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.

Proteasomes tether to two distinct sites at the nuclear pore complex

This study compares the native structures of cytosolic and nuclear proteasomes, visualized directly within cells. The assembly states and functional states of proteasomes in each compartment were similar, indicating comparable levels of proteolytic activity per proteasome. Nuclear proteasomes were tethered to two different sites at the nuclear pore complex (NPC): the inner nuclear membrane and the NPC basket. Structural analysis revealed mechanistic details of the two tethering interactions. These results present direct evidence that proteasomes bind at NPCs, establishing a cellular hub for protein degradation at the gateway between the nucleus and cytoplasm. This work demonstrates how cryo-electron tomography can reveal biological mechanisms by directly observing the interactions between molecular complexes within the native cellular environment.

The partitioning of cellular components between the nucleus and cytoplasm is the defining feature of eukaryotic life. The nuclear pore complex (NPC) selectively gates the transport of macromolecules between these compartments, but it is unknown whether surveillance mechanisms exist to reinforce this function. By leveraging in situ cryo-electron tomography to image the native cellular environment of Chlamydomonas reinhardtii, we observed that nuclear 26S proteasomes crowd around NPCs. Through a combination of subtomogram averaging and nanometer-precision localization, we identified two classes of proteasomes tethered via their Rpn9 subunits to two specific NPC locations: binding sites on the NPC basket that reflect its eightfold symmetry and more abundant binding sites at the inner nuclear membrane that encircle the NPC. These basket-tethered and membrane-tethered proteasomes, which have similar substrate-processing state frequencies as proteasomes elsewhere in the cell, are ideally positioned to regulate transcription and perform quality control of both soluble and membrane proteins transiting the NPC.

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.

Revealing the Cell-Material Interface with Nanometer Resolution by Focused Ion Beam/Scanning Electron Microscopy

The interface between cells and nonbiological surfaces regulates cell attachment, chronic tissue responses, and ultimately the success of medical implants or biosensors. Clinical and laboratory studies show that topological features of the surface profoundly influence cellular responses; for example, titanium surfaces with nano- and microtopographical structures enhance osteoblast attachment and host-implant integration as compared to a smooth surface. To understand how cells and tissues respond to different topographical features, it is of critical importance to directly visualize the cell-material interface at the relevant nanometer length scale. Here, we present a method for in situ examination of the cell-to-material interface at any desired location, based on focused ion beam milling and scanning electron microscopy imaging to resolve the cell membrane-to-material interface with 10 nm resolution. By examining how cell membranes interact with topographical features such as nanoscale protrusions or invaginations, we discovered that the cell membrane readily deforms inward and wraps around protruding structures, but hardly deforms outward to contour invaginating structures. This asymmetric membrane response (inward vs outward deformation) causes the cleft width between the cell membrane and the nanostructure surface to vary by more than an order of magnitude. Our results suggest that surface topology is a crucial consideration for the development of medical implants or biosensors whose performances are strongly influenced by the cell-to-material interface. We anticipate that the method can be used to explore the direct interaction of cells/tissue with medical devices such as metal implants in the future.

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.

Role of 4-tert-Butylpyridine as a Hole Transport Layer Morphological Controller in Perovskite Solar Cells

Hybrid organic-inorganic materials for high-efficiency, low-cost photovoltaic devices have seen rapid progress since the introduction of lead based perovskites and solid-state hole transport layers. Although majority of the materials used for perovskite solar cells (PSC) are introduced from dye-sensitized solar cells (DSSCs), the presence of a perovskite capping layer as opposed to a single dye molecule (in DSSCs) changes the interactions between the various layers in perovskite solar cells. 4-tert-Butylpyridine (tBP), commonly used in PSCs, is assumed to function as a charge recombination inhibitor, similar to DSSCs. However, the presence of a perovskite capping layer calls for a re-evaluation of its function in PSCs. Using TEM (transmission electron microscopy), we first confirm the role of tBP as a HTL morphology controller in PSCs. Our observations suggest that tBP significantly improves the uniformity of the HTL and avoids accumulation of Li salt. We also study degradation pathways by using FTIR (Fourier transform infrared spectroscopy) and APT (atom probe tomography) to investigate and visualize in 3-dimensions the moisture content associated with the Li salt. Long-term effects, over 1000 h, due to evaporation of tBP have also been studied. Based on our findings, a PSC failure mechanism associated with the morphological change of the HTL is proposed. tBP, the morphology controller in HTL, plays a key role in this process, and thus this study highlights the need for additive materials with higher boiling points for consistent long-term performance of PSCs.

In situ structural analysis of Golgi intracisternal protein arrays

We acquired molecular-resolution structures of the Golgi within its native cellular environment. Vitreous Chlamydomonas cells were thinned by cryo-focused ion beam milling and then visualized by cryo-electron tomography. These tomograms revealed structures within the Golgi cisternae that have not been seen before. Narrow trans-Golgi lumina were spanned by asymmetric membrane-associated protein arrays that had ∼6-nm lateral periodicity. Subtomogram averaging showed that the arrays may determine the narrow central spacing of the trans-Golgi cisternae through zipper-like interactions, thereby forcing cargo to the trans-Golgi periphery. Additionally, we observed dense granular aggregates within cisternae and intracisternal filament bundles associated with trans-Golgi buds. These native in situ structures provide new molecular insights into Golgi architecture and function.

A nanostructure platform for live-cell manipulation of membrane curvature

Membrane curvatures are involved in essential cellular processes, such as endocytosis and exocytosis, in which they are believed to act as microdomains for protein interactions and intracellular signaling. These membrane curvatures appear and disappear dynamically, and their locations are difficult or impossible to predict. In addition, the size of these curvatures is usually below the diffraction limit of visible light, making it impossible to resolve their values using live-cell imaging. Therefore, precise manipulation of membrane curvature is important to understanding how membrane curvature is involved in intracellular processes. Recent studies show that membrane curvatures can be induced by surface topography when cells are in direct contact with engineered substrates. Here, we present detailed procedures for using nanoscale structures to manipulate membrane curvatures and probe curvature-induced phenomena in live cells. We first describe detailed procedures for the design of nanoscale structures and their fabrication using electron-beam (E-beam) lithography. The fabrication process takes 2 d, but the resultant chips can be cleaned and reused repeatedly over the course of 2 years. Then we describe how to use these nanostructures to manipulate local membrane curvatures and probe intracellular protein responses, discussing surface coating, cell plating, and fluorescence imaging in detail. Finally, we describe a procedure to characterize the nanostructure-cell membrane interface using focused ion beam and scanning electron microscopy (FIB-SEM). Nanotopography-based methods can induce stable membrane curvatures with well-defined curvature values and locations in live cells, which enables the generation of a library of curvatures for probing curvature-related intracellular processes.

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.

Structural and Chemical Changes to CH3 NH3 PbI3 Induced by Electron and Gallium Ion Beams

Organic-inorganic hybrid perovskites, such as CH₃ NH₃ PbI_3, have shown highly promising photovoltaic performance. Electron microscopy (EM) is a powerful tool for studying the crystallography, morphology, interfaces, lattice defects, composition, and charge carrier collection and recombination properties at the nanoscale. Here, the sensitivity of CH₃ NH₃ PbI₃ to electron beam irradiation is examined. CH₃ NH₃ PbI₃ undergoes continuous structural and compositional changes with increasing electron dose, with the total dose, rather than dose rate, being the key operative parameter. Importantly, the first structural change is subtle and easily missed and occurs after an electron dose significantly smaller than that typically applied in conventional EM techniques. The electron dose conditions under which these structural changes occur are identified. With appropriate dose-minimization techniques, electron diffraction patterns can be obtained from pristine material consistent with the tetragonal CH₃ NH₃ PbI₃ phases determined by X-ray diffraction. Radiation damage incurred at liquid nitrogen temperatures and using Ga⁺ irradiation in a focused ion beam instrument are also examined. Finally, some simple guidelines for how to minimize electron-beam-induced artifacts when using EM to study hybrid perovskite materials are provided.

Deterministic Quantum Emitter Formation in Hexagonal Boron Nitride via Controlled Edge Creation

Quantum emitters (QEs) in 2D hexagonal boron nitride (hBN) are extremely bright and are stable at high temperature and under harsh chemical conditions. Because they reside within an atomically thin 2D material, these QEs have a unique potential to couple strongly to hybrid optoelectromechanical and quantum devices. However, this potential for coupling has been underexplored because of challenges in nanofabrication and patterning of hBN QEs. Motivated by recent studies showing that QEs in hBN tend to form at edges, we use a focused ion beam (FIB) to mill an array of patterned holes into hBN. Using optical confocal microscopy, we find arrays of bright, localized photoluminescence that match the geometry of the patterned holes. Furthermore, second-order photon correlation measurements on these bright spots reveal that they contain single and multiple QEs. By optimizing the FIB parameters, we create patterned single QEs with a yield of 31%, a value close to Poissonian limit. Using atomic force microscopy to study the morphology near emission sites, we find that single QE yield is highest with smoothly milled holes on unwrinkled hBN. This technique dramatically broadens the utility and convenience of hBN QEs and achieves a vital step toward the facile integration of the QEs into large-scale photonic, plasmonic, nanomechanical, or optoelectronic devices.

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

Noninvasive Nanoscopy Uncovers the Impact of the Hierarchical Porous Structure on the Catalytic Activity of Single Dealuminated Mordenite Crystals

Spatial restrictions around catalytic sites, provided by molecular-sized micropores, are beneficial to reaction selectivity but also inherently limit diffusion. The molecular transport can be enhanced by introducing meso- and macropores. However, the impact of this extraframework porosity on the local nanoscale reactivity is relatively unexplored. Herein we show that the area of enhanced reactivity in hierarchical zeolite, examined with super-resolution fluorescence microscopy, is spatially restricted to narrow zones around meso- and macropores, as observed with focused ion-beam-assisted scanning electron microscopy. This comparison indicates that reagent molecules efficiently reach catalytic active sites only in the micropores surrounding extraframework porosity and that extensive macroporosity does not warrant optimal reactivity distribution throughout a hierarchical porous zeolite.

Toward Two-Dimensional All-Carbon Heterostructures via Ion Beam Patterning of Single-Layer Graphene

Graphene has many claims to fame: it is the thinnest possible membrane, it has unique electronic and excellent mechanical properties, and it provides the perfect model structure for studying materials science at the atomic level. However, for many practical studies and applications the ordered hexagon arrangement of carbon atoms in graphene is not directly suitable. Here, we show that the atoms can be locally either removed or rearranged into a random pattern of polygons using a focused ion beam (FIB). The atomic structure of the disordered regions is confirmed with atomic-resolution scanning transmission electron microscopy images. These structural modifications can be made on macroscopic scales with a spatial resolution determined only by the size of the ion beam. With just one processing step, three types of structures can be defined within a graphene layer: chemically inert graphene, chemically active amorphous 2D carbon, and empty areas. This, along with the changes in properties, gives promise that FIB patterning of graphene will open the way for creating all-carbon heterostructures to be used in fields ranging from nanoelectronics and chemical sensing to composite materials.

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.

Ultra-thin resin embedding method for scanning electron microscopy of individual cells on high and low aspect ratio 3D nanostructures

The preparation of biological cells for either scanning or transmission electron microscopy requires a complex process of fixation, dehydration and drying. Critical point drying is commonly used for samples investigated with a scanning electron beam, whereas resin-infiltration is typically used for transmission electron microscopy. Critical point drying may cause cracks at the cellular surface and a sponge-like morphology of nondistinguishable intracellular compartments. Resin-infiltrated biological samples result in a solid block of resin, which can be further processed by mechanical sectioning, however that does not allow a top view examination of small cell-cell and cell-surface contacts. Here, we propose a method for removing resin excess on biological samples before effective polymerization. In this way the cells result to be embedded in an ultra-thin layer of epoxy resin. This novel method highlights in contrast to standard methods the imaging of individual cells not only on nanostructured planar surfaces but also on topologically challenging substrates with high aspect ratio three-dimensional features by scanning electron microscopy.

Crystal Morphologies of Organolead Trihalide in Mesoscopic/Planar Perovskite Solar Cells

The crystal morphology of organolead trihalide perovskite (OTP) light absorbers can have profound influence on the perovskite solar cells (PSCs) performance. Here we have used a combination of conventional transmission electron microscopy (TEM) and high-resolution TEM (HRTEM), in cross-section and plan-view, to characterize the morphologies of a solution-processed OTP (CH3NH3PbI3 or MAPbI3) within mesoporous TiO2 scaffolds and within capping and planar layers. Studies of TEM specimens prepared with and without the use of focused ion beam (FIB) show that FIBing is a viable method for preparing TEM specimens. HRTEM studies, in conjunction with quantitative X-ray diffraction, show that MAPbI3 perovskite within mesoporous TiO2 scaffold has equiaxed grains of size 10-20 nm and relatively low crystallinity. In contrast, the grain size of MAPbI3 perovskite in the capping and the planar layers can be larger than 100 nm in our PSCs, and the grains can be elongated and textured, with relatively high crystallinity. The observed differences in the performance of planar and mesoscopic-planar hybrid PSCs can be attributed in part to the striking differences in their perovskite-grain morphologies.

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.

The internal plumbing of algal chloroplasts

High-resolution images of chloroplast structure in the alga Chlamydomonas offer new insights into photosynthesis.

Ultraefficient Ultraviolet and Visible Light Sensing and Ohmic Contacts in High-Mobility InSe Nanoflake Photodetectors Fabricated by the Focused Ion Beam Technique

A photodetector using a two-dimensional (2D) low-direct band gap indium selenide (InSe) nanostructure fabricated by the focused ion beam (FIB) technique has been investigated. The FIB-fabricated InSe photodetectors with a low contact resistance exhibit record high responsivity and detectivity to the ultraviolet and visible lights. The optimal responsivity and detectivity up to 1.8 × 10⁷ A W^-1 and 1.1 × 10¹⁵ Jones, respectively, are much higher than those of the other 2D material-based photoconductors and phototransistors. Moreover, the inherent photoconductivity (PC) quantified by the value of normalized gain has also been discussed and compared. By excluding the contribution of artificial parameters, the InSe nanoflakes exhibit an ultrahigh normalized gain of 3.2 cm² V^-1, which is several orders of magnitude higher than those of MoS₂, GaS, and other layer material nanostructures. A high electron mobility at room temperature reaching 450 cm² V^-1 s^-1 has been confirmed to be one of the major causes of the inherent superior PC in the InSe nanoflakes. The oxygen-sensitized PC mechanism that enhances carrier lifetime and carrier collection efficiency has also been proposed. This work demonstrates the devices fabricated by the FIB technique using InSe nanostructures for highly efficient broad-band optical sensing and light harvesting, which is critical for development of the 2D material-based ultrathin flexible optoelectronics.

Optimization of FIB-SEM Tomography and Reconstruction for Soft, Porous, and Poorly Conducting Materials

Tomography using a focused ion beam (FIB) combined with a scanning electron microscope (SEM) is well-established for a wide range of conducting materials. However, performing FIB–SEM tomography on ion- and electron-beam-sensitive materials as well as poorly conducting soft materials remains challenging. Some common challenges include cross-sectioning artifacts, shadowing effects, and charging. Fully dense materials provide a planar cross section, whereas pores also expose subsurface areas of the planar cross-section surface. The image intensity of the subsurface areas gives rise to overlap between the grayscale intensity levels of the solid and pore areas, which complicates image processing and segmentation for three-dimensional (3D) reconstruction. To avoid the introduction of artifacts, the goal is to examine porous and poorly conducting soft materials as close as possible to their original state. This work presents a protocol for the optimization of FIB–SEM tomography parameters for porous and poorly conducting soft materials. The protocol reduces cross-sectioning artifacts, charging, and eliminates shadowing effects. In addition, it handles the subsurface and grayscale intensity overlap problems in image segmentation. The protocol was evaluated on porous polymer films which have both poor conductivity and pores. 3D reconstructions, with automated data segmentation, from three films with different porosities were successfully obtained.

Comparison between Focused Electron/Ion Beam-Induced Deposition at Room Temperature and under Cryogenic Conditions

In this contribution, we compare the performance of Focused Electron Beam-induced Deposition (FEBID) and Focused Ion Beam-induced Deposition (FIBID) at room temperature and under cryogenic conditions (the prefix “Cryo” is used here for cryogenic). Under cryogenic conditions, the precursor material condensates on the substrate, forming a layer that is several nm thick. Its subsequent exposure to a focused electron or ion beam and posterior heating to 50 °C reveals the deposit. Due to the extremely low charge dose required, Cryo-FEBID and Cryo-FIBID are found to excel in terms of growth rate, which is typically a few hundred/thousand times higher than room-temperature deposition. Cryo-FIBID using the W(CO)₆ precursor has demonstrated the growth of metallic deposits, with resistivity not far from the corresponding deposits grown at room temperature. This paves the way for its application in circuit edit and the fast and direct growth of micro/nano-electrical contacts with decreased ion damage. The last part of the contribution is dedicated to the comparison of these techniques with other charge-based lithography techniques in terms of the charge dose required and process complexity. The comparison indicates that Cryo-FIBID is very competitive and shows great potential for future lithography developments.

Engineering Optically Active Defects in Hexagonal Boron Nitride Using Focused Ion Beam and Water

Hexagonal boron nitride (hBN) has emerged as a promising material platform for nanophotonics and quantum sensing, hosting optically active defects with exceptional properties such as high brightness and large spectral tuning. However, precise control over deterministic spatial positioning of emitters in hBN remained elusive for a long time, limiting their proper correlative characterization and applications in hybrid devices. Recently, focused ion beam (FIB) systems proved to be useful to engineer several types of spatially defined emitters with various structural and photophysical properties. Here we systematically explore the physical processes leading to the creation of optically active defects in hBN using FIB and find that beam-substrate interaction plays a key role in the formation of defects. These findings are confirmed using transmission electron microscopy, which reveals local mechanical deterioration of the hBN layers and local amorphization of ion beam irradiated hBN. Additionally, we show that, upon exposure to water, amorphized hBN undergoes a structural and optical transition between two defect types with distinctive emission properties. Moreover, using super-resolution optical microscopy combined with atomic force microscopy, we pinpoint the exact location of emitters within the defect sites, confirming the role of defected edges as primary sources of fluorescent emission. This lays the foundation for FIB-assisted engineering of optically active defects in hBN with high spatial and spectral control for applications ranging from integrated photonics, to nanoscale sensing, and to nanofluidics.

High-Resolution Microscopical Studies of Contact Killing Mechanisms on Copper-Based Surfaces

The mechanisms of bacterial contact killing induced by Cu surfaces were explored through high-resolution studies based on combinations of the focused ion beam (FIB), scanning transmission electron microscopy (STEM), high-resolution TEM, and nanoscale Fourier transform infrared spectroscopy (nano-FTIR) microscopy of individual bacterial cells of Gram-positive Bacillus subtilis in direct contact with Cu metal and Cu5Zn5Al1Sn surfaces after high-touch corrosion conditions. This approach permitted subcellular information to be extracted from the bioinorganic interface between a single bacterium and Cu/Cu5Zn5Al1Sn surfaces after complete contact killing. Early stages of interaction between individual bacteria and the metal/alloy surfaces include cell leakage of extracellular polymeric substances (EPSs) from the bacterium and changes in the metal/alloy surface composition upon adherence of bacteria. Three key observations responsible for Cu-induced contact killing include cell membrane damage, formation of nanosized copper-containing particles within the bacteria cell, and intracellular copper redox reactions. Direct evidence of cell membrane damage was observed upon contact with both Cu metal and Cu5Zn5Al1Sn surfaces. Cell membrane damage permits copper to enter into the cell interior through two possible routes, as small fragmentized Cu₂O particles from the corrosion product layer and/or as released copper ions. This results in the presence of intracellular copper oxide nanoparticles inside the cell. The nanosized particles consist primarily of CuO with smaller amounts of Cu₂O. The existence of two oxidation states of copper suggests that intracellular redox reactions play an important role. The nanoparticle formation can be regarded as a detoxification process of copper, which immobilizes copper ions via transformation processes within the bacteria into poorly soluble or even insoluble nanosized Cu structures. Similarly, the formation of primarily Cu(II) oxide nanoparticles could be a possible way for the bacteria to deactivate the toxic effects induced by copper ions via conversion of Cu(I) to Cu(II).

Multimode Fabry⁻Perot Interferometer Probe Based on Vernier Effect for Enhanced Temperature Sensing

New miniaturized sensors for biological and medical applications must be adapted to the measuring environments and they should provide a high measurement resolution to sense small changes. The Vernier effect is an effective way of magnifying the sensitivity of a device, allowing for higher resolution sensing. We applied this concept to the development of a small-size optical fiber Fabry–Perot interferometer probe that presents more than 60-fold higher sensitivity to temperature than the normal Fabry–Perot interferometer without the Vernier effect. This enables the sensor to reach higher temperature resolutions. The silica Fabry–Perot interferometer is created by focused ion beam milling of the end of a tapered multimode fiber. Multiple Fabry–Perot interferometers with shifted frequencies are generated in the cavity due to the presence of multiple modes. The reflection spectrum shows two main components in the Fast Fourier transform that give rise to the Vernier effect. The superposition of these components presents an enhancement of sensitivity to temperature. The same effect is also obtained by monitoring the reflection spectrum node without any filtering. A temperature sensitivity of −654 pm/°C was obtained between 30 °C and 120 °C, with an experimental resolution of 0.14 °C. Stability measurements are also reported.