Microscope Configuration Research Articles

Tip-induced local Fermi level alignment: A Stark shift in vacuum level in scanning tunneling microscope configurations

Electric fields in the junction of a scanning tunneling microscope (STM) are generally considered to have a negligible impact on the vacuum level (VL) of materials. We employed field emission resonance (FER) in the STM, combined with the triangular potential model, to measure the VL of the Ag(100) surface under varying electric currents. Unexpectedly, our results reveal that the VL exhibits a linear positive energy shift with increasing electric field strength. We suggest that this Stark shift in the VL arises from local Fermi level alignment induced by the STM tip. Additionally, we examined the VL of Ag islands grown on Cu(111) and Au(111) surfaces under different currents. Despite the Ag island having a lower work function than the Cu(111) and Au(111) surfaces, the energy shift in the VL with respect to the electric field on the Ag island is almost identical to that on the substrate under the same tip structure. This suggests that the Stark shift of the VL is insensitive to the work function. These findings are crucial for utilizing FER to measure local work function variations on surfaces, as the measured value is not influenced by the STM tip structure or the tunneling current, both of which can alter the electric field.

Sub-60-nm isotropic 3D super-resolution microscopy through self-interference field excitation

Due to its unique optical sectioning capability, confocal laser scanning microscopy (CLSM) can provide highly sensitive, highly specific imaging of specimens in three dimensions and has been recognized as an indispensable tool for biological and medical studies. Nonetheless, the spatial resolution of CLSM is constrained by the diffraction nature, with λ/2 resolution laterally (xy) and 1.5λ resolution axially (z). To improve the imaging resolution beyond the diffraction limit as well as to achieve its isotropy, we present a strategy of mirror-assisted self-interference field excitation (SIEx) highly nonlinear microscopy. The imaging principle has been theoretically modeled and investigated in accordance with the Wolf vector diffraction theory. The experimental demonstration of isotropic three-dimensional SIEx nanoscopy, assisted with the ultrahigh-order optical nonlinearity of photon avalanching nanoparticles, was achieved utilizing a common laser-scanning microscope configuration, resulting in a lateral resolution of 54 nm (λ/15) and an axial resolution of 57 nm (λ/15) with one single beam from a low-power, continuous-wave, near-infrared laser (19kW⋅cm−2). We further extended the applicability of the SIEx scheme to biological imaging and demonstrated super-resolution imaging for immunolabeled actin filaments of BSC-1 cells with an isotropic full width at half maximum of ∼67nm (λ/13). Our facile SIEx methodology can, in principle, be seamlessly integrated with the existing and widely available laser-scanning fluorescence microscopes without adding any complexity, thereby enabling their capability of 3D isotropic super-resolution imaging.

Development of a four-color quasimonochromatic X-ray microscope for laser plasma research

X-ray multicolor imaging diagnosis obtains the spatial distribution of the imploding core during laser inertial confinement fusion. We propose a four-color quasimonochromatic X-ray microscope based on the Kirkpatrick–Baez microscope configuration, covering the medium-to-high-energy X-ray range. Composed of single-layer film mirrors and periodic multilayer film mirrors, the microscope features high spatial resolution and spectral resolution. Furthermore, zoned coating technology achieves common field-of-view (FOV) imaging at four energy points: 4.51, 6.4, 8.4, and 9.67 keV. When assembled and calibrated in the laboratory, the microscope achieved central FOV spatial resolutions of 3.9, 3.7, 4.0, and 4.1 µm at 4.51, 6.4, 8.04, and 9.67 keV, respectively. Finally, a spectral calibration experiment confirmed spectral selectivity at the four energy points.

EMinsight: a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition.

The widespread adoption of cryoEM technologies for structural biology has pushed the discipline to new frontiers. A significant worldwide effort has refined the single-particle analysis (SPA) workflow into a reasonably standardized procedure. Significant investments of development time have been made, particularly in sample preparation, microscope data-collection efficiency, pipeline analyses and data archiving. The widespread adoption of specific commercial microscopes, software for controlling them and best practices developed at facilities worldwide has also begun to establish a degree of standardization to data structures coming from the SPA workflow. There is opportunity to capitalize on this moment in the maturation of the field, to capture metadata from SPA experiments and correlate the metadata with experimental outcomes, which is presented here in a set of programs called EMinsight. This tool aims to prototype the framework and types of analyses that could lead to new insights into optimal microscope configurations as well as to define methods for metadata capture to assist with the archiving of cryoEM SPA data. It is also envisaged that this tool will be useful to microscope operators and facilities looking to rapidly generate reports on SPA data-collection and screening sessions.

Dynamic structured illumination for confocal microscopy.

Structured illumination enables the tailoring of an imaging device's optical transfer function to enhance resolution. We propose the incorporation of a temporal periodic modulation, specifically a rotating mask, to encode multiple transfer functions in the temporal domain. This approach is demonstrated using a confocal microscope configuration. At each scanning position, a temporal periodic signal is recorded. By filtering around each harmonic of the rotation frequency, multiple images of the same object can be constructed. The image carried by the nth harmonic is a convolution of the object with a phase vortex of topological charge n, similar to the outcome when using a vortex phase plate as an illumination. This enables the collection of chosen high spatial frequencies from the sample, thereby enhancing the spatial resolution of the confocal microscope.

Assessing spontaneous sensory neuron activity using in vivo calcium imaging.

Heightened spontaneous activity in sensory neurons is often reported in individuals living with chronic pain. It is possible to study this activity in rodents using electrophysiology, but these experiments require great skill and can be prone to bias. Here, we have examined whether in vivo calcium imaging with GCaMP6s can be used as an alternative approach. We show that spontaneously active calcium transients can be visualised in the fourth lumbar dorsal root ganglion (L4 DRG) through in vivo imaging in a mouse model of inflammatory pain. Application of lidocaine to the nerve, between the inflamed site and the DRG, silenced spontaneous firing and revealed the true baseline level of calcium for spontaneously active neurons. We used these data to train a machine learning algorithm to predict when a neuron is spontaneously active. We show that our algorithm is accurate in 2 different models of pain: intraplantar complete Freund adjuvant and antigen-induced arthritis, with accuracies of 90.0% ±1.2 and 85.9% ±2.1, respectively, assessed against visual inspection by an experienced observer. The algorithm can also detect neuronal activity in imaging experiments generated in a different laboratory using a different microscope configuration (accuracy = 94.0% ±2.2). We conclude that in vivo calcium imaging can be used to assess spontaneous activity in sensory neurons and provide a Google Colaboratory Notebook to allow anyone easy access to our novel analysis tool, for the assessment of spontaneous neuronal activity in their own imaging setups.

Measuring the Effect of Ice Thickness and Microscope Configuration on Resolution in Single Particle Cryo-EM.

Measuring the Effect of Ice Thickness and Microscope Configuration on Resolution in Single Particle Cryo-EM.

TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation.

An interactive simulation of a transmission electron microscope (TEM) called TEMGYM Basic is developed here, which enables users to understand how to operate and control an electron beam without the need to access an instrument. TEMGYM Basic allows users to familiarize themselves with alignment procedures offline, reducing the time and money required to become a proficient TEM operator. In addition to teaching the basics of electron beam alignments, the software enables users to create bespoke microscope configurations and develop an understanding of how to operate the configurations without sitting at a microscope. TEMGYM Basic also creates static ray diagram figures for a given lens configuration. The available components include apertures, lenses, quadrupoles, deflectors and biprisms. The software design uses first-order ray transfer matrices to calculate ray paths through each electron microscope component, and the program is developed entirely in Python to facilitate compatibility with machine-learning packages for future exploration of automated control.

Gap plasmon modes and plasmon-exciton coupling in a hybrid Au/MoSe2/Au tunneling junction.

The light-matter interaction between plasmonic nanocavity modes and excitons at the nanometer scale is here addressed in the scanning tunneling microscope configuration where an MoSe2 monolayer is located between the tip and the substrate. We investigate by optical excitation the electromagnetic modes of this hybrid Au/MoSe2/Au tunneling junction using numerical simulations where electron tunneling and the anisotropic character of the MoSe2 layer are taken into account. In particular, we pointed out gap plasmon modes and Fano-type plasmon-exciton coupling taking place at the MoSe2/Au substrate interface. The spectral properties and spatial localization of these modes are studied as a function of the tunneling parameters and incident polarization.

Tailored Supramolecular Cage for Efficient Bio-Labeling.

Fluorescent chemosensors are powerful imaging tools used in a broad range of biomedical fields. However, the application of fluorescent dyes in bioimaging still remains challenging, with small Stokes shifts, interfering signals, background noise, and self-quenching on current microscope configurations. In this work, we reported a supramolecular cage (CA) by coordination-driven self-assembly of benzothiadiazole derivatives and Eu(OTf)3. The CA exhibited high fluorescence with a quantum yield (QY) of 38.57%, good photoluminescence (PL) stability, and a large Stokes shift (153 nm). Furthermore, the CCK-8 assay against U87 glioblastoma cells verified the low cytotoxicity of CA. We revealed that the designed probes could be used as U87 cells targeting bioimaging.

Line-scanning technique using a PDMS grating in a microscope configuration.

We report the concept of a 1550nm laser line scanning microscope based on a polydimethylsiloxane (PDMS) grating with scanning by stretching the PDMS grating to improve the scanning speed and enable low-cost scanning. Zemax is used to verify the possibility of realizing the system by simulating the illumination light path and the emission light path. The scanning field of view is 0.11m m×0.11m m, and the modulation transfer function (MTF) data of the 0th, ±1st, and ±2 nd diffraction orders in the illumination light path and the emission light path, respectively, meet the requirements of the diffraction limit resolution at the cutoff frequencies.

Analysis of the surface plasmon resonance interferometric imaging performance of scanning confocal surface plasmon microscopy.

Here, we apply rigorous coupled-wave theory to analyze the optical phase imaging performance of scanning confocal surface plasmon microscope. The scanning confocal surface plasmon resonance microscope is an embedded interferometric microscope interfering between two integrated optical beams. One beam is provided by the central part around the normal incident angle of the back focal plane, and the other beam is the incident angles beyond the critical angle, exciting the surface plasmon. Furthermore, the two beams can form an interference signal inside a confocal pinhole in the image plane, which provides a well-defined path for the surface plasmon propagation. The scanning confocal surface plasmon resonance microscope operates by scanning the sample along the optical axis z, so-called V(z). The study investigates two imaging modes: non-quantitative imaging and quantitative imaging modes. We also propose a theoretical framework to analyze the scanning confocal surface plasmon resonance microscope compared to non-interferometric surface plasmon microscopes and quantify quantitative performance parameters including spatial resolution and optical contrast for non-quantitative imaging; sensitivity and crosstalk for quantitative imaging. The scanning confocal SPR microscope can provide a higher spatial resolution, better sensitivity, and lower crosstalk measurement. The confocal SPR microscope configuration is a strong candidate for high throughput measurements since it requires a smaller sensing channel than the other SPR microscopes.

Planar photonic chips with tailored angular transmission for high-contrast-imaging devices

A limitation of standard brightfield microscopy is its low contrast images, especially for thin specimens of weak absorption, and biological species with refractive indices very close in value to that of their surroundings. We demonstrate, using a planar photonic chip with tailored angular transmission as the sample substrate, a standard brightfield microscopy can provide both darkfield and total internal reflection (TIR) microscopy images with one experimental configuration. The image contrast is enhanced without altering the specimens and the microscope configurations. This planar chip consists of several multilayer sections with designed photonic band gaps and a central region with dielectric nanoparticles, which does not require top-down nanofabrication and can be fabricated in a larger scale. The photonic chip eliminates the need for a bulky condenser or special objective to realize darkfield or TIR illumination. Thus, it can work as a miniaturized high-contrast-imaging device for the developments of versatile and compact microscopes.

Advanced Electron Energy Loss Spectroscopy for Battery Studies

AbstractAs a powerful tool for chemical compositional analyses, electron energy loss spectroscopy (EELS) can reveal an abundance of information regarding the atomic‐level electron state in a variety of materials, including the elemental types as well as their valence and concentration distributions, and the structure‐related atom radial distribution. Benefiting from its unique capabilities and the newly developed advanced transmission electron microscope (TEM) configurations (i.e., in situ bias, in situ heating, cryo‐TEM, etc.), EELS has facilitated the battery studies in various aspects. Here, a brief introduction of EELS is provided. Thereafter, a description of the recent progress in studying battery materials using EELS is provided, and finally a look ahead on the future development of EELS techniques and their applications in battery studies is provided.

Neuroblastoma Cells Classification Through Learning Approaches by Direct Analysis of Digital Holograms

The label-free single cell analysis by machine and Deep Learning, in combination with digital holography in transmission microscope configuration, is becoming a powerful framework exploited for phenotyping biological samples. Usually, quantitative phase images of cells are retrieved from the reconstructed complex diffraction patterns and used as inputs of a deep neural network. However, the phase retrieval process can be very time consuming and prone to errors. Here we address the classification of cells by using learning strategies with images coming directly from the raw recorded digital holograms, i.e. without any data processing or refocusing involved. Indeed, in the raw digital hologram the entire complex amplitude information of the sample is intrinsically embedded in the form of modulated fringes. We develop a training strategy, based on deep and feature based machine learning models, in order extract such information by skipping the classical reconstruction process for classifying different neuroblastoma cells. We provided an experimental validation by using the proposed strategy to classify two neuroblastoma cell lines.

Validating pore size estimates in a complex microfiber environment on a human MRI system.

Recent advances in diffusion-weighted MRI provide "restricted diffusion signal fraction" and restricting pore size estimates. Materials based on co-electrospun oriented hollow cylinders have been introduced to provide validation for such methods. This study extends this work, exploring accuracy and repeatability using an extended acquisition on a 300 mT/m gradient human MRI scanner, in substrates closely mimicking tissue, that is, non-circular cross-sections, intra-voxel fiber crossing, intra-voxel distributions of pore-sizes, and smaller pore-sizes overall. In a single-blind experiment, diffusion-weighted data were collected from a biomimetic phantom on a 3T Connectom system using multiple gradient directions/diffusion times. Repeated scans established short-term and long-term repeatability. The total scan time (54 min) matched similar protocols used in human studies. The number of distinct fiber populations was estimated using spherical deconvolution, and median pore size estimated through the combination of CHARMED and AxCaliber3D framework. Diffusion-based estimates were compared with measurements derived from scanning electron microscopy. The phantom contained substrates with different orientations, fiber configurations, and pore size distributions. Irrespective of one or two populations within the voxel, the pore-size estimates (~5 μm) and orientation-estimates showed excellent agreement with the median values of pore-size derived from scanning electron microscope and phantom configuration. Measurement repeatability depended on substrate complexity, with lower values seen in samples containing crossing-fibers. Sample-level repeatability was found to be good. While no phantom mimics tissue completely, this study takes a step closer to validating diffusion microstructure measurements for use in vivo by demonstrating the ability to quantify microgeometry in relatively complex configurations.

PiAutoStage: An Open‐Source 3D Printed Tool for the Automatic Collection of High‐Resolution Microscope Imagery

AbstractWe have created an open‐source 3D printable microscope automatic stage and integrated camera system capable of providing a means for imaging microscope slides—the PiAutoStage. The PiAutoStage was developed to interface with the high‐quality optics of existing microscopes by creating an adaptable system that can be used in conjunction with a range of microscope configurations. The PiAutoStage automatically captures the entire area of a microscope slide in a series of overlapping high‐resolution images, which can then be stitched into a single panoramic image. We have demonstrated the utility of the PiAutoStage when attached to a transmitted light microscope by creating high‐fidelity image stacks of rock specimens in plane polarized and cross‐polarized light. We have shown that the PiAutoStage is compatible with microscopes that do not currently have a camera attachment by using two different optical trains within the same microscope: one set of imagery collected through the photography tube of a trinocular microscope, and a second set through a camera mounted to an ocular. We furthermore establish the broad adaptability of the PiAutoStage system by attaching it to a reflected light stereo dissection microscope to capture images of microfossils. We discuss strategies for the online delivery of these large‐sized images in a data efficient manner through the application of tiled imagery and open‐source Java‐based web viewers. The low cost of the PiAutoStage system, combined with the data‐efficient mechanisms of online delivery make this system an important tool in promoting the universal accessibility of high‐resolution microscope imagery.

Micro and Nanoplastics Identification: Classic Methods and Innovative Detection Techniques.

Micro and nanoplastics are fragments with dimensions less than a millimeter invading all terrestrial and marine environments. They have become a major global environmental issue in recent decades and, indeed, recent scientific studies have highlighted the presence of these fragments all over the world even in environments that were thought to be unspoiled. Analysis of micro/nanoplastics in isolated samples from abiotic and biotic environmental matrices has become increasingly common. Hence, the need to find valid techniques to identify these micro and nano-sized particles. In this review, we discuss the current and potential identification methods used in microplastic analyses along with their advantages and limitations. We discuss the most suitable techniques currently available, from physical to chemical ones, as well as the challenges to enhance the existing methods and develop new ones. Microscopical techniques (i.e., dissect, polarized, fluorescence, scanning electron, and atomic force microscopy) are one of the most used identification methods for micro/nanoplastics, but they have the limitation to produce incomplete results in analyses of small particles. At present, the combination with chemical analysis (i.e., spectroscopy) overcome this limit together with recently introduced alternative approaches. For example, holographic imaging in microscope configuration images microplastics directly in unfiltered water, thus discriminating microplastics from diatoms and differentiates different sizes, shapes, and plastic types. The development of new analytical instruments coupled with each other or with conventional and innovative microscopy could solve the current problems in the identification of micro/nanoplastics.

Heterodyne phase shifting method in scanning probe microscopy.

The present paper describes a novel implementation of the continuous phase shifting method (PSM), named heterodyne holography, in a scanning probe microscope configuration, able to retrieve the complex scattered field in on-axis configuration. This can be achieved by acquiring a continuous sequence of holograms at different wavelengths in just a single scan through the combination of scanning interference microscopy and a low-coherent signal acquired in the frequency domain. This method exploits the main advantages of the phase shifting technique and avoids some limits relative to off-axis holography in providing quantitative phase imaging.

An Intravital Microscopy-Based Approach to Assess Intestinal Permeability and Epithelial Cell Shedding Performance.

Intravital microscopy of the gut using confocal imaging allows real time observation of epithelial cell shedding and barrier leakage in living animals. Therefore, the intestinal mucosa of anesthetized mice is topically stained with unspecific staining (acriflavine) and a fluorescent tracer (rhodamine-B dextran), mounted on a saline solution-rinsed plate and directly imaged using a confocal microscope. This technique can complement other non-invasive techniques to identify leakage of intestinal permeability, such as transmucosal passage of orally administered tracers. Besides this, the approach presented here allows the direct observation of cell shedding events at real-time. In combination with appropriate fluorescent reporter mice, this approach is suitable for shedding light into cellular and molecular mechanisms controlling intestinal epithelial cell extrusion, as well as to other biological processes. In the last decades, interesting studies using intravital microscopy have contributed to knowledge on endothelial permeability, immune cell gut homing, immune-epithelial communication and invasion of luminal components, among others. Together, the protocol presented here would not only help increase the understanding of mechanisms controlling epithelial cell extrusion, but could also be the basis for the developmental of other approaches to be used as instruments to visualize other highly dynamic cellular process, even in other tissues. Among technical limitations, optical properties of the specific tissue, as well as the selected imaging technology and microscope configuration, would in turn, determine the imaging working distance, and resolution of acquired images.