Standard Optical Microscope Research Articles

Distinguishing Depositional Setting For Sandy Deposits In Coastal Landscapes Using Grain Shape

Abstract: Several methods exist that use sediment properties to characterize depositional setting and related mechanisms of transport, including analysis of grain-size distributions, sediment petrology, micromorphology, and grain structure. Techniques that rely on electron or optical microscopy produce results with varying degrees of success and applicability. Here, a new method is presented and used to differentiate between littoral and eolian sands that were extracted from recently formed landforms, as well as landforms that are from mid to late Holocene in age. The method utilizes a standard optical microscope with a mounted digital camera, paired with freely available software (ImageJ) to characterize grain shape parameters. The method was tested on nearly 6000 sand grains from samples with varied transport histories, and it was found that grain solidity was the most distinguishable characteristic between eolian and littoral samples, differentiating them 86% of the time for calibration samples. The method was used to correctly identify the mechanism of transport for 76% of the samples. Patterns in the results indicated that this method could be extended to link potential sediment sources to various depositional basins, and future work includes testing the method in areas with a different mineralogy and/or landscape history.

THz Time-Domain Spectroscopy of Human Skin Tissue for In-Body Nanonetworks

This paper presents experimental study of real human skin material parameter extraction based on terahertz (THz) time-domain spectroscopy in the band 0.1–2.5 THz. Results in this paper show that electromagnetic properties of the human skin distinctively affect the path loss and noise temperature parameters of the communication link, which are vital for channel modeling of in-body nanonetworks. Refractive index and absorption coefficient values are evaluated for dermis layer of the human skin. Repeatability and consistency of the data are accounted for in the experimental investigation and the morphology of the skin tissue is verified using a standard optical microscope. Finally, the results of this paper are compared with the available work in the literature, which shows the effects of dehydration on the path loss and noise temperature. The measured parameters, i.e., the refractive index and absorption coefficient are 2.1 and 18.45 cm−1, respectively, at 1 THz for a real human skin, which are vital for developing and optimizing future in-body nanonetworks.

Monitoring and Evaluating Cutting Tool Wear using a IFM G4 Microscope

Evaluation of cutting tool wear is the technique generally used when monitoring cutting tool life. Different tool wear types increase depending on the cutting conditions and machined material on the cutting edge surface. The evaluated parameters depend on the tool wear type and where the tool wear is created. All these parameters are described by ISO 3685 standards. When a standard optical microscope is used, it is very difficult to determine the volumetric parameters and, in many cases, the actual (real) area of the tool wear. A standard optical microscope works on the basis of 2D screening. The new microscope works on the basis of 3D scanning, so the user has full information about the surface. This article is focused on the evaluation of the volumetric parameters on the cutting edge, on the size of the built up edge (BUE), and on the formation of the crater. Different coating types on the cutting inserts were used for the testing, and a IFM G4 microscope was used for monitoring and evaluating the tool wear.

AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis.

Segmenting axon and myelin from microscopic images is relevant for studying the peripheral and central nervous system and for validating new MRI techniques that aim at quantifying tissue microstructure. While several software packages have been proposed, their interface is sometimes limited and/or they are designed to work with a specific modality (e.g., scanning electron microscopy (SEM) only). Here we introduce AxonSeg, which allows to perform automatic axon and myelin segmentation on histology images, and to extract relevant morphometric information, such as axon diameter distribution, axon density and the myelin g-ratio. AxonSeg includes a simple and intuitive MATLAB-based graphical user interface (GUI) and can easily be adapted to a variety of imaging modalities. The main steps of AxonSeg consist of: (i) image pre-processing; (ii) pre-segmentation of axons over a cropped image and discriminant analysis (DA) to select the best parameters based on axon shape and intensity information; (iii) automatic axon and myelin segmentation over the full image; and (iv) atlas-based statistics to extract morphometric information. Segmentation results from standard optical microscopy (OM), SEM and coherent anti-Stokes Raman scattering (CARS) microscopy are presented, along with validation against manual segmentations. Being fully-automatic after a quick manual intervention on a cropped image, we believe AxonSeg will be useful to researchers interested in large throughput histology. AxonSeg is open source and freely available at: https://github.com/neuropoly/axonseg.

Versatile optical determination of two-dimensional atomic crystal layers

An efficient method has been developed to facilitate the identification of the layer number of two-dimensional atomic crystals from their optical images. By analyzing the image contrasts of two-dimensional atomic crystals with different layers, such as graphene, hexagonal boron nitride (h-BN) and molybdenum disulfide (MoS2), on silicon substrates, it was found that the image contrasts of these two-dimensional materials showed the distinct relation with the layer number, which was well explained by the theoretical analysis. This method proved the importance of proper choices of the substrate to achieve a clear linear relation between the image contrast and the layer number. Since the method only relies on a standard optical microscope with a charge-coupled device (CCD) camera and simple calculation of the contrast from the optical images, the entire process of layer identification can be finished in a short time and with low cost, thus speeding up the exploration of the big family of two-dimensional atomic crystals.

Automated Micro-Object Detection for Mobile Diagnostics Using Lens-Free Imaging Technology.

Lens-free imaging technology has been extensively used recently for microparticle and biological cell analysis because of its high throughput, low cost, and simple and compact arrangement. However, this technology still lacks a dedicated and automated detection system. In this paper, we describe a custom-developed automated micro-object detection method for a lens-free imaging system. In our previous work (Roy et al.), we developed a lens-free imaging system using low-cost components. This system was used to generate and capture the diffraction patterns of micro-objects and a global threshold was used to locate the diffraction patterns. In this work we used the same setup to develop an improved automated detection and analysis algorithm based on adaptive threshold and clustering of signals. For this purpose images from the lens-free system were then used to understand the features and characteristics of the diffraction patterns of several types of samples. On the basis of this information, we custom-developed an automated algorithm for the lens-free imaging system. Next, all the lens-free images were processed using this custom-developed automated algorithm. The performance of this approach was evaluated by comparing the counting results with standard optical microscope results. We evaluated the counting results for polystyrene microbeads, red blood cells, HepG2, HeLa, and MCF7 cells lines. The comparison shows good agreement between the systems, with a correlation coefficient of 0.91 and linearity slope of 0.877. We also evaluated the automated size profiles of the microparticle samples. This Wi-Fi-enabled lens-free imaging system, along with the dedicated software, possesses great potential for telemedicine applications in resource-limited settings.

Quartz types of the Eocene Broken River Formation, Mount Somers, South Island, New Zealand

ABSTRACTQuartz arenites are a very common geological feature on the South Island of New Zealand. The provenance of the quartz grains that form these arenites is not well constrained because standard point-counting techniques do not provide enough detailed information. In this study we distinguish different quartz types using scanning electron microscopy–cathodoluminescence combined with standard optical microscopy on the same individual quartz grains. This is done on a suite of samples collected from shallow marine quartz arenites of the Paleocene–Eocene Blondin Sand Member of the Broken River Formation (Eyre Group) at Mt Somers in the Canterbury basin on the South Island of New Zealand. Our results show that the volcanic quartz grains were derived from local volcanic source rocks, whereas metamorphic quartz grains may have been derived from either local source rocks of the Torlesse Supergroup or from distant metamorphic sources rocks via longshore transport. Plutonic quartz grains were exclusively derived by long-distance transport. Warm and humid climatic conditions and the presence of humic acids in the associated coal-forming depositional environment probably increased the proportion of quartz in the sampled rocks.

Rapid thickness reading of CH3NH3PbI3 nanowire thin films from color maps

Hybrid halide perovskite photovoltaic materials show a remarkable light conversion efficiency in various optoelectronic devices. In the fabrication of these solar cells, light emitting diodes, laser and photodetector prototypes the thickness of the perovskite is an important parameter since the light is absorbed within a thin layer of a few hundred nanometers. Nevertheless, making perovskite coatings with various solution‐based and evaporation methods showing highly reproducible thickness and area coverage is still an issue. Therefore, rapid and reliable quality‐control of the film morphology is needed. This report shows a simple, rapid, and calibration‐free method for reading the thickness directly from the color map of nanowire perovskite films seen in standard optical microscope with visible light.

Making graphene visible on transparent dielectric substrates: Brewster angle imaging

The visibility of graphene is greatly increased by illuminating samples deposited on transparent dielectrics at the substrates’ Brewster angle. Using a commercial ellipsometer, the reflectivity of monolayers of chemical vapour deposition (CVD) graphene is found to be up to 33 times higher than that of the substrate, i.e., an optical contrast as high as 3200% is obtained, more than 380 times higher than with standard optical microscopy. Also, with a simpler, homemade, experimental setup, a 1400% optical contrast was measured for a monolayer of CVD graphene and linear features as small as ∼20 μm were visible in a monolayer, while ∼6 × 17 μm2 trilayers could still be imaged in exfoliated samples. It is also shown that the reflectance/transmittance ratio increases quadratically with the number of graphene layers, which may allow for counting layer numbers and identifying wrinkles and folds in transferred samples.

Fungal colonization of the rooting system of the early land plantAsteroxylon mackieifrom the 407-Myr-old Rhynie Chert (Scotland, UK)

Associations between plants and fungi were an important and varied feature of early terrestrial ecosystems, but in most instances their biological functions remain poorly understood. We document a new species of fungus colonizing the rooting system of the early lycopod Asteroxylon mackiei, based on exceptionally well-preserved fossils from the Rhynie Chert. We investigated historical petrographic thin sections using standard optical microscopy and confocal laser scanning microscopy. Palaeozoosporites renaultii gen. nov., sp. nov. colonized the inner cortex of the plant rooting system. The fungus had an aseptate thallus with isotomous or sympodial branching. The mycelium bore distinctive porate, globose to elongated structures that we interpret as zoosporangia and resting sporangia. Doubts remain over the precise systematic affinity of P. renaultii, which closely resembles chytrids. Whereas most of the Rhynie Chert plants developed symbiotic associations of the mycorrhizal type, it seems that this was not the case for Asteroxylon mackiei, which possessed the most evolved rooting system among the Rhynie Chert plants. We argue that the new root-borne fungus was probably parasitic. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 201–213.

Nitrogen-Vacancy centers in diamond for current imaging at the redistributive layer level of Integrated Circuits

We present a novel technique based on an ensemble of Nitrogen-Vacancy (NV) centers of diamond to perform Magnetic Current Imaging (MCI) on an Integrated Circuit (IC). NV centers of diamond permit to measure the three components of the magnetic fields generated by mA range current in an IC structure over a field of 50×200μm with sub-micrometric resolution. Vector measurements allow the use of a more robust algorithm than those used for MCI using GMR or SQUID sensors and it is opening new current reconstruction prospects. Calculated MCI from these measurements shows a very good agreement with theoretical current path. Acquisition time is around 10s, which is much faster than scanning measurements using Superconducting Quantum Interference Device (SQUID) or Giant Magneto Resistance (GMR). The experimental set-up relies on a standard optical microscope, and the measurements can be performed at room temperature and atmospheric pressure. These early experiences, not optimized for IC, show that NV centers in diamond could become a real alternative for MCI in IC.

Controlled preferential oxidation of grain boundaries in monolayer tungsten disulfide for direct optical imaging.

Synthetic 2D crystal films grown by chemical vapor deposition are typically polycrystalline, and determining grain size within domains and continuous films is crucial for determining their structure. Here we show that grain boundaries in the 2D transition metal dichalcogenide WS2, grown by CVD, can be preferentially oxidized by controlled heating in air. Under our developed conditions, preferential degradation at the grain boundaries causes an increase in their physical size due to oxidation. This increase in size enables their clear and rapid identification using a standard optical microscope. We demonstrate that similar treatments in an Ar environment do no show this effect, confirming that oxidation is the main role in the structural change. Statistical analysis of grain boundary (GB) angles shows dominant mirror formation. Electrical biasing across the GB is shown to lead to changes at the GB and their observation under an optical microscope. Our approach enables high-throughput screening of as-synthesized WS2 domains and continuous films to determine their crystallinity and should enable improvements in future CVD growth of these materials.

On the use of CR-39 PNTD with AFM analysis in measuring proton-induced target fragmentation particles

In addition to energy loss by ionization process, protons of energy >∼50MeV, such as those used in proton radiotherapy, can undergo nuclear interactions with nuclei of Z>1, resulting in the production of short range (<20μm), high-LET (linear energy transfer) target fragment particles. One of the few methods to detect these short-range particles is by means of CR-39 plastic nuclear track detector (PNTD) analyzed with an atomic force microscope (AFM). However, due to the LET-dependent angular sensitivity of CR-39 PNTD, multiple detectors exposed at a range of incident angles to the primary proton beam, must be analyzed in order to accurately determine the LET spectrum, absorbed dose and dose equivalent. The LET spectrum of 160MeV proton-induced secondary particles was experimentally measured with CR-39 PNTDs, which were exposed at six different incident angles to take into account the intrinsic sensitivity of the critical angle for track registration. The irradiated detectors were chemically processed to remove a 1μm thick volume of CR-39 PNTD. The measured LET range of short range tracks was from 15keV/μm up to 1.5MeV/μm. The absorbed dose contribution (Ds/Dp) from secondary particles to primary proton dose was ∼1%, while the dose equivalent contribution (Hs/Dp) was found to be ∼20%. Analysis of CR-39 PNTD by AFM yielded ∼60% higher value for absorbed dose compared to standard optical microscopy analysis.

Rapid super-resolution imaging of sub-surface nanostructures beyond diffraction limit by high refractive index microsphere optical nanoscopy

Sub-surface nanostructures cannot be observed by scanning electronic microscopy or standard scanning probe microscopy. They are also outside the resolution limit of standard optical microscopes. In this paper, we demonstrate super-resolution imaging of sub-surface nanostructures beyond the optical diffraction limit. Sub-surface Blu-ray recorded data structures (100–200nm) have been observed directly with submerged microsphere optical nanoscopy (SMON) using TiO2–BaO–ZnO glass microspheres (refractive index=2.2) of 60µm diameter immersed in water coupled with a standard optical microscope. Theoretical analysis of the imaging phenomena was carried out by the characteristics of electrical field Poynting vectors and photonic nanojets.

Subdiffraction-limited radius measurements of microcylinders using conventional bright-field optical microscopy.

A technique for measuring the radius of dielectric microcylinders with subdiffraction-limited precision is presented. Diffraction fringes arising from the dielectric cylinder are measured using conventional bright-field optical microscopy and compared with theory to deduce the radii. The technique has been demonstrated measuring the radii of the major-ampullate silks from Plebs eburnus spiders. Precision better than 50 nm is demonstrated, using a standard optical microscope with a numerical aperture of 0.6 for the objective. Accuracy was verified using scanning electron microscopy. This technique will facilitate rapid, precise measurement of dielectric microcylinder radii, enabling a new optical-microscopy-based measurement approach for these challenging micro-optics.

Laser spectrometry for multi-elemental imaging of biological tissues.

An increasing interest has arisen in research focused on metallic and organic ions that play crucial roles in both physiological and pathological metabolic processes. Current methods for the observation of trace elements in biological tissues at microscopic spatial resolution often require equipment with high complexity. We demonstrate a novel approach with an all-optical design and multi-elemental scanning imaging, which is unique among methods of elemental detection because of its full compatibility with standard optical microscopy. This approach is based on laser-induced breakdown spectroscopy (LIBS), which allows the elements in a tissue sample to be directly detected and quantified under atmospheric pressure. We successfully applied this method to murine kidneys with 10 µm resolution and a ppm-level detection limit to analyze the renal clearance of nanoparticles. These results offer new insight into the use of laser spectrometry in biomedical applications in the field of label-free elemental mapping of biological tissues.

Solid state detectors based on point defects in lithium fluoride for advanced proton beam diagnostics

Proton beams of 3 and 7MeV energies, produced by a linear accelerator, were used to irradiate lithium fluoride crystals and thermally evaporated LiF thin films in the fluence range of 1011–1015protons/cm2. The irradiation induces the formation of stable colour centres, mainly the primary F centre and the aggregate F2 and F3+ defects. By optical pumping in the blue spectral region, the F2 and F3+ centres emit broad photoluminescence bands in the visible spectral range. By conventional fluorescence microscopy, the integrated photoluminescence intensity was carefully measured in LiF crystals and thin films as a function of the irradiation fluence: a linear optical response was obtained in a large range of fluence, which is dependent on the used LiF samples and the selected beam energy. It was possible to record the transversal proton beam intensity profile by acquiring the photoluminescence image of the irradiated spots on LiF films by a standard optical microscope. Using LiF films grown on silicon substrates irradiated in a particular geometry, the same optical reading microscopy technique allowed one to measure the distribution of colour centres photoluminescence along the depth and direct imaging the Bragg peak position, which gives a rough estimation of the initial proton beam energy.

Laser-induced breakdown spectroscopy: a new approach for nanoparticle's mapping and quantification in organ tissue.

Emission spectroscopy of laser-induced plasma was applied to elemental analysis of biological samples. Laser-induced breakdown spectroscopy (LIBS) performed on thin sections of rodent tissues: kidneys and tumor, allows the detection of inorganic elements such as (i) Na, Ca, Cu, Mg, P, and Fe, naturally present in the body and (ii) Si and Gd, detected after the injection of gadolinium-based nanoparticles. The animals were euthanized 1to 24 hrafter intravenous injection of particles. A two-dimensional scan of the sample, performed using a motorized micrometric 3D-stage, allowed the infrared laser beam exploring the surface with a lateral resolution less than 100 μm. Quantitative chemical images of Gd element inside the organ were obtained with sub-mM sensitivity. LIBS offers a simple and robust method to study the distribution of inorganic materials without any specific labeling. Moreover, the compatibility of the setup with standard optical microscopy emphasizes its potential to provide multiple images of the same biological tissue with different types of response:elemental, molecular, or cellular.

Optical imaging of individual plasmonic nanoparticles in biological samples.

Imaging of plasmonic nanoparticles (PNP) with optical microscopy has aroused considerable attention in recent years. The unique localized surface plasmon resonance (LSPR) from metal nanoparticles facilitates the transduction of a chemical or physical stimulus into optical signals in a highly efficient way. It is therefore possible to perform chemical or biological assays at the single object level with the help of standard optical microscopes. Because the source of background noise from different samples is different, distinct imaging modalities have been developed to discern the signals of interest in complex surroundings. With these convenient yet powerful techniques, great improvements in chemical and biological assays have been demonstrated, and many interesting phenomena and dynamic processes have also been elucidated. Further development and application of optical imaging methods for plasmonic probes should lead to many exciting results in chemistry and biology in the future.

Quantitative Optical Microscopy: Measurement of Cellular Biophysical Features with a Standard Optical Microscope

We describe the use of a standard optical microscope to perform quantitative measurements of mass, volume, and density on cellular specimens through a combination of bright field and differential interference contrast imagery. Two primary approaches are presented: noninterferometric quantitative phase microscopy (NIQPM), to perform measurements of total cell mass and subcellular density distribution, and Hilbert transform differential interference contrast microscopy (HTDIC) to determine volume. NIQPM is based on a simplified model of wave propagation, termed the paraxial approximation, with three underlying assumptions: low numerical aperture (NA) illumination, weak scattering, and weak absorption of light by the specimen. Fortunately, unstained cellular specimens satisfy these assumptions and low NA illumination is easily achieved on commercial microscopes. HTDIC is used to obtain volumetric information from through-focus DIC imagery under high NA illumination conditions. High NA illumination enables enhanced sectioning of the specimen along the optical axis. Hilbert transform processing on the DIC image stacks greatly enhances edge detection algorithms for localization of the specimen borders in three dimensions by separating the gray values of the specimen intensity from those of the background. The primary advantages of NIQPM and HTDIC lay in their technological accessibility using “off-the-shelf” microscopes. There are two basic limitations of these methods: slow z-stack acquisition time on commercial scopes currently abrogates the investigation of phenomena faster than 1 frame/minute, and secondly, diffraction effects restrict the utility of NIQPM and HTDIC to objects from 0.2 up to 10 (NIQPM) and 20 (HTDIC) μm in diameter, respectively. Hence, the specimen and its associated time dynamics of interest must meet certain size and temporal constraints to enable the use of these methods. Excitingly, most fixed cellular specimens are readily investigated with these methods.