3D imaging of the early embryonic chicken heart with focused ion beam scanning electron microscopy

Early embryonic heart development is a period of dynamic growth and remodeling, with rapid changes occurring at the tissue, cell, and subcellular levels. A detailed understanding of the events that establish the components of the heart wall has been hampered by a lack of methodologies for three-dimensional (3D), high-resolution imaging. Focused ion beam scanning electron microscopy (FIB-SEM) is a novel technology for imaging 3D tissue volumes at the subcellular level. FIB-SEM alternates between imaging the block face with a scanning electron beam and milling away thin sections of tissue with a FIB, allowing for collection and analysis of 3D data. FIB-SEM was used to image the three layers of the day 4 chicken embryo heart: myocardium, cardiac jelly, and endocardium. Individual images obtained with FIB-SEM were comparable in quality and resolution to those obtained with transmission electron microscopy. Up to 1,100 serial images were obtained in 4 nm increments at 4.88 nm resolution, and image stacks were aligned to create volumes 800-1,500 μm3 in size. Segmentation of organelles revealed their organization and distinct volume fractions between cardiac wall layers. We conclude that FIB-SEM is a powerful modality for 3D subcellular imaging of the embryonic heart wall.

Role of α2β1 integrins in mediating cell shape on microtextured titanium surfaces

Surface microroughness plays an important role in determining osteoblast behavior on titanium. Previous studies have shown that osteoblast differentiation on microtextured titanium substrates is dependent on alpha-2 beta-1 (α2β1) integrin signaling. This study used focused ion beam milling and scanning electron microscopy, combined with three-dimensional image reconstruction, to investigate early interactions of individual cells with their substrate and the role of integrin α2β1 in determining cell shape. MG63 osteoblast-like cells on sand blasted/acid etched (SLA) Ti surfaces after 3 days of culturing indicated decreased cell number, increased cell differentiation, and increased expression of mRNA levels for α1, α2, αV, and β1 integrin subunits compared to cells on smooth Ti (PT) surfaces. α2 or β1 silenced cells exhibited increased cell number and decreased differentiation on SLA compared to wild-type cells. Wild-type cells on SLA possessed an elongated morphology with reduced cell area, increased cell thickness, and more apparent contact points. Cells on PT exhibited greater spreading and were relatively flat. Silenced cells possessed a morphology and phenotype similar to wild-type cells grown on PT. These observations indicate that surface microroughness affects cell response via α2β1 integrin signaling, resulting in a cell shape that promotes osteoblastic differentiation.

Resolving the CaP-bone interface: a review of discoveries with light and electron microscopy

It has long been known that the interfacial relationship between synthetic materials and tissue is influential in the success of implant materials. Instability at the implant interface has been shown, in some cases, to lead to complete implant failure. Bioceramics, and in particular calcium phosphates, form a large fraction of the implantable devices on the market today due to the biocompatibility they exhibit in contact with bone and tooth-like tissues. The characterization of such bioceramic-tissue interfaces has played a crucial role in understanding the behavior of bioceramics in vivo. In this review, we shed light on the preparation methods, technological approaches and key advances in resolving the interface between calcium phosphate bioceramics and bone, and share a future outlook on this field.

Focused ion beam processing to fabricate ohmic contact electrodes on a bismuth nanowire for Hall measurements

Ohmic contact electrodes for four-wire resistance and Hall measurements were fabricated on an individual single-crystal bismuth nanowire encapsulated in a cylindrical quartz template. Focused ion beam processing was utilized to expose the side surfaces of the bismuth nanowire in the template, and carbon and tungsten electrodes were deposited on the bismuth nanowire in situ to achieve electrical contacts. The temperature dependence of the four-wire resistance was successfully measured for the bismuth nanowire, and a difference between the resistivities of the two-wire and four-wire methods was observed. It was concluded that the two-wire method was unsuitable for estimation of the resistivity due to the influence of contact resistance, even if the magnitude of the bismuth nanowire resistance was greater than the kilo-ohm order. Furthermore, Hall measurement of a 4-μm-diameter bismuth microwire was also performed as a trial, and the evaluated temperature dependence of the carrier mobility was in agreement with that for bulk bismuth, which indicates that the carrier mobility was successfully measured using this technique. PACS: 81.07.Gf.

Controlling FIB-SBEM slice thickness by monitoring the transmitted ion beam

Serial block-face electron microscopy with focused ion beam cutting suffers from cutting artefacts caused by changes in the relative position of beam and sample, which are, for example, inevitable when reconditioning the ion gun. The latter has to be done periodically, which limits the continuous stack-acquisition time to several days. Here, we describe a method for controlling the ion-beam position that is based on detecting that part of the ion beam that passes the sample (transmitted beam). We find that the transmitted-beam current decreases monotonically as the beam approaches the sample and can be used to determine the relative position of beam and sample to an accuracy of around one nanometre. By controlling the beam approach using this current as the feedback parameter, it is possible to ion-mill consecutive 5 nm slices without detectable variations in thickness even in the presence of substantial temperature fluctuations and to restart the acquisition of a stack seamlessly. In addition, the use of a silicon junction detector instead of the in-column detector is explored.

Direct observation of CD4 T cell morphologies and their cross-sectional traction force derivation on quartz nanopillar substrates using focused ion beam technique

Direct observations of the primary mouse CD4 T cell morphologies, e.g., cell adhesion and cell spreading by culturing CD4 T cells in a short period of incubation (e.g., 20 min) on streptavidin-functionalized quartz nanopillar arrays (QNPA) using a high-content scanning electron microscopy method were reported. Furthermore, we first demonstrated cross-sectional cell traction force distribution of surface-bound CD4 T cells on QNPA substrates by culturing the cells on top of the QNPA and further analysis in deflection of underlying QNPA via focused ion beam-assisted technique.

Correlative analysis of immunoreactivity in confocal laser-scanning microscopy and scanning electron microscopy with focused ion beam milling

Recently, three-dimensional reconstruction of ultrastructure of the brain has been realized with minimal effort by using scanning electron microscopy (SEM) combined with focused ion beam (FIB) milling (FIB-SEM). Application of immunohistochemical staining in electron microscopy (EM) provides a great advantage in that molecules of interest are specifically localized in ultrastructures. Thus, we applied immunocytochemistry for FIB-SEM and correlated this immunoreactivity with that in confocal laser-scanning microcopy (CF-LSM). Dendrites of medium-sized spiny neurons in the rat neostriatum were visualized using a recombinant viral vector, which labeled the infected neurons with membrane-targeted GFP in a Golgi stain-like fashion. Moreover, the thalamostriatal afferent terminals were immunolabeled with Cy5 fluorescence for vesicular glutamate transporter 2 (VGluT2). After detection of the sites of terminals apposed to the dendrites by using CF-LSM, GFP and VGluT2 immunoreactivities were further developed for EM by using immunogold/silver enhancement and immunoperoxidase/diaminobenzidine (DAB) methods, respectively. In contrast-inverted FIB-SEM images, silver precipitations and DAB deposits were observed as fine dark grains and diffuse dense profiles, respectively, indicating that these immunoreactivities were as easily recognizable as those in the transmission electron microscopy (TEM) images. Furthermore, in the sites of interest, some appositions displayed synaptic specializations of an asymmetric type. Thus, the present method was useful in the three-dimensional analysis of immunocytochemically differentiated synaptic connections in the central neural circuit.

Analysis of the 3D distribution of stacked self-assembled quantum dots by electron tomography

The 3D distribution of self-assembled stacked quantum dots (QDs) is a key parameter to obtain the highest performance in a variety of optoelectronic devices. In this work, we have measured this distribution in 3D using a combined procedure of needle-shaped specimen preparation and electron tomography. We show that conventional 2D measurements of the distribution of QDs are not reliable, and only 3D analysis allows an accurate correlation between the growth design and the structural characteristics.

Preparation of bismuth nanowire encased in quartz template for Hall measurements using focused ion beam processing

Forming electrodes on opposite sides of an individual bismuth nanowire was attempted to prepare for Hall measurements. Although a 1-mm-long bismuth nanowire which is completely covered with a quartz template has been successfully fabricated to prevent oxidation, it is very difficult to attach Hall electrodes on the opposite sides of the nanowire due to the quartz covering. One side of the cylindrical quartz template was removed by polishing without exposure of the nanowire to the atmosphere; the thickness between the polished template surface and the nanowire was estimated to be several micrometers. Focused ion beam processing was successfully employed to expose both surfaces of the nanowire under high vacuum by removing part of the quartz template. A carbon thin film was then deposited in situ on the wire surface to fabricate an electrical contact on the bismuth nanowire sample. Furthermore, the energy dispersive X-ray analysis was performed to the area processed by focused ion beam, and the bismuth component of the nanowire was successfully detected. It was confirmed that the focused ion beam processing was applicable to attach electrodes to bismuth nanowire for Hall measurement.

Microfiber-based Bragg gratings for sensing applications: a review

Microfiber-based Bragg gratings (MFBGs) are an emerging concept in ultra-small optical fiber sensors. They have attracted great attention among researchers in the fiber sensing area because of their large evanescent field and compactness. In this review, the basic techniques for the fabrication of MFBGs are introduced first. Then, the sensing properties and applications of MFBGs are discussed, including measurement of refractive index (RI), temperature, and strain/force. Finally a summary of selected MFBG sensing elements from previous literature are tabulated.

Critical aspects of substrate nanopatterning for the ordered growth of GaN nanocolumns

Precise and reproducible surface nanopatterning is the key for a successful ordered growth of GaN nanocolumns. In this work, we point out the main technological issues related to the patterning process, mainly surface roughness and cleaning, and mask adhesion to the substrate. We found that each of these factors, process-related, has a dramatic impact on the subsequent selective growth of the columns inside the patterned holes. We compare the performance of e-beam lithography, colloidal lithography, and focused ion beam in the fabrication of hole-patterned masks for ordered columnar growth. These results are applicable to the ordered growth of nanocolumns of different materials.

Espina: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images

The synapses in the cerebral cortex can be classified into two main types, Gray's type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed, and quantified from large 3D tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation, and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes.

Fabrication of sub-5 nm nanochannels in insulating substrates using focused ion beam milling

The use of focused ion beam (FIB) milling to fabricate nanochannels with critical dimensions extending below 5 nm is described. FIB milled lines have narrowing widths as they are milled deeper into a substrate. This focusing characteristic is coupled with a two-layered architecture consisting of a relatively thick (>100 nm) metal film deposited onto a substrate. A channel is milled through the metal layer until it penetrates a prescribed depth into the substrate material. The metal is then removed, leaving a nanochannel with smooth surfaces and lateral dimensions as small as sub-5 nm. These open nanochannels can be sealed with a cover plate and the resulting devices are well-suited for single-molecule DNA transport studies. This methodology is used with quartz, single-crystal silicon, and polydimethylsiloxane substrates to demonstrate its general utility.

Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides

We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO(2) and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide.

Counting Synapses Using FIB/SEM Microscopy: A True Revolution for Ultrastructural Volume Reconstruction

The advent of transmission electron microscopy (TEM) in the 1950s represented a fundamental step in the study of neuronal circuits. The application of this technique soon led to the realization that the number of synapses changes during the course of normal life, as well as under certain pathological or experimental circumstances. Since then, one of the main goals in neurosciences has been to define simple and accurate methods to estimate the magnitude of these changes. Contrary to analysing single sections, TEM reconstructions are extremely time-consuming and difficult. Therefore, most quantitative studies use stereological methods to define the three-dimensional characteristics of synaptic junctions that are studied in two dimensions. Here, to count the exact number of synapses per unit of volume we have applied a new three-dimensional reconstruction method that involves the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM). We show that the images obtained with FIB/SEM are similar to those obtained with TEM, but with the advantage that FIB/SEM permits serial reconstructions of large volumes of tissue to be generated rapidly and automatically. Furthermore, we compared the estimates of the number of synapses obtained with stereological methods with the values obtained by FIB/SEM reconstructions. We concluded that FIB/SEM not only provides the actual number of synapses per volume but it is also much easier and faster to use than other currently available TEM methods. More importantly, it also avoids most of the errors introduced by stereological methods and overcomes the difficulties associated with these techniques.

Cathodoluminescence and Cross-sectional Transmission Electron Microscopy Studies for Deformation Behaviors of GaN Thin Films Under Berkovich Nanoindentation

In this study, details of Berkovich nanoindentation-induced mechanical deformation mechanisms of metal-organic chemical-vapor deposition-derived GaN thin films have been systematic investigated with the aid of the cathodoluminescence (CL) and the cross-sectional transmission electron microscopy (XTEM) techniques. The multiple “pop-in” events were observed in the load-displacement (P–h) curve and appeared to occur randomly by increasing the indentation load. These instabilities are attributed to the dislocation nucleation and propagation. The CL images of nanoindentation show very well-defined rosette structures with the hexagonal system and, clearly display the distribution of deformation-induced extended defects/dislocations which affect CL emission. By using focused ion beam milling to accurately position the cross-section of an indented area, XTEM results demonstrate that the major plastic deformation is taking place through the propagation of dislocations. The present observations are in support to the massive dislocations activities occurring underneath the indenter during the loading cycle. No evidence of either phase transformation or formation of micro-cracking was observed by means of scanning electron microscopy and XTEM observations. We also discuss how these features correlate with Berkovich nanoindentation produced defects/dislocations structures.

Mechanical Deformation Induced in Si and GaN Under Berkovich Nanoindentation

Details of Berkovich nanoindentation-induced mechanical deformation mechanisms of single-crystal Si(100) and the metal-organic chemical-vapor deposition (MOCVD) derived GaN thin films have been systematic investigated by means of micro-Raman spectroscopy and cross-sectional transmission electron microscopy (XTEM) techniques. The XTEM samples were prepared by using focused ion beam (FIB) milling to accurately position the cross-section of the nanoindented area. The behaviors of the discontinuities displayed in the loading and unloading segments of the load-displacement curves of Si and GaN thin films performed with a Berkovich diamond indenter tip were explained by the observed microstructure features obtained from XTEM analyses. According to the observations of micro-Raman and XTEM, the nanoindentation-induced mechanical deformation is due primarily to the generation and propagation of dislocations gliding along the pyramidal and basal planes specific to the hexagonal structure of GaN thin films rather than by indentation-induced phase transformations displayed in Si.