Brain tumor classification using AFM in combination with data mining techniques.

PubMed

Huml, Marlene; Silye, René; Zauner, Gerald; Hutterer, Stephan; Schilcher, Kurt

2013-01-01

Although classification of astrocytic tumors is standardized by the WHO grading system, which is mainly based on microscopy-derived, histomorphological features, there is great interobserver variability. The main causes are thought to be the complexity of morphological details varying from tumor to tumor and from patient to patient, variations in the technical histopathological procedures like staining protocols, and finally the individual experience of the diagnosing pathologist. Thus, to raise astrocytoma grading to a more objective standard, this paper proposes a methodology based on atomic force microscopy (AFM) derived images made from histopathological samples in combination with data mining techniques. By comparing AFM images with corresponding light microscopy images of the same area, the progressive formation of cavities due to cell necrosis was identified as a typical morphological marker for a computer-assisted analysis. Using genetic programming as a tool for feature analysis, a best model was created that achieved 94.74% classification accuracy in distinguishing grade II tumors from grade IV ones. While utilizing modern image analysis techniques, AFM may become an important tool in astrocytic tumor diagnosis. By this way patients suffering from grade II tumors are identified unambiguously, having a less risk for malignant transformation. They would benefit from early adjuvant therapies.

Brain morphology imaging by 3D microscopy and fluorescent Nissl staining.

PubMed

Lazutkin, A A; Komissarova, N V; Toptunov, D M; Anokhin, K V

2013-07-01

Modern optical methods (multiphoton and light-sheet fluorescent microscopy) allow 3D imaging of large specimens of the brain with cell resolution. It is therefore essential to refer the resultant 3D pictures of expression of transgene, protein, and other markers in the brain to the corresponding structures in the atlas. This implies counterstaining of specimens with morphological dyes. However, there are no methods for contrasting large samples of the brain without their preliminary slicing. We have developed a method for fluorescent Nissl staining of whole brain samples. 3D reconstructions of specimens of the hippocampus, olfactory bulbs, and cortex were created. The method can be used for morphological control and evaluation of the effects of various factors on the brain using 3D microscopy technique.

Application of Nomarski DIC and cathodoluminescence (CL) microscopy to building materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goetze, J., E-mail: goetze@mineral.tu-freiberg.de

2009-07-15

The present study discusses the potential of an integrated application of Nomarski differential interference contrast and cathodoluminescence microscopy for the investigation of building materials such as natural stone, cement, mortar and concrete. Nomarski differential interference contrast microscopy is a modern technique applied in materials sciences to visualize different phases and/or to image the surface relief on the scale of 50 nm. It is based on the principle of beam splitting by a double-crystal prism split, resulting in the superposition of laterally shifted wave fronts. In cathodoluminescence microscopy, the luminescence signal is excited by an electron beam and is generated bymore » different point defects within the material. Therefore, cathodoluminescence is a powerful method to characterize the defect structure of solid materials, to distinguish different phases and to reveal detailed information about their chemical composition. By combining Nomarski differential interference contrast and cathodoluminescence microscopy, textural, crystallographic and chemical information can be obtained from the same sample area in a polished thin section.« less

Advances in the microrheology of complex fluids

NASA Astrophysics Data System (ADS)

Waigh, Thomas Andrew

2016-07-01

New developments in the microrheology of complex fluids are considered. Firstly the requirements for a simple modern particle tracking microrheology experiment are introduced, the error analysis methods associated with it and the mathematical techniques required to calculate the linear viscoelasticity. Progress in microrheology instrumentation is then described with respect to detectors, light sources, colloidal probes, magnetic tweezers, optical tweezers, diffusing wave spectroscopy, optical coherence tomography, fluorescence correlation spectroscopy, elastic- and quasi-elastic scattering techniques, 3D tracking, single molecule methods, modern microscopy methods and microfluidics. New theoretical techniques are also reviewed such as Bayesian analysis, oversampling, inversion techniques, alternative statistical tools for tracks (angular correlations, first passage probabilities, the kurtosis, motor protein step segmentation etc), issues in micro/macro rheological agreement and two particle methodologies. Applications where microrheology has begun to make some impact are also considered including semi-flexible polymers, gels, microorganism biofilms, intracellular methods, high frequency viscoelasticity, comb polymers, active motile fluids, blood clots, colloids, granular materials, polymers, liquid crystals and foods. Two large emergent areas of microrheology, non-linear microrheology and surface microrheology are also discussed.

Advanced 3D Optical Microscopy in ENS Research.

PubMed

Vanden Berghe, Pieter

2016-01-01

Microscopic techniques are among the few approaches that have survived the test of time. Being invented half way the seventeenth century by Antonie van Leeuwenhoek and Robert Hooke, this technology is still essential in modern biomedical labs. Many microscopy techniques have been used in ENS research to guide researchers in their dissections and later to enable electrode recordings. Apart from this, microscopy has been instrumental in the identification of subpopulations of cells in the ENS, using a variety of staining methods. A significant step forward in the use of microscopy was the introduction of fluorescence approaches. Due to the fact that intense excitation light is now filtered away from the longer wavelength emission light, the contrast can be improved drastically, which helped to identify subpopulations of enteric neurons in a variety of species. Later functionalized fluorescent probes were used to measure and film activity in muscle and neuronal cells. Another important impetus to the use of microscopy was the discovery and isolation of the green fluorescent protein (GFP), as it gave rise to the development of many different color variants and functionalized constructs. Recent advances in microscopy are the result of a continuous search to enhance contrast between the item of interest and its background but also to improve resolving power to tell two small objects apart. In this chapter three different microscopy approaches will be discussed that can aid to improve our understanding of ENS function within the gut wall.

Nanoscale infrared spectroscopy as a non-destructive probe of extraterrestrial samples.

PubMed

Dominguez, Gerardo; Mcleod, A S; Gainsforth, Zack; Kelly, P; Bechtel, Hans A; Keilmann, Fritz; Westphal, Andrew; Thiemens, Mark; Basov, D N

2014-12-09

Advances in the spatial resolution of modern analytical techniques have tremendously augmented the scientific insight gained from the analysis of natural samples. Yet, while techniques for the elemental and structural characterization of samples have achieved sub-nanometre spatial resolution, infrared spectral mapping of geochemical samples at vibrational 'fingerprint' wavelengths has remained restricted to spatial scales >10 μm. Nevertheless, infrared spectroscopy remains an invaluable contactless probe of chemical structure, details of which offer clues to the formation history of minerals. Here we report on the successful implementation of infrared near-field imaging, spectroscopy and analysis techniques capable of sub-micron scale mineral identification within natural samples, including a chondrule from the Murchison meteorite and a cometary dust grain (Iris) from NASA's Stardust mission. Complementary to scanning electron microscopy, energy-dispersive X-ray spectroscopy and transmission electron microscopy probes, this work evidences a similarity between chondritic and cometary materials, and inaugurates a new era of infrared nano-spectroscopy applied to small and invaluable extraterrestrial samples.

Extracting elastic properties of an atomically thin interfacial layer by time-domain analysis of femtosecond acoustics

NASA Astrophysics Data System (ADS)

Chen, H.-Y.; Huang, Y.-R.; Shih, H.-Y.; Chen, M.-J.; Sheu, J.-K.; Sun, C.-K.

2017-11-01

Modern devices adopting denser designs and complex 3D structures have created much more interfaces than before, where atomically thin interfacial layers could form. However, fundamental information such as the elastic property of the interfacial layers is hard to measure. The elastic property of the interfacial layer is of great importance in both thermal management and nano-engineering of modern devices. Appropriate techniques to probe the elastic properties of interfacial layers as thin as only several atoms are thus critically needed. In this work, we demonstrated the feasibility of utilizing the time-resolved femtosecond acoustics technique to extract the elastic properties and mass density of a 1.85-nm-thick interfacial layer, with the aid of transmission electron microscopy. We believe that this femtosecond acoustics approach will provide a strategy to measure the absolute elastic properties of atomically thin interfacial layers.

Atomic force microscopy – looking at mechanosensors on the cell surface

PubMed Central

Heinisch, Jürgen J.; Lipke, Peter N.; Beaussart, Audrey; El Kirat Chatel, Sofiane; Dupres, Vincent; Alsteens, David; Dufrêne, Yves F.

2012-01-01

Summary Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment. However, the way in which these proteins respond to mechanical stimuli and assemble into large complexes remains poorly understood at the molecular level. In the past years, atomic force microscopy (AFM) has revolutionized the way in which biologists analyze cell surface proteins to molecular resolution. In this Commentary, we discuss how the powerful set of advanced AFM techniques (e.g. live-cell imaging and single-molecule manipulation) can be integrated with the modern tools of molecular genetics (i.e. protein design) to study the localization and molecular elasticity of individual mechanosensors on the surface of living cells. Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells. PMID:23077172

In vivo confocal microscopy, an inner vision of the cornea - a major review.

PubMed

Guthoff, Rudolf F; Zhivov, Andrey; Stachs, Oliver

2009-01-01

The demands of modern ophthalmology have evolved from descriptive findings from the slit lamp to in vivo assessment of cellular level changes. Nowadays, the latter can be provided by in vivo confocal microscopy. This article gives an overview of confocal principles using tandem scanning, scanning slit and laser scanning techniques used in ophthalmology. The main part of the paper describes the clinical applications emphasizing the anatomy of the normal and pathological cornea, and illustrates side-effects of topical medication, contact lens wear, cross-linking and refractive surgery. Finally, a summary about experimental applications, including animal studies, surface characterization and volume rendering as well as future developments, is given.

Handheld Fluorescence Microscopy based Flow Analyzer.

PubMed

Saxena, Manish; Jayakumar, Nitin; Gorthi, Sai Siva

2016-03-01

Fluorescence microscopy has the intrinsic advantages of favourable contrast characteristics and high degree of specificity. Consequently, it has been a mainstay in modern biological inquiry and clinical diagnostics. Despite its reliable nature, fluorescence based clinical microscopy and diagnostics is a manual, labour intensive and time consuming procedure. The article outlines a cost-effective, high throughput alternative to conventional fluorescence imaging techniques. With system level integration of custom-designed microfluidics and optics, we demonstrate fluorescence microscopy based imaging flow analyzer. Using this system we have imaged more than 2900 FITC labeled fluorescent beads per minute. This demonstrates high-throughput characteristics of our flow analyzer in comparison to conventional fluorescence microscopy. The issue of motion blur at high flow rates limits the achievable throughput in image based flow analyzers. Here we address the issue by computationally deblurring the images and show that this restores the morphological features otherwise affected by motion blur. By further optimizing concentration of the sample solution and flow speeds, along with imaging multiple channels simultaneously, the system is capable of providing throughput of about 480 beads per second.

[Morphology, biology and life-cycle of Plasmodium parasites].

PubMed

Hommel, Marcel

2007-10-01

Laveran first discovered that an infectious agent was responsible for malaria by using a simple microscope, without the assistance of specific stains. Our knowledge of the Plasmodium life cycle and cellular biology has progressed with each technological advance, from Romanovsky staining and histology to electron microscopy, immunocytochemistry, molecular methods and modern imaging techniques. The use of bird, primate and rodent models also made a major contribution, notably in the development of antimalarial drugs that are still in use today.

Rapid detection of biofilms and adherent pathogens using scanning confocal laser microscopy and episcopic differential interference contrast microscopy.

PubMed

Keevil, C W

2003-01-01

Knowledge of biofilm structure and function has changed significantly in the last few years due to advances in light microscopy. One pertinent example is the use of scanning confocal laser microscopy (SCLM) to visualise corrosion pits caused by the biofilm mosaic footprint on corroding metal surfaces. Nevertheless, SCLM has some limitations as to its widespread use, including cost, inability to observe motile bacteria and eukaryotic grazers within biofilms, and difficulty to scan a curved surface. By contrast, episcopic differential interference contrast (EDIC) microscopy has provided a rapid, real time analysis of biofilms on opaque, curved, natural or man-made surfaces without the need for cover slips and oil. EDIC, coupled with epi-fluorescence (EDIC/EF), microscopy has been used successfully to visualise the 3-D biofilm structure, physiological niches, protozoal grazing and iron biomineralization, and the location of specific pathogens such as Legionella pneumophila, Campylobacter jejuni and Cryptosporidium parvum. These species were identified using gold nanoparticles or fluorophores coupled to monoclonal antibodies or 16S rRNA probes, respectively. Among its many potential uses, the EDIC technique will provide a rapid procedure to facilitate the calibration of the modern generation of biofilm-sensing electrodes.

Resolution enhancement techniques in microscopy

NASA Astrophysics Data System (ADS)

Cremer, Christoph; Masters, Barry R.

2013-05-01

We survey the history of resolution enhancement techniques in microscopy and their impact on current research in biomedicine. Often these techniques are labeled superresolution, or enhanced resolution microscopy, or light-optical nanoscopy. First, we introduce the development of diffraction theory in its relation to enhanced resolution; then we explore the foundations of resolution as expounded by the astronomers and the physicists and describe the conditions for which they apply. Then we elucidate Ernst Abbe's theory of optical formation in the microscope, and its experimental verification and dissemination to the world wide microscope communities. Second, we describe and compare the early techniques that can enhance the resolution of the microscope. Third, we present the historical development of various techniques that substantially enhance the optical resolution of the light microscope. These enhanced resolution techniques in their modern form constitute an active area of research with seminal applications in biology and medicine. Our historical survey of the field of resolution enhancement uncovers many examples of reinvention, rediscovery, and independent invention and development of similar proposals, concepts, techniques, and instruments. Attribution of credit is therefore confounded by the fact that for understandable reasons authors stress the achievements from their own research groups and sometimes obfuscate their contributions and the prior art of others. In some cases, attribution of credit is also made more complex by the fact that long term developments are difficult to allocate to a specific individual because of the many mutual connections often existing between sometimes fiercely competing, sometimes strongly collaborating groups. Since applications in biology and medicine have been a major driving force in the development of resolution enhancing approaches, we focus on the contribution of enhanced resolution to these fields.

The quest for four-dimensional imaging in plant cell biology: it's just a matter of time

PubMed Central

Domozych, David S.

2012-01-01

Background Analysis of plant cell dynamics over time, or four-dimensional imaging (4-DI), represents a major goal of plant science. The ability to resolve structures in the third dimension within the cell or tissue during developmental events or in response to environmental or experimental stresses (i.e. 4-DI) is critical to our understanding of gene expression, post-expression modulations of macromolecules and sub-cellular system interactions. Scope Microscopy-based technologies have been profoundly integral to this type of investigation, and new and refined microscopy technologies now allow for the visualization of cell dynamics with unprecedented resolution, contrast and experimental versatility. However, certain realities of light and electron microscopy, choice of specimen and specimen preparation techniques limit the scope of readily attaining 4-DI. Today, the plant microscopist must use a combinatorial strategy whereby multiple microscopy-based investigations are used. Modern fluorescence, confocal laser scanning, transmission electron and scanning electron microscopy provide effective conduits for synthesizing data detailing live cell dynamics and highly resolved snapshots of specific cell structures that will ultimately lead to 4-DI. This review provides a synopsis of such technologies available. PMID:22628381

The BioImage Database Project: organizing multidimensional biological images in an object-relational database.

PubMed

Carazo, J M; Stelzer, E H

1999-01-01

The BioImage Database Project collects and structures multidimensional data sets recorded by various microscopic techniques relevant to modern life sciences. It provides, as precisely as possible, the circumstances in which the sample was prepared and the data were recorded. It grants access to the actual data and maintains links between related data sets. In order to promote the interdisciplinary approach of modern science, it offers a large set of key words, which covers essentially all aspects of microscopy. Nonspecialists can, therefore, access and retrieve significant information recorded and submitted by specialists in other areas. A key issue of the undertaking is to exploit the available technology and to provide a well-defined yet flexible structure for dealing with data. Its pivotal element is, therefore, a modern object relational database that structures the metadata and ameliorates the provision of a complete service. The BioImage database can be accessed through the Internet. Copyright 1999 Academic Press.

Topography of Cells Revealed by Variable-Angle Total Internal Reflection Fluorescence Microscopy.

PubMed

Cardoso Dos Santos, Marcelina; Déturche, Régis; Vézy, Cyrille; Jaffiol, Rodolphe

2016-09-20

We propose an improved version of variable-angle total internal reflection fluorescence microscopy (vaTIRFM) adapted to modern TIRF setup. This technique involves the recording of a stack of TIRF images, by gradually increasing the incident angle of the light beam on the sample. A comprehensive theory was developed to extract the membrane/substrate separation distance from fluorescently labeled cell membranes. A straightforward image processing was then established to compute the topography of cells with a nanometric axial resolution, typically 10-20 nm. To highlight the new opportunities offered by vaTIRFM to quantify adhesion process of motile cells, adhesion of MDA-MB-231 cancer cells on glass substrate coated with fibronectin was examined. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Richardson-Lucy deconvolution as a general tool for combining images with complementary strengths.

PubMed

Ingaramo, Maria; York, Andrew G; Hoogendoorn, Eelco; Postma, Marten; Shroff, Hari; Patterson, George H

2014-03-17

We use Richardson-Lucy (RL) deconvolution to combine multiple images of a simulated object into a single image in the context of modern fluorescence microscopy techniques. RL deconvolution can merge images with very different point-spread functions, such as in multiview light-sheet microscopes,1, 2 while preserving the best resolution information present in each image. We show that RL deconvolution is also easily applied to merge high-resolution, high-noise images with low-resolution, low-noise images, relevant when complementing conventional microscopy with localization microscopy. We also use RL deconvolution to merge images produced by different simulated illumination patterns, relevant to structured illumination microscopy (SIM)3, 4 and image scanning microscopy (ISM). The quality of our ISM reconstructions is at least as good as reconstructions using standard inversion algorithms for ISM data, but our method follows a simpler recipe that requires no mathematical insight. Finally, we apply RL deconvolution to merge a series of ten images with varying signal and resolution levels. This combination is relevant to gated stimulated-emission depletion (STED) microscopy, and shows that merges of high-quality images are possible even in cases for which a non-iterative inversion algorithm is unknown. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light Sheet Fluorescence Microscopy (LSFM)

PubMed Central

Adams, Michael W.; Loftus, Andrew F.; Dunn, Sarah E.; Joens, Matthew S.; Fitzpatrick, James A.J.

2015-01-01

The development of confocal microscopy techniques introduced the ability to optically section fluorescent samples in the axial dimension, perpendicular to the image plane. These approaches, via the placement of a pinhole in the conjugate image plane, provided superior resolution in the axial (z) dimension resulting in nearly isotropic optical sections. However, increased axial resolution, via pinhole optics, comes at the cost of both speed and excitation efficiency. Light Sheet Fluorescent Microscopy (LSFM), a century old idea (Siedentopf and Zsigmondy, 1902) made possible with modern developments in both excitation and detection optics, provides sub-cellular resolution and optical sectioning capabilities without compromising speed or excitation efficiency. Over the past decade, several variations of LSFM have been implemented each with its own benefits and deficiencies. Here we discuss LSFM fundamentals and outline the basic principles of several major light sheet based imaging modalities (SPIM, inverted SPIM, multi-view SPIM, Bessel beam SPIM, and stimulated emission depletion SPIM while considering their biological relevance in terms of intrusiveness, temporal resolution, and sample requirements. PMID:25559221

Creating a histology-embryology free digital image database using high-end microscopy and computer techniques for on-line biomedical education.

PubMed

Silva-Lopes, Victor W; Monteiro-Leal, Luiz H

2003-07-01

The development of new technology and the possibility of fast information delivery by either Internet or Intranet connections are changing education. Microanatomy education depends basically on the correct interpretation of microscopy images by students. Modern microscopes coupled to computers enable the presentation of these images in a digital form by creating image databases. However, the access to this new technology is restricted entirely to those living in cities and towns with an Information Technology (IT) infrastructure. This study describes the creation of a free Internet histology database composed by high-quality images and also presents an inexpensive way to supply it to a greater number of students through Internet/Intranet connections. By using state-of-the-art scientific instruments, we developed a Web page (http://www2.uerj.br/~micron/atlas/atlasenglish/index.htm) that, in association with a multimedia microscopy laboratory, intends to help in the reduction of the IT educational gap between developed and underdeveloped regions. Copyright 2003 Wiley-Liss, Inc.

Determination of Dynamics of Plant Plasma Membrane Proteins with Fluorescence Recovery and Raster Image Correlation Spectroscopy.

PubMed

Laňková, Martina; Humpolíčková, Jana; Vosolsobě, Stanislav; Cit, Zdeněk; Lacek, Jozef; Čovan, Martin; Čovanová, Milada; Hof, Martin; Petrášek, Jan

2016-04-01

A number of fluorescence microscopy techniques are described to study dynamics of fluorescently labeled proteins, lipids, nucleic acids, and whole organelles. However, for studies of plant plasma membrane (PM) proteins, the number of these techniques is still limited because of the high complexity of processes that determine the dynamics of PM proteins and the existence of cell wall. Here, we report on the usage of raster image correlation spectroscopy (RICS) for studies of integral PM proteins in suspension-cultured tobacco cells and show its potential in comparison with the more widely used fluorescence recovery after photobleaching method. For RICS, a set of microscopy images is obtained by single-photon confocal laser scanning microscopy (CLSM). Fluorescence fluctuations are subsequently correlated between individual pixels and the information on protein mobility are extracted using a model that considers processes generating the fluctuations such as diffusion and chemical binding reactions. As we show here using an example of two integral PM transporters of the plant hormone auxin, RICS uncovered their distinct short-distance lateral mobility within the PM that is dependent on cytoskeleton and sterol composition of the PM. RICS, which is routinely accessible on modern CLSM instruments, thus represents a valuable approach for studies of dynamics of PM proteins in plants.

Coherent x-ray diffraction imaging with nanofocused illumination.

PubMed

Schroer, C G; Boye, P; Feldkamp, J M; Patommel, J; Schropp, A; Schwab, A; Stephan, S; Burghammer, M; Schöder, S; Riekel, C

2008-08-29

Coherent x-ray diffraction imaging is an x-ray microscopy technique with the potential of reaching spatial resolutions well beyond the diffraction limits of x-ray microscopes based on optics. However, the available coherent dose at modern x-ray sources is limited, setting practical bounds on the spatial resolution of the technique. By focusing the available coherent flux onto the sample, the spatial resolution can be improved for radiation-hard specimens. A small gold particle (size <100 nm) was illuminated with a hard x-ray nanobeam (E=15.25 keV, beam dimensions approximately 100 x 100 nm2) and is reconstructed from its coherent diffraction pattern. A resolution of about 5 nm is achieved in 600 s exposure time.

Silicifying Biofilm Exopolymers on a Hot-Spring Microstromatolite: Templating Nanometer-Thick Laminae

NASA Astrophysics Data System (ADS)

Handley, Kim M.; Turner, Sue J.; Campbell, Kathleen A.; Mountain, Bruce W.

2008-08-01

Exopolymeric substances (EPS) are an integral component of microbial biofilms; however, few studies have addressed their silicification and preservation in hot-spring deposits. Through comparative analyses with the use of a range of microscopy techniques, we identified abundant EPS significant to the textural development of spicular, microstromatolitic, siliceous sinter at Champagne Pool, Waiotapu, New Zealand. Examination of biofilms coating sinter surfaces by confocal laser scanning microscopy (CLSM), environmental scanning electron microscopy (ESEM), cryo-scanning electron microscopy (cryo-SEM), and transmission electron microscopy (TEM) revealed contraction of the gelatinous EPS matrix into films (approximately 10 nm thick) or fibrillar structures, which is common in conventional SEM analyses and analogous to products of naturally occurring desiccation. Silicification of fibrillar EPS contributed to the formation of filamentous sinter. Matrix surfaces or dehydrated films templated sinter laminae (nanometers to microns thick) that, in places, preserved fenestral voids beneath. Laminae of similar thickness are, in general, common to spicular geyserites. This is the first report to demonstrate EPS templation of siliceous stromatolite laminae. Considering the ubiquity of biofilms on surfaces in hot-spring environments, EPS silicification studies are likely to be important to a better understanding of the origins of laminae in other modern and ancient stromatolitic sinters, and EPS potentially may serve as biosignatures in extraterrestrial rocks.

Wide-field optical mapping of neural activity and brain haemodynamics: considerations and novel approaches

PubMed Central

Ma, Ying; Shaik, Mohammed A.; Kozberg, Mariel G.; Thibodeaux, David N.; Zhao, Hanzhi T.; Yu, Hang

2016-01-01

Although modern techniques such as two-photon microscopy can now provide cellular-level three-dimensional imaging of the intact living brain, the speed and fields of view of these techniques remain limited. Conversely, two-dimensional wide-field optical mapping (WFOM), a simpler technique that uses a camera to observe large areas of the exposed cortex under visible light, can detect changes in both neural activity and haemodynamics at very high speeds. Although WFOM may not provide single-neuron or capillary-level resolution, it is an attractive and accessible approach to imaging large areas of the brain in awake, behaving mammals at speeds fast enough to observe widespread neural firing events, as well as their dynamic coupling to haemodynamics. Although such wide-field optical imaging techniques have a long history, the advent of genetically encoded fluorophores that can report neural activity with high sensitivity, as well as modern technologies such as light emitting diodes and sensitive and high-speed digital cameras have driven renewed interest in WFOM. To facilitate the wider adoption and standardization of WFOM approaches for neuroscience and neurovascular coupling research, we provide here an overview of the basic principles of WFOM, considerations for implementation of wide-field fluorescence imaging of neural activity, spectroscopic analysis and interpretation of results. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’. PMID:27574312

Applications of emerging transmission electron microscopy technology in PCD research and diagnosis.

PubMed

Shoemark, Amelia

2017-01-01

Primary Ciliary Dyskinesia (PCD) is a heterogeneous genetic condition characterized by dysfunction of motile cilia. Patients suffer from chronic infection and inflammation of the upper and lower respiratory tract. Diagnosis of PCD is confirmed by identification of a hallmark defect of ciliary ultrastructure or by identification of biallelic pathogenic mutations in a known PCD gene. Since the first description of PCD in 1976, assessment of ciliary ultrastructure by transmission electron microscopy (TEM) has been central to diagnosis and research. Electron tomography is a technique whereby a series of transmission electron micrographs are collected at different angles and reconstructed into a single 3D model of a specimen. Electron tomography provides improved spatial information and resolution compared to a single micrograph. Research by electron tomography has revealed new insight into ciliary ultrastructure and consequently ciliary function at a molecular and cellular level. Gene discovery studies in PCD have utilized electron tomography to define the structural consequences of variants in cilia genes. Modern transmission electron microscopes capable of electron tomography are increasingly being installed in clinical laboratories. This presents the possibility for the use of tomography technique in a diagnostic setting. This review describes the electron tomography technique, the contribution tomography has made to the understanding of basic cilia structure and function and finally the potential of the technique for use in PCD diagnosis.

Identification of surface terminations of iron pnictides with low-temperature STM/STS

NASA Astrophysics Data System (ADS)

Wang, Jihui; Li, Ang; Ma, Jihua; Wu, Zheng; Yin, Jiaxin; Lv, Bing; Chu, C. W.; Sefat, A.; McGuire, M.; Sales, B.; Mandrus, D.; Zhang, Chenglin; Dai, Pengcheng; Jin, Rongying; Zhang, Jiandi; Plummer, E. W.; Chen, Genfu; Ding, Hong; Pan, Shuheng H.

2013-03-01

The alkaline-earth metal iron pnictide superconductor AEFe2As2 (AE =Ca, Sr, Ba) have been studied extensively with modern surface techniques, such as scanning tunneling microscopy/spectroscopy (STM/STS) and Angle Resolved Photoemission Spectroscopy (ARPES). Yet the surface termination upon cleaving is still controversial. Hence, the interpretation of those results of STM/STS and reconcile with results of other surface techniques tend to be challenging. We have performed a systematic low-temperature STM/STS study on a series of (Ca,Na)Fe2As2, (Ba,K)Fe2As2, Ba(Fe,Co)2As2, and BaFe2(As,P)2. We found that, with cryogenic cleaving method, all three crystalline atomic layers can be revealed and identified. We will discuss their identities and their implications.

Microstructures of ancient and modern cast silver–copper alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Northover, S.M., E-mail: s.m.northover@open.ac.uk; Northover, J.P., E-mail: peter.northover@materials.ox.ac.uk

The microstructures of modern cast Sterling silver and of cast silver objects about 2500 years old have been compared using optical microscopy (OM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), energy dispersive X-ray microanalysis (EDX) and electron backscatter diffraction (EBSD). Microstructures of both ancient and modern alloys were typified by silver-rich dendrites with a few pools of eutectic and occasional cuprite particles with an oxidised rim on the outer surface. EBSD showed the dendrites to have a complex internal structure, often involving extensive twinning. There was copious intragranular precipitation within the dendrites, in themore » form of very fine copper-rich rods which TEM, X-ray diffraction (XRD), SEM and STEM suggest to be of a metastable face-centred-cubic (FCC) phase with a cube–cube orientation relationship to the silver-rich matrix but a higher silver content than the copper-rich β in the eutectic. Samples from ancient objects displayed a wider range of microstructures including a fine scale interpenetration of the adjoining grains not seen in the modern material. Although this study found no unambiguous evidence that this resulted from microstructural change produced over archaeological time, the copper supersaturation remaining after intragranular precipitation suggests that such changes, previously proposed for wrought and annealed material, may indeed occur in ancient silver castings. - Highlights: • Similar twinned structures and oxidised surfaces seen in ancient and modern cast silver • General precipitation of fine Cu-rich rods apparently formed by discontinuous precipitation is characteristic of as-cast silver. • The fine rods are cube-cube related to the matrix in contrast with the eutectic. • The silver-rich phase remains supersaturated with copper. • Possibly age-related grain boundary features seen in ancient cast silver.« less

X-ray imaging of spin currents and magnetisation dynamics at the nanoscale

NASA Astrophysics Data System (ADS)

Bonetti, Stefano

2017-04-01

Understanding how spins move in time and space is the aim of both fundamental and applied research in modern magnetism. Over the past three decades, research in this field has led to technological advances that have had a major impact on our society, while improving the understanding of the fundamentals of spin physics. However, important questions still remain unanswered, because it is experimentally challenging to directly observe spins and their motion with a combined high spatial and temporal resolution. In this article, we present an overview of the recent advances in x-ray microscopy that allow researchers to directly watch spins move in time and space at the microscopically relevant scales. We discuss scanning x-ray transmission microscopy (STXM) at resonant soft x-ray edges, which is available at most modern synchrotron light sources. This technique measures magnetic contrast through the x-ray magnetic circular dichroism (XMCD) effect at the resonant absorption edges, while focusing the x-ray radiation at the nanometre scale, and using the intrinsic pulsed structure of synchrotron-generated x-rays to create time-resolved images of magnetism at the nanoscale. In particular, we discuss how the presence of spin currents can be detected by imaging spin accumulation, and how the magnetisation dynamics in thin ferromagnetic films can be directly imaged. We discuss how a direct look at the phenomena allows for a deeper understanding of the the physics at play, that is not accessible to other, more indirect techniques. Finally, we present an overview of the exciting opportunities that lie ahead to further understand the fundamentals of novel spin physics, opportunities offered by the appearance of diffraction limited storage rings and free electron lasers.

X-ray imaging of spin currents and magnetisation dynamics at the nanoscale.

PubMed

Bonetti, Stefano

2017-04-05

Understanding how spins move in time and space is the aim of both fundamental and applied research in modern magnetism. Over the past three decades, research in this field has led to technological advances that have had a major impact on our society, while improving the understanding of the fundamentals of spin physics. However, important questions still remain unanswered, because it is experimentally challenging to directly observe spins and their motion with a combined high spatial and temporal resolution. In this article, we present an overview of the recent advances in x-ray microscopy that allow researchers to directly watch spins move in time and space at the microscopically relevant scales. We discuss scanning x-ray transmission microscopy (STXM) at resonant soft x-ray edges, which is available at most modern synchrotron light sources. This technique measures magnetic contrast through the x-ray magnetic circular dichroism (XMCD) effect at the resonant absorption edges, while focusing the x-ray radiation at the nanometre scale, and using the intrinsic pulsed structure of synchrotron-generated x-rays to create time-resolved images of magnetism at the nanoscale. In particular, we discuss how the presence of spin currents can be detected by imaging spin accumulation, and how the magnetisation dynamics in thin ferromagnetic films can be directly imaged. We discuss how a direct look at the phenomena allows for a deeper understanding of the the physics at play, that is not accessible to other, more indirect techniques. Finally, we present an overview of the exciting opportunities that lie ahead to further understand the fundamentals of novel spin physics, opportunities offered by the appearance of diffraction limited storage rings and free electron lasers.

Hominid cranial bone structure: a histological study of Omo 1 specimens from Ethiopia using different microscopic techniques.

PubMed

Bartsiokas, Antonis

2002-05-01

The microstructure of a hominid cranial vault has not previously been studied to determine its tissue histology, and differences in comparison with that of modern humans. We selected the parietals of Omo-Kibish 1, regarded as one of the oldest (about 130,000 years old) anatomically modern humans, and Omo 1 (Howell), which is a very recent human (about 2,000 years old)-both from the same area of Ethiopia. A combination of macrophotography, polarizing microscopy in the incident and transmission illumination mode, and confocal laser scanning microscopy (CLSM) was employed to examine thin sections, as well as polished and unpolished block faces of unembedded bone fragments, to minimize specimen destruction as much as possible. The methods enabled remarkably detailed information on bone microstructure and remodeling to be gleaned from tiny fragments of bone. The best method for examining fossilized human bones was shown to be that of incident light microscopy, which was the least destructive while producing the most amount of information. Unless the above methods are used, bone-filling minerals, such as calcite, can cause erroneous estimations of bone thickness, as observations with the naked eye or even a magnifying glass cannot determine the limit between the cortex and the diploe. This is particularly important for sciences such as paleoanthropology, in which, for instance, a thick cranial bone of Homo erectus may be confused with a pathological one of H. sapiens and vice versa. Cross sections of parietal bones revealed differences between Omo-Kibish 1 and Omo 1 (Howell) in diploic histology and in the relative thickness between the cortex and diploe, with the former specimen having an H. erectus ratio despite its H. sapiens gross anatomy. Omo-Kibish 1 may still retain some affinities with H. erectus despite its being classified as H. sapiens. Newly described histological structures, such as the reverse type II osteons, the multicanalled osteons, and the osteocytomata are presented here. A modern human skeletal anatomy does not necessarily imply a modern human cranial bone histology. The outer circumferential lamellae of cranial bones are in essence growth lines. Cranial histology of hominids may provide useful information concerning their taxonomy and life history, including such factors as growth rate, developmental stress, and diet. Copyright 2002 Wiley-Liss, Inc.

Applicability of confocal laser scanning microscopy for evaluation and monitoring of cutaneous wound healing

NASA Astrophysics Data System (ADS)

Lange-Asschenfeldt, Susanne; Bob, Adrienne; Terhorst, Dorothea; Ulrich, Martina; Fluhr, Joachim; Mendez, Gil; Roewert-Huber, Hans-Joachim; Stockfleth, Eggert; Lange-Asschenfeldt, Bernhard

2012-07-01

There is a high demand for noninvasive imaging techniques for wound assessment. In vivo reflectance confocal laser scanning microscopy (CLSM) represents an innovative optical technique for noninvasive evaluation of normal and diseased skin in vivo at near cellular resolution. This study was designed to test the feasibility of CLSM for noninvasive analysis of cutaneous wound healing in 15 patients (7 male/8 female), including acute and chronic, superficial and deep dermal skin wounds. A commercially available CLSM system was used for the assessment of wound bed and wound margins in order to obtain descriptive cellular and morphological parameters of cutaneous wound repair noninvasively and over time. CLSM was able to visualize features of cutaneous wound repair in epidermal and superficial dermal wounds, including aspects of inflammation, neovascularisation, and tissue remodelling in vivo. Limitations include the lack of mechanic fixation of the optical system on moist surfaces restricting the analysis of chronic skin wounds to the wound margins, as well as a limited optical resolution in areas of significant slough formation. By describing CLSM features of cutaneous inflammation, vascularisation, and epithelialisation, the findings of this study support the role of CLSM in modern wound research and management.

Capturing the Surface Texture and Shape of Pollen: A Comparison of Microscopy Techniques

PubMed Central

Sivaguru, Mayandi; Mander, Luke; Fried, Glenn; Punyasena, Surangi W.

2012-01-01

Research on the comparative morphology of pollen grains depends crucially on the application of appropriate microscopy techniques. Information on the performance of microscopy techniques can be used to inform that choice. We compared the ability of several microscopy techniques to provide information on the shape and surface texture of three pollen types with differing morphologies. These techniques are: widefield, apotome, confocal and two-photon microscopy (reflected light techniques), and brightfield and differential interference contrast microscopy (DIC) (transmitted light techniques). We also provide a first view of pollen using super-resolution microscopy. The three pollen types used to contrast the performance of each technique are: Croton hirtus (Euphorbiaceae), Mabea occidentalis (Euphorbiaceae) and Agropyron repens (Poaceae). No single microscopy technique provided an adequate picture of both the shape and surface texture of any of the three pollen types investigated here. The wavelength of incident light, photon-collection ability of the optical technique, signal-to-noise ratio, and the thickness and light absorption characteristics of the exine profoundly affect the recovery of morphological information by a given optical microscopy technique. Reflected light techniques, particularly confocal and two-photon microscopy, best capture pollen shape but provide limited information on very fine surface texture. In contrast, transmitted light techniques, particularly differential interference contrast microscopy, can resolve very fine surface texture but provide limited information on shape. Texture comprising sculptural elements that are spaced near the diffraction limit of light (∼250 nm; NDL) presents an acute challenge to optical microscopy. Super-resolution structured illumination microscopy provides data on the NDL texture of A. repens that is more comparable to textural data from scanning electron microscopy than any other optical microscopy technique investigated here. Maximizing the recovery of morphological information from pollen grains should lead to more robust classifications, and an increase in the taxonomic precision with which ancient vegetation can be reconstructed. PMID:22720050

Electron Microscopy and Analytical X-ray Characterization of Compositional and Nanoscale Structural Changes in Fossil Bone

NASA Astrophysics Data System (ADS)

Boatman, Elizabeth Marie

The nanoscale structure of compact bone contains several features that are direct indicators of bulk tissue mechanical properties. Fossil bone tissues represent unique opportunities to understand the compact bone structure/property relationships from a deep time perspective, offering a possible array of new insights into bone diseases, biomimicry of composite materials, and basic knowledge of bioapatite composition and nanoscale bone structure. To date, most work with fossil bone has employed microscale techniques and has counter-indicated the survival of bioapatite and other nanoscale structural features. The obvious disconnect between the use of microscale techniques and the discernment of nanoscale structure has prompted this work. The goal of this study was to characterize the nanoscale constituents of fossil compact bone by applying a suite of diffraction, microscopy, and spectrometry techniques, representing the highest levels of spatial and energy resolution available today, and capable of complementary structural and compositional characterization from the micro- to the nanoscale. Fossil dinosaur and crocodile long bone specimens, as well as modern ratite and crocodile femurs, were acquired from the UC Museum of Paleontology. Preserved physiological features of significance were documented with scanning electron microscopy back-scattered imaging. Electron microprobe wavelength-dispersive X-ray spectroscopy (WDS) revealed fossil bone compositions enriched in fluorine with a complementary loss of oxygen. X-ray diffraction analyses demonstrated that all specimens were composed of apatite. Transmission electron microscopy (TEM) imaging revealed preserved nanocrystallinity in the fossil bones and electron diffraction studies further identified these nanocrystallites as apatite. Tomographic analyses of nanoscale elements imaged by TEM and small angle X-ray scattering were performed, with the results of each analysis further indicating that nanoscale structure is highly conserved in these four fossil specimens. Finally, the results of this study indicate that bioapatite can be preserved in even the most ancient vertebrate specimens, further supporting the idea that fossilization is a preservational process. This work also underlines the importance of using appropriately selected characterization and analytical techniques for the study of fossil bone, especially from the perspective of spatial resolution and the scale of the bone structural features in question.

Electron Microscopy Imaging of Zinc Soaps Nucleation in Oil Paint.

PubMed

Hermans, Joen; Osmond, Gillian; van Loon, Annelies; Iedema, Piet; Chapman, Robyn; Drennan, John; Jack, Kevin; Rasch, Ronald; Morgan, Garry; Zhang, Zhi; Monteiro, Michael; Keune, Katrien

2018-06-04

Using the recently developed techniques of electron tomography, we have explored the first stages of disfiguring formation of zinc soaps in modern oil paintings. The formation of complexes of zinc ions with fatty acids in paint layers is a major threat to the stability and appearance of many late 19th and early 20th century oil paintings. Moreover, the occurrence of zinc soaps in oil paintings leading to defects is disturbingly common, but the chemical reactions and migration mechanisms leading to large zinc soap aggregates or zones remain poorly understood. State-of-the-art scanning (SEM) and transmission (TEM) electron microscopy techniques, primarily developed for biological specimens, have enabled us to visualize the earliest stages of crystalline zinc soap growth in a reconstructed zinc white (ZnO) oil paint sample. In situ sectioning techniques and sequential imaging within the SEM allowed three-dimensional tomographic reconstruction of sample morphology. Improvements in the detection and discrimination of backscattered electrons enabled us to identify local precipitation processes with small atomic number contrast. The SEM images were correlated to low-dose and high-sensitivity TEM images, with high-resolution tomography providing unprecedented insight into the structure of nucleating zinc soaps at the molecular level. The correlative approach applied here to study phase separation, and crystallization processes specific to a problem in art conservation creates possibilities for visualization of phase formation in a wide range of soft materials.

ADHESION AND DE-ADHESION MECHANISMS AT POLYMER/METAL INTERFACES: Mechanistic Understanding Based on In Situ Studies of Buried Interfaces

NASA Astrophysics Data System (ADS)

Grundmeier, G.; Stratmann, M.

2005-08-01

The review highlights the state-of-the-art research regarding the application of modern in situ spectroscopic, microscopic, and electrochemical techniques to improve the understanding of the interaction of organic molecules with metal surfaces. We also consider the chemical and electrochemical processes that lead to a de-adhesion of polymers from metal surfaces. Spectroscopic techniques such as surface-enhanced infrared or Raman spectroscopy provide molecular understanding of organic molecules and water at buried metal surfaces. This information is complementary to adhesion studies by means of atomic force microscopy and de-adhesion studies of polymer layers from metals by means of a scanning Kelvin probe. Adhesion and de-adhesion mechanisms are discussed, especially those involving humid and corrosive environments, which are the predominant and most important for metal/polymer composites in engineering applications.

Unlocking the spatial inversion of large scanning magnetic microscopy datasets

NASA Astrophysics Data System (ADS)

Myre, J. M.; Lascu, I.; Andrade Lima, E.; Feinberg, J. M.; Saar, M. O.; Weiss, B. P.

2013-12-01

Modern scanning magnetic microscopy provides the ability to perform high-resolution, ultra-high sensitivity moment magnetometry, with spatial resolutions better than 10^-4 m and magnetic moments as weak as 10^-16 Am^2. These microscopy capabilities have enhanced numerous magnetic studies, including investigations of the paleointensity of the Earth's magnetic field, shock magnetization and demagnetization of impacts, magnetostratigraphy, the magnetic record in speleothems, and the records of ancient core dynamos of planetary bodies. A common component among many studies utilizing scanning magnetic microscopy is solving an inverse problem to determine the non-negative magnitude of the magnetic moments that produce the measured component of the magnetic field. The two most frequently used methods to solve this inverse problem are classic fast Fourier techniques in the frequency domain and non-negative least squares (NNLS) methods in the spatial domain. Although Fourier techniques are extremely fast, they typically violate non-negativity and it is difficult to implement constraints associated with the space domain. NNLS methods do not violate non-negativity, but have typically been computation time prohibitive for samples of practical size or resolution. Existing NNLS methods use multiple techniques to attain tractable computation. To reduce computation time in the past, typically sample size or scan resolution would have to be reduced. Similarly, multiple inversions of smaller sample subdivisions can be performed, although this frequently results in undesirable artifacts at subdivision boundaries. Dipole interactions can also be filtered to only compute interactions above a threshold which enables the use of sparse methods through artificial sparsity. To improve upon existing spatial domain techniques, we present the application of the TNT algorithm, named TNT as it is a "dynamite" non-negative least squares algorithm which enhances the performance and accuracy of spatial domain inversions. We show that the TNT algorithm reduces the execution time of spatial domain inversions from months to hours and that inverse solution accuracy is improved as the TNT algorithm naturally produces solutions with small norms. Using sIRM and NRM measures of multiple synthetic and natural samples we show that the capabilities of the TNT algorithm allow very large samples to be inverted without the need for alternative techniques to make the problems tractable. Ultimately, the TNT algorithm enables accurate spatial domain analysis of scanning magnetic microscopy data on an accelerated time scale that renders spatial domain analyses tractable for numerous studies, including searches for the best fit of unidirectional magnetization direction and high-resolution step-wise magnetization and demagnetization.

Digital and Conventional Microscopy--Learning Effects Detected through Eye Tracking and the Use of Interactive Whiteboards

ERIC Educational Resources Information Center

Berg, Julia; Jäkel, Lissy; Penzes, Anamarija

2016-01-01

Learning the meaningful use of the microscope is an essential requirement in school curricula. Modern science and medicine is hardly conceivable without the inclusion of microscopy. The number of didactic studies in this area, however, is negligible. Real microscopy is rarely used to gain knowledge in higher school years. Could the understanding…

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

PubMed

Prosa, Ty J; Larson, David J

2017-04-01

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.

Large area scanning probe microscope in ultra-high vacuum demonstrated for electrostatic force measurements on high-voltage devices.

PubMed

Gysin, Urs; Glatzel, Thilo; Schmölzer, Thomas; Schöner, Adolf; Reshanov, Sergey; Bartolf, Holger; Meyer, Ernst

2015-01-01

The resolution in electrostatic force microscopy (EFM), a descendant of atomic force microscopy (AFM), has reached nanometre dimensions, necessary to investigate integrated circuits in modern electronic devices. However, the characterization of conducting or semiconducting power devices with EFM methods requires an accurate and reliable technique from the nanometre up to the micrometre scale. For high force sensitivity it is indispensable to operate the microscope under high to ultra-high vacuum (UHV) conditions to suppress viscous damping of the sensor. Furthermore, UHV environment allows for the analysis of clean surfaces under controlled environmental conditions. Because of these requirements we built a large area scanning probe microscope operating under UHV conditions at room temperature allowing to perform various electrical measurements, such as Kelvin probe force microscopy, scanning capacitance force microscopy, scanning spreading resistance microscopy, and also electrostatic force microscopy at higher harmonics. The instrument incorporates beside a standard beam deflection detection system a closed loop scanner with a scan range of 100 μm in lateral and 25 μm in vertical direction as well as an additional fibre optics. This enables the illumination of the tip-sample interface for optically excited measurements such as local surface photo voltage detection. We present Kelvin probe force microscopy (KPFM) measurements before and after sputtering of a copper alloy with chromium grains used as electrical contact surface in ultra-high power switches. In addition, we discuss KPFM measurements on cross sections of cleaved silicon carbide structures: a calibration layer sample and a power rectifier. To demonstrate the benefit of surface photo voltage measurements, we analysed the contact potential difference of a silicon carbide p/n-junction under illumination.

Functional characterization of neotropical snakes peripheral blood leukocytes subsets: Linking flow cytometry cell features, microscopy images and serum corticosterone levels.

PubMed

de Carvalho, Marcelo Pires Nogueira; Queiroz-Hazarbassanov, Nicolle Gilda Teixeira; de Oliveira Massoco, Cristina; Sant'Anna, Sávio Stefanini; Lourenço, Mariana Mathias; Levin, Gabriel; Sogayar, Mari Cleide; Grego, Kathleen Fernandes; Catão-Dias, José Luiz

2017-09-01

Reptiles are the unique ectothermic amniotes, providing the key link between ectothermic anamniotes fish and amphibians, and endothermic birds and mammals; becoming an important group to study with the aim of providing significant knowledge into the evolutionary history of vertebrate immunity. Classification systems for reptiles' leukocytes have been described by their appearance rather than function, being still inconsistent. With the advent of modern techniques and the establishment of analytical protocols for snakes' blood by flow cytometry, we bring a qualitative and quantitative assessment of innate activities presented by snakes' peripheral blood leukocytes, thereby linking flow cytometric features with fluorescent and light microscopy images. Moreover, since corticosterone is an important immunomodulator in reptiles, hormone levels of all blood samples were measured. We provide novel and additional information which should contribute to better understanding of the development of the immune system of reptiles and vertebrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Towards nano-physiology of insects with atomic force microscopy.

PubMed

Dokukin, M E; Guz, N V; Sokolov, I

2011-02-01

Little study of insects with modern nanotechnology tools has been done so far. Here we use one of such tool, atomic force microscopy (AFM) to study surface oscillations of the ladybird beetles (Hippodamia convergens) measured in different parts of the insect at picometer level. This allows us to record a much broader spectral range of possible surface vibrations (up to several kHz) than the previously studied oscillations due to breathing, heartbeat cycles, coelopulses, etc. (up to 5-10Hz). Here we demonstrate three different ways with which one can identify the origins of the observed peaks - by physical positioning the probe near a specific organ, and by using biological or chemical stimuli. We report on identification of high frequency peaks associated with H. convergens heart, spiracular closer muscles, and oscillations associated with muscles activated while drinking. The method, being a relatively non-invasive technique providing a new type of information, may be useful in developing "nanophysiology" of insects. Copyright © 2010 Elsevier Ltd. All rights reserved.

XRF, μ-XRD and μ-spectroscopic techniques for revealing the composition and structure of paint layers on polychrome sculptures after multiple restorations.

PubMed

Franquelo, M L; Duran, A; Castaing, J; Arquillo, D; Perez-Rodriguez, J L

2012-01-30

This paper presents the novel application of recently developed analytical techniques to the study of paint layers on sculptures that have been restored/repainted several times across centuries. Analyses were performed using portable XRF, μ-XRD and μ-Raman instruments. Other techniques, such as optical microscopy, SEM-EDX and μ-FTIR, were also used. Pigments and other materials including vermilion, minium, red lac, ivory black, lead white, barium white, zinc white (zincite), titanium white (rutile and anatase), lithopone, gold and brass were detected. Pigments from both ancient and modern times were found due to the different restorations/repaintings carried out. μ-Raman was very useful to characterise some pigments that were difficult to determine by μ-XRD. In some cases, pigments identification was only possible by combining results from the different analytical techniques used in this work. This work is the first article devoted to the study of sculpture cross-section samples using laboratory-made μ-XRD systems. Copyright © 2011 Elsevier B.V. All rights reserved.

A new diagnostic technique for tinea incognito: in vivo reflectance confocal microscopy. Report of five cases.

PubMed

Turan, Enver; Erdemir, Asli Turgut; Gurel, Mehmet Salih; Yurt, Nurdan

2013-02-01

In vivo confocal laser scanning microscopy (CLSM) is a modern non-invasive method for investigation of the skin that allows real-time visualization of individual cells and subcellular structures with the highest resolution imaging comparable to the routine histopathology. Our aim was to demonstrate the potential of CLSM for non-invasive diagnosis of difficult tinea incognito cases. Clinically atypical lesions in five cases of tinea incognito due to dermatophyte spp. were demonstrated using reflectance confocal laser scanning microscopy (RCM), parallel to KOH preparation and fungal culture of skin scrapings performed in the same patients. The morphological features characteristic for tinea incognito, namely linear branched hyphae in the intercellular area of the stratum corneum, were readily detectable by means of CLSM. In vivo tissue imaging were performed at three different wavelengths (785, 658, 445 nm) and the best images of fungal elements were obtained at 445 nm. All of our five cases had similar reflectance confocal microscopical findings. Our findings suggest the potential of CLSM as a non-invasive tool for the diagnosis of tinea incognito having atypical clinical appearance. Although at present the reflectance confocal microscopy cannot replace the current diagnostic standards for tinea incognito, it may be successfully used as in vivo non-invasive screening tool to facilitate the diagnosis and point to the need for further investigation of the patient. © 2012 John Wiley & Sons A/S.

Review of advanced imaging techniques

PubMed Central

Chen, Yu; Liang, Chia-Pin; Liu, Yang; Fischer, Andrew H.; Parwani, Anil V.; Pantanowitz, Liron

2012-01-01

Pathology informatics encompasses digital imaging and related applications. Several specialized microscopy techniques have emerged which permit the acquisition of digital images (“optical biopsies”) at high resolution. Coupled with fiber-optic and micro-optic components, some of these imaging techniques (e.g., optical coherence tomography) are now integrated with a wide range of imaging devices such as endoscopes, laparoscopes, catheters, and needles that enable imaging inside the body. These advanced imaging modalities have exciting diagnostic potential and introduce new opportunities in pathology. Therefore, it is important that pathology informaticists understand these advanced imaging techniques and the impact they have on pathology. This paper reviews several recently developed microscopic techniques, including diffraction-limited methods (e.g., confocal microscopy, 2-photon microscopy, 4Pi microscopy, and spatially modulated illumination microscopy) and subdiffraction techniques (e.g., photoactivated localization microscopy, stochastic optical reconstruction microscopy, and stimulated emission depletion microscopy). This article serves as a primer for pathology informaticists, highlighting the fundamentals and applications of advanced optical imaging techniques. PMID:22754737

Introducing bio- and micro-technology into undergraduate thermal-fluids courses: investigating pipe pressure loss via atomic force microscopy.

PubMed

Müller, Marcus; Traum, Matthew J

2012-01-01

To introduce bio- and micro-technologies into general undergraduate thermal-fluids classes, a hands-on interdisciplinary in-class demonstration is described that juxtaposes classical pressure loss pipe flow experiments against a modern micro-characterization technique, AFM profilometry. Both approaches measure surface roughness and can segue into classroom discussions related to material selection and design of bio-medical devices to handle biological fluids such as blood. Appealing to the range of engineering students populating a general thermal-fluids course, a variety of pipe/hose/tube materials representing a spectrum of disciplines can be tested using both techniques. This in-class demonstration relies on technical content already available in standard thermal-fluids textbooks, provides experimental juxtaposition between classical and micro-technology-enabled approaches to the same experiment, and can be taught by personnel with no specialized micro- or bio-technology expertise.

Nondestructive Analysis of Apollo Samples by Micro-CT and Micro-XRF Analysis: A PET Style Examination

NASA Technical Reports Server (NTRS)

Zeigler, Ryan A.

2014-01-01

An integral part of any sample return mission is the initial description and classification of returned samples by the preliminary examination team (PET). The goal of a PET is to characterize and classify the returned samples, making this information available to the general research community who can then conduct more in-depth studies on the samples. A PET strives to minimize the impact their work has on the sample suite, which often limits the PET work to largely visual measurements and observations like optical microscopy. More modern techniques can also be utilized by future PET to nondestructively characterize astromaterials in a more rigorous way. Here we present our recent analyses of Apollo samples 14321 and 14305 by micro-CT and micro-XRF (respectively), assess the potential for discovery of "new" Apollo samples for scientific study, and evaluate the usefulness of these techniques in future PET efforts.

Alternative techniques in root canal debridement

NASA Astrophysics Data System (ADS)

Luca, Ruxandra; Todea, Carmen; Bǎlǎbuc, Cosmin; Nica, Luminita; Armani, Giacomo; Locovei, Cosmin

2014-01-01

Studies have demonstrated that conventional chemo-mechanical preparation is limited regarding the decontamination of the endodontic space, which is why alternative techniques such as laser radiation have their importance in the modern endodontic treatment. The present study aims to assess the possibility of improving the debridement of the root canals by removing smear layer using Er: YAG laser radiation. We used 18 extracted teeth, which were subjected to the same initial protocol and then divided into 5 study groups: the control group has not been treated with laser; the other 4 groups were exposed to laser radiation using two different geometries peaks of quartz and two energy levels. Scanning electronic microscopy revealed an increased efficiency in the debridement of all interested areas when using PIPS and XPulse tips at proper energy. In the two groups treated with inferior laser energy, the debridement didn't prove to be superior to the conventional treatment.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.

PubMed

Agulleiro, J I; Garzón, E M; García, I; Fernández, J J

2010-06-01

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

Radiation microscope for SEE testing using GeV ions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doyle, Barney Lee; Knapp, James Arthur; Rossi, Paolo

2009-09-01

Radiation Effects Microscopy is an extremely useful technique in failure analysis of electronic parts used in radiation environment. It also provides much needed support for development of radiation hard components used in spacecraft and nuclear weapons. As the IC manufacturing technology progresses, more and more overlayers are used; therefore, the sensitive region of the part is getting farther and farther from the surface. The thickness of these overlayers is so large today that the traditional microbeams, which are used for REM are unable to reach the sensitive regions. As a result, higher ion beam energies have to be used (>more » GeV), which are available only at cyclotrons. Since it is extremely complicated to focus these GeV ion beams, a new method has to be developed to perform REM at cyclotrons. We developed a new technique, Ion Photon Emission Microscopy, where instead of focusing the ion beam we use secondary photons emitted from a fluorescence layer on top of the devices being tested to determine the position of the ion hit. By recording this position information in coincidence with an SEE signal we will be able to indentify radiation sensitive regions of modern electronic parts, which will increase the efficiency of radiation hard circuits.« less

Monet's Painting under the Microscope

NASA Astrophysics Data System (ADS)

Dredge, Paula; Wuhrer, Richard; Phillips, Matthew R.

2003-04-01

An oil painting by Claude Monet, Port-Goulphar, Belle-Ile 1887 (collection of the Art Gallery of New South Wales), was examined to determine both the identity of the pigments used by the artist in this painting and his technique of mixing colors and laying paint on the canvas. The extremely complex construction of the painting was revealed by optical microscopy, scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDS), and X-ray mapping (XRM) analysis of cross sections of paint flakes excised from damaged regions of Port-Goulphar, Belle-Ile. Nine different pigments were found on the painting. Many of the identified colors were modern pigments that became available only late in the 19th century as a result of scientific advances in pigment chemistry. Although similar colors were available in a natural mineral form, they lacked the vivid color of their manufactured counterparts. The use of these new synthetic metallic oxide colors by Monet accounts for the brilliance of his paintings. In addition, a separation between successive paint layers was observed in some areas of paint chip cross sections, indicating that oil-based paint was applied to paint that had dried, and consequently, Port-Goulphar, Belle-Ile was painted over a long period of time. This observation is contrary to the general perception of Monet's technique of painting freely and quickly.

Quantitative high dynamic range beam profiling for fluorescence microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, T. J., E-mail: t.j.mitchell@dur.ac.uk; Saunter, C. D.; O’Nions, W.

2014-10-15

Modern developmental biology relies on optically sectioning fluorescence microscope techniques to produce non-destructive in vivo images of developing specimens at high resolution in three dimensions. As optimal performance of these techniques is reliant on the three-dimensional (3D) intensity profile of the illumination employed, the ability to directly record and analyze these profiles is of great use to the fluorescence microscopist or instrument builder. Though excitation beam profiles can be measured indirectly using a sample of fluorescent beads and recording the emission along the microscope detection path, we demonstrate an alternative approach where a miniature camera sensor is used directly withinmore » the illumination beam. Measurements taken using our approach are solely concerned with the illumination optics as the detection optics are not involved. We present a miniature beam profiling device and high dynamic range flux reconstruction algorithm that together are capable of accurately reproducing quantitative 3D flux maps over a large focal volume. Performance of this beam profiling system is verified within an optical test bench and demonstrated for fluorescence microscopy by profiling the low NA illumination beam of a single plane illumination microscope. The generality and success of this approach showcases a widely flexible beam amplitude diagnostic tool for use within the life sciences.« less

Monet's painting under the microscope.

PubMed

Dredge, Paula; Wuhrer, Richard; Phillips, Matthew R

2003-04-01

An oil painting by Claude Monet, Port-Goulphar, Belle-Ile 1887 (collection of the Art Gallery of New South Wales), was examined to determine both the identity of the pigments used by the artist in this painting and his technique of mixing colors and laying paint on the canvas. The extremely complex construction of the painting was revealed by optical microscopy, scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDS), and X-ray mapping (XRM) analysis of cross sections of paint flakes excised from damaged regions of Port-Goulphar, Belle-Ile. Nine different pigments were found on the painting. Many of the identified colors were modern pigments that became available only late in the 19th century as a result of scientific advances in pigment chemistry. Although similar colors were available in a natural mineral form, they lacked the vivid color of their manufactured counterparts. The use of these new synthetic metallic oxide colors by Monet accounts for the brilliance of his paintings. In addition, a separation between successive paint layers was observed in some areas of paint chip cross sections, indicating that oil-based paint was applied to paint that had dried, and consequently, Port-Goulphar, Belle-Ile was painted over a long period of time. This observation is contrary to the general perception of Monet's technique of painting freely and quickly.

Accumulative Roll Bonding for Bladesmithing: From Book to Burrito to Blade

NASA Astrophysics Data System (ADS)

Hawgood, Mary; Hasier, John; Ho, Kathy

2016-12-01

A bladesmithing program was undertaken with the aim of producing superior decorative steel from dissimilar starting metals using severe plastic deformation. Accumulative roll bonding using an antiquated rolling mill was performed on 1095, CPM S30V, and 15N20 Hi-Contrast steel. Original attempts using the CPM S30V and the 1095 were unsuccessful, while later attempts using the 1095 and 15N20 Hi-Contrast steels produced a more desirable ingot. Characterization and testing, consisting of both optical and scanning electron microscopy, of the starting and wrought materials as well as the challenges in producing knife steel via synthesis of modern and traditional forging techniques, are discussed and failures analyzed.

Backside imaging of a microcontroller with common-path digital holography

NASA Astrophysics Data System (ADS)

Finkeldey, Markus; Göring, Lena; Schellenberg, Falk; Gerhardt, Nils C.; Hofmann, Martin

2017-03-01

The investigation of integrated circuits (ICs), such as microcontrollers (MCUs) and system on a chip (SoCs) devices is a topic with growing interests. The need for fast and non-destructive imaging methods is given by the increasing importance of hardware Trojans, reverse engineering and further security related analysis of integrated cryptographic devices. In the field of side-channel attacks, for instance, the precise spot for laser fault attacks is important and could be determined by using modern high resolution microscopy methods. Digital holographic microscopy (DHM) is a promising technique to achieve high resolution phase images of surface structures. These phase images provide information about the change of the refractive index in the media and the topography. For enabling a high phase stability, we use the common-path geometry to create the interference pattern. The interference pattern, or hologram, is captured with a water cooled sCMOS camera. This provides a fast readout while maintaining a low level of noise. A challenge for these types of holograms is the interference of the reflected waves from the different interfaces inside the media. To distinguish between the phase signals from the buried layer and the surface reflection we use specific numeric filters. For demonstrating the performance of our setup we show results with devices under test (DUT), using a 1064 nm laser diode as light source. The DUTs are modern microcontrollers thinned to different levels of thickness of the Si-substrate. The effect of the numeric filter compared to unfiltered images is analyzed.

Introduction to the Minireview Series on Modern Technologies for In-cell Biochemistry.

PubMed

Lutsenko, Svetlana

2016-02-19

The last decade has seen enormous progress in the exploration and understanding of the behavior of molecules in their natural cellular environments at increasingly high spatial and temporal resolution. Advances in microscopy and the development of new fluorescent reagents as well as genetic editing techniques have enabled quantitative analysis of protein interactions, intracellular trafficking, metabolic changes, and signaling. Modern biochemistry now faces new and exciting challenges. Can traditionally "in vitro" experiments, e.g. analysis of protein folding and conformational transitions, be done in cells? Can the structure and behavior of endogenous and/or non-tagged recombinant proteins be analyzed and altered within the cell or in cellular compartments? How can molecules and their actions be studied mechanistically in tissues and organs? Is personalized cellular biochemistry a reality? This thematic series summarizes recent studies that illustrate some first steps toward successfully answering these modern biochemical questions. The first minireview focuses on utilization of three-dimensional primary enteroids and organoids for mechanistic studies of intestinal biology with molecular resolution. The second minireview describes application of single chain antibodies (nanobodies) for monitoring and regulating protein dynamics in vitro and in cells. The third minireview highlights advances in using NMR spectroscopy for analysis of protein folding and assembly in cells. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as a Tool in Cell Biology Education.

PubMed

Augusto, Ingrid; Monteiro, Douglas; Girard-Dias, Wendell; Dos Santos, Thaisa Oliveira; Rosa Belmonte, Simone Letícia; Pinto de Oliveira, Jairo; Mauad, Helder; da Silva Pacheco, Marcos; Lenz, Dominik; Stefanon Bittencourt, Athelson; Valentim Nogueira, Breno; Lopes Dos Santos, Jorge Roberto; Miranda, Kildare; Guimarães, Marco Cesar Cunegundes

2016-01-01

The cell biology discipline constitutes a highly dynamic field whose concepts take a long time to be incorporated into the educational system, especially in developing countries. Amongst the main obstacles to the introduction of new cell biology concepts to students is their general lack of identification with most teaching methods. The introduction of elaborated figures, movies and animations to textbooks has given a tremendous contribution to the learning process and the search for novel teaching methods has been a central goal in cell biology education. Some specialized tools, however, are usually only available in advanced research centers or in institutions that are traditionally involved with the development of novel teaching/learning processes, and are far from becoming reality in the majority of life sciences schools. When combined with the known declining interest in science among young people, a critical scenario may result. This is especially important in the field of electron microscopy and associated techniques, methods that have greatly contributed to the current knowledge on the structure and function of different cell biology models but are rarely made accessible to most students. In this work, we propose a strategy to increase the engagement of students into the world of cell and structural biology by combining 3D electron microscopy techniques and 3D prototyping technology (3D printing) to generate 3D physical models that accurately and realistically reproduce a close-to-the native structure of the cell and serve as a tool for students and teachers outside the main centers. We introduce three strategies for 3D imaging, modeling and prototyping of cells and propose the establishment of a virtual platform where different digital models can be deposited by EM groups and subsequently downloaded and printed in different schools, universities, research centers and museums, thereby modernizing teaching of cell biology and increasing the accessibility to modern approaches in basic science.

Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as a Tool in Cell Biology Education

PubMed Central

Girard-Dias, Wendell; dos Santos, Thaisa Oliveira; Rosa Belmonte, Simone Letícia; Pinto de Oliveira, Jairo; Mauad, Helder; da Silva Pacheco, Marcos; Lenz, Dominik; Stefanon Bittencourt, Athelson; Valentim Nogueira, Breno; Lopes dos Santos, Jorge Roberto; Miranda, Kildare; Guimarães, Marco Cesar Cunegundes

2016-01-01

The cell biology discipline constitutes a highly dynamic field whose concepts take a long time to be incorporated into the educational system, especially in developing countries. Amongst the main obstacles to the introduction of new cell biology concepts to students is their general lack of identification with most teaching methods. The introduction of elaborated figures, movies and animations to textbooks has given a tremendous contribution to the learning process and the search for novel teaching methods has been a central goal in cell biology education. Some specialized tools, however, are usually only available in advanced research centers or in institutions that are traditionally involved with the development of novel teaching/learning processes, and are far from becoming reality in the majority of life sciences schools. When combined with the known declining interest in science among young people, a critical scenario may result. This is especially important in the field of electron microscopy and associated techniques, methods that have greatly contributed to the current knowledge on the structure and function of different cell biology models but are rarely made accessible to most students. In this work, we propose a strategy to increase the engagement of students into the world of cell and structural biology by combining 3D electron microscopy techniques and 3D prototyping technology (3D printing) to generate 3D physical models that accurately and realistically reproduce a close-to-the native structure of the cell and serve as a tool for students and teachers outside the main centers. We introduce three strategies for 3D imaging, modeling and prototyping of cells and propose the establishment of a virtual platform where different digital models can be deposited by EM groups and subsequently downloaded and printed in different schools, universities, research centers and museums, thereby modernizing teaching of cell biology and increasing the accessibility to modern approaches in basic science. PMID:27526196

In Vivo and Ex Vivo Confocal Microscopy for Dermatologic and Mohs Surgeons.

PubMed

Longo, Caterina; Ragazzi, Moira; Rajadhyaksha, Milind; Nehal, Kishwer; Bennassar, Antoni; Pellacani, Giovanni; Malvehy Guilera, Josep

2016-10-01

Confocal microscopy is a modern imaging device that has been extensively applied in skin oncology. More specifically, for tumor margin assessment, it has been used in two modalities: reflectance mode (in vivo on skin patient) and fluorescence mode (on freshly excised specimen). Although in vivo reflectance confocal microscopy is an add-on tool for lentigo maligna mapping, fluorescence confocal microscopy is far superior for basal cell carcinoma and squamous cell carcinoma margin assessment in the Mohs setting. This article provides a comprehensive overview of the use of confocal microscopy for skin cancer margin evaluation. Copyright © 2016 Elsevier Inc. All rights reserved.

Microscopy techniques in flavivirus research.

PubMed

Chong, Mun Keat; Chua, Anthony Jin Shun; Tan, Terence Tze Tong; Tan, Suat Hoon; Ng, Mah Lee

2014-04-01

The Flavivirus genus is composed of many medically important viruses that cause high morbidity and mortality, which include Dengue and West Nile viruses. Various molecular and biochemical techniques have been developed in the endeavour to study flaviviruses. However, microscopy techniques still have irreplaceable roles in the identification of novel virus pathogens and characterization of morphological changes in virus-infected cells. Fluorescence microscopy contributes greatly in understanding the fundamental viral protein localizations and virus-host protein interactions during infection. Electron microscopy remains the gold standard for visualizing ultra-structural features of virus particles and infected cells. New imaging techniques and combinatory applications are continuously being developed to push the limit of resolution and extract more quantitative data. Currently, correlative live cell imaging and high resolution three-dimensional imaging have already been achieved through the tandem use of optical and electron microscopy in analyzing biological specimens. Microscopy techniques are also used to measure protein binding affinities and determine the mobility pattern of proteins in cells. This chapter will consolidate on the applications of various well-established microscopy techniques in flavivirus research, and discuss how recently developed microscopy techniques can potentially help advance our understanding in these membrane viruses. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Inheritance and evolution of acupuncture manipulation techniques of Zhejiang acupuncture masters in modern times].

PubMed

Yu, Daxiong; Ma, Ruijie; Fang, Jianqiao

2015-05-01

There are many eminent acupuncture masters in modern times in the regions of Zhejiang province, which has developed the acupuncture schools of numerous characteristics and induces the important impacts at home and abroad. Through the literature collection on the acupuncture schools in Zhejiang and the interviews to the parties involved, it has been discovered that the acupuncture manipulation techniques of acupuncture masters in modern times are specifically featured. Those techniques are developed on the basis of Neijing (Internal Classic), Jinzhenfu (Ode to Gold Needle) and Zhenjiu Dacheng (Great Compendium of Acupuncture and Moxibustion). No matter to obey the old maxim or study by himself, every master lays the emphasis on the research and interpretation of classical theories and integrates the traditional with the modern. In the paper, the acupuncture manipulation techniques of Zhejiang acupuncture masters in modern times are stated from four aspects, named needling techniques in Internal Classic, feijingzouqi needling technique, penetrating needling technique and innovation of acupuncture manipulation.

Increasing the reliability of ecological models using modern software engineering techniques

Treesearch

Robert M. Scheller; Brian R. Sturtevant; Eric J. Gustafson; Brendan C. Ward; David J. Mladenoff

2009-01-01

Modern software development techniques are largely unknown to ecologists. Typically, ecological models and other software tools are developed for limited research purposes, and additional capabilities are added later, usually in an ad hoc manner. Modern software engineering techniques can substantially increase scientific rigor and confidence in ecological models and...

A new systematic and quantitative approach to characterization of surface nanostructures using fuzzy logic

NASA Astrophysics Data System (ADS)

Al-Mousa, Amjed A.

Thin films are essential constituents of modern electronic devices and have a multitude of applications in such devices. The impact of the surface morphology of thin films on the device characteristics where these films are used has generated substantial attention to advanced film characterization techniques. In this work, we present a new approach to characterize surface nanostructures of thin films by focusing on isolating nanostructures and extracting quantitative information, such as the shape and size of the structures. This methodology is applicable to any Scanning Probe Microscopy (SPM) data, such as Atomic Force Microscopy (AFM) data which we are presenting here. The methodology starts by compensating the AFM data for some specific classes of measurement artifacts. After that, the methodology employs two distinct techniques. The first, which we call the overlay technique, proceeds by systematically processing the raster data that constitute the scanning probe image in both vertical and horizontal directions. It then proceeds by classifying points in each direction separately. Finally, the results from both the horizontal and the vertical subsets are overlaid, where a final decision on each surface point is made. The second technique, based on fuzzy logic, relies on a Fuzzy Inference Engine (FIE) to classify the surface points. Once classified, these points are clustered into surface structures. The latter technique also includes a mechanism which can consistently distinguish crowded surfaces from those with sparsely distributed structures and then tune the fuzzy technique system uniquely for that surface. Both techniques have been applied to characterize organic semiconductor thin films of pentacene on different substrates. Also, we present a case study to demonstrate the effectiveness of our methodology to identify quantitatively particle sizes of two specimens of gold nanoparticles of different nominal dimensions dispersed on a mica surface. A comparison with other techniques like: thresholding, watershed and edge detection is presented next. Finally, we present a systematic study of the fuzzy logic technique by experimenting with synthetic data. These results are discussed and compared along with the challenges of the two techniques.

Automatic tracking of cells for video microscopy in patch clamp experiments

PubMed Central

2014-01-01

Background Visualisation of neurons labeled with fluorescent proteins or compounds generally require exposure to intense light for a relatively long period of time, often leading to bleaching of the fluorescent probe and photodamage of the tissue. Here we created a technique to drastically shorten light exposure and improve the targeting of fluorescent labeled cells that is specially useful for patch-clamp recordings. We applied image tracking and mask overlay to reduce the time of fluorescence exposure and minimise mistakes when identifying neurons. Methods Neurons are first identified according to visual criteria (e.g. fluorescence protein expression, shape, viability etc.) and a transmission microscopy image Differential Interference Contrast (DIC) or Dodt contrast containing the cell used as a reference for the tracking algorithm. A fluorescence image can also be acquired later to be used as a mask (that can be overlaid on the target during live transmission video). As patch-clamp experiments require translating the microscope stage, we used pattern matching to track reference neurons in order to move the fluorescence mask to match the new position of the objective in relation to the sample. For the image processing we used the Open Source Computer Vision (OpenCV) library, including the Speeded-Up Robust Features (SURF) for tracking cells. The dataset of images (n = 720) was analyzed under normal conditions of acquisition and with influence of noise (defocusing and brightness). Results We validated the method in dissociated neuronal cultures and fresh brain slices expressing Enhanced Yellow Fluorescent Protein (eYFP) or Tandem Dimer Tomato (tdTomato) proteins, which considerably decreased the exposure to fluorescence excitation, thereby minimising photodamage. We also show that the neuron tracking can be used in differential interference contrast or Dodt contrast microscopy. Conclusion The techniques of digital image processing used in this work are an important addition to the set of microscopy tools used in modern electrophysiology, specially in experiments with neuron cultures and brain slices. PMID:24946774

Automatic tracking of cells for video microscopy in patch clamp experiments.

PubMed

Peixoto, Helton M; Munguba, Hermany; Cruz, Rossana M S; Guerreiro, Ana M G; Leao, Richardson N

2014-06-20

Visualisation of neurons labeled with fluorescent proteins or compounds generally require exposure to intense light for a relatively long period of time, often leading to bleaching of the fluorescent probe and photodamage of the tissue. Here we created a technique to drastically shorten light exposure and improve the targeting of fluorescent labeled cells that is specially useful for patch-clamp recordings. We applied image tracking and mask overlay to reduce the time of fluorescence exposure and minimise mistakes when identifying neurons. Neurons are first identified according to visual criteria (e.g. fluorescence protein expression, shape, viability etc.) and a transmission microscopy image Differential Interference Contrast (DIC) or Dodt contrast containing the cell used as a reference for the tracking algorithm. A fluorescence image can also be acquired later to be used as a mask (that can be overlaid on the target during live transmission video). As patch-clamp experiments require translating the microscope stage, we used pattern matching to track reference neurons in order to move the fluorescence mask to match the new position of the objective in relation to the sample. For the image processing we used the Open Source Computer Vision (OpenCV) library, including the Speeded-Up Robust Features (SURF) for tracking cells. The dataset of images (n = 720) was analyzed under normal conditions of acquisition and with influence of noise (defocusing and brightness). We validated the method in dissociated neuronal cultures and fresh brain slices expressing Enhanced Yellow Fluorescent Protein (eYFP) or Tandem Dimer Tomato (tdTomato) proteins, which considerably decreased the exposure to fluorescence excitation, thereby minimising photodamage. We also show that the neuron tracking can be used in differential interference contrast or Dodt contrast microscopy. The techniques of digital image processing used in this work are an important addition to the set of microscopy tools used in modern electrophysiology, specially in experiments with neuron cultures and brain slices.

Modern Micro and Nanoparticle-Based Imaging Techniques

PubMed Central

Ryvolova, Marketa; Chomoucka, Jana; Drbohlavova, Jana; Kopel, Pavel; Babula, Petr; Hynek, David; Adam, Vojtech; Eckschlager, Tomas; Hubalek, Jaromir; Stiborova, Marie; Kaiser, Jozef; Kizek, Rene

2012-01-01

The requirements for early diagnostics as well as effective treatment of insidious diseases such as cancer constantly increase the pressure on development of efficient and reliable methods for targeted drug/gene delivery as well as imaging of the treatment success/failure. One of the most recent approaches covering both the drug delivery as well as the imaging aspects is benefitting from the unique properties of nanomaterials. Therefore a new field called nanomedicine is attracting continuously growing attention. Nanoparticles, including fluorescent semiconductor nanocrystals (quantum dots) and magnetic nanoparticles, have proven their excellent properties for in vivo imaging techniques in a number of modalities such as magnetic resonance and fluorescence imaging, respectively. In this article, we review the main properties and applications of nanoparticles in various in vitro imaging techniques, including microscopy and/or laser breakdown spectroscopy and in vivo methods such as magnetic resonance imaging and/or fluorescence-based imaging. Moreover the advantages of the drug delivery performed by nanocarriers such as iron oxides, gold, biodegradable polymers, dendrimers, lipid based carriers such as liposomes or micelles are also highlighted. PMID:23202187

Tracking flow of leukocytes in blood for drug analysis

NASA Astrophysics Data System (ADS)

Basharat, Arslan; Turner, Wesley; Stephens, Gillian; Badillo, Benjamin; Lumpkin, Rick; Andre, Patrick; Perera, Amitha

2011-03-01

Modern microscopy techniques allow imaging of circulating blood components under vascular flow conditions. The resulting video sequences provide unique insights into the behavior of blood cells within the vasculature and can be used as a method to monitor and quantitate the recruitment of inflammatory cells at sites of vascular injury/ inflammation and potentially serve as a pharmacodynamic biomarker, helping screen new therapies and individualize dose and combinations of drugs. However, manual analysis of these video sequences is intractable, requiring hours per 400 second video clip. In this paper, we present an automated technique to analyze the behavior and recruitment of human leukocytes in whole blood under physiological conditions of shear through a simple multi-channel fluorescence microscope in real-time. This technique detects and tracks the recruitment of leukocytes to a bioactive surface coated on a flow chamber. Rolling cells (cells which partially bind to the bioactive matrix) are detected counted, and have their velocity measured and graphed. The challenges here include: high cell density, appearance similarity, and low (1Hz) frame rate. Our approach performs frame differencing based motion segmentation, track initialization and online tracking of individual leukocytes.

Joint denoising and distortion correction of atomic scale scanning transmission electron microscopy images

NASA Astrophysics Data System (ADS)

Berkels, Benjamin; Wirth, Benedikt

2017-09-01

Nowadays, modern electron microscopes deliver images at atomic scale. The precise atomic structure encodes information about material properties. Thus, an important ingredient in the image analysis is to locate the centers of the atoms shown in micrographs as precisely as possible. Here, we consider scanning transmission electron microscopy (STEM), which acquires data in a rastering pattern, pixel by pixel. Due to this rastering combined with the magnification to atomic scale, movements of the specimen even at the nanometer scale lead to random image distortions that make precise atom localization difficult. Given a series of STEM images, we derive a Bayesian method that jointly estimates the distortion in each image and reconstructs the underlying atomic grid of the material by fitting the atom bumps with suitable bump functions. The resulting highly non-convex minimization problems are solved numerically with a trust region approach. Existence of minimizers and the model behavior for faster and faster rastering are investigated using variational techniques. The performance of the method is finally evaluated on both synthetic and real experimental data.

Interface formation in monolayer graphene-boron nitride heterostructures.

PubMed

Sutter, P; Cortes, R; Lahiri, J; Sutter, E

2012-09-12

The ability to control the formation of interfaces between different materials has become one of the foundations of modern materials science. With the advent of two-dimensional (2D) crystals, low-dimensional equivalents of conventional interfaces can be envisioned: line boundaries separating different materials integrated in a single 2D sheet. Graphene and hexagonal boron nitride offer an attractive system from which to build such 2D heterostructures. They are isostructural, nearly lattice-matched, and isoelectronic, yet their different band structures promise interesting functional properties arising from their integration. Here, we use a combination of in situ microscopy techniques to study the growth and interface formation of monolayer graphene-boron nitride heterostructures on ruthenium. In a sequential chemical vapor deposition process, boron nitride grows preferentially at the edges of existing monolayer graphene domains, which can be exploited for synthesizing continuous 2D membranes of graphene embedded in boron nitride. High-temperature growth leads to intermixing near the interface, similar to interfacial alloying in conventional heterostructures. Using real-time microscopy, we identify processes that eliminate this intermixing and thus pave the way to graphene-boron nitride heterostructures with atomically sharp interfaces.

Application of gold nanoparticles as contrast agents in confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Lemelle, A.; Veksler, B.; Kozhevnikov, I. S.; Akchurin, G. G.; Piletsky, S. A.; Meglinski, I.

2009-01-01

Confocal laser scanning microscopy (CLSM) is a modern high-resolution optical technique providing detailed image of tissue structure with high (down to microns) spatial resolution. Aiming at a concurrent improvement of imaging depth and image quality the CLSM requires the use of contrast agents. Commonly employed fluorescent contrast agents, such as fluorescent dyes and proteins, suffer from toxicity, photo-bleaching and overlapping with the tissues autofluorescence. Gold nanoparticles are potentially highly attractive to be applied as a contrast agent since they are not subject to photo-bleaching and can target biochemical cells markers associated with the specific diseases. In current report we consider the applicability of gold nano-spheres as a contrast agent to enhance quality of CLSM images of skin tissues in vitro versus the application of optical clearing agent, such as glycerol. The enhancement of CLSM image contrast was observed with an application of gold nano-spheres diffused within the skin tissues. We show that optical clearing agents such as a glycerol provide better CLSM image contrast than gold nano-spheres.

Application of scanning acoustic microscopy to advanced structural ceramics

NASA Technical Reports Server (NTRS)

Vary, Alex; Klima, Stanley J.

1987-01-01

A review is presentod of research investigations of several acoustic microscopy techniques for application to structural ceramics for advanced heat engines. Results obtained with scanning acoustic microscopy (SAM), scanning laser acoustic microscopy (SLAM), scanning electron acoustic microscopy (SEAM), and photoacoustic microscopy (PAM) are compared. The techniques were evaluated on research samples of green and sintered monolithic silicon nitrides and silicon carbides in the form of modulus-of-rupture bars containing deliberately introduced flaws. Strengths and limitations of the techniques are described with emphasis on statistics of detectability of flaws that constitute potential fracture origins.

Characterization of Apollo Regolith by X-Ray and Electron Microbeam Techniques: An Analog for Future Sample Return Missions

NASA Technical Reports Server (NTRS)

Zeigler, Ryan A.

2015-01-01

The Apollo missions collected 382 kg of rock and regolith from the Moon; approximately 1/3 of the sample mass collected was regolith. Lunar regolith consists of well mixed rocks, minerals, and glasses less than 1-centimeter n size. The majority of most surface regolith samples were sieved into less than 1, 1-2, 2-4, and 4-10- millimiter size fractions; a portion of most samples was re-served unsieved. The initial characterization and classification of most Apollo regolith particles was done primarily by binocular microscopy. Optical classification of regolith is difficult because (1) the finest fraction of the regolith coats and obscures the textures of the larger particles, and (b) not all lithologies or minerals are uniquely identifiable optically. In recent years, we have begun to use more modern x-ray beam techniques [1-3], coupled with high resolution 3D optical imaging techniques [4] to characterize Apollo and meteorite samples as part of the curation process. These techniques, particularly in concert with SEM imaging of less than 1-millimeter regolith grain mounts, allow for the rapid characterization of the components within a regolith.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boussaa, S. Anas, E-mail: sabiha.anas@gmail.com; Kheloufi, A.; Kefaifi, A.

Raw materials are essential for the functioning of modern societies, and access to these raw materials is vital to the world economy. Sustainable development, both globally level, raises important new challenges associated with access and efficient use of raw materials. High purity quartz, is consider as a critical raw material and it is a rare commodity that only forms under geological conditions where a narrow set of chemical and physical parameters is fulfilled. When identified and following special beneficiation techniques, high purity quartz obtains very attractive prices and is applied in high technology sectors that currently are under rapid expansionmore » such as photovoltaic solar cells, silicon metal - oxide wafers in the semiconductor industry and long distance optical fibers that are used in communication networks. Crystalline silicon remains the principal material for photovoltaic technology. Metallurgical silicon is produced industrially by the reduction of silica with carbon in an electric arc furnace at temperatures higher than 2000 °C in the hottest parts, by a reaction that can be written ideally as: SiO{sub 2} + 2C = Si + 2CO. The aim of this study has been to test experimental methods for investigating the various physical and chemical proprieties of Hoggar quartz with different techniques: X Ray Fluorescence, infra-red spectroscopy, Scanning Electron Microscopy, Optic Microscopy, Carbon Analyzer and Vickers Hardness. The results show finally that the quartz has got good result in purity but need enrichment for the photovoltaic application.« less

Progress in the Correlative Atomic Force Microscopy and Optical Microscopy

PubMed Central

Zhou, Lulu; Cai, Mingjun; Tong, Ti; Wang, Hongda

2017-01-01

Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed. To overcome the technical limitations, it is necessary to combine AFM with other complementary techniques, such as fluorescence microscopy. The combination of several complementary techniques in one instrument has increasingly become a vital approach to investigate the details of the interactions among molecules and molecular dynamics. In this review, we reported the principles of AFM and optical microscopy, such as confocal microscopy and single-molecule localization microscopy, and focused on the development and use of correlative AFM and optical microscopy. PMID:28441775

Nanoscale Phase-Separated Structure in Core-Shell Nanoparticles of SiO2-Si1-xGexO2 Glass Revealed by Electron Microscopy.

PubMed

Kubo, Yugo; Yonezawa, Kazuhiro

2017-09-05

SiO 2 -based optical fibers are indispensable components of modern information communication technologies. It has recently become increasingly important to establish a technique for visualizing the nanoscale phase-separated structure inside SiO 2 -GeO 2 glass nanoparticles during the manufacturing of SiO 2 -GeO 2 fibers. This is because the rapidly increasing price of Ge has made it necessary to improve the Ge yield by clarifying the detailed mechanism of Ge diffusion into SiO 2 . However, direct observation of the internal nanostructure of glass particles has been extremely difficult, mainly due to electrostatic charging and the damage induced by electron and X-ray irradiation. In the present study, we used state-of-the-art scanning electron microscopy (SEM), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDX) to examine cross-sectional samples of SiO 2 -GeO 2 particles embedded in an epoxy resin, which were fabricated using a broad Ar ion beam and a focused Ga ion beam. These advanced techniques enabled us to observe the internal phase-separated structure of the nanoparticles. We have for the first time clearly determined the SiO 2 -Si 1-x Ge x O 2 core-shell structure of such particles, the element distribution, the degree of crystallinity, and the quantitative chemical composition of microscopic regions, and we discuss the formation mechanism for the observed structure. The proposed imaging protocol is highly promising for studying the internal structure of various core-shell nanoparticles, which affects their catalytic, optical, and electronic properties.

Biotic Control of Skeletal Growth by Scleractinian Corals in Aragonite–Calcite Seas

PubMed Central

Higuchi, Tomihiko; Fujimura, Hiroyuki; Yuyama, Ikuko; Harii, Saki; Agostini, Sylvain; Oomori, Tamotsu

2014-01-01

Modern scleractinian coral skeletons are commonly composed of aragonite, the orthorhombic form of CaCO3. Under certain conditions, modern corals produce calcite as a secondary precipitate to fill pore space. However, coral construction of primary skeletons from calcite has yet to be demonstrated. We report a calcitic primary skeleton produced by the modern scleractinian coral Acropora tenuis. When uncalcified juveniles were incubated from the larval stage in seawater with low mMg/Ca levels, the juveniles constructed calcitic crystals in parts of the primary skeleton such as the septa; the deposits were observable under Raman microscopy. Using scanning electron microscopy, we observed different crystal morphologies of aragonite and calcite in a single juvenile skeleton. Quantitative analysis using X-ray diffraction showed that the majority of the skeleton was composed of aragonite even though we had exposed the juveniles to manipulated seawater before their initial crystal nucleation and growth processes. Our results indicate that the modern scleractinian coral Acropora mainly produces aragonite skeletons in both aragonite and calcite seas, but also has the ability to use calcite for part of its skeletal growth when incubated in calcite seas. PMID:24609012

Investigation of biomaterials by human epithelial gingiva cells: an in vitro study

PubMed Central

2012-01-01

Introduction In modern medicine and dentistry the use of biomaterials is a fast developing field of increasing interest. Especially in dentistry the interaction between biomaterials like implant materials and the soft tissue in the oral cavity is in the focus of daily research. In this context the high importance of testing materials and their surfaces concerning their biocompatibility towards corresponding cells is very likely. For this purpose this study investigates cells derived from human gingival biopsies on different materials and surfaces. Methods Cells in this study were cultivated out of human biopsies by a grow out explant technique and were sub cultivated on titanium, zirconium dioxide and collagen membrane specimens. To characterise the cells on the material surfaces used in this study immunohistochemical and histological staining techniques as well as different methods of microscopy (light microscopy and SEM) were applied. Results With the aid of the explant technique and the chosen cell cultivation method it was possible to investigate the human gingiva derived cells on different materials. The data of the present study show that the human gingival cells attach and proliferate on all three tested materials by exhibiting characteristic gingival keratinocyte protein expression even after long periods of culture e.g. up to 70 days. Conclusions It could be shown that the three tested materials titanium, zirconium dioxide and collagen membrane (and their special surfaces) are good candidates for the application as materials in the dental gingival environment or, in the case of the collagen membrane as scaffold/cell-carrier for human gingival cells in tissue engineering. PMID:23241143

Comparative morphology analysis of live blood platelets using scanning ion conductance and robotic dark-field microscopy.

PubMed

Kraus, Max-Joseph; Seifert, Jan; Strasser, Erwin F; Gawaz, Meinrad; Schäffer, Tilman E; Rheinlaender, Johannes

2016-09-01

Many conventional microscopy techniques for investigating platelet morphology such as electron or fluorescence microscopy require highly invasive treatment of the platelets such as fixation, drying and metal coating or staining. Here, we present two unique but entirely different microscopy techniques for direct morphology analysis of live, unstained platelets: scanning ion conductance microscopy (SICM) and robotic dark-field microscopy (RDM). We demonstrate that both techniques allow for a quantitative evaluation of the morphological features of live adherent platelets. We show that their morphology can be quantified by both techniques using the same geometric parameters and therefore can be directly compared. By imaging the same identical platelets subsequently with SICM and RDM, we found that area, perimeter and circularity of the platelets are directly correlated between SICM and dark-field microscopy (DM), while the fractal dimension (FD) differed between the two microscopy techniques. We show that SICM and RDM are both valuable tools for the ex vivo investigation of the morphology of live platelets, which might contribute to new insights into the physiological and pathophysiological role of platelet spreading.

Automated data collection in single particle electron microscopy

PubMed Central

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

In vivo correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh; Leahy, Martin

2016-04-01

To facilitate regular assessment of the microcirculation in vivo, noninvasive imaging techniques such as nailfold capillaroscopy are required in clinics. Recently, a correlation mapping technique has been applied to optical coherence tomography (OCT), which extends the capabilities of OCT to microcirculation morphology imaging. This technique, known as correlation mapping optical coherence tomography, has been shown to extract parameters, such as capillary density and vessel diameter, and key clinical markers associated with early changes in microvascular diseases. However, OCT has limited spatial resolution in both the transverse and depth directions. Here, we extend this correlation mapping technique to other microscopy modalities, including confocal microscopy, and take advantage of the higher spatial resolution offered by these modalities. The technique is achieved as a processing step on microscopy images and does not require any modification to the microscope hardware. Results are presented which show that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution in both the transverse and depth directions.

Subcutaneous transplantation of embryonic pancreas for correction of type 1 diabetes

PubMed Central

Gunawardana, Subhadra C.; Benninger, Richard K. P.; Piston, David W.

2009-01-01

Islet transplantation is a promising therapeutic approach for type 1 diabetes. However, current success rates are low due to progressive graft failure in the long term and inability to monitor graft development in vivo. Other limitations include the necessity of initial invasive surgery and continued immunosuppressive therapy. We report an alternative transplantation strategy with the potential to overcome these problems. This technique involves transplantation of embryonic pancreatic tissue into recipients’ subcutaneous space, eliminating the need for invasive surgery and associated risks. Current results in mouse models of type 1 diabetes show that embryonic pancreatic transplants in the subcutaneous space can normalize blood glucose homeostasis and achieve extensive endocrine differentiation and vascularization. Furthermore, modern imaging techniques such as two-photon excitation microscopy (TPEM) can be employed to monitor transplants through the intact skin in a completely noninvasive manner. Thus, this strategy is a convenient alternative to islet transplantation in diabetic mice and has the potential to be translated to human clinical applications with appropriate modifications. PMID:19066321

Red blood cell-deformability measurement: review of techniques.

PubMed

Musielak, M

2009-01-01

Cell-deformability characterization involves general measurement of highly complex relationships between cell biology and physical forces to which the cell is subjected. The review takes account of the modern technical solutions simulating the action of the force applied to the red blood cell in macro- and microcirculation. Diffraction ektacytometers and rheoscopes measure the mean deformability value for the total red blood cell population investigated and the deformation distribution index of individual cells, respectively. Deformation assays of a whole single cell are possible by means of optical tweezers. The single cell-measuring setups for micropipette aspiration and atomic force microscopy allow conducting a selective investigation of deformation parameters (e.g., cytoplasm viscosity, viscoelastic membrane properties). The distinction between instrument sensitivity to various RBC-rheological features as well as the influence of temperature on measurement are discussed. The reports quoted confront fascinating possibilities of the techniques with their medical applications since the RBC-deformability has the key position in the etiology of a wide range of conditions.

The Development of Teaching and Learning in Bright-Field Microscopy Technique

ERIC Educational Resources Information Center

Iskandar, Yulita Hanum P.; Mahmud, Nurul Ethika; Wahab, Wan Nor Amilah Wan Abdul; Jamil, Noor Izani Noor; Basir, Nurlida

2013-01-01

E-learning should be pedagogically-driven rather than technologically-driven. The objectives of this study are to develop an interactive learning system in bright-field microscopy technique in order to support students' achievement of their intended learning outcomes. An interactive learning system on bright-field microscopy technique was…

NicoLase—An open-source diode laser combiner, fiber launch, and sequencing controller for fluorescence microscopy

PubMed Central

Walsh, James; Böcking, Till; Gaus, Katharina

2017-01-01

Modern fluorescence microscopy requires software-controlled illumination sources with high power across a wide range of wavelengths. Diode lasers meet the power requirements and combining multiple units into a single fiber launch expands their capability across the required spectral range. We present the NicoLase, an open-source diode laser combiner, fiber launch, and software sequence controller for fluorescence microscopy and super-resolution microscopy applications. Two configurations are described, giving four or six output wavelengths and one or two single-mode fiber outputs, with all CAD files, machinist drawings, and controller source code openly available. PMID:28301563

Correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh M.; Leahy, Martin J.

2015-03-01

Changes in the microcirculation are associated with conditions such as Raynauds disease. Current modalities used to assess the microcirculation such as nailfold capillaroscopy are limited due to their depth ambiguity. A correlation mapping technique was recently developed to extend the capabilities of Optical Coherence Tomography to generate depth resolved images of the microcirculation. Here we present the extension of this technique to microscopy modalities, including confocal microscopy. It is shown that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution.

Current role of modern radiotherapy techniques in the management of breast cancer

PubMed Central

Ozyigit, Gokhan; Gultekin, Melis

2014-01-01

Breast cancer is the most common type of malignancy in females. Advances in systemic therapies and radiotherapy (RT) provided long survival rates in breast cancer patients. RT has a major role in the management of breast cancer. During the past 15 years several developments took place in the field of imaging and irradiation techniques, intensity modulated RT, hypofractionation and partial-breast irradiation. Currently, improvements in the RT technology allow us a subsequent decrease in the treatment-related complications such as fibrosis and long-term cardiac toxicity while improving the loco-regional control rates and cosmetic results. Thus, it is crucial that modern radiotherapy techniques should be carried out with maximum care and efficiency. Several randomized trials provided evidence for the feasibility of modern radiotherapy techniques in the management of breast cancer. However, the role of modern radiotherapy techniques in the management of breast cancer will continue to be defined by the mature results of randomized trials. Current review will provide an up-to-date evidence based data on the role of modern radiotherapy techniques in the management of breast cancer. PMID:25114857

Atomic force microscopy and nanoindentation investigation of polydimethylsiloxane elastomeric substrate compliancy for various sputtered thin film morphologies.

PubMed

Maji, Debashis; Das, Soumen

2018-03-01

Crack free electrically continuous metal thin films over soft elastomeric substrates play an integral part in realization of modern day flexible bioelectronics and biosensors. Under nonoptimized deposition conditions, delamination, and/or cracking of the top film as well as the underlying soft substrate hinders optimal performance of these devices. Hence it is very important to understand and control not only the various deposition factors like power, time, or deposition pressure but also investigate the various interfacial physics playing a critical role in assuring thin film adhesion and substrate compliancy. In the present study, various nanomechanical information of the underlying substrate, namely, crack profile, average roughness, Young's modulus, and adhesion force were studied for uncracked and cracked polydimethylsiloxane (PDMS) surfaces along with pristine and conventional plasma treated PDMS samples as control. Quantification of the above parameters were done using three-dimensional surface profiler, scanning electron microscopy, nanoindentation, and atomic force microscopy techniques to elucidate the modulus range, average roughness, and adhesion force. Comparative analysis with control revealed remarkable similarity between increased modulus values, increased surface roughness, and reduced adhesion force accounting for reduced substrate compliancy and resulting in film cracking or buckling which are critical for development of various bioflexible devices. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 725-737, 2018. © 2017 Wiley Periodicals, Inc.

Evaluation of mobile digital light-emitting diode fluorescence microscopy in Hanoi, Viet Nam.

PubMed

Chaisson, L H; Reber, C; Phan, H; Switz, N; Nilsson, L M; Myers, F; Nhung, N V; Luu, L; Pham, T; Vu, C; Nguyen, H; Nguyen, A; Dinh, T; Nahid, P; Fletcher, D A; Cattamanchi, A

2015-09-01

Hanoi Lung Hospital, Hanoi, Viet Nam. To compare the accuracy of CellScopeTB, a manually operated mobile digital fluorescence microscope, with conventional microscopy techniques. Patients referred for sputum smear microscopy to the Hanoi Lung Hospital from May to September 2013 were included. Ziehl-Neelsen (ZN) smear microscopy, conventional light-emitting diode (LED) fluorescence microscopy (FM), CellScopeTB-based LED FM and Xpert(®) MTB/RIF were performed on sputum samples. The sensitivity and specificity of microscopy techniques were determined in reference to Xpert results, and differences were compared using McNemar's paired test of proportions. Of 326 patients enrolled, 93 (28.5%) were Xpert-positive for TB. The sensitivity of ZN microscopy, conventional LED FM, and CellScopeTB-based LED FM was respectively 37.6% (95%CI 27.8-48.3), 41.9% (95%CI 31.8-52.6), and 35.5% (95%CI 25.8-46.1). The sensitivity of CellScopeTB was similar to that of conventional LED FM (difference -6.5%, 95%CI -18.2 to 5.3, P = 0.33) and ZN microscopy (difference -2.2%, 95%CI -9.2 to 4.9, P = 0.73). The specificity was >99% for all three techniques. CellScopeTB performed similarly to conventional microscopy techniques in the hands of experienced TB microscopists. However, the sensitivity of all sputum microscopy techniques was low. Options enabled by digital microscopy, such as automated imaging with real-time computerized analysis, should be explored to increase sensitivity.

Direct Determination of the Equilibrium Unbinding Potential Profile for a Short DNA Duplex from Force Spectroscopy Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noy, A

2004-05-04

Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in non-equilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of non-equilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNAmore » duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.« less

The origins and evolution of freeze-etch electron microscopy

PubMed Central

Heuser, John E.

2011-01-01

The introduction of the Balzers freeze-fracture machine by Moor in 1961 had a much greater impact on the advancement of electron microscopy than he could have imagined. Devised originally to circumvent the dangers of classical thin-section techniques, as well as to provide unique en face views of cell membranes, freeze-fracturing proved to be crucial for developing modern concepts of how biological membranes are organized and proved that membranes are bilayers of lipids within which proteins float and self-assemble. Later, when freeze-fracturing was combined with methods for freezing cells that avoided the fixation and cryoprotection steps that Moor still had to use to prepare the samples for his original invention, it became a means for capturing membrane dynamics on the millisecond time-scale, thus allowing a deeper understanding of the functions of biological membranes in living cells as well as their static ultrastructure. Finally, the realization that unfixed, non-cryoprotected samples could be deeply vacuum-etched or even freeze-dried after freeze-fracturing opened up a whole new way to image all the other molecular components of cells besides their membranes and also provided a powerful means to image the interactions of all the cytoplasmic components with the various membranes of the cell. The purpose of this review is to outline the history of these technical developments, to describe how they are being used in electron microscopy today and to suggest how they can be improved in order to further their utility for biological electron microscopy in the future. PMID:21844598

Enhancing multi-spot structured illumination microscopy with fluorescence difference

NASA Astrophysics Data System (ADS)

Ward, Edward N.; Torkelsen, Frida H.; Pal, Robert

2018-03-01

Structured illumination microscopy is a super-resolution technique used extensively in biological research. However, this technique is limited in the maximum possible resolution increase. Here we report the results of simulations of a novel enhanced multi-spot structured illumination technique. This method combines the super-resolution technique of difference microscopy with structured illumination deconvolution. Initial results give at minimum a 1.4-fold increase in resolution over conventional structured illumination in a low-noise environment. This new technique also has the potential to be expanded to further enhance axial resolution with three-dimensional difference microscopy. The requirement for precise pattern determination in this technique also led to the development of a new pattern estimation algorithm which proved more efficient and reliable than other methods tested.

A scientific approach to the characterization of the painting materials of Fra Mattia della Robbia polychrome terracotta altarpiece

NASA Astrophysics Data System (ADS)

Amadori, M. L.; Barcelli, S.; Casoli, A.; Mazzeo, R.; Prati, S.

2013-12-01

During the last restoration (2008-2011) of the polychrome terracotta altarpiece called Coronation of Virgin between Saints Rocco, Sebastian, Peter martyr and Antonio abbot, located in the collegiate church of S. Maria Assunta in Montecassiano (Macerata, Italy), scientific investigations were carried out to acquire detailed information about the painting technique. The identification of materials allowed a correct restoration. The altarpiece is almost entirely realized by Marco della Robbia (Fra Mattia), dates back to the first half of the XVI century and represents an interesting example of painted terracotta produced by using two different techniques: glazed polychrome terracotta and the "cold painting" technique. The characterization of the samples' material constituents was obtained by analysing the cross-sections and the fragments by different techniques (optical, SEM-EDS and ATR-FTIR microscopy as well as GC-MS), as the real nature of a component is often difficult to assess with one single technique. The optical microscope examination of paint cross-sections shows the presence of many layers, indicating the complexity of the paint stratigraphic morphologies. The original polychromy of della Robbia's masterpiece is constituted of cinnabar, red lake, red lead, orpiment, red ochre, lead white, lead tin yellow, green earth and raw umber. Two different types of gilding technique have been distinguished. The first one presents a glue mordant, and the second one shows an oil mordant composed by a mixture of red lead, red ochre, cinnabar and orpiment. The GC-MS analysis allowed the characterisation of linseed oil and a mixture of animal glue and egg as binding media stratigraphically located by the use of ATR-FTIR mapping microscopy. The analytical results of the painted terracotta integrated investigations show that original technique adopted is characterised by the application of pigments in an oil-binding medium directly applied on the substrates, probably treated with oil and animal glue. A large number of overpaintings above the original scheme of polychromy was found, which could be ascribed to almost three different interventions; the absence of modern pigments suggests that they could be realized long ago.

Tissue reactions to modern suturing material in colorectal surgery.

PubMed

Molokova, O A; Kecherukov, A I; Aliev, F Sh; Chernov, I A; Bychkov, V G; Kononov, V P

2007-06-01

Morphological changes in the wall of the large intestine were studied after its manual suturing by a double-row interrupted suture with modern suture threads. Light and scanning electron microscopy showed "fuse properties" and "sawing effect" of polyfilament twisted threads (e.g. vicryl). Monofilament threads were free from these drawbacks and therefore were preferable. Metal elastic threads on the basis of titanium-nickelide alloys caused no inflammatory changes in tissues.

Plant cell wall characterization using scanning probe microscopy techniques

PubMed Central

Yarbrough, John M; Himmel, Michael E; Ding, Shi-You

2009-01-01

Lignocellulosic biomass is today considered a promising renewable resource for bioenergy production. A combined chemical and biological process is currently under consideration for the conversion of polysaccharides from plant cell wall materials, mainly cellulose and hemicelluloses, to simple sugars that can be fermented to biofuels. Native plant cellulose forms nanometer-scale microfibrils that are embedded in a polymeric network of hemicelluloses, pectins, and lignins; this explains, in part, the recalcitrance of biomass to deconstruction. The chemical and structural characteristics of these plant cell wall constituents remain largely unknown today. Scanning probe microscopy techniques, particularly atomic force microscopy and its application in characterizing plant cell wall structure, are reviewed here. We also further discuss future developments based on scanning probe microscopy techniques that combine linear and nonlinear optical techniques to characterize plant cell wall nanometer-scale structures, specifically apertureless near-field scanning optical microscopy and coherent anti-Stokes Raman scattering microscopy. PMID:19703302

Realistic representation of Bacillus subtilis biofilms architecture using combined microscopy (CLSM, ESEM and FESEM).

PubMed

Bridier, A; Meylheuc, T; Briandet, R

2013-05-01

In this contribution, we used a set of microscopic techniques including confocal laser scanning microscopy (CLSM), environmental scanning electron microscopy (ESEM) and field emission scanning electron microscopy (FESEM) to analyze the three-dimensional spatial arrangement of cells and their surrounding matrix in Bacillus subtilis biofilm. The combination of the different techniques enabled a deeper and realistic deciphering of biofilm architecture by providing the opportunity to overcome the limits of each single technique. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metabolomic and high-throughput sequencing analysis-modern approach for the assessment of biodeterioration of materials from historic buildings.

PubMed

Gutarowska, Beata; Celikkol-Aydin, Sukriye; Bonifay, Vincent; Otlewska, Anna; Aydin, Egemen; Oldham, Athenia L; Brauer, Jonathan I; Duncan, Kathleen E; Adamiak, Justyna; Sunner, Jan A; Beech, Iwona B

2015-01-01

Preservation of cultural heritage is of paramount importance worldwide. Microbial colonization of construction materials, such as wood, brick, mortar, and stone in historic buildings can lead to severe deterioration. The aim of the present study was to give modern insight into the phylogenetic diversity and activated metabolic pathways of microbial communities colonized historic objects located in the former Auschwitz II-Birkenau concentration and extermination camp in Oświecim, Poland. For this purpose we combined molecular, microscopic and chemical methods. Selected specimens were examined using Field Emission Scanning Electron Microscopy (FESEM), metabolomic analysis and high-throughput Illumina sequencing. FESEM imaging revealed the presence of complex microbial communities comprising diatoms, fungi and bacteria, mainly cyanobacteria and actinobacteria, on sample surfaces. Microbial diversity of brick specimens appeared higher than that of the wood and was dominated by algae and cyanobacteria, while wood was mainly colonized by fungi. DNA sequences documented the presence of 15 bacterial phyla representing 99 genera including Halomonas, Halorhodospira, Salinisphaera, Salinibacterium, Rubrobacter, Streptomyces, Arthrobacter and nine fungal classes represented by 113 genera including Cladosporium, Acremonium, Alternaria, Engyodontium, Penicillium, Rhizopus, and Aureobasidium. Most of the identified sequences were characteristic of organisms implicated in deterioration of wood and brick. Metabolomic data indicated the activation of numerous metabolic pathways, including those regulating the production of primary and secondary metabolites, for example, metabolites associated with the production of antibiotics, organic acids and deterioration of organic compounds. The study demonstrated that a combination of electron microscopy imaging with metabolomic and genomic techniques allows to link the phylogenetic information and metabolic profiles of microbial communities and to shed new light on biodeterioration processes.

Metabolomic and high-throughput sequencing analysis—modern approach for the assessment of biodeterioration of materials from historic buildings

PubMed Central

Gutarowska, Beata; Celikkol-Aydin, Sukriye; Bonifay, Vincent; Otlewska, Anna; Aydin, Egemen; Oldham, Athenia L.; Brauer, Jonathan I.; Duncan, Kathleen E.; Adamiak, Justyna; Sunner, Jan A.; Beech, Iwona B.

2015-01-01

Preservation of cultural heritage is of paramount importance worldwide. Microbial colonization of construction materials, such as wood, brick, mortar, and stone in historic buildings can lead to severe deterioration. The aim of the present study was to give modern insight into the phylogenetic diversity and activated metabolic pathways of microbial communities colonized historic objects located in the former Auschwitz II–Birkenau concentration and extermination camp in Oświecim, Poland. For this purpose we combined molecular, microscopic and chemical methods. Selected specimens were examined using Field Emission Scanning Electron Microscopy (FESEM), metabolomic analysis and high-throughput Illumina sequencing. FESEM imaging revealed the presence of complex microbial communities comprising diatoms, fungi and bacteria, mainly cyanobacteria and actinobacteria, on sample surfaces. Microbial diversity of brick specimens appeared higher than that of the wood and was dominated by algae and cyanobacteria, while wood was mainly colonized by fungi. DNA sequences documented the presence of 15 bacterial phyla representing 99 genera including Halomonas, Halorhodospira, Salinisphaera, Salinibacterium, Rubrobacter, Streptomyces, Arthrobacter and nine fungal classes represented by 113 genera including Cladosporium, Acremonium, Alternaria, Engyodontium, Penicillium, Rhizopus, and Aureobasidium. Most of the identified sequences were characteristic of organisms implicated in deterioration of wood and brick. Metabolomic data indicated the activation of numerous metabolic pathways, including those regulating the production of primary and secondary metabolites, for example, metabolites associated with the production of antibiotics, organic acids and deterioration of organic compounds. The study demonstrated that a combination of electron microscopy imaging with metabolomic and genomic techniques allows to link the phylogenetic information and metabolic profiles of microbial communities and to shed new light on biodeterioration processes. PMID:26483760

Non-invasive diagnosis of sweat gland dysplasia using optical coherence tomography and reflectance confocal microscopy in a family with anhidrotic ectodermal dysplasia (Christ-Siemens-Touraine syndrome).

PubMed

Reinholz, M; Gauglitz, G G; Giehl, K; Braun-Falco, M; Schwaiger, H; Schauber, J; Ruzicka, T; Berneburg, M; von Braunmühl, T

2016-04-01

Anhidrotic ectodermal dysplasia (AED) is an inherited syndrome, which originates mainly from genetic alteration of the ectodysplasin A (EDA) gene. It regularly affects the adnexa of the skin which results in a characteristic phenotype of the patients including hypo- or anhidrosis leading to severe disturbances in the regulation of body temperature. To prevent the development of the symptoms in early childhood promising therapeutic approaches are currently under clinical investigation. In this context, timely diagnosis of this genetic syndrome is crucial. The purpose of our study was the investigation of modern non-invasive imaging methods such as optical coherence tomography (OCT) and reflectance confocal microscopy (RCM) in the immediate diagnosis of AED. We examined a 3-year-old boy with the suspicion for an AED syndrome and his family members with RCM and OCT to document presence and characteristic features of sweat glands in comparison to non-affected individuals. The patient and the affected brother showed significantly reduced sweat glands in the imaging compared to the controls. The genetic analysis revealed a mutation of the EDA gene for hemizygosity previously associated with AED and the mother was revealed as the conductor of the genetic alteration. With the help of non-invasive imaging, we were able to detect sweat gland dysplasia in the affected family members without performing a biopsy which led us to the diagnosis of an AED. The application of modern dermatological imaging techniques might serve as valuable supplementary tools in the immediate, non-invasive diagnosis of genetic syndromes especially in newborns when early therapeutic approaches are planned. © 2015 European Academy of Dermatology and Venereology.

What can we tell from particle morphology in Mesozoic charcoal assemblages?

NASA Astrophysics Data System (ADS)

Crawford, Alastair; Belcher, Claire

2015-04-01

Sedimentary charcoal particles provide a valuable record of palaeofire activity on both human and geological timescales. Charcoal is both an unambiguous indicator of wildfire, and a means of preservation of plant material in an inert form; thus it records not only the occurrence and extent of wildfire, but also the species affected. While scanning electron microscopy can be usefully employed for precise taxonomic identification of charcoals, the time and cost associated with this limit the extent to which the technique is employed. Morphometric analysis of mesocharcoal particles (c. 125-1000 µm) potentially provides a simple method for obtaining useful information from optical microscopy images. Grass fires have been shown to produce mesocharcoal particles with a higher length-to-width ratio than woodland fuel sources. In Holocene archives, aspect ratio measurements are thus used to infer the broad taxonomic affinity of the burned vegetation. Since Mesozoic charcoals display similarly heterogeneous morphologies, we investigate whether there is a similar potential to infer the broad botanical affinities of Mesozoic charcoal assemblages from simple morphological metrics. We have used image analysis to analyse a range of Jurassic and Cretaceous sedimentary rocks representing different vegetation communities and depositional environments, and also to determine the range of charcoal particle morphologies which can be produced from different modern taxa under laboratory conditions. We find that modern charcoals break down into mesocharcoal particles of very variable aspect ratio, and this appears to be dependent on taxonomic position. Our analysis of fragmented laboratory-produced charcoals indicates that pteridophytes produce much more elongate particles than either conifers or non-grass angiosperms. We suggest that for charcoal assemblages that predate the evolution of grasses, high average aspect ratios may be a useful indicator of the burning of a pteridophyte-dominated flora.

Enhancing multi-spot structured illumination microscopy with fluorescence difference

PubMed Central

Torkelsen, Frida H.

2018-01-01

Structured illumination microscopy is a super-resolution technique used extensively in biological research. However, this technique is limited in the maximum possible resolution increase. Here we report the results of simulations of a novel enhanced multi-spot structured illumination technique. This method combines the super-resolution technique of difference microscopy with structured illumination deconvolution. Initial results give at minimum a 1.4-fold increase in resolution over conventional structured illumination in a low-noise environment. This new technique also has the potential to be expanded to further enhance axial resolution with three-dimensional difference microscopy. The requirement for precise pattern determination in this technique also led to the development of a new pattern estimation algorithm which proved more efficient and reliable than other methods tested. PMID:29657751

Application of microscopy in authentication of traditional Tibetan medicinal plants of five Rhodiola (Crassulaceae) alpine species by comparative anatomy and micromorphology.

PubMed

Li, Tao; Zhang, Hao

2008-06-01

A comparative analysis was undertaken to conduct an anatomical and micromorphological study of five species of Rhodiola-R. kirilowii, R. yunnanensis, R. crenulata, R. fastigata, and R. quadrifida-collected from the western Sichuan province plateau of China. Rhodiola plants are a popularly used ethnodrug from the Qinghai-Tibetan plateau of China. Modern studies have shown that the plants of Rhodiola possess different pharmacological activities, chemical constituents, and efficiencies in clinical application. To distinguish five main species of Rhodiola and ensure their safety and efficacy, microscopic characteristics of roots, rhizomes, and stems, including transverse sections, stem and foliar epidermis, as well as the crude drug powder, were observed. The fixed, sectioned, and stained plant materials, as well as the crude powder, were studied using a light microscope according to the usual microscopic techniques. The results of the microscopic features were systematically and comparatively described and illustrated. The five species have distinct microscopic characteristic differences, thus allowing us to distinguish between the species. Also, semi-quantitative and quantitative micrographic parameter tables were simultaneously presented. Further, a key to the five species and a comparative chart of the key authentication parameters based on these anatomic characteristics analyzed was drawn up and is presented for the Rhodiola species studied. The study indicated that light microscopy and related techniques provide a method that is convenient, feasible, and can be unambiguously applied to the authentication of species of Rhodiola. (c) 2008 Wiley-Liss, Inc.

Applications of microscopy to genetic therapy of cystic fibrosis and other human diseases.

PubMed

Moninger, Thomas O; Nessler, Randy A; Moore, Kenneth C

2006-01-01

Gene therapy has become an extremely important and active field of biomedical research. Microscopy is an integral component of this effort. This chapter presents an overview of imaging techniques used in our facility in support of cystic fibrosis gene therapy research. Instrumentation used in these studies includes light and confocal microscopy, transmission electron microscopy, and scanning electron microscopy. Techniques outlined include negative staining, cryo-electron microscopy, three-dimentional reconstruction, enzyme cytochemistry, immunocytochemistry, and fluorescence imaging.

Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities.

PubMed

Hauser, Meghan; Wojcik, Michal; Kim, Doory; Mahmoudi, Morteza; Li, Wan; Xu, Ke

2017-06-14

Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.

Investigating Microbe-Mineral Interactions: Recent Advances in X-Ray and Electron Microscopy and Redox-Sensitive Methods

NASA Astrophysics Data System (ADS)

Miot, Jennyfer; Benzerara, Karim; Kappler, Andreas

2014-05-01

Microbe-mineral interactions occur in diverse modern environments, from the deep sea and subsurface rocks to soils and surface aquatic environments. They may have played a central role in the geochemical cycling of major (e.g., C, Fe, Ca, Mn, S, P) and trace (e.g., Ni, Mo, As, Cr) elements over Earth's history. Such interactions include electron transfer at the microbe-mineral interface that left traces in the rock record. Geomicrobiology consists in studying interactions at these organic-mineral interfaces in modern samples and looking for traces of past microbe-mineral interactions recorded in ancient rocks. Specific tools are required to probe these interfaces and to understand the mechanisms of interaction between microbes and minerals from the scale of the biofilm to the nanometer scale. In this review, we focus on recent advances in electron microscopy, in particular in cryoelectron microscopy, and on a panel of electrochemical and synchrotron-based methods that have recently provided new understanding and imaging of the microbe-mineral interface, ultimately opening new fields to be explored.

Portable, battery-operated, fluorescence field microscope for the developing world

NASA Astrophysics Data System (ADS)

Miller, Andrew R.; Davis, Gregory; Pierce, Mark; Oden, Z. Maria; Richards-Kortum, Rebecca

2010-02-01

In many areas of the world, current methods for diagnosis of infectious diseases such as malaria and tuberculosis involve microscopic evaluation of a patient specimen. Advances in fluorescence microscopy can improve diagnostic sensitivity and reduce time and expertise necessary to interpret diagnostic results. However, modern research-grade microscopes are neither available nor appropriate for use in many settings in the developing world. To address this need, we designed, fabricated, and tested a portable, battery-powered, bright field and fluorescence inverted field microscope, optimized for infrastructural constraints of the developing world. We characterized an initial prototype constructed with rapidprototyping techniques, which utilized low-cost, over-the-counter components such as a battery-powered LED flashlight as the light source. The microscope exhibited suitable spatial resolution (0.8 μm) in fluorescence mode to resolve M. tuberculosis bacilli. In bright field mode, malaria parasites were resolvable at 1000x magnification. The initial prototype cost 480 USD and we estimate that the microscope can be manufactured for 230 USD. While future studies are planned to evaluate ease-of-use and reliability, our current system serves as a proof of concept that combined fluorescence and bright field microscopy is possible in a low-cost and portable system.

Innovative Teaching Practice: Traditional and Alternative Methods (Challenges and Implications)

ERIC Educational Resources Information Center

Nurutdinova, Aida R.; Perchatkina, Veronika G.; Zinatullina, Liliya M.; Zubkova, Guzel I.; Galeeva, Farida T.

2016-01-01

The relevance of the present issue is caused be the strong need in alternative methods of learning foreign language and the need in language training and retraining for the modern professionals. The aim of the article is to identify the basic techniques and skills in using various modern techniques in the context of modern educational tasks. The…

An Improved Fungal Mounting Technique for Nomarski Microscopy.

ERIC Educational Resources Information Center

Fairclough, Andrew; And Others

1985-01-01

Conventional sellotape techniques for fungal mounting produce interference patterns when using Normarsky microscopy. A technique is described which overcomes this problem and produces a permanent mount with a completely clear background. (Author/JN)

In vivo microscopy of the mouse brain using multiphoton laser scanning techniques

NASA Astrophysics Data System (ADS)

Yoder, Elizabeth J.

2002-06-01

The use of multiphoton microscopy for imaging mouse brain in vivo offers several advantages and poses several challenges. This tutorial begins by briefly comparing multiphoton microscopy with other imaging modalities used to visualize the brain and its activity. Next, an overview of the techniques for introducing fluorescence into whole animals to generate contrast for in vivo microscopy using two-photon excitation is presented. Two different schemes of surgically preparing mice for brain imaging with multiphoton microscopy are reviewed. Then, several issues and problems with in vivo microscopy - including motion artifact, respiratory and cardiac rhythms, maintenance of animal health, anesthesia, and the use of fiducial markers - are discussed. Finally, examples of how these techniques have been applied to visualize the cerebral vasculature and its response to hypercapnic stimulation are provided.

Dictionary of Microscopy

NASA Astrophysics Data System (ADS)

Heath, Julian

2005-10-01

The past decade has seen huge advances in the application of microscopy in all areas of science. This welcome development in microscopy has been paralleled by an expansion of the vocabulary of technical terms used in microscopy: terms have been coined for new instruments and techniques and, as microscopes reach even higher resolution, the use of terms that relate to the optical and physical principles underpinning microscopy is now commonplace. The Dictionary of Microscopy was compiled to meet this challenge and provides concise definitions of over 2,500 terms used in the fields of light microscopy, electron microscopy, scanning probe microscopy, x-ray microscopy and related techniques. Written by Dr Julian P. Heath, Editor of Microscopy and Analysis, the dictionary is intended to provide easy navigation through the microscopy terminology and to be a first point of reference for definitions of new and established terms. The Dictionary of Microscopy is an essential, accessible resource for: students who are new to the field and are learning about microscopes equipment purchasers who want an explanation of the terms used in manufacturers' literature scientists who are considering using a new microscopical technique experienced microscopists as an aide mémoire or quick source of reference librarians, the press and marketing personnel who require definitions for technical reports.

Hierarchy of adhesion forces in patterns of photoreactive surface layers

NASA Astrophysics Data System (ADS)

Hlawacek, Gregor; Shen, Quan; Teichert, Christian; Lex, Alexandra; Trimmel, Gregor; Kern, Wolfgang

2009-01-01

Precise control of surface properties including electrical characteristics, wettability, and friction is a prerequisite for manufacturing modern organic electronic devices. The successful combination of bottom up approaches for aligning and orienting the molecules and top down techniques to structure the substrate on the nano- and micrometer scale allows the cost efficient fabrication and integration of future organic light emitting diodes and organic thin film transistors. One possibility for the top down patterning of a surface is to utilize different surface free energies or wetting properties of a functional group. Here, we used friction force microscopy (FFM) to reveal chemical patterns inscribed by a photolithographic process into a photosensitive surface layer. FFM allowed the simultaneous visualization of at least three different chemical surface terminations. The underlying mechanism is related to changes in the chemical interaction between probe and film surface.

[Development of an incubation system for an inverted microscopy for long-term observation of cell cultures using chamber slides].

PubMed

Feicht, W; Buchner, A; Riesenberg, R

2001-05-01

Trifunctional bispecific antibodies open up new immunological possibilities in tumour treatment. Prior to clinical application, comprehensive investigations using animal models and in vitro examinations need to be done. To investigate long-term interactions between various immunologically active blood cells and individual tumour cells in the presence of antibodies, we developed an incubation system for experimental cell cultures on an inverted microscope. The system consists of a perspex box with a central moisture chamber with integrated water reservoir, external air circulation heating, and a CO2 supply. The sterile cell cultures are located in the wells of a slide positioned within a depression in the water reservoir. The newly developed incubation system enables continuous observation over the long term of experiments under optimal cell cultures conditions in combination with modern video techniques.

Imaging mammalian cells with soft x rays: The importance of specimen preparation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, J.T.; Meyer-Ilse, W.

1997-04-01

Studies of mammalian cell structure and spatial organization are a very prominent part of modern cell biology. The interest in them as well as their size make them very accommodating subject specimens for imaging with soft x-rays using the XM-1 transmission microscope built and operated by The Center for X-ray Optics on Beam Line 6.1 at the Advanced Light Source. The purpose of these experiments was to determine if the fixative protocols normally used in electron or visible light microscopy were adequate to allow imaging cells, either fibroblasts or neurons, with minimal visible radiation damage due to imaging with softmore » x-rays at 2.4 nm. Two cell types were selected. Fibroblasts are easily cultured but fragile cells which are commonly used as models for the detailed study of cell physiology. Neurons are complex and sensitive cells which are difficult to prepare and to culture for study in isolation from their connections with surrounding cells. These cell types pose problems in their preparation for any microscopy. To improve the contrast and to prevent postmortem alteration of the chemistry and hence the structure of cells extracted from culture or from living organisms, fixation and staining techniques are employed in electron and visible light microscopy. It has been accepted by biologists for years that these treatments create artifacts and false structure. The authors have begun to develop protocols for specimens of each of these two cell types for soft x-ray microscopy which will preserve them in as near normal state as possible using minimal fixation, and make it possible to image them in either a hydrated or dried state free of secondary addition of stains or other labels.« less

Techniques for 3D tracking of single molecules with nanometer accuracy in living cells

NASA Astrophysics Data System (ADS)

Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S.

2013-06-01

We describe a microscopy technique that, combining wide-field single molecule microscopy, bifocal imaging and Highly Inclined and Laminated Optical sheet (HILO) microscopy, allows a 3D tracking with nanometer accuracy of single fluorescent molecules in vitro and in living cells.

Flexible use and technique extension of logistics management

NASA Astrophysics Data System (ADS)

Xiong, Furong

2011-10-01

As we all know, the origin of modern logistics was in the United States, developed in Japan, became mature in Europe, and expanded in China. This is a historical development of the modern logistics recognized track. Due to China's economic and technological development, and with the construction of Shanghai International Shipping Center and Shanghai Yangshan International Deepwater development, China's modern logistics industry will attain a leap-forward development of a strong pace, and will also catch up with developed countries in the Western modern logistics level. In this paper, the author explores the flexibility of China's modern logistics management techniques to extend the use, and has certain practical and guidance significances.

Surface Characterization.

ERIC Educational Resources Information Center

Fulghum, J. E.; And Others

1989-01-01

This review is divided into the following analytical methods: ion spectroscopy, electron spectroscopy, scanning tunneling microscopy, atomic force microscopy, optical spectroscopy, desorption techniques, and X-ray techniques. (MVL)

Applying modern psychometric techniques to melodic discrimination testing: Item response theory, computerised adaptive testing, and automatic item generation.

PubMed

Harrison, Peter M C; Collins, Tom; Müllensiefen, Daniel

2017-06-15

Modern psychometric theory provides many useful tools for ability testing, such as item response theory, computerised adaptive testing, and automatic item generation. However, these techniques have yet to be integrated into mainstream psychological practice. This is unfortunate, because modern psychometric techniques can bring many benefits, including sophisticated reliability measures, improved construct validity, avoidance of exposure effects, and improved efficiency. In the present research we therefore use these techniques to develop a new test of a well-studied psychological capacity: melodic discrimination, the ability to detect differences between melodies. We calibrate and validate this test in a series of studies. Studies 1 and 2 respectively calibrate and validate an initial test version, while Studies 3 and 4 calibrate and validate an updated test version incorporating additional easy items. The results support the new test's viability, with evidence for strong reliability and construct validity. We discuss how these modern psychometric techniques may also be profitably applied to other areas of music psychology and psychological science in general.

Fluorescent probes for lipid rafts: from model membranes to living cells.

PubMed

Klymchenko, Andrey S; Kreder, Rémy

2014-01-16

Membrane microdomains (rafts) remain one of the controversial issues in biophysics. Fluorescent molecular probes, which make these lipid nanostructures visible through optical techniques, are one of the tools currently used to study lipid rafts. The most common are lipophilic fluorescent probes that partition specifically into liquid ordered or liquid disordered phase. Their partition depends on the lipid composition of a given phase, which complicates their use in cellular membranes. A second class of probes is based on environment-sensitive dyes, which partition into both phases, but stain them by different fluorescence color, intensity, or lifetime. These probes can directly address the properties of each separate phase, but their cellular applications are still limited. The present review focuses on summarizing the current state in the field of developing and applying fluorescent molecular probes to study lipid rafts. We highlight an urgent need to develop new probes, specifically adapted for cell plasma membranes and compatible with modern fluorescence microscopy techniques to push the understanding of membrane microdomains forward. Copyright © 2014 Elsevier Ltd. All rights reserved.

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2016-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:27248784

High-resolution non-destructive three-dimensional imaging of integrated circuits.

PubMed

Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H R; Dinapoli, Roberto; Müller, Elisabeth; Bunk, Oliver; Raabe, Jörg; Aeppli, Gabriel

2017-03-15

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography-a high-resolution coherent diffractive imaging technique-can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

A molecular method to assess bioburden embedded within silicon-based resins used on modern spacecraft materials

NASA Astrophysics Data System (ADS)

Stam, Christina N.; Bruckner, James; Spry, J. Andy; Venkateswaran, Kasthuri; La Duc, Myron T.

2012-07-01

Current assessments of bioburden embedded in spacecraft materials are based on work performed in the Viking era (1970s), and the ability to culture organisms extracted from such materials. To circumvent the limitations of such approaches, DNA-based techniques were evaluated alongside established culturing techniques to determine the recovery and survival of bacterial spores encapsulated in spacecraft-qualified polymer materials. Varying concentrations of Bacillus pumilus SAFR-032 spores were completely embedded in silicone epoxy. An organic dimethylacetamide-based solvent was used to digest the epoxy and spore recovery was evaluated via gyrB-targeted qPCR, direct agar plating, most probably number analysis, and microscopy. Although full-strength solvent was shown to inhibit the germination and/or outgrowth of spores, dilution in excess of 100-fold allowed recovery with no significant decrease in cultivability. Similarly, qPCR (quantitative PCR) detection sensitivities as low as ~103 CFU ml-1 were achieved upon removal of inhibitory substances associated with the epoxy and/or solvent. These detection and enumeration methods show promise for use in assessing the embedded bioburden of spacecraft hardware.

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2010-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy and neutron diffraction are well established and have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches and high-speed computing and visualization, now provide specialists and non-specialists alike with a steady flow of molecular images of unprecedented detail. The present chapter combines a general overview of diffraction methods with a step-by-step description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:20517991

Diffraction Techniques in Structural Biology.

PubMed

Egli, Martin

2016-06-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Pump-probe Kelvin-probe force microscopy: Principle of operation and resolution limits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murawski, J.; Graupner, T.; Milde, P., E-mail: peter.milde@tu-dresden.de

Knowledge on surface potential dynamics is crucial for understanding the performance of modern-type nanoscale devices. We describe an electrical pump-probe approach in Kelvin-probe force microscopy that enables a quantitative measurement of dynamic surface potentials at nanosecond-time and nanometer-length scales. Also, we investigate the performance of pump-probe Kelvin-probe force microscopy with respect to the relevant experimental parameters. We exemplify a measurement on an organic field effect transistor that verifies the undisturbed functionality of our pump-probe approach in terms of simultaneous and quantitative mapping of topographic and electronic information at a high lateral and temporal resolution.

The future of electron microscopy

DOE PAGES

Zhu, Yimei; Durr, Hermann

2015-04-01

Seeing is believing. So goes the old adage and seen evidence is undoubtedly satisfying because it can be interpreted easily, though not always correctly. For centuries, humans have developed such instruments as telescopes that observe the heavens and microscopes that reveal bacteria and viruses. The 2014 Nobel Prize in Chemistry was awarded to Eric Betzig, Stefan Hell, and William Moerner for their foundational work on superresolution fluorescence microscopy in which they overcame the Abbe diffraction limit for the resolving power of conventional light microscopes. (See Physics Today, December 2014, page 18.) That breakthrough enabled discoveries in biological research and testifiesmore » to the importance of modern microscopy.« less

Integration of terrestrial laser scanner, ultrasonic and petrographical data in the diagnostic process on stone building materials

NASA Astrophysics Data System (ADS)

Casula, Giuseppe; Fais, Silvana; Giovanna Bianchi, Maria; Cuccuru, Francesco; Ligas, Paola

2015-04-01

The Terrestrial Laser Scanner (TLS) is a modern contactless non-destructive technique (NDT) useful to 3D-model complex-shaped objects with a few hours' field survey. A TLS survey produces very dense point clouds made up of coordinates of point and radiometric information given by the reflectivity parameter i.e. the ratio between the amount of energy emitted by the sensor and the energy reflected by the target object. Modern TLSs used in architecture are phase instruments where the phase difference obtained by comparing the emitted laser pulse with the reflected one is proportional to the sensor-target distance expressed as an integer multiple of the half laser wavelength. TLS data are processed by registering point clouds i.e. by referring them to the same reference frame and by aggregation after a fine registration procedure. The resulting aggregate point cloud can be compared with graphic primitives as single or multiple planes, cylinders or spheres, and the resulting residuals give a morphological map that affords information about the state of conservation of the building materials used in historical or modern buildings, in particular when compared with other NDT techniques. In spite of its great productivity, the TLS technique is limited in that it is unable to penetrate the investigated materials. For this reason both the 3D residuals map and the reflectivity map need to be correlated with the results of other NDT techniques such as the ultrasonic method, and a complex study of the composition of building materials is also necessary. The application of a methodology useful to evaluate the quality of stone building materials and locate altered or damaged zones is presented in this study based on the integrated application of three independent techniques, two non destructive such as the TLS and the ultrasonic techniques in the 24-54 kHz range, and a third to analyze the petrographical characteristics of the stone materials, mainly the texture, with optical and scanning electronic microscopy (SEM). A very interesting case study is presented on a carbonate stone door of great architectural and historical interest, well suited to a high definition survey . This architectural element is inside the "Palazzo di Città" museum in the historical center of the Town of Cagliari, Sardinia (Italy). The integrated application of TLS and in situ and laboratory ultrasonic techniques, enhanced by the knowledge of the petrographic characteristics of the rocks, improves the diagnostic process and affords reliable information on the state of conservation of the stones used to build it. The integrated use of the above non destructive techniques also provides suitable data for a possible restoration and future preservation. Acknowledgments: This work was financially supported by Sardinian Local Administration (RAS - LR 7,August 2007, n.7, Promotion of Scientific Research and Innovation in Sardinia - Italy, Responsible Scientist: S.Fais).

Precambrian animal diversity: putative phosphatized embryos from the Doushantuo Formation of China

NASA Technical Reports Server (NTRS)

Chen, J. Y.; Oliveri, P.; Li, C. W.; Zhou, G. Q.; Gao, F.; Hagadorn, J. W.; Peterson, K. J.; Davidson, E. H.

2000-01-01

Putative fossil embryos and larvae from the Precambrian phosphorite rocks of the Doushantuo Formation in Southwest China have been examined in thin section by bright field and polarized light microscopy. Although we cannot completely exclude a nonbiological or nonmetazoan origin, we identified what appear to be modern cnidarian developmental stages, including both anthozoan planula larvae and hydrozoan embryos. Most importantly, the sections contain a variety of small (

Serial block face scanning electron microscopy--the future of cell ultrastructure imaging.

PubMed

Hughes, Louise; Hawes, Chris; Monteith, Sandy; Vaughan, Sue

2014-03-01

One of the major drawbacks in transmission electron microscopy has been the production of three-dimensional views of cells and tissues. Currently, there is no one suitable 3D microscopy technique that answers all questions and serial block face scanning electron microscopy (SEM) fills the gap between 3D imaging using high-end fluorescence microscopy and the high resolution offered by electron tomography. In this review, we discuss the potential of the serial block face SEM technique for studying the three-dimensional organisation of animal, plant and microbial cells.

Superresolution Microscopy of the Nuclear Envelope and Associated Proteins.

PubMed

Xie, Wei; Horn, Henning F; Wright, Graham D

2016-01-01

Superresolution microscopy is undoubtedly one of the most exciting technologies since the invention of the optical microscope. Capable of nanometer-scale resolution to surpass the diffraction limit and coupled with the versatile labeling techniques available, it is revolutionizing the study of cell biology. Our understanding of the nucleus, the genetic and architectural center of the cell, has gained great advancements through the application of various superresolution microscopy techniques. This chapter describes detailed procedures of multichannel superresolution imaging of the mammalian nucleus, using structured illumination microscopy and single-molecule localization microscopy.

State of the art in treatment of facial paralysis with temporalis tendon transfer.

PubMed

Sidle, Douglas M; Simon, Patrick

2013-08-01

Temporalis tendon transfer is a technique for dynamic facial reanimation. Since its inception, nearly 80 years ago, it has undergone a wealth of innovation to produce the modern operation. The purpose of this review is to update the literature as to the current techniques and perioperative management of patients undergoing temporalis tendon transfer. The modern technique focuses on the minimally invasive approaches and aesthetic refinements to enhance the final product of the operation. The newest techniques as well as preoperative assessment and postoperative rehabilitation are discussed. When temporalis tendon transfer is indicated for facial reanimation, the modern operation offers a refined technique that produces an aesthetically acceptable outcome. Preoperative smile assessment and postoperative smile rehabilitation are necessary and are important adjuncts to a successful operation.

Analysis of nanomechanical properties of Borrelia burgdorferi spirochetes under the influence of lytic factors in an in vitro model using atomic force microscopy.

PubMed

Tokarska-Rodak, Małgorzata; Kozioł-Montewka, Maria; Skrzypiec, Krzysztof; Chmielewski, Tomasz; Mendyk, Ewaryst; Tylewska-Wierzbanowska, Stanisława

2015-11-12

Atomic force microscopy (AFM) is an experimental technique which recently has been used in biology, microbiology, and medicine to investigate the topography of surfaces and in the evaluation of mechanical properties of cells. The aim of this study was to evaluate the influence of the complement system and specific anti-Borrelia antibodies in in vitro conditions on the modification of nanomechanical features of B. burgdorferi B31 cells. In order to assess the influence of the complement system and anti-Borrelia antibodies on B. burgdorferi s.s. B31 spirochetes, the bacteria were incubated together with plasma of identified status. The samples were applied on the surface of mica disks. Young's modulus and adhesive forces were analyzed with a NanoScope V, MultiMode 8 AFM microscope (Bruker) by the PeakForce QNM technique in air using NanoScope Analysis 1.40 software (Bruker). The average value of flexibility of spirochetes' surface expressed by Young's modulus was 10185.32 MPa, whereas the adhesion force was 3.68 nN. AFM is a modern tool with a broad spectrum of observational and measurement abilities. Young's modulus and the adhesion force can be treated as parameters in the evaluation of intensity and changes which take place in pathogenic microorganisms under the influence of various lytic factors. The visualization of the changes in association with nanomechanical features provides a realistic portrayal of the lytic abilities of the elements of the innate and adaptive human immune system.

One- and two-dimensional dopant/carrier profiling for ULSI

NASA Astrophysics Data System (ADS)

Vandervorst, W.; Clarysse, T.; De Wolf, P.; Trenkler, T.; Hantschel, T.; Stephenson, R.; Janssens, T.

1998-11-01

Dopant/carrier profiles constitute the basis of the operation of a semiconductor device and thus play a decisive role in the performance of a transistor and are subjected to the same scaling laws as the other constituents of a modern semiconductor device and continuously evolve towards shallower and more complex configurations. This evolution has increased the demands on the profiling techniques in particular in terms of resolution and quantification such that a constant reevaluation and improvement of the tools is required. As no single technique provides all the necessary information (dopant distribution, electrical activation,..) with the requested spatial and depth resolution, the present paper attempts to provide an assessment of those tools which can be considered as the main metrology technologies for ULSI-applications. For 1D-dopant profiling secondary ion mass spectrometry (SIMS) has progressed towards a generally accepted tool meeting the requirements. For 1D-carrier profiling spreading resistance profiling and microwave surface impedance profiling are envisaged as the best choices but extra developments are required to promote them to routinely applicable methods. As no main metrology tool exist for 2D-dopant profiling, main emphasis is on 2D-carrier profiling tools based on scanning probe microscopy. Scanning spreading resistance (SSRM) and scanning capacitance microscopy (SCM) are the preferred methods although neither of them already meets all the requirements. Complementary information can be extracted from Nanopotentiometry which samples the device operation in more detail. Concurrent use of carrier profiling tools, Nanopotentiometry, analysis of device characteristics and simulations is required to provide a complete characterization of deep submicron devices.

Applying Superresolution Localization-Based Microscopy to Neurons

PubMed Central

ZHONG, HAINING

2016-01-01

Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue. PMID:25648102

Bacterial cell identification in differential interference contrast microscopy images.

PubMed

Obara, Boguslaw; Roberts, Mark A J; Armitage, Judith P; Grau, Vicente

2013-04-23

Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several widely used non-fluorescence, interference-based microscopy imaging modalities. For example in differential interference contrast microscopy which plays an important role in modern bacterial cell biology. Therefore, new revolutions in the field require the development of tools, technologies and work-flows to extract and exploit information from interference-based imaging data so as to achieve new fundamental biological insights and understanding. We have developed and evaluated a high-throughput image analysis and processing approach to detect and characterize bacterial cells and chemotaxis proteins. Its performance was evaluated using differential interference contrast and fluorescence microscopy images of Rhodobacter sphaeroides. Results demonstrate that the proposed approach provides a fast and robust method for detection and analysis of spatial relationship between bacterial cells and their chemotaxis proteins.

Chapter 14: Electron Microscopy on Thin Films for Solar Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romero, Manuel; Abou-Ras, Daniel; Nichterwitz, Melanie

2016-07-22

This chapter overviews the various techniques applied in scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and highlights their possibilities and also limitations. It gives the various imaging and analysis techniques applied on a scanning electron microscope. The chapter shows that imaging is divided into that making use of secondary electrons (SEs) and of backscattered electrons (BSEs), resulting in different contrasts in the images and thus providing information on compositions, microstructures, and surface potentials. Whenever aiming for imaging and analyses at scales of down to the angstroms range, TEM and its related techniques are appropriate tools. In many cases,more » also SEM techniques provide the access to various material properties of the individual layers, not requiring specimen preparation as time consuming as TEM techniques. Finally, the chapter dedicates to cross-sectional specimen preparation for electron microscopy. The preparation decides indeed on the quality of imaging and analyses.« less

Microscopy basics and the study of actin-actin-binding protein interactions.

PubMed

Thomasson, Maggie S; Macnaughtan, Megan A

2013-12-15

Actin is a multifunctional eukaryotic protein with a globular monomer form that polymerizes into a thin, linear microfilament in cells. Through interactions with various actin-binding proteins (ABPs), actin plays an active role in many cellular processes, such as cell motility and structure. Microscopy techniques are powerful tools for determining the role and mechanism of actin-ABP interactions in these processes. In this article, we describe the basic concepts of fluorescent speckle microscopy, total internal reflection fluorescence microscopy, atomic force microscopy, and cryoelectron microscopy and review recent studies that utilize these techniques to visualize the binding of actin with ABPs. Copyright © 2013 Elsevier Inc. All rights reserved.

Porosity characterization for heterogeneous shales using integrated multiscale microscopy

NASA Astrophysics Data System (ADS)

Rassouli, F.; Andrew, M.; Zoback, M. D.

2016-12-01

Pore size distribution analysis plays a critical role in gas storage capacity and fluid transport characterization of shales. Study of the diverse distribution of pore size and structure in such low permeably rocks is withheld by the lack of tools to visualize the microstructural properties of shale rocks. In this paper we try to use multiple techniques to investigate the full pore size range in different sample scales. Modern imaging techniques are combined with routine analytical investigations (x-ray diffraction, thin section analysis and mercury porosimetry) to describe pore size distribution of shale samples from Haynesville formation in East Texas to generate a more holistic understanding of the porosity structure in shales, ranging from standard core plug down to nm scales. Standard 1" diameter core plug samples were first imaged using a Versa 3D x-ray microscope at lower resolutions. Then we pick several regions of interest (ROIs) with various micro-features (such as micro-cracks and high organic matters) in the rock samples to run higher resolution CT scans using a non-destructive interior tomography scans. After this step, we cut the samples and drill 5 mm diameter cores out of the selected ROIs. Then we rescan the samples to measure porosity distribution of the 5 mm cores. We repeat this step for samples with diameter of 1 mm being cut out of the 5 mm cores using a laser cutting machine. After comparing the pore structure and distribution of the samples measured form micro-CT analysis, we move to nano-scale imaging to capture the ultra-fine pores within the shale samples. At this stage, the diameter of the 1 mm samples will be milled down to 70 microns using the laser beam. We scan these samples in a nano-CT Ultra x-ray microscope and calculate the porosity of the samples by image segmentation methods. Finally, we use images collected from focused ion beam scanning electron microscopy (FIB-SEM) to be able to compare the results of porosity measurements from all different imaging techniques. These multi-scale characterization techniques are then compared with traditional analytical techniques such as Mercury Porosimetry.

Natural cement in the nineteenth century city of Madrid. Identification of their application, conservation status and their compatibility with moderns cements.

NASA Astrophysics Data System (ADS)

Corrochano, Cristina Mayo; Lasheras Merino, Felix; Sanz-Arauz, David

2016-04-01

Roman cement was patented in 1796 and it arrived to Spain in 1835. Although the natural cement used in Madrid came mainly from Guipúzcoa's factories, there were a few small factories producing natural cement in the area. In the south east of Madrid, in "Morata de Tajuña", are the marl quarries of the Madrid Community. Natural cement was extensively used to decorate buildings in Madrid during the 19th century and the beginning of the 20th. It was highly demanded in various sectors of civil engineering: sewerage, water supply, canals, ports and tunnels. In the building sector, at first the use of cements was limited to building foundations and masonry mortars, but never as render mortar because it was considered an unsightly and vulgar material. For renders still traditional lime mortar was used. And is not till the end of the 19th century when it was used in facade decorations for the first time. We have analysed 25 buildings in Madrid built in that period of time. It was used microscopy techniques for the identification of these cements, checking how many of them used natural cement, how they used it, what is its conservation status and their compatibility with modern cements.

Focus on membrane differentiation and membrane domains in the prokaryotic cell.

PubMed

Boekema, Egbert J; Scheffers, Dirk-Jan; van Bezouwen, Laura S; Bolhuis, Henk; Folea, I Mihaela

2013-01-01

A summary is presented of membrane differentiation in the prokaryotic cell, with an emphasis on the organization of proteins in the plasma/cell membrane. Many species belonging to the Eubacteria and Archaea have special membrane domains and/or membrane proliferation, which are vital for different cellular processes. Typical membrane domains are found in bacteria where a specific membrane protein is abundantly expressed. Lipid rafts form another example. Despite the rareness of conventional organelles as found in eukaryotes, some bacteria are known to have an intricate internal cell membrane organization. Membrane proliferation can be divided into curvature and invaginations which can lead to internal compartmentalization. This study discusses some of the clearest examples of bacteria with such domains and internal membranes. The need for membrane specialization is highest among the heterogeneous group of bacteria which harvest light energy, such as photosynthetic bacteria and halophilic archaea. Most of the highly specialized membranes and domains, such as the purple membrane, chromatophore and chlorosome, are found in these autotrophic organisms. Otherwise the need for membrane differentiation is lower and variable, except for those structures involved in cell division. Microscopy techniques have given essential insight into bacterial membrane morphology. As microscopy will further contribute to the unraveling of membrane organization in the years to come, past and present technology in electron microscopy and light microscopy is discussed. Electron microscopy was the first to unravel bacterial morphology because it can directly visualize membranes with inserted proteins, which no other technique can do. Electron microscopy techniques developed in the 1950s and perfected in the following decades involve the thin sectioning and freeze fractioning of cells. Several studies from the golden age of these techniques show amazing examples of cell membrane morphology. More recently, light microscopy in combination with the use of fluorescent dyes has become an attractive technique for protein localization with the natural membrane. However, the resolution problem in light microscopy remains and overinterpretation of observed phenomena is a pitfall. Thus, light microscopy as a stand-alone technique is not sufficient to prove, for instance, the long-range helical distribution of proteins in membrane such as MinD spirals in Bacillus subtilis. Electron tomography is an emerging electron microscopy technique that can provide three-dimensional reconstructions of small, nonchemically fixed bacteria. It will become a useful tool for studying prokaryotic membranes in more detail and is expected to collect information complementary to those of advanced light microscopy. Together, microscopy techniques can meet the challenge of the coming years: to specify membrane structures in more detail and to bring them to the level of specific protein-protein interactions. Copyright © 2013 S. Karger AG, Basel.

Green synthesis of silver nanoparticles using leaf extract of medicinally potent plant Saraca indica: a novel study

NASA Astrophysics Data System (ADS)

Perugu, Shyam; Nagati, Veerababu; Bhanoori, Manjula

2016-06-01

Eco-friendly silver nanoparticles (AgNPs) have various applications in modern biotechnology for better outcomes and benefits to the society. In the present study, we report an eco-friendly synthesis of silver nanoparticles using Saraca indica leaf extract. Characterization of S. indica silver nanoparticles (SAgNPs) was carried out by Fourier transform infrared spectroscopy, scanning electron microscopy, energy dispersive spectrometry, Zeta potential, and transmission electron microscopy. SAgNPs showed antimicrobial activity against Gram-negative and Gram-positive bacteria.

Microchemical Analysis Of Space Operation Debris

NASA Technical Reports Server (NTRS)

Cummings, Virginia J.; Kim, Hae Soo

1995-01-01

Report discusses techniques used in analyzing debris relative to space shuttle operations. Debris collected from space shuttle, expendable launch vehicles, payloads carried by space shuttle, and payloads carried by expendable launch vehicles. Optical microscopy, scanning electron microscopy with energy-dispersive spectrometry, analytical electron microscopy with wavelength-dispersive spectrometry, and X-ray diffraction chosen as techniques used in examining samples of debris.

Thermometry of Silicon Nanoparticles

NASA Astrophysics Data System (ADS)

Mecklenburg, Matthew; Zutter, Brian; Regan, B. C.

2018-01-01

Current thermometry techniques lack the spatial resolution required to see the temperature gradients in typical, highly scaled modern transistors. As a step toward addressing this problem, we measure the temperature dependence of the volume plasmon energy in silicon nanoparticles from room temperature to 1250 °C , using a chip-style heating sample holder in a scanning transmission electron microscope (STEM) equipped with electron energy loss spectroscopy (EELS). The plasmon energy changes as expected for an electron gas subject to the thermal expansion of silicon. Reversing this reasoning, we find that measurements of the plasmon energy provide an independent measure of the nanoparticle temperature consistent with that of the heater chip's macroscopic, dual-function heater-and-thermometer to within the 5% accuracy of the thermometer's calibration. Thus, silicon has the potential to provide its own high-spatial-resolution thermometric readout signal via measurements of its volume plasmon energy. Furthermore, nanoparticles can, in general, serve as convenient nanothermometers for in situ electron-microscopy experiments.

Bird embryos uncover homology and evolution of the dinosaur ankle.

PubMed

Ossa-Fuentes, Luis; Mpodozis, Jorge; Vargas, Alexander O

2015-11-13

The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the 'ascending process' (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin-disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.

Mastering fundamentals of supramolecular design with carboxylic acids. Common lessons from X-ray crystallography and scanning tunneling microscopy.

PubMed

Ivasenko, Oleksandr; Perepichka, Dmitrii F

2011-01-01

Hydrogen bonding is one of the most important non-covalent interactions in both biological (DNA, peptides, saccharides etc.) and artificial systems (various soft materials, host-guest architectures, molecular networks, etc.). Carboxylic acids are some of the most simple yet powerful hydrogen-bonding building blocks, that possess a particularly rich supramolecular chemistry. This tutorial review focuses on the structural diversity of supramolecular architectures accessible via hydrogen bonding of carboxylic acids, as observed both in single crystals using X-ray analysis and in monolayers on surfaces using scanning probe techniques. It provides a concise overview of the key concepts and principles of modern supramolecular design and is given in the form of case studies of finely selected literature examples, covering formation of macrocycles, chains, ladders, rotaxanes, catenanes, various 2D and 3D nets, host-guest systems and some applications thereof.

Early bases of modern embryology in Spain: microscopical anatomy and the introduction of cell theory and histology in their scientific and social European context.

PubMed

Marco-Cuellar, Roberto; Aréchaga, Juan

2009-01-01

We present a survey of the introduction and evolution of microscopy techniques in Spain, and the concepts and lines of research developed around this instrument, particularly in the field of Biomedical research. We cover in our article the long period from the XVII Century to the arrival of the great figure of Santiago Ramon y Cajal (1853-1934). We particularly want to mention many of the previously neglected pioneers who certainly paved the route for his discoveries and, we believe that without them, he would never have arrived to his important position in the annals of Biology and Medicine. The historical, scientific and social framework of that period also helped the approach to important biological concepts such as the cell and tissue, which are previous and essential ideas for a correct understanding of Development.

Polarization-controlled directional scattering for nanoscopic position sensing

PubMed Central

Neugebauer, Martin; Woźniak, Paweł; Bag, Ankan; Leuchs, Gerd; Banzer, Peter

2016-01-01

Controlling the propagation and coupling of light to sub-wavelength antennas is a crucial prerequisite for many nanoscale optical devices. Recently, the main focus of attention has been directed towards high-refractive-index materials such as silicon as an integral part of the antenna design. This development is motivated by the rich spectral properties of individual high-refractive-index nanoparticles. Here we take advantage of the interference of their magnetic and electric resonances to achieve strong lateral directionality. For controlled excitation of a spherical silicon nanoantenna, we use tightly focused radially polarized light. The resultant directional emission depends on the antenna's position relative to the focus. This approach finds application as a novel position sensing technique, which might be implemented in modern nanometrology and super-resolution microscopy set-ups. We demonstrate in a proof-of-concept experiment that a lateral resolution in the Ångström regime can be achieved. PMID:27095171

FIB–SEM tomography of 4th generation PWA 1497 superalloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ziętara, Maciej, E-mail: zietara@agh.edu.pl; Kruk, Adam, E-mail: kruczek@agh.edu.pl; Gruszczyński, Adam, E-mail: gruszcz@agh.edu.pl

2014-01-15

The effect of creep deformation on the microstructure of the PWA 1497 single crystal Ni-base superalloy developed for turbine blade applications was investigated. The aim of the present study was to characterize quantitatively a superalloy microstructure and subsequent development of rafted γ′ precipitates in the PWA 1497 during creep deformation at 982 °C and 248 MPa up to rupture. The PWA1497 microstructure was characterized by scanning electron microscopy and FIB–SEM electron tomography. The 3D reconstruction of the PWA1497 microstructure is presented and discussed. - Highlights: • The microstructure of PWA1497 superalloy was examined using FIB–SEM tomography. • In case ofmore » modern single crystal superalloys, measurements of A{sub A} are adequate for V{sub V}. • During creep the γ channel width increases from 65 to 193 nm for ruptured specimen. • Tomography is a useful technique for quantitative studies of material microstructure.« less

Bird embryos uncover homology and evolution of the dinosaur ankle

PubMed Central

Ossa-Fuentes, Luis; Mpodozis, Jorge; Vargas, Alexander O

2015-01-01

The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the ‘ascending process' (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin–disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution. PMID:26563435

In situ wavefront correction and its application to micromanipulation

NASA Astrophysics Data System (ADS)

Čižmár, Tomáš; Mazilu, Michael; Dholakia, Kishan

2010-06-01

In any optical system, distortions to a propagating wavefront reduce the spatial coherence of a light field, making it increasingly difficult to obtain the theoretical diffraction-limited spot size. Such aberrations are severely detrimental to optimal performance in imaging, nanosurgery, nanofabrication and micromanipulation, as well as other techniques within modern microscopy. We present a generic method based on complex modulation for true in situ wavefront correction that allows compensation of all aberrations along the entire optical train. The power of the method is demonstrated for the field of micromanipulation, which is very sensitive to wavefront distortions. We present direct trapping with optimally focused laser light carrying power of a fraction of a milliwatt as well as the first trapping through highly turbid and diffusive media. This opens up new perspectives for optical micromanipulation in colloidal and biological physics and may be useful for various forms of advanced imaging.

Fluorescence of sanguinarine: fundamental characteristics and analysis of interconversion between various forms.

PubMed

Janovská, Marika; Kubala, Martin; Simánek, Vilím; Ulrichová, Jitka

2009-09-01

The quaternary isoquinoline alkaloid, sanguinarine (SG) plays an important role in both traditional and modern medicine, exhibiting a wide range of biological activities. Under physiological conditions, there is an equilibrium between the quaternary cation (SG+) and a pseudobase (SGOH) forms of SG. In the gastrointestinal tract, SG is converted to dihydrosanguinarine (DHSG). All forms exhibit bright fluorescence. However, their spectra overlap, which limited the use of powerful techniques based on fluorescence spectroscopy/microscopy. Our experiments using a combination of steady-state and time-resolved techniques enabled the separation of individual components. The results revealed that (a) the equilibrium constant between SG+ and SGOH is pKa = 8.06, while fluorescence of DHSG exhibited no changes in the pH range 5-12, (b) the SGOH has excitation/emission spectra with maxima at 327/418 nm and excited-state lifetime 3.2 ns, the spectra of the SG+ have maxima at 475/590 nm and excited-state lifetime 2.4 ns. The DHSG spectra have maxima at 327/446 nm and 2-exponential decay with components 4.2 and 2.0 ns, (c) NADH is able to convert SG to DHSG, while there is no apparent interaction between NADH and DHSG. These techniques are applicable for monitoring the SG to DHSG conversion in hepatocytes.

Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures.

PubMed

Lidke, Diane S; Lidke, Keith A

2012-06-01

A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.

Modern modelling techniques are data hungry: a simulation study for predicting dichotomous endpoints.

PubMed

van der Ploeg, Tjeerd; Austin, Peter C; Steyerberg, Ewout W

2014-12-22

Modern modelling techniques may potentially provide more accurate predictions of binary outcomes than classical techniques. We aimed to study the predictive performance of different modelling techniques in relation to the effective sample size ("data hungriness"). We performed simulation studies based on three clinical cohorts: 1282 patients with head and neck cancer (with 46.9% 5 year survival), 1731 patients with traumatic brain injury (22.3% 6 month mortality) and 3181 patients with minor head injury (7.6% with CT scan abnormalities). We compared three relatively modern modelling techniques: support vector machines (SVM), neural nets (NN), and random forests (RF) and two classical techniques: logistic regression (LR) and classification and regression trees (CART). We created three large artificial databases with 20 fold, 10 fold and 6 fold replication of subjects, where we generated dichotomous outcomes according to different underlying models. We applied each modelling technique to increasingly larger development parts (100 repetitions). The area under the ROC-curve (AUC) indicated the performance of each model in the development part and in an independent validation part. Data hungriness was defined by plateauing of AUC and small optimism (difference between the mean apparent AUC and the mean validated AUC <0.01). We found that a stable AUC was reached by LR at approximately 20 to 50 events per variable, followed by CART, SVM, NN and RF models. Optimism decreased with increasing sample sizes and the same ranking of techniques. The RF, SVM and NN models showed instability and a high optimism even with >200 events per variable. Modern modelling techniques such as SVM, NN and RF may need over 10 times as many events per variable to achieve a stable AUC and a small optimism than classical modelling techniques such as LR. This implies that such modern techniques should only be used in medical prediction problems if very large data sets are available.

Analytical electron microscopy of biogenic and inorganic carbonates

NASA Technical Reports Server (NTRS)

Blake, David F.

1989-01-01

In the terrestrial sedimentary environment, the mineralogically predominant carbonates are calcite-type minerals (rhombohedral carbonates) and aragonite-type minerals (orthorhombic carbonates). Most common minerals precipitating either inorganically or biogenically are high magnesium calcite and aragonite. High magnesium calcite (with magnesium carbonate substituting for more than 7 mole percent of the calcium carbonate) is stable only at temperatures greater than 700 C or thereabouts, and aragonite is stable only at pressures exceeding several kilobars of confining pressure. Therefore, these carbonates are expected to undergo chemical stabilization in the diagenetic environment to ultimately form stable calcite and dolomite. Because of the strong organic control of carbonate deposition in organisms during biomineralization, the microchemistry and microstructure of invertebrate skeletal material is much different than that present in inorganic carbonate cements. The style of preservation of microstructural features in skeletal material is therefore often quite distinctive when compared to that of inorganic carbonate even though wholesale recrystallization of the sediment has taken place. Microstructural and microchemical comparisons are made between high magnesium calcite echinoderm skeletal material and modern inorganic high magnesium calcite inorganic cements, using analytical electron microscopy and related techniques. Similar comparisons are made between analogous materials which have undergone stabilization in the diagenetic environment. Similar analysis schemes may prove useful in distinguishing between biogenic and inorganic carbonates in returned Martian carbonate samples.

Simple technique for high-throughput marking of distinguishable micro-areas for microscopy.

PubMed

Henrichs, Leonard F; Chen, L I; Bell, Andrew J

2016-04-01

Today's (nano)-functional materials, usually exhibiting complex physical properties require local investigation with different microscopy techniques covering different physical aspects such as dipolar and magnetic structure. However, often these must be employed on the very same sample position to be able to truly correlate those different information and corresponding properties. This can be very challenging if not impossible especially when samples lack prominent features for orientation. Here, we present a simple but effective method to mark hundreds of approximately 15×15 μm sample areas at one time by using a commercial transmission electron microscopy grid as shadow mask in combination with thin-film deposition. Areas can be easily distinguished when using a reference or finder grid structure as shadow mask. We show that the method is suitable to combine many techniques such as light microscopy, scanning probe microscopy and scanning electron microscopy. Furthermore, we find that best results are achieved when depositing aluminium on a flat sample surface using electron-beam evaporation which ensures good line-of-sight deposition. This inexpensive high-throughput method has several advantageous over other marking techniques such as focused ion-beam processing especially when batch processing or marking of many areas is required. Nevertheless, the technique could be particularly valuable, when used in junction with, for example focused ion-beam sectioning to obtain a thin lamellar of a particular pre-selected area. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Backscattered Electron Microscopy as an Advanced Technique in Petrography.

ERIC Educational Resources Information Center

Krinsley, David Henry; Manley, Curtis Robert

1989-01-01

Three uses of this method with sandstone, desert varnish, and granite weathering are described. Background information on this technique is provided. Advantages of this type of microscopy are stressed. (CW)

Digital differential confocal microscopy based on spatial shift transformation.

PubMed

Liu, J; Wang, Y; Liu, C; Wilson, T; Wang, H; Tan, J

2014-11-01

Differential confocal microscopy is a particularly powerful surface profilometry technique in industrial metrology due to its high axial sensitivity and insensitivity to noise. However, the practical implementation of the technique requires the accurate positioning of point detectors in three-dimensions. We describe a simple alternative based on spatial transformation of a through-focus series of images obtained from a homemade beam scanning confocal microscope. This digital differential confocal microscopy approach is described and compared with the traditional Differential confocal microscopy approach. The ease of use of the digital differential confocal microscopy system is illustrated by performing measurements on a 3D standard specimen. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Methods for characterizing plant fibers.

PubMed

Cruthers, Natasha; Carr, Debra; Niven, Brian; Girvan, Elizabeth; Laing, Raechel

2005-08-01

The effectiveness of different microscopy techniques for measuring the dimensions of ultimate fibers from harakeke (Phormium tenax, New Zealand flax) was investigated using a factorial experimental design. Constant variables were geographical location, location of specimens along the leaf, season (winter), individual plant, a fourth leaf from a north-facing fan, age of plant, and cultivars (two). Experimental variables were microscopy techniques and measurement axis. Measurements of width and length of harakeke ultimate fibers depended on the microscopic preparation/technique used as well as the cultivar examined. The best methods were (i) transverse sections of leaf specimens 4 microm thick, embedded in Paraplast and observed using light microscopy, and (ii) nonfixed ultimate fibers observed using scanning electron microscopy. (c) 2005 Wiley-Liss, Inc.

Invited Review Article: Imaging techniques for harmonic and multiphoton absorption fluorescence microscopy

PubMed Central

Carriles, Ramón; Schafer, Dawn N.; Sheetz, Kraig E.; Field, Jeffrey J.; Cisek, Richard; Barzda, Virginijus; Sylvester, Anne W.; Squier, Jeffrey A.

2009-01-01

We review the current state of multiphoton microscopy. In particular, the requirements and limitations associated with high-speed multiphoton imaging are considered. A description of the different scanning technologies such as line scan, multifoci approaches, multidepth microscopy, and novel detection techniques is given. The main nonlinear optical contrast mechanisms employed in microscopy are reviewed, namely, multiphoton excitation fluorescence, second harmonic generation, and third harmonic generation. Techniques for optimizing these nonlinear mechanisms through a careful measurement of the spatial and temporal characteristics of the focal volume are discussed, and a brief summary of photobleaching effects is provided. Finally, we consider three new applications of multiphoton microscopy: nonlinear imaging in microfluidics as applied to chemical analysis and the use of two-photon absorption and self-phase modulation as contrast mechanisms applied to imaging problems in the medical sciences. PMID:19725639

Even illumination in total internal reflection fluorescence microscopy using laser light.

PubMed

Fiolka, R; Belyaev, Y; Ewers, H; Stemmer, A

2008-01-01

In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode. 2007 Wiley-Liss, Inc

An Introduction to Modern Missing Data Analyses

ERIC Educational Resources Information Center

Baraldi, Amanda N.; Enders, Craig K.

2010-01-01

A great deal of recent methodological research has focused on two modern missing data analysis methods: maximum likelihood and multiple imputation. These approaches are advantageous to traditional techniques (e.g. deletion and mean imputation techniques) because they require less stringent assumptions and mitigate the pitfalls of traditional…

Preservation of protein globules and peptidoglycan in the mineralized cell wall of nitrate-reducing, iron(II)-oxidizing bacteria: a cryo-electron microscopy study.

PubMed

Miot, J; Maclellan, K; Benzerara, K; Boisset, N

2011-11-01

Iron-oxidizing bacteria are important actors of the geochemical cycle of iron in modern environments and may have played a key role all over Earth's history. However, in order to better assess that role on the modern and the past Earth, there is a need for better understanding the mechanisms of bacterial iron oxidation and for defining potential biosignatures to be looked for in the geologic record. In this study, we investigated experimentally and at the nanometre scale the mineralization of iron-oxidizing bacteria with a combination of synchrotron-based scanning transmission X-ray microscopy (STXM), scanning transmission electron microscopy (STEM) and cryo-transmission electron microscopy (cryo-TEM). We show that the use of cryo-TEM instead of conventional microscopy provides detailed information of the successive iron biomineralization stages in anaerobic nitrate-reducing iron-oxidizing bacteria. These results suggest the existence of preferential Fe-binding and Fe-oxidizing sites on the outer face of the plasma membrane leading to the nucleation and growth of Fe minerals within the periplasm of these cells that eventually become completely encrusted. In contrast, the septa of dividing cells remain nonmineralized. In addition, the use of cryo-TEM offers a detailed view of the exceptional preservation of protein globules and the peptidoglycan within the Fe-mineralized cell walls of these bacteria. These organic molecules and ultrastructural details might be protected from further degradation by entrapment in the mineral matrix down to the nanometre scale. This is discussed in the light of previous studies on the properties of Fe-organic interactions and more generally on the fossilization of mineral-organic assemblies. © 2011 Blackwell Publishing Ltd.

Large scale superres 3D imaging: light-sheet single-molecule localization microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lu, Chieh Han; Chen, Peilin; Chen, Bi-Chang

2017-02-01

Optical imaging techniques provide much important information in understanding life science especially cellular structure and morphology because "seeing is believing". However, the resolution of optical imaging is limited by the diffraction limit, which is discovered by Ernst Abbe, i.e. λ/2(NA) (NA is the numerical aperture of the objective lens). Fluorescence super-resolution microscopic techniques such as Stimulated emission depletion microscopy (STED), Photoactivated localization microscopy (PALM), and Stochastic optical reconstruction microscopy (STORM) are invented to have the capability of seeing biological entities down to molecular level that are smaller than the diffraction limit (around 200-nm in lateral resolution). These techniques do not physically violate the Abbe limit of resolution but exploit the photoluminescence properties and labelling specificity of fluorescence molecules to achieve super-resolution imaging. However, these super-resolution techniques limit most of their applications to the 2D imaging of fixed or dead samples due to the high laser power needed or slow speed for the localization process. Extended from 2D imaging, light sheet microscopy has been proven to have a lot of applications on 3D imaging at much better spatiotemporal resolutions due to its intrinsic optical sectioning and high imaging speed. Herein, we combine the advantage of localization microscopy and light-sheet microscopy to have super-resolved cellular imaging in 3D across large field of view. With high-density labeled spontaneous blinking fluorophore and wide-field detection of light-sheet microscopy, these allow us to construct 3D super-resolution multi-cellular imaging at high speed ( minutes) by light-sheet single-molecule localization microscopy.

Photoinduced force microscopy: A technique for hyperspectral nanochemical mapping

NASA Astrophysics Data System (ADS)

Murdick, Ryan A.; Morrison, William; Nowak, Derek; Albrecht, Thomas R.; Jahng, Junghoon; Park, Sung

2017-08-01

Advances in nanotechnology have intensified the need for tools that can characterize newly synthesized nanomaterials. A variety of techniques has recently been shown which combines atomic force microscopy (AFM) with optical illumination including tip-enhanced Raman spectroscopy (TERS), scattering-type scanning near-field optical microscopy (sSNOM), and photothermal induced resonance microscopy (PTIR). To varying degrees, these existing techniques enable optical spectroscopy with the nanoscale spatial resolution inherent to AFM, thereby providing nanochemical interrogation of a specimen. Here we discuss photoinduced force microscopy (PiFM), a recently developed technique for nanoscale optical spectroscopy that exploits image forces acting between an AFM tip and sample to detect wavelength-dependent polarization within the sample to generate absorption spectra. This approach enables ∼10 nm spatial resolution with spectra that show correlation with macroscopic optical absorption spectra. Unlike other techniques, PiFM achieves this high resolution with virtually no constraints on sample or substrate properties. The applicability of PiFM to a variety of archetypal systems is reported here, highlighting the potential of PiFM as a useful tool for a wide variety of industrial and academic investigations, including semiconducting nanoparticles, nanocellulose, block copolymers, and low dimensional systems, as well as chemical and morphological mixing at interfaces.

Housing Improvements and Malaria Risk in Sub-Saharan Africa: A Multi-Country Analysis of Survey Data.

PubMed

Tusting, Lucy S; Bottomley, Christian; Gibson, Harry; Kleinschmidt, Immo; Tatem, Andrew J; Lindsay, Steve W; Gething, Peter W

2017-02-01

Improvements to housing may contribute to malaria control and elimination by reducing house entry by malaria vectors and thus exposure to biting. We tested the hypothesis that the odds of malaria infection are lower in modern, improved housing compared to traditional housing in sub-Saharan Africa (SSA). We analysed 15 Demographic and Health Surveys (DHS) and 14 Malaria Indicator Surveys (MIS) conducted in 21 countries in SSA between 2008 and 2015 that measured malaria infection by microscopy or rapid diagnostic test (RDT). DHS/MIS surveys record whether houses are built with finished materials (e.g., metal) or rudimentary materials (e.g., thatch). This information was used to develop a binary housing quality variable where houses built using finished wall, roof, and floor materials were classified as "modern", and all other houses were classified as "traditional". Conditional logistic regression was used to determine the association between housing quality and prevalence of malaria infection in children aged 0-5 y, adjusting for age, gender, insecticide-treated net (ITN) use, indoor residual spraying, household wealth, and geographic cluster. Individual survey odds ratios (ORs) were combined to determine a summary OR using a random effects meta-analysis. Of 284,532 total children surveyed, 139,318 were tested for malaria infection using microscopy (n = 131,652) or RDT (n = 138,540). Within individual surveys, malaria prevalence measured by microscopy ranged from 0.4% (Madagascar 2011) to 45.5% (Burkina Faso 2010) among children living in modern houses and from 0.4% (The Gambia 2013) to 70.6% (Burkina Faso 2010) in traditional houses, and malaria prevalence measured by RDT ranged from 0.3% (Senegal 2013-2014) to 61.2% (Burkina Faso 2010) in modern houses and from 1.5% (The Gambia 2013) to 79.8% (Burkina Faso 2010) in traditional houses. Across all surveys, modern housing was associated with a 9% to 14% reduction in the odds of malaria infection (microscopy: adjusted OR 0.91, 95% CI 0.85-0.97, p = 0.003; RDT: adjusted OR 0.86, 95% CI 0.80-0.92, p < 0.001). This association was consistent regardless of ITN usage. As a comparison, the odds of malaria infection were 15% to 16% lower among ITN users versus non-users (microscopy: adjusted OR 0.84, 95% CI 0.79-0.90, p < 0.001; RDT: adjusted OR 0.85, 95% CI 0.80-0.90, p < 0.001). The main limitation of this study is that residual confounding by household wealth of the observed association between housing quality and malaria prevalence is possible, since the wealth index may not have fully captured differences in socioeconomic position; however, the use of multiple national surveys offers the advantage of a large sample size and the elimination of many biases typically associated with pooling observational data. Housing quality is an important risk factor for malaria infection across the spectrum of malaria endemicity in SSA, with a strength of association between housing quality and malaria similar to that observed between ITN use and malaria. Improved housing should be considered a promising intervention for malaria control and elimination and long-term prevention of reintroduction.

Application of modern autoradiography to nuclear forensic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parsons-Davis, Tashi; Knight, Kim; Fitzgerald, Marc

Modern autoradiography techniques based on phosphorimaging technology using image plates (IPs) and digital scanning can identify heterogeneities in activity distributions and reveal material properties, serving to inform subsequent analyses. Here, we have adopted these advantages for applications in nuclear forensics, the technical analysis of radioactive or nuclear materials found outside of legal control to provide data related to provenance, production history, and trafficking route for the materials. IP autoradiography is a relatively simple, non-destructive method for sample characterization that records an image reflecting the relative intensity of alpha and beta emissions from a two-dimensional surface. Such data are complementary tomore » information gathered from radiochemical characterization via bulk counting techniques, and can guide the application of other spatially resolved techniques such as scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS). IP autoradiography can image large 2-dimenstional areas (up to 20 × 40 cm), with relatively low detection limits for actinides and other radioactive nuclides, and sensitivity to a wide dynamic range (10 5) of activity density in a single image. Distributions of radioactivity in nuclear materials can be generated with a spatial resolution of approximately 50 μm using IP autoradiography and digital scanning. While the finest grain silver halide films still provide the best possible resolution (down to ~10 μm), IP autoradiography has distinct practical advantages such as shorter exposure times, no chemical post-processing, reusability, rapid plate scanning, and automated image digitization. Sample preparation requirements are minimal, and the analytical method does not consume or alter the sample. These advantages make IP autoradiography ideal for routine screening of nuclear materials, and for the identification of areas of interest for subsequent micro-characterization methods. Here in this article we present a summary of our setup, as modified for nuclear forensic sample analysis and related research, and provide examples of data from select samples from the nuclear fuel cycle and historical nuclear test debris.« less

Application of modern autoradiography to nuclear forensic analysis

DOE PAGES

Parsons-Davis, Tashi; Knight, Kim; Fitzgerald, Marc; ...

2018-05-20

Modern autoradiography techniques based on phosphorimaging technology using image plates (IPs) and digital scanning can identify heterogeneities in activity distributions and reveal material properties, serving to inform subsequent analyses. Here, we have adopted these advantages for applications in nuclear forensics, the technical analysis of radioactive or nuclear materials found outside of legal control to provide data related to provenance, production history, and trafficking route for the materials. IP autoradiography is a relatively simple, non-destructive method for sample characterization that records an image reflecting the relative intensity of alpha and beta emissions from a two-dimensional surface. Such data are complementary tomore » information gathered from radiochemical characterization via bulk counting techniques, and can guide the application of other spatially resolved techniques such as scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS). IP autoradiography can image large 2-dimenstional areas (up to 20 × 40 cm), with relatively low detection limits for actinides and other radioactive nuclides, and sensitivity to a wide dynamic range (10 5) of activity density in a single image. Distributions of radioactivity in nuclear materials can be generated with a spatial resolution of approximately 50 μm using IP autoradiography and digital scanning. While the finest grain silver halide films still provide the best possible resolution (down to ~10 μm), IP autoradiography has distinct practical advantages such as shorter exposure times, no chemical post-processing, reusability, rapid plate scanning, and automated image digitization. Sample preparation requirements are minimal, and the analytical method does not consume or alter the sample. These advantages make IP autoradiography ideal for routine screening of nuclear materials, and for the identification of areas of interest for subsequent micro-characterization methods. Here in this article we present a summary of our setup, as modified for nuclear forensic sample analysis and related research, and provide examples of data from select samples from the nuclear fuel cycle and historical nuclear test debris.« less

Assessing open-system behavior of 14C in terrestrial gastropod shells

USGS Publications Warehouse

Rech, Jason A.; Pigati, Jeffrey S.; Lehmann, Sophie B.; McGimpsey, Chelsea N.; Grimley, David A.; Nekola, Jeffrey C.

2011-01-01

In order to assess open-system behavior of radiocarbon in fossil gastropod shells, we measured the 14C activity on 10 aliquots of shell material recovered from Illinoian (~190-130 ka) and pre-Illinoian (~800 ka) loess and lacustrine deposits in the Midwestern USA. Eight of the 10 aliquots yielded measurable 14C activities that ranged from 0.25 to 0.53 percent modern carbon (pMC), corresponding to apparent 14C ages between 48.2 and 42.1 ka. This small level of open-system behavior is common in many materials that are used for 14C dating (e.g. charcoal), and typically sets the upper practical limit of the technique. Two aliquots of gastropod shells from the Illinoian-aged Petersburg Silt (Petersburg Section) in central Illinois, USA, however, yielded elevated 14C activities of 1.26 and 1.71 pMC, which correspond to apparent 14C ages of 35.1 and 32.7 ka. Together, these results suggest that while many fossil gastropods shells may not suffer from major (>1%) open-system problems, this is not always the case. We then examined the mineralogy, trace element chemistry, and physical characteristics of a suite of fossil and modern gastropod shells to identify the source of contamination in the Petersburg shells and assess the effectiveness of these screening techniques at identifying samples suitable for 14C dating. Mineralogical (XRD) and trace element analyses were inconclusive, which suggests that these techniques are not suitable for assessing open-system behavior in terrestrial gastropod shells. Analysis with scanning electron microscopy (SEM), however, identified secondary mineralization (calcium carbonate) primarily within the inner whorls of the Petersburg shells. This indicates that SEM examination, or possibly standard microscope examination, of the interior of gastropod shells should be used when selecting fossil gastropod shells for 14C dating.

Assessing open-system behavior of 14C in terrestrial gastropod shells

USGS Publications Warehouse

Rech, J.A.; Pigati, J.S.; Lehmann, S.B.; McGimpsey, C.N.; Grimley, D.A.; Nekola, J.C.

2011-01-01

In order to assess open-system behavior of radiocarbon in fossil gastropod shells, we measured the 14C activity on 10 aliquots of shell material recovered from Illinoian (~190-130 ka) and pre-Illinoian (~800 ka) loess and lacustrine deposits in the Midwestern USA. Eight of the 10 aliquots yielded measurable 14C activities that ranged from 0.25 to 0.53 percent modern carbon (pMC), corresponding to apparent 14C ages between 48.2 and 42.1 ka. This small level of open-system behavior is common in many materials that are used for 14C dating (e.g. charcoal), and typically sets the upper practical limit of the technique. Two aliquots of gastropod shells from the Illinoian-aged Petersburg Silt (Petersburg Section) in central Illinois, USA, however, yielded elevated 14C activities of 1.26 and 1.71 pMC, which correspond to apparent 14C ages of 35.1 and 32.7 ka. Together, these results suggest that while many fossil gastropods shells may not suffer from major (>1%) open-system problems, this is not always the case. We then examined the mineralogy, trace element chemistry, and physical characteristics of a suite of fossil and modern gastropod shells to identify the source of contamination in the Petersburg shells and assess the effectiveness of these screening techniques at identifying samples suitable for 14C dating. Mineralogical (XRD) and trace element analyses were inconclusive, which suggests that these techniques are not suitable for assessing open-system behavior in terrestrial gastropod shells. Analysis with scanning electron microscopy (SEM), however, identified secondary mineralization (calcium carbonate) primarily within the inner whorls of the Petersburg shells. This indicates that SEM examination, or possibly standard microscope examination, of the interior of gastropod shells should be used when selecting fossil gastropod shells for 14C dating. ?? 2011 by the Arizona Board of Regents on behalf of the University of Arizona.

Application of modern autoradiography to nuclear forensic analysis.

PubMed

Parsons-Davis, Tashi; Knight, Kim; Fitzgerald, Marc; Stone, Gary; Caldeira, Lee; Ramon, Christina; Kristo, Michael

2018-05-01

Modern autoradiography techniques based on phosphorimaging technology using image plates (IPs) and digital scanning can identify heterogeneities in activity distributions and reveal material properties, serving to inform subsequent analyses. Here, we have adopted these advantages for applications in nuclear forensics, the technical analysis of radioactive or nuclear materials found outside of legal control to provide data related to provenance, production history, and trafficking route for the materials. IP autoradiography is a relatively simple, non-destructive method for sample characterization that records an image reflecting the relative intensity of alpha and beta emissions from a two-dimensional surface. Such data are complementary to information gathered from radiochemical characterization via bulk counting techniques, and can guide the application of other spatially resolved techniques such as scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS). IP autoradiography can image large 2-dimenstional areas (up to 20×40cm), with relatively low detection limits for actinides and other radioactive nuclides, and sensitivity to a wide dynamic range (10 5 ) of activity density in a single image. Distributions of radioactivity in nuclear materials can be generated with a spatial resolution of approximately 50μm using IP autoradiography and digital scanning. While the finest grain silver halide films still provide the best possible resolution (down to ∼10μm), IP autoradiography has distinct practical advantages such as shorter exposure times, no chemical post-processing, reusability, rapid plate scanning, and automated image digitization. Sample preparation requirements are minimal, and the analytical method does not consume or alter the sample. These advantages make IP autoradiography ideal for routine screening of nuclear materials, and for the identification of areas of interest for subsequent micro-characterization methods. In this paper we present a summary of our setup, as modified for nuclear forensic sample analysis and related research, and provide examples of data from select samples from the nuclear fuel cycle and historical nuclear test debris. Copyright © 2018 Elsevier B.V. All rights reserved.

Fluorescence Live Cell Imaging

PubMed Central

Ettinger, Andreas

2014-01-01

Fluorescence microscopy of live cells has become an integral part of modern cell biology. Fluorescent protein tags, live cell dyes, and other methods to fluorescently label proteins of interest provide a range of tools to investigate virtually any cellular process under the microscope. The two main experimental challenges in collecting meaningful live cell microscopy data are to minimize photodamage while retaining a useful signal-to-noise ratio, and to provide a suitable environment for cells or tissues to replicate physiological cell dynamics. This chapter aims to give a general overview on microscope design choices critical for fluorescence live cell imaging that apply to most fluorescence microscopy modalities, and on environmental control with a focus on mammalian tissue culture cells. In addition, we provide guidance on how to design and evaluate fluorescent protein constructs by spinning disk confocal microscopy. PMID:24974023

On the state of crystallography at the dawn of the electron microscopy revolution.

PubMed

Higgins, Matthew K; Lea, Susan M

2017-10-01

While protein crystallography has, for many years, been the most used method for structural analysis of macromolecular complexes, remarkable recent advances in high-resolution electron cryo-microscopy led to suggestions that 'the revolution will not be crystallised'. Here we highlight the current success rate, speed and ease of modern crystallographic structure determination and some recent triumphs of both 'classical' crystallography and the use of X-ray free electron lasers. We also outline fundamental differences between structure determination using X-ray crystallography and electron microscopy. We suggest that crystallography will continue to co-exist with electron microscopy as part of an integrated array of methods, allowing structural biologists to focus on fundamental biological questions rather than being constrained by the methods available. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Degradation of glass artifacts: application of modern surface analytical techniques.

PubMed

Melcher, Michael; Wiesinger, Rita; Schreiner, Manfred

2010-06-15

A detailed understanding of the stability of glasses toward liquid or atmospheric attack is of considerable importance for preserving numerous objects of our cultural heritage. Glasses produced in the ancient periods (Egyptian, Greek, or Roman glasses), as well as modern glass, can be classified as soda-lime-silica glasses. In contrast, potash was used as a flux in medieval Northern Europe for the production of window panes for churches and cathedrals. The particular chemical composition of these potash-lime-silica glasses (low in silica and rich in alkali and alkaline earth components), in combination with increased levels of acidifying gases (such as SO(2), CO(2), NO(x), or O(3)) and airborne particulate matter in today's urban or industrial atmospheres, has resulted in severe degradation of important cultural relics, particularly over the last century. Rapid developments in the fields of microelectronics and computer sciences, however, have contributed to the development of a variety of nondestructive, surface analytical techniques for the scientific investigation and material characterization of these unique and valuable objects. These methods include scanning electron microscopy in combination with energy- or wavelength-dispersive spectrometry (SEM/EDX or SEM/WDX), secondary ion mass spectrometry (SIMS), and atomic force microscopy (AFM). In this Account, we address glass analysis and weathering mechanisms, exploring the possibilities (and limitations) of modern analytical techniques. Corrosion by liquid substances is well investigated in the glass literature. In a tremendous number of case studies, the basic reaction between aqueous solutions and the glass surfaces was identified as an ion-exchange reaction between hydrogen-bearing species of the attacking liquid and the alkali and alkaline earth ions in the glass, causing a depletion of the latter in the outermost surface layers. Although mechanistic analogies to liquid corrosion are obvious, atmospheric attack on glass ("weathering") is much more complex due to the multiphase system (atmosphere, water film, glass surface, and bulk glass) and added complexities (such as relative humidity and atmospheric pollutant concentration). Weathered medieval stained glass objects, as well as artifacts under controlled museum conditions, typically have less transparent or translucent surfaces, often with a thick weathering crust on top, consisting of sulfates of the glass constituents K, Ca, Na, or Mg. In this Account, we try to answer questions about glass analysis and weathering in three main categories. (i) Which chemical reactions are involved in the weathering of glass surfaces? (ii) Which internal factors (such as the glass composition or surface properties) play a dominant role for the weathering process? Can certain environmental or climatic factors be identified as more harmful for glasses than others? Is it possible to set up a quantitative relationship or at least an approximation between the degree of weathering and the factors described above? (iii) What are the consequences for the restoration and conservation strategies of endangered glass objects? How can a severe threat to precious glass objects be avoided, or at least minimized, to preserve these artifacts of our cultural heritage for future generations?

Single-molecule fluorescence microscopy review: shedding new light on old problems

PubMed Central

Shashkova, Sviatlana

2017-01-01

Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilize light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples. For example, the discovery of GFP, initiating the so-called ‘green revolution’, has pushed experimental tools in the biosciences to a completely new level of functional imaging of living samples, culminating in single fluorescent protein molecule detection. Today, fluorescence microscopy is an indispensable tool in single-molecule investigations, providing a high signal-to-noise ratio for visualization while still retaining the key features in the physiological context of native biological systems. In this review, we discuss some of the recent discoveries in the life sciences which have been enabled using single-molecule fluorescence microscopy, paying particular attention to the so-called ‘super-resolution’ fluorescence microscopy techniques in live cells, which are at the cutting-edge of these methods. In particular, how these tools can reveal new insights into long-standing puzzles in biology: old problems, which have been impossible to tackle using other more traditional tools until the emergence of new single-molecule fluorescence microscopy techniques. PMID:28694303

Yoga and mental health: A dialogue between ancient wisdom and modern psychology

PubMed Central

Vorkapic, Camila Ferreira

2016-01-01

Background: Many yoga texts make reference to the importance of mental health and the use of specific techniques in the treatment of mental disorders. Different concepts utilized in modern psychology may not come with contemporary ideas, instead, they seem to share a common root with ancient wisdom. Aims: The goal of this perspective article is to correlate modern techniques used in psychology and psychiatry with yogic practices, in the treatment of mental disorders. Materials and Methods: The current article presented a dialogue between the yogic approach for the treatment of mental disorder and concepts used in modern psychology, such as meta-cognition, disidentification, deconditioning and interoceptive exposure. Conclusions: Contemplative research found out that modern interventions in psychology might not come from modern concepts after all, but share great similarity with ancient yogic knowledge, giving us the opportunity to integrate the psychological wisdom of both East and West. PMID:26865774

Advances in Modern Botnet Understanding and the Accurate Enumeration of Infected Hosts

ERIC Educational Resources Information Center

Nunnery, Christopher Edward

2011-01-01

Botnets remain a potent threat due to evolving modern architectures, inadequate remediation methods, and inaccurate measurement techniques. In response, this research exposes the architectures and operations of two advanced botnets, techniques to enumerate infected hosts, and pursues the scientific refinement of infected-host enumeration data by…

Stochastic Optical Reconstruction Microscopy (STORM).

PubMed

Xu, Jianquan; Ma, Hongqiang; Liu, Yang

2017-07-05

Super-resolution (SR) fluorescence microscopy, a class of optical microscopy techniques at a spatial resolution below the diffraction limit, has revolutionized the way we study biology, as recognized by the Nobel Prize in Chemistry in 2014. Stochastic optical reconstruction microscopy (STORM), a widely used SR technique, is based on the principle of single molecule localization. STORM routinely achieves a spatial resolution of 20 to 30 nm, a ten-fold improvement compared to conventional optical microscopy. Among all SR techniques, STORM offers a high spatial resolution with simple optical instrumentation and standard organic fluorescent dyes, but it is also prone to image artifacts and degraded image resolution due to improper sample preparation or imaging conditions. It requires careful optimization of all three aspects-sample preparation, image acquisition, and image reconstruction-to ensure a high-quality STORM image, which will be extensively discussed in this unit. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Measuring Roughnesses Of Optical Surfaces

NASA Technical Reports Server (NTRS)

Coulter, Daniel R.; Al-Jumaily, Gahnim A.; Raouf, Nasrat A.; Anderson, Mark S.

1994-01-01

Report discusses use of scanning tunneling microscopy and atomic force microscopy to measure roughnesses of optical surfaces. These techniques offer greater spatial resolution than other techniques. Report notes scanning tunneling microscopes and atomic force microscopes resolve down to 1 nm.

Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping.

PubMed

Roth, Gary A; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M; Tahiliani, Sahil; Brenner, Sara A

2015-12-08

Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy.

Pump-probe optical microscopy for imaging nonfluorescent chromophores.

PubMed

Wei, Lu; Min, Wei

2012-06-01

Many chromophores absorb light intensely but have undetectable fluorescence. Hence microscopy techniques other than fluorescence are highly desirable for imaging these chromophores inside live cells, tissues, and organisms. The recently developed pump-probe optical microscopy techniques provide fluorescence-free contrast mechanisms by employing several fundamental light-molecule interactions including excited state absorption, stimulated emission, ground state depletion, and the photothermal effect. By using the pump pulse to excite molecules and the subsequent probe pulse to interrogate the created transient states on a laser scanning microscope, pump-probe microscopy offers imaging capability with high sensitivity and specificity toward nonfluorescent chromophores. Single-molecule sensitivity has even been demonstrated. Here we review and summarize the underlying principles of this emerging class of molecular imaging techniques.

Quantitative fluorescence microscopy and image deconvolution.

PubMed

Swedlow, Jason R

2013-01-01

Quantitative imaging and image deconvolution have become standard techniques for the modern cell biologist because they can form the basis of an increasing number of assays for molecular function in a cellular context. There are two major types of deconvolution approaches--deblurring and restoration algorithms. Deblurring algorithms remove blur but treat a series of optical sections as individual two-dimensional entities and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed in this chapter. Image deconvolution in fluorescence microscopy has usually been applied to high-resolution imaging to improve contrast and thus detect small, dim objects that might otherwise be obscured. Their proper use demands some consideration of the imaging hardware, the acquisition process, fundamental aspects of photon detection, and image processing. This can prove daunting for some cell biologists, but the power of these techniques has been proven many times in the works cited in the chapter and elsewhere. Their usage is now well defined, so they can be incorporated into the capabilities of most laboratories. A major application of fluorescence microscopy is the quantitative measurement of the localization, dynamics, and interactions of cellular factors. The introduction of green fluorescent protein and its spectral variants has led to a significant increase in the use of fluorescence microscopy as a quantitative assay system. For quantitative imaging assays, it is critical to consider the nature of the image-acquisition system and to validate its response to known standards. Any image-processing algorithms used before quantitative analysis should preserve the relative signal levels in different parts of the image. A very common image-processing algorithm, image deconvolution, is used to remove blurred signal from an image. There are two major types of deconvolution approaches, deblurring and restoration algorithms. Deblurring algorithms remove blur, but treat a series of optical sections as individual two-dimensional entities, and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed. Copyright © 1998 Elsevier Inc. All rights reserved.

Deciphering complex, functional structures with synchrotron-based absorption and phase contrast tomographic microscopy

NASA Astrophysics Data System (ADS)

Stampanoni, M.; Reichold, J.; Weber, B.; Haberthür, D.; Schittny, J.; Eller, J.; Büchi, F. N.; Marone, F.

2010-09-01

Nowadays, thanks to the high brilliance available at modern, third generation synchrotron facilities and recent developments in detector technology, it is possible to record volumetric information at the micrometer scale within few minutes. High signal-to-noise ratio, quantitative information on very complex structures like the brain micro vessel architecture, lung airways or fuel cells can be obtained thanks to the combination of dedicated sample preparation protocols, in-situ acquisition schemes and cutting-edge imaging analysis instruments. In this work we report on recent experiments carried out at the TOMCAT beamline of the Swiss Light Source [1] where synchrotron-based tomographic microscopy has been successfully used to obtain fundamental information on preliminary models for cerebral fluid flow [2], to provide an accurate mesh for 3D finite-element simulation of the alveolar structure of the pulmonary acinus [3] and to investigate the complex functional mechanism of fuel cells [4]. Further, we introduce preliminary results on the combination of absorption and phase contrast microscopy for the visualization of high-Z nanoparticles in soft tissues, a fundamental information when designing modern drug delivery systems [5]. As an outlook we briefly discuss the new possibilities offered by high sensitivity, high resolution grating interferomtery as well as Zernike Phase contrast nanotomography [6].

Applications of surface analytical techniques in Earth Sciences

NASA Astrophysics Data System (ADS)

Qian, Gujie; Li, Yubiao; Gerson, Andrea R.

2015-03-01

This review covers a wide range of surface analytical techniques: X-ray photoelectron spectroscopy (XPS), scanning photoelectron microscopy (SPEM), photoemission electron microscopy (PEEM), dynamic and static secondary ion mass spectroscopy (SIMS), electron backscatter diffraction (EBSD), atomic force microscopy (AFM). Others that are relatively less widely used but are also important to the Earth Sciences are also included: Auger electron spectroscopy (AES), low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM). All these techniques probe only the very top sample surface layers (sub-nm to several tens of nm). In addition, we also present several other techniques i.e. Raman microspectroscopy, reflection infrared (IR) microspectroscopy and quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN) that penetrate deeper into the sample, up to several μm, as all of them are fundamental analytical tools for the Earth Sciences. Grazing incidence synchrotron techniques, sensitive to surface measurements, are also briefly introduced at the end of this review. (Scanning) transmission electron microscopy (TEM/STEM) is a special case that can be applied to characterisation of mineralogical and geological sample surfaces. Since TEM/STEM is such an important technique for Earth Scientists, we have also included it to draw attention to the capability of TEM/STEM applied as a surface-equivalent tool. While this review presents most of the important techniques for the Earth Sciences, it is not an all-inclusive bibliography of those analytical techniques. Instead, for each technique that is discussed, we first give a very brief introduction about its principle and background, followed by a short section on approaches to sample preparation that are important for researchers to appreciate prior to the actual sample analysis. We then use examples from publications (and also some of our known unpublished results) within the Earth Sciences to show how each technique is applied and used to obtain specific information and to resolve real problems, which forms the central theme of this review. Although this review focuses on applications of these techniques to study mineralogical and geological samples, we also anticipate that researchers from other research areas such as Material and Environmental Sciences may benefit from this review.

New quality assurance program integrating "modern radiotherapy" within the German Hodgkin Study Group.

PubMed

Kriz, J; Baues, C; Engenhart-Cabillic, R; Haverkamp, U; Herfarth, K; Lukas, P; Schmidberger, H; Marnitz-Schulze, S; Fuchs, M; Engert, A; Eich, H T

2017-02-01

Field design changed substantially from extended-field RT (EF-RT) to involved-field RT (IF-RT) and now to involved-node RT (IN-RT) and involved-site RT (IS-RT) as well as treatment techniques in radiotherapy (RT) of Hodgkin's lymphoma (HL). The purpose of this article is to demonstrate the establishment of a quality assurance program (QAP) including modern RT techniques and field designs within the German Hodgkin Study Group (GHSG). In the era of modern conformal RT, this QAP had to be fundamentally adapted and a new evaluation process has been intensively discussed by the radiotherapeutic expert panel of the GHSG. The expert panel developed guidelines and criteria to analyse "modern" field designs and treatment techniques. This work is based on a dataset of 11 patients treated within the sixth study generation (HD16-17). To develop a QAP of "modern RT", the expert panel defined criteria for analysing current RT procedures. The consensus of a modified QAP in ongoing and future trials is presented. With this schedule, the QAP of the GHSG could serve as a model for other study groups.

Cathodoluminescence in the scanning transmission electron microscope.

PubMed

Kociak, M; Zagonel, L F

2017-05-01

Cathodoluminescence (CL) is a powerful tool for the investigation of optical properties of materials. In recent years, its combination with scanning transmission electron microscopy (STEM) has demonstrated great success in unveiling new physics in the field of plasmonics and quantum emitters. Most of these results were not imaginable even twenty years ago, due to conceptual and technical limitations. The purpose of this review is to present the recent advances that broke these limitations, and the new possibilities offered by the modern STEM-CL technique. We first introduce the different STEM-CL operating modes and the technical specificities in STEM-CL instrumentation. Two main classes of optical excitations, namely the coherent one (typically plasmons) and the incoherent one (typically light emission from quantum emitters) are investigated with STEM-CL. For these two main classes, we describe both the physics of light production under electron beam irradiation and the physical basis for interpreting STEM-CL experiments. We then compare STEM-CL with its better known sister techniques: scanning electron microscope CL, photoluminescence, and electron energy-loss spectroscopy. We finish by comprehensively reviewing recent STEM-CL applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Cathodoluminescence in the scanning transmission electron microscope.

PubMed

Kociak, M; Zagonel, L F

2016-12-19

Cathodoluminescence (CL) is a powerful tool for the investigation of optical properties of materials. In recent years, its combination with scanning transmission electron microscopy (STEM) has demonstrated great success in unveiling new physics in the field of plasmonics and quantum emitters. Most of these results were not imaginable even twenty years ago, due to conceptual and technical limitations. The purpose of this review is to present the recent advances that broke these limitations, and the new possibilities offered by the modern STEM-CL technique. We first introduce the different STEM-CL operating modes and the technical specificities in STEM-CL instrumentation. Two main classes of optical excitations, namely the coherent one (typically plasmons) and the incoherent one (typically light emission from quantum emitters) are investigated with STEM-CL. For these two main classes, we describe both the physics of light production under electron beam irradiation and the physical basis for interpreting STEM-CL experiments. We then compare STEM-CL with its better known sister techniques: scanning electron microscope CL, photoluminescence, and electron energy-loss spectroscopy. We finish by comprehensively reviewing recent STEM-CL applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Active and Passive Microrheology: Theory and Simulation

NASA Astrophysics Data System (ADS)

Zia, Roseanna N.

2018-01-01

Microrheological study of complex fluids traces its roots to the work of the botanist Robert Brown in the early nineteenth century. Indeed, passive microrheology and Brownian motion are one and the same. Once thought to reveal a fundamental life force, the phenomenon was ultimately leveraged by Einstein in proof of the atomic nature of matter ( Haw 2006 ). His work simultaneously paved the way for modern-day passive microrheology by connecting observable particle motion—diffusion—to solvent properties—the viscosity—via the well-known Stokes-Einstein relation. Advances in microscopy techniques in the last two decades have prompted extensions of the original model to generalized forms for passive probing of complex fluids. In the last decade, active microrheology has emerged as a means by which to interrogate the nonequilibrium behavior of complex fluids, in particular, the non-Newtonian rheology of dynamically heterogeneous and microscopically small systems. Here we review theoretical and computational approaches and advances in both passive and active microrheology, with a focus on the extent to which these techniques preserve the connection between single-particle motion and flow properties, as well as the rather surprising recovery of non-Newtonian flow behavior observed in bulk rheology.

Professional Competence of a Teacher in Higher Educational Institution

ERIC Educational Resources Information Center

Abykanova, Bakytgul; Tashkeyeva, Gulmira; Idrissov, Salamat; Bilyalova, Zhupar; Sadirbekova, Dinara

2016-01-01

Modern reality brings certain corrections to the understanding of forms and methods of teaching various courses in higher educational institution. A special role among the educational techniques and means in the college educational environment is taken by the modern technologies, such as using the techniques, means and ways, which are aimed at…

An Investigative Graduate Laboratory Course for Teaching Modern DNA Techniques

ERIC Educational Resources Information Center

de Lencastre, Alexandre; Torello, A. Thomas; Keller, Lani C.

2017-01-01

This graduate-level DNA methods laboratory course is designed to model a discovery-based research project and engages students in both traditional DNA analysis methods and modern recombinant DNA cloning techniques. In the first part of the course, students clone the "Drosophila" ortholog of a human disease gene of their choosing using…

Community to Classroom: Reflections on Community-Centered Pedagogy in Contemporary Modern Dance Technique

ERIC Educational Resources Information Center

Fitzgerald, Mary

2017-01-01

This article reflects on the ways in which socially engaged arts practices can contribute to reconceptualizing the contemporary modern dance technique class as a powerful site of social change. Specifically, the author considers how incorporating socially engaged practices into pedagogical models has the potential to foster responsible citizenship…

Techniques for super-resolution microscopy using NV-diamond

NASA Astrophysics Data System (ADS)

Trifonov, Alexei; Glenn, David; Bar-Gill, Nir; Le Sage, David; Walsworth, Ronald

2011-05-01

We discuss the development and application of techniques for super-resolution microscopy using NV centers in diamond: stimulated emission depletion (STED), metastable ground state depletion (GSD), and stochastic optical reconstruction microscopy (STORM). NV centers do not bleach under optical excitation, are not biotoxic, and have long-lived electronic spin coherence and spin-state-dependent fluorescence. Thus NV-diamond has great potential as a fluorescent biomarker and as a magnetic biosensor.

Non-contact lateral force microscopy.

PubMed

Weymouth, A J

2017-08-16

The goal of atomic force microscopy (AFM) is to measure the short-range forces that act between the tip and the surface. The signal recorded, however, includes long-range forces that are often an unwanted background. Lateral force microscopy (LFM) is a branch of AFM in which a component of force perpendicular to the surface normal is measured. If we consider the interaction between tip and sample in terms of forces, which have both direction and magnitude, then we can make a very simple yet profound observation: over a flat surface, long-range forces that do not yield topographic contrast have no lateral component. Short-range interactions, on the other hand, do. Although contact-mode is the most common LFM technique, true non-contact AFM techniques can be applied to perform LFM without the tip depressing upon the sample. Non-contact lateral force microscopy (nc-LFM) is therefore ideal to study short-range forces of interest. One of the first applications of nc-LFM was the study of non-contact friction. A similar setup is used in magnetic resonance force microscopy to detect spin flipping. More recently, nc-LFM has been used as a true microscopy technique to systems unsuitable for normal force microscopy.

Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy.

PubMed

Avti, Pramod K; Hu, Song; Favazza, Christopher; Mikos, Antonios G; Jansen, John A; Shroyer, Kenneth R; Wang, Lihong V; Sitharaman, Balaji

2012-01-01

In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Optical-resolution (OR) and acoustic-resolution (AR)--Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs.

Techniques for the Cellular and Subcellular Localization of Endocannabinoid Receptors and Enzymes in the Mammalian Brain.

PubMed

Cristino, Luigia; Imperatore, Roberta; Di Marzo, Vincenzo

2017-01-01

This chapter attempts to piece together knowledge about new advanced microscopy techniques to study the neuroanatomical distribution of endocannabinoid receptors and enzymes at the level of cellular and subcellular structures and organelles in the brain. Techniques ranging from light to electron microscopy up to the new advanced LBM, PALM, and STORM super-resolution microscopy will be discussed in the context of their contribution to define the spatial distribution and organization of receptors and enzymes of the endocannabinoid system (ECS), and to better understand ECS brain functions. © 2017 Elsevier Inc. All rights reserved.

Fluorescence microscopy for the characterization of structural integrity

NASA Technical Reports Server (NTRS)

Street, Kenneth W.; Leonhardt, Todd A.

1991-01-01

The absorption characteristics of light and the optical technique of fluorescence microscopy for enhancing metallographic interpretation are presented. Characterization of thermally sprayed coatings by optical microscopy suffers because of the tendency for misidentification of the microstructure produced by metallographic preparation. Gray scale, in bright field microscopy, is frequently the only means of differentiating the actual structural details of porosity, cracking, and debonding of coatings. Fluorescence microscopy is a technique that helps to distinguish the artifacts of metallographic preparation (pullout, cracking, debonding) from the microstructure of the specimen by color contrasting structural differences. Alternative instrumentation and the use of other dye systems are also discussed. The combination of epoxy vacuum infiltration with fluorescence microscopy to verify microstructural defects is an effective means to characterize advanced materials and to assess structural integrity.

High-sensitivity chemical imaging for biomedicine by SRS microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Min, Wei

2017-02-01

Innovations in spectroscopy principles and microscopy technology have significantly impacted modern biology and medicine. While most of the contemporary bio-imaging modalities harness electronic transition, nuclear spin or radioactivity, vibrational spectroscopy has not been widely used yet. Here we will discuss an emerging chemical imaging platform, stimulated Raman scattering (SRS) microscopy, which can enhance the otherwise feeble spontaneous Raman eight orders of magnitude by virtue of stimulated emission. When coupled with stable isotopes (e.g., deuterium and 13C) or bioorthogonal chemical moieties (e.g., alkynes), SRS microscopy is well suited for probing in vivo metabolic dynamics of small bio-molecules which cannot be labeled by bulky fluorophores. Physical principle of the underlying optical spectroscopy and exciting biomedical applications such as imaging lipid metabolism, protein synthesis, DNA replication, protein degradation, RNA synthesis, glucose uptake, drug trafficking and tumor metabolism will be presented.

Cement paste surface roughness analysis using coherence scanning interferometry and confocal microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Apedo, K.L., E-mail: apedo@unistra.fr; Munzer, C.; He, H.

2015-02-15

Scanning electron microscopy and scanning probe microscopy have been used for several decades to better understand the microstructure of cementitious materials. Very limited work has been performed to date to study the roughness of cementitious materials by optical microscopy such as coherence scanning interferometry (CSI) and chromatic confocal sensing (CCS). The objective of this paper is to better understand how CSI can be used as a tool to analyze surface roughness and topography of cement pastes. Observations from a series of images acquired using this technique on both polished and unpolished samples are described. The results from CSI are comparedmore » with those from a STIL confocal microscopy technique (SCM). Comparison between both optical techniques demonstrates the ability of CSI to measure both polished and unpolished cement pastes. - Highlights: • Coherence scanning interferometry (CSI) was used to analyze cement paste surfaces. • The results from the CSI were compared with those from a confocal microscopy. • 3D roughness parameters were obtained using the window resizing method. • Polished and unpolished cement pastes were studied.« less

SRRF: Universal live-cell super-resolution microscopy.

PubMed

Culley, Siân; Tosheva, Kalina L; Matos Pereira, Pedro; Henriques, Ricardo

2018-08-01

Super-resolution microscopy techniques break the diffraction limit of conventional optical microscopy to achieve resolutions approaching tens of nanometres. The major advantage of such techniques is that they provide resolutions close to those obtainable with electron microscopy while maintaining the benefits of light microscopy such as a wide palette of high specificity molecular labels, straightforward sample preparation and live-cell compatibility. Despite this, the application of super-resolution microscopy to dynamic, living samples has thus far been limited and often requires specialised, complex hardware. Here we demonstrate how a novel analytical approach, Super-Resolution Radial Fluctuations (SRRF), is able to make live-cell super-resolution microscopy accessible to a wider range of researchers. We show its applicability to live samples expressing GFP using commercial confocal as well as laser- and LED-based widefield microscopes, with the latter achieving long-term timelapse imaging with minimal photobleaching. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

A review of cellphone microscopy for disease detection.

PubMed

Dendere, R; Myburg, N; Douglas, T S

2015-12-01

The expansion in global cellphone network coverage coupled with advances in cellphone imaging capabilities present an opportunity for the advancement of cellphone microscopy as a low-cost alternative to conventional microscopy for disease detection in resource-limited regions. The development of cellphone microscopy has also benefitted from the availability of low-cost miniature microscope components such as low-power light-emitting diodes and ball lenses. As a result, researchers are developing hardware and software techniques that would enable such microscopes to produce high-resolution, diagnostic-quality images. This approach may lead to more widespread delivery of diagnostic services in resource-limited areas where there is a shortage of the skilled labour required for conventional microscopy and where prevalence of infectious and other diseases is still high. In this paper, we review current techniques, clinical applications and challenges faced in the field of cellphone microscopy. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Infrared spectroscopy of molecular submonolayers on surfaces by infrared scanning tunneling microscopy: tetramantane on Au111.

PubMed

Pechenezhskiy, Ivan V; Hong, Xiaoping; Nguyen, Giang D; Dahl, Jeremy E P; Carlson, Robert M K; Wang, Feng; Crommie, Michael F

2013-09-20

We have developed a new scanning-tunneling-microscopy-based spectroscopy technique to characterize infrared (IR) absorption of submonolayers of molecules on conducting crystals. The technique employs a scanning tunneling microscope as a precise detector to measure the expansion of a molecule-decorated crystal that is irradiated by IR light from a tunable laser source. Using this technique, we obtain the IR absorption spectra of [121]tetramantane and [123]tetramantane on Au(111). Significant differences between the IR spectra for these two isomers show the power of this new technique to differentiate chemical structures even when single-molecule-resolved scanning tunneling microscopy (STM) images look quite similar. Furthermore, the new technique was found to yield significantly better spectral resolution than STM-based inelastic electron tunneling spectroscopy, and to allow determination of optical absorption cross sections. Compared to IR spectroscopy of bulk tetramantane powders, infrared scanning tunneling microscopy (IRSTM) spectra reveal narrower and blueshifted vibrational peaks for an ordered tetramantane adlayer. Differences between bulk and surface tetramantane vibrational spectra are explained via molecule-molecule interactions.

Cornea and anterior eye assessment with slit lamp biomicroscopy, specular microscopy, confocal microscopy, and ultrasound biomicroscopy

PubMed Central

Martin, Raul

2018-01-01

Current corneal assessment technologies make the process of corneal evaluation extremely fast and simple, and several devices and technologies show signs that help in identification of different diseases thereby, helping in diagnosis, management, and follow-up of patients. The purpose of this review is to present and update readers on the evaluation of cornea and ocular surface. This first part reviews a description of slit lamp biomicroscopy (SLB), endothelial specular microscopy, confocal microscopy, and ultrasound biomicroscopy examination techniques and the second part describes the corneal topography and tomography, providing up-to-date information on the clinical recommendations of these techniques in eye care practice. Although the SLB is a traditional technique, it is of paramount importance in clinical diagnosis and compulsory when an eye test is conducted in primary or specialist eye care practice. Different techniques allow the early diagnosis of many diseases, especially when clinical signs have not yet become apparent and visible with SLB. These techniques also allow for patient follow-up in several clinical conditions or diseases, facilitating clinical decisions and improving knowledge regarding the corneal anatomy. PMID:29380757

Hypothesis Testing, "p" Values, Confidence Intervals, Measures of Effect Size, and Bayesian Methods in Light of Modern Robust Techniques

ERIC Educational Resources Information Center

Wilcox, Rand R.; Serang, Sarfaraz

2017-01-01

The article provides perspectives on p values, null hypothesis testing, and alternative techniques in light of modern robust statistical methods. Null hypothesis testing and "p" values can provide useful information provided they are interpreted in a sound manner, which includes taking into account insights and advances that have…

Teaching Earth Signals Analysis Using the Java-DSP Earth Systems Edition: Modern and Past Climate Change

ERIC Educational Resources Information Center

Ramamurthy, Karthikeyan Natesan; Hinnov, Linda A.; Spanias, Andreas S.

2014-01-01

Modern data collection in the Earth Sciences has propelled the need for understanding signal processing and time-series analysis techniques. However, there is an educational disconnect in the lack of instruction of time-series analysis techniques in many Earth Science academic departments. Furthermore, there are no platform-independent freeware…

Multiple excitation nano-spot generation and confocal detection for far-field microscopy.

PubMed

Mondal, Partha Pratim

2010-03-01

An imaging technique is developed for the controlled generation of multiple excitation nano-spots for far-field microscopy. The system point spread function (PSF) is obtained by interfering two counter-propagating extended depth-of-focus PSF (DoF-PSF), resulting in highly localized multiple excitation spots along the optical axis. The technique permits (1) simultaneous excitation of multiple planes in the specimen; (2) control of the number of spots by confocal detection; and (3) overcoming the point-by-point based excitation. Fluorescence detection from the excitation spots can be efficiently achieved by Z-scanning the detector/pinhole assembly. The technique complements most of the bioimaging techniques and may find potential application in high resolution fluorescence microscopy and nanoscale imaging.

Multiple excitation nano-spot generation and confocal detection for far-field microscopy

NASA Astrophysics Data System (ADS)

Mondal, Partha Pratim

2010-03-01

An imaging technique is developed for the controlled generation of multiple excitation nano-spots for far-field microscopy. The system point spread function (PSF) is obtained by interfering two counter-propagating extended depth-of-focus PSF (DoF-PSF), resulting in highly localized multiple excitation spots along the optical axis. The technique permits (1) simultaneous excitation of multiple planes in the specimen; (2) control of the number of spots by confocal detection; and (3) overcoming the point-by-point based excitation. Fluorescence detection from the excitation spots can be efficiently achieved by Z-scanning the detector/pinhole assembly. The technique complements most of the bioimaging techniques and may find potential application in high resolution fluorescence microscopy and nanoscale imaging.

Superresolution microscopy for microbiology

PubMed Central

Coltharp, Carla; Xiao, Jie

2014-01-01

Summary This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of super-resolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate super-resolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments. PMID:22947061

Nano-Optics for Chemical and Materials Characterization

NASA Astrophysics Data System (ADS)

Beversluis, Michael; Stranick, Stephan

2007-03-01

Light microscopy can provide non-destructive, real-time, three-dimensional imaging with chemically-specific contrast, but diffraction frequently limits the resolution to roughly 200 nm. Recently, structured illumination techniques have allowed fluorescence imaging to reach 50 nm resolution [1]. Since these fluorescence techniques were developed for use in microbiology, a key challenge is to take the resolution-enhancing features and apply them to contrast mechanisms like vibrational spectroscopy (e.g., Raman and CARS microscopy) that provide morphological and chemically specific imaging.. We are developing a new hybrid technique that combines the resolution enhancement of structured illumination microscopy with scanning techniques that can record hyperspectral images with 100 nm spatial resolution. We will show such superresolving images of semiconductor nanostructures and discuss the advantages and requirements for this technique. Referenence: 1. M. G. L. Gustafsson, P. Natl. Acad. Sci. USA 102, 13081-13086 (2005).

Identifying Nanoscale Structure-Function Relationships Using Multimodal Atomic Force Microscopy, Dimensionality Reduction, and Regression Techniques.

PubMed

Kong, Jessica; Giridharagopal, Rajiv; Harrison, Jeffrey S; Ginger, David S

2018-05-31

Correlating nanoscale chemical specificity with operational physics is a long-standing goal of functional scanning probe microscopy (SPM). We employ a data analytic approach combining multiple microscopy modes, using compositional information in infrared vibrational excitation maps acquired via photoinduced force microscopy (PiFM) with electrical information from conductive atomic force microscopy. We study a model polymer blend comprising insulating poly(methyl methacrylate) (PMMA) and semiconducting poly(3-hexylthiophene) (P3HT). We show that PiFM spectra are different from FTIR spectra, but can still be used to identify local composition. We use principal component analysis to extract statistically significant principal components and principal component regression to predict local current and identify local polymer composition. In doing so, we observe evidence of semiconducting P3HT within PMMA aggregates. These methods are generalizable to correlated SPM data and provide a meaningful technique for extracting complex compositional information that are impossible to measure from any one technique.

A contribution to the characterization of the silicate-water interface - Part I: Implication of a new polished sample hydration technique.

PubMed

Sowoidnich, T; Gordon, L; Naber, C; Bellmann, F; Neubauer, J; Joester, D

2018-06-11

The analysis of the atomic composition of the interface between tricalcium silicate (C 3 S), the main compound of Ordinary Portland Cement, and surrounding solution is still a challenging task. At the same time, that knowledge is of profound importance for describing the basic processes during hydration. By means of Scanning Electron Microscopy (SEM) and Atom Probe Tomography (APT) we combine modern techniques in order to shed light on this topic in the present study. The results of these methods are compared with conduction calorimetry as a standard technique to study the hydration kinetics of cement. The tests were carried out on powders as well as on polished C 3 S samples. Results indicate that the progress of hydration is strongly increased when the C 3 S is used in the form of polished specimen. First C-S-H phases are detected in the powder 2.2 h after contact with water, on the polished section after 5 min. Besides SEM, the formation of C-S-H phases can be detected by APT, leading to an advantageous atomic resolution compared to EDX analysis. We propose that the use of APT will lead to deeper insights on the hydration progress and on the composition of the sensitive C-S-H phases based on these first results. Copyright © 2018 Elsevier Ltd. All rights reserved.

Environmental scanning electron microscopy in cell biology.

PubMed

McGregor, J E; Staniewicz, L T L; Guthrie Neé Kirk, S E; Donald, A M

2013-01-01

Environmental scanning electron microscopy (ESEM) (1) is an imaging technique which allows hydrated, insulating samples to be imaged under an electron beam. The resolution afforded by this technique is higher than conventional optical microscopy but lower than conventional scanning electron microscopy (CSEM). The major advantage of the technique is the minimal sample preparation needed, making ESEM quick to use and the images less susceptible to the artifacts that the extensive sample preparation usually required for CSEM may introduce. Careful manipulation of both the humidity in the microscope chamber and the beam energy are nevertheless essential to prevent dehydration and beam damage artifacts. In some circumstances it is possible to image live cells in the ESEM (2).In the following sections we introduce the fundamental principles of ESEM imaging before presenting imaging protocols for plant epidermis, mammalian cells, and bacteria. In the first two cases samples are imaged using the secondary electron (topographic) signal, whereas a transmission technique is employed to image bacteria.

3D digital image processing for biofilm quantification from confocal laser scanning microscopy: Multidimensional statistical analysis of biofilm modeling

NASA Astrophysics Data System (ADS)

Zielinski, Jerzy S.

The dramatic increase in number and volume of digital images produced in medical diagnostics, and the escalating demand for rapid access to these relevant medical data, along with the need for interpretation and retrieval has become of paramount importance to a modern healthcare system. Therefore, there is an ever growing need for processed, interpreted and saved images of various types. Due to the high cost and unreliability of human-dependent image analysis, it is necessary to develop an automated method for feature extraction, using sophisticated mathematical algorithms and reasoning. This work is focused on digital image signal processing of biological and biomedical data in one- two- and three-dimensional space. Methods and algorithms presented in this work were used to acquire data from genomic sequences, breast cancer, and biofilm images. One-dimensional analysis was applied to DNA sequences which were presented as a non-stationary sequence and modeled by a time-dependent autoregressive moving average (TD-ARMA) model. Two-dimensional analyses used 2D-ARMA model and applied it to detect breast cancer from x-ray mammograms or ultrasound images. Three-dimensional detection and classification techniques were applied to biofilm images acquired using confocal laser scanning microscopy. Modern medical images are geometrically arranged arrays of data. The broadening scope of imaging as a way to organize our observations of the biophysical world has led to a dramatic increase in our ability to apply new processing techniques and to combine multiple channels of data into sophisticated and complex mathematical models of physiological function and dysfunction. With explosion of the amount of data produced in a field of biomedicine, it is crucial to be able to construct accurate mathematical models of the data at hand. Two main purposes of signal modeling are: data size conservation and parameter extraction. Specifically, in biomedical imaging we have four key problems that were addressed in this work: (i) registration, i.e. automated methods of data acquisition and the ability to align multiple data sets with each other; (ii) visualization and reconstruction, i.e. the environment in which registered data sets can be displayed on a plane or in multidimensional space; (iii) segmentation, i.e. automated and semi-automated methods to create models of relevant anatomy from images; (iv) simulation and prediction, i.e. techniques that can be used to simulate growth end evolution of researched phenomenon. Mathematical models can not only be used to verify experimental findings, but also to make qualitative and quantitative predictions, that might serve as guidelines for the future development of technology and/or treatment.

Aberrations and adaptive optics in super-resolution microscopy.

PubMed

Booth, Martin; Andrade, Débora; Burke, Daniel; Patton, Brian; Zurauskas, Mantas

2015-08-01

As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy - or rather nanoscopy - to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy.

Polarized Light Microscopy

NASA Technical Reports Server (NTRS)

Frandsen, Athela F.

2016-01-01

Polarized light microscopy (PLM) is a technique which employs the use of polarizing filters to obtain substantial optical property information about the material which is being observed. This information can be combined with other microscopy techniques to confirm or elucidate the identity of an unknown material, determine whether a particular contaminant is present (as with asbestos analysis), or to provide important information that can be used to refine a manufacturing or chemical process. PLM was the major microscopy technique in use for identification of materials for nearly a century since its introduction in 1834 by William Fox Talbot, as other techniques such as SEM (Scanning Electron Microscopy), FTIR (Fourier Transform Infrared spectroscopy), XPD (X-ray Powder Diffraction), and TEM (Transmission Electron Microscopy) had not yet been developed. Today, it is still the only technique approved by the Environmental Protection Agency (EPA) for asbestos analysis, and is often the technique first applied for identification of unknown materials. PLM uses different configurations in order to determine different material properties. With each configuration additional clues can be gathered, leading to a conclusion of material identity. With no polarizing filter, the microscope can be used just as a stereo optical microscope, and view qualities such as morphology, size, and number of phases. With a single polarizing filter (single polars), additional properties can be established, such as pleochroism, individual refractive indices, and dispersion staining. With two polarizing filters (crossed polars), even more can be deduced: isotropy vs. anisotropy, extinction angle, birefringence/degree of birefringence, sign of elongation, and anomalous polarization colors, among others. With the use of PLM many of these properties can be determined in a matter of seconds, even for those who are not highly trained. McCrone, a leader in the field of polarized light microscopy, often advised, If you cant determine a specific optical property of a particle after two minutes, move onto another configuration. Since optical properties can be seen so very quickly and easily under polarized light, it is only necessary to spend a maximum of two minutes on a technique to determine a particular property, though often only a few seconds are required.

Insights into the prominent effect of mahanimbine on Acanthamoeba castellanii: Cell profiling analysis based on microscopy techniques

NASA Astrophysics Data System (ADS)

Hashim, Fatimah; Amin, Nakisah Mat

2017-02-01

Mahanimbine (MH), has been shown to have antiamoeba properties. Therefore, the aim of this study was to assess the growth inhibitory mechanisms of MH on Acanthamoeba castellanii, a causative agents for Acanthamoeba keratitis. The IC50 value obtained for MH against A. castellanii was 1.18 µg/ml. Light and scanning electron microscopy observation showed that most cells were in cystic appearance. While transmission electron microscopy observation revealed changes at the ultrastructural level and fluorescence microscopy observation indicated the induction of apoptosis and autophagic activity in the amoeba cytoplasms. In conclusion, MH has very potent anti-amoebic properties on A. castellanii as is shown by cytotoxicity analyses based on microscopy techniques.

Tip-Enhanced Raman Scattering Microscopy: A Step toward Nanoscale Control of Intrinsic Molecular Properties

NASA Astrophysics Data System (ADS)

Yano, Taka-aki; Hara, Masahiko

2018-06-01

Tip-enhanced Raman scattering microscopy, a family of scanning probe microscopy techniques, has been recognized as a powerful surface analytical technique with both single-molecule sensitivity and angstrom-scale spatial resolution. This review covers the current status of tip-enhanced Raman scattering microscopy in surface and material nanosciences, including a brief history, the basic principles, and applications for the nanoscale characterization of a variety of nanomaterials. The focus is on the recent trend of combining tip-enhanced Raman scattering microscopy with various external stimuli such as pressure, voltage, light, and temperature, which enables the local control of the molecular properties and functions and also enables chemical reactions to be induced on a nanometer scale.

Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison.

PubMed

Wegel, Eva; Göhler, Antonia; Lagerholm, B Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M

2016-06-06

Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques.

In-situ Isotopic Analysis at Nanoscale using Parallel Ion Electron Spectrometry: A Powerful New Paradigm for Correlative Microscopy

NASA Astrophysics Data System (ADS)

Yedra, Lluís; Eswara, Santhana; Dowsett, David; Wirtz, Tom

2016-06-01

Isotopic analysis is of paramount importance across the entire gamut of scientific research. To advance the frontiers of knowledge, a technique for nanoscale isotopic analysis is indispensable. Secondary Ion Mass Spectrometry (SIMS) is a well-established technique for analyzing isotopes, but its spatial-resolution is fundamentally limited. Transmission Electron Microscopy (TEM) is a well-known method for high-resolution imaging down to the atomic scale. However, isotopic analysis in TEM is not possible. Here, we introduce a powerful new paradigm for in-situ correlative microscopy called the Parallel Ion Electron Spectrometry by synergizing SIMS with TEM. We demonstrate this technique by distinguishing lithium carbonate nanoparticles according to the isotopic label of lithium, viz. 6Li and 7Li and imaging them at high-resolution by TEM, adding a new dimension to correlative microscopy.

Axial range of conjugate adaptive optics in two-photon microscopy

PubMed Central

Paudel, Hari P.; Taranto, John; Mertz, Jerome; Bifano, Thomas

2015-01-01

We describe an adaptive optics technique for two-photon microscopy in which the deformable mirror used for aberration compensation is positioned in a plane conjugate to the plane of the aberration. We demonstrate in a proof-of-principle experiment that this technique yields a large field of view advantage in comparison to standard pupil-conjugate adaptive optics. Further, we show that the extended field of view in conjugate AO is maintained over a relatively large axial translation of the deformable mirror with respect to the conjugate plane. We conclude with a discussion of limitations and prospects for the conjugate AO technique in two-photon biological microscopy. PMID:26367938

Axial range of conjugate adaptive optics in two-photon microscopy.

PubMed

Paudel, Hari P; Taranto, John; Mertz, Jerome; Bifano, Thomas

2015-08-10

We describe an adaptive optics technique for two-photon microscopy in which the deformable mirror used for aberration compensation is positioned in a plane conjugate to the plane of the aberration. We demonstrate in a proof-of-principle experiment that this technique yields a large field of view advantage in comparison to standard pupil-conjugate adaptive optics. Further, we show that the extended field of view in conjugate AO is maintained over a relatively large axial translation of the deformable mirror with respect to the conjugate plane. We conclude with a discussion of limitations and prospects for the conjugate AO technique in two-photon biological microscopy.

Surface Diagnostics in Tribology Technology and Advanced Coatings Development

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1999-01-01

This paper discusses the methodologies used for surface property measurement of thin films and coatings, lubricants, and materials in the field of tribology. Surface diagnostic techniques include scanning electron microscopy, transmission electron microscopy, atomic force microscopy, stylus profilometry, x-ray diffraction, electron diffraction, Raman spectroscopy, Rutherford backscattering, elastic recoil spectroscopy, and tribology examination. Each diagnostic technique provides specific measurement results in its own unique way. In due course it should be possible to coordinate the different pieces of information provided by these diagnostic techniques into a coherent self-consistent description of the surface properties. Examples are given on the nature and character of thin diamond films.

The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.

PubMed

Dorfman, Kevin D

2018-02-01

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

Davisson-Germer Prize in Atomic or Surface Physics Talk: Soft X-Ray Studies of Surfaces, Interfaces and Thin Films: From Spectroscopy to Ultrafast Nanoscale Movies

NASA Astrophysics Data System (ADS)

Stöhr, Joachim

2011-03-01

My talk will review the development of soft x-ray spectroscopy and microscopy and its impact on our understanding of chemical bonding, magnetism and dynamics at surfaces and interfaces. I will first outline important soft x-ray spectroscopy and microscopy techniques that have been developed over the last 30 years and their key strengths such as elemental and chemical specificity, sensitivity to small atomic concentrations, separation of charge and spin properties, spatial resolution down to the nanometer scale, and temporal resolution down to the intrinsic femtosecond timescale of atomic and electronic motions. I will then present scientific breakthroughs based on soft x-ray studies in three selected areas: the nature of molecular bonding and reactivity on metal surfaces, the molecular origin of liquid crystal alignment on surfaces, and the microscopic origin of interface-mediated spin alignments in modern magnetic devices. My talk will also cover the use of soft x-rays for revealing the temporal evolution of electronic structure, addressing the key problem of ``function,'' down to the intrinsic femtosecond time scale of charge and spin configuration changes. As examples I will present the formation and breaking of chemical bonds in surface complexes and the motion of the magnetization in magnetic devices. Work supported by the Office of Basic Energy Science of the US Department of Energy.

Structural and Galvanomagnetic properties in Mn-Bi2Te3 thin films

NASA Astrophysics Data System (ADS)

Bidinakis, K.; Speliotis, Th.

2017-12-01

Bismuth-based binary chalcogenide compounds such as Bi2Te3 and Bi2Se3 are well known materials for their excellent thermoelectric properties due to their near-gap electronic structure. In the last few years these materials have received attention for exhibiting new physics of 3D topological insulators (TI). Possible applications of TI based devices range from quantum computing, spin based logic and memory to electrodynamics. The 3D TIs present spin-momentum-locked surface states by time reversal symmetry (TRS). Introducing magnetic doping in a TI, brakes the TRS and is predicted to open the gap at Dirac point, resulting in exotic quantum phenomena. This interaction between magnetism and topologically protected states is of potential attention for applications in modern spintronics. Quantum phenomena such as weak antilocalization observed in these nanostructures are described. In this work, granular Mn-Bi2Te3 thin films were grown by DC magnetron sputtering on Si(111) substrates and were submitted to ex situ annealing. We present results for the crystal structure of sputtered and annealed films characterized with X-ray diffraction and high-resolution scanning electron microscopy (HRSEM). The surface analysis was studied with atomic force microscopy (AFM). Magnetotransport measurements were performed using standard four probe technique with Hall and MR configurations, with perpendicular magnetic fields up to 9T and temperatures from 300 to 3K.

Correlation of two-photon in vivo imaging and FIB/SEM microscopy

PubMed Central

Blazquez-Llorca, L; Hummel, E; Zimmerman, H; Zou, C; Burgold, S; Rietdorf, J; Herms, J

2015-01-01

Advances in the understanding of brain functions are closely linked to the technical developments in microscopy. In this study, we describe a correlative microscopy technique that offers a possibility of combining two-photon in vivo imaging with focus ion beam/scanning electron microscope (FIB/SEM) techniques. Long-term two-photon in vivo imaging allows the visualization of functional interactions within the brain of a living organism over the time, and therefore, is emerging as a new tool for studying the dynamics of neurodegenerative diseases, such as Alzheimer’s disease. However, light microscopy has important limitations in revealing alterations occurring at the synaptic level and when this is required, electron microscopy is mandatory. FIB/SEM microscopy is a novel tool for three-dimensional high-resolution reconstructions, since it acquires automated serial images at ultrastructural level. Using FIB/SEM imaging, we observed, at 10 nm isotropic resolution, the same dendrites that were imaged in vivo over 9 days. Thus, we analyzed their ultrastructure and monitored the dynamics of the neuropil around them. We found that stable spines (present during the 9 days of imaging) formed typical asymmetric contacts with axons, whereas transient spines (present only during one day of imaging) did not form a synaptic contact. Our data suggest that the morphological classification that was assigned to a dendritic spine according to the in vivo images did not fit with its ultrastructural morphology. The correlative technique described herein is likely to open opportunities for unravelling the earlier unrecognized complexity of the nervous system. Lay Description Neuroscience and the understanding of brain functions are closely linked to the technical advances in microscopy. In this study we performed a correlative microscopy technique that offers the possibility to combine 2 photon in vivo imaging and FIB/SEM microscopy. Long term 2 photon in vivo imaging allows the visualization of functional interactions within the brain of a living organism over the time, and therefore, is emerging as a new tool to study the dynamics of neurodegenerative diseases, such as Alzheimer’s disease. However, light microscopy has important limitations in revealing synapses that are the connections between neurons, and for this purpose, the electron microscopy is necessary. FIB/SEM microscopy is a novel tool for three-dimensional (3D) high resolution reconstructions since it acquires automated serial images at ultrastructural level. This correlative technique will open up new horizons and opportunities for unravelling the complexity of the nervous system. PMID:25786682

Integral refractive index imaging of flowing cell nuclei using quantitative phase microscopy combined with fluorescence microscopy.

PubMed

Dardikman, Gili; Nygate, Yoav N; Barnea, Itay; Turko, Nir A; Singh, Gyanendra; Javidi, Barham; Shaked, Natan T

2018-03-01

We suggest a new multimodal imaging technique for quantitatively measuring the integral (thickness-average) refractive index of the nuclei of live biological cells in suspension. For this aim, we combined quantitative phase microscopy with simultaneous 2-D fluorescence microscopy. We used 2-D fluorescence microscopy to localize the nucleus inside the quantitative phase map of the cell, as well as for measuring the nucleus radii. As verified offline by both 3-D confocal fluorescence microscopy and 2-D fluorescence microscopy while rotating the cells during flow, the nucleus of cells in suspension that are not during division can be assumed to be an ellipsoid. The entire shape of a cell in suspension can be assumed to be a sphere. Then, the cell and nucleus 3-D shapes can be evaluated based on their in-plain radii available from the 2-D phase and fluorescent measurements, respectively. Finally, the nucleus integral refractive index profile is calculated. We demonstrate the new technique on cancer cells, obtaining nucleus refractive index values that are lower than those of the cytoplasm, coinciding with recent findings. We believe that the proposed technique has the potential to be used for flow cytometry, where full 3-D refractive index tomography is too slow to be implemented during flow.

Detection, Mapping, and Quantification of Single Walled Carbon Nanotubes in Histological Specimens with Photoacoustic Microscopy

PubMed Central

Mikos, Antonios G.; Jansen, John A.; Shroyer, Kenneth R.; Wang, Lihong V.; Sitharaman, Balaji

2012-01-01

Aims In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Materials and Methods Optical-resolution (OR) and acoustic-resolution (AR) - Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Results Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. Conclusions The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs. PMID:22496892

Widefield fluorescence sectioning with HiLo microscopy.

PubMed

Mertz, Jerome; Lim, Daryl; Chu, Kengyeh K; Bozinovic, Nenad; Ford, Timothy

2009-01-01

HiLo microscopy is a widefield fluorescence imaging technique that provides depth discrimination by combining two images, one with non-uniform illumination and one with uniform illumination. We discuss the theory of this technique and a variety of practical implementations in brain-tissue imaging and fluorescence endomicroscopy.

Holographic techniques for cellular fluorescence microscopy

NASA Astrophysics Data System (ADS)

Kim, Myung K.

2017-04-01

We have constructed a prototype instrument for holographic fluorescence microscopy (HFM) based on self-interference incoherent digital holography (SIDH) and demonstrate novel imaging capabilities such as differential 3D fluorescence microscopy and optical sectioning by compressive sensing.

Teaching Plasmonics, Scanning Probe Microscopy and Other Useful Experiments at the Upper Level

NASA Astrophysics Data System (ADS)

Sanchez, Erik

2012-10-01

It is important to teach students concepts and experimental skills relating to modern research being performed today. Experiments that help educate students about the latest research helps them get jobs and into the doors at many great academic institutions. PSU's Advanced Experimental Class for physics undergraduates offers many novel experiments to help the students accomplish this task. Labs involving Plasmonics, thin film deposition, scanning probe microscopy (SPM) and more will be discussed. In addition, a new NSF funded project involving the building of a Do-It-Yourself (DIY) SPM will be discussed.

Non-invasive current and voltage imaging techniques for integrated circuits using scanning probe microscopy. Final report, LDRD Project FY93 and FY94

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, A.N.; Cole, E.I. Jr.; Tangyunyong, Paiboon

This report describes the first practical, non-invasive technique for detecting and imaging currents internal to operating integrated circuits (ICs). This technique is based on magnetic force microscopy and was developed under Sandia National Laboratories` LDRD (Laboratory Directed Research and Development) program during FY 93 and FY 94. LDRD funds were also used to explore a related technique, charge force microscopy, for voltage probing of ICs. This report describes the technical work performed under this LDRD as well as the outcomes of the project in terms of publications and awards, intellectual property and licensing, synergistic work, potential future work, hiring ofmore » additional permanent staff, and benefits to DOE`s defense programs (DP).« less

Molecular and Cellular Quantitative Microscopy: theoretical investigations, technological developments and applications to neurobiology

NASA Astrophysics Data System (ADS)

Esposito, Alessandro

2006-05-01

This PhD project aims at the development and evaluation of microscopy techniques for the quantitative detection of molecular interactions and cellular features. The primarily investigated techniques are Fαrster Resonance Energy Transfer imaging and Fluorescence Lifetime Imaging Microscopy. These techniques have the capability to quantitatively probe the biochemical environment of fluorophores. An automated microscope capable of unsupervised operation has been developed that enables the investigation of molecular and cellular properties at high throughput levels and the analysis of cellular heterogeneity. State-of-the-art Förster Resonance Energy Transfer imaging, Fluorescence Lifetime Imaging Microscopy, Confocal Laser Scanning Microscopy and the newly developed tools have been combined with cellular and molecular biology techniques for the investigation of protein-protein interactions, oligomerization and post-translational modifications of α-Synuclein and Tau, two proteins involved in Parkinson’s and Alzheimer’s disease, respectively. The high inter-disciplinarity of this project required the merging of the expertise of both the Molecular Biophysics Group at the Debye Institute - Utrecht University and the Cell Biophysics Group at the European Neuroscience Institute - Gαttingen University. This project was conducted also with the support and the collaboration of the Center for the Molecular Physiology of the Brain (Göttingen), particularly with the groups associated with the Molecular Quantitative Microscopy and Parkinson’s Disease and Aggregopathies areas. This work demonstrates that molecular and cellular quantitative microscopy can be used in combination with high-throughput screening as a powerful tool for the investigation of the molecular mechanisms of complex biological phenomena like those occurring in neurodegenerative diseases.

Diagnostic performance of direct wet mount microscopy in detecting intestinal helminths among pregnant women attending ante-natal care (ANC) in East Wollega, Oromia, Ethiopia.

PubMed

Mengist, Hylemariam Mihiretie; Demeke, Gebreselassie; Zewdie, Olifan; Belew, Adugna

2018-05-04

The aim of this study was to evaluate the diagnostic performance of direct wet mount microscopy compared to formalin ether concentration (FEC) technique in detecting intestinal helminths in pregnant women. The total prevalence of intestinal helminths was 18.8% (70/372) by direct wet mount microscopy and 24.7% (92/372) by FEC technique (P < 0.001). The sensitivity, negative predictive value (NPV) and test efficiency (TE) of direct wet mount microscopy in diagnosing intestinal helminths was 76, 92.7 and 94%, respectively. The sensitivity of direct w et mount microscopy was very low in detecting ova of Hymenolepis nana. The two methods showed excellent agreement in detecting ova of Hook worm and Ascaris lumbricoides (Kappa > 0.81) but they fairly agreed in detecting ova of Hymenolepis nana (Kappa = 0.39). Intestinal helminths were underdiagnosed and the total diagnostic performance of direct wet mount microscopy was significantly poor in detecting intestinal helminths as compared to FEC technique. Routine use of FEC method is recommended for the diagnosis of intestinal helminths in pregnant women.

Leakage radiation interference microscopy.

PubMed

Descrovi, Emiliano; Barakat, Elsie; Angelini, Angelo; Munzert, Peter; De Leo, Natascia; Boarino, Luca; Giorgis, Fabrizio; Herzig, Hans Peter

2013-09-01

We present a proof of principle for a new imaging technique combining leakage radiation microscopy with high-resolution interference microscopy. By using oil immersion optics it is demonstrated that amplitude and phase can be retrieved from optical fields, which are evanescent in air. This technique is illustratively applied for mapping a surface mode propagating onto a planar dielectric multilayer on a thin glass substrate. The surface mode propagation constant estimated after Fourier transformation of the measured complex field is well matched with an independent measurement based on back focal plane imaging.

Molecular expressions: exploring the world of optics and microscopy. http://microscopy.fsu.edu.

PubMed

Eliceiri, Kevin W

2004-08-01

Our knowledge of the structure, dynamics and physiology of a cell has increased significantly in the last ten years through the emergence of new optical imaging modalities such as optical sectioning microscopy, computer- enhanced video microscopy and laser-scanning microscopy. These techniques together with the use of genetically engineered fluorophores have helped scientists visualize the 3-dimensional dynamic processes of living cells. However as powerful as these imaging tools are, they can often be difficult to understand and fully utilize. Below I will discuss my favorite website: The Molecular Expressions Web Site that endeavors to present the power of microscopy to its visitors. The Molecular Expressions group does a remarkable job of not only clearly presenting the principles behind these techniques in a manner approachable by lay and scientific audiences alike but also provides representative data from each as well.

Virtual microscopy and digital pathology in training and education.

PubMed

Hamilton, Peter W; Wang, Yinhai; McCullough, Stephen J

2012-04-01

Traditionally, education and training in pathology has been delivered using textbooks, glass slides and conventional microscopy. Over the last two decades, the number of web-based pathology resources has expanded dramatically with centralized pathological resources being delivered to many students simultaneously. Recently, whole slide imaging technology allows glass slides to be scanned and viewed on a computer screen via dedicated software. This technology is referred to as virtual microscopy and has created enormous opportunities in pathological training and education. Students are able to learn key histopathological skills, e.g. to identify areas of diagnostic relevance from an entire slide, via a web-based computer environment. Students no longer need to be in the same room as the slides. New human-computer interfaces are also being developed using more natural touch technology to enhance the manipulation of digitized slides. Several major initiatives are also underway introducing online competency and diagnostic decision analysis using virtual microscopy and have important future roles in accreditation and recertification. Finally, researchers are investigating how pathological decision-making is achieved using virtual microscopy and modern eye-tracking devices. Virtual microscopy and digital pathology will continue to improve how pathology training and education is delivered. © 2012 The Authors APMIS © 2012 APMIS.

Characterization of microstructure and property evolution in advanced cladding and duct: Materials exposed to high dose and elevated temperature

DOE PAGES

Allen, Todd R.; Kaoumi, Djamel; Wharry, Janelle P.; ...

2015-05-20

Designing materials for performance in high-radiation fields can be accelerated through a carefully chosen combination of advanced multiscale modeling paired with appropriate experimental validation. Here, the studies reported in this work, the combined efforts of six universities working together as the Consortium on Cladding and Structural Materials, use that approach to focus on improving the scientific basis for the response of ferritic–martensitic steels to irradiation. A combination of modern modeling techniques with controlled experimentation has specifically focused on improving the understanding of radiation-induced segregation, precipitate formation and growth under radiation, the stability of oxide nanoclusters, and the development of dislocationmore » networks under radiation. Experimental studies use both model and commercial alloys, irradiated with both ion beams and neutrons. Lastly, transmission electron microscopy and atom probe are combined with both first-principles and rate theory approaches to advance the understanding of ferritic–martensitic steels.« less

Single-shot full resolution region-of-interest (ROI) reconstruction in image plane digital holographic microscopy

NASA Astrophysics Data System (ADS)

Singh, Mandeep; Khare, Kedar

2018-05-01

We describe a numerical processing technique that allows single-shot region-of-interest (ROI) reconstruction in image plane digital holographic microscopy with full pixel resolution. The ROI reconstruction is modelled as an optimization problem where the cost function to be minimized consists of an L2-norm squared data fitting term and a modified Huber penalty term that are minimized alternately in an adaptive fashion. The technique can provide full pixel resolution complex-valued images of the selected ROI which is not possible to achieve with the commonly used Fourier transform method. The technique can facilitate holographic reconstruction of individual cells of interest from a large field-of-view digital holographic microscopy data. The complementary phase information in addition to the usual absorption information already available in the form of bright field microscopy can make the methodology attractive to the biomedical user community.

Nonlinear dynamic phase contrast microscopy for microfluidic and microbiological applications

NASA Astrophysics Data System (ADS)

Denz, C.; Holtmann, F.; Woerdemann, M.; Oevermann, M.

2008-08-01

In live sciences, the observation and analysis of moving living cells, molecular motors or motion of micro- and nano-objects is a current field of research. At the same time, microfluidic innovations are needed for biological and medical applications on a micro- and nano-scale. Conventional microscopy techniques are reaching considerable limits with respect to these issues. A promising approach for this challenge is nonlinear dynamic phase contrast microscopy. It is an alternative full field approach that allows to detect motion as well as phase changes of living unstained micro-objects in real-time, thereby being marker free, without contact and non destructive, i.e. fully biocompatible. The generality of this system allows it to be combined with several other microscope techniques such as conventional bright field or fluorescence microscopy. In this article we will present the dynamic phase contrast technique and its applications in analysis of micro organismic dynamics, micro flow velocimetry and micro-mixing analysis.

Going glass to digital: virtual microscopy as a simulation-based revolution in pathology and laboratory science.

PubMed

Nelson, Danielle; Ziv, Amitai; Bandali, Karim S

2012-10-01

The recent technological advance of digital high resolution imaging has allowed the field of pathology and medical laboratory science to undergo a dramatic transformation with the incorporation of virtual microscopy as a simulation-based educational and diagnostic tool. This transformation has correlated with an overall increase in the use of simulation in medicine in an effort to address dwindling clinical resource availability and patient safety issues currently facing the modern healthcare system. Virtual microscopy represents one such simulation-based technology that has the potential to enhance student learning and readiness to practice while revolutionising the ability to clinically diagnose pathology collaboratively across the world. While understanding that a substantial amount of literature already exists on virtual microscopy, much more research is still required to elucidate the full capabilities of this technology. This review explores the use of virtual microscopy in medical education and disease diagnosis with a unique focus on key requirements needed to take this technology to the next level in its use in medical education and clinical practice.

Republished: going glass to digital: virtual microscopy as a simulation-based revolution in pathology and laboratory science.

PubMed

Nelson, Danielle; Ziv, Amitai; Bandali, Karim S

2013-10-01

The recent technological advance of digital high resolution imaging has allowed the field of pathology and medical laboratory science to undergo a dramatic transformation with the incorporation of virtual microscopy as a simulation-based educational and diagnostic tool. This transformation has correlated with an overall increase in the use of simulation in medicine in an effort to address dwindling clinical resource availability and patient safety issues currently facing the modern healthcare system. Virtual microscopy represents one such simulation-based technology that has the potential to enhance student learning and readiness to practice while revolutionising the ability to clinically diagnose pathology collaboratively across the world. While understanding that a substantial amount of literature already exists on virtual microscopy, much more research is still required to elucidate the full capabilities of this technology. This review explores the use of virtual microscopy in medical education and disease diagnosis with a unique focus on key requirements needed to take this technology to the next level in its use in medical education and clinical practice.

A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images

PubMed Central

Afshar, Yaser; Sbalzarini, Ivo F.

2016-01-01

Modern fluorescence microscopy modalities, such as light-sheet microscopy, are capable of acquiring large three-dimensional images at high data rate. This creates a bottleneck in computational processing and analysis of the acquired images, as the rate of acquisition outpaces the speed of processing. Moreover, images can be so large that they do not fit the main memory of a single computer. We address both issues by developing a distributed parallel algorithm for segmentation of large fluorescence microscopy images. The method is based on the versatile Discrete Region Competition algorithm, which has previously proven useful in microscopy image segmentation. The present distributed implementation decomposes the input image into smaller sub-images that are distributed across multiple computers. Using network communication, the computers orchestrate the collectively solving of the global segmentation problem. This not only enables segmentation of large images (we test images of up to 1010 pixels), but also accelerates segmentation to match the time scale of image acquisition. Such acquisition-rate image segmentation is a prerequisite for the smart microscopes of the future and enables online data compression and interactive experiments. PMID:27046144

A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images.

PubMed

Afshar, Yaser; Sbalzarini, Ivo F

2016-01-01

Modern fluorescence microscopy modalities, such as light-sheet microscopy, are capable of acquiring large three-dimensional images at high data rate. This creates a bottleneck in computational processing and analysis of the acquired images, as the rate of acquisition outpaces the speed of processing. Moreover, images can be so large that they do not fit the main memory of a single computer. We address both issues by developing a distributed parallel algorithm for segmentation of large fluorescence microscopy images. The method is based on the versatile Discrete Region Competition algorithm, which has previously proven useful in microscopy image segmentation. The present distributed implementation decomposes the input image into smaller sub-images that are distributed across multiple computers. Using network communication, the computers orchestrate the collectively solving of the global segmentation problem. This not only enables segmentation of large images (we test images of up to 10(10) pixels), but also accelerates segmentation to match the time scale of image acquisition. Such acquisition-rate image segmentation is a prerequisite for the smart microscopes of the future and enables online data compression and interactive experiments.

Aberrations and adaptive optics in super-resolution microscopy

PubMed Central

Booth, Martin; Andrade, Débora; Burke, Daniel; Patton, Brian; Zurauskas, Mantas

2015-01-01

As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy – or rather nanoscopy – to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem. PMID:26124194

Collection efficiency and acceptance maps of electron detectors for understanding signal detection on modern scanning electron microscopy.

PubMed

Agemura, Toshihide; Sekiguchi, Takashi

2018-02-01

Collection efficiency and acceptance maps of typical detectors in modern scanning electron microscopes (SEMs) were investigated. Secondary and backscattered electron trajectories from a specimen to through-the-lens and under-the-lens detectors placed on an electron optical axis and an Everhart-Thornley detector mounted on a specimen chamber were simulated three-dimensionally. The acceptance maps were drawn as the relationship between the energy and angle of collected electrons under different working distances. The collection efficiency considering the detector sensitivity was also estimated for the various working distances. These data indicated that the acceptance maps and collection efficiency are keys to understand the detection mechanism and image contrast for each detector in the modern SEMs. Furthermore, the working distance is the dominant parameter because electron trajectories are drastically changed with the working distance.

Tackling the Challenges of Dynamic Experiments Using Liquid-Cell Transmission Electron Microscopy.

PubMed

Parent, Lucas R; Bakalis, Evangelos; Proetto, Maria; Li, Yiwen; Park, Chiwoo; Zerbetto, Francesco; Gianneschi, Nathan C

2018-01-16

Revolutions in science and engineering frequently result from the development, and wide adoption, of a new, powerful characterization or imaging technique. Beginning with the first glass lenses and telescopes in astronomy, to the development of visual-light microscopy, staining techniques, confocal microscopy, and fluorescence super-resolution microscopy in biology, and most recently aberration-corrected, cryogenic, and ultrafast (4D) electron microscopy, X-ray microscopy, and scanning probe microscopy in nanoscience. Through these developments, our perception and understanding of the physical nature of matter at length-scales beyond ordinary perception have been fundamentally transformed. Despite this progression in microscopy, techniques for observing nanoscale chemical processes and solvated/hydrated systems are limited, as the necessary spatial and temporal resolution presents significant technical challenges. However, the standard reliance on indirect or bulk phase characterization of nanoscale samples in liquids is undergoing a shift in recent times with the realization ( Williamson et al. Nat. Mater . 2003 , 2 , 532 - 536 ) of liquid-cell (scanning) transmission electron microscopy, LC(S)TEM, where picoliters of solution are hermetically sealed between electron-transparent "windows," which can be directly imaged or videoed at the nanoscale using conventional transmission electron microscopes. This Account seeks to open a discussion on the topic of standardizing strategies for conducting imaging experiments with a view to characterizing dynamics and motion of nanoscale materials. This is a challenge that could be described by critics and proponents alike, as analogous to doing chemistry in a lightning storm; where the nature of the solution, the nanomaterial, and the dynamic behaviors are all potentially subject to artifactual influence by the very act of our observation.

"Reinventing" Techniques for the Estimation of the Area of Irregular Plane Figures: From the Eighteenth Century to the Modern Classroom

ERIC Educational Resources Information Center

Papadopoulos, Ioannis

2010-01-01

The issue of the area of irregular shapes is absent from the modern mathematical textbooks in elementary education in Greece. However, there exists a collection of books written for educational purposes by famous Greek scholars dating from the eighteenth century, which propose certain techniques concerning the estimation of the area of such…

Micro-Eukaryote Diversity in Freshwater Ponds That Harbor the Amphibian Pathogen "Batrachochytrium Dendrobatidis" ("Bd")

ERIC Educational Resources Information Center

Lauer, Antje; McConnel, Lonnie; Singh, Navdeep

2012-01-01

We designed a microbiology project that fully engaged undergraduate biology students, high school students, and their teachers in a summer research program as part of the Research Education Vitalizing Science University Program conducted at California State University Bakersfield. Modern molecular biological methods and microscopy were used to…

Engaging Students in Early Exploration of Nanoscience Topics Using Hands-On Activities and Scanning Tunneling Microscopy

ERIC Educational Resources Information Center

Furlan, Ping Y.

2009-01-01

This manuscript reports on efforts to introduce beginning college students to the modern nanoscience field. These include: implementing selected experiments into sequencing core first-year and second-year chemistry laboratory courses; providing students with a first research experience; and engaging them in service learning and outreach programs…

Detection of stiff nanoparticles within cellular structures by contact resonance atomic force microscopy subsurface nanomechanical imaging.

PubMed

Reggente, Melania; Passeri, Daniele; Angeloni, Livia; Scaramuzzo, Francesca Anna; Barteri, Mario; De Angelis, Francesca; Persiconi, Irene; De Stefano, Maria Egle; Rossi, Marco

2017-05-04

Detecting stiff nanoparticles buried in soft biological matrices by atomic force microscopy (AFM) based techniques represents a new frontier in the field of scanning probe microscopies, originally developed as surface characterization methods. Here we report the detection of stiff (magnetic) nanoparticles (NPs) internalized in cells by using contact resonance AFM (CR-AFM) employed as a potentially non-destructive subsurface characterization tool. Magnetite (Fe 3 O 4 ) NPs were internalized in microglial cells from cerebral cortices of mouse embryos of 18 days by phagocytosis. Nanomechanical imaging of cells was performed by detecting the contact resonance frequencies (CRFs) of an AFM cantilever held in contact with the sample. Agglomerates of NPs internalized in cells were visualized on the basis of the local increase in the contact stiffness with respect to the surrounding biological matrix. A second AFM-based technique for nanomechanical imaging, i.e., HarmoniX™, as well as magnetic force microscopy and light microscopy were used to confirm the CR-AFM results. Thus, CR-AFM was demonstrated as a promising technique for subsurface imaging of nanomaterials in biological samples.

Quantitative Aspects of Single Molecule Microscopy

PubMed Central

Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

2015-01-01

Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

Gamete competence assessment by polarizing optics in assisted reproduction.

PubMed

Montag, Markus; Köster, Maria; van der Ven, Katrin; van der Ven, Hans

2011-01-01

The purpose of this study was first to give an overview of the historical development of polarization microscopy, second to describe the various applications of this technique in assisted reproduction techniques (ART) and third to discuss the potential benefit of polarization microscopy as a predictor for IVF success. The history of polarization microscopy was undertaken by performing a backward search in the scientific literature using Google and internet sites of several Societies for Microscopy and Cell Biology. Studies of polarization microscopy in ART were identified by using a systematic literature search in PubMed and Scopus. A total of 62 articles were identified by the direct search and further relevant articles were found by screening the cited literature in these articles. The topics relevant for assisted reproduction were spindle and zona imaging in combination with IVF success, meiotic cell cycle progression, pharmaceutical studies and cryopreservation. A separate topic was the use of sperm birefringence in ART. The majority of studies are observational studies and were not performed in a randomized manner and there is no direct comparison of techniques using other gamete selection markers. Despite this, most studies show that polarization microscopy may help us to further increase our knowledge on gametes and meiosis. Whether certain applications such as spindle or zona imaging may lead to an increase in IVF success is unclear at present. Publications on the use of polarization microscopy on sperm are still very limited.

Comparative measurement of collagen bundle orientation by Fourier analysis and semiquantitative evaluation: reliability and agreement in Masson's trichrome, Picrosirius red and confocal microscopy techniques.

PubMed

Marcos-Garcés, V; Harvat, M; Molina Aguilar, P; Ferrández Izquierdo, A; Ruiz-Saurí, A

2017-08-01

Measurement of collagen bundle orientation in histopathological samples is a widely used and useful technique in many research and clinical scenarios. Fourier analysis is the preferred method for performing this measurement, but the most appropriate staining and microscopy technique remains unclear. Some authors advocate the use of Haematoxylin-Eosin (H&E) and confocal microscopy, but there are no studies comparing this technique with other classical collagen stainings. In our study, 46 human skin samples were collected, processed for histological analysis and stained with Masson's trichrome, Picrosirius red and H&E. Five microphotographs of the reticular dermis were taken with a 200× magnification with light microscopy, polarized microscopy and confocal microscopy, respectively. Two independent observers measured collagen bundle orientation with semiautomated Fourier analysis with the Image-Pro Plus 7.0 software and three independent observers performed a semiquantitative evaluation of the same parameter. The average orientation for each case was calculated with the values of the five pictures. We analyzed the interrater reliability, the consistency between Fourier analysis and average semiquantitative evaluation and the consistency between measurements in Masson's trichrome, Picrosirius red and H&E-confocal. Statistical analysis for reliability and agreement was performed with the SPSS 22.0 software and consisted of intraclass correlation coefficient (ICC), Bland-Altman plots and limits of agreement and coefficient of variation. Interrater reliability was almost perfect (ICC > 0.8) with all three histological and microscopy techniques and always superior in Fourier analysis than in average semiquantitative evaluation. Measurements were consistent between Fourier analysis by one observer and average semiquantitative evaluation by three observers, with an almost perfect agreement with Masson's trichrome and Picrosirius red techniques (ICC > 0.8) and a strong agreement with H&E-confocal (0.7 < ICC < 0.8). Comparison of measurements between the three techniques for the same observer showed an almost perfect agreement (ICC > 0.8), better with Fourier analysis than with semiquantitative evaluation (single and average). These results in nonpathological skin samples were also confirmed in a preliminary analysis in eight scleroderma skin samples. Our results show that Masson's trichrome and Picrosirius red are consistent with H&E-confocal for measuring collagen bundle orientation in histological samples and could thus be used indistinctly for this purpose. Fourier analysis is superior to average semiquantitative evaluation and should keep being used as the preferred method. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Demonstration of transmission high energy electron microscopy

DOE PAGES

Merrill, F. E.; Goett, J.; Gibbs, J. W.; ...

2018-04-06

High energy electrons have been used to investigate an extension of transmission electron microscopy. This technique, transmission high energy electron microscopy (THEEM), provides two additional capabilities to electron microscopy. First, high energy electrons are more penetrating than low energy electrons, and thus, they are able to image through thicker samples. Second, the accelerating mode of a radio-frequency linear accelerator provides fast exposures, down to 1 ps, which are ideal for flash radiography, making THEEM well suited to study the evolution of fast material processes under dynamic conditions. Lastly, initial investigations with static objects and during material processing have been performedmore » to investigate the capabilities of this technique.« less

Open-source do-it-yourself multi-color fluorescence smartphone microscopy

PubMed Central

Sung, Yulung; Campa, Fernando; Shih, Wei-Chuan

2017-01-01

Fluorescence microscopy is an important technique for cellular and microbiological investigations. Translating this technique onto a smartphone can enable particularly powerful applications such as on-site analysis, on-demand monitoring, and point-of-care diagnostics. Current fluorescence smartphone microscope setups require precise illumination and imaging alignment which altogether limit its broad adoption. We report a multi-color fluorescence smartphone microscope with a single contact lens-like add-on lens and slide-launched total-internal-reflection guided illumination for three common tasks in investigative fluorescence microscopy: autofluorescence, fluorescent stains, and immunofluorescence. The open-source, simple and cost-effective design has the potential for do-it-yourself fluorescence smartphone microscopy. PMID:29188104

Coherent nonlinear optical imaging: beyond fluorescence microscopy.

PubMed

Min, Wei; Freudiger, Christian W; Lu, Sijia; Xie, X Sunney

2011-01-01

The quest for ultrahigh detection sensitivity with spectroscopic contrasts other than fluorescence has led to various novel approaches to optical microscopy of biological systems. Coherent nonlinear optical imaging, especially the recently developed nonlinear dissipation microscopy (including stimulated Raman scattering and two-photon absorption) and pump-probe microscopy (including excited-state absorption, stimulated emission, and ground-state depletion), provides new image contrasts for nonfluorescent species. Thanks to the high-frequency modulation transfer scheme, these imaging techniques exhibit superb detection sensitivity. By directly interrogating vibrational and/or electronic energy levels of molecules, they offer high molecular specificity. Here we review the underlying principles and excitation and detection schemes, as well as exemplary biomedical applications of this emerging class of molecular imaging techniques.

Use of Kelvin probe force microscopy for identification of CVD grown graphene flakes on copper foil

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Mehta, B. R.; Kanjilal, D.

2017-05-01

Graphene flakes have been grown by chemical vapour deposition (CVD) method on Cu foils. The obtained graphene flakes have been characterized by optical microscopy, field emission scanning electron microscopy, Kelvin probe force microscopy (KPFM) and Raman spectroscopy. The graphene flakes grown on Cu foil comprise mainly single layer graphene and confirm that the nucleation for graphene growth starts very quickly. Moreover, KPFM has been found to be a valuable technique to differentiate between covered and uncovered portion of Cu foil by graphene flakes deposited for shorter duration. The results show that KPFM can be a very useful technique in understanding the mechanism of graphene growth.

Airborne asbestos in Colorado public schools.

PubMed

Chadwick, D A; Buchan, R M; Beaulieu, H J

1985-02-01

Levels of airborne asbestos for six Colorado public school facilities with sprayed-on asbestos materials were documented using three analytical techniques. Phase contrast microscopy showed levels up to the thousandths of a fiber per cubic centimeter (f/cc), scanning electron microscopy (SEM) up to the hundredths of a f/cc, and transmission electron microscopy coupled to selected area electron diffraction and energy dispersive X-ray analysis (TEM-SAED-EDXA) up to the tenths of an asbestos f/cc. Phase contrast microscopy was found to be an inadequate analytical technique for documenting the levels of airborne asbestos fibers in the schools: only large fibers which were not embedded in the filter were counted, and asbestos fibers were not distinguished from nonasbestos.

Laser beam shaping for biomedical microscopy techniques

NASA Astrophysics Data System (ADS)

Laskin, Alexander; Kaiser, Peter; Laskin, Vadim; Ostrun, Aleksei

2016-04-01

Uniform illumination of a working field is very important in optical systems of confocal microscopy and various implementations of fluorescence microscopy like TIR, SSIM, STORM, PALM to enhance performance of these laser-based research techniques. Widely used TEM00 laser sources are characterized by essentially non-uniform Gaussian intensity profile which leads usually to non-uniform intensity distribution in a microscope working field or in a field of microlenses array of a confocal microscope optical system, this non-uniform illumination results in instability of measuring procedure and reducing precision of quantitative measurements. Therefore transformation of typical Gaussian distribution of a TEM00 laser to flat-top (top hat) profile is an actual technical task, it is solved by applying beam shaping optics. Due to high demands to optical image quality the mentioned techniques have specific requirements to a uniform laser beam: flatness of phase front and extended depth of field, - from this point of view the microscopy techniques are similar to holography and interferometry. There are different refractive and diffractive beam shaping approaches used in laser industrial and scientific applications, but only few of them are capable to fulfil the optimum conditions for beam quality required in discussed microscopy techniques. We suggest applying refractive field mapping beam shapers πShaper, which operational principle presumes almost lossless transformation of Gaussian to flat-top beam with flatness of output wavefront, conserving of beam consistency, providing collimated low divergent output beam, high transmittance, extended depth of field, negligible wave aberration, and achromatic design provides capability to work with several lasers with different wavelengths simultaneously. The main function of a beam shaper is transformation of laser intensity profile, further beam transformation to provide optimum for a particular technique spot size and shape has to be realized by an imaging optical system which can include microscope objectives and tube lenses. This paper will describe design basics of refractive beam shapers and optical layouts of their applying in microscopy systems. Examples of real implementations and experimental results will be presented as well.

Application of high-angle annular dark field scanning transmission electron microscopy, scanning transmission electron microscopy-energy dispersive X-ray spectrometry, and energy-filtered transmission electron microscopy to the characterization of nanoparticles in the environment.

PubMed

Utsunomiya, Satoshi; Ewing, Rodney C

2003-02-15

A major challenge to the development of a fundamental understanding of transport and retardation mechanisms of trace metal contaminants (<10 ppm) is their identification and characterization at the nanoscale. Atomic-scale techniques, such as conventional transmission electron microscopy, although powerful, are limited by the extremely small amounts of material that are examined. However, recent advances in electron microscopy provide a number of new analytical techniques that expand its application in environmental studies, particularly those concerning heavy metals on airborne particulates or water-borne colloids. High-angle annular dark field scanning transmission electron microscopy (HAADF-STEM), STEM-energy-dispersive X-ray spectrometry (EDX), and energy-filtered TEM (EFTEM) can be effectively used to identify and characterize nanoparticles. The image contrast in HAADF-STEM is strongly correlated to the atomic mass: heavier elements contribute to brighter contrast. Gold nanocrystals in pyrite and uranium nanocrystals in atmospheric aerosols have been identified by HAADF-STEM and STEM-EDX mapping and subsequently characterized by high-resolution TEM (HRTEM). EFTEM was used to identify U and Fe nanocrystals embedded in an aluminosilicate. A rare, As-bearing nanophase, westerveldite (FeAs), was identified by STEM-EDX and HRTEM. The combined use of these techniques greatly expands the effective application of electron microscopy in environmental studies, especially when applied to metals of very low concentrations. This paper describes examples of how these electron microbeam techniques can be used in combination to characterize a low concentration of heavy metals (a few ppm) on nanoscale particles.

Applications of microscopy in Salmonella research.

PubMed

Malt, Layla M; Perrett, Charlotte A; Humphrey, Suzanne; Jepson, Mark A

2015-01-01

Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals. Understanding the mechanisms by which Salmonella induces disease has been the focus of intensive research. This has revealed that Salmonella invasion requires dynamic cross-talk between the microbe and host cells, in which bacterial adherence rapidly leads to a complex sequence of cellular responses initiated by proteins translocated into the host cell by a type 3 secretion system. Once these Salmonella-induced responses have resulted in bacterial invasion, proteins translocated by a second type 3 secretion system initiate further modulation of cellular activities to enable survival and replication of the invading pathogen. Elucidation of the complex and highly dynamic pathogen-host interactions ultimately requires analysis at the level of single cells and single infection events. To achieve this goal, researchers have applied a diverse range of microscopy techniques to analyze Salmonella infection in models ranging from whole animal to isolated cells and simple eukaryotic organisms. For example, electron microscopy and high-resolution light microscopy techniques such as confocal microscopy can reveal the precise location of Salmonella and its relationship to cellular components. Widefield light microscopy is a simpler approach with which to study the interaction of bacteria with host cells and often has advantages for live cell imaging, enabling detailed analysis of the dynamics of infection and cellular responses. Here we review the use of imaging techniques in Salmonella research and compare the capabilities of different classes of microscope to address specific types of research question. We also provide protocols and notes on some microscopy techniques used routinely in our own research.

Feasibility of Tactical Air Delivery Resupply Using Gliders

DTIC Science & Technology

2016-12-01

using modern design and manufacturing techniques including AutoCAD, 3D printing , laser cutting and CorelDraw, and conducting field testing and...Sparrow,” using modern design and manufacturing techniques including AutoCAD, 3D printing , laser cutting and CorelDraw, and conducting field testing and...the desired point(s) of impact due to the atmospheric three-dimensional ( 3D ) wind and density field encountered by the descending load under canopy

Development of Self-made LSM Software using in Neuroscience

NASA Astrophysics Data System (ADS)

Doronin, Maxim; Makovkin, Sergey; Popov, Alexander

2017-07-01

One of the main and modern visualization method in neuroscience is two-photon microscopy. However, scientists need to upgrade their microscopy system so regular because they are interested to get more specific data. Self-developed microscopy system allows to modify the construction of microscope in not-complicated manner depending on specialized experimental models and scientific tasks. Earlier we reported about building of self-made laser scanning microscope (LSM) using in neuroscience both for in vivo and in vitro experiments. Here we will report how to create software AMAScan for LSM controlling in MATLAB. The work was performed with financial support of the government represented by the Ministry of Education and Science of the Russian Federation, the unique identifier of the project is RFMEFI58115X0016, the agreement on granting a subsidy №14.581.21.0016 dated 14.10.2015.

Use of synchrotron tomography to image naturalistic anatomy in insects

NASA Astrophysics Data System (ADS)

Socha, John J.; De Carlo, Francesco

2008-08-01

Understanding the morphology of anatomical structures is a cornerstone of biology. For small animals, classical methods such as histology have provided a wealth of data, but such techniques can be problematic due to destruction of the sample. More importantly, fixation and physical slicing can cause deformation of anatomy, a critical limitation when precise three-dimensional data are required. Modern techniques such as confocal microscopy, MRI, and tabletop x-ray microCT provide effective non-invasive methods, but each of these tools each has limitations including sample size constraints, resolution limits, and difficulty visualizing soft tissue. Our research group at the Advanced Photon Source (Argonne National Laboratory) studies physiological processes in insects, focusing on the dynamics of breathing and feeding. To determine the size, shape, and relative location of internal anatomy in insects, we use synchrotron microtomography at the beamline 2-BM to image structures including tracheal tubes, muscles, and gut. Because obtaining naturalistic, undeformed anatomical information is a key component of our studies, we have developed methods to image fresh and non-fixed whole animals and tissues. Although motion artifacts remain a problem, we have successfully imaged multiple species including beetles, ants, fruit flies, and butterflies. Here we discuss advances in biological imaging and highlight key findings in insect morphology.

Optical sectioning microscopes with no moving parts using a micro-stripe array light emitting diode.

PubMed

Poher, V; Zhang, H X; Kennedy, G T; Griffin, C; Oddos, S; Gu, E; Elson, D S; Girkin, M; French, P M W; Dawson, M D; Neil, M A

2007-09-03

We describe an optical sectioning microscopy system with no moving parts based on a micro-structured stripe-array light emitting diode (LED). By projecting arbitrary line or grid patterns onto the object, we are able to implement a variety of optical sectioning microscopy techniques such as grid-projection structured illumination and line scanning confocal microscopy, switching from one imaging technique to another without modifying the microscope setup. The micro-structured LED and driver are detailed and depth discrimination capabilities are measured and calculated.

Multilayer mounting for long-term light sheet microscopy of zebrafish.

PubMed

Weber, Michael; Mickoleit, Michaela; Huisken, Jan

2014-02-27

Light sheet microscopy is the ideal imaging technique to study zebrafish embryonic development. Due to minimal photo-toxicity and bleaching, it is particularly suited for long-term time-lapse imaging over many hours up to several days. However, an appropriate sample mounting strategy is needed that offers both confinement and normal development of the sample. Multilayer mounting, a new embedding technique using low-concentration agarose in optically clear tubes, now overcomes this limitation and unleashes the full potential of light sheet microscopy for real-time developmental biology.

Immunoelectron Microscopy of Cryofixed and Freeze-Substituted Plant Tissues.

PubMed

Takeuchi, Miyuki; Takabe, Keiji; Mineyuki, Yoshinobu

2016-01-01

Cryofixation and freeze-substitution techniques provide excellent preservation of plant ultrastructure. The advantage of cryofixation is not only in structural preservation, as seen in the smooth plasma membrane, but also in the speed in arresting cell activity. Immunoelectron microscopy reveals the subcellular localization of molecules within cells. Immunolabeling in combination with cryofixation and freeze-substitution techniques provides more detailed information on the immunoelectron-microscopic localization of molecules in the plant cell than can be obtained from chemically fixed tissues. Here, we introduce methods for immunoelectron microscopy of cryofixed and freeze-substituted plant tissues.

Single-Shot Optical Sectioning Using Two-Color Probes in HiLo Fluorescence Microscopy

PubMed Central

Muro, Eleonora; Vermeulen, Pierre; Ioannou, Andriani; Skourides, Paris; Dubertret, Benoit; Fragola, Alexandra; Loriette, Vincent

2011-01-01

We describe a wide-field fluorescence microscope setup which combines HiLo microscopy technique with the use of a two-color fluorescent probe. It allows one-shot fluorescence optical sectioning of thick biological moving sample which is illuminated simultaneously with a flat and a structured pattern at two different wavelengths. Both homogenous and structured fluorescence images are spectrally separated at detection and combined similarly with the HiLo microscopy technique. We present optically sectioned full-field images of Xenopus laevis embryos acquired at 25 images/s frame rate. PMID:21641327

Correlative light-electron fractography for fatigue striations characterization in metallic alloys.

PubMed

Hein, Luis Rogerio de Oliveira; de Oliveira, José Alberto; de Campos, Kamila Amato

2013-09-01

The correlative light-electron fractography technique combines correlative microscopy concepts to the extended depth-from-focus reconstruction method, associating the reliable topographic information of 3-D maps from light microscopy ordered Z-stacks to the finest lateral resolution and large focus depth from scanning electron microscopy. Fatigue striations spacing analysis can be precisely measured, by correcting the mean surface tilting with the knowledge of local elevation data from elevation maps. This new technique aims to improve the accuracy of quantitative fractography in fatigue fracture investigations. Copyright © 2013 Wiley Periodicals, Inc.

Multilayer Mounting for Long-term Light Sheet Microscopy of Zebrafish

PubMed Central

Weber, Michael; Mickoleit, Michaela; Huisken, Jan

2014-01-01

Light sheet microscopy is the ideal imaging technique to study zebrafish embryonic development. Due to minimal photo-toxicity and bleaching, it is particularly suited for long-term time-lapse imaging over many hours up to several days. However, an appropriate sample mounting strategy is needed that offers both confinement and normal development of the sample. Multilayer mounting, a new embedding technique using low-concentration agarose in optically clear tubes, now overcomes this limitation and unleashes the full potential of light sheet microscopy for real-time developmental biology. PMID:24637614

Modern Education in China. Bulletin, 1919, No. 44

ERIC Educational Resources Information Center

Edmunds, Charles K.

1919-01-01

The Chinese conception of life's values is so different from that of western peoples that they have failed to develop modern technique and scientific knowledge. Now that they have come to see the value of these, rapid and fundamental changes are taking place. When modern scientific knowledge is added to the skill which the Chinese already have in…

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

PubMed Central

Neuman, Keir C.; Nagy, Attila

2012-01-01

Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations. PMID:18511917

Fourier ptychographic microscopy at telecommunication wavelengths using a femtosecond laser

NASA Astrophysics Data System (ADS)

Ahmed, Ishtiaque; Alotaibi, Maged; Skinner-Ramos, Sueli; Dominguez, Daniel; Bernussi, Ayrton A.; de Peralta, Luis Grave

2017-12-01

We report the implementation of the Fourier Ptychographic Microscopy (FPM) technique, a phase retrieval technique, at telecommunication wavelengths using a low-coherence ultrafast pulsed laser source. High quality images, near speckle-free, were obtained with the proposed approach. We demonstrate that FPM can also be used to image periodic features through a silicon wafer.

A profile of the demographics and training characteristics of professional modern dancers.

PubMed

Weiss, David S; Shah, Selina; Burchette, Raoul J

2008-01-01

Modern dancers are a unique group of artists, performing a diverse repertoire in dance companies of various sizes. In this study, 184 professional modern dancers in the United States (males N=49, females N=135), including members of large and small companies as well as freelance dancers, were surveyed regarding their demographics and training characteristics. The mean age of the dancers was 30.1 +/- 7.3 years, and they had danced professionally for 8.9 +/- 7.2 years. The average Body Mass Index (BMI) was 23.6 +/- 2.4 for males and 20.5 +/- 1.7 for females. Females had started taking dance class earlier (age 6.5 +/- 4.2 years) as compared to males (age 15.6 +/- 6.2 years). Females were more likely to have begun their training in ballet, while males more often began with modern classes (55% and 51% respectively, p < 0.0001). The professional modern dancers surveyed spent 8.3 +/- 6.0 hours in class and 17.2 +/- 12.6 hours in rehearsal each week. Eighty percent took modern technique class and 67% reported that they took ballet technique class. The dancers who specified what modern technique they studied (N=84) reported between two and four different techniques. The dancers also participated in a multitude of additional exercise regimens for a total of 8.2 +/- 6.6 hours per week, with the most common types being Pilates, yoga, and upper body weightlifting. The dancers wore many different types of footwear, depending on the style of dance being performed. For modern dance alone, dancers wore 12 different types of footwear. Reflecting the diversity of the dancers and companies surveyed, females reported performing for 23.3 +/- 14.0 weeks (range: 2-52 weeks) per year; males reported performing 20.4 +/- 13.9 weeks (range: 1-40) per year. Only 18% of the dancers did not have any health insurance, with 54% having some type of insurance provided by their employer. However, 23% of the dancers purchased their own insurance, and 22% had insurance provided by their families. Only 16% of dancers reported that they had Workers' Compensation coverage, despite the fact that they were all professionals, including many employed by major modern dance companies across the United States. It is concluded that understanding the training profile of the professional modern dancer should assist healthcare providers in supplying appropriate medical care for these performers.

NDE of structural ceramics

NASA Technical Reports Server (NTRS)

Klima, S. J.; Vary, A.

1986-01-01

Radiographic, ultrasonic, scanning laser acoustic microscopy (SLAM), and thermo-acoustic microscopy techniques were used to characterize silicon nitride and silicon carbide modulus-of-rupture test specimens in various stages of fabrication. Conventional and microfocus X-ray techniques were found capable of detecting minute high density inclusions in as-received powders, green compacts, and fully densified specimens. Significant density gradients in sintered bars were observed by radiography, ultrasonic velocity, and SLAM. Ultrasonic attenuation was found sensitive to microstructural variations due to grain and void morphology and distribution. SLAM was also capable of detecting voids, inclusions and cracks in finished test bars. Consideration is given to the potential for applying thermo-acoustic microscopy techniques to green and densified ceramics. The detection probability statistics and some limitations of radiography and SLAM also are discussed.

Looking ahead in systems engineering

NASA Technical Reports Server (NTRS)

Feigenbaum, Donald S.

1966-01-01

Five areas that are discussed in this paper are: (1) the technological characteristics of systems engineering; (2) the analytical techniques that are giving modern systems work its capability and power; (3) the management, economics, and effectiveness dimensions that now frame the modern systems field; (4) systems engineering's future impact upon automation, computerization and managerial decision-making in industry - and upon aerospace and weapons systems in government and the military; and (5) modern systems engineering's partnership with modern quality control and reliability.

High-resolution measurements of the multilayer ultra-structure of articular cartilage and their translational potential

PubMed Central

2014-01-01

Current musculoskeletal imaging techniques usually target the macro-morphology of articular cartilage or use histological analysis. These techniques are able to reveal advanced osteoarthritic changes in articular cartilage but fail to give detailed information to distinguish early osteoarthritis from healthy cartilage, and this necessitates high-resolution imaging techniques measuring cells and the extracellular matrix within the multilayer structure of articular cartilage. This review provides a comprehensive exploration of the cellular components and extracellular matrix of articular cartilage as well as high-resolution imaging techniques, including magnetic resonance image, electron microscopy, confocal laser scanning microscopy, second harmonic generation microscopy, and laser scanning confocal arthroscopy, in the measurement of multilayer ultra-structures of articular cartilage. This review also provides an overview for micro-structural analysis of the main components of normal or osteoarthritic cartilage and discusses the potential and challenges associated with developing non-invasive high-resolution imaging techniques for both research and clinical diagnosis of early to late osteoarthritis. PMID:24946278

Evidence and role of phlebitis and lipid infiltration in the onset and pathogenesis of Wooden Breast Disease in modern broiler chickens.

PubMed

Papah, Michael B; Brannick, Erin M; Schmidt, Carl J; Abasht, Behnam

2017-12-01

Wooden Breast Disease (WBD), a myopathy that frequently affects modern broiler chickens, is a disorder that has been associated with significant economic losses in the poultry industry. To examine tissue changes associated with the onset and early pathogenesis of this disorder, a time-series experiment was conducted using chickens from a high-breast-muscle-yield, purebred commercial broiler line. Birds were raised for up to seven weeks, with a subset of birds sampled weekly. Breast muscle tissues were extracted at necropsy and processed for analysis by light microscopy and transmission electron microscopy. Histologic presentation indicated localized phlebitis with lipogranulomas in Week 1, focal single-myofibril degeneration in Week 2 preceding an inflammatory response that started in Week 3. Lesions in Week 4 were characterized by multifocal to diffuse muscle fibre degeneration, necrosis, interstitial oedema accompanied by increased lipid and inflammatory cell infiltration. Lesions in Weeks 5-7 revealed diffuse muscle degeneration, necrosis, fibrosis and fatty infiltration with lipogranulomas. Ultrastructural examination showed myofibrillar splitting and degeneration, irregular, displaced and degenerated Z-lines, mitochondrial degeneration and interstitial fibrosis with dense regular collagen fibres. This study, therefore, demonstrates that WBD exhibits an earlier onset in modern broilers than when detectable by clinical examination. Further, this study shows that the disease assumes a progressive course with acute vasculitis, lipid deposition and myodegeneration occurring in the earlier stages, followed by a chronic fibrotic phase.

The development of optical microscopy techniques for the advancement of single-particle studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marchuk, Kyle

2013-05-15

Single particle orientation and rotational tracking (SPORT) has recently become a powerful optical microscopy tool that can expose many molecular motions. Unfortunately, there is not yet a single microscopy technique that can decipher all particle motions in all environmental conditions, thus there are limitations to current technologies. Within, the two powerful microscopy tools of total internal reflection and interferometry are advanced to determine the position, orientation, and optical properties of metallic nanoparticles in a variety of environments. Total internal reflection is an optical phenomenon that has been applied to microscopy to produce either fluorescent or scattered light. The non-invasive far-fieldmore » imaging technique is coupled with a near-field illumination scheme that allows for better axial resolution than confocal microscopy and epi-fluorescence microscopy. By controlling the incident illumination angle using total internal reflection fluorescence (TIRF) microscopy, a new type of imaging probe called “non-blinking” quantum dots (NBQDs) were super-localized in the axial direction to sub-10-nm precision. These particles were also used to study the rotational motion of microtubules being propelled by the motor protein kinesin across the substrate surface. The same instrument was modified to function under total internal reflection scattering (TIRS) microscopy to study metallic anisotropic nanoparticles and their dynamic interactions with synthetic lipid bilayers. Utilizing two illumination lasers with opposite polarization directions at wavelengths corresponding to the short and long axis surface plasmon resonance (SPR) of the nanoparticles, both the in-plane and out-of-plane movements of many particles could be tracked simultaneously. When combined with Gaussian point spread function (PSF) fitting for particle super-localization, the binding status and rotational movement could be resolved without degeneracy. TIRS microscopy was also used to find the 3D orientation of stationary metallic anisotropic nanoparticles utilizing only long-axis SPR enhancement. The polarization direction of the illuminating light was rotated causing the relative intensity of p-polarized and s-polarized light within the evanescent field to change. The interaction of the evanescent field with the particles is dependent on the orientation of the particle producing an intensity curve. This curve and the in-plane angle can be compared with simulations to accurately determine the 3D orientation. Differential interference contrast (DIC) microscopy is another non-invasive far-field technique based upon interferometry that does not rely on staining or other contrast enhancing techniques. In addition, high numerical aperture condensers and objectives can be used to give a very narrow depth of field allowing for the optical tomography of samples, which makes it an ideal candidate to study biological systems. DIC microscopy has also proven itself in determining the orientation of gold nanorods in both engineered environments and within cells. Many types of nanoparticles and nanostructures have been synthesized using lithographic techniques on silicon wafer substrates. Traditionally, reflective mode DIC microscopes have been developed and applied to the topographical study of reflective substrates and the imaging of chips on silicon wafers. Herein, a laser-illuminated reflected-mode DIC was developed for studying nanoparticles on reflective surfaces.« less

The development of optical microscopy techniques for the advancement of single-particle studies

NASA Astrophysics Data System (ADS)

Marchuk, Kyle

Single particle orientation and rotational tracking (SPORT) has recently become a powerful optical microscopy tool that can expose many molecular motions. Unfortunately, there is not yet a single microscopy technique that can decipher all particle motions in all environmental conditions, thus there are limitations to current technologies. Within, the two powerful microscopy tools of total internal reflection and interferometry are advanced to determine the position, orientation, and optical properties of metallic nanoparticles in a variety of environments. Total internal reflection is an optical phenomenon that has been applied to microscopy to produce either fluorescent or scattered light. The non-invasive far-field imaging technique is coupled with a near-field illumination scheme that allows for better axial resolution than confocal microscopy and epi-fluorescence microscopy. By controlling the incident illumination angle using total internal reflection fluorescence (TIRF) microscopy, a new type of imaging probe called "non-blinking" quantum dots (NBQDs) were super-localized in the axial direction to sub-10-nm precision. These particles were also used to study the rotational motion of microtubules being propelled by the motor protein kinesin across the substrate surface. The same instrument was modified to function under total internal reflection scattering (TIRS) microscopy to study metallic anisotropic nanoparticles and their dynamic interactions with synthetic lipid bilayers. Utilizing two illumination lasers with opposite polarization directions at wavelengths corresponding to the short and long axis surface plasmon resonance (SPR) of the nanoparticles, both the in-plane and out-of-plane movements of many particles could be tracked simultaneously. When combined with Gaussian point spread function (PSF) fitting for particle super-localization, the binding status and rotational movement could be resolved without degeneracy. TIRS microscopy was also used to find the 3D orientation of stationary metallic anisotropic nanoparticles utilizing only long-axis SPR enhancement. The polarization direction of the illuminating light was rotated causing the relative intensity of p-polarized and s-polarized light within the evanescent field to change. The interaction of the evanescent field with the particles is dependent on the orientation of the particle producing an intensity curve. This curve and the in-plane angle can be compared with simulations to accurately determine the 3D orientation. Differential interference contrast (DIC) microscopy is another non-invasive far-field technique based upon interferometry that does not rely on staining or other contrast enhancing techniques. In addition, high numerical aperture condensers and objectives can be used to give a very narrow depth of field allowing for the optical tomography of samples, which makes it an ideal candidate to study biological systems. DIC microscopy has also proven itself in determining the orientation of gold nanorods in both engineered environments and within cells. Many types of nanoparticles and nanostructures have been synthesized using lithographic techniques on silicon wafer substrates. Traditionally, reflective mode DIC microscopes have been developed and applied to the topographical study of reflective substrates and the imaging of chips on silicon wafers. Herein, a laser-illuminated reflected-mode DIC was developed for studying nanoparticles on reflective surfaces.

Quantification of surface displacements and electromechanical phenomena via dynamic atomic force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balke, Nina; Jesse, Stephen; Yu, Pu

Detection of dynamic surface displacements associated with local changes in material strain provides access to a number of phenomena and material properties. Contact resonance-enhanced methods of atomic force microscopy (AFM) have been shown capable of detecting ~1–3 pm-level surface displacements, an approach used in techniques such as piezoresponse force microscopy, atomic force acoustic microscopy, and ultrasonic force microscopy. Here, based on an analytical model of AFM cantilever vibrations, we demonstrate a guideline to quantify surface displacements with high accuracy by taking into account the cantilever shape at the first resonant contact mode, depending on the tip–sample contact stiffness. The approachmore » has been experimentally verified and further developed for piezoresponse force microscopy (PFM) using well-defined ferroelectric materials. These results open up a way to accurate and precise measurements of surface displacement as well as piezoelectric constants at the pm-scale with nanometer spatial resolution and will allow avoiding erroneous data interpretations and measurement artifacts. Furthermore, this analysis is directly applicable to all cantilever-resonance-based scanning probe microscopy (SPM) techniques.« less

Quantification of surface displacements and electromechanical phenomena via dynamic atomic force microscopy

DOE PAGES

Balke, Nina; Jesse, Stephen; Yu, Pu; ...

2016-09-15

Detection of dynamic surface displacements associated with local changes in material strain provides access to a number of phenomena and material properties. Contact resonance-enhanced methods of atomic force microscopy (AFM) have been shown capable of detecting ~1–3 pm-level surface displacements, an approach used in techniques such as piezoresponse force microscopy, atomic force acoustic microscopy, and ultrasonic force microscopy. Here, based on an analytical model of AFM cantilever vibrations, we demonstrate a guideline to quantify surface displacements with high accuracy by taking into account the cantilever shape at the first resonant contact mode, depending on the tip–sample contact stiffness. The approachmore » has been experimentally verified and further developed for piezoresponse force microscopy (PFM) using well-defined ferroelectric materials. These results open up a way to accurate and precise measurements of surface displacement as well as piezoelectric constants at the pm-scale with nanometer spatial resolution and will allow avoiding erroneous data interpretations and measurement artifacts. Furthermore, this analysis is directly applicable to all cantilever-resonance-based scanning probe microscopy (SPM) techniques.« less

A correlative optical microscopy and scanning electron microscopy approach to locating nanoparticles in brain tumors.

PubMed

Kempen, Paul J; Kircher, Moritz F; de la Zerda, Adam; Zavaleta, Cristina L; Jokerst, Jesse V; Mellinghoff, Ingo K; Gambhir, Sanjiv S; Sinclair, Robert

2015-01-01

The growing use of nanoparticles in biomedical applications, including cancer diagnosis and treatment, demands the capability to exactly locate them within complex biological systems. In this work a correlative optical and scanning electron microscopy technique was developed to locate and observe multi-modal gold core nanoparticle accumulation in brain tumor models. Entire brain sections from mice containing orthotopic brain tumors injected intravenously with nanoparticles were imaged using both optical microscopy to identify the brain tumor, and scanning electron microscopy to identify the individual nanoparticles. Gold-based nanoparticles were readily identified in the scanning electron microscope using backscattered electron imaging as bright spots against a darker background. This information was then correlated to determine the exact location of the nanoparticles within the brain tissue. The nanoparticles were located only in areas that contained tumor cells, and not in the surrounding healthy brain tissue. This correlative technique provides a powerful method to relate the macro- and micro-scale features visible in light microscopy with the nanoscale features resolvable in scanning electron microscopy. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Aerobic methylobacteria as promising objects of modern biotechnology].

PubMed

Doronina, N V; Toronskava, L; Fedorov, D N; Trotsenko, Yu A

2015-01-01

The experimental data of the past decade concerning the metabolic peculiarities of aerobic meth ylobacteria and the prospects for their use in different fields of modern biotechnology, including genetic engineering techniques, have been summarized.

Characterization of the host response to the myxosporean parasite, Ceratomyxa shasta (Noble), by histology, scanning electron microscopy, and immunological techniques

USGS Publications Warehouse

Bartholomew, J.L.; Smith, C.E.; Rohovec, J.S.; Fryer, J.L.

1989-01-01

The tissue response of Salmo gairdneri Richardson, against the myxosporean parasite. Ceratomyxa shasta (Noble), was investigated using histological techniques, scanning electron microscopy and immunological methods. The progress of infection in C. shasta-susceptible and resistant steelhead and rainbow trout was examined by standard histological techniques and by indirect fluorescent antibody methods using monoclonal antibodies directed against C. shasta antigens. Trophozoite stages were first observed in the posterior intestine and there was indication that resistance was due to the inability of the parasite to penetrate this tissue rather than to an inflammatory response. Examination of a severely infected intestine by scanning electron microscopy showed extensive destruction of the mucosal folds of the posterior intestine. Western blotting and indirect fluorescent antibody techniques were used to investigate the immunological component of the host response. No antibodies specific for C. shasta were detected by either method.

Measurements and Diagnostics of Diamond Films and Coatings

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa; Wu, Richard L. C.

1999-01-01

The commercial potential of chemical-vapor-deposited (CVD) diamond films has been established and a number of applications have been identified through university, industry, and government research studies. This paper discusses the methodologies used for property measurement and diagnostic of CVD diamond films and coatings. Measurement and diagnostic techniques studied include scanning electron microscopy, transmission electron microscopy, atomic force microscopy, stylus profilometry, x-ray diffraction, electron diffraction, Raman spectroscopy, Rutherford backscattering, elastic recoil spectroscopy, and friction examination. Each measurement and diagnostic technique provides unique information. A combination of techniques can provide the technical information required to understand the quality and properties of CVD diamond films, which are important to their application in specific component systems and environments. In this study the combination of measurement and diagnostic techniques was successfully applied to correlate deposition parameters and resultant diamond film composition, crystallinity, grain size, surface roughness, and coefficient of friction.

Microscopy Images as Interactive Tools in Cell Modeling and Cell Biology Education

ERIC Educational Resources Information Center

Araujo-Jorge, Tania C.; Cardona, Tania S.; Mendes, Claudia L. S.; Henriques-Pons, Andrea; Meirelles, Rosane M. S.; Coutinho, Claudia M. L. M.; Aguiar, Luiz Edmundo V.; Meirelles, Maria de Nazareth L.; de Castro, Solange L.; Barbosa, Helene S.; Luz, Mauricio R. M. P.

2004-01-01

The advent of genomics, proteomics, and microarray technology has brought much excitement to science, both in teaching and in learning. The public is eager to know about the processes of life. In the present context of the explosive growth of scientific information, a major challenge of modern cell biology is to popularize basic concepts of…

Ancient Chinese medicine and mechanistic evidence of acupuncture physiology.

PubMed

Yang, Edward S; Li, Pei-Wen; Nilius, Bernd; Li, Geng

2011-11-01

Acupuncture has been widely used in China for three millennia as an art of healing. Yet, its physiology is not yet understood. The current interest in acupuncture started in 1971. Soon afterward, extensive research led to the concept of neural signaling with possible involvement of opioid peptides, glutamate, adenosine and identifying responsive parts in the central nervous system. In the last decade scientists began investigating the subject with anatomical and molecular imaging. It was found that mechanical movements of the needle, ignored in the past, appear to be central to the method and intracellular calcium ions may play a pivotal role. In this review, we trace the technique of clinical treatment from the first written record about 2,200 years ago to the modern time. The ancient texts have been used to introduce the concepts of yin, yang, qi, de qi, and meridians, the traditional foundation of acupuncture. We explore the sequence of the physiological process, from the turning of the needle, the mechanical wave activation of calcium ion channel to beta-endorphin secretion. By using modern terminology to re-interpret the ancient texts, we have found that the 2nd century B.C.: physiologists were meticulous investigators and their explanation fits well with the mechanistic model derived from magnetic resonance imaging (MRI) and confocal microscopy. In conclusion, the ancient model appears to have withstood the test of time surprisingly well confirming the popular axiom that the old wine is better than the new.

Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

PubMed Central

Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

2009-01-01

Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

Two-Photon Excitation, Fluorescence Microscopy, and Quantitative Measurement of Two-Photon Absorption Cross Sections

NASA Astrophysics Data System (ADS)

DeArmond, Fredrick Michael

As optical microscopy techniques continue to improve, most notably the development of super-resolution optical microscopy which garnered the Nobel Prize in Chemistry in 2014, renewed emphasis has been placed on the development and use of fluorescence microscopy techniques. Of particular note is a renewed interest in multiphoton excitation due to a number of inherent properties of the technique including simplified optical filtering, increased sample penetration, and inherently confocal operation. With this renewed interest in multiphoton fluorescence microscopy, comes an increased demand for robust non-linear fluorescent markers, and characterization of the associated tool set. These factors have led to an experimental setup to allow a systematized approach for identifying and characterizing properties of fluorescent probes in the hopes that the tool set will provide researchers with additional information to guide their efforts in developing novel fluorophores suitable for use in advanced optical microscopy techniques as well as identifying trends for their synthesis. Hardware was setup around a software control system previously developed. Three experimental tool sets were set up, characterized, and applied over the course of this work. These tools include scanning multiphoton fluorescence microscope with single molecule sensitivity, an interferometric autocorrelator for precise determination of the bandwidth and pulse width of the ultrafast Titanium Sapphire excitation source, and a simplified fluorescence microscope for the measurement of two-photon absorption cross sections. Resulting values for two-photon absorption cross sections and two-photon absorption action cross sections for two standardized fluorophores, four commercially available fluorophores, and ten novel fluorophores are presented as well as absorption and emission spectra.

Report on the 18th International Conference on X-ray and Inner-Shell Processes (X99).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gemmell, D. S.; Physics

2000-01-01

The 18th conference of the series served as a forum for discussing fundamental issues in the field of x-ray and inner-shell processes and their application in various disciplines of science and technology. Special emphasis was given to the opportunities offered by modern synchrotron x-ray sources. The program included plenary talks, progress reports and poster presentations relating to new developments in the field of x-ray and inner-shell processes. The range of topics included: X-ray interactions with atoms, molecules, clusters, surfaces and solids; Decay processes for inner-shell vacancies; X-ray absorption and emission spectroscopy - Photoionization processes; Phenomena associated with highly charged ionsmore » and collisions with energetic particles; Electron-spin and -momentum spectroscopy; X-ray scattering and spectroscopy in the study of magnetic systems; Applications in materials science, biology, geosciences, and other disciplines; Elastic and inelastic x-ray scattering processes in atoms and molecules; Threshold phenomena (post-collision interaction, resonant Raman processes, etc.); Nuclear absorption and scattering of x-rays; 'Fourth-generation' x-ray sources; Processes exploiting the polarization and coherence properties of x-ray beams; Developments in experimental techniques (x-ray optics, temporal techniques, detectors); Microscopy, spectromicroscopy, and various imaging techniques; Non-linear processes and x-ray lasers; Ionization and excitation induced by charged particles and by x-rays; and Exotic atoms (including 'hollow' atoms and atoms that contain 'exotic' particles).« less

Impact of the macroeconomic factors on university budgeting the US and Russia

NASA Astrophysics Data System (ADS)

Bogomolova, Arina; Balk, Igor; Ivachenko, Natalya; Temkin, Anatoly

2017-10-01

This paper discuses impact of macroeconomics factor on the university budgeting. Modern developments in the area of data science and machine learning made it possible to utilise automated techniques to address several problems of humankind ranging from genetic engineering and particle physics to sociology and economics. This paper is the first step to create a robust toolkit which will help universities sustain macroeconomic challenges utilising modern predictive analytics techniques.

Identification of Microorganisms by Modern Analytical Techniques.

PubMed

Buszewski, Bogusław; Rogowska, Agnieszka; Pomastowski, Paweł; Złoch, Michał; Railean-Plugaru, Viorica

2017-11-01

Rapid detection and identification of microorganisms is a challenging and important aspect in a wide range of fields, from medical to industrial, affecting human lives. Unfortunately, classical methods of microorganism identification are based on time-consuming and labor-intensive approaches. Screening techniques require the rapid and cheap grouping of bacterial isolates; however, modern bioanalytics demand comprehensive bacterial studies at a molecular level. Modern approaches for the rapid identification of bacteria use molecular techniques, such as 16S ribosomal RNA gene sequencing based on polymerase chain reaction or electromigration, especially capillary zone electrophoresis and capillary isoelectric focusing. However, there are still several challenges with the analysis of microbial complexes using electromigration technology, such as uncontrolled aggregation and/or adhesion to the capillary surface. Thus, an approach using capillary electrophoresis of microbial aggregates with UV and matrix-assisted laser desorption ionization time-of-flight MS detection is presented.

Nano-Electrochemistry and Nano-Electrografting with an Original Combined AFM-SECM

PubMed Central

Ghorbal, Achraf; Grisotto, Federico; Charlier, Julienne; Palacin, Serge; Goyer, Cédric; Demaille, Christophe; Ben Brahim, Ammar

2013-01-01

This study demonstrates the advantages of the combination between atomic force microscopy and scanning electrochemical microscopy. The combined technique can perform nano-electrochemical measurements onto agarose surface and nano-electrografting of non-conducting polymers onto conducting surfaces. This work was achieved by manufacturing an original Atomic Force Microscopy-Scanning ElectroChemical Microscopy (AFM-SECM) electrode. The capabilities of the AFM-SECM-electrode were tested with the nano-electrografting of vinylic monomers initiated by aryl diazonium salts. Nano-electrochemical and technical processes were thoroughly described, so as to allow experiments reproducing. A plausible explanation of chemical and electrochemical mechanisms, leading to the nano-grafting process, was reported. This combined technique represents the first step towards improved nano-processes for the nano-electrografting. PMID:28348337

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

Application of Multiphoton Microscopy in Dermatological Studies: a Mini-Review

PubMed Central

Yew, Elijah; Rowlands, Christopher

2014-01-01

This review summarizes the historical and more recent developments of multiphoton microscopy, as applied to dermatology. Multiphoton microscopy offers several advantages over competing microscopy techniques: there is an inherent axial sectioning, penetration depths that compete well with confocal microscopy on account of the use of near-infrared light, and many two-photon contrast mechanisms, such as second-harmonic generation, have no analogue in one-photon microscopy. While the penetration depths of photons into tissue are typically limited on the order of hundreds of microns, this is of less concern in dermatology, as the skin is thin and readily accessible. As a result, multiphoton microscopy in dermatology has generated a great deal of interest, much of which is summarized here. The review covers the interaction of light and tissue, as well as the various considerations that must be made when designing an instrument. The state of multiphoton microscopy in imaging skin cancer and various other diseases is also discussed, along with the investigation of aging and regeneration phenomena, and finally, the use of multiphoton microscopy to analyze the transdermal transport of drugs, cosmetics and other agents is summarized. The review concludes with a look at potential future research directions, especially those that are necessary to push these techniques into widespread clinical acceptance. PMID:25075226

Simultaneous off-axis multiplexed holography and regular fluorescence microscopy of biological cells.

PubMed

Nygate, Yoav N; Singh, Gyanendra; Barnea, Itay; Shaked, Natan T

2018-06-01

We present a new technique for obtaining simultaneous multimodal quantitative phase and fluorescence microscopy of biological cells, providing both quantitative phase imaging and molecular specificity using a single camera. Our system is based on an interferometric multiplexing module, externally positioned at the exit of an optical microscope. In contrast to previous approaches, the presented technique allows conventional fluorescence imaging, rather than interferometric off-axis fluorescence imaging. We demonstrate the presented technique for imaging fluorescent beads and live biological cells.

Combining Textural Techniques to Explore Effects of Diagenesis and Low-grade Metamorphism on Iron Mineralogy and Iron Speciation

NASA Astrophysics Data System (ADS)

Slotznick, S. P.; Webb, S.; Eiler, J. M.; Kirschvink, J. L.; Fischer, W. W.

2016-12-01

Iron chemistry and mineralogy in the sedimentary rocks provide a valuable tool for studying paleoenvironmental conditions due to the fact that iron atoms can take on either the +II or +III valence state under geological redox conditions. One method utilizing this redox chemistry is `iron speciation', a bulk chemical sequential extraction technique that maps proportions of iron species to redox conditions empirically calibrated from modern sediments. However, all Precambrian and many Phanerozoic rocks have experienced post-depositional processes; it is vital to explore their effects on iron mineralogy and speciation. We combined light and electron microscopy, magnetic microscopy, (synchrotron-based) microprobe x-ray spectroscopy, and rock magnetic measurements in order to deconvolve secondary overprints from primary phases and provide quantitative measurement of iron minerals. These techniques were applied to excellently-preserved shale and siltstone samples of the 1.4 Ga lower Belt Supergroup, Montana and Idaho, USA, spanning a metamorphic gradient from sub-biotite to garnet zone. Previously measured Silurian-Devonian shales, sandstones, and carbonates in Maine and Vermont, USA spanning from the chlorite to kyanite zone provided additional well-constrained, quantitative data for comparison and to extend our analysis. In all of the studied samples, pyrrhotite formation occurred at the sub-biotite or sub-chlorite zone. Pyrrhotite was interpreted to form from pyrite and/or other iron phases based on lithology; these reactions can affect the paleoredox proxy. Iron carbonates can also severely influence iron speciation results since they often form in anoxic pore fluids during diagenesis; textural analyses of the Belt Supergroup samples highlighted that iron-bearing carbonates were early diagenetic cements or later diagenetic overprints. The inclusion of iron from diagenetic minerals during iron speciation analyses will skew results by providing a view of pore-fluid redox, not ancient water column chemistry. While our analyses and biological indicators suggest that the studied samples of the lower Belt Supergroup and New England were deposited in oxic water columns, iron speciation results imply anoxic/ferruginous conditions due to diagenetic alterations affecting the record.

Transition to Virtual Microscopy in Medical Undergraduate Pathology Education: First Experience of Turkey in Dokuz Eylül University Hospital.

PubMed

Sağol, Özgül; Yörükoğlu, Kutsal; Lebe, Banu; Durak, Merih Güray; Ulukuş, Çağnur; Tuna, Burçin; Musal, Berna; Canda, Tülay; Özer, Erdener

2015-01-01

Pathology education includes an important visual part supporting a wide range of theoretical knowledge. However, the use of traditional microscopes in pathology education has declined over the last decade and there is a lack of interest for microscopy. Virtual microscopy, which was first described in 1985 and has experienced a revolution since 2000, is an alternative technique to conventional microscopy, in which microscopic slides are scanned to form digital images and stored in the web. The aim of this study was to evaluate the use of virtual microscopy in practical pathology sessions and its effects on our students and undergraduate education at our faculty. Second and third year medical students who were used to conventional microscopes were included in the study. The practical sessions were carried out via virtual slides and the effect of the new technique was investigated by a scale at the end of each session. Academic staff from the pathology department joined sessions to promote discussion and respond to questions. Student ratings were analysed statistically. The evaluation of the ratings showed that the students were easily adapted to the use of virtual microscopy. They found it user-friendly and thought that the opportunity of viewing slides at home was advantageous. Collaboration between students and interactive discussions was also improved with this technique. It was concluded that the use of virtual microscopy could contribute to the pathology education of our students.

Nanoscale characterization of vesicle adhesion by normalized total internal reflection fluorescence microscopy.

PubMed

Cardoso Dos Santos, Marcelina; Vézy, Cyrille; Jaffiol, Rodolphe

2016-06-01

We recently proposed a straightforward fluorescence microscopy technique to study adhesion of Giant Unilamellar Vesicles. This technique is based on dual observations which combine epi-fluorescence microscopy and total internal reflection fluorescence (TIRF) microscopy: TIRF images are normalized by epi-fluorescence ones. By this way, it is possible to map the membrane/substrate separation distance with a nanometric resolution, typically ~20 nm, with a maximal working range of 300-400 nm. The purpose of this paper is to demonstrate that this technique is useful to quantify vesicle adhesion from ultra-weak to strong membrane-surface interactions. Thus, we have examined unspecific and specific adhesion conditions. Concerning unspecific adhesion, we have controlled the strength of electrostatic forces between negatively charged vesicles and various functionalized surfaces which exhibit a positive or a negative effective charge. Specific adhesion was highlighted with lock-and-key forces mediated by the well defined biotin/streptavidin recognition. Copyright © 2016 Elsevier B.V. All rights reserved.

Biomolecular Imaging with Coherent Nonlinear Vibrational Microscopy

PubMed Central

Chung, Chao-Yu; Boik, John; Potma, Eric O.

2014-01-01

Optical imaging with spectroscopic vibrational contrast is a label-free solution for visualizing, identifying, and quantifying a wide range of biomolecular compounds in biological materials. Both linear and nonlinear vibrational microscopy techniques derive their imaging contrast from infrared active or Raman allowed molecular transitions, which provide a rich palette for interrogating chemical and structural details of the sample. Yet nonlinear optical methods, which include both second-order sum-frequency generation (SFG) and third-order coherent Raman scattering (CRS) techniques, offer several improved imaging capabilities over their linear precursors. Nonlinear vibrational microscopy features unprecedented vibrational imaging speeds, provides strategies for higher spatial resolution, and gives access to additional molecular parameters. These advances have turned vibrational microscopy into a premier tool for chemically dissecting live cells and tissues. This review discusses the molecular contrast of SFG and CRS microscopy and highlights several of the advanced imaging capabilities that have impacted biological and biomedical research. PMID:23245525

Grinding and polishing instead of sectioning for the tissue samples with a graft: Implications for light and electron microscopy.

PubMed

Mukhamadiyarov, Rinat A; Sevostyanova, Victoria V; Shishkova, Daria K; Nokhrin, Andrey V; Sidorova, Olga D; Kutikhin, Anton G

2016-06-01

A broad use of the graft replacement requires a detailed investigation of the host-graft interaction, including both histological examination and electron microscopy. A high quality sectioning of the host tissue with a graft seems to be complicated; in addition, it is difficult to examine the same tissue area by both of the mentioned microscopy techniques. To solve these problems, we developed a new technique of epoxy resin embedding with the further grinding, polishing, and staining. Graft-containing tissues prepared by grinding and polishing preserved their structure; however, sectioning frequently required the explantation of the graft and led to tissue disintegration. Moreover, stained samples prepared by grinding and polishing may then be assessed by both light microscopy and backscattered scanning electron microscopy. Therefore, grinding and polishing outperform sectioning when applied to the tissues with a graft. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tomographic phase microscopy and its biological applications

NASA Astrophysics Data System (ADS)

Choi, Wonshik

2012-12-01

Conventional interferometric microscopy techniques such as digital holographic microscopy and quantitative phase microscopy are often classified as 3D imaging techniques because a recorded complex field image can be numerically propagated to a different depth. In a strict sense, however, a single complex field image contains only 2D information on a specimen. The measured 2D image is only a subset of the 3D structure. For the 3D mapping of an object, multiple independent 2D images are to be taken, for example at multiple incident angles or wavelengths, and then combined by the so-called optical diffraction tomography (ODT). In this Letter, tomographic phase microscopy (TPM) is reviewed that experimentally realizes the concept of the ODT for the 3D mapping of biological cells in their native state, and some of its interesting biological and biomedical applications are introduced. [Figure not available: see fulltext.

Multi-scale Observation of Biological Interactions of Nanocarriers: from Nano to Macro

PubMed Central

Jin, Su-Eon; Bae, Jin Woo; Hong, Seungpyo

2010-01-01

Microscopic observations have played a key role in recent advancements in nanotechnology-based biomedical sciences. In particular, multi-scale observation is necessary to fully understand the nano-bio interfaces where a large amount of unprecedented phenomena have been reported. This review describes how to address the physicochemical and biological interactions of nanocarriers within the biological environments using microscopic tools. The imaging techniques are categorized based on the size scale of detection. For observation of the nano-scale biological interactions of nanocarriers, we discuss atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). For the micro to macro-scale (in vitro and in vivo) observation, we focus on confocal laser scanning microscopy (CLSM) as well as in vivo imaging systems such as magnetic resonance imaging (MRI), superconducting quantum interference devices (SQUIDs), and IVIS®. Additionally, recently developed combined techniques such as AFM-CLSM, correlative Light and Electron Microscopy (CLEM), and SEM-spectroscopy are also discussed. In this review, we describe how each technique helps elucidate certain physicochemical and biological activities of nanocarriers such as dendrimers, polymers, liposomes, and polymeric/inorganic nanoparticles, thus providing a toolbox for bioengineers, pharmaceutical scientists, biologists, and research clinicians. PMID:20232368

Adequacy of surface analytical tools for studying the tribology of ceramics

NASA Technical Reports Server (NTRS)

Sliney, H. E.

1986-01-01

Surface analytical tools are very beneficial in tribological studies of ceramics. Traditional methods of optical microscopy, XRD, XRF, and SEM should be combined with newer surface sensitive techniques especially AES and XPS. ISS and SIMS can also be useful in providing additional compositon details. Tunneling microscopy and electron energy loss spectroscopy are less known techniques that may also prove useful.

Scalp imaging techniques

NASA Astrophysics Data System (ADS)

Otberg, Nina; Shapiro, Jerry; Lui, Harvey; Wu, Wen-Yu; Alzolibani, Abdullateef; Kang, Hoon; Richter, Heike; Lademann, Jürgen

2017-05-01

Scalp imaging techniques are necessary tools for the trichological practice and for visualization of permeation, penetration and absorption processes into and through the scalp and for the research on drug delivery and toxicology. The present letter reviews different scalp imaging techniques and discusses their utility. Moreover, two different studies on scalp imaging techniques are presented in this letter: (1) scalp imaging with phototrichograms in combination with laser scanning microscopy, and (2) follicular measurements with cyanoacrylate surface replicas and light microscopy in combination with laser scanning microscopy. The experiments compare different methods for the determination of hair density on the scalp and different follicular measures. An average terminal hair density of 132 hairs cm-2 was found in 6 Caucasian volunteers and 135 hairs cm-2 in 6 Asian volunteers. The area of the follicular orifices accounts to 16.3% of the skin surface on average measured with laser scanning microscopy images. The potential volume of the follicular infundibulum was calculated based on the laser scanning measurements and is found to be 4.63 mm3 per cm2 skin on average. The experiments show that hair follicles are quantitatively relevant pathways and potential reservoirs for topically applied drugs and cosmetics.

High-spatial-resolution sub-surface imaging using a laser-based acoustic microscopy technique.

PubMed

Balogun, Oluwaseyi; Cole, Garrett D; Huber, Robert; Chinn, Diane; Murray, Todd W; Spicer, James B

2011-01-01

Scanning acoustic microscopy techniques operating at frequencies in the gigahertz range are suitable for the elastic characterization and interior imaging of solid media with micrometer-scale spatial resolution. Acoustic wave propagation at these frequencies is strongly limited by energy losses, particularly from attenuation in the coupling media used to transmit ultrasound to a specimen, leading to a decrease in the depth in a specimen that can be interrogated. In this work, a laser-based acoustic microscopy technique is presented that uses a pulsed laser source for the generation of broadband acoustic waves and an optical interferometer for detection. The use of a 900-ps microchip pulsed laser facilitates the generation of acoustic waves with frequencies extending up to 1 GHz which allows for the resolution of micrometer-scale features in a specimen. Furthermore, the combination of optical generation and detection approaches eliminates the use of an ultrasonic coupling medium, and allows for elastic characterization and interior imaging at penetration depths on the order of several hundred micrometers. Experimental results illustrating the use of the laser-based acoustic microscopy technique for imaging micrometer-scale subsurface geometrical features in a 70-μm-thick single-crystal silicon wafer with a (100) orientation are presented.

Immunogold scanning electron microscopy can reveal the polysaccharide architecture of xylem cell walls

PubMed Central

Sun, Yuliang; Juzenas, Kevin

2017-01-01

Abstract Immunofluorescence microscopy (IFM) and immunogold transmission electron microscopy (TEM) are the two main techniques commonly used to detect polysaccharides in plant cell walls. Both are important in localizing cell wall polysaccharides, but both have major limitations, such as low resolution in IFM and restricted sample size for immunogold TEM. In this study, we have developed a robust technique that combines immunocytochemistry with scanning electron microscopy (SEM) to study cell wall polysaccharide architecture in xylem cells at high resolution over large areas of sample. Using multiple cell wall monoclonal antibodies (mAbs), this immunogold SEM technique reliably localized groups of hemicellulosic and pectic polysaccharides in the cell walls of five different xylem structures (vessel elements, fibers, axial and ray parenchyma cells, and tyloses). This demonstrates its important advantages over the other two methods for studying cell wall polysaccharide composition and distribution in these structures. In addition, it can show the three-dimensional distribution of a polysaccharide group in the vessel lateral wall and the polysaccharide components in the cell wall of developing tyloses. This technique, therefore, should be valuable for understanding the cell wall polysaccharide composition, architecture and functions of diverse cell types. PMID:28398585

A comparative analysis of microscopic alterations in modern and ancient undecalcified and decalcified dry bones.

PubMed

Caruso, Valentina; Cummaudo, Marco; Maderna, Emanuela; Cappella, Annalisa; Caudullo, Giorgio; Scarpulla, Valentina; Cattaneo, Cristina

2018-02-01

The present study aims to evaluate the preservation of the microstructure of skeletal remains collected from four different known burial sites (archaeological and contemporary). Histological analysis on undecalcified and decalcified thin sections was performed in order to assess which of the two techniques is more affected by taphonomic insults. A histological analysis was performed on both undecalcified and decalcified thin sections of 40 long bones and the degree of diagenetic change was evaluated using transmitted and polarized light microscopy according to the Oxford Histological Index (OHI). In order to test the optical behavior of bone tissue, thin sections were observed by polarized light microscopy and the intensity of birefringence was evaluated. The more ancient samples are generally characterized by a low OHI (0-1) with extensive microscopic focal destruction; recent samples exhibited a better preservation of bone micromorphology. When comparing undecalcified to decalcified thin sections, the latter showed an amelioration in the conservation of microscopic structure. As regards the birefringence, it was very low in all the undecalcified thin sections, whereas decalcification process seems to improve its visibility. The preservation of the bone microscopic structure appears to be influenced not only by age, but also by the burial context. Undecalcified bones appear to be more affected by taphonomical alterations, probably because of the thickness of the thin sections; on the contrary, decalcified thin sections proved to be able to tackle this issue allowing a better reading of the bone tissue. © 2017 Wiley Periodicals, Inc.

A comparative study of modern and fossil cone scales and seeds of conifers: A geochemical approach

USGS Publications Warehouse

Artur, Stankiewicz B.; Mastalerz, Maria; Kruge, M.A.; Van Bergen, P. F.; Sadowska, A.

1997-01-01

Modern cone scales and seeds of Pinus strobus and Sequoia sempervirens, and their fossil (Upper Miocene, c. 6 Mar) counterparts Pinus leitzii and Sequoia langsdorfi have been studied using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), electron-microprobe and scanning electron microscopy. Microscopic observations revealed only minor microbial activity and high-quality structural preservation of the fossil material. The pyrolysates of both modern genera showed the presence of ligno-cellulose characteristic of conifers. However, the abundance of (alkylated)phenols and 1,2-benzenediols in modern S. sempervirens suggests the presence of non-hydrolysable tannins or abundant polyphenolic moieties not previously reported in modern conifers. The marked differences between the pyrolysis products of both modern genera are suggested to be of chemosystematic significance. The fossil samples also contained ligno-cellulose which exhibited only partial degradation, primarily of the carbohydrate constituents. Comparison between the fossil cone scale and seed pyrolysates indicated that the ligno-cellulose complex present in the seeds is chemically more resistant than that in the cone scales. Principal component analysis (PCA) of the pyrolysis data allowed for the determination of the discriminant functions used to assess the extent of degradation and the chemosystematic differences between both genera and between cone scales and seeds. Elemental composition (C, O, S), obtained using electron-microprobe, corroborated the pyrolysis results. Overall, the combination of chemical, microscopic and statistical methods allowed for a detailed characterization and chemosystematic interpretations of modern and fossil conifer cone scales and seeds.

A Simplified, Low-Cost Method for Polarized Light Microscopy

PubMed Central

Maude, Richard J.; Buapetch, Wanchana; Silamut, Kamolrat

2009-01-01

Malaria pigment is an intracellular inclusion body that appears in blood and tissue specimens on microscopic examination and can help in establishing the diagnosis of malaria. In simple light microscopy, it can be difficult to discern from cellular background and artifacts. It has long been known that if polarized light microscopy is used, malaria pigment can be much easier to distinguish. However, this technique is rarely used because of the need for a relatively costly polarization microscope. We describe a simple and economical technique to convert any standard light microscope suitable for examination of malaria films into a polarization microscope. PMID:19861611

Microscopy and Image Analysis.

PubMed

McNamara, George; Difilippantonio, Michael; Ried, Thomas; Bieber, Frederick R

2017-07-11

This unit provides an overview of light microscopy, including objectives, light sources, filters, film, and color photography for fluorescence microscopy and fluorescence in situ hybridization (FISH). We believe there are excellent opportunities for cytogeneticists, pathologists, and other biomedical readers, to take advantage of specimen optical clearing techniques and expansion microscopy-we briefly point to these new opportunities. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Direct Microscopy: A Useful Tool to Diagnose Oral Candidiasis in Children and Adolescents.

PubMed

Marty, Mathieu; Bourrat, Emmanuelle; Vaysse, Frédéric; Bonner, Mark; Bailleul-Forestier, Isabelle

2015-12-01

Oral candidiasis is one of the most common opportunistic fungal infections of the oral cavity in human. Among children, this condition represents one of the most frequent affecting the mucosa. Although most diagnoses are made based on clinical signs and features, a microbiological analysis is sometimes necessary. We performed a literature review on the diagnosis of oral candidiasis to identify the techniques most commonly employed in routine clinical practice. A Medline-PubMed search covering the last 10 years was performed. Microbiological techniques were used in cases requiring confirmation of the clinical diagnosis. In such cases, direct microscopy was the method most commonly used for diagnosing candidiasis. Direct microscopy appears as the method of choice for confirming clinical diagnosis and could become a routine chair-side technique.

Far-Field High-Energy Diffraction Microscopy: A Non-Destructive Tool for Characterizing the Microstructure and Micromechanical State of Polycrystalline Materials

DOE PAGES

Park, Jun-Sang; Zhang, Xuan; Kenesei, Peter; ...

2017-08-31

A suite of non-destructive, three-dimensional X-ray microscopy techniques have recently been developed and used to characterize the microstructures of polycrystalline materials. These techniques utilize high-energy synchrotron radiation and include near-field and far-field diffraction microscopy (NF- and FF-HEDM, respectively) and absorption tomography. Several compatible sample environments have also been developed, enabling a wide range of 3D studies of material evolution. In this article, the FF-HEDM technique is described in detail, including its implementation at the 1-ID beamline of the Advanced Photon Source. Examples of how the information obtained from FF-HEDM can be used to deepen our understanding of structure-property-processing relationships inmore » selected materials are presented.« less

Laser scanning confocal microscopy: history, applications, and related optical sectioning techniques.

PubMed

Paddock, Stephen W; Eliceiri, Kevin W

2014-01-01

Confocal microscopy is an established light microscopical technique for imaging fluorescently labeled specimens with significant three-dimensional structure. Applications of confocal microscopy in the biomedical sciences include the imaging of the spatial distribution of macromolecules in either fixed or living cells, the automated collection of 3D data, the imaging of multiple labeled specimens and the measurement of physiological events in living cells. The laser scanning confocal microscope continues to be chosen for most routine work although a number of instruments have been developed for more specific applications. Significant improvements have been made to all areas of the confocal approach, not only to the instruments themselves, but also to the protocols of specimen preparation, to the analysis, the display, the reproduction, sharing and management of confocal images using bioinformatics techniques.

Dermatopathology education in the era of modern technology.

PubMed

Shahriari, Neda; Grant-Kels, Jane; Murphy, Michael J

2017-09-01

Continuing technological advances are inevitably impacting the study and practice of dermatopathology (DP). We are seeing the transition from glass slide microscopy to virtual microscopy, which is serving both as an accessible educational medium for medical students, residents and fellows in the form of online databases and atlases, as well as a research tool to better inform us regarding the development of visual diagnostic expertise. Expansion in mobile technology is simplifying slide image attainment and providing greater opportunities for phone- and tablet-based microscopy, including teledermatopathology instruction and consultation in resource-poor areas with lack of specialists. Easily accessible mobile and computer-based applications ("apps"), including myDermPath and Clearpath, are providing an interactive medium for DP instruction. The Internet and social networking sites are enabling rapid global communication of DP information and image-sharing, promoting collaborative diagnostic research and scholastic endeavors. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Deep Learning Neural Networks and Bayesian Neural Networks in Data Analysis

NASA Astrophysics Data System (ADS)

Chernoded, Andrey; Dudko, Lev; Myagkov, Igor; Volkov, Petr

2017-10-01

Most of the modern analyses in high energy physics use signal-versus-background classification techniques of machine learning methods and neural networks in particular. Deep learning neural network is the most promising modern technique to separate signal and background and now days can be widely and successfully implemented as a part of physical analysis. In this article we compare Deep learning and Bayesian neural networks application as a classifiers in an instance of top quark analysis.

A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

PubMed Central

2013-01-01

Background In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of information. Here we demonstrate the advantages of the correlative use of microCT, light microscopy, and transmission electron microscopy for the analysis of small biological samples. Results We used a small juvenile bivalve mollusc (Mytilus galloprovincialis, approximately 0.8 mm length) to demonstrate the workflow of a correlative examination by microCT, LM serial section analysis, and TEM-re-sectioning. Initially these three datasets were analyzed separately, and subsequently they were fused in one 3D scene. This workflow is very straightforward. The specimen was processed as usual for transmission electron microscopy including post-fixation in osmium tetroxide and embedding in epoxy resin. Subsequently it was imaged with microCT. Post-fixation in osmium tetroxide yielded sufficient X-ray contrast for microCT imaging, since the X-ray absorption of epoxy resin is low. Thereafter, the same specimen was serially sectioned for LM investigation. The serial section images were aligned and specific organ systems were reconstructed based on manual segmentation and surface rendering. According to the region of interest (ROI), specific LM sections were detached from the slides, re-mounted on resin blocks and re-sectioned (ultrathin) for TEM. For analysis, image data from the three different modalities was co-registered into a single 3D scene using the software AMIRA®. We were able to register both the LM section series volume and TEM slices neatly to the microCT dataset, with small geometric deviations occurring only in the peripheral areas of the specimen. Based on co-registered datasets the excretory organs, which were chosen as ROI for this study, could be investigated regarding both their ultrastructure as well as their position in the organism and their spatial relationship to adjacent tissues. We found structures typical for mollusc excretory systems, including ultrafiltration sites at the pericardial wall, and ducts leading from the pericardium towards the kidneys, which exhibit a typical basal infolding system. Conclusions The presented approach allows a comprehensive analysis and presentation of small objects regarding both the overall organization as well as cellular and subcellular details. Although our protocol involves a variety of different equipment and procedures, we maintain that it offers savings in both effort and cost. Co-registration of datasets from different imaging modalities can be accomplished with high-end desktop computers and offers new opportunities for understanding and communicating structural relationships within organisms and tissues. In general, the correlative use of different microscopic imaging techniques will continue to become more widespread in morphological and structural research in zoology. Classical TEM serial section investigations are extremely time consuming, and modern methods for 3D analysis of ultrastructure such as SBF-SEM and FIB-SEM are limited to very small volumes for examination. Thus the re-sectioning of LM sections is suitable for speeding up TEM examination substantially, while microCT could become a key-method for complementing ultrastructural examinations. PMID:23915384

Subminiature eddy current transducers for studying boride coatings

NASA Astrophysics Data System (ADS)

Dmitriev, S. F.; Ishkov, A. V.; Malikov, V. N.; Sagalakov, A. M.

2016-07-01

Strengthening of parts and units of machines, increased reliability and longer service life is an important task of modern mechanical engineering. The main objects of study in the work were selected steel 65G and 50HGA, wear-resistant boride coatings ternary system Fe-B-Fe n B which were investigated by scanning electron microscopy and eddy-current nondestructive methods.

Widely Accepted Modern Views of Cell Structure are Fundamentally Correct: A Reply to Hillman and Sartory.

ERIC Educational Resources Information Center

Michell, R. H.; And Others

1982-01-01

Argues against Hillman and Sartory's views of cell structure (EJ242880), pointing out that they are erroneous in their analysis of the motives and working methods of the scientific community, in their total rejection of information coming from electron microscopy, and in their claim that lysosomes and endoplasmic reticulum are imaginary. (DC)

Quantitative photothermal phase imaging of red blood cells using digital holographic photothermal microscope.

PubMed

Vasudevan, Srivathsan; Chen, George C K; Lin, Zhiping; Ng, Beng Koon

2015-05-10

Photothermal microscopy (PTM), a noninvasive pump-probe high-resolution microscopy, has been applied as a bioimaging tool in many biomedical studies. PTM utilizes a conventional phase contrast microscope to obtain highly resolved photothermal images. However, phase information cannot be extracted from these photothermal images, as they are not quantitative. Moreover, the problem of halos inherent in conventional phase contrast microscopy needs to be tackled. Hence, a digital holographic photothermal microscopy technique is proposed as a solution to obtain quantitative phase images. The proposed technique is demonstrated by extracting phase values of red blood cells from their photothermal images. These phase values can potentially be used to determine the temperature distribution of the photothermal images, which is an important study in live cell monitoring applications.

Domain imaging in ferroelectric thin films via channeling-contrast backscattered electron microscopy

DOE PAGES

Ihlefeld, Jon F.; Michael, Joseph R.; McKenzie, Bonnie B.; ...

2016-09-16

We report that ferroelastic domain walls provide opportunities for deterministically controlling mechanical, optical, electrical, and thermal energy. Domain wall characterization in micro- and nanoscale systems, where their spacing may be of the order of 100 nm or less is presently limited to only a few techniques, such as piezoresponse force microscopy and transmission electron microscopy. These respective techniques cannot, however, independently characterize domain polarization orientation and domain wall motion in technologically relevant capacitor structures or in a non-destructive manner, thus presenting a limitation of their utility. In this work, we show how backscatter scanning electron microscopy utilizing channeling contrast yieldmore » can image the ferroelastic domain structure of ferroelectric films with domain wall spacing as narrow as 10 nm.« less

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

PubMed Central

Smith, Selena Y.; Collinson, Margaret E.; Rudall, Paula J.; Simpson, David A.; Marone, Federica; Stampanoni, Marco

2009-01-01

While more commonly applied in zoology, synchrotron radiation X-ray tomographic microscopy (SRXTM) is well-suited to nondestructive study of the morphology and anatomy of both fossil and modern plants. SRXTM uses hard X-rays and a monochromatic light source to provide high-resolution data with little beam-hardening, resulting in slice data with clear boundaries between materials. Anatomy is readily visualized, including various planes of section from a single specimen, as clear as in traditional histological sectioning at low magnifications. Thus, digital sectioning of rare or difficult material is possible. Differential X-ray attenuation allows visualization of different layers or chemistries to enable virtual 3-dimensional (3D) dissections of material. Virtual potential fossils can be visualized and digital tissue removal reveals cryptic underlying morphology. This is essential for fossil identification and for comparisons between assemblages where fossils are preserved by different means. SRXTM is a powerful approach for botanical studies using morphology and anatomy. The ability to gain search images in both 2D and 3D for potential fossils gives paleobotanists a tool—virtual taphonomy—to improve our understanding of plant evolution and paleobiogeography. PMID:19574457

Two-photon speckle illumination for super-resolution microscopy.

PubMed

Negash, Awoke; Labouesse, Simon; Chaumet, Patrick C; Belkebir, Kamal; Giovannini, Hugues; Allain, Marc; Idier, Jérôme; Sentenac, Anne

2018-06-01

We present a numerical study of a microscopy setup in which the sample is illuminated with uncontrolled speckle patterns and the two-photon excitation fluorescence is collected on a camera. We show that, using a simple deconvolution algorithm for processing the speckle low-resolution images, this wide-field imaging technique exhibits resolution significantly better than that of two-photon excitation scanning microscopy or one-photon excitation bright-field microscopy.

Locality-Aware CTA Clustering For Modern GPUs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Ang; Song, Shuaiwen; Liu, Weifeng

2017-04-08

In this paper, we proposed a novel clustering technique for tapping into the performance potential of a largely ignored type of locality: inter-CTA locality. We first demonstrated the capability of the existing GPU hardware to exploit such locality, both spatially and temporally, on L1 or L1/Tex unified cache. To verify the potential of this locality, we quantified its existence in a broad spectrum of applications and discussed its sources of origin. Based on these insights, we proposed the concept of CTA-Clustering and its associated software techniques. Finally, We evaluated these techniques on all modern generations of NVIDIA GPU architectures. Themore » experimental results showed that our proposed clustering techniques could significantly improve on-chip cache performance.« less

Modern adjuncts and technologies in microsurgery: an historical and evidence-based review.

PubMed

Pratt, George F; Rozen, Warren M; Chubb, Daniel; Whitaker, Iain S; Grinsell, Damien; Ashton, Mark W; Acosta, Rafael

2010-11-01

While modern reconstructive surgery was revolutionized with the introduction of microsurgical techniques, microsurgery itself has seen the introduction of a range of technological aids and modern techniques aiming to improve dissection times, anastomotic times, and overall outcomes. These include improved preoperative planning, anastomotic aides, and earlier detection of complications with higher salvage rates. Despite the potential for substantial impact, many of these techniques have been evaluated in a limited fashion, and the evidence for each has not been universally explored. The purpose of this review was to establish and quantify the evidence for each technique. A search of relevant medical databases was performed to identify literature providing evidence for each technology. Levels of evidence were thus accumulated and applied to each technique. There is a relative paucity of evidence for many of the more recent technologies described in the field of microsurgery, with no randomized controlled trials, and most studies in the field comprising case series only. Current evidence-based suggestions include the use of computed tomographic angiography (CTA) for the preoperative planning of perforator flaps, the intraoperative use of a mechanical anastomotic coupling aide (particularly the Unilink® coupler), and postoperative flap monitoring with strict protocols using clinical bedside monitoring and/or the implantable Doppler probe. Despite the breadth of technologies introduced into the field of microsurgery, there is substantial variation in the degree of evidence presented for each, suggesting the role for much future research, particularly from emerging technologies such as robotics and modern simulators. Copyright © 2010 Wiley-Liss, Inc.

Nanoscale elasticity mappings of micro-constituents of abalone shell by band excitation-contact resonance force microscopy

NASA Astrophysics Data System (ADS)

Li, Tao; Zeng, Kaiyang

2014-01-01

The macroscopic mechanical properties of the abalone shell have been studied extensively in the literature, but the in situ nanoscale elasticity of various micro-constituents in the shell have not been characterized and reported yet. In this study, the nanoscale elasticity mappings including different micro-constituents in abalone shell were observed by using the Contact Resonance Force Microscopy (CR-FM) technique. CR-FM is one of the advanced scanning probe microscopy techniques that is able to quantify the local elastic moduli of various materials in a non-destructive manner. Instead of an average value, an elasticity mapping that reveals the nanoscale variations of elastic moduli with location can be extracted and correlated with the topography of the structure. Therefore in this study, by adopting the CR-FM technique that is incorporated with the band excitation technique, the elasticity variations of the abalone shell caused by different micro-constituents and crystal orientations are reported, and the elasticity values of the aragonite and calcite nanograins are quantified.The macroscopic mechanical properties of the abalone shell have been studied extensively in the literature, but the in situ nanoscale elasticity of various micro-constituents in the shell have not been characterized and reported yet. In this study, the nanoscale elasticity mappings including different micro-constituents in abalone shell were observed by using the Contact Resonance Force Microscopy (CR-FM) technique. CR-FM is one of the advanced scanning probe microscopy techniques that is able to quantify the local elastic moduli of various materials in a non-destructive manner. Instead of an average value, an elasticity mapping that reveals the nanoscale variations of elastic moduli with location can be extracted and correlated with the topography of the structure. Therefore in this study, by adopting the CR-FM technique that is incorporated with the band excitation technique, the elasticity variations of the abalone shell caused by different micro-constituents and crystal orientations are reported, and the elasticity values of the aragonite and calcite nanograins are quantified. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr05292c

A Survey of Architectural Techniques For Improving Cache Power Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mittal, Sparsh

Modern processors are using increasingly larger sized on-chip caches. Also, with each CMOS technology generation, there has been a significant increase in their leakage energy consumption. For this reason, cache power management has become a crucial research issue in modern processor design. To address this challenge and also meet the goals of sustainable computing, researchers have proposed several techniques for improving energy efficiency of cache architectures. This paper surveys recent architectural techniques for improving cache power efficiency and also presents a classification of these techniques based on their characteristics. For providing an application perspective, this paper also reviews several real-worldmore » processor chips that employ cache energy saving techniques. The aim of this survey is to enable engineers and researchers to get insights into the techniques for improving cache power efficiency and motivate them to invent novel solutions for enabling low-power operation of caches.« less

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

High-resolution imaging by scanning electron microscopy of semithin sections in correlation with light microscopy.

PubMed

Koga, Daisuke; Kusumi, Satoshi; Shodo, Ryusuke; Dan, Yukari; Ushiki, Tatsuo

2015-12-01

In this study, we introduce scanning electron microscopy (SEM) of semithin resin sections. In this technique, semithin sections were adhered on glass slides, stained with both uranyl acetate and lead citrate, and observed with a backscattered electron detector at a low accelerating voltage. As the specimens are stained in the same manner as conventional transmission electron microscopy (TEM), the contrast of SEM images of semithin sections was similar to TEM images of ultrathin sections. Using this technique, wide areas of semithin sections were also observed by SEM, without the obstruction of grids, which was inevitable for traditional TEM. This study also applied semithin section SEM to correlative light and electron microscopy. Correlative immunofluorescence microscopy and immune-SEM were performed in semithin sections of LR white resin-embedded specimens using a FluoroNanogold-labeled secondary antibody. Because LR white resin is hydrophilic and electron stable, this resin is suitable for immunostaining and SEM observation. Using correlative microscopy, the precise localization of the primary antibody was demonstrated by fluorescence microscopy and SEM. This method has great potential for studies examining the precise localization of molecules, including Golgi- and ER-associated proteins, in correlation with LM and SEM. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

X-ray microscopy of live biological micro-organisms

NASA Astrophysics Data System (ADS)

Raja Al-Ani, Ma'an Nassar

Real-time, compact x-ray microscopy has the potential to benefit many scientific fields, including microbiology, pharmacology, organic chemistry, and physics. Single frame x-ray micro-radiography, produced by a compact, solid-state laser plasma source, allows scientists to use x-ray emission for elemental analysis, and to observe biological specimens in their natural state. In this study, x-ray images of mouse kidney tissue, live bacteria, Pseudomonas aeruginosa and Burkholderia cepacia, and the bacteria's interaction with the antibiotic gentamicin, are examined using x-ray microscopy. For the purposes of comparing between confocal microscopy and x-ray microscopy, we introduced to our work the technique of gold labeling. Indirect immunofluorescence staining and immuno-gold labeling were applied on human lymphocytes and human tumor cells. Differential interference contrast microscopy (DIC) showed the lymphocyte body and nucleus, as did x-ray microscopy. However, the high resolution of x-ray microscopy allows us to differentiate between the gold particles bound to the antibodies and the free gold. A compact, tabletop Nd: glass laser is used in this study to produce x-rays from an Yttrium target. An atomic force microscope is used to scan the x-ray images from the developed photo-resist. The use of compact, tabletop laser plasma sources, in conjunction with x-ray microscopy, is a new technique that has great potential as a flexible, user-friendly scientific research tool.

Strategies for Fermentation Medium Optimization: An In-Depth Review

PubMed Central

Singh, Vineeta; Haque, Shafiul; Niwas, Ram; Srivastava, Akansha; Pasupuleti, Mukesh; Tripathi, C. K. M.

2017-01-01

Optimization of production medium is required to maximize the metabolite yield. This can be achieved by using a wide range of techniques from classical “one-factor-at-a-time” to modern statistical and mathematical techniques, viz. artificial neural network (ANN), genetic algorithm (GA) etc. Every technique comes with its own advantages and disadvantages, and despite drawbacks some techniques are applied to obtain best results. Use of various optimization techniques in combination also provides the desirable results. In this article an attempt has been made to review the currently used media optimization techniques applied during fermentation process of metabolite production. Comparative analysis of the merits and demerits of various conventional as well as modern optimization techniques have been done and logical selection basis for the designing of fermentation medium has been given in the present review. Overall, this review will provide the rationale for the selection of suitable optimization technique for media designing employed during the fermentation process of metabolite production. PMID:28111566

Determination of the electrical resistivity of vertically aligned carbon nanotubes by scanning probe microscopy

NASA Astrophysics Data System (ADS)

Ageev, O. A.; Il'in, O. I.; Rubashkina, M. V.; Smirnov, V. A.; Fedotov, A. A.; Tsukanova, O. G.

2015-07-01

Techniques are developed to determine the resistance per unit length and the electrical resistivity of vertically aligned carbon nanotubes (VA CNTs) using atomic force microscopy (AFM) and scanning tunneling microscopy (STM). These techniques are used to study the resistance of VA CNTs. The resistance of an individual VA CNT calculated with the AFM-based technique is shown to be higher than the resistance of VA CNTs determined by the STM-based technique by a factor of 200, which is related to the influence of the resistance of the contact of an AFM probe to VA CNTs. The resistance per unit length and the electrical resistivity of an individual VA CNT 118 ± 39 nm in diameter and 2.23 ± 0.37 μm in height that are determined by the STM-based technique are 19.28 ± 3.08 kΩ/μm and 8.32 ± 3.18 × 10-4 Ω m, respectively. The STM-based technique developed to determine the resistance per unit length and the electrical resistivity of VA CNTs can be used to diagnose the electrical parameters of VA CNTs and to create VA CNT-based nanoelectronic elements.

Cassette Series Designed for Live-Cell Imaging of Proteins and High Resolution Techniques in Yeast

PubMed Central

Young, Carissa L.; Raden, David L.; Caplan, Jeffrey; Czymmek, Kirk; Robinson, Anne S.

2012-01-01

During the past decade, it has become clear that protein function and regulation are highly dependent upon intracellular localization. Although fluorescent protein variants are ubiquitously used to monitor protein dynamics, localization, and abundance; fluorescent light microscopy techniques often lack the resolution to explore protein heterogeneity and cellular ultrastructure. Several approaches have been developed to identify, characterize, and monitor the spatial localization of proteins and complexes at the sub-organelle level; yet, many of these techniques have not been applied to yeast. Thus, we have constructed a series of cassettes containing codon-optimized epitope tags, fluorescent protein variants that cover the full spectrum of visible light, a TetCys motif used for FlAsH-based localization, and the first evaluation in yeast of a photoswitchable variant – mEos2 – to monitor discrete subpopulations of proteins via confocal microscopy. This series of modules, complete with six different selection markers, provides the optimal flexibility during live-cell imaging and multicolor labeling in vivo. Furthermore, high-resolution imaging techniques include the yeast-enhanced TetCys motif that is compatible with diaminobenzidine photooxidation used for protein localization by electron microscopy and mEos2 that is ideal for super-resolution microscopy. We have examined the utility of our cassettes by analyzing all probes fused to the C-terminus of Sec61, a polytopic membrane protein of the endoplasmic reticulum of moderate protein concentration, in order to directly compare fluorescent probes, their utility and technical applications. Our series of cassettes expand the repertoire of molecular tools available to advance targeted spatiotemporal investigations using multiple live-cell, super-resolution or electron microscopy imaging techniques. PMID:22473760

Nondestructive evaluation of structural ceramics by photoacoustic microscopy

NASA Technical Reports Server (NTRS)

Khandelwal, Pramod K.

1987-01-01

A photoacoustic microscopy (PAM) digital imaging system was developed and utilized to characterize silicon nitride material at the various stages of the ceramic fabrication process. Correlation studies revealed that photoacoustic microscopy detected failure initiating defects in substantially more specimens than microradiography and ultrasonic techniques. Photoacoustic microscopy detected 10 to 100 micron size surface and subsurface pores and inclusions, respectively, up to 80 microns below the interrogating surface in machined sintered silicon nitride. Microradiography detected 50 micron diameter fracture controlling pores and inclusions. Subsurface holes were detected up to a depth of 570 microns and 1.00 mm in sintered silicon nitride and silicon carbide, respectively. Seeded voids of 20 to 30 micron diameters at the surface and 50 microns below the interrogating surface were detected by photoacoustic microscopy and microradiography with 1 percent X-ray thickness sensitivity. Tight surface cracks of 96 micron length x 48 micron depth were detected by photoacoustic microscopy. PAM volatilized and removed material in the green state which resulted in linear shallow microcracks after sintering. This significantly limits the use of PAM as an in-process NDE technique.

Application of modern tools and techniques to maximize engineering productivity in the development of orbital operations plans for the space station progrm

NASA Technical Reports Server (NTRS)

Manford, J. S.; Bennett, G. R.

1985-01-01

The Space Station Program will incorporate analysis of operations constraints and considerations in the early design phases to avoid the need for later modifications to the Space Station for operations. The application of modern tools and administrative techniques to minimize the cost of performing effective orbital operations planning and design analysis in the preliminary design phase of the Space Station Program is discussed. Tools and techniques discussed include: approach for rigorous analysis of operations functions, use of the resources of a large computer network, and providing for efficient research and access to information.

Genetically encoded sensors and fluorescence microscopy for anticancer research

NASA Astrophysics Data System (ADS)

Zagaynova, Elena V.; Shirmanova, Marina V.; Sergeeva, Tatiana F.; Klementieva, Natalia V.; Mishin, Alexander S.; Gavrina, Alena I.; Zlobovskay, Olga A.; Furman, Olga E.; Dudenkova, Varvara V.; Perelman, Gregory S.; Lukina, Maria M.; Lukyanov, Konstantin A.

2017-02-01

Early response of cancer cells to chemical compounds and chemotherapeutic drugs were studied using novel fluorescence tools and microscopy techniques. We applied confocal microscopy, two-photon fluorescence lifetime imaging microscopy and super-resolution localization-based microscopy to assess structural and functional changes in cancer cells in vitro. The dynamics of energy metabolism, intracellular pH, caspase-3 activation during staurosporine-induced apoptosis as well as actin cytoskeleton rearrangements under chemotherapy were evaluated. We have showed that new genetically encoded sensors and advanced fluorescence microscopy methods provide an efficient way for multiparameter analysis of cell activities

Scanning probe recognition microscopy investigation of tissue scaffold properties

PubMed Central

Fan, Yuan; Chen, Qian; Ayres, Virginia M; Baczewski, Andrew D; Udpa, Lalita; Kumar, Shiva

2007-01-01

Scanning probe recognition microscopy is a new scanning probe microscopy technique which enables selective scanning along individual nanofibers within a tissue scaffold. Statistically significant data for multiple properties can be collected by repetitively fine-scanning an identical region of interest. The results of a scanning probe recognition microscopy investigation of the surface roughness and elasticity of a series of tissue scaffolds are presented. Deconvolution and statistical methods were developed and used for data accuracy along curved nanofiber surfaces. Nanofiber features were also independently analyzed using transmission electron microscopy, with results that supported the scanning probe recognition microscopy-based analysis. PMID:18203431

Scanning probe recognition microscopy investigation of tissue scaffold properties.

PubMed

Fan, Yuan; Chen, Qian; Ayres, Virginia M; Baczewski, Andrew D; Udpa, Lalita; Kumar, Shiva

2007-01-01

Scanning probe recognition microscopy is a new scanning probe microscopy technique which enables selective scanning along individual nanofibers within a tissue scaffold. Statistically significant data for multiple properties can be collected by repetitively fine-scanning an identical region of interest. The results of a scanning probe recognition microscopy investigation of the surface roughness and elasticity of a series of tissue scaffolds are presented. Deconvolution and statistical methods were developed and used for data accuracy along curved nanofiber surfaces. Nanofiber features were also independently analyzed using transmission electron microscopy, with results that supported the scanning probe recognition microscopy-based analysis.

A study of reduced chromium content in a nickel-base superalloy via element substitution and rapid solidification processing. Ph.D. ThesisFinal Report

NASA Technical Reports Server (NTRS)

Powers, William O.

1987-01-01

A study of reduced chromium content in a nickel base superalloy via element substitution and rapid solidification processing was performed. The two elements used as partial substitutes for chromium were Si and Zr. The microstructure of conventionally solidified materials was characterized using microscopy techniques. These alloys were rapidly solidified using the chill block melt spinning technique and the rapidly solidified microstructures were characterized using electron microscopy. The spinning technique and the rapidly solidified microstructures was assessed following heat treatments at 1033 and 1272 K. Rapidly solidified material of three alloys was reduced to particulate form and consolidated using hot isostatic pressing (HIP). The consolidated materials were also characterized using microscopy techniques. In order to evaluate the relative strengths of the consolidated alloys, compression tests were performed at room temperature and 1033 K on samples of as-HIPed and HIPed plus solution treated material. Yield strength, porosity, and oxidation resistance characteristics are given and compared.

Infrared and Raman Microscopy in Cell Biology

PubMed Central

Matthäus, Christian; Bird, Benjamin; Miljković, Miloš; Chernenko, Tatyana; Romeo, Melissa; Diem, Max

2009-01-01

This chapter presents novel microscopic methods to monitor cell biological processes of live or fixed cells without the use of any dye, stains, or other contrast agent. These methods are based on spectral techniques that detect inherent spectroscopic properties of biochemical constituents of cells, or parts thereof. Two different modalities have been developed for this task. One of them is infrared micro-spectroscopy, in which an average snapshot of a cell’s biochemical composition is collected at a spatial resolution of typically 25 mm. This technique, which is extremely sensitive and can collect such a snapshot in fractions of a second, is particularly suited for studying gross biochemical changes. The other technique, Raman microscopy (also known as Raman micro-spectroscopy), is ideally suited to study variations of cellular composition on the scale of subcellular organelles, since its spatial resolution is as good as that of fluorescence microscopy. Both techniques exhibit the fingerprint sensitivity of vibrational spectroscopy toward biochemical composition, and can be used to follow a variety of cellular processes. PMID:19118679

A simple approach to characterizing block copolymer assemblies: graphene oxide supports for high contrast multi-technique imaging†

PubMed Central

Patterson, Joseph P.; Sanchez, Ana M.; Petzetakis, Nikos; Smart, Thomas P.; Epps, Thomas H.; Portman, Ian

2013-01-01

Block copolymers are well-known to self-assemble into a range of 3-dimensional morphologies. However, due to their nanoscale dimensions, resolving their exact structure can be a challenge. Transmission electron microscopy (TEM) is a powerful technique for achieving this, but for polymeric assemblies chemical fixing/staining techniques are usually required to increase image contrast and protect specimens from electron beam damage. Graphene oxide (GO) is a robust, water-dispersable, and nearly electron transparent membrane: an ideal support for TEM. We show that when using GO supports no stains are required to acquire high contrast TEM images and that the specimens remain stable under the electron beam for long periods, allowing sample analysis by a range of electron microscopy techniques. GO supports are also used for further characterization of assemblies by atomic force microscopy. The simplicity of sample preparation and analysis, as well as the potential for significantly increased contrast background, make GO supports an attractive alternative for the analysis of block copolymer assemblies. PMID:24049544

Correlative fractography: combining scanning electron microscopy and light microscopes for qualitative and quantitative analysis of fracture surfaces.

PubMed

Hein, Luis Rogerio de Oliveira; de Oliveira, José Alberto; de Campos, Kamila Amato

2013-04-01

Correlative fractography is a new expression proposed here to describe a new method for the association between scanning electron microscopy (SEM) and light microscopy (LM) for the qualitative and quantitative analysis of fracture surfaces. This article presents a new method involving the fusion of one elevation map obtained by extended depth from focus reconstruction from LM with exactly the same area by SEM and associated techniques, as X-ray mapping. The true topographic information is perfectly associated to local fracture mechanisms with this new technique, presented here as an alternative to stereo-pair reconstruction for the investigation of fractured components. The great advantage of this technique resides in the possibility of combining any imaging methods associated with LM and SEM for the same observed field from fracture surface.

Morphology of one-time coated palladium-alumina composite membrane prepared by sol-gel process and electroless plating technique

NASA Astrophysics Data System (ADS)

Sari, R.; Dewi, R.; Pardi; Hakim, L.; Diana, S.

2018-03-01

Palladium coated porous alumina ceramic membrane tube was obtained using a combination of sol-gel process and electroless plating technique. The thickness, structure and composition of palladium-alumina composite membrane were analyzed by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), and atomic force microscopy (AFM). Palladium particle size was 6.18 to 7.64 nm. Palladium membrane with thickness of approximately 301.5 to 815.1 nm was formed at the outer surface of the alumina layer. EDX data confirmed the formation of palladium-alumina membrane containing 45% of palladium. From this research it shows the combination of sol-gel process and electroless plating technique with one-time coating can produce a homogeneous and smoother palladium nano layer film on alumina substrate.

A combined confocal and magnetic resonance microscope for biological studies

NASA Astrophysics Data System (ADS)

Majors, Paul D.; Minard, Kevin R.; Ackerman, Eric J.; Holtom, Gary R.; Hopkins, Derek F.; Parkinson, Christopher I.; Weber, Thomas J.; Wind, Robert A.

2002-12-01

Complementary data acquired with different microscopy techniques provide a basis for establishing a more comprehensive understanding of cell function in health and disease, particularly when results acquired with different methodologies can be correlated in time and space. In this article, a novel microscope is described for studying live cells simultaneously with both confocal scanning laser fluorescence optical microscopy and magnetic resonance microscopy. The various design considerations necessary for integrating these two complementary techniques are discussed, the layout and specifications of the instrument are given, and examples of confocal and magnetic resonance images of large frog cells and model tumor spheroids obtained with the compound microscope are presented.

Room temperature chemical synthesis of lead selenide thin films with preferred orientation

NASA Astrophysics Data System (ADS)

Kale, R. B.; Sartale, S. D.; Ganesan, V.; Lokhande, C. D.; Lin, Yi-Feng; Lu, Shih-Yuan

2006-11-01

Room temperature chemical synthesis of PbSe thin films was carried out from aqueous ammoniacal solution using Pb(CH3COO)2 as Pb2+ and Na2SeSO3 as Se2- ion sources. The films were characterized by a various techniques including, X-ray diffraction (XRD), energy dispersive X-ray analysis (EDAX), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high resolution transmission electron microscopy (HR-TEM), selected area electron diffraction (SAED), Fast Fourier transform (FFT) and UV-vis-NIR techniques. The study revealed that the PbSe thin film consists of preferentially oriented nanocubes with energy band gap of 0.5 eV.

Single-shot optical sectioning using two-color probes in HiLo fluorescence microscopy.

PubMed

Muro, Eleonora; Vermeulen, Pierre; Ioannou, Andriani; Skourides, Paris; Dubertret, Benoit; Fragola, Alexandra; Loriette, Vincent

2011-06-08

We describe a wide-field fluorescence microscope setup which combines HiLo microscopy technique with the use of a two-color fluorescent probe. It allows one-shot fluorescence optical sectioning of thick biological moving sample which is illuminated simultaneously with a flat and a structured pattern at two different wavelengths. Both homogenous and structured fluorescence images are spectrally separated at detection and combined similarly with the HiLo microscopy technique. We present optically sectioned full-field images of Xenopus laevis embryos acquired at 25 images/s frame rate. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Enhanced Axial Resolution of Wide-Field Two-Photon Excitation Microscopy by Line Scanning Using a Digital Micromirror Device.

PubMed

Park, Jong Kang; Rowlands, Christopher J; So, Peter T C

2017-01-01

Temporal focusing multiphoton microscopy is a technique for performing highly parallelized multiphoton microscopy while still maintaining depth discrimination. While the conventional wide-field configuration for temporal focusing suffers from sub-optimal axial resolution, line scanning temporal focusing, implemented here using a digital micromirror device (DMD), can provide substantial improvement. The DMD-based line scanning temporal focusing technique dynamically trades off the degree of parallelization, and hence imaging speed, for axial resolution, allowing performance parameters to be adapted to the experimental requirements. We demonstrate this new instrument in calibration specimens and in biological specimens, including a mouse kidney slice.

Enhanced Axial Resolution of Wide-Field Two-Photon Excitation Microscopy by Line Scanning Using a Digital Micromirror Device

PubMed Central

Park, Jong Kang; Rowlands, Christopher J.; So, Peter T. C.

2017-01-01

Temporal focusing multiphoton microscopy is a technique for performing highly parallelized multiphoton microscopy while still maintaining depth discrimination. While the conventional wide-field configuration for temporal focusing suffers from sub-optimal axial resolution, line scanning temporal focusing, implemented here using a digital micromirror device (DMD), can provide substantial improvement. The DMD-based line scanning temporal focusing technique dynamically trades off the degree of parallelization, and hence imaging speed, for axial resolution, allowing performance parameters to be adapted to the experimental requirements. We demonstrate this new instrument in calibration specimens and in biological specimens, including a mouse kidney slice. PMID:29387484

Physicochemical characterization and failure analysis of military coating systems

NASA Astrophysics Data System (ADS)

Keene, Lionel Thomas

Modern military coating systems, as fielded by all branches of the U.S. military, generally consist of a diverse array of organic and inorganic components that can complicate their physicochemical analysis. These coating systems consist of VOC-solvent/waterborne automotive grade polyurethane matrix containing a variety of inorganic pigments and flattening agents. The research presented here was designed to overcome the practical difficulties regarding the study of such systems through the combined application of several cross-disciplinary techniques, including vibrational spectroscopy, electron microscopy, microtomy, ultra-fast laser ablation and optical interferometry. The goal of this research has been to determine the degree and spatial progression of weathering-induced alteration of military coating systems as a whole, as well as to determine the failure modes involved, and characterizing the impact of these failures on the physical barrier performance of the coatings. Transmission-mode Fourier Transform Infrared (FTIR) spectroscopy has been applied to cross-sections of both baseline and artificially weathered samples to elucidate weathering-induced spatial gradients to the baseline chemistry of the coatings. A large discrepancy in physical durability (as indicated by the spatial progression of these gradients) has been found between older and newer generation coatings. Data will be shown implicating silica fillers (previously considered inert) as the probable cause for this behavioral divergence. A case study is presented wherein the application of the aforementioned FTIR technique fails to predict the durability of the coating system as a whole. The exploitation of the ultra-fast optical phenomenon of femtosecond (10-15S) laser ablation is studied as a potential tool to facilitate spectroscopic depth profiling of composite materials. Finally, the interferometric technique of Phase Shifting was evaluated as a potential high-sensitivity technique applied to the problem of determining internal stress evolution in curing and aging coatings.

Microbiologically influenced corrosion: looking to the future.

PubMed

Videla, Héctor A; Herrera, Liz K

2005-09-01

This review discusses the state-of-the-art of research into biocorrosion and the biofouling of metals and alloys of industrial usage. The key concepts needed to understand the main effects of microorganisms on metal decay, and current trends in monitoring and control strategies to mitigate the deleterious effects of biocorrosion and biofouling are also described. Several relevant cases of biocorrosion studied by our research group are provided as examples: (i) biocorrosion of aluminum and its alloys by fungal contaminants of jet fuels; (ii) sulfate-reducing bacteria (SRB)-induced corrosion of steel; (iii) biocorrosion and biofouling interactions in the marine environment; (iv) monitoring strategies for assessing biocorrosion in industrial water systems; (v) microbial inhibition of corrosion; (vi) use and limitations of electrochemical techniques for evaluating biocorrosion effects. Future prospects in the field are described with respect to the potential of innovative techniques in microscopy (environmental scanning electron microscopy, confocal scanning laser microscopy, atomic force microscopy), new spectroscopic techniques for the study of corrosion products and biofilms (energy dispersion X-ray analysis, X-ray photoelectron spectroscopy, electron microprobe analysis) and electrochemistry (electrochemical impedance spectroscopy, electrochemical noise analysis).

Review of combined isotopic and optical nanoscopy

PubMed Central

Richter, Katharina N.; Rizzoli, Silvio O.; Jähne, Sebastian; Vogts, Angela; Lovric, Jelena

2017-01-01

Abstract. Investigating the detailed substructure of the cell is beyond the ability of conventional optical microscopy. Electron microscopy, therefore, has been the only option for such studies for several decades. The recent implementation of several super-resolution optical microscopy techniques has rendered the investigation of cellular substructure easier and more efficient. Nevertheless, optical microscopy only provides an image of the present structure of the cell, without any information on its long-temporal changes. These can be investigated by combining super-resolution optics with a nonoptical imaging technique, nanoscale secondary ion mass spectrometry, which investigates the isotopic composition of the samples. The resulting technique, combined isotopic and optical nanoscopy, enables the investigation of both the structure and the “history” of the cellular elements. The age and the turnover of cellular organelles can be read by isotopic imaging, while the structure can be analyzed by optical (fluorescence) approaches. We present these technologies, and we discuss their implementation for the study of biological samples. We conclude that, albeit complex, this type of technology is reliable enough for mass application to cell biology. PMID:28466025

Coherent optical adaptive technique improves the spatial resolution of STED microscopy in thick samples

PubMed Central

Yan, Wei; Yang, Yanlong; Tan, Yu; Chen, Xun; Li, Yang; Qu, Junle; Ye, Tong

2018-01-01

Stimulated emission depletion microscopy (STED) is one of far-field optical microscopy techniques that can provide sub-diffraction spatial resolution. The spatial resolution of the STED microscopy is determined by the specially engineered beam profile of the depletion beam and its power. However, the beam profile of the depletion beam may be distorted due to aberrations of optical systems and inhomogeneity of specimens’ optical properties, resulting in a compromised spatial resolution. The situation gets deteriorated when thick samples are imaged. In the worst case, the sever distortion of the depletion beam profile may cause complete loss of the super resolution effect no matter how much depletion power is applied to specimens. Previously several adaptive optics approaches have been explored to compensate aberrations of systems and specimens. However, it is hard to correct the complicated high-order optical aberrations of specimens. In this report, we demonstrate that the complicated distorted wavefront from a thick phantom sample can be measured by using the coherent optical adaptive technique (COAT). The full correction can effectively maintain and improve the spatial resolution in imaging thick samples. PMID:29400356

Orbital angular momentum light in microscopy

PubMed Central

2017-01-01

Light with a helical phase has had an impact on optical imaging, pushing the limits of resolution or sensitivity. Here, special emphasis will be given to classical light microscopy of phase samples and to Fourier filtering techniques with a helical phase profile, such as the spiral phase contrast technique in its many variants and areas of application. This article is part of the themed issue ‘Optical orbital angular momentum’. PMID:28069768

Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope.

PubMed

Kaufmann, Anna; Mickoleit, Michaela; Weber, Michael; Huisken, Jan

2012-09-01

Light sheet microscopy techniques, such as selective plane illumination microscopy (SPIM), are ideally suited for time-lapse imaging of developmental processes lasting several hours to a few days. The success of this promising technology has mainly been limited by the lack of suitable techniques for mounting fragile samples. Embedding zebrafish embryos in agarose, which is common in conventional confocal microscopy, has resulted in severe growth defects and unreliable results. In this study, we systematically quantified the viability and mobility of zebrafish embryos mounted under more suitable conditions. We found that tubes made of fluorinated ethylene propylene (FEP) filled with low concentrations of agarose or methylcellulose provided an optimal balance between sufficient confinement of the living embryo in a physiological environment over 3 days and optical clarity suitable for fluorescence imaging. We also compared the effect of different concentrations of Tricaine on the development of zebrafish and provide guidelines for its optimal use depending on the application. Our results will make light sheet microscopy techniques applicable to more fields of developmental biology, in particular the multiview long-term imaging of zebrafish embryos and other small organisms. Furthermore, the refinement of sample preparation for in toto and in vivo imaging will promote other emerging optical imaging techniques, such as optical projection tomography (OPT).

Application of microscopy technique and high performance liquid chromatography for quality assessment of Polygonum multiflorum Thunb. (Heshouwu)

PubMed Central

Liang, Li; Zhao, Zhongzhen; Kang, Tingguo

2014-01-01

Background: The technique of microscopy has been applied for identification of Chinese materia medica (CMM) since decades. However, very few scientific publications report the combination of conventional microscopy and high performance liquid chromatography (HPLC) techniques for further application to quality assessment of CMM. Objective: The objective of this study is to analyze the quality of the dried root tuber of Polygonum multiflorum Thunb. (Heshouwu) and to establish the relationships between 2,3,5,4’-tetrahydroxystilbene-2-O-β-glucoside, combined anthraquinone (CAQ) and quantity of clusters of calcium oxalate. Materials and Methods: In this study, microscopy and HPLC techniques were applied to assess the quality of P. multiflorum Thunb., and SPSS software was used to establish the relationship between microscopic characteristics and chemical components. Results: The results showed close and direct correlations between the quantity of clusters of calcium oxalate in P. multiflorum Thunb. and the contents of 2,3,5,4’-tetrahydroxystilbene-2-O-β-glucoside and CAQ. From these results, it can be deduced that Polygoni Multiflori Radix with a higher quantity of clusters of calcium oxalate should be of better quality. Conclusion: The established method can be helpful for evaluating the quality of CMM based upon the identification and quantitation of chemical and ergastic substance of cells. PMID:25422540

Housing Improvements and Malaria Risk in Sub-Saharan Africa: A Multi-Country Analysis of Survey Data

PubMed Central

Bottomley, Christian; Gibson, Harry; Kleinschmidt, Immo; Tatem, Andrew J.; Gething, Peter W.

2017-01-01

Background Improvements to housing may contribute to malaria control and elimination by reducing house entry by malaria vectors and thus exposure to biting. We tested the hypothesis that the odds of malaria infection are lower in modern, improved housing compared to traditional housing in sub-Saharan Africa (SSA). Methods and Findings We analysed 15 Demographic and Health Surveys (DHS) and 14 Malaria Indicator Surveys (MIS) conducted in 21 countries in SSA between 2008 and 2015 that measured malaria infection by microscopy or rapid diagnostic test (RDT). DHS/MIS surveys record whether houses are built with finished materials (e.g., metal) or rudimentary materials (e.g., thatch). This information was used to develop a binary housing quality variable where houses built using finished wall, roof, and floor materials were classified as “modern”, and all other houses were classified as “traditional”. Conditional logistic regression was used to determine the association between housing quality and prevalence of malaria infection in children aged 0–5 y, adjusting for age, gender, insecticide-treated net (ITN) use, indoor residual spraying, household wealth, and geographic cluster. Individual survey odds ratios (ORs) were combined to determine a summary OR using a random effects meta-analysis. Of 284,532 total children surveyed, 139,318 were tested for malaria infection using microscopy (n = 131,652) or RDT (n = 138,540). Within individual surveys, malaria prevalence measured by microscopy ranged from 0.4% (Madagascar 2011) to 45.5% (Burkina Faso 2010) among children living in modern houses and from 0.4% (The Gambia 2013) to 70.6% (Burkina Faso 2010) in traditional houses, and malaria prevalence measured by RDT ranged from 0.3% (Senegal 2013–2014) to 61.2% (Burkina Faso 2010) in modern houses and from 1.5% (The Gambia 2013) to 79.8% (Burkina Faso 2010) in traditional houses. Across all surveys, modern housing was associated with a 9% to 14% reduction in the odds of malaria infection (microscopy: adjusted OR 0.91, 95% CI 0.85–0.97, p = 0.003; RDT: adjusted OR 0.86, 95% CI 0.80–0.92, p < 0.001). This association was consistent regardless of ITN usage. As a comparison, the odds of malaria infection were 15% to 16% lower among ITN users versus non-users (microscopy: adjusted OR 0.84, 95% CI 0.79–0.90, p < 0.001; RDT: adjusted OR 0.85, 95% CI 0.80–0.90, p < 0.001). The main limitation of this study is that residual confounding by household wealth of the observed association between housing quality and malaria prevalence is possible, since the wealth index may not have fully captured differences in socioeconomic position; however, the use of multiple national surveys offers the advantage of a large sample size and the elimination of many biases typically associated with pooling observational data. Conclusions Housing quality is an important risk factor for malaria infection across the spectrum of malaria endemicity in SSA, with a strength of association between housing quality and malaria similar to that observed between ITN use and malaria. Improved housing should be considered a promising intervention for malaria control and elimination and long-term prevention of reintroduction. PMID:28222094

Coherent Anti-Stokes Raman Scattering Spectroscopy of Single Molecules in Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sunney Xie, Wei Min, Chris Freudiger, Sijia Lu

2012-01-18

During this funding period, we have developed two breakthrough techniques. The first is stimulated Raman scattering microscopy, providing label-free chemical contrast for chemical and biomedical imaging based on vibrational spectroscopy. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. We developed a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-freemore » and readily interpretable chemical contrast. We demonstrated a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis. This technology offers exciting prospect for medical imaging. The second technology we developed is stimulated emission microscopy. Many chromophores, such as haemoglobin and cytochromes, absorb but have undetectable fluorescence because the spontaneous emission is dominated by their fast non-radiative decay. Yet the detection of their absorption is difficult under a microscope. We use stimulated emission, which competes effectively with the nonradiative decay, to make the chromophores detectable, as a new contrast mechanism for optical microscopy. We demonstrate a variety of applications of stimulated emission microscopy, such as visualizing chromoproteins, non-fluorescent variants of the green fluorescent protein, monitoring lacZ gene expression with a chromogenic reporter, mapping transdermal drug distribu- tions without histological sectioning, and label-free microvascular imaging based on endogenous contrast of haemoglobin. For all these applications, sensitivity is orders of magnitude higher than for spontaneous emission or absorption contrast, permitting nonfluorescent reporters for molecular imaging. Although we did not accomplish the original goal of detecting single-molecule by CARS, our quest for high sensitivity of nonlinear optical microscopy paid off in providing the two brand new enabling technologies. Both techniques were greatly benefited from the use of high frequency modulation for microscopy, which led to orders of magnitude increase in sensitivity. Extensive efforts have been made on optics and electronics to accomplish these breakthroughs.« less

Modern Radiation Therapy for Nodal Non-Hodgkin Lymphoma—Target Definition and Dose Guidelines From the International Lymphoma Radiation Oncology Group

DOE Office of Scientific and Technical Information (OSTI.GOV)

Illidge, Tim, E-mail: Tim.Illidge@ics.manchester.ac.uk; Specht, Lena; Yahalom, Joachim

2014-05-01

Radiation therapy (RT) is the most effective single modality for local control of non-Hodgkin lymphoma (NHL) and is an important component of therapy for many patients. Many of the historic concepts of dose and volume have recently been challenged by the advent of modern imaging and RT planning tools. The International Lymphoma Radiation Oncology Group (ILROG) has developed these guidelines after multinational meetings and analysis of available evidence. The guidelines represent an agreed consensus view of the ILROG steering committee on the use of RT in NHL in the modern era. The roles of reduced volume and reduced doses aremore » addressed, integrating modern imaging with 3-dimensional planning and advanced techniques of RT delivery. In the modern era, in which combined-modality treatment with systemic therapy is appropriate, the previously applied extended-field and involved-field RT techniques that targeted nodal regions have now been replaced by limiting the RT to smaller volumes based solely on detectable nodal involvement at presentation. A new concept, involved-site RT, defines the clinical target volume. For indolent NHL, often treated with RT alone, larger fields should be considered. Newer treatment techniques, including intensity modulated RT, breath holding, image guided RT, and 4-dimensional imaging, should be implemented, and their use is expected to decrease significantly the risk for normal tissue damage while still achieving the primary goal of local tumor control.« less

Imaging TiO2 nanoparticles on GaN nanowires with electrostatic force microscopy

NASA Astrophysics Data System (ADS)

Xie, Ting; Wen, Baomei; Liu, Guannan; Guo, Shiqi; Motayed, Abhishek; Murphy, Thomas; Gomez, R. D.

Gallium nitride (GaN) nanowires that are functionalized with metal-oxides nanoparticles have been explored extensively for gas sensing applications in the past few years. These sensors have several advantages over conventional schemes, including miniature size, low-power consumption and fast response and recovery times. The morphology of the oxide functionalization layer is critical to achieve faster response and recovery times, with the optimal size distribution of nanoparticles being in the range of 10 to 30 nm. However, it is challenging to characterize these nanoparticles on GaN nanowires using common techniques such as scanning electron microscopy, transmission electron microscopy, and x-ray diffraction. Here, we demonstrate electrostatic force microscopy in combination with atomic force microscopy as a non-destructive technique for morphological characterization of the dispersed TiO2 nanoparticles on GaN nanowires. We also discuss the applicability of this method to other material systems with a proposed tip-surface capacitor model. This project was sponsored through N5 Sensors and the Maryland Industrial Partnerships (MIPS, #5418).

Fluorescence Imaging of Posterior Spiracles from Second and Third Instars of Forensically-important Chrysomya rufifacies (Diptera: Calliphoridae)*

PubMed Central

Flores, Danielle; Miller, Amy L.; Showman, Angelique; Tobita, Caitlyn; Shimoda, Lori M.N.; Sung, Carl; Stokes, Alexander J.; Tomberlin, Jeffrey K.; Carter, David O.; Turner, Helen

2016-01-01

Entomological protocols for aging blow fly (Diptera: Calliphoridae) larvae to estimate the time of colonization (TOC) are commonly used to assist in death investigations. While the methodologies for analysing fly larvae differ, most rely on light microscopy, genetic analysis or, more rarely, electron microscopy. This pilot study sought to improve resolution of larval stage in the forensically-important blow fly Chrysomya rufifacies using high-content fluorescence microscopy and biochemical measures of developmental marker proteins. We established fixation and mounting protocols, defined a set of measurable morphometric criteria and captured developmental transitions of 2nd instar to 3rd instar using both fluorescence microscopy and anti-ecdysone receptor Western blot analysis. The data show that these instars can be distinguished on the basis of robust, non-bleaching, autofluorescence of larval posterior spiracles. High content imaging techniques using confocal microscopy, combined with morphometric and biochemical techniques, may therefore aid forensic entomologists in estimating TOC. PMID:27706817

Analysis-Preserving Video Microscopy Compression via Correlation and Mathematical Morphology

PubMed Central

Shao, Chong; Zhong, Alfred; Cribb, Jeremy; Osborne, Lukas D.; O’Brien, E. Timothy; Superfine, Richard; Mayer-Patel, Ketan; Taylor, Russell M.

2015-01-01

The large amount video data produced by multi-channel, high-resolution microscopy system drives the need for a new high-performance domain-specific video compression technique. We describe a novel compression method for video microscopy data. The method is based on Pearson's correlation and mathematical morphology. The method makes use of the point-spread function (PSF) in the microscopy video acquisition phase. We compare our method to other lossless compression methods and to lossy JPEG, JPEG2000 and H.264 compression for various kinds of video microscopy data including fluorescence video and brightfield video. We find that for certain data sets, the new method compresses much better than lossless compression with no impact on analysis results. It achieved a best compressed size of 0.77% of the original size, 25× smaller than the best lossless technique (which yields 20% for the same video). The compressed size scales with the video's scientific data content. Further testing showed that existing lossy algorithms greatly impacted data analysis at similar compression sizes. PMID:26435032

Modern quantitative schlieren techniques

NASA Astrophysics Data System (ADS)

Hargather, Michael; Settles, Gary

2010-11-01

Schlieren optical techniques have traditionally been used to qualitatively visualize refractive flowfields in transparent media. Modern schlieren optics, however, are increasingly focused on obtaining quantitative information such as temperature and density fields in a flow -- once the sole purview of interferometry -- without the need for coherent illumination. Quantitative data are obtained from schlieren images by integrating the measured refractive index gradient to obtain the refractive index field in an image. Ultimately this is converted to a density or temperature field using the Gladstone-Dale relationship, an equation of state, and geometry assumptions for the flowfield of interest. Several quantitative schlieren methods are reviewed here, including background-oriented schlieren (BOS), schlieren using a weak lens as a "standard," and "rainbow schlieren." Results are presented for the application of these techniques to measure density and temperature fields across a supersonic turbulent boundary layer and a low-speed free-convection boundary layer in air. Modern equipment, including digital cameras, LED light sources, and computer software that make this possible are also discussed.

Formation of porous silicon oxide from substrate-bound silicon rich silicon oxide layers by continuous-wave laser irradiation

NASA Astrophysics Data System (ADS)

Wang, Nan; Fricke-Begemann, Th.; Peretzki, P.; Ihlemann, J.; Seibt, M.

2018-03-01

Silicon nanocrystals embedded in silicon oxide that show room temperature photoluminescence (PL) have great potential in silicon light emission applications. Nanocrystalline silicon particle formation by laser irradiation has the unique advantage of spatially controlled heating, which is compatible with modern silicon micro-fabrication technology. In this paper, we employ continuous wave laser irradiation to decompose substrate-bound silicon-rich silicon oxide films into crystalline silicon particles and silicon dioxide. The resulting microstructure is studied using transmission electron microscopy techniques with considerable emphasis on the formation and properties of laser damaged regions which typically quench room temperature PL from the nanoparticles. It is shown that such regions consist of an amorphous matrix with a composition similar to silicon dioxide which contains some nanometric silicon particles in addition to pores. A mechanism referred to as "selective silicon ablation" is proposed which consistently explains the experimental observations. Implications for the damage-free laser decomposition of silicon-rich silicon oxides and also for controlled production of porous silicon dioxide films are discussed.

High-resolution non-destructive three-dimensional imaging of integrated circuits

NASA Astrophysics Data System (ADS)

Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H. R.; Dinapoli, Roberto; Müller, Elisabeth; Bunk, Oliver; Raabe, Jörg; Aeppli, Gabriel

2017-03-01

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography—a high-resolution coherent diffractive imaging technique—can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

Forensic geoscience: applications of geology, geomorphology and geophysics to criminal investigations

NASA Astrophysics Data System (ADS)

Ruffell, Alastair; McKinley, Jennifer

2005-03-01

One hundred years ago Georg Popp became the first scientist to present in court a case where the geological makeup of soils was used to secure a criminal conviction. Subsequently there have been significant advances in the theory and practice of forensic geoscience: many of them subsequent to the seminal publication of "Forensic Geology" by Murray and Tedrow [Murray, R., Tedrow, J.C.F. 1975 (republished 1986). Forensic Geology: Earth Sciences and Criminal Investigation. Rutgers University Press, New York, 240 pp.]. Our review places historical development in the modern context of how the allied disciplines of geology (mineralogy, sedimentology, microscopy), geophysics, soil science, microbiology, anthropology and geomorphology have been used as tool to aid forensic (domestic, serious, terrorist and international) crime investigations. The latter half of this paper uses the concept of scales of investigation, from large-scale landforms through to microscopic particles as a method of categorising the large number of geoscience applications to criminal investigation. Forensic geoscience has traditionally used established non-forensic techniques: 100 years after Popp's seminal work, research into forensic geoscience is beginning to lead, as opposed to follow other scientific disciplines.

Application of Pinniped Vibrissae to Aeropropulsion

NASA Technical Reports Server (NTRS)

Shyam, Vikram; Ameri, Ali; Poinsatte, Philip; Thurman, Douglas; Wroblewski, Adam; Snyder, Christopher

2015-01-01

Vibrissae of Phoca Vitulina (Harbor Seal) and Mirounga Angustirostris (Elephant Seal) possessundulations along their length. Harbor Seal Vibrissae were shown to reduce vortex induced vibrations and reduce dragcompared to appropriately scaled cylinders and ellipses. Samples of Harbor Seal vibrissae, Elephant Seal vibrissae andCalifornia Sea Lion vibrissae were collected from the Marine Mammal Center in California. CT scanning, microscopy and3D scanning techniques were utilized to characterize the whiskers. Computational fluid dynamics simulations of thewhiskers were carried out to compare them to an ellipse and a cylinder. Leading edge parameters from the whiskerswere used to create a 3D profile based on a modern power turbine blade. The NASA SW-2 facility was used to performwind tunnel cascade testing on the 'Seal Blades'. Computational Fluid Dynamics simulations were used to studyincidence angles from -37 to +10 degrees on the aerodynamic performance of the Seal Blade. The tests and simulationswere conducted at a Reynolds number of 100,000. The Seal Blades showed consistent performance improvements overthe baseline configuration. It was determined that a fuel burn reduction of approximately 5 could be achieved for a fixedwing aircraft. Noise reduction potential is also explored

Influence of Fe3O4 Nanoparticles in Hydroxyapatite Scaffolds on Proliferation of Primary Human Fibroblast Cells

NASA Astrophysics Data System (ADS)

Maleki-Ghaleh, H.; Aghaie, E.; Nadernezhad, A.; Zargarzadeh, M.; Khakzad, A.; Shakeri, M. S.; Beygi Khosrowshahi, Y.; Siadati, M. H.

2016-06-01

Modern techniques for expanding stem cells play a substantial role in tissue engineering: the raw material that facilitates regeneration of damaged tissues and treats diseases. The environmental conditions and bioprocessing methods are the primary determinants of the rate of cultured stem cell proliferation. Bioceramic scaffolds made of calcium phosphate are effective substrates for optimal cell proliferation. The present study investigates the effects of two bioceramic scaffolds on proliferating cells in culture media. One scaffold was made of hydroxyapatite and the other was a mixture of hydroxyapatite and ferromagnetic material (Fe3O4 nanoparticles). Disk-shaped (10 mm × 2 mm) samples of the two scaffolds were prepared. Primary human fibroblast proliferation was 1.8- and 2.5-fold faster, respectively, when cultured in the presence of hydroxyapatite or ferrous nanoparticle/hydroxyapatite mixtures. Optical microscopy images revealed that the increased proliferation was due to enhanced cell-cell contact. The presence of magnetic Fe3O4 nanoparticles in the ceramic scaffolds significantly increased cell proliferation compared to hydroxyapatite scaffolds and tissue culture polystyrene.

Ancient Coins and their Modern Fakes: An Attempt of Physico-Chemical Unmasking.

NASA Astrophysics Data System (ADS)

Mezzasalma, A. M.; Mondio, G.; Serafino, T.; De Fulvio, G.; Romeo, M.; Salici, A.

As a consequence of police operations in Messina (Sicily), a huge quantity of perfect imitations of ancient coins, realized by a sicilian forger, has been recently found. Such fakes have been realized by the lost wax casting technique and reproduce coins issued by different authorities in different historical epochs. In order to overcome the obvious subjectivity of the traditional (autoptical) numismatic analysis, which sometime provides contrasting interpretations, five of these fakes have been analysed by Scanning Electron Microscopy (SEM) and Energy Dispersed X-Ray Fluorescence (EDXRF). The results obtained have given information on the microstructure, the homogeneity and the elemental composition of the alloys used by the forger. Furthermore, evident traces of the chemical treatment utilized for the artificial ageing of the coins have been found. Due to the presumable and dangerous large diffusion of these sicilian fakes in the international market, the results of such analyses may certainly be of noticeable interest for Numismatics and forensic applications as well, representing a set of proofs to be used in the unmasking of analogous counterfeiting cases.

Controlled nanopatterning of a polymerized ionic liquid in a strong electric field

DOE PAGES

Bocharova, Vera; Agapov, Alexander L.; Tselev, Alexander; ...

2014-12-17

Nanolithography has become a driving force in advancements of the modern day's electronics, allowing for miniaturization of devices and a steady increase of the calculation, power, and storage densities. Among various nanofabrication approaches, scanning probe techniques, including atomic force microscopy (AFM), are versatile tools for creating nanoscale patterns utilizing a range of physical stimuli such as force, heat, or electric field confined to the nanoscale. In this study, the potential of using the electric field localized at the apex of an AFM tip to induce and control changes in the mechanical properties of an ion containing polymer—a polymerized ionic liquidmore » (PolyIL)—on a very localized scale is explored. In particular, it is demonstrated that by means of AFM, one can form topographical features on the surface of PolyIL-based thin films with a significantly lower electric potential and power consumption as compared to nonconductive polymer materials. Lastly,, by tuning the applied voltage and ambient air humidity, control over dimensions of the formed structures is reproducibly achieved.« less

Teledermatology: from historical perspective to emerging techniques of the modern era: part II: Emerging technologies in teledermatology, limitations and future directions.

PubMed

Coates, Sarah J; Kvedar, Joseph; Granstein, Richard D

2015-04-01

Telemedicine is the use of telecommunications technology to support health care at a distance. Dermatology relies on visual cues that are easily captured by imaging technologies, making it ideally suited for this care model. Advances in telecommunications technology have made it possible to deliver high-quality skin care when patient and provider are separated by both time and space. Most recently, mobile devices that connect users through cellular data networks have enabled teledermatologists to instantly communicate with primary care providers throughout the world. The availability of teledermoscopy provides an additional layer of visual information to enhance the quality of teleconsultations. Teledermatopathology has become increasingly feasible because of advances in digitization of entire microscopic slides and robot-assisted microscopy. Barriers to additional expansion of these services include underdeveloped infrastructure in remote regions, fragmented electronic medical records, and varying degrees of reimbursement. Teleconsultants also confront special legal and ethical challenges as they work toward building a global network of practicing physicians. Copyright © 2014 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Fossilization processes in siliceous thermal springs: trends in preservation along thermal gradients

NASA Technical Reports Server (NTRS)

Cady, S. L.; Farmer, J. D.

1996-01-01

To enhance our ability to extract palaeobiological and palaeoenvironmental information from ancient thermal spring deposits, we have studied the processes responsible for the development and preservation of stromatolites in modern subaerial thermal spring systems in Yellowstone National Park (USA). We investigated specimens collected from silica-depositing thermal springs along the thermal gradient using petrographic techniques and scanning electron microscopy. Although it is known that thermophilic cyanobacteria control the morphogenesis of thermal spring stromatolites below 73 degrees C, we have found that biofilms which contain filamentous thermophiles contribute to the microstructural development of subaerial geyserites that occur along the inner rims of thermal spring pools and geyser effluents. Biofilms intermittently colonize the surfaces of subaerial geyserites and provide a favoured substrate for opaline silica precipitation. We have also found that the preservation of biotically produced microfabrics of thermal spring sinters reflects dynamic balances between rates of population growth, decomposition of organic matter, silica deposition and early diagenesis. Major trends in preservation of thermophilic organisms along the thermal gradient are defined by differences in the mode of fossilization, including replacement, encrustation and permineralization.

Low-energy electron holographic imaging of individual tobacco mosaic virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Longchamp, Jean-Nicolas, E-mail: longchamp@physik.uzh.ch; Latychevskaia, Tatiana; Escher, Conrad

2015-09-28

Modern structural biology relies on Nuclear Magnetic Resonance (NMR), X-ray crystallography, and cryo-electron microscopy for gaining information on biomolecules at nanometer, sub-nanometer, or atomic resolution. All these methods, however, require averaging over a vast ensemble of entities, and hence knowledge on the conformational landscape of an individual particle is lost. Unfortunately, there are now strong indications that even X-ray free electron lasers will not be able to image individual molecules but will require nanocrystal samples. Here, we show that non-destructive structural biology of single particles has now become possible by means of low-energy electron holography. As an example, individual tobaccomore » mosaic virions deposited on ultraclean freestanding graphene are imaged at 1 nm resolution revealing structural details arising from the helical arrangement of the outer protein shell of the virus. Since low-energy electron holography is a lens-less technique and since electrons with a deBroglie wavelength of approximately 1 Å do not impose radiation damage to biomolecules, the method has the potential for Angstrom resolution imaging of single biomolecules.« less

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

NASA Astrophysics Data System (ADS)

Benza, Vincenzo G.; Bassetti, Bruno; Dorfman, Kevin D.; Scolari, Vittore F.; Bromek, Krystyna; Cicuta, Pietro; Cosentino Lagomarsino, Marco

2012-07-01

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.

Atom Probe Tomography Analysis of Gallium-Nitride-Based Light-Emitting Diodes

NASA Astrophysics Data System (ADS)

Prosa, Ty J.; Olson, David; Giddings, A. Devin; Clifton, Peter H.; Larson, David J.; Lefebvre, Williams

2014-03-01

Thin-film light-emitting diodes (LEDs) composed of GaN/InxGa1-xN/GaN quantum well (QW) structures are integrated into modern optoelectronic devices because of the tunable InGaN band-gap enabling emission of the full visible spectrum. Atom probe tomography (APT) offers unique capabilities for 3D device characterization including compositional mapping of nano-volumes (>106 nm3) , high detection efficiency (>50%), and good sensitivity. In this study, APT is used to understand the distribution of dopants as well as Al and In alloying agents in a GaN device. Measurements using transmission electron microscopy (TEM) and secondary ion mass spectrometry (SIMS) have also been made to improve the accuracy of the APT analysis by correlating the information content of these complimentary techniques. APT analysis reveals various QW and other optoelectronic structures including a Mg p-GaN layer, an Al-rich electron blocking layer, an In-rich multi-QW region, and an In-based super-lattice structure. The multi-QW composition shows good quantitative agreement with layer thickness and spacing extracted from a high resolution TEM image intensity analysis.

Recent advances in magnetic resonance microscopy to the physical structure characterization of carbonaceous and inorganic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory, D.M.; Gerald, R.E.; Cody, G.D.

1997-04-01

Magnetic resonance microscopy (MRM) techniques have been employed to study the molecular architectures and properties of structural polymers, fossil fuels, microporous carbons and inorganic catalysts.

Application of contrast media in post-mortem imaging (CT and MRI).

PubMed

Grabherr, Silke; Grimm, Jochen; Baumann, Pia; Mangin, Patrice

2015-09-01

The application of contrast media in post-mortem radiology differs from clinical approaches in living patients. Post-mortem changes in the vascular system and the absence of blood flow lead to specific problems that have to be considered for the performance of post-mortem angiography. In addition, interpreting the images is challenging due to technique-related and post-mortem artefacts that have to be known and that are specific for each applied technique. Although the idea of injecting contrast media is old, classic methods are not simply transferable to modern radiological techniques in forensic medicine, as they are mostly dedicated to single-organ studies or applicable only shortly after death. With the introduction of modern imaging techniques, such as post-mortem computed tomography (PMCT) and post-mortem magnetic resonance (PMMR), to forensic death investigations, intensive research started to explore their advantages and limitations compared to conventional autopsy. PMCT has already become a routine investigation in several centres, and different techniques have been developed to better visualise the vascular system and organ parenchyma in PMCT. In contrast, the use of PMMR is still limited due to practical issues, and research is now starting in the field of PMMR angiography. This article gives an overview of the problems in post-mortem contrast media application, the various classic and modern techniques, and the issues to consider by using different media.

Lensless microscopy technique for static and dynamic colloidal systems.

PubMed

Alvarez-Palacio, D C; Garcia-Sucerquia, J

2010-09-15

We present the application of a lensless microscopy technique known as digital in-line holographic microscopy (DIHM) to image dynamic and static colloidal systems of microspheres. DIHM has been perfected up to the point that submicrometer lateral resolution with several hundreds of micrometers depth of field is achieved with visible light; it is shown that the lateral resolution of DIHM is enough to resolve self-assembled colloidal monolayers built up from polystyrene spheres with submicrometer diameters. The time resolution of DIHM is of the order of 4 frames/s at 2048 x 2048 pixels, which represents an overall improvement of 16 times the time resolution of confocal scanning microscopy. This feature is applied to the visualization of the migration of dewetting fronts in dynamic colloidal systems and the formation of front-like arrangements of particles. Copyright 2010 Elsevier Inc. All rights reserved.

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

PubMed

Sosinsky, G E; Baker, T S; Hand, G; Ellisman, M H

1999-01-01

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise. Copyright 1999 Academic Press.

Setting up and running an advanced light microscopy and imaging facility.

PubMed

Sánchez, Carlos; Muñoz, Ma Ángeles; Villalba, Maite; Labrador, Verónica; Díez-Guerra, F Javier

2011-07-01

During the last twenty years, interest in light microscopy and imaging techniques has grown in various fields, such as molecular and cellular biology, developmental biology, and neurobiology. In addition, the number of scientific articles and journals using these techniques is rapidly increasing. Nowadays, most research institutions require sophisticated microscopy systems to cover their investigation demands. In general, such instruments are too expensive and complex to be purchased and managed by a single laboratory or research group, so they have to be shared with other groups and supervised by specialized personnel. This is the reason why microscopy and imaging facilities are becoming so important at research institutions nowadays. In this unit, we have gathered and presented a number of issues and considerations from our own experience that we hope will be helpful when planning or setting up a new facility.

Not all that glitters is gold-Electron microscopy study on uptake of gold nanoparticles in Daphnia magna and related artifacts.

PubMed

Jensen, Louise Helene Søgaard; Skjolding, Lars Michael; Thit, Amalie; Sørensen, Sara Nørgaard; Købler, Carsten; Mølhave, Kristian; Baun, Anders

2017-06-01

Increasing use of engineered nanoparticles has led to extensive research into their potential hazards to the environment and human health. Cellular uptake from the gut is sparsely investigated, and microscopy techniques applied for uptake studies can result in misinterpretations. Various microscopy techniques were used to investigate internalization of 10-nm gold nanoparticles in Daphnia magna gut lumen and gut epithelial cells following 24-h exposure and outline potential artifacts (i.e., high-contrast precipitates from sample preparation related to these techniques). Light sheet microscopy confirmed accumulation of gold nanoparticles in the gut lumen. Scanning transmission electron microscopy and elemental analysis revealed gold nanoparticles attached to the microvilli of gut cells. Interestingly, the peritrophic membrane appeared to act as a semipermeable barrier between the lumen and the gut epithelium, permitting only single particles through. Structures resembling nanoparticles were also observed inside gut cells. Elemental analysis could not verify these to be gold, and they were likely artifacts from the preparation, such as osmium and iron. Importantly, gold nanoparticles were found inside holocrine cells with disrupted membranes. Thus, false-positive observations of nanoparticle internalization may result from either preparation artifacts or mistaking disrupted cells for intact cells. These findings emphasize the importance of cell integrity and combining elemental analysis with the localization of internalized nanoparticles using transmission electron microscopy. Environ Toxicol Chem 2017;36:1503-1509. © 2016 SETAC. © 2016 SETAC.

The application of laser scanning confocal microscopy to the examination of hairs and textile fibers: an initial investigation.

PubMed

Kirkbride, K Paul; Tridico, Silvana R

2010-02-25

An initial investigation of the application of laser scanning confocal microscopy to the examination of hairs and fibers has been conducted. This technique allows the production of virtual transverse and longitudinal cross-sectional images of a wide range of hairs and fibers. Special mounting techniques are not required; specimens that have been mounted for conventional microscopy require no further treatment. Unlike physical cross-sectioning, in which it is difficult to produce multiple cross-sections from a single hair or fiber and the process is destructive, confocal microscopy allows the examiner to image the cross-section at any point in the field of view along the hair or fiber and it is non-destructive. Confocal microscopy is a fluorescence-based technique. The images described in this article were collected using only the autofluorescence exhibited by the specimen (i.e. fluorescence staining was not necessary). Colorless fibers generally and hairs required excitation at 405 nm in order to stimulate useful autofluorescence; longer wavelength excitation was suitable for dyed fibers. Although confocal microscopy was found to be generally applicable to the generation virtual transverse cross-sections from a wide range of hairs and fibers, on some occasions the autofluorescence signal was attenuated by heavy pigmentation or the presence of an opaque medulla in hairs, and by heavy delustering or the presence of air-filled voids in the case of fibers. In these situations only partial cross-sections were obtained. 2009 Elsevier Ireland Ltd. All rights reserved.

Lensfree On-Chip Microscopy and Tomography for Bio-Medical Applications

PubMed Central

Isikman, Serhan O.; Bishara, Waheb; Mudanyali, Onur; Sencan, Ikbal; Su, Ting-Wei; Tseng, Derek; Yaglidere, Oguzhan; Sikora, Uzair; Ozcan, Aydogan

2012-01-01

Lensfree on-chip holographic microscopy is an emerging technique that offers imaging of biological specimens over a large field-of-view without using any lenses or bulky optical components. Lending itself to a compact, cost-effective and mechanically robust architecture, lensfree on-chip holographic microscopy can offer an alternative toolset addressing some of the emerging needs of microscopic analysis and diagnostics in low-resource settings, especially for telemedicine applications. In this review, we summarize the latest achievements in lensfree optical microscopy based on partially coherent on-chip holography, including portable telemedicine microscopy, cell-phone based microscopy and field-portable optical tomographic microscopy. We also discuss some of the future directions for telemedicine microscopy and its prospects to help combat various global health challenges. PMID:24478572

Crystal structure of stacking faults in InGaAs/InAlAs/InAs heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trunkin, I. N.; Presniakov, M. Yu.; Vasiliev, A. L., E-mail: a.vasiliev56@gmail.com

Stacking faults and dislocations in InGaAs/InAlAs/InAs heterostructures have been studied by electron microscopy. The use of different techniques of transmission electron microscopy (primarily, highresolution dark-field scanning transmission electron microscopy) has made it possible to determine the defect structure at the atomic level.

Injuries in students of three different dance techniques.

PubMed

Echegoyen, Soledad; Acuña, Eugenia; Rodríguez, Cristina

2010-06-01

As with any athlete, the dancer has a high risk for injury. Most studies carried out relate to classical and modern dance; however, there is a lack of reports on injuries involving other dance techniques. This study is an attempt to determine the differences in the incidence, the exposure-related rates, and the kind of injuries in three different dance techniques. A prospective study about dance injuries was carried out between 2004 and 2007 on students of modern, Mexican folkloric, and Spanish dance at the Escuela Nacional de Danza. A total of 1,168 injuries were registered in 444 students; the injury rate was 4 injuries/student for modern dance and 2 injuries/student for Mexican folkloric and Spanish dance. The rate per training hours was 4 for modern, 1.8 for Mexican folkloric, and 1.5 injuries/1,000 hr of training for Spanish dance. The lower extremity is the most frequent structure injured (70.47%), and overuse injuries comprised 29% of the total. The most frequent injuries were strain, sprain, back pain, and patellofemoral pain. This study has a consistent medical diagnosis of the injuries and is the first attempt in Mexico to compare the incidence of injuries in different dance techniques. To decrease the frequency of student injury, it is important to incorporate prevention programs into dance program curricula. More studies are necessary to define causes and mechanisms of injury, as well as an analysis of training methodology, to decrease the incidence of the muscle imbalances resulting in injury.

Ceria-based model catalysts: fundamental studies on the importance of the metal–ceria interface in CO oxidation, the water–gas shift, CO 2 hydrogenation, and methane and alcohol reforming

DOE PAGES

Rodriguez, José A.; Grinter, David C.; Liu, Zongyuan; ...

2017-02-17

Model metal/ceria and ceria/metal catalysts have been shown to be excellent systems for studying fundamental phenomena linked to the operation of technical catalysts. In the last fifteen years, many combinations of well-defined systems involving different kinds of metals and ceria have been prepared and characterized using the modern techniques of surface science. So far most of the catalytic studies have been centered on a few reactions: CO oxidation, the hydrogenation of CO 2, and the production of hydrogen through the water–gas shift reaction and the reforming of methane or alcohols. By using model catalysts it is been possible to examinemore » in detail correlations between the structural, electronic and catalytic properties of ceria–metal interfaces. In situ techniques (X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, infrared spectroscopy, scanning tunneling microscopy) have been combined to study the morphological changes under reaction conditions and investigate the evolution of active phases involved in the cleavage of C–O, C–H and C–C bonds. Several studies with model ceria catalysts have shown the importance of strong metal–support interactions. Generally, a substantial body of knowledge has been acquired and concepts have been developed for a more rational approach to the design of novel technical catalysts containing ceria.« less

The History of Epidemic Typhus.

PubMed

Angelakis, Emmanouil; Bechah, Yassina; Raoult, Didier

2016-08-01

Epidemic typhus caused by Rickettsia prowazekii is one of the oldest pestilential diseases of humankind. The disease is transmitted to human beings by the body louse Pediculus humanus corporis and is still considered a major threat by public health authorities, despite the efficacy of antibiotics, because poor sanitary conditions are conducive to louse proliferation. Epidemic typhus has accompanied disasters that impact humanity and has arguably determined the outcome of more wars than have soldiers and generals. The detection, identification, and characterization of microorganisms in ancient remains by paleomicrobiology has permitted the diagnosis of past epidemic typhus outbreaks through the detection of R. prowazekii. Various techniques, including microscopy and immunodetection, can be used in paleomicrobiology, but most of the data have been obtained by using PCR-based molecular techniques on dental pulp samples. Paleomicrobiology enabled the identification of the first outbreak of epidemic typhus in the 18th century in the context of a pan-European great war in the city of Douai, France, and supported the hypothesis that typhus was imported into Europe by Spanish soldiers returning from America. R. prowazekii was also detected in the remains of soldiers of Napoleon's Grand Army in Vilnius, Lithuania, which indicates that Napoleon's soldiers had epidemic typhus. The purpose of this article is to underscore the modern comprehension of clinical epidemic typhus, focus on the historical relationships of the disease, and examine the use of paleomicrobiology in the detection of past epidemic typhus outbreaks.

Study of Deformation Phenomena in TRIP/TWIP Steels by Acoustic Emission and Scanning Electron Microscopy

NASA Astrophysics Data System (ADS)

Linderov, M. L.; Segel, C.; Weidner, A.; Biermann, H.; Vinogradov, A. Yu.

2018-04-01

Modern metastable steels with TRIP/TWIP effects have a unique set of physical-mechanical properties. They combine both high-strength and high-plasticity characteristics, which is governed by processes activated during deformation, namely, twinning, the formation of stacking faults, and martensitic transformations. To study the behavior of these phenomena in CrMnNi TRIP/TWIP steels and stainless CrNiMo steel, which does not have these effects in the temperature range under study, we used the method of acoustic emission and modern methods of signal processing, including the cluster analysis of spectral-density functions. The results of this study have been compared with a detailed microstructural analysis performed with a scanning electron microscope using electron backscatter diffraction (EBSD).

Developing single-laser sources for multimodal coherent anti-Stokes Raman scattering microscopy

NASA Astrophysics Data System (ADS)

Pegoraro, Adrian Frank

Coherent anti-Stokes Raman scattering (CARS) microscopy has developed rapidly and is opening the door to new types of experiments. This work describes the development of new laser sources for CARS microscopy and their use for different applications. It is specifically focused on multimodal nonlinear optical microscopy—the simultaneous combination of different imaging techniques. This allows us to address a diverse range of applications, such as the study of biomaterials, fluid inclusions, atherosclerosis, hepatitis C infection in cells, and ice formation in cells. For these applications new laser sources are developed that allow for practical multimodal imaging. For example, it is shown that using a single Ti:sapphire oscillator with a photonic crystal fiber, it is possible to develop a versatile multimodal imaging system using optimally chirped laser pulses. This system can perform simultaneous two photon excited fluorescence, second harmonic generation, and CARS microscopy. The versatility of the system is further demonstrated by showing that it is possible to probe different Raman modes using CARS microscopy simply by changing a time delay between the excitation beams. Using optimally chirped pulses also enables further simplification of the laser system required by using a single fiber laser combined with nonlinear optical fibers to perform effective multimodal imaging. While these sources are useful for practical multimodal imaging, it is believed that for further improvements in CARS microscopy sensitivity, new excitation schemes are necessary. This has led to the design of a new, high power, extended cavity oscillator that should be capable of implementing new excitation schemes for CARS microscopy as well as other techniques. Our interest in multimodal imaging has led us to other areas of research as well. For example, a fiber-coupling scheme for signal collection in the forward direction is demonstrated that allows for fluorescence lifetime imaging without significant temporal distortion. Also highlighted is an imaging artifact that is unique to CARS microscopy that can alter image interpretation, especially when using multimodal imaging. By combining expertise in nonlinear optics, laser development, fiber optics, and microscopy, we have developed systems and techniques that will be of benefit for multimodal CARS microscopy.

High-resolution high-sensitivity elemental imaging by secondary ion mass spectrometry: from traditional 2D and 3D imaging to correlative microscopy

NASA Astrophysics Data System (ADS)

Wirtz, T.; Philipp, P.; Audinot, J.-N.; Dowsett, D.; Eswara, S.

2015-10-01

Secondary ion mass spectrometry (SIMS) constitutes an extremely sensitive technique for imaging surfaces in 2D and 3D. Apart from its excellent sensitivity and high lateral resolution (50 nm on state-of-the-art SIMS instruments), advantages of SIMS include high dynamic range and the ability to differentiate between isotopes. This paper first reviews the underlying principles of SIMS as well as the performance and applications of 2D and 3D SIMS elemental imaging. The prospects for further improving the capabilities of SIMS imaging are discussed. The lateral resolution in SIMS imaging when using the microprobe mode is limited by (i) the ion probe size, which is dependent on the brightness of the primary ion source, the quality of the optics of the primary ion column and the electric fields in the near sample region used to extract secondary ions; (ii) the sensitivity of the analysis as a reasonable secondary ion signal, which must be detected from very tiny voxel sizes and thus from a very limited number of sputtered atoms; and (iii) the physical dimensions of the collision cascade determining the origin of the sputtered ions with respect to the impact site of the incident primary ion probe. One interesting prospect is the use of SIMS-based correlative microscopy. In this approach SIMS is combined with various high-resolution microscopy techniques, so that elemental/chemical information at the highest sensitivity can be obtained with SIMS, while excellent spatial resolution is provided by overlaying the SIMS images with high-resolution images obtained by these microscopy techniques. Examples of this approach are given by presenting in situ combinations of SIMS with transmission electron microscopy (TEM), helium ion microscopy (HIM) and scanning probe microscopy (SPM).

Contributions of in situ microscopy to the current understanding of stone biodeterioration.

PubMed

de Los Ríos, Asunción; Ascaso, Carmen

2005-09-01

In situ microscopy consists of simultaneously applying several microscopy techniques without separating the biological component from its habitat. Over the past few years, this strategy has allowed characterization of the biofilms involved in biodeterioration processes affecting stone monuments and has revealed the biogeophysical and biogeochemical impact of the microbiota present. In addition, through in situ microscopy diagnosis, appropriate treatments can be designed to resolve the problems related to microbial colonization of stone monuments.

Enhanced weak-signal sensitivity in two-photon microscopy by adaptive illumination.

PubMed

Chu, Kengyeh K; Lim, Daryl; Mertz, Jerome

2007-10-01

We describe a technique to enhance both the weak-signal relative sensitivity and the dynamic range of a laser scanning optical microscope. The technique is based on maintaining a fixed detection power by fast feedback control of the illumination power, thereby transferring high measurement resolution to weak signals while virtually eliminating the possibility of image saturation. We analyze and demonstrate the benefits of adaptive illumination in two-photon fluorescence microscopy.

Nanoscale live cell imaging using hopping probe ion conductance microscopy

PubMed Central

Novak, Pavel; Li, Chao; Shevchuk, Andrew I.; Stepanyan, Ruben; Caldwell, Matthew; Hughes, Simon; Smart, Trevor G.; Gorelik, Julia; Ostanin, Victor P.; Lab, Max J.; Moss, Guy W. J.; Frolenkov, Gregory I.; Klenerman, David; Korchev, Yuri E.

2009-01-01

We describe a major advance in scanning ion conductance microscopy: a new hopping mode that allows non-contact imaging of the complex surfaces of live cells with resolution better than 20 nm. The effectiveness of this novel technique was demonstrated by imaging networks of cultured rat hippocampal neurons and mechanosensory stereocilia of mouse cochlear hair cells. The technique allows studying nanoscale phenomena on the surface of live cells under physiological conditions. PMID:19252505

Deposition And Characterization of (Ti,Zr)N Thin Films Grown Through PAPVD By The Pulsed Arc Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marulanda, D. M.; Trujillo, O.; Devia, A.

The Plasma Assisted Physic Vapor Deposition (PAPVD) by the pulsed arc technique has been used for deposition of Titanium Zirconium Nitride (Ti,Zr)N coatings, using a segmented target of TiZr. The deposition was performed in a vacuum chamber with two faced electrodes (target and substrate) using nitrogen as working gas, and a power-controlled source used to produce the arc discharges. Films were deposited on stainless steel 304, and they were characterized using the X-Ray Photoelectron Spectroscopy (XPS), X-Ray Diffraction (XRD), Energy Dispersion Spectroscopy (EDS) and Scanning Probe Microscopy (SPM) techniques. The XRD patterns show different planes in which the film grows.more » Through SPM, using Atomic Force Microscopy (AFM) and Lateral Force Microscopy (LFM) modes, a nanotribologic study of the thin film was made, determining hardness and friction coefficient.« less

Two-dimensional dopant profiling of gallium nitride p-n junctions by scanning capacitance microscopy

NASA Astrophysics Data System (ADS)

Lamhamdi, M.; Cayrel, F.; Frayssinet, E.; Bazin, A. E.; Yvon, A.; Collard, E.; Cordier, Y.; Alquier, D.

2016-04-01

Two-dimensional imaging of dopant profiles for n and p-type regions are relevant for the development of new power semiconductors, especially for gallium nitride (GaN) for which classical profiling techniques are not adapted. This is a challenging task since it needs a technique with simultaneously good sensitivity, high spatial resolution and high dopant gradient resolution. To face these challenges, scanning capacitance microscopy combined with Atomic Force Microscopy is a good candidate, presenting reproducible results, as demonstrated in literature. In this work, we attempt to distinguish reliably and qualitatively the various doping concentrations and type at p-n and unipolar junctions. For both p-n and unipolar junctions three kinds of samples were prepared and measured separately. The space-charge region of the p-n metallurgical junction, giving rise to different contrasts under SCM imaging, is clearly observed, enlightening the interest of the SCM technique.

Single-molecule imaging of cytoplasmic dynein in vivo.

PubMed

Ananthanarayanan, Vaishnavi; Tolić, Iva M

2015-01-01

While early fluorescence microscopy experiments employing fluorescent probes afforded snapshots of the cell, the power of live-cell microscopy is required to understand complex dynamics in biological processes. The first successful cloning of green fluorescent protein in the 1990s paved the way for development of approaches that we now utilize for visualization in a living cell. In this chapter, we discuss a technique to observe fluorescently tagged single molecules in fission yeast. With a few simple modifications to the established total internal reflection fluorescence microscopy, cytoplasmic dynein molecules in the cytoplasm and on the microtubules can be visualized and their intracellular dynamics can be studied. We illustrate a technique to study motor behavior, which is not apparent in conventional ensemble studies of motors. In general, this technique can be employed to study single-molecule dynamics of fluorescently tagged proteins in the cell interior. Copyright © 2015 Elsevier Inc. All rights reserved.

An historical account of the development and applications of the negative staining technique to the electron microscopy of viruses.

PubMed

Horne, R W; Wildy, P

1979-09-01

A brief historical account of the development and applications of the negative staining techniques to the study of the structure of viruses and their components as observed in the electron microscope is presented. Although the basic method of surrounding or embedding specimens in opaque dyes was used in light microscopy dating from about 1884, the equivalent preparative techniques applied to electron microscopy were comparatively recent. The combination of experiments on a sophisticated bacterial virus and the installation of a high resolution electron microscope in the Cavendish Laboratory, Cambridge, during 1954, subsequently led to the analysis of several important morphological features of animal, plant and bacterial viruses. The implications of the results from these early experiments on viruses and recent developments in negative staining methods for high resolution image analysis of electron micrographs are also discussed.

Nanoscale deformation analysis with high-resolution transmission electron microscopy and digital image correlation

DOE PAGES

Wang, Xueju; Pan, Zhipeng; Fan, Feifei; ...

2015-09-10

We present an application of the digital image correlation (DIC) method to high-resolution transmission electron microscopy (HRTEM) images for nanoscale deformation analysis. The combination of DIC and HRTEM offers both the ultrahigh spatial resolution and high displacement detection sensitivity that are not possible with other microscope-based DIC techniques. We demonstrate the accuracy and utility of the HRTEM-DIC technique through displacement and strain analysis on amorphous silicon. Two types of error sources resulting from the transmission electron microscopy (TEM) image noise and electromagnetic-lens distortions are quantitatively investigated via rigid-body translation experiments. The local and global DIC approaches are applied for themore » analysis of diffusion- and reaction-induced deformation fields in electrochemically lithiated amorphous silicon. As a result, the DIC technique coupled with HRTEM provides a new avenue for the deformation analysis of materials at the nanometer length scales.« less

Combining atomic force and fluorescence microscopy for analysis of quantum-dot labeled protein–DNA complexes

PubMed Central

Ebenstein, Yuval; Gassman, Natalie; Kim, Soohong; Weiss, Shimon

2011-01-01

Atomic force microscopy (AFM) and fluorescence microscopy are widely used for the study of protein-DNA interactions. While AFM excels in its ability to elucidate structural detail and spatial arrangement, it lacks the ability to distinguish between similarly sized objects in a complex system. This information is readily accessible to optical imaging techniques via site-specific fluorescent labels, which enable the direct detection and identification of multiple components simultaneously. Here, we show how the utilization of semiconductor quantum dots (QDs), serving as contrast agents for both AFM topography and fluorescence imaging, facilitates the combination of both imaging techniques, and with the addition of a flow based DNA extension method for sample deposition, results in a powerful tool for the study of protein-DNA complexes. We demonstrate the inherent advantages of this novel combination of techniques by imaging individual RNA polymerases (RNAP) on T7 genomic DNA. PMID:19452448

Optical Spectroscopy for Noninvasive Monitoring of Stem Cell Differentiation

PubMed Central

Downes, Andrew; Mouras, Rabah; Elfick, Alistair

2010-01-01

There is a requirement for a noninvasive technique to monitor stem cell differentiation. Several candidates based on optical spectroscopy are discussed in this review: Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, and coherent anti-Stokes Raman scattering (CARS) microscopy. These techniques are briefly described, and the ability of each to distinguish undifferentiated from differentiated cells is discussed. FTIR spectroscopy has demonstrated its ability to distinguish between stem cells and their derivatives. Raman spectroscopy shows a clear reduction in DNA and RNA concentrations during embryonic stem cell differentiation (agreeing with the well-known reduction in the nucleus to cytoplasm ratio) and also shows clear increases in mineral content during differentiation of mesenchymal stem cells. CARS microscopy can map these DNA, RNA, and mineral concentrations at high speed, and Mutliplex CARS spectroscopy/microscopy is highlighted as the technique with most promise for future applications. PMID:20182537

Loop shaping design for tracking performance in machine axes.

PubMed

Schinstock, Dale E; Wei, Zhouhong; Yang, Tao

2006-01-01

A modern interpretation of classical loop shaping control design methods is presented in the context of tracking control for linear motor stages. Target applications include noncontacting machines such as laser cutters and markers, water jet cutters, and adhesive applicators. The methods are directly applicable to the common PID controller and are pertinent to many electromechanical servo actuators other than linear motors. In addition to explicit design techniques a PID tuning algorithm stressing the importance of tracking is described. While the theory behind these techniques is not new, the analysis of their application to modern systems is unique in the research literature. The techniques and results should be important to control practitioners optimizing PID controller designs for tracking and in comparing results from classical designs to modern techniques. The methods stress high-gain controller design and interpret what this means for PID. Nothing in the methods presented precludes the addition of feedforward control methods for added improvements in tracking. Laboratory results from a linear motor stage demonstrate that with large open-loop gain very good tracking performance can be achieved. The resultant tracking errors compare very favorably to results from similar motions on similar systems that utilize much more complicated controllers.

Planar Diffractive Lenses: Fundamentals, Functionalities, and Applications.

PubMed

Huang, Kun; Qin, Fei; Liu, Hong; Ye, Huapeng; Qiu, Cheng-Wei; Hong, Minghui; Luk'yanchuk, Boris; Teng, Jinghua

2018-06-01

Traditional objective lenses in modern microscopy, based on the refraction of light, are restricted by the Rayleigh diffraction limit. The existing methods to overcome this limit can be categorized into near-field (e.g., scanning near-field optical microscopy, superlens, microsphere lens) and far-field (e.g., stimulated emission depletion microscopy, photoactivated localization microscopy, stochastic optical reconstruction microscopy) approaches. However, they either operate in the challenging near-field mode or there is the need to label samples in biology. Recently, through manipulation of the diffraction of light with binary masks or gradient metasurfaces, some miniaturized and planar lenses have been reported with intriguing functionalities such as ultrahigh numerical aperture, large depth of focus, and subdiffraction-limit focusing in far-field, which provides a viable solution for the label-free superresolution imaging. Here, the recent advances in planar diffractive lenses (PDLs) are reviewed from a united theoretical account on diffraction-based focusing optics, and the underlying physics of nanofocusing via constructive or destructive interference is revealed. Various approaches of realizing PDLs are introduced in terms of their unique performances and interpreted by using optical aberration theory. Furthermore, a detailed tutorial about applying these planar lenses in nanoimaging is provided, followed by an outlook regarding future development toward practical applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wide-field two-photon microscopy with temporal focusing and HiLo background rejection

NASA Astrophysics Data System (ADS)

Yew, Elijah Y. S.; Choi, Heejin; Kim, Daekeun; So, Peter T. C.

2011-03-01

Scanningless depth-resolved microscopy is achieved through spatial-temporal focusing and has been demonstrated previously. The advantage of this method is that a large area may be imaged without scanning resulting in higher throughput of the imaging system. Because it is a widefield technique, the optical sectioning effect is considerably poorer than with conventional spatial focusing two-photon microscopy. Here we propose wide-field two-photon microscopy based on spatio-temporal focusing and employing background rejection based on the HiLo microscope principle. We demonstrate the effects of applying HiLo microscopy to widefield temporally focused two-photon microscopy.

Hyperspectral imaging with laser-scanning sum-frequency generation microscopy

PubMed Central

Hanninen, Adam; Shu, Ming Wai; Potma, Eric O.

2017-01-01

Vibrationally sensitive sum-frequency generation (SFG) microscopy is a chemically selective imaging technique sensitive to non-centrosymmetric molecular arrangements in biological samples. The routine use of SFG microscopy has been hampered by the difficulty of integrating the required mid-infrared excitation light into a conventional, laser-scanning nonlinear optical (NLO) microscope. In this work, we describe minor modifications to a regular laser-scanning microscope to accommodate SFG microscopy as an imaging modality. We achieve vibrationally sensitive SFG imaging of biological samples with sub-μm resolution at image acquisition rates of 1 frame/s, almost two orders of magnitude faster than attained with previous point-scanning SFG microscopes. Using the fast scanning capability, we demonstrate hyperspectral SFG imaging in the CH-stretching vibrational range and point out its use in the study of molecular orientation and arrangement in biologically relevant samples. We also show multimodal imaging by combining SFG microscopy with second-harmonic generation (SHG) and coherent anti-Stokes Raman scattering (CARS) on the same imaging platfrom. This development underlines that SFG microscopy is a unique modality with a spatial resolution and image acquisition time comparable to that of other NLO imaging techniques, making point-scanning SFG microscopy a valuable member of the NLO imaging family. PMID:28966861

Two-photon excitation fluorescence bioassays.

PubMed

Hänninen, Pekka; Soukka, Jori; Soini, Juhani T

2008-01-01

Application of two-photon excitation of fluorescence in microscopy is one of the major discoveries of the "renaissance" of light microscopy that started in the 1980s. The technique derives its advantages from the biologically "smooth" wavelength of the excitation light and the confinement of the excitation. Difficult, and seemingly nontransparent, samples may be imaged with the technique with good resolution. Although the bioresearch has been concentrating mostly on the positive properties of the technique for imaging, the same properties may be applied successfully to nonimaging bioassays. This article focuses on the development path of two-photon excitation-based assay system.

Crossroads: Modern Interactive Intersections and Accessible Pedestrian Signals

ERIC Educational Resources Information Center

Barlow, Janet M.; Franck, Lukas

2005-01-01

This article discusses the interactive nature of modern actuated intersections and the effect of that interface on pedestrians who are visually impaired. Information is provided about accessible pedestrian signals (APS), the role of blindness professionals in APS installation decisions, and techniques for crossing streets with APS.

Assessing the functional mechanical properties of bioengineered organs with emphasis on the lung.

PubMed

Suki, Béla

2014-09-01

Recently, an exciting new approach has emerged in regenerative medicine pushing the forefront of tissue engineering to create bioartificial organs. The basic idea is to create biological scaffolds made of extracellular matrix (ECM) that preserves the three-dimensional architecture of an entire organ. These scaffolds are then used as templates for functional tissue and organ reconstruction after re-seeding the structure with stem cells or appropriately differentiated cells. In order to make sure that these bioartificial organs will be able to function in the mechanical environment of the native tissue, it is imperative to fully characterize their mechanical properties and match them with those of the normal native organs. This mini-review briefly summarizes modern measurement techniques of mechanical function characterized mostly by the material or volumetric stiffness. Micro-scale and macro-scale techniques such as atomic force microscopy and the tissue strip stress-strain approach are discussed with emphasis on those that combine mechanical measurements with structural visualization. Proper micro-scale stiffness helps attachment and differentiation of cells in the bioartificial organ whereas macro-scale functionality is provided by the overall mechanical properties of the construct. Several approaches including failure mechanics are also described, which specifically probe the contributions of the main ECM components including collagen, elastin, and proteoglycans to organ level ECM function. Advantages, drawbacks, and possible pitfalls as well as interpretation of the data are given throughout. Finally, specific techniques to assess the functionality of the ECM of bioartificial lungs are separately discussed. © 2014 Wiley Periodicals, Inc.

Sample preparation for the analysis of isoflavones from soybeans and soy foods.

PubMed

Rostagno, M A; Villares, A; Guillamón, E; García-Lafuente, A; Martínez, J A

2009-01-02

This manuscript provides a review of the actual state and the most recent advances as well as current trends and future prospects in sample preparation and analysis for the quantification of isoflavones from soybeans and soy foods. Individual steps of the procedures used in sample preparation, including sample conservation, extraction techniques and methods, and post-extraction treatment procedures are discussed. The most commonly used methods for extraction of isoflavones with both conventional and "modern" techniques are examined in detail. These modern techniques include ultrasound-assisted extraction, pressurized liquid extraction, supercritical fluid extraction and microwave-assisted extraction. Other aspects such as stability during extraction and analysis by high performance liquid chromatography are also covered.

The research and realization of digital management platform for ultra-precision optical elements within life-cycle

NASA Astrophysics Data System (ADS)

Wang, Juan; Wang, Jian; Li, Lijuan; Zhou, Kun

2014-08-01

In order to solve the information fusion, process integration, collaborative design and manufacturing for ultra-precision optical elements within life-cycle management, this paper presents a digital management platform which is based on product data and business processes by adopting the modern manufacturing technique, information technique and modern management technique. The architecture and system integration of the digital management platform are discussed in this paper. The digital management platform can realize information sharing and interaction for information-flow, control-flow and value-stream from user's needs to offline in life-cycle, and it can also enhance process control, collaborative research and service ability of ultra-precision optical elements.

Visualizing and quantifying the in vivo structure and dynamics of the Arabidopsis cortical cytoskeleton using CLSM and VAEM.

PubMed

Rosero, Amparo; Zárský, Viktor; Cvrčková, Fatima

2014-01-01

The cortical microtubules, and to some extent also the actin meshwork, play a central role in the shaping of plant cells. Transgenic plants expressing fluorescent protein markers specifically tagging the two main cytoskeletal systems are available, allowing noninvasive in vivo studies. Advanced microscopy techniques, in particular confocal laser scanning microscopy (CLSM) and variable angle epifluorescence microscopy (VAEM), can be nowadays used for imaging the cortical cytoskeleton of living cells with unprecedented spatial and temporal resolution. With the aid of suitable computing techniques, quantitative information can be extracted from microscopic images and video sequences, providing insight into both architecture and dynamics of the cortical cytoskeleton.

Determination of the Subcellular Distribution of Liposomes Using Confocal Microscopy.

PubMed

Solomon, Melani A

2017-01-01

It is being increasingly recognized that therapeutics need to be delivered to specific organelle targets within cells. Liposomes are versatile lipid-based drug delivery vehicles that can be surface-modified to deliver the loaded cargo to specific subcellular locations within the cell. Hence, the development of such technology requires a means of measuring the subcellular distribution possibly by utilizing imaging techniques that can visualize and quantitate the extent of this subcellular localization. The apparent increase of resolution along the Z-axis offered by confocal microscopy makes this technique suitable for such studies. In this chapter, we describe the application of confocal laser scanning microscopy (CLSM) to determine the subcellular distribution of fluorescently labeled mitochondriotropic liposomes.

Visualizing molecular polar order in tissues via electromechanical coupling

PubMed Central

Denning, Denise; Alilat, Sofiane; Habelitz, Stefan; Fertala, Andrzej; Rodriguez, Brian J.

2015-01-01

Electron microscopy (EM) and atomic force microscopy (AFM) techniques have long been used to characterize collagen fibril ordering and alignment in connective tissues. These techniques, however, are unable to map collagen fibril polarity, i.e., the polar orientation that is directed from the amine to the carboxyl termini. Using a voltage modulated AFM-based technique called piezoresponse force microscopy (PFM), we show it is possible to visualize both the alignment of collagen fibrils within a tissue and the polar orientation of the fibrils with minimal sample preparation. We demonstrate the technique on rat tail tendon and porcine eye tissues in ambient conditions. In each sample, fibrils are arranged into domains whereby neighboring domains exhibit opposite polarizations, which in some cases extend to the individual fibrillar level. Uniform polarity has not been observed in any of the tissues studied. Evidence of anti-parallel ordering of the amine to carboxyl polarity in bundles of fibrils or in individual fibrils is found in all tissues, which has relevance for understanding mechanical and biofunctional properties and the formation of connective tissues. The technique can be applied to any biological material containing piezoelectric biopolymers or polysaccharides. PMID:22985991

Applications of SLR

NASA Technical Reports Server (NTRS)

Schutz, Bob E.

1993-01-01

Satellite Laser Ranging (SLR) has a rich history of development which began in the 1960s with 10 meter-level first generation systems. These systems evolved with order of magnitude improvements to the systems that now produce several millimeter single shot range precisions. What began, in part, as an interesting application of the new laser technology has become an essential component of modern, precision space geodesy, which in turn enables contributions to a variety of science areas. Modern space geodesy is the beneficiary of technological developments which have enabled precision geodetic measurements. Aside from SLR and its closely related technique, Lunar Laser Ranging (LLR), Very Long Baseline Interferometry (VLBI) has made prominent science contributions also. In recent years, the Global Positioning System (GPS) has demonstrated a rapidly growing popularity as the result of demonstrated low cost with high precision instrumentation. Other modern techniques such as DORIS have demonstrated the ability to make significant science contributions; furthermore, PRARE can be expected to contribute in its own right. An appropriate question is 'why should several techniques be financially supported'? While there are several answers, I offer the opinion that, in consideration of the broad science areas that are the benefactors of space geodesy, no single technique can meet all the requirements and/or expectations of the science areas in which space geodesy contributes or has the potential for contributing. The more well-known science areas include plate tectonics, earthquake processes, Earth rotation/orientation, gravity (static and temporal), ocean circulation, land, and ice topography, to name a few applications. It is unfortunate that the modern space geodesy techniques are often viewed as competitive, but this view is usually encouraged by funding competition, especially in an era of growing needs but diminishing budgets. The techniques are, for the most part, complementary and the ability to reduce the data to geodetic parameters from several techniques promotes confidence in the geophysical interpretations. In the following sections, the current SLR applications are reviewed in the context of the other techniques. The strengths and limitations of SLR are reviewed and speculation about the future prospects are offered.

DURIP: Super-Resolution Module for Confocal Microscopy of Reconfigurable Matter

DTIC Science & Technology

2014-09-28

Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 superresolution microscopy, colloidal particles, self-assembly REPORT...previously have been resolved by optical microscopy. Results of Super Resolution Technique Evaluation Commercially available superresolution imaging...Weaknesses of the method are that is fundamentally a measurement that can only be deployed for fixed samples. Because superresolution is obtained by

Nobel Prize Recipient Eric Betzig Presents Lecture on Efforts to Improve High-Resolution Microscopy | Poster

Cancer.gov

Eric Betzig, Ph.D., a 2014 recipient of the Nobel Prize in Chemistry and a scientist at Janelia Research Campus (JRC), Howard Hughes Medical Institute, in Ashburn, Va., visited NCI at Frederick on Sept. 10 to present a Distinguished Scientist lecture and discuss the latest high-resolution microscopy techniques. Betzig co-invented photoactivation localization microscopy (PALM)

Dark-field X-ray microscopy for multiscale structural characterization

NASA Astrophysics Data System (ADS)

Simons, H.; King, A.; Ludwig, W.; Detlefs, C.; Pantleon, W.; Schmidt, S.; Snigireva, I.; Snigirev, A.; Poulsen, H. F.

2015-01-01

Many physical and mechanical properties of crystalline materials depend strongly on their internal structure, which is typically organized into grains and domains on several length scales. Here we present dark-field X-ray microscopy; a non-destructive microscopy technique for the three-dimensional mapping of orientations and stresses on lengths scales from 100 nm to 1 mm within embedded sampling volumes. The technique, which allows ‘zooming’ in and out in both direct and angular space, is demonstrated by an annealing study of plastically deformed aluminium. Facilitating the direct study of the interactions between crystalline elements is a key step towards the formulation and validation of multiscale models that account for the entire heterogeneity of a material. Furthermore, dark-field X-ray microscopy is well suited to applied topics, where the structural evolution of internal nanoscale elements (for example, positioned at interfaces) is crucial to the performance and lifetime of macro-scale devices and components thereof.

Magnetic resonance microscopy: concepts, challenges, and state-of-the-art.

PubMed

Gimi, Barjor

2006-01-01

Recent strides in targeted therapy and regenerative medicine have created a need to identify molecules and metabolic pathways implicated in a disease and its treatment. These molecules and pathways must be discerned at the cellular level to meaningfully reveal the biochemical underpinnings of the disease and to identify key molecular targets for therapy. Magnetic resonance (MR) techniques are well suited for molecular and functional imaging because of their noninvasive nature and their versatility in extracting physiological, biochemical, and functional information over time. However, MR is an insensitive technique; MR microscopy seeks to increase detection sensitivity, thereby localizing biochemical and functional information at the level of single cells or small cellular clusters. Here, we discuss some of the challenges facing MR microscopy and the technical and phenomenological strategies used to overcome these challenges. Some of the applications of MR microscopy are highlighted in this chapter.

Acousto-optical tunable filter for combined wideband, spectral, and optical coherence microscopy.

PubMed

Machikhin, Alexander S; Pozhar, Vitold E; Viskovatykh, Alexander V; Burmak, Ludmila I

2015-09-01

A multimodal technique for inspection of microscopic objects by means of wideband optical microscopy, spectral microscopy, and optical coherence microscopy is described, implemented, and tested. The key feature is the spectral selection of light in the output arm of an interferometer with use of the specialized imaging acousto-optical tunable filter. In this filter, two interfering optical beams are diffracted via the same ultrasound wave without destruction of interference image structure. The basic requirements for the acousto-optical tunable filter are defined, and mathematical formulas for calculation of its parameters are derived. Theoretical estimation of the achievable accuracy of the 3D image reconstruction is presented and experimental proofs are given. It is demonstrated that spectral imaging can also be accompanied by measurement of the quantitative reflectance spectra. Examples of inspection of optically transparent and nontransparent samples demonstrate the applicability of the technique.

Correlative Fluorescence and Electron Microscopy

PubMed Central

Schirra, Randall T.; Zhang, Peijun

2014-01-01

Correlative fluorescence and electron microscopy (CFEM) is a multimodal technique that combines dynamic and localization information from fluorescence methods with ultrastructural data from electron microscopy, to give new information about how cellular components change relative to the spatiotemporal dynamics within their environment. In this review, we will discuss some of the basic techniques and tools of the trade for utilizing this attractive research method, which is becoming a very powerful tool for biology labs. The information obtained from correlative methods has proven to be invaluable in creating consensus between the two types of microscopy, extending the capability of each, and cutting the time and expense associate with using each method separately for comparative analysis. The realization of the advantages of these methods in cell biology have led to rapid improvement in the protocols and have ushered in a new generation of instruments to reach the next level of correlation – integration. PMID:25271959

Numerical tilting compensation in microscopy based on wavefront sensing using transport of intensity equation method

NASA Astrophysics Data System (ADS)

Hu, Junbao; Meng, Xin; Wei, Qi; Kong, Yan; Jiang, Zhilong; Xue, Liang; Liu, Fei; Liu, Cheng; Wang, Shouyu

2018-03-01

Wide-field microscopy is commonly used for sample observations in biological research and medical diagnosis. However, the tilting error induced by the oblique location of the image recorder or the sample, as well as the inclination of the optical path often deteriorates the imaging quality. In order to eliminate the tilting in microscopy, a numerical tilting compensation technique based on wavefront sensing using transport of intensity equation method is proposed in this paper. Both the provided numerical simulations and practical experiments prove that the proposed technique not only accurately determines the tilting angle with simple setup and procedures, but also compensates the tilting error for imaging quality improvement even in the large tilting cases. Considering its simple systems and operations, as well as image quality improvement capability, it is believed the proposed method can be applied for tilting compensation in the optical microscopy.

Wavefront correction using machine learning methods for single molecule localization microscopy

NASA Astrophysics Data System (ADS)

Tehrani, Kayvan F.; Xu, Jianquan; Kner, Peter

2015-03-01

Optical Aberrations are a major challenge in imaging biological samples. In particular, in single molecule localization (SML) microscopy techniques (STORM, PALM, etc.) a high Strehl ratio point spread function (PSF) is necessary to achieve sub-diffraction resolution. Distortions in the PSF shape directly reduce the resolution of SML microscopy. The system aberrations caused by the imperfections in the optics and instruments can be compensated using Adaptive Optics (AO) techniques prior to imaging. However, aberrations caused by the biological sample, both static and dynamic, have to be dealt with in real time. A challenge for wavefront correction in SML microscopy is a robust optimization approach in the presence of noise because of the naturally high fluctuations in photon emission from single molecules. Here we demonstrate particle swarm optimization for real time correction of the wavefront using an intensity independent metric. We show that the particle swarm algorithm converges faster than the genetic algorithm for bright fluorophores.

Fabrication and optical characterization of imaging fiber-based nanoarrays.

PubMed

Tam, Jenny M; Song, Linan; Walt, David R

2005-09-15

In this paper, we present a technique for fabricating arrays containing a density at least 90 times higher than previously published. Specifically, we discuss the fabrication of two imaging fiber-based nanoarrays, one with 700nm features, another with 300nm features. With arrays containing up to 4.5x10(6) array elements/mm(2), these nanoarrays have an ultra-high packing density. A straightforward etching protocol is used to create nanowells into which beads can be deposited. These beads comprise the sensing elements of the nanoarray. Deposition of the nanobeads into the nanowells using two techniques is described. The surface characteristics of the etched arrays are examined with atomic force microscopy and scanning electron microscopy. Fluorescence microscopy was used to observe the arrays. The 300nm array features and the 500nm center-to-center distance approach the minimum feature sizes viewable using conventional light microscopy.

Scanning electron microscopy of cells and tissues under fully hydrated conditions

PubMed Central

Thiberge, Stephan; Nechushtan, Amotz; Sprinzak, David; Gileadi, Opher; Behar, Vered; Zik, Ory; Chowers, Yehuda; Michaeli, Shulamit; Schlessinger, Joseph; Moses, Elisha

2004-01-01

A capability for scanning electron microscopy of wet biological specimens is presented. A membrane that is transparent to electrons protects the fully hydrated sample from the vacuum. The result is a hybrid technique combining the ease of use and ability to see into cells of optical microscopy with the higher resolution of electron microscopy. The resolution of low-contrast materials is ≈100 nm, whereas in high-contrast materials the resolution can reach 10 nm. Standard immunogold techniques and heavy-metal stains can be applied and viewed in the fluid to improve the contrast. Images present a striking combination of whole-cell morphology with a wealth of internal details. A possibility for direct inspection of tissue slices transpires, imaging only the external layer of cells. Simultaneous imaging with photons excited by the electrons incorporates data on material distribution, indicating a potential for multilabeling and specific scintillating markers. PMID:14988502

Three-dimensional textures and defects of soft material layering revealed by thermal sublimation.

PubMed

Yoon, Dong Ki; Kim, Yun Ho; Kim, Dae Seok; Oh, Seong Dae; Smalyukh, Ivan I; Clark, Noel A; Jung, Hee-Tae

2013-11-26

Layering is found and exploited in a variety of soft material systems, ranging from complex macromolecular self-assemblies to block copolymer and small-molecule liquid crystals. Because the control of layer structure is required for applications and characterization, and because defects reveal key features of the symmetries of layered phases, a variety of techniques have been developed for the study of soft-layer structure and defects, including X-ray diffraction and visualization using optical transmission and fluorescence confocal polarizing microscopy, atomic force microscopy, and SEM and transmission electron microscopy, including freeze-fracture transmission electron microscopy. Here, it is shown that thermal sublimation can be usefully combined with such techniques to enable visualization of the 3D structure of soft materials. Sequential sublimation removes material in a stepwise fashion, leaving a remnant layer structure largely unchanged and viewable using SEM, as demonstrated here using a lamellar smectic liquid crystal.

Comparing high-resolution microscopy techniques for potential intraoperative use in guiding low-grade glioma resections.

PubMed

Meza, Daphne; Wang, Danni; Wang, Yu; Borwege, Sabine; Sanai, Nader; Liu, Jonathan T C

2015-04-01

Fluorescence image-guided surgery (FIGS), with contrast provided by 5-ALA-induced PpIX, has been shown to enable a higher extent of resection of high-grade gliomas. However, conventional FIGS with low-power microscopy lacks the sensitivity to aid in low-grade glioma (LGG) resection because PpIX signal is weak and sparse in such tissues. Intraoperative high-resolution microscopy of PpIX fluorescence has been proposed as a method to guide LGG resection, where sub-cellular resolution allows for the visualization of sparse and punctate mitochondrial PpIX production in tumor cells. Here, we assess the performance of three potentially portable high-resolution microscopy techniques that may be used for the intraoperative imaging of human LGG tissue samples with PpIX contrast: high-resolution fiber-optic microscopy (HRFM), high-resolution wide-field microscopy (WFM), and dual-axis confocal (DAC) microscopy. Thick unsectioned human LGG tissue samples (n = 7) with 5-ALA-induced PpIX contrast were imaged using three imaging techniques (HRFM, WFM, DAC). The average signal-to-background ratio (SBR) was then calculated for each imaging modality (5 images per tissue, per modality). HRFM provides the ease of use and portability of a flexible fiber bundle, and is simple and inexpensive to build. However, in most cases (6/7), HRFM is not capable of detecting PpIX signal from LGGs due to high autofluorescence, generated by the fiber bundle under laser illumination at 405 nm, which overwhelms the PpIX signal and impedes its visualization. WFM is a camera-based method possessing high lateral resolution but poor axial resolution, resulting in sub-optimal image contrast. Consistent successful detection of PpIX signal throughout our human LGG tissue samples (n = 7), with an acceptable image contrast (SBR >2), was only achieved using DAC microscopy, which offers superior image resolution and contrast that is comparable to histology, but requires a laser-scanning mechanism to achieve optical sectioning. © 2015 Wiley Periodicals, Inc.

A Simple Laser Microphone for Classroom Demonstration

ERIC Educational Resources Information Center

Moses, James M.; Trout, K. P.

2006-01-01

Communication through the modulation of electromagnetic radiation has become a foundational technique in modern technology. In this paper we discuss a modern day method of eavesdropping based upon the modulation of laser light reflected from a window pane. A simple and affordable classroom demonstration of a "laser microphone" is…

Characterization of articular cartilage by combining microscopic analysis with a fibril-reinforced finite-element model.

PubMed

Julkunen, Petro; Kiviranta, Panu; Wilson, Wouter; Jurvelin, Jukka S; Korhonen, Rami K

2007-01-01

Load-bearing characteristics of articular cartilage are impaired during tissue degeneration. Quantitative microscopy enables in vitro investigation of cartilage structure but determination of tissue functional properties necessitates experimental mechanical testing. The fibril-reinforced poroviscoelastic (FRPVE) model has been used successfully for estimation of cartilage mechanical properties. The model includes realistic collagen network architecture, as shown by microscopic imaging techniques. The aim of the present study was to investigate the relationships between the cartilage proteoglycan (PG) and collagen content as assessed by quantitative microscopic findings, and model-based mechanical parameters of the tissue. Site-specific variation of the collagen network moduli, PG matrix modulus and permeability was analyzed. Cylindrical cartilage samples (n=22) were harvested from various sites of the bovine knee and shoulder joints. Collagen orientation, as quantitated by polarized light microscopy, was incorporated into the finite-element model. Stepwise stress-relaxation experiments in unconfined compression were conducted for the samples, and sample-specific models were fitted to the experimental data in order to determine values of the model parameters. For comparison, Fourier transform infrared imaging and digital densitometry were used for the determination of collagen and PG content in the same samples, respectively. The initial and strain-dependent fibril network moduli as well as the initial permeability correlated significantly with the tissue collagen content. The equilibrium Young's modulus of the nonfibrillar matrix and the strain dependency of permeability were significantly associated with the tissue PG content. The present study demonstrates that modern quantitative microscopic methods in combination with the FRPVE model are feasible methods to characterize the structure-function relationships of articular cartilage.

Distributed force probe bending model of critical dimension atomic force microscopy bias

NASA Astrophysics Data System (ADS)

Ukraintsev, Vladimir A.; Orji, Ndubuisi G.; Vorburger, Theodore V.; Dixson, Ronald G.; Fu, Joseph; Silver, Rick M.

2013-04-01

Critical dimension atomic force microscopy (CD-AFM) is a widely used reference metrology technique. To characterize modern semiconductor devices, small and flexible probes, often 15 to 20 nm in diameter, are used. Recent studies have reported uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements. To understand the source of these variations, tip-sample interactions between high aspect ratio features and small flexible probes, and their influence on measurement bias, should be carefully studied. Using theoretical and experimental procedures, one-dimensional (1-D) and two-dimensional (2-D) models of cylindrical probe bending relevant to carbon nanotube (CNT) AFM probes were developed and tested. An earlier 1-D bending model was refined, and a new 2-D distributed force (DF) model was developed. Contributions from several factors were considered, including: probe misalignment, CNT tip apex diameter variation, probe bending before snapping, and distributed van der Waals-London force. A method for extracting Hamaker probe-surface interaction energy from experimental probe-bending data was developed. Comparison of the new 2-D model with 1-D single point force (SPF) model revealed a difference of about 28% in probe bending. A simple linear relation between biases predicted by the 1-D SPF and 2-D DF models was found. The results suggest that probe bending can be on the order of several nanometers and can partially explain the observed CD-AFM probe-to-probe variation. New 2-D and three-dimensional CD-AFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Towards atomically precise manipulation of 2D nanostructures in the electron microscope

NASA Astrophysics Data System (ADS)

Susi, Toma; Kepaptsoglou, Demie; Lin, Yung-Chang; Ramasse, Quentin M.; Meyer, Jannik C.; Suenaga, Kazu; Kotakoski, Jani

2017-12-01

Despite decades of research, the ultimate goal of nanotechnology—top-down manipulation of individual atoms—has been directly achieved with only one technique: scanning probe microscopy. In this review, we demonstrate that scanning transmission electron microscopy (STEM) is emerging as an alternative method for the direct assembly of nanostructures, with possible applications in plasmonics, quantum technologies, and materials science. Atomically precise manipulation with STEM relies on recent advances in instrumentation that have enabled non-destructive atomic-resolution imaging at lower electron energies. While momentum transfer from highly energetic electrons often leads to atom ejection, interesting dynamics can be induced when the transferable kinetic energies are comparable to bond strengths in the material. Operating in this regime, very recent experiments have revealed the potential for single-atom manipulation using the Ångström-sized electron beam. To truly enable control, however, it is vital to understand the relevant atomic-scale phenomena through accurate dynamical simulations. Although excellent agreement between experiment and theory for the specific case of atomic displacements from graphene has been recently achieved using density functional theory molecular dynamics, in many other cases quantitative accuracy remains a challenge. We provide a comprehensive reanalysis of available experimental data on beam-driven dynamics in light of the state-of-the-art in simulations, and identify important targets for improvement. Overall, the modern electron microscope has great potential to become an atom-scale fabrication platform, especially for covalently bonded 2D nanostructures. We review the developments that have made this possible, argue that graphene is an ideal starting material, and assess the main challenges moving forward.

Recent Advances in Fiber Lasers for Nonlinear Microscopy

PubMed Central

Xu, C.; Wise, F. W.

2013-01-01

Nonlinear microscopy techniques developed over the past two decades have provided dramatic new capabilities for biological imaging. The initial demonstrations of nonlinear microscopies coincided with the development of solid-state femtosecond lasers, which continue to dominate applications of nonlinear microscopy. Fiber lasers offer attractive features for biological and biomedical imaging, and recent advances are leading to high-performance sources with the potential for robust, inexpensive, integrated instruments. This article discusses recent advances, and identifies challenges and opportunities for fiber lasers in nonlinear bioimaging. PMID:24416074

Super-resolution optical microscopy for studying membrane structure and dynamics.

PubMed

Sezgin, Erdinc

2017-07-12

Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.

Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells.

PubMed

Spahn, Christoph; Glaesmann, Mathilda; Gao, Yunfeng; Foo, Yong Hwee; Lampe, Marko; Kenney, Linda J; Heilemann, Mike

2017-01-01

Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.

Bessel light sheet structured illumination microscopy

NASA Astrophysics Data System (ADS)

Noshirvani Allahabadi, Golchehr

Biomedical study researchers using animals to model disease and treatment need fast, deep, noninvasive, and inexpensive multi-channel imaging methods. Traditional fluorescence microscopy meets those criteria to an extent. Specifically, two-photon and confocal microscopy, the two most commonly used methods, are limited in penetration depth, cost, resolution, and field of view. In addition, two-photon microscopy has limited ability in multi-channel imaging. Light sheet microscopy, a fast developing 3D fluorescence imaging method, offers attractive advantages over traditional two-photon and confocal microscopy. Light sheet microscopy is much more applicable for in vivo 3D time-lapsed imaging, owing to its selective illumination of tissue layer, superior speed, low light exposure, high penetration depth, and low levels of photobleaching. However, standard light sheet microscopy using Gaussian beam excitation has two main disadvantages: 1) the field of view (FOV) of light sheet microscopy is limited by the depth of focus of the Gaussian beam. 2) Light-sheet images can be degraded by scattering, which limits the penetration of the excitation beam and blurs emission images in deep tissue layers. While two-sided sheet illumination, which doubles the field of view by illuminating the sample from opposite sides, offers a potential solution, the technique adds complexity and cost to the imaging system. We investigate a new technique to address these limitations: Bessel light sheet microscopy in combination with incoherent nonlinear Structured Illumination Microscopy (SIM). Results demonstrate that, at visible wavelengths, Bessel excitation penetrates up to 250 microns deep in the scattering media with single-side illumination. Bessel light sheet microscope achieves confocal level resolution at a lateral resolution of 0.3 micron and an axial resolution of 1 micron. Incoherent nonlinear SIM further reduces the diffused background in Bessel light sheet images, resulting in confocal quality images in thick tissue. The technique was applied to live transgenic zebra fish tg(kdrl:GFP), and the sub-cellular structure of fish vasculature genetically labeled with GFP was captured in 3D. The superior speed of the microscope enables us to acquire signal from 200 layers of a thick sample in 4 minutes. The compact microscope uses exclusively off-the-shelf components and offers a low-cost imaging solution for studying small animal models or tissue samples.

Chondrocytes provide a model for in-situ confocal microscopy and 3D reconstructions

NASA Astrophysics Data System (ADS)

Hirsch, Michelle S.; Svoboda, Kathy K. H.

1994-04-01

Hyaline cartilage is composed of chondrocytes that reside in lacunae surrounded by extracellular matrix molecules. Microscopic and histochemical features of cartilage have been studied with many techniques. Many of these techniques can be time consuming and may alter natural cartilage characteristics. In addition, the orientation and order of sectioned tissue must be maintained to create 3D reconstructions. We show that confocal laser scanning microscopy may replace traditional methods for studying cartilage.

Characterization of the Roman curse tablet

NASA Astrophysics Data System (ADS)

Liu, Wen; Zhang, Boyang; Fu, Lin

2017-08-01

The Roman curse tablet, produced in ancient Rome period, is a metal plate that inscribed with curses. In this research, several techniques were used to find out the physical structure and chemical composition of the Roman curse tablet, and testified the hypothesis that whether the tablet is made of pure lead or lead alloy. A sample of Roman Curse Tablet from the Johns Hopkins Archaeological Museum was analyzed using several different characterization techniques to determine the physical structure and chemical composition. The characterization techniques used were including optical microscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), and differential scanning calorimetry (DSC). Because of the small sample size, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and X-ray fluorescence (XRF) cannot test the sample. Results from optical microscopy and SEM, enlarged images of the sample surface were studied. The result revealed that the sample surface has a rough, non-uniform, and grainy surface. AFM provides three-dimensional topography of the sample surface, studying the sample surface in atomic level. DSC studies the thermal property, which is most likely a lead-alloy, not a pure lead. However, none of these tests indicated anything about the chemical composition. Future work will be required due to the lack of measures finding out its chemical composition. Therefore, from these characterization techniques above, the Roman curse tablet sample is consisted of lead alloy, not pure lead.

Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems

NASA Astrophysics Data System (ADS)

Cerbino, Roberto; Cicuta, Pietro

2017-09-01

Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.

A simple 2D composite image analysis technique for the crystal growth study of L-ascorbic acid.

PubMed

Kumar, Krishan; Kumar, Virender; Lal, Jatin; Kaur, Harmeet; Singh, Jasbir

2017-06-01

This work was destined for 2D crystal growth studies of L-ascorbic acid using the composite image analysis technique. Growth experiments on the L-ascorbic acid crystals were carried out by standard (optical) microscopy, laser diffraction analysis, and composite image analysis. For image analysis, the growth of L-ascorbic acid crystals was captured as digital 2D RGB images, which were then processed to composite images. After processing, the crystal boundaries emerged as white lines against the black (cancelled) background. The crystal boundaries were well differentiated by peaks in the intensity graphs generated for the composite images. The lengths of crystal boundaries measured from the intensity graphs of composite images were in good agreement (correlation coefficient "r" = 0.99) with the lengths measured by standard microscopy. On the contrary, the lengths measured by laser diffraction were poorly correlated with both techniques. Therefore, the composite image analysis can replace the standard microscopy technique for the crystal growth studies of L-ascorbic acid. © 2017 Wiley Periodicals, Inc.

Harvey Guthrey | NREL

Science.gov Websites

advanced electron-microscopy-based characterization techniques to the study of photovoltaics and energy -storage materials. Research Interests Combining structural and chemical characterization techniques to

Three-Dimensional Visualization of Interfacial Phenomena Using Confocal Microscopy

NASA Astrophysics Data System (ADS)

Shieh, Ian C.

Surfactants play an integral role in numerous functions ranging from stabilizing the emulsion in a favorite salad dressing to organizing the cellular components that make life possible. We are interested in lung surfactant, which is a mixture of lipids and proteins essential for normal respiration because it modulates the surface tension of the air-liquid interface of the thin fluid lining in the lungs. Through this surface tension modulation, lung surfactant ensures effortless lung expansion and prevents lung collapse during exhalation, thereby effecting proper oxygenation of the bloodstream. The function of lung surfactant, as well as numerous interfacial lipid systems, is not solely dictated by the behavior of materials confined to the two-dimensional interface. Rather, the distributions of materials in the liquid subphase also greatly influence the performance of interfacial films of lung surfactant. Therefore, to better understand the behavior of lung surfactant and other interfacial lipid systems, we require a three-dimensional characterization technique. In this dissertation, we have developed a novel confocal microscopy methodology for investigating the interfacial phenomena of surfactants at the air-liquid interface of a Langmuir trough. Confocal microscopy provides the excellent combination of in situ, fast, three-dimensional visualization of multiple components of the lung surfactant system that other characterization techniques lack. We detail the solutions to the numerous challenges encountered when imaging a dynamic air-liquid interface with a high-resolution technique like confocal microscopy. We then use confocal microscopy to elucidate the distinct mechanisms by which a polyelectrolyte (chitosan) and nonadsorbing polymer (polyethylene glycol) restore the function of lung surfactant under inhibitory conditions mimicking the effects of lung trauma. Beyond this physiological model, we also investigate several one- and two-component interfacial films of the various lipid constituents of lung surfactant. Confocal microscopy allows us to use a water-soluble, cationic fluorophore that partitions into the disordered phases of lipid monolayers. By exploiting the properties of this water-soluble fluorophore, we investigate both the phase behavior and electrostatics of the interfacial lipid systems. Overall, we believe the work presented in this dissertation provides the building blocks for establishing confocal microscopy as a ubiquitous characterization technique in the interfacial and surface sciences.

PREFACE: European Microbeam Analysis Society's 14th European Workshop on Modern Developments and Applications in Microbeam Analysis (EMAS 2015), Portorož, Slovenia, 3-7 May 2015

NASA Astrophysics Data System (ADS)

Llovet, Xavier; Matthews, Michael B.; Čeh, Miran; Langer, Enrico; Žagar, Kristina

2016-02-01

This volume of the IOP Conference Series: Materials Science and Engineering contains papers from the 14th Workshop of the European Microbeam Analysis Society (EMAS) on Modern Developments and Applications in Microbeam Analysis which took place from the 3rd to the 7th of May 2015 in the Grand Hotel Bernardin, Portorož, Slovenia. The primary aim of this series of workshops is to assess the state-of-the-art and reliability of microbeam analysis techniques. The workshops also provide a forum where students and young scientists starting out on a career in microbeam analysis can meet and discuss with the established experts. The workshops have a unique format comprising invited plenary lectures by internationally recognized experts, poster presentations by the participants and round table discussions on the key topics led by specialists in the field.This workshop was organized in collaboration with the Jožef Stefan Institute and SDM - Slovene Society for Microscopy. The technical programme included the following topics: electron probe microanalysis, STEM and EELS, materials applications, cathodoluminescence and electron backscatter diffraction (EBSD), and their applications. As at previous workshops there was also a special oral session for young scientists. The best presentation by a young scientist was awarded with an invitation to attend the 2016 Microscopy and Microanalysis meeting at Columbus, Ohio. The prize went to Shirin Kaboli, of the Department of Metals and Materials Engineering of McGill University (Montréal, Canada), for her talk entitled "Electron channelling contrast reconstruction with electron backscattered diffraction". The continuing relevance of the EMAS workshops and the high regard in which they are held internationally can be seen from the fact that 71 posters from 16 countries were on display at the meeting and that the participants came from as far away as Japan, Canada, USA, and Australia. A selection of participants with posters was invited to give a short oral presentation of their work in three dedicated sessions. The prize for the best poster was an invitation to participate in the 24th Australian Conference on Microscopy and Microanalysis (ACMM 24) in Melbourne, Australia. The prize was awarded to Aurélien Moy of the University of Montpellier (France) for his poster entitled: "Standardless quantification of heavy metals by electron probe microanalysis". This proceedings volume contains the full texts of 9 of the invited plenary lectures and of 12 papers on related topics originating from the posters presented at the workshop. All the papers have been subjected to peer review by a least two referees.

Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks.

PubMed

Stegmaier, Johannes; Otte, Jens C; Kobitski, Andrei; Bartschat, Andreas; Garcia, Ariel; Nienhaus, G Ulrich; Strähle, Uwe; Mikut, Ralf

2014-01-01

Automated analysis of multi-dimensional microscopy images has become an integral part of modern research in life science. Most available algorithms that provide sufficient segmentation quality, however, are infeasible for a large amount of data due to their high complexity. In this contribution we present a fast parallelized segmentation method that is especially suited for the extraction of stained nuclei from microscopy images, e.g., of developing zebrafish embryos. The idea is to transform the input image based on gradient and normal directions in the proximity of detected seed points such that it can be handled by straightforward global thresholding like Otsu's method. We evaluate the quality of the obtained segmentation results on a set of real and simulated benchmark images in 2D and 3D and show the algorithm's superior performance compared to other state-of-the-art algorithms. We achieve an up to ten-fold decrease in processing times, allowing us to process large data sets while still providing reasonable segmentation results.

Unconventional methods of imaging: computational microscopy and compact implementations

NASA Astrophysics Data System (ADS)

McLeod, Euan; Ozcan, Aydogan

2016-07-01

In the past two decades or so, there has been a renaissance of optical microscopy research and development. Much work has been done in an effort to improve the resolution and sensitivity of microscopes, while at the same time to introduce new imaging modalities, and make existing imaging systems more efficient and more accessible. In this review, we look at two particular aspects of this renaissance: computational imaging techniques and compact imaging platforms. In many cases, these aspects go hand-in-hand because the use of computational techniques can simplify the demands placed on optical hardware in obtaining a desired imaging performance. In the first main section, we cover lens-based computational imaging, in particular, light-field microscopy, structured illumination, synthetic aperture, Fourier ptychography, and compressive imaging. In the second main section, we review lensfree holographic on-chip imaging, including how images are reconstructed, phase recovery techniques, and integration with smart substrates for more advanced imaging tasks. In the third main section we describe how these and other microscopy modalities have been implemented in compact and field-portable devices, often based around smartphones. Finally, we conclude with some comments about opportunities and demand for better results, and where we believe the field is heading.

Evaluation of agave fiber delignification by means of microscopy techniques and image analysis.

PubMed

Hernández-Hernández, Hilda M; Chanona-Pérez, Jorge J; Calderón-Domínguez, Georgina; Perea-Flores, María J; Mendoza-Pérez, Jorge A; Vega, Alberto; Ligero, Pablo; Palacios-González, Eduardo; Farrera-Rebollo, Reynold R

2014-10-01

Recently, the use of different types of natural fibers to produce paper and textiles from agave plants has been proposed. Agave atrovirens can be a good source of cellulose and lignin; nevertheless, the microstructural changes that happen during delignification have scarcely been studied. The aim of this work was to study the microstructural changes that occur during the delignification of agave fibers by means of microscopy techniques and image analysis. The fibers of A. atrovirens were obtained from leaves using convective drying, milling, and sieving. Fibers were processed using the Acetosolv pulping method at different concentrations of acetic acid; increasing acid concentration promoted higher levels of delignification, structural damage, and the breakdown of fiber clumps. Delignification followed by spectrometric analysis and microstructural studies were carried out by light, confocal laser scanning and scanning electron microscopy and showed that the delignification process follows three stages: initial, bulk, and residual. Microscopy techniques and image analysis were efficient tools for microstructural characterization during delignification of agave fibers, allowing quantitative evaluation of the process and the development of linear prediction models. The data obtained integrated numerical and microstructural information that could be valuable for the study of pulping of lignocellulosic materials.

Modern Observational Techniques for Comets

NASA Technical Reports Server (NTRS)

Brandt, J. C. (Editor); Greenberg, J. M. (Editor); Donn, B. (Editor); Rahe, J. (Editor)

1981-01-01

Techniques are discussed in the following areas: astrometry, photometry, infrared observations, radio observations, spectroscopy, imaging of coma and tail, image processing of observation. The determination of the chemical composition and physical structure of comets is highlighted.

A Photomicrography Primer.

ERIC Educational Resources Information Center

Davidson, Michael W.

1991-01-01

Describes techniques and equipment which allows school microscopes to perform crossed-polarized light microscopy, reflected light microscopy, and photomicrography. Provides information on using chemicals from a high school stockroom to view crystals, viewing integrated circuits, and capturing images on film. Lists possible independent student…

Lipids in cheese

USDA-ARS?s Scientific Manuscript database

Lipids are present in cheese at levels above 20 percent and are analyzed by several techniques. Scanning electron microscopy and confocal laser scanning microscopy are used to examine the microstructure, gas chromatography is employed to look at fatty acid composition, and differential scanning cal...

Fundamental limits to superresolution fluorescence microscopy

NASA Astrophysics Data System (ADS)

Small, Alex

2013-02-01

Superresolution fluorescence microscopy techniques such as PALM, STORM, STED, and Structured Illumination Microscopy (SIM) enable imaging of live cells at nanometer resolution. The common theme in all of these techniques is that the diffraction limit is circumvented by controlling the states of fluorescent molecules. Although the samples are labeled very densely (i.e. with spacing much smaller than the Airy distance), not all of the molecules are emitting at the same time. Consequently, one does not encounter overlapping blurs. In the deterministic techniques (STED, SIM) the achievable resolution scales as the wavelength of light divided by the square root of the intensity of a beam used to control the fluorescent state. In the stochastic techniques (PALM, STORM), the achievable resolution scales as the wavelength of light divided by the square root of the number of photons collected. Although these limits arise from very different mechanisms (parabolic beam profiles for STED and SIM, statistics for PALM and STORM), in all cases the resolution scales inversely with the square root of a measure of the number of photons used in the experiment. We have developed a proof that this relationship between resolution and photon count is universal to techniques that control the states of fluorophores using classical light. Our proof encompasses linear and nonlinear optics, as well as computational post-processing techniques for extracting information beyond the diffraction limit. If there are techniques that can achieve a more efficient relationship between resolution and photon count, those techniques will require light exhibiting non-classical correlations.

Modified glass fibre reinforced polymer composites

NASA Astrophysics Data System (ADS)

Cao, Yumei

A high ratio of strength to density and relatively low-cost are some of the significant features of glass fibre reinforced polymer composites (GFRPCs) that made them one of the most rapidly developed materials in recent years. They are widely used as the material of construction in the areas of aerospace, marine and everyday life, such as airplane, helicopter, boat, canoe, fishing rod, racket, etc. Traditionally, researchers tried to raise the mechanical properties and keep a high strength/weight ratio using all or some of the following methods: increasing the volume fraction of the fibre; using different polymeric matrix material; or changing the curing conditions. In recent years, some new techniques and processing methods were developed to further improve the mechanical properties of glass fibre (GF) reinforced polymer composite. For example, by modifying the surface condition of the GF, both the interface strength between the GF and the polymer matrix and the shear strength of the final composite can be significantly increased. Also, by prestressing the fibre during the curing process of the composite, the tensile, flexural and the impact properties of the composite can be greatly improved. In this research project, a new method of preparing GFRPCs, which combined several traditional and modern techniques together, was developed. This new method includes modification of the surface of the GF with silica particles, application of different levels of prestressing on the GF during the curing process, and the change of the fibre volume fraction and curing conditions in different sets of experiments. The results of the new processing were tested by the three-point bend test, the short beam shear test and the impact test to determine the new set of properties so formed in the composite material. Scanning electronic microscopy (SEM) was used to study the fracture surface of the new materials after the mechanical tests were performed. By taking advantages of the traditional and modern techniques at the same time, the newly developed modified glass fibre reinforced epoxy matrix composites (MGFRECs) have much improved comprehensive properties. The flexural strength, the flexural modulus, the shear modulus and the impact energy (Izod impact test) of the composites were improved up to 87%, 74%, 30% and 89% respectively when modified samples were compared to the samples made by the traditional methods.

From experimental imaging techniques to virtual embryology.

PubMed

Weninger, Wolfgang J; Tassy, Olivier; Darras, Sébastien; Geyer, Stefan H; Thieffry, Denis

2004-01-01

Modern embryology increasingly relies on descriptive and functional three dimensional (3D) and four dimensional (4D) analysis of physically, optically, or virtually sectioned specimens. To cope with the technical requirements, new methods for high detailed in vivo imaging, as well as the generation of high resolution digital volume data sets for the accurate visualisation of transgene activity and gene product presence, in the context of embryo morphology, were recently developed and are under construction. These methods profoundly change the scientific applicability, appearance and style of modern embryo representations. In this paper, we present an overview of the emerging techniques to create, visualise and administrate embryo representations (databases, digital data sets, 3-4D embryo reconstructions, models, etc.), and discuss the implications of these new methods on the work of modern embryologists, including, research, teaching, the selection of specific model organisms, and potential collaborators.

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy

PubMed Central

Lim, Daryl; Ford, Tim N.; Chu, Kengyeh K.; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish. PMID:21280920

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy.

PubMed

Lim, Daryl; Ford, Tim N; Chu, Kengyeh K; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish.

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy

NASA Astrophysics Data System (ADS)

Lim, Daryl; Ford, Tim N.; Chu, Kengyeh K.; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish.

A Simple Configuration for Quantitative Phase Contrast Microscopy of Transmissible Samples

NASA Astrophysics Data System (ADS)

Sengupta, Chandan; Dasgupta, Koustav; Bhattacharya, K.

Phase microscopy attempts to visualize and quantify the phase distribution of samples which are otherwise invisible under microscope without the use of stains. The two principal approaches to phase microscopy are essentially those of Fourier plane modulation and interferometric techniques. Although the former, first proposed by Zernike, had been the harbinger of phase microscopy, it was the latter that allowed for quantitative evaluation of phase samples. However interferometric techniques are fraught with associated problems such as complicated setup involving mirrors and beam-splitters, the need for a matched objective in the reference arm and also the need for vibration isolation. The present work proposes a single element cube beam-splitter (CBS) interferometer combined with a microscope objective (MO) for interference microscopy. Because of the monolithic nature of the interferometer, the system is almost insensitive to vibrations and relatively simple to align. It will be shown that phase shifting properties may also be introduced by suitable and proper use of polarizing devices. Initial results showing the quantitative three dimensional phase profiles of simulated and actual biological specimens are presented.

Observation and manipulation of magnetic domains in sol gel derived thin films of spinel ferrites

NASA Astrophysics Data System (ADS)

Datar, Ashwini A.; Mathe, Vikas L.

2017-12-01

Thin films of spinel ferrites, namely zinc substituted nickel, cobalt ferrite, and manganese substituted cobalt ferrite, were synthesized using sol-gel derived spin-coating techniques. The films were characterized using x-ray diffraction, field emission scanning electron microscopy, Fourier transform infrared spectroscopy and Raman spectroscopy techniques for the analysis of structural, morphological and vibrational band transition properties, which confirm the spinel phase formation of the films. The magnetic force microscopy (MFM) technique was used to observe the magnetic domain structure present in the synthesized films. Further, the films were subjected to an external DC magnetic field of 2 kG to orient the magnetic domains and analyzed using an ex situ MFM technique.

Investigation of wear phenomena by microscopy

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1982-01-01

The various wear mechanisms involved in the loss of material from metallic and nonmetallic surfaces are discussed. The results presented indicate how various microscopy techniques used in conjunction with other analytical tools can assist in the elucidation of a wear mechanism. Without question, microscopy is the single most important tool for the study of the wear of surfaces, to assess and address inherent mechanisms of the material removal process.

Image correlation microscopy for uniform illumination.

PubMed

Gaborski, T R; Sealander, M N; Ehrenberg, M; Waugh, R E; McGrath, J L

2010-01-01

Image cross-correlation microscopy is a technique that quantifies the motion of fluorescent features in an image by measuring the temporal autocorrelation function decay in a time-lapse image sequence. Image cross-correlation microscopy has traditionally employed laser-scanning microscopes because the technique emerged as an extension of laser-based fluorescence correlation spectroscopy. In this work, we show that image correlation can also be used to measure fluorescence dynamics in uniform illumination or wide-field imaging systems and we call our new approach uniform illumination image correlation microscopy. Wide-field microscopy is not only a simpler, less expensive imaging modality, but it offers the capability of greater temporal resolution over laser-scanning systems. In traditional laser-scanning image cross-correlation microscopy, lateral mobility is calculated from the temporal de-correlation of an image, where the characteristic length is the illuminating laser beam width. In wide-field microscopy, the diffusion length is defined by the feature size using the spatial autocorrelation function. Correlation function decay in time occurs as an object diffuses from its original position. We show that theoretical and simulated comparisons between Gaussian and uniform features indicate the temporal autocorrelation function depends strongly on particle size and not particle shape. In this report, we establish the relationships between the spatial autocorrelation function feature size, temporal autocorrelation function characteristic time and the diffusion coefficient for uniform illumination image correlation microscopy using analytical, Monte Carlo and experimental validation with particle tracking algorithms. Additionally, we demonstrate uniform illumination image correlation microscopy analysis of adhesion molecule domain aggregation and diffusion on the surface of human neutrophils.

Nanoparticles as smart treatment-delivery systems in plants: assessment of different techniques of microscopy for their visualization in plant tissues.

PubMed

González-Melendi, P; Fernández-Pacheco, R; Coronado, M J; Corredor, E; Testillano, P S; Risueño, M C; Marquina, C; Ibarra, M R; Rubiales, D; Pérez-de-Luque, A

2008-01-01

The great potential of using nanodevices as delivery systems to specific targets in living organisms was first explored for medical uses. In plants, the same principles can be applied for a broad range of uses, in particular to tackle infections. Nanoparticles tagged to agrochemicals or other substances could reduce the damage to other plant tissues and the amount of chemicals released into the environment. To explore the benefits of applying nanotechnology to agriculture, the first stage is to work out the correct penetration and transport of the nanoparticles into plants. This research is aimed (a) to put forward a number of tools for the detection and analysis of core-shell magnetic nanoparticles introduced into plants and (b) to assess the use of such magnetic nanoparticles for their concentration in selected plant tissues by magnetic field gradients. Cucurbita pepo plants were cultivated in vitro and treated with carbon-coated Fe nanoparticles. Different microscopy techniques were used for the detection and analysis of these magnetic nanoparticles, ranging from conventional light microscopy to confocal and electron microscopy. Penetration and translocation of magnetic nanoparticles in whole living plants and into plant cells were determined. The magnetic character allowed nanoparticles to be positioned in the desired plant tissue by applying a magnetic field gradient there; also the graphitic shell made good visualization possible using different microscopy techniques. The results open a wide range of possibilities for using magnetic nanoparticles in general plant research and agronomy. The nanoparticles can be charged with different substances, introduced within the plants and, if necessary, concentrated into localized areas by using magnets. Also simple or more complex microscopical techniques can be used in localization studies.

Nanoparticles as Smart Treatment-delivery Systems in Plants: Assessment of Different Techniques of Microscopy for their Visualization in Plant Tissues

PubMed Central

González-Melendi, P.; Fernández-Pacheco, R.; Coronado, M. J.; Corredor, E.; Testillano, P. S.; Risueño, M. C.; Marquina, C.; Ibarra, M. R.; Rubiales, D.; Pérez-de-Luque, A.

2008-01-01

Background and Aims The great potential of using nanodevices as delivery systems to specific targets in living organisms was first explored for medical uses. In plants, the same principles can be applied for a broad range of uses, in particular to tackle infections. Nanoparticles tagged to agrochemicals or other substances could reduce the damage to other plant tissues and the amount of chemicals released into the environment. To explore the benefits of applying nanotechnology to agriculture, the first stage is to work out the correct penetration and transport of the nanoparticles into plants. This research is aimed (a) to put forward a number of tools for the detection and analysis of core-shell magnetic nanoparticles introduced into plants and (b) to assess the use of such magnetic nanoparticles for their concentration in selected plant tissues by magnetic field gradients. Methods Cucurbita pepo plants were cultivated in vitro and treated with carbon-coated Fe nanoparticles. Different microscopy techniques were used for the detection and analysis of these magnetic nanoparticles, ranging from conventional light microscopy to confocal and electron microscopy. Key Results Penetration and translocation of magnetic nanoparticles in whole living plants and into plant cells were determined. The magnetic character allowed nanoparticles to be positioned in the desired plant tissue by applying a magnetic field gradient there; also the graphitic shell made good visualization possible using different microscopy techniques. Conclusions The results open a wide range of possibilities for using magnetic nanoparticles in general plant research and agronomy. The nanoparticles can be charged with different substances, introduced within the plants and, if necessary, concentrated into localized areas by using magnets. Also simple or more complex microscopical techniques can be used in localization studies. PMID:17998213

Complementary Imaging of Silver Nanoparticle Interactions with Green Algae: Dark-Field Microscopy, Electron Microscopy, and Nanoscale Secondary Ion Mass Spectrometry.

PubMed

Sekine, Ryo; Moore, Katie L; Matzke, Marianne; Vallotton, Pascal; Jiang, Haibo; Hughes, Gareth M; Kirby, Jason K; Donner, Erica; Grovenor, Chris R M; Svendsen, Claus; Lombi, Enzo

2017-11-28

Increasing consumer use of engineered nanomaterials has led to significantly increased efforts to understand their potential impact on the environment and living organisms. Currently, no individual technique can provide all the necessary information such as their size, distribution, and chemistry in complex biological systems. Consequently, there is a need to develop complementary instrumental imaging approaches that provide enhanced understanding of these "bio-nano" interactions to overcome the limitations of individual techniques. Here we used a multimodal imaging approach incorporating dark-field light microscopy, high-resolution electron microscopy, and nanoscale secondary ion mass spectrometry (NanoSIMS). The aim was to gain insight into the bio-nano interactions of surface-functionalized silver nanoparticles (Ag-NPs) with the green algae Raphidocelis subcapitata, by combining the fidelity, spatial resolution, and elemental identification offered by the three techniques, respectively. Each technique revealed that Ag-NPs interact with the green algae with a dependence on the size (10 nm vs 60 nm) and surface functionality (tannic acid vs branched polyethylenimine, bPEI) of the NPs. Dark-field light microscopy revealed the presence of strong light scatterers on the algal cell surface, and SEM imaging confirmed their nanoparticulate nature and localization at nanoscale resolution. NanoSIMS imaging confirmed their chemical identity as Ag, with the majority of signal concentrated at the cell surface. Furthermore, SEM and NanoSIMS provided evidence of 10 nm bPEI Ag-NP internalization at higher concentrations (40 μg/L), correlating with the highest toxicity observed from these NPs. This multimodal approach thus demonstrated an effective approach to complement dose-response studies in nano-(eco)-toxicological investigations.

Multimodal biophotonic workstation for live cell analysis.

PubMed

Esseling, Michael; Kemper, Björn; Antkowiak, Maciej; Stevenson, David J; Chaudet, Lionel; Neil, Mark A A; French, Paul W; von Bally, Gert; Dholakia, Kishan; Denz, Cornelia

2012-01-01

A reliable description and quantification of the complex physiology and reactions of living cells requires a multimodal analysis with various measurement techniques. We have investigated the integration of different techniques into a biophotonic workstation that can provide biological researchers with these capabilities. The combination of a micromanipulation tool with three different imaging principles is accomplished in a single inverted microscope which makes the results from all the techniques directly comparable. Chinese Hamster Ovary (CHO) cells were manipulated by optical tweezers while the feedback was directly analyzed by fluorescence lifetime imaging, digital holographic microscopy and dynamic phase-contrast microscopy. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic study of Pbs nano-structured layer prepared by Pld utilized as a Hall-effect magnetic sensor

NASA Astrophysics Data System (ADS)

Atwa, D. M.; Aboulfotoh, N.; El-magd, A. Abo; Badr, Y.

2013-10-01

Lead sulfide (PbS) nano-structured films have been grown on quartz substrates using PLD technique. The deposited films were characterized by several structural techniques, including scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Selected-area electron diffraction patterns (SAED). The results prove the formation of cubic phase of PbS nanocrystals. Elemental analysis of the deposited films compared to the bulk target was obtained via laser induced fluorescence of the produced plasma particles and the energy dispersive X-ray "EDX" technique. The Hall coefficient measurements indicate an efficient performance of the deposited films as a magnetic sensor.

Developments in flow visualization methods for flight research

NASA Technical Reports Server (NTRS)

Holmes, Bruce J.; Obara, Clifford J.; Manuel, Gregory S.; Lee, Cynthia C.

1990-01-01

With the introduction of modern airplanes utilizing laminar flow, flow visualization has become an important diagnostic tool in determining aerodynamic characteristics such as surface flow direction and boundary-layer state. A refinement of the sublimating chemical technique has been developed to define both the boundary-layer transition location and the transition mode. In response to the need for flow visualization at subsonic and transonic speeds and altitudes above 20,000 feet, the liquid crystal technique has been developed. A third flow visualization technique that has been used is infrared imaging, which offers non-intrusive testing over a wide range of test conditions. A review of these flow visualization methods and recent flight results is presented for a variety of modern aircraft and flight conditions.

Characterization of human carotid atherosclerotic tissues imaged by combining multiple multiphoton microscopy techniques

NASA Astrophysics Data System (ADS)

Baria, E.; Cicchi, R.; Nesi, G.; Massi, D.; Pavone, F. S.

2017-07-01

We combined Second Harmonic Generation, Two-Photon Fluorescence and Fluorescence Lifetime Imaging Microscopy for studying human carotid ex vivo tissue sections affected by atherosclerosis, resulting in the discrimination of different arterial regions within the plaques.

Confocal microscopy imaging of solid tissue

EPA Science Inventory

Confocal laser scanning microscopy (CLSM) is a technique that is capable of generating serial sections of whole-mount tissue and then reassembling the computer acquired images as a virtual 3-dimensional structure. In many ways CLSM offers an alternative to traditional sectioning ...

Speckle-field digital holographic microscopy.

PubMed

Park, YongKeun; Choi, Wonshik; Yaqoob, Zahid; Dasari, Ramachandra; Badizadegan, Kamran; Feld, Michael S

2009-07-20

The use of coherent light in conventional holographic phase microscopy (HPM) poses three major drawbacks: poor spatial resolution, weak depth sectioning, and fixed pattern noise due to unwanted diffraction. Here, we report a technique which can overcome these drawbacks, but maintains the advantage of phase microscopy - high contrast live cell imaging and 3D imaging. A speckle beam of a complex spatial pattern is used for illumination to reduce fixed pattern noise and to improve optical sectioning capability. By recording of the electric field of speckle, we demonstrate high contrast 3D live cell imaging without the need for axial scanning - neither objective lens nor sample stage. This technique has great potential in studying biological samples with improved sensitivity, resolution and optical sectioning capability.

Assembly and microscopic characterization of DNA origami structures.

PubMed

Scheible, Max; Jungmann, Ralf; Simmel, Friedrich C

2012-01-01

DNA origami is a revolutionary method for the assembly of molecular nanostructures from DNA with precisely defined dimensions and with an unprecedented yield. This can be utilized to arrange nanoscale components such as proteins or nanoparticles into pre-defined patterns. For applications it will now be of interest to arrange such components into functional complexes and study their geometry-dependent interactions. While commonly DNA nanostructures are characterized by atomic force microscopy or electron microscopy, these techniques often lack the time-resolution to study dynamic processes. It is therefore of considerable interest to also apply fluorescence microscopic techniques to DNA nanostructures. Of particular importance here is the utilization of novel super-resolved microscopy methods that enable imaging beyond the classical diffraction limit.

Image contrast mechanisms in dynamic friction force microscopy: Antimony particles on graphite

NASA Astrophysics Data System (ADS)

Mertens, Felix; Göddenhenrich, Thomas; Dietzel, Dirk; Schirmeisen, Andre

2017-01-01

Dynamic Friction Force Microscopy (DFFM) is a technique based on Atomic Force Microscopy (AFM) where resonance oscillations of the cantilever are excited by lateral actuation of the sample. During this process, the AFM tip in contact with the sample undergoes a complex movement which consists of alternating periods of sticking and sliding. Therefore, DFFM can give access to dynamic transition effects in friction that are not accessible by alternative techniques. Using antimony nanoparticles on graphite as a model system, we analyzed how combined influences of friction and topography can effect different experimental configurations of DFFM. Based on the experimental results, for example, contrast inversion between fractional resonance and band excitation imaging strategies to extract reliable tribological information from DFFM images are devised.

Higher-eigenmode piezoresponse force microscopy: a path towards increased sensitivity and the elimination of electrostatic artifacts

NASA Astrophysics Data System (ADS)

MacDonald, Gordon A.; DelRio, Frank W.; Killgore, Jason P.

2018-03-01

Piezoresponse force microscopy (PFM) and related bias-induced strain sensing atomic force microscopy techniques provide unique characterization of material-functionality at the nanoscale. However, these techniques are prone to unwanted artifact signals that influence the vibration amplitude of the detecting cantilever. Here, we show that higher-order contact resonance eigenmodes can be readily excited in PFM. The benefits of using the higher-order eigenmodes include absolute sensitivity enhancement, electrostatic artifact reduction, and lateral versus normal strain decoupling. This approach can significantly increase the proportion of total signal arising from desired strain (as opposed to non-strain artifacts) in measurements with cantilevers exhibiting typical, few N m‑1 spring constants to cantilevers up to 1000× softer than typically used.

Detection of living Sarcoptes scabiei larvae by reflectance mode confocal microscopy in the skin of a patient with crusted scabies

NASA Astrophysics Data System (ADS)

Levi, Assi; Mumcuoglu, Kosta Y.; Ingber, Arieh; Enk, Claes D.

2012-06-01

Scabies is an intensely pruritic disorder induced by a delayed type hypersensitivity reaction to infestation of the skin by the mite Sarcoptes scabiei. The diagnosis of scabies is established clinically and confirmed by identifying mites or eggs by microscopic examination of scrapings from the skin or by surface microscopy using a dermatoscope. Reflectance-mode confocal microscopy is a novel technique used for noninvasive imaging of skin structures and lesions at a resolution compatible to that of conventional histology. Recently, the technique was employed for the confirmation of the clinical diagnosis of scabies. We demonstrate the first ever documentation of a larva moving freely inside the skin of a patient infected with scabies.

Instrumentation and fusion for congenital spine deformities.

PubMed

Hedequist, Daniel J

2009-08-01

A retrospective clinical review. To review the use of modern instrumentation of the spine for congenital spinal deformities. Spinal instrumentation has evolved since the advent of the Harrington rod. There is a paucity of literature, which discusses the use of modern spinal instrumentation in congenital spine deformity cases. This review focuses on modern instrumentation techniques for congenital scoliosis and kyphosis. A systematic review was performed of the literature to discuss spinal implant use for congenital deformities. Spinal instrumentation may be safely and effectively used in cases of congenital spinal deformity. Spinal surgeons taking care of children with congenital spine deformities need to be trained in all aspects of modern spinal instrumentation.

Quantitative nondestructive evaluation of materials and structures

NASA Technical Reports Server (NTRS)

Smith, Barry T.

1991-01-01

An experimental investigation was undertaken to quantify damage tolerance and resistance in composite materials impacted using the drop-weight method. Tests were conducted on laminates of several different carbon-fiber composite systems, such as epoxies, modified epoxies, and amorphous and semicrystalline thermoplastics. Impacted composite specimens were examined using destructive and non-destructive techniques to establish the characteristic damage states. Specifically, optical microscopy, ultrasonic, and scanning electron microscopy techniques were used to identify impact induced damage mechanisms. Damage propagation during post impact compression was also studied.

Bulk microstructure and local elastic properties of carbon nanocomposites studied by impulse acoustic microscopy technique

NASA Astrophysics Data System (ADS)

Levin, V.; Petronyuk, Yu.; Morokov, E.; Chernozatonskii, L.; Kuzhir, P.; Fierro, V.; Celzard, A.; Bellucci, S.; Bistarelli, S.; Mastrucci, M.; Tabacchioni, I.

2016-05-01

Bulk microstructure and elastic properties of epoxy-nanocarbon nanocomposites for diverse types and different content of carbon nanofiller has been studied by using impulse acoustic microscopy technique. It has been shown occurrence of various types of mesoscopic structure formed by nanoparticles inside the bulk of nanocomposite materials, including nanoparticle conglomerates and nanoparticle aerogel systems. In spite of the bulk microstructure, nanocarbon composites demonstrate elastic uniformity and negligible influence of nanofiller on elastic properties of carbon nanocomposite materials.

Synthesis of samarium doped gadolinium oxide nanorods, its spectroscopic and physical properties

NASA Astrophysics Data System (ADS)

Boopathi, G.; Gokul Raj, S.; Ramesh Kumar, G.; Mohan, R.; Mohan, S.

2018-06-01

One-dimensional samarium doped gadolinium oxide [Sm:Gd2O3] nanorods have been synthesized successfully through co-precipitation technique in aqueous solution. The as-synthesized and calcined products were characterized by using powder X-ray diffraction pattern, Fourier transform Raman spectroscopy, thermogravimetric/differential thermal analysis, scanning electron microscopy with energy-dispersive X-ray analysis, transmission electron microscopy, Fourier transform infrared spectroscopy, Ultraviolet-Visible spectrometry, photoluminescence spectrophotometer and X-ray photoelectron spectroscopy techniques. The obtained results are discussed in detailed manner.

Helium ion microscopy and ultra-high-resolution scanning electron microscopy analysis of membrane-extracted cells reveals novel characteristics of the cytoskeleton of Giardia intestinalis.

PubMed

Gadelha, Ana Paula Rocha; Benchimol, Marlene; de Souza, Wanderley

2015-06-01

Giardia intestinalis presents a complex microtubular cytoskeleton formed by specialized structures, such as the adhesive disk, four pairs of flagella, the funis and the median body. The ultrastructural organization of the Giardia cytoskeleton has been analyzed using different microscopic techniques, including high-resolution scanning electron microscopy. Recent advances in scanning microscopy technology have opened a new venue for the characterization of cellular structures and include scanning probe microscopy techniques such as ultra-high-resolution scanning electron microscopy (UHRSEM) and helium ion microscopy (HIM). Here, we studied the organization of the cytoskeleton of G. intestinalis trophozoites using UHRSEM and HIM in membrane-extracted cells. The results revealed a number of new cytoskeletal elements associated with the lateral crest and the dorsal surface of the parasite. The fine structure of the banded collar was also observed. The marginal plates were seen linked to a network of filaments, which were continuous with filaments parallel to the main cell axis. Cytoplasmic filaments that supported the internal structures were seen by the first time. Using anti-actin antibody, we observed a labeling in these filamentous structures. Taken together, these data revealed new surface characteristics of the cytoskeleton of G. intestinalis and may contribute to an improved understanding of the structural organization of trophozoites. Copyright © 2015 Elsevier Inc. All rights reserved.

How Farmers Learn about Environmental Issues: Reflections on a Sociobiographical Approach

ERIC Educational Resources Information Center

Vandenabeele, Joke; Wildemeersch, Danny

2012-01-01

At the time of this research, protests of farmers against new environmental policy measures received much media attention. News reports suggested that farmers' organizations rejected the idea that modern farming techniques cause damage to the environment and even tried to undermine attempts to reconcile the goals of modern agriculture with…

Older Learning Engagement in the Modern City

ERIC Educational Resources Information Center

Lido, Catherine; Osborne, Michael; Livingston, Mark; Thakuriah, Piyushimita; Sila-Nowicka, Katarzyna

2016-01-01

This research employs novel techniques to examine older learners' journeys, educationally and physically, in order to gain a "three-dimensional" picture of lifelong learning in the modern urban context of Glasgow. The data offers preliminary analyses of an ongoing 1,500 household survey by the Urban Big Data Centre (UBDC). A sample of…

Commodification of Ghana's Volta River: An Example of Ellul's Autonomy of Technique

ERIC Educational Resources Information Center

Agbemabiese, Lawrence; Byrne, John

2005-01-01

Jacques Ellul argued that modernity's nearly exclusive reliance on science and technology to design society would threaten human freedom. Of particular concern for Ellul was the prospect of the technical milieu overwhelming culture. The commodification of the Volta River in order to modernize Ghana illustrates the Ellulian dilemma of the autonomy…

Modern Methodology and Techniques Aimed at Developing the Environmentally Responsible Personality

ERIC Educational Resources Information Center

Ponomarenko, Yelena V.; Zholdasbekova, Bibisara A.; Balabekov, Aidarhan T.; Kenzhebekova, Rabiga I.; Yessaliyev, Aidarbek A.; Larchenkova, Liudmila A.

2016-01-01

The article discusses the positive impact of an environmentally responsible individual as the social unit able to live in harmony with the natural world, himself/herself and other people. The purpose of the article is to provide theoretical substantiation of modern teaching methods. The authors considered the experience of philosophy, psychology,…

[Significance of bone mineral density and modern cementing technique for in vitro cement penetration in total shoulder arthroplasty].

PubMed

Pape, G; Raiss, P; Kleinschmidt, K; Schuld, C; Mohr, G; Loew, M; Rickert, M

2010-12-01

Loosening of the glenoid component is one of the major causes of failure in total shoulder arthroplasty. Possible risk factors for loosening of cemented components include an eccentric loading, poor bone quality, inadequate cementing technique and insufficient cement penetration. The application of a modern cementing technique has become an established procedure in total hip arthroplasty. The goal of modern cementing techniques in general is to improve the cement-penetration into the cancellous bone. Modern cementing techniques include the cement vacuum-mixing technique, retrograde filling of the cement under pressurisation and the use of a pulsatile lavage system. The main purpose of this study was to analyse cement penetration into the glenoid bone by using modern cement techniques and to investigate the relationship between the bone mineral density (BMD) and the cement penetration. Furthermore we measured the temperature at the glenoid surface before and after jet-lavage of different patients during total shoulder arthroplasty. It is known that the surrounding temperature of the bone has an effect on the polymerisation of the cement. Data from this experiment provide the temperature setting for the in-vitro study. The glenoid surface temperature was measured in 10 patients with a hand-held non-contact temperature measurement device. The bone mineral density was measured by DEXA. Eight paired cadaver scapulae were allocated (n = 16). Each pair comprised two scapulae from one donor (matched-pair design). Two different glenoid components were used, one with pegs and the other with a keel. The glenoids for the in-vitro study were prepared with the bone compaction technique by the same surgeon in all cases. Pulsatile lavage was used to clean the glenoid of blood and bone fragments. Low viscosity bone cement was applied retrogradely into the glenoid by using a syringe. A constant pressure was applied with a modified force sensor impactor. Micro-computed tomography scans were applied to analyse the cement penetration into the cancellous bone. The mean temperature during the in-vivo arthroplasty of the glenoid was 29.4 °C (27.2-31 °C) before and 26.2 °C (25-27.5 °C) after jet-lavage. The overall peak BMD was 0.59 (range 0.33-0.99) g/cm (2). Mean cement penetration was 107.9 (range 67.6-142.3) mm (2) in the peg group and 128.3 (range 102.6-170.8) mm (2) in the keel group. The thickness of the cement layer varied from 0 to 2.1 mm in the pegged group and from 0 to 2.4 mm in the keeled group. A strong negative correlation between BMD and mean cement penetration was found for the peg group (r (2) = -0.834; p < 0.01) and for the keel group (r (2) = -0.727; p < 0.041). Micro-CT shows an inhomogenous dispersion of the cement into the cancellous bone. Data from the in-vivo temperature measurement indicate that the temperature at the glenohumeral surface under operation differs from the body core temperature and should be considered in further in-vitro studies with human specimens. Bone mineral density is negatively correlated to cement penetration in the glenoid. The application of a modern cementing technique in the glenoid provides sufficient cementing penetration although there is an inhomogenous dispersion of the cement. The findings of this study should be considered in further discussions about cementing technique and cement penetration into the cancellous bone of the glenoid. © Georg Thieme Verlag KG Stuttgart · New York.

Cache Energy Optimization Techniques For Modern Processors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mittal, Sparsh

2013-01-01

Modern multicore processors are employing large last-level caches, for example Intel's E7-8800 processor uses 24MB L3 cache. Further, with each CMOS technology generation, leakage energy has been dramatically increasing and hence, leakage energy is expected to become a major source of energy dissipation, especially in last-level caches (LLCs). The conventional schemes of cache energy saving either aim at saving dynamic energy or are based on properties specific to first-level caches, and thus these schemes have limited utility for last-level caches. Further, several other techniques require offline profiling or per-application tuning and hence are not suitable for product systems. In thismore » book, we present novel cache leakage energy saving schemes for single-core and multicore systems; desktop, QoS, real-time and server systems. Also, we present cache energy saving techniques for caches designed with both conventional SRAM devices and emerging non-volatile devices such as STT-RAM (spin-torque transfer RAM). We present software-controlled, hardware-assisted techniques which use dynamic cache reconfiguration to configure the cache to the most energy efficient configuration while keeping the performance loss bounded. To profile and test a large number of potential configurations, we utilize low-overhead, micro-architecture components, which can be easily integrated into modern processor chips. We adopt a system-wide approach to save energy to ensure that cache reconfiguration does not increase energy consumption of other components of the processor. We have compared our techniques with state-of-the-art techniques and have found that our techniques outperform them in terms of energy efficiency and other relevant metrics. The techniques presented in this book have important applications in improving energy-efficiency of higher-end embedded, desktop, QoS, real-time, server processors and multitasking systems. This book is intended to be a valuable guide for both newcomers and veterans in the field of cache power management. It will help graduate students, CAD tool developers and designers in understanding the need of energy efficiency in modern computing systems. Further, it will be useful for researchers in gaining insights into algorithms and techniques for micro-architectural and system-level energy optimization using dynamic cache reconfiguration. We sincerely believe that the ``food for thought'' presented in this book will inspire the readers to develop even better ideas for designing ``green'' processors of tomorrow.« less

Avoid lost discoveries, because of violations of standard assumptions, by using modern robust statistical methods.

PubMed

Wilcox, Rand; Carlson, Mike; Azen, Stan; Clark, Florence

2013-03-01

Recently, there have been major advances in statistical techniques for assessing central tendency and measures of association. The practical utility of modern methods has been documented extensively in the statistics literature, but they remain underused and relatively unknown in clinical trials. Our objective was to address this issue. STUDY DESIGN AND PURPOSE: The first purpose was to review common problems associated with standard methodologies (low power, lack of control over type I errors, and incorrect assessments of the strength of the association). The second purpose was to summarize some modern methods that can be used to circumvent such problems. The third purpose was to illustrate the practical utility of modern robust methods using data from the Well Elderly 2 randomized controlled trial. In multiple instances, robust methods uncovered differences among groups and associations among variables that were not detected by classic techniques. In particular, the results demonstrated that details of the nature and strength of the association were sometimes overlooked when using ordinary least squares regression and Pearson correlation. Modern robust methods can make a practical difference in detecting and describing differences between groups and associations between variables. Such procedures should be applied more frequently when analyzing trial-based data. Copyright © 2013 Elsevier Inc. All rights reserved.

The 2015 super-resolution microscopy roadmap

NASA Astrophysics Data System (ADS)

Hell, Stefan W.; Sahl, Steffen J.; Bates, Mark; Zhuang, Xiaowei; Heintzmann, Rainer; Booth, Martin J.; Bewersdorf, Joerg; Shtengel, Gleb; Hess, Harald; Tinnefeld, Philip; Honigmann, Alf; Jakobs, Stefan; Testa, Ilaria; Cognet, Laurent; Lounis, Brahim; Ewers, Helge; Davis, Simon J.; Eggeling, Christian; Klenerman, David; Willig, Katrin I.; Vicidomini, Giuseppe; Castello, Marco; Diaspro, Alberto; Cordes, Thorben

2015-11-01

Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, the applicability of the optical microscope is limited, since the diffraction of light imposes limitations on the spatial resolution of the image. Consequently the details of, for example, cellular protein distributions, can be visualized only to a certain extent. Fortunately, recent years have witnessed the development of ‘super-resolution’ far-field optical microscopy (nanoscopy) techniques such as stimulated emission depletion (STED), ground state depletion (GSD), reversible saturated optical (fluorescence) transitions (RESOLFT), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) or saturated structured illumination microscopy (SSIM), all in one way or another addressing the problem of the limited spatial resolution of far-field optical microscopy. While SIM achieves a two-fold improvement in spatial resolution compared to conventional optical microscopy, STED, RESOLFT, PALM/STORM, or SSIM have all gone beyond, pushing the limits of optical image resolution to the nanometer scale. Consequently, all super-resolution techniques open new avenues of biomedical research. Because the field is so young, the potential capabilities of different super-resolution microscopy approaches have yet to be fully explored, and uncertainties remain when considering the best choice of methodology. Thus, even for experts, the road to the future is sometimes shrouded in mist. The super-resolution optical microscopy roadmap of Journal of Physics D: Applied Physics addresses this need for clarity. It provides guidance to the outstanding questions through a collection of short review articles from experts in the field, giving a thorough discussion on the concepts underlying super-resolution optical microscopy, the potential of different approaches, the importance of label optimization (such as reversible photoswitchable proteins) and applications in which these methods will have a significant impact. Mark Bates, Christian Eggeling

The effects of modern cementing techniques on the longevity of total hip arthroplasty.

PubMed

Poss, R; Brick, G W; Wright, R J; Roberts, D W; Sledge, C B

1988-07-01

Modern prosthetic design and cementing techniques have dramatically improved femoral component fixation. Compared to studies reported in the 1970s, the incidence of radiographic loosening for periods up to 5 years postoperatively has been reduced by at least a factor of 10. These results are the benchmark by which alternative forms of femoral component fixation must be measured. With the likelihood of increased longevity of total hip arthroplasty resulting from improved fixation, the problems of wear debris from the bearing surfaces and loss of bone stock with time will become preeminent.

[Modern biology, imagery and forensic medicine: contributions and limitations in examination of skeletal remains].

PubMed

Lecomte, Dominique; Plu, Isabelle; Froment, Alain

2012-06-01

Forensic examination is often requested when skeletal remains are discovered. Detailed visual observation can provide much information, such as the human or animal origin, sex, age, stature, and ancestry, and approximate time since death. New three-dimensional imaging techniques can provide further information (osteometry, facial reconstruction). Bone chemistry, and particularly measurement of stable or unstable carbon and nitrogen isotopes, yields information on diet and time since death, respectively. Genetic analyses of ancient DNA are also developing rapidly. Although seldom used in a judicial context, these modern anthropologic techniques are nevertheless available for the most complex cases.

In situ study of Li-ions diffusion and deformation in Li-rich cathode materials by using scanning probe microscopy techniques

NASA Astrophysics Data System (ADS)

Zeng, Kaiyang; Li, Tao; Tian, Tian

2017-08-01

In this paper, the scanning probe microscopy (SPM) based techniques, namely, conductive-AFM, electrochemical strain microscopy (ESM) and AM-FM (amplitude modulation-frequency modulation) techniques, are used to in situ characterize the changes in topography, conductivity and elastic properties of Li-rich layered oxide cathode (Li1.2Mn0.54Ni0.13Co0.13O2) materials, in the form of nanoparticles, when subject to the external electric field. Nanoparticles are the basic building blocks for composite cathode in a Li-ion rechargeable battery. Characterization of the structure and electrochemical properties of the nanoparticles is very important to understand the performance and reliability of the battery materials and devices. In this study, the conductivity, deformation and mechanical properties of the Li-rich oxide nanoparticles under different polarities of biases are studied using the above-mentioned SPM techniques. This information can be correlated with the Li+-ion diffusion and migration in the particles under external electrical field. The results also confirm that the SPM techniques are ideal tools to study the changes in various properties of electrode materials at nano- to micro-scales during or after the ‘simulated’ battery operation conditions. These techniques can also be used to in situ characterize the electrochemical performances of other energy storage materials, especially in the form of the nanoparticles.