bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Introduction to 3D Microscopy Techniques
Authors: MacNeil Megan , McMillan Duncan 
Published: May 2018

Abstract
In the earliest years of microscopy, it was well understood that visualization of the finest details was often limited by the ‘intrusion’ of light from out-of-focus planes. For many decades the only solution to this dilemma was to limit microscopic studies to very thin samples or to physically squash or slice thicker samples. More recently, biomedical research has driven the need for microscopes that can resolve very fine detail in 3 dimensions within intact, and often living, specimens. The use of fluorescence labeling further exacerbates the problem of out-of-focus light because signal is generated throughout the volume of the sample. The following article describes the most prevalent techniques for 3D imaging and important optical considerations for achieving highest image quality.
Nanoelectromechanics of Inorganic and Biological Systems: From Structural Imaging to Local Functionalities
Authors: Rodriguez Brian J , Kalinin Sergei V , Jesse Stephen , Thompson G , Vertegel A , Hohlbauch Sophia , Proksch Roger 
Published: May 2018

Abstract
Coupling between electrical and mechanical phenomena is extremely common in inorganic materials, and nearly ubiquitous in biological systems, underpinning phenomena and devices ranging from SONAR to cardiac activity and hearing. This paper briefly summarizes the Scanning Probe Microscopy (SPM) approach, referred to as Piezoresponse Force Microscopy (PFM), for probing electromechanical coupling on the nanometer scales, and delineates some existing and emerging applications to probe local structure and functionality in inorganic ferroelectrics, calcified and connective tissues, and complex biosystems based on electromechanical detection.
Lab-Tek Chamber Slide for TEM Prep: A Simple, Rapid, and Reliable Protocol for In Situ Embedding Monolayer Cell Cultures in Epoxy and LR White Resin
Authors: Ning Gang 
Published: May 2018

Abstract
Preparation for TEM of resin-embedded monolayer cell cultures usually requires scraping cells from the culture substrate before or after primary fixation, which disturbs the monolayer and often results in mechanical trauma to the cells. After harvest, the cells are centrifuged and processed as a pellet in a microcentrifuge tube through a prolonged procedure of post-fixation, dehydration, infiltration, and finally embedding to ensure a “well done” sample block for subsequent sectioning, staining, and observing under a transmission electron microscope. Other disadvantages to this method include the loss of cellular orientation and information on cellular interaction, as well as difficulty in collecting a large quantity of cells to form a sizable pellet for processing, which is of special importance when samples are differentiated cells and neurons cultured in low density. In an alternative method, cells can be seeded on either glass or plastic cover slips or Petri dishes, and then processed and embedded directly as a monolayer.
Simplification and Variation in TEM Focus Techniques
Authors: Chapman Steve 
Published: May 2018

Abstract
In order to understand the focusing action of a TEM objective lens, a simple imaging system (figure 1) is best considered. This system consists of an objective lens and a single projector. In operation, the projector is adjusted as required within the total imaging system to achieve a magnification, M2, on the screen. This results in a focal length of F1, with the lens seeking to find an image in the position M1. If the objective lens does not place the image at M1 the result on the screen is an out of focus condition. The objective lens may have produced an image short of M1, overfocus, or beyond M1, underfocus.
Wide Field and Deep Focus imaging in Photomicrography Optical and Software-Based Techniques
Authors: Piper Jörg 
Published: May 2018

Abstract
In photomicrography, two fundamental problems often arise in practice: The higher the magnification and the higher the thickness or three dimensional extension of the specimen, the lower is the depth of focus which can result in parts of the specimen being indistinct. The larger the area of the specimen, the lower is the resolution in images showing the specimen in a total view. Additional problems will occur, when the lowest magnification of the respective microscope is not low enough for inclusion of the specimen’s total size so that only parts of the specimen will be visible in photo micrographic images. Table 1 presents the focal depth and lateral resolution of microscopic objectives with regard to their magnification and numerical aperture (modified from [4] and [7]).
Identifying Foreign Material Contamination in Food and Food Ingredients
Authors: Jeor V L St , Lape A , Muroski A R , McGuire C , Kruger JS , Elmore D L 
Published: May 2018

Abstract
Between the Biological and Materials sciences resides the food industry, where both biological and materials methods and techniques are employed for both production and analysis. Often referred to as “Black Specs,” one of the biggest concerns for the food industry is contamination of the food, or its additives and ingredients, with foreign material (FM). Many of our customers seek assistance in solving their FM issues, which may require multiple instrumentation, several methods, and considerable open communication with the customer before a satisfactory result can be achieved. An additional level of difficulty is often present when we learn that the FM is so small we can barely detect it with the unaided eye. Particularly difficult is what might be referred to as “chemical contamination.” We present here in example (and in the upcoming Microscopy and Microanalysis meeting in Albuquerque this August), several of the methods employed in assisting our customers with FM issues.
Development of TV-rate CCD Cameras for in-situ Electron Microscopy
Authors: Tsung Lancy , Mollon Bill , Pan Ming , Jia Yan , Mooney Paul , Mao Chengye 
Published: May 2018

Abstract
We have all heard the quote “A picture is worth a thousand words” when describing how much information can really be represented by a single image. Many of you may have written and published pages of results all based sometimes on a single piece of important data such as an electron micrograph. Of course, if one image is worth a thousand words, as the saying goes, how much would 30 or more be worth? With the advent of better performing electronics and development of newer CCD (charge couple device) technology, it is now possible to extend the famous saying and complete it with “but a movie tells the whole story”. By extending the single acquired image into a series of fast-acquired frames, movie creation is possible. This capability allows us to record dynamic events in many different applications, leading towards sharing the sequence of images and telling a more complete story that cannot be done with one image alone. A brief background on how this technique is used in electron microscopy follows.
Automated Image Acquisition of Polymer Blend Morphology in an SEM
Authors: Todd Clifford S , Blackson John , Bar Georg , Garcia-Meitin Eddy , Reuschle David , Janus Michael , Darus Mark , Nickles Annabel 
Published: May 2018

Abstract
Modern semi-crystalline polymers based on olefin chemistry are receiving a lot of attention due to their low cost of manufacture and the ability to tailor properties by controlling polymer morphology. A common technique to visualize polymer morphology is transmission electron microscopy (TEM), with the use of appropriate contrast-enhancing heavy metal stains. One of the difficulties in obtaining a TEM image is the need to prepare an ultra-thin section. Alternative approaches that do not rely on sectioning, such as AFM and SEM imaging of a prepared block face, have shown some promise for gross morphology characterization (μm-scale) but in most cases lacked the detail that can be observed by TEM.
Functional Collaborative Remote Microscopy: Inter-Continental Atomic Resolution Imaging
Authors: Perkins J M , Blom D A , McComb D W , Allard L F 
Published: May 2018

Abstract
In recent years the development of remote microscopy, specifically in electron microscopes, has begun to emerge as a useful research tool rather than simply an educational or teaching aid. Scientists have long been able to work collaboratively at a distance; however, it is often in terms of receiving data or sending some instructions where there may be a delay in receipt of the information. When defining remote control it is important to note that electron microscopy requires instantaneous control and receipt of the feedback (in most cases via images on a screen). Without realtime control it is impossible to conduct high resolution imaging and analysis work. In terms of electron microscopy, there are several reasons for conducting experiments remotely: With sub-Ångström aberration-corrected scanning transmission electron microscopes, the environment within which the microscope itself sits is of utmost importance.
Why is it Difficult to Simulate EBSD Patterns Accurately?
Authors: Eades Alwyn , Deal Andrew 
Published: May 2018

Abstract
Electron backscattering diffraction (EBSD) has become a technique of great importance in scanning electron microscopy. The diffraction patterns obtained by this method are of value in identifying phases and in determining the orientation of samples. The technique was initially developed about thirty years ago and has enjoyed widespread use in the last decade or so. It is therefore something of a surprise that there do not exist computer programs that simulate the patterns well. In fairness, we must make it clear that a number of programs exist and others are being implemented, which represent important steps towards the simulation of EBSD patterns. However, as we hope these notes will make clear, a satisfactory simulation will be very difficult and we are not aware of any existing or forthcoming program that does a job that can be guaranteed to give accurate values for the intensities in the experimental patterns.
Signature Analysis Applied to EDS Microanalysis
Authors: Colby JW , Ward D C 
Published: May 2018

Abstract
Most spectroscopies (FTIR, XRD, RAMAN, MS, etc.), were developed in order to identify materials. This is accomplished by capturing the spectral “signature” of an unknown and matching it to those of a comprehensive database of reference materials. Development of these spectroscopies has included efforts to embellish the associated database. EDS evolved as a resource to provide qual/quant, and development has been to improve the accuracy of quantation. Until recently, EDS was not considered a spectroscopy to provide identification of materials.
Cryo-Fracture or Freeze-Fracture, a Method to Expose Internal Tissue Surfaces and Cell Surfaces for Viewing in the Scanning Electron Microscope
Authors: Taylor Jeannette 
Published: May 2018

Abstract
Cryo-fracture, in conjunction with critical point drying is a method used to prepare biological samples in order to expose, for viewing via scanning electron microscopy, those naturally occurring surfaces which might otherwise remain obscure. For example, the Bowman’s capsule and tubules of a kidney, tiny blood vessels on any organ, inter-cellular spaces in liver or alveoli in the lungs. Also, some surfaces, not normally exposed at all such as the membrane surface of a nuclear envelope, mitochondria or chloroplasts or the cytoplasm of a cell, can be brought to light with this method. Herein is a review of the development of cryo-fracture and how it is currently used at our facility.
SEM Remote Control with a 3D Option
Authors: Mighela F , Perra C , Pintus R , Podda S , Vanzi M 
Published: May 2018

Abstract
Remote control of a scientific instrument is a topic gaining more and more attention between instrument users and operators. The project presented in this article reports results obtained from two distinct research efforts. The main outcome from the first research was the realization of an application to remote-control a Scanning Electron Microscope (SEM), while the main outcome from the second research was the implementation of a procedure to reconstruct 3D surfaces.
Coloring Pictures for Electron Microscopists or Elements of Digital Image Manipulation for Students
Authors: Dusevich VM , Purk JH , Eick JD 
Published: May 2018

Abstract
Coloring pictures is an educational exercise, which is fun, and helps develop important skills. Coloring SEM micrographs is especially suitable for electron microscopists. Color micrographs are not just great looking on a lab wall; they inspire both microscopists and students to exercise digital picture manipulation. Many microscopists enjoyed looking at the beautiful color micrographs by D. Scharf, but were frustrated to learn they needed a very particular scanning electron microscope equipped with multiple secondary electron detectors in order to color their own pictures. Fortunately, there are other ways to color SEM micrographs. Most SEMs are equipped with at least two detectors, for secondary and backscattered electrons.
Atom-Probe Tomography – Different Analysis Tools for Three-Dimensional Atomic-Resolution Data
Authors: Ulfig Robert M , Larson David J , Reinhard David A , Kelly Thomas F 
Published: May 2018

Abstract
Like no other microscopy technique, atom-probe tomography (APT) requires detailed data analysis algorithms specific to the knowledge desired, as the data are both complex due to their three-dimensional nature and can only be collected in a digital format. With recent increases in speed and field of view available in contemporary instruments like the Imago Scientific Instruments LEAP™ microscopes, these challenges and significant benefits are exacerbated. In practice, ‘data collection’ in APT, as understood in complementary techniques like scanning electron microscopy (SEM) or transmission electron microscopy (TEM), does not even begin until after the atom-probe experiment is over and the microscopist leaves the laboratory. The sample is prepared into the appropriate needle-shaped geometry, field evaporated atom by atom, and the ‘experiment’ part of the specimen analysis is over as soon as the ions are detected and stored in a digital file.
Characterization of Surface and Sub- Surface Defects on Devices using Complimentary Techniques
Authors: Smentkowski Vincent S , Ostrowski Sara G , Denault Lauraine , Woychik Charles G 
Published: May 2018

Abstract
Being able to differentiate surface from bulk defects on devices requires the use of complimentary characterization tools. In this article, we show how light microscopy, scanning electron microscopy, energy dispersive X-ray analysis, and time of flight secondary ion mass spectrometry provides complimentary information about the surface and sub-surface composition, topography, and microstructure of a semiconductor device.
To create a gamma-ray spectroscopy detector, electrical contacts consisting of a blanket coated cathode and a pixilated anode can be deposited directly on opposite faces of a cadmium zinc telluride (CZT) crystal. The contact metallization must adhere to the surfaces, and the streets between adjacent anode pads must be free of residual metal and contaminants to avoid excessive interpixel leakage currents. The analysis reported below was used to validate the structure and composition of the contact metal stack and to characterize the streets of the anode pad array.
Ultrafast Confocal Raman Imaging
Authors: Fischer Harald , Dieing Thomas , Hollricher Olaf 
Published: May 2018

Abstract
A thorough knowledge of structural and chemical properties is essential in the fields of nanotechnology, materials research, and life science, leading to a growing demand for characterization methods for heterogeneous systems on the nanometer scale. However, certain properties are difficult to study with conventional characterization techniques due to either limited resolution or the inability to differentiate materials chemically without inflicting damage or using invasive techniques such as staining. Confocal Raman Imaging can effectively overcome these fundamental obstacles. In Confocal Raman Imaging, the acquisition time for one Raman spectrum is a crucial value, as it determines the acquisition time of the image, which typically consists of tens of thousands of Raman spectra. This article describes how the use of a spectroscopic Electron Multiplying-CCD (EMCCD) as the detector can significantly reduce the acquisition time to a few milliseconds per spectrum, as well as tremendously improve sensitivity.
Breaking the Resolution Barrier in the Scanning Electron Microscope
Authors: Vanderlinde William 
Published: May 2018

Abstract
Everyone always wants better resolution from his or her microscopes. With semiconductor manufacturers now shipping product with sub-100 nm gates, measuring features and defects has become a challenge, even for the scanning electron microscope (SEM). For metrology below 100 nm, some manufacturers have begun routinely using TEM (transmission electron microscopy) which is tedious and expensive. As a microscopist, I find this quite disappointing since, in principle, the SEM should be capable of providing more than enough resolution well below 100 nm. Why is it that SEMs with 1 nm spot size can’t provide adequate resolution for 100 nm gates? It turns out that at very high magnification, SEM resolution is limited by how the electron beam interacts with the sample rather than simply the spot size of the beam.
Improving Image Quality and Reducing Drift Problems via Automated Data Acquisition and Averaging in a Cs-Corrected TEM
Authors: Voelkl E , Jiang B , Dai ZR , Bradley JP 
Published: May 2018

Abstract
Image acquisition with a CCD camera is a single-press-button activity: after selecting exposure time and adjusting illumination, a button is pressed and the acquired image is perceived as the final, unmodified proof of what was seen in the microscope. Thus it is generally assumed that the image processing steps of e.g., “darkcurrent correction” and “gain normalization” do not alter the information content of the image, but rather eliminate unwanted artifacts.
Single Cell Force Measurements and Cell Adhesion
Authors: Mueller Torsten , Neumann Tanja 
Published: May 2018

Abstract
This short review describes the relevance of cell adhesion in cell biology. Starting with a short overview of the force range of adhesion related biological events and the current biophysical techniques for investigating these events, it will conclude with a description of the use of single cell force spectroscopy for quantifying mechanical properties such as stiffness, surface tension, and bond disruption forces.
The McCrone Atlas of Microscopic Particles: The Modern Dynamic Particle Reference Resource
Authors: Wiley David A 
Published: May 2018

Abstract
Microscopists have been identifying particulate matter since the seventeenth century. Reference sets of study slides, identification keys, and even atlases of specific groups of microscopic substances were prepared throughout the eighteenth and nineteenth centuries. During the latter half of the nineteenth century and the early twentieth century, these types of resources grew in volume, but none of them attempted to be a comprehensive source.
In 1967, Dr. Walter C. McCrone and his colleagues changed the practice of microscopy with the publication of The Particle Atlas, Edition I. This single volume first edition, a photomicrographic atlas, illustrated and described 404 substances based on analyses using the polarized light microscope.
A cryoSEM Method for Preservation and Visualization of Calcified Shark Cartilage (And Other Stubborn Heterogeneous Skeletal Tissues)
Authors: Dean Mason N , Gorb Stanislav N , Summers Adam P 
Published: May 2018

Abstract
Biological materials interest biologists and engineers for their complex interactions among constituents and unique mechanical properties. While the heterogeneous tissue structure and its material properties are responsible for intriguing biomechanics, they pose challenges for sectioning, particularly in regions with stark tissue boundaries. Microscopists level this playing field when sectioning samples by embedding them in paraffin or plastic; but for scanning electron microscopy, natural morphology must be preserved without sacrificing the sample’s surface contours. Here we outline a simple preparation method for visualizing in cryoSEM the calcified cartilage of sharks and rays (elasmobranch fishes), a layered biocomposite that has traditionally been considered difficult to prepare for microscopy.
Nannobacteria, Organic Matter, and Precipitation in Hot Springs, Viterbo, Italy: Distinctions and Relevance
Authors: Kirkland B L , Lynch F L , Folk R L , Lawrence AM , Corley ME 
Published: May 2018

Abstract
Tiny (50-200 nm) spheroids were first discovered by Folk through SEM work on the hot springs of Viterbo Italy. He termed these small, spherical structures “nannobacteria,” and proposed that they may be important agents in precipitation of CaCO3, as needle-like crystals of the mineral aragonite, and as bundles of such needle-like crystals (termed “fuzzy dumbbells”), or as elongated crystals of the mineral calcite.
During the past 15 years, nanometer-scale spheroids have been discovered in the geological, medical, and astronomical worlds. There can be no doubt as to their existence, but their significance and origin remain a subject of continuing controversy. Even the spelling (“nanno-“), which has been the standard in biology, geology, and paleontology going back to the 19th century, has been questioned. Whether or not they are truly bacteria or any form of life has been a subject of heated debate.
The Ghost of the IEL: A Halloween Photoshop Exercise
Authors: Bradford Emily , Shull Gary , Miller Marian 
Published: May 2018

Abstract
Image of an intraepithelial lymphocyte (IEL) from a CLIC5 mutant mouse small intestine. The CLIC (Chloride Intracellular Channel) family of proteins is expressed in a wide variety of cell types, and several isoforms are known to cycle between soluble and membranebound forms. As well as being widely expressed, the CLICs are involved in diverse functions, including tubulogenesis, immune cell activation, apoptosis and calcium handling. CLIC5 has been shown to associate with cytoskeletal proteins in placental microvilli and inner ear cells, and is required for proper maintenence of hair cell steriocilia. It has also been localized to the cytosol of human intestinal epithelial cells, though its function there remains unclear. The study in which this particular “IEL” was found, involved a search to see what function CLIC5 played in the modulation of tubulovesicles and microvillar apical membranes in the process of acid secretion. In particular, the relative amounts and structural characteristics of these two membrane types was quantified in parietal cells.
A Simple, Inexpensive Method Of Sample Preparation For Infrared Microscopy
Authors: Feltovich Kathy , Goldfinger Gerry 
Published: May 2018

Abstract
The use of infrared microspectroscopy for examining polymer systems has been well known for some time. Fibers, inclusions in polymers and multilayered films have been examined by this technique. One limitation of the technique is the difficulty of sample preparation. A variety of methods have been proposed to prepare the sample including excising an inclusion, microtoming and the use of diamond cells to squeeze the sample into an appropriate thickness. Spectra-Tech purveys a diamond Micro Plane to prepare thin sections of polymers as well as an ATR objective to avoid the necessity of preparing thin sections. Ing Shaw et al. have proposed the use of a fiber microtome to prepare samples and claims that this technique is faster and easier than conventional microtoming.