to TEM. FIB-SEM can provide serial section volume imaging not easily obtained with TEM, but it is time-consuming to locate CNTs in the tissue. We demonstrate that protruding CNTs after ultramicrotomy can be used to locate the region of interest, and we present FIB-SEM images of CNTs in lung tissue. FIB-SEM imaging was applied to lung tissue from mice which had been intratracheally instilled with two different multiwalled CNTs; one being short and thin, and the other longer and thicker. FIB-SEM was found to be most suitable for detection of the large CNTs (Ø ca. 70 nm), and to be well suited for studying CNT agglomerates in biological samples which is challenging using standard TEM techniques.

| S-EPMC4039996 | biostudies-literature

Photothermal excitation efficiency enhancement of cantilevers by electron beam deposition of amorphous carbon thin films.

Project description:In recent years, the atomic force microscope has proven to be a powerful tool for studying biological systems, mainly for its capability to measure in liquids with nanoscale resolution. Measuring tissues, cells or proteins in their physiological conditions gives us access to valuable information about their real 'in vivo' structure, dynamics and functionality which could then fuel disruptive medical and biological applications. The main problem faced by the atomic force microscope when working in liquid environments is the difficulty to generate clear cantilever resonance spectra, essential for stable operation and for high resolution imaging. Photothermal actuation overcomes this problem, as it generates clear resonance spectra free from spurious peaks. However, relatively high laser powers are required to achieve the desired cantilever oscillation amplitude, which could potentially damage biological samples. In this study, we demonstrate that the photothermal excitation efficiency can be enhanced by coating the cantilever with a thin amorphous carbon layer to increase the heat absorption from the laser, reducing the required excitation laser power and minimizing the damage to biological samples.

| S-EPMC7562866 | biostudies-literature

Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition.

Project description:Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.

| S-EPMC9802471 | biostudies-literature

Electrospray ion beam deposition plus low-energy electron holography as a tool for imaging individual biomolecules.

Project description:Inline low-energy electron holography (LEEH) in conjunction with sample preparation by electrospray ion beam deposition (ES-IBD) has recently emerged as a promising method for the sub-nanometre-scale single-molecule imaging of biomolecules. The single-molecule nature of the LEEH measurement allows for the mapping of the molecules' conformational space and thus for the imaging of structurally variable biomolecules, thereby providing valuable complementary information to well-established biomolecular structure determination methods. Here, after briefly tracing the development of inline LEEH in bioimaging, we present the state-of-the-art of native ES-IBD + LEEH as a method of single-protein imaging, discuss its applications, specifically regarding the imaging of structurally flexible protein systems and the amplitude and phase information encoded in a low-energy electron hologram, and provide an outlook regarding the considerable possibilities for the future advancement of the approach.

| S-EPMC10070476 | biostudies-literature

SEM3De: image restoration for FIB-SEM.

Project description:MotivationFIB-SEM (Focused Ion Beam-Scanning Electron Microscopy) is a technique to generate 3D images of samples up to several microns in depth. The principle is based on the alternate use of SEM to image the surface of the sample (a few nanometers thickness) and of FIB to mill the surface of the sample a few nanometers at the time. In this way, huge stacks of images can thus be acquired.Although this technique has proven useful in imaging biological systems, the presence of some visual artifacts (stripes due to sample milling, detector saturation, charge effects, focus or sample drift, etc.) still raises some challenges for image interpretation and analyses.ResultsWith the aim of meeting these challenges, we developed a freeware (SEM3De) that either corrects artifacts with state-of-the-art approaches or, when artifacts are impossible to correct, enables the replacement of artifactual slices by an in-painted image created from adjacent non-artifactual slices. Thus, SEM3De improves the overall usability of FIB-SEM acquisitions.Availability and implementationSEM3De can be downloaded from https://sourceforge.net/projects/sem3de/ as a plugin for ImageJ.

| S-EPMC10516526 | biostudies-literature

Ligand Size and Carbon-Chain Length Study of Silver Carboxylates in Focused Electron-Beam-Induced Deposition.

Project description:Gas-assisted focused electron-beam-induced deposition is a versatile tool for the direct writing of complex-shaped nanostructures with unprecedented shape fidelity and resolution. While the technique is well-established for various materials, the direct electron beam writing of silver is still in its infancy. Here, we examine and compare five different silver carboxylates, three perfluorinated: [Ag2(µ-O2CCF3)2], [Ag2(µ-O2CC2F5)2], and [Ag2(µ-O2CC3F7)2], and two containing branched substituents: [Ag2(µ-O2CCMe2Et)2] and [Ag2(µ-O2CtBu)2], as potential precursors for focused electron-beam-induced deposition. All of the compounds show high sensitivity to electron dissociation and efficient dissociation of Ag-O bonds. The as-deposited materials have silver contents from 42 at.% to above 70 at.% and are composed of silver nano-crystals with impurities of carbon and fluorine between them. Precursors with the shortest carbon-fluorine chain ligands yield the highest silver contents. In addition, the deposited silver content depends on the balance of electron-induced ligand co-deposition and ligand desorption. For all of the tested compounds, low electron flux was related to high silver content. Our findings demonstrate that silver carboxylates constitute a promising group of precursors for gas-assisted focused electron beam writing of high silver content materials.

| S-EPMC10180361 | biostudies-literature

Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition.

Project description:Imaging of proteins at the single-molecule level can reveal conformational variability, which is essential for the understanding of biomolecules. To this end, a biologically relevant state of the sample must be retained during both sample preparation and imaging. Native electrospray ionization (ESI) can transfer even the largest protein complexes into the gas phase while preserving their stoichiometry and overall shape. High-resolution imaging of protein structures following native ESI is thus of fundamental interest for establishing the relation between gas phase and solution structure. Taking advantage of low-energy electron holography's (LEEH) unique capability of imaging individual proteins with subnanometer resolution, we investigate the conformational flexibility of Herceptin, a monoclonal IgG antibody, deposited by native electrospray mass-selected ion beam deposition (ES-IBD) on graphene. Images reconstructed from holograms reveal a large variety of conformers. Some of these conformations can be mapped to the crystallographic structure of IgG, while others suggest that a compact, gas-phase-related conformation, adopted by the molecules during ES-IBD, is retained. We can steer the ratio of those two types of conformations by changing the landing energy of the protein on the single-layer graphene surface. Overall, we show that LEEH can elucidate the conformational heterogeneity of inherently flexible proteins, exemplified here by IgG antibodies, and thereby distinguish gas-phase collapse from rearrangement on surfaces.

| S-EPMC8713884 | biostudies-literature

Ion-to-electron capacitance of single-walled carbon nanotube layers before and after ion-selective membrane deposition.

Project description:The capacitance of the ion-to-electron transducer layer helps to maintain a high potential stability of solid-contact ion-selective electrodes (SC-ISEs), and its estimation is therefore an essential step of SC-ISE characterization. The established chronopotentiometric protocol used to evaluate the capacitance of the single-walled carbon nanotube transducer layer was revised in order to obtain more reliable and better reproducible values and also to allow capacitance to be measured before membrane deposition for electrode manufacturing quality control purposes. The capacitance values measured with the revised method increased linearly with the number of deposited carbon nanotube-based transducer layers and were also found to correlate linearly before and after ion-selective membrane deposition, with correlation slopes close to 1 for nitrate-selective electrodes, to 0.7 and to 0.5 for potassium- and calcium-selective electrodes.

| S-EPMC8018922 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data