WorldWideScience

Sample records for ion microscopic imaging

  1. Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging.

    Science.gov (United States)

    Kiss, András; Smith, Donald F; Jungmann, Julia H; Heeren, Ron M A

    2013-12-30

    Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging. Copyright © 2013 John Wiley & Sons, Ltd.

  2. Comparative study of image contrast in scanning electron microscope and helium ion microscope.

    Science.gov (United States)

    O'Connell, R; Chen, Y; Zhang, H; Zhou, Y; Fox, D; Maguire, P; Wang, J J; Rodenburg, C

    2017-12-01

    Images of Ga + -implanted amorphous silicon layers in a 110 n-type silicon substrate have been collected by a range of detectors in a scanning electron microscope and a helium ion microscope. The effects of the implantation dose and imaging parameters (beam energy, dwell time, etc.) on the image contrast were investigated. We demonstrate a similar relationship for both the helium ion microscope Everhart-Thornley and scanning electron microscope Inlens detectors between the contrast of the images and the Ga + density and imaging parameters. These results also show that dynamic charging effects have a significant impact on the quantification of the helium ion microscope and scanning electron microscope contrast. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  3. A Simple Metric for Determining Resolution in Optical, Ion, and Electron Microscope Images.

    Science.gov (United States)

    Curtin, Alexandra E; Skinner, Ryan; Sanders, Aric W

    2015-06-01

    A resolution metric intended for resolution analysis of arbitrary spatially calibrated images is presented. By fitting a simple sigmoidal function to pixel intensities across slices of an image taken perpendicular to light-dark edges, the mean distance over which the light-dark transition occurs can be determined. A fixed multiple of this characteristic distance is then reported as the image resolution. The prefactor is determined by analysis of scanning transmission electron microscope high-angle annular dark field images of Si. This metric has been applied to optical, scanning electron microscope, and helium ion microscope images. This method provides quantitative feedback about image resolution, independent of the tool on which the data were collected. In addition, our analysis provides a nonarbitrary and self-consistent framework that any end user can utilize to evaluate the resolution of multiple microscopes from any vendor using the same metric.

  4. Helium Ion Microscope: A New Tool for Sub-nanometer Imaging of Soft Materials

    Science.gov (United States)

    Shutthanandan, V.; Arey, B.; Smallwood, C. R.; Evans, J. E.

    2017-12-01

    High-resolution inspection of surface details is needed in many biological and environmental researches to understand the Soil organic material (SOM)-mineral interactions along with identifying microbial communities and their interactions. SOM shares many imaging characteristics with biological samples and getting true surface details from these materials are challenging since they consist of low atomic number materials. FE-SEM imaging is the main imagining technique used to image these materials in the past. These SEM images often show loss of resolution and increase noise due to beam damage and charging issues. Newly developed Helium Ion Microscope (HIM), on the other hand can overcome these difficulties and give very fine details. HIM is very similar to scanning electron microscopy (SEM) but instead of using electrons as a probe beam, HIM uses helium ions with energy ranges from 5 to 40 keV. HIM offers a series of advantages compared to SEM such as nanometer and sub-nanometer image resolutions (about 0.35 nm), detailed surface topography, high surface sensitivity, low Z material imaging (especially for polymers and biological samples), high image contrast, and large depth of field. In addition, HIM also has the ability to image insulating materials without any conductive coatings so that surface details are not modified. In this presentation, several scientific applications across biology and geochemistry will be presented to highlight the effectiveness of this powerful microscope. Acknowledgements: Research was performed using the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at PNNL. Work was supported by DOE-BER Mesoscale to Molecules Bioimaging Project FWP# 66382.

  5. Microscope mode secondary ion mass spectrometry imaging with a Timepix detector.

    NARCIS (Netherlands)

    Kiss, A.; Jungmann, JH; Smith, D.F.; Heeren, R.M.A.

    2013-01-01

    In-vacuum active pixel detectors enable high sensitivity, highly parallel time- and space-resolved detection of ions from complex surfaces. For the first time, a Timepix detector assembly was combined with a secondary ion mass spectrometer for microscope mode secondary ion mass spectrometry (SIMS)

  6. Ion emission microscope microanalyzer

    International Nuclear Information System (INIS)

    Cherepin, V.T.; Olckovsky, V.L.

    1977-01-01

    In the ion microanalyzer (microprobe) the object is exposed to the bombardment of a highly focused ion beam, the secondary ions emitted from the object being analyzed by means of a mass filter. In order to be able to control the position of an analysis synchronous to the local analysis of an object an ion-optical converter (electron image with a fluorescent screen) is placed behind the aperture diaphragm in the direction of the secondary ion beam. The converter allows to make visible in front of the mass filter a non-split ion image characterizing the surface of the surface investigated. Then a certain section may be selected for performing chemical and isotope analyses. (DG) [de

  7. Macro-SICM: A Scanning Ion Conductance Microscope for Large-Range Imaging.

    Science.gov (United States)

    Schierbaum, Nicolas; Hack, Martin; Betz, Oliver; Schäffer, Tilman E

    2018-04-17

    The scanning ion conductance microscope (SICM) is a versatile, high-resolution imaging technique that uses an electrolyte-filled nanopipet as a probe. Its noncontact imaging principle makes the SICM uniquely suited for the investigation of soft and delicate surface structures in a liquid environment. The SICM has found an ever-increasing number of applications in chemistry, physics, and biology. However, a drawback of conventional SICMs is their relatively small scan range (typically 100 μm × 100 μm in the lateral and 10 μm in the vertical direction). We have developed a Macro-SICM with an exceedingly large scan range of 25 mm × 25 mm in the lateral and 0.25 mm in the vertical direction. We demonstrate the high versatility of the Macro-SICM by imaging at different length scales: from centimeters (fingerprint, coin) to millimeters (bovine tongue tissue, insect wing) to micrometers (cellular extensions). We applied the Macro-SICM to the study of collective cell migration in epithelial wound healing.

  8. Imaging arrangement and microscope

    Science.gov (United States)

    Pertsinidis, Alexandros; Chu, Steven

    2015-12-15

    An embodiment of the present invention is an imaging arrangement that includes imaging optics, a fiducial light source, and a control system. In operation, the imaging optics separate light into first and second tight by wavelength and project the first and second light onto first and second areas within first and second detector regions, respectively. The imaging optics separate fiducial light from the fiducial light source into first and second fiducial light and project the first and second fiducial light onto third and fourth areas within the first and second detector regions, respectively. The control system adjusts alignment of the imaging optics so that the first and second fiducial light projected onto the first and second detector regions maintain relatively constant positions within the first and second detector regions, respectively. Another embodiment of the present invention is a microscope that includes the imaging arrangement.

  9. Techniques for improving material fidelity and contrast consistency in secondary electron mode helium ion microscope (HIM) imaging

    Science.gov (United States)

    Thompson, William; Stern, Lewis; Ferranti, Dave; Huynh, Chuong; Scipioni, Larry; Notte, John; Sanford, Colin

    2010-06-01

    Recent helium ion microscope (HIM) imaging studies have shown the strong sensitivity of HIM induced secondary electron (SE) yields [1] to the sample physical and chemical properties and to its surface topography. This SE yield sensitivity is due to the low recoil energy of the HIM initiated electrons and their resulting short mean free path. Additionally, a material's SE escape probability is modulated by changes in the material's work function and surface potential. Due to the escape electrons' roughly 2eV mean energy and their nanometer range mean free path, HIM SE mode image contrast has significant material and surface sensitivity. The latest generation of HIM has a 0.35 nanometer resolution specification and is equipped with a plasma cleaning process to mitigate the effects of hydrocarbon contamination. However, for surfaces that may have native oxide chemistries influencing the secondary electron yield, a new process of low energy, shallow angle argon sputtering, was evaluated. The intent of this work was to study the effect of removing pre-existing native oxides and any in-situ deposited surface contaminants. We will introduce the sputter yield predictions of two established computer models and the sputter yield and sample modification forecasts of the molecular dynamics program, Kalypso. We will review the experimental technique applied to copper samples and show the copper grain contrast improvement that resulted when argon cleaned samples were imaged in HIM SE mode.

  10. Microscopic studies of RIB target materials and ion induced nanostructures

    International Nuclear Information System (INIS)

    Karmakar, Prasanta; Bhattacharya, Shampa; Roy, Tapatee Kundu; Bhowmick, Debasis; Chakrabarti, Alok

    2010-01-01

    The invention of electron microscope and scanning probe microscope has empowered us to visualize the tiny world that has explored many fundamental laws of natures. Further technological advancements have made these tools capable to probe micron size structures to individual atom. These microscopes are used to image and study micron size fibers or grain structures used for high yield radioactive products, to few nanometer size ripple, dot and hole structures produced by ion irradiation. Electron Microscope has also been used to characterize the ion beam synthesized dilute magnetic systems

  11. A high resolution ion microscope for cold atoms

    International Nuclear Information System (INIS)

    Stecker, Markus; Schefzyk, Hannah; Fortágh, József; Günther, Andreas

    2017-01-01

    We report on an ion-optical system that serves as a microscope for ultracold ground state and Rydberg atoms. The system is designed to achieve a magnification of up to 1000 and a spatial resolution in the 100 nm range, thereby surpassing many standard imaging techniques for cold atoms. The microscope consists of four electrostatic lenses and a microchannel plate in conjunction with a delay line detector in order to achieve single particle sensitivity with high temporal and spatial resolution. We describe the design process of the microscope including ion-optical simulations of the imaging system and characterize aberrations and the resolution limit. Furthermore, we present the experimental realization of the microscope in a cold atom setup and investigate its performance by patterned ionization with a structure size down to 2.7 μ m. The microscope meets the requirements for studying various many-body effects, ranging from correlations in cold quantum gases up to Rydberg molecule formation. (paper)

  12. Differential magnetic force microscope imaging.

    Science.gov (United States)

    Wang, Ying; Wang, Zuobin; Liu, Jinyun; Hou, Liwei

    2015-01-01

    This paper presents a method for differential magnetic force microscope imaging based on a two-pass scanning procedure to extract differential magnetic forces and eliminate or significantly reduce background forces with reversed tip magnetization. In the work, the difference of two scanned images with reversed tip magnetization was used to express the local magnetic forces. The magnetic sample was first scanned with a low lift distance between the MFM tip and the sample surface, and the magnetization direction of the probe was then changed after the first scan to perform the second scan. The differential magnetic force image was obtained through the subtraction of the two images from the two scans. The theoretical and experimental results have shown that the proposed method for differential magnetic force microscope imaging is able to reduce the effect of background or environment interference forces, and offers an improved image contrast and signal to noise ratio (SNR). © Wiley Periodicals, Inc.

  13. Focal depth measurement of scanning helium ion microscope

    International Nuclear Information System (INIS)

    Guo, Hongxuan; Itoh, Hiroshi; Wang, Chunmei; Zhang, Han; Fujita, Daisuke

    2014-01-01

    When facing the challenges of critical dimension measurement of complicated nanostructures, such as of the three dimension integrated circuit, characterization of the focal depth of microscopes is important. In this Letter, we developed a method for characterizing the focal depth of a scanning helium ion microscope (HIM) by using an atomic force microscope tip characterizer (ATC). The ATC was tilted in a sample chamber at an angle to the scanning plan. Secondary electron images (SEIs) were obtained at different positions of the ATC. The edge resolution of the SEIs shows the nominal diameters of the helium ion beam at different focal levels. With this method, the nominal shapes of the helium ion beams were obtained with different apertures. Our results show that a small aperture is necessary to get a high spatial resolution and high depth of field images with HIM. This work provides a method for characterizing and improving the performance of HIM.

  14. Surface charge compensation for a highly charged ion emission microscope

    International Nuclear Information System (INIS)

    McDonald, J.W.; Hamza, A.V.; Newman, M.W.; Holder, J.P.; Schneider, D.H.G.; Schenkel, T.

    2003-01-01

    A surface charge compensation electron flood gun has been added to the Lawrence Livermore National Laboratory (LLNL) highly charged ion (HCI) emission microscope. HCI surface interaction results in a significant charge residue being left on the surface of insulators and semiconductors. This residual charge causes undesirable aberrations in the microscope images and a reduction of the Time-Of-Flight (TOF) mass resolution when studying the surfaces of insulators and semiconductors. The benefits and problems associated with HCI microscopy and recent results of the electron flood gun enhanced HCI microscope are discussed

  15. Highly charged ion based time-of-flight emission microscope

    International Nuclear Information System (INIS)

    Hamza, Alex V.; Barnes, Alan V.; Magee, Ed; Newman, Mike; Schenkel, Thomas; McDonald, Joseph W.; Schneider, Dieter H.

    2000-01-01

    An emission microscope using highly charged ions as the excitation source has been designed, constructed, and operated. A novel ''acorn'' objective lens has been used to simultaneously image electron and secondary ion emission. A resistive anode-position sensitive detector is used to determine the x-y position and time of arrival of the secondary events at the microscope image plane. Contrast in the image can be based on the intensity of the electron emission and/or the presence of particular secondary ions. Spatial resolution of better than 1 μm and mass resolution m/Δm of better than 400 were demonstrated. Background rejection from uncorrelated events of greater than an order of magnitude is also achieved. (c) 2000 American Institute of Physics

  16. A new ion sensing deep atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Drake, Barney; Randall, Connor; Bridges, Daniel; Hansma, Paul K. [Department of Physics, University of California, Santa Barbara, California 93106 (United States)

    2014-08-15

    Here we describe a new deep atomic force microscope (AFM) capable of ion sensing. A novel probe assembly incorporates a micropipette that can be used both for sensing ion currents and as the tip for AFM imaging. The key advance of this instrument over previous ion sensing AFMs is that it uses conventional micropipettes in a novel suspension system. This paper focuses on sensing the ion current passively while using force feedback for the operation of the AFM in contact mode. Two images are obtained simultaneously: (1) an AFM topography image and (2) an ion current image. As an example, two images of a MEMS device with a microchannel show peaks in the ion current as the pipette tip goes over the edges of the channel. This ion sensing AFM can also be used in other modes including tapping mode with force feedback as well as in non-contact mode by utilizing the ion current for feedback, as in scanning ion conductance microscopy. The instrument is gentle enough to be used on some biological samples such as plant leaves.

  17. High-voltage scanning ion microscope: Beam optics and design

    Energy Technology Data Exchange (ETDEWEB)

    Magilin, D., E-mail: dmitrymagilin@gmail.com; Ponomarev, A.; Rebrov, V.; Ponomarov, A.

    2015-05-01

    This article is devoted to the conceptual design of a compact high-voltage scanning ion microscope (HVSIM). In an HVSIM design, the ion optical system is based on a high-brightness ion source. Specifically, the ion optical system is divided into two components: an ion injector and a probe-forming system (PFS) that consists of an accelerating tube and a multiplet of quadrupole lenses. The crossover is formed and controlled by the injector, which acts as an object collimator, and is focused on the image plane by the PFS. The ion microprobe has a size of 0.1 μm and an energy of 2 MeV. When the influence of the chromatic and third-order aberrations is theoretically taken into account, the HVSIM forms an ion microprobe.

  18. Ion microscopic imaging of calcium transport in the intestinal tissue of vitamin D-deficient and vitamin D-replete chickens: A 44Ca stable isotope study

    International Nuclear Information System (INIS)

    Chandra, S.; Fullmer, C.S.; Smith, C.A.; Wasserman, R.H.; Morrison, G.H.

    1990-01-01

    The intestinal absorption of calcium includes at least three definable steps; transfer across the microvillar membrane, movement through the cytosolic compartment, and energy-dependent extrusion into the lamina propria, Tracing the movement of calcium through the epithelium has been hampered by lack of suitable techniques and, in this study, advantage was taken of ion microscopy in conjunction with cryosectioning and use of the stable isotope 44Ca to visualize calcium in transit during the absorptive process. The effect of vitamin D, required for optimal calcium absorption, was investigated. Twenty millimolar 44Ca was injected into the duodenal lumen in situ of vitamin D-deficient and vitamin D-replete chickens. At 2.5, 5.0, and 20.0 min after injection, duodenal tissue was obtained and processed for ion microscopic imaging. At 2.5 min. 44Ca was seen to be concentrated in the region subjacent to the microvillar membrane in tissue from both groups. At 5.0 and 20.0 min, a similar pattern of localization was evident in D-deficient tissues. In D-replete tissues, the distribution of 44Ca became more homogenous, indicating that vitamin D increased the rate of transfer of Ca2+ from the apical to the basolateral membrane, a function previously ascribed to the vitamin D-induced calcium-binding protein (28-kDa calbindin-D). Quantitative aspects of the calcium absorptive process were determined in parallel experiments with the radionuclide 47Ca. Complementary information on the localization of the naturally occurring isotopes of calcium (40Ca) and potassium (39K) is also described

  19. Co-Registered In Situ Secondary Electron and Mass Spectral Imaging on the Helium Ion Microscope Demonstrated Using Lithium Titanate and Magnesium Oxide Nanoparticles.

    Science.gov (United States)

    Dowsett, D; Wirtz, T

    2017-09-05

    The development of a high resolution elemental imaging platform combining coregistered secondary ion mass spectrometry and high resolution secondary electron imaging is reported. The basic instrument setup and operation are discussed and in situ image correlation is demonstrated on a lithium titanate and magnesium oxide nanoparticle mixture. The instrument uses both helium and neon ion beams generated by a gas field ion source to irradiate the sample. Both secondary electrons and secondary ions may be detected. Secondary ion mass spectrometry (SIMS) is performed using an in-house developed double focusing magnetic sector spectrometer with parallel detection. Spatial resolutions of 10 nm have been obtained in SIMS mode. Both the secondary electron and SIMS image data are very surface sensitive and have approximately the same information depth. While the spatial resolutions are approximately a factor of 10 different, switching between the different images modes may be done in situ and extremely rapidly, allowing for simple imaging of the same region of interest and excellent coregistration of data sets. The ability to correlate mass spectral images on the 10 nm scale with secondary electron images on the nanometer scale in situ has the potential to provide a step change in our understanding of nanoscale phenomena in fields from materials science to life science.

  20. A novel ion imager for secondary ion mass spectrometry

    International Nuclear Information System (INIS)

    Matsumoto, Kazuya; Miyata, Kenji; Nakamura, Tsutomu

    1993-01-01

    This paper describes a new area detector for secondary ion mass spectrometry (SIMS) ion microscope, and its performance. The operational principle is based on detecting the change in potential of a floating photodiode caused by the ion-induced secondary-electron emission and the incoming ion itself. The experiments demonstrated that 10 1 -10 5 aluminum ions per pixel can be detected with good linear response. Moreover, relative ion sensitivities from hydrogen to lead were constant within a factor of 2. The performance of this area detector provides the potential for detection of kiloelectronvolt ion images with current ion microscopy

  1. Towards vortex imaging with scanning tunneling microscope

    International Nuclear Information System (INIS)

    Fuchs, Dan T.

    1994-02-01

    A low temperature, Besocke beetle type scanning tunneling microscope, with a scan range of 10 by 10 microns was built. The scanning tunneling microscope was calibrates for various temperatures and tested on several samples. Gold monolayers evaporated at 400 deg C were resolved and their dynamic behavior observed. Atomic resolution images of graphite were obtained. The scanning tunneling microscope was designed for future applications of vortex imaging in superconductors. The special design considerations for this application are discussed and the physics underlying it reviewed. (author)

  2. MIAMI: Microscope and ion accelerator for materials investigations

    International Nuclear Information System (INIS)

    Hinks, J. A.; Berg, J. A. van den; Donnelly, S. E.

    2011-01-01

    A transmission electron microscope (TEM) with in situ ion irradiation has been built at the University of Salford, U.K. The system consists of a Colutron G-2 ion source connected to a JEOL JEM-2000FX TEM via an in-house designed and constructed ion beam transport system. The ion source can deliver ion energies from 0.5 to 10 keV for singly charged ions and can be floated up to 100 kV to allow acceleration to higher energies. Ion species from H to Xe can be produced for the full range of energies allowing the investigation of implantation with light ions such as helium as well as the effects of displacing irradiation with heavy inert or self-ions. The ability to implant light ions at energies low enough such that they come to rest within the thickness of a TEM sample and to also irradiate with heavier species at energies sufficient to cause large numbers of atomic displacements makes this facility ideally suited to the study of materials for use in nuclear environments. TEM allows the internal microstructure of a sample to be imaged at the nanoscale. By irradiating in situ it is possible to observe the dynamic evolution of radiation damage which can occur during irradiation as a result of competing processes within the system being studied. Furthermore, experimental variables such as temperature can be controlled and maintained throughout both irradiation and observation. This combination of capabilities enables an understanding of the underlying atomistic processes to be gained and thus gives invaluable insights into the fundamental physics governing the response of materials to irradiation. Details of the design and specifications of the MIAMI facility are given along with examples of initial experimental results in silicon and silicon carbide.

  3. Image processing for HTS SQUID probe microscope

    International Nuclear Information System (INIS)

    Hayashi, T.; Koetitz, R.; Itozaki, H.; Ishikawa, T.; Kawabe, U.

    2005-01-01

    An HTS SQUID probe microscope has been developed using a high-permeability needle to enable high spatial resolution measurement of samples in air even at room temperature. Image processing techniques have also been developed to improve the magnetic field images obtained from the microscope. Artifacts in the data occur due to electromagnetic interference from electric power lines, line drift and flux trapping. The electromagnetic interference could successfully be removed by eliminating the noise peaks from the power spectrum of fast Fourier transforms of line scans of the image. The drift between lines was removed by interpolating the mean field value of each scan line. Artifacts in line scans occurring due to flux trapping or unexpected noise were removed by the detection of a sharp drift and interpolation using the line data of neighboring lines. Highly detailed magnetic field images were obtained from the HTS SQUID probe microscope by the application of these image processing techniques

  4. Imaging differential polarization microscope with electronic readout

    International Nuclear Information System (INIS)

    Mickols, W.; Tinoco, I.; Katz, J.E.; Maestre, M.F.; Bustamante, C.

    1985-01-01

    A differential polarization microscope forms two images: one of the transmitted intensity and the other due to the change in intensity between images formed when different polarizations of light are used. The interpretation of these images for linear dichroism and circular dichroism are described. The design constraints on the data acquisition systems and the polarization modulation are described. The advantage of imaging several biological systems which contain optically anisotropic structures are described

  5. Multi-compartment microscopic diffusion imaging

    OpenAIRE

    Kaden, Enrico; Kelm, Nathaniel D.; Carson, Robert P.; Does, Mark D.; Alexander, Daniel C.

    2016-01-01

    This paper introduces a multi-compartment model for microscopic diffusion anisotropy imaging. The aim is to estimate microscopic features specific to the intra- and extra-neurite compartments in nervous tissue unconfounded by the effects of fibre crossings and orientation dispersion, which are ubiquitous in the brain. The proposed MRI method is based on the Spherical Mean Technique (SMT), which factors out the neurite orientation distribution and thus provides direct estimates of the microsco...

  6. Seamless stitching of tile scan microscope images.

    Science.gov (United States)

    Legesse, F B; Chernavskaia, O; Heuke, S; Bocklitz, T; Meyer, T; Popp, J; Heintzmann, R

    2015-06-01

    For diagnostic purposes, optical imaging techniques need to obtain high-resolution images of extended biological specimens in reasonable time. The field of view of an objective lens, however, is often smaller than the sample size. To image the whole sample, laser scanning microscopes acquire tile scans that are stitched into larger mosaics. The appearance of such image mosaics is affected by visible edge artefacts that arise from various optical aberrations which manifest in grey level jumps across tile boundaries. In this contribution, a technique for stitching tiles into a seamless mosaic is presented. The stitching algorithm operates by equilibrating neighbouring edges and forcing the brightness at corners to a common value. The corrected image mosaics appear to be free from stitching artefacts and are, therefore, suited for further image analysis procedures. The contribution presents a novel method to seamlessly stitch tiles captured by a laser scanning microscope into a large mosaic. The motivation for the work is the failure of currently existing methods for stitching nonlinear, multimodal images captured by our microscopic setups. Our method eliminates the visible edge artefacts that appear between neighbouring tiles by taking into account the overall illumination differences among tiles in such mosaics. The algorithm first corrects the nonuniform brightness that exists within each of the tiles. It then compensates for grey level differences across tile boundaries by equilibrating neighbouring edges and forcing the brightness at the corners to a common value. After these artefacts have been removed further image analysis procedures can be applied on the microscopic images. Even though the solution presented here is tailored for the aforementioned specific case, it could be easily adapted to other contexts where image tiles are assembled into mosaics such as in astronomical or satellite photos. © 2015 The Authors Journal of Microscopy © 2015 Royal

  7. Dual ion beam irradiation system for in situ observation with electron microscope

    International Nuclear Information System (INIS)

    Tsukamoto, Tetuo; Hojou, Kiiti; Furuno, Sigemi; Otsu, Hitosi; Izui, Kazuhiko.

    1993-01-01

    We have developed a new in situ observation system for dynamic processes under dual ion beam irradiation. The system consists of a modified 400 keV analytical electron microscope (JEOL, JEM-4000FX) and two 40 kV ion beam accelerators. This system allows evaluation of microscopic changes of structure and chemical bonding state of materials in the dynamic processes under two kinds of ion beam irradiations, that is required for the simulation test of the first wall of nuclear fusion reactors onto which He + , H + , and H 2 + ions are irradiated simultaneously. These two ion accelerators were equipped symmetrically both sides of the electron microscope and individually controlled. Each ion beam extracted from a duo-plasmatron ion gun is bent downward by an angle of 30deg with a mass-separating magnet, and introduced into specimen chamber of the electron microscope. Inside the specimen chamber the beam is deflected again by an angle of 30deg with an electrostatic prism so as to be incident on the specimen surface. Finally, two ion beams from both side are incident on the specimen surface at an angle of 60deg. The maximum ion current density of helium is more than 250μA/cm 2 at the specimen at an ion energy of 17 keV. Images of the electron microscope during dual ion beam irradiation are observed through a TV camera and recorded with a VTR. (author)

  8. Scanning laser microscope for imaging nanostructured superconductors

    International Nuclear Information System (INIS)

    Ishida, Takekazu; Arai, Kohei; Akita, Yukio; Miyanari, Mitsunori; Minami, Yusuke; Yotsuya, Tsutomu; Kato, Masaru; Satoh, Kazuo; Uno, Mayumi; Shimakage, Hisashi; Miki, Shigehito; Wang, Zhen

    2010-01-01

    The nanofabrication of superconductors yields various interesting features in superconducting properties. A variety of different imaging techniques have been developed for probing the local superconducting profiles. A scanning pulsed laser microscope has been developed by the combination of the XYZ piezo-driven stages and an optical fiber with an aspheric focusing lens. The scanning laser microscope is used to understand the position-dependent properties of a superconducting MgB 2 stripline of length 100 μm and width of 3 μm under constant bias current. Our results show that the superconducting stripline can clearly be seen in the contour image of the scanning laser microscope on the signal voltage. It is suggested from the observed image that the inhomogeneity is relevant in specifying the operating conditions such as detection efficiency of the sensor.

  9. Scanning laser microscope for imaging nanostructured superconductors

    Science.gov (United States)

    Ishida, Takekazu; Arai, Kohei; Akita, Yukio; Miyanari, Mitsunori; Minami, Yusuke; Yotsuya, Tsutomu; Kato, Masaru; Satoh, Kazuo; Uno, Mayumi; Shimakage, Hisashi; Miki, Shigehito; Wang, Zhen

    2010-10-01

    The nanofabrication of superconductors yields various interesting features in superconducting properties. A variety of different imaging techniques have been developed for probing the local superconducting profiles. A scanning pulsed laser microscope has been developed by the combination of the XYZ piezo-driven stages and an optical fiber with an aspheric focusing lens. The scanning laser microscope is used to understand the position-dependent properties of a superconducting MgB 2 stripline of length 100 μm and width of 3 μm under constant bias current. Our results show that the superconducting stripline can clearly be seen in the contour image of the scanning laser microscope on the signal voltage. It is suggested from the observed image that the inhomogeneity is relevant in specifying the operating conditions such as detection efficiency of the sensor.

  10. IMIS: An intelligence microscope imaging system

    Science.gov (United States)

    Caputo, Michael; Hunter, Norwood; Taylor, Gerald

    1994-01-01

    Until recently microscope users in space relied on traditional microscopy techniques that required manual operation of the microscope and recording of observations in the form of written notes, drawings, or photographs. This method was time consuming and required the return of film and drawings from space for analysis. No real-time data analysis was possible. Advances in digital and video technologies along with recent developments in article intelligence will allow future space microscopists to have a choice of three additional modes of microscopy: remote coaching, remote control, and automation. Remote coaching requires manual operations of the microscope with instructions given by two-way audio/video transmission during critical phases of the experiment. When using the remote mode of microscopy, the Principal Investigator controls the microscope from the ground. The automated mode employs artificial intelligence to control microscope functions and is the only mode that can be operated in the other three modes as well. The purpose of this presentation is to discuss the advantages and disadvantages of the four modes of of microscopy and how the IMIS, a proposed intelligent microscope imaging system, can be used as a model for developing and testing concepts, operating procedures, and equipment design of specifications required to provide a comprehensive microscopy/imaging capability onboard Space Station Freedom.

  11. Quantitative Imaging with a Mobile Phone Microscope

    Science.gov (United States)

    Skandarajah, Arunan; Reber, Clay D.; Switz, Neil A.; Fletcher, Daniel A.

    2014-01-01

    Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone–based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications. PMID:24824072

  12. Quantitative imaging with a mobile phone microscope.

    Directory of Open Access Journals (Sweden)

    Arunan Skandarajah

    Full Text Available Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone-based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications.

  13. DHM (Digital Holography Microscope) for imaging cells

    International Nuclear Information System (INIS)

    Emery, Yves; Cuche, Etienne; Colomb, Tristan; Depeursinge, Christian; Rappaz, Benjamin; Marquet, Pierre; Magistretti, Pierre

    2007-01-01

    Light interaction with a sample modifies both intensity and phase of the illuminating wave. Any available supports for image recording are only sensitive to intensity, but Denis Gabor [P. Marquet, B. Rappaz, P. Magistretti, et. al. Digital Holography for quantitative phase-contrast imaging, Optics Letters, 30, 5, pp 291-93 (2005)] invented in 1948 a way to encode the phase as an intensity variation: the h ologram . Digital Holographic Microscopy (DHM) [D. Gabor, A new microscopic principle, Nature, 1948] implements digitally this powerful hologram. Characterization of various pollen grains and of morphology changes of neurones associated with hypotonic shock demonstrates the potential of DHM for imaging cells

  14. Improved Scanners for Microscopic Hyperspectral Imaging

    Science.gov (United States)

    Mao, Chengye

    2009-01-01

    Improved scanners to be incorporated into hyperspectral microscope-based imaging systems have been invented. Heretofore, in microscopic imaging, including spectral imaging, it has been customary to either move the specimen relative to the optical assembly that includes the microscope or else move the entire assembly relative to the specimen. It becomes extremely difficult to control such scanning when submicron translation increments are required, because the high magnification of the microscope enlarges all movements in the specimen image on the focal plane. To overcome this difficulty, in a system based on this invention, no attempt would be made to move either the specimen or the optical assembly. Instead, an objective lens would be moved within the assembly so as to cause translation of the image at the focal plane: the effect would be equivalent to scanning in the focal plane. The upper part of the figure depicts a generic proposed microscope-based hyperspectral imaging system incorporating the invention. The optical assembly of this system would include an objective lens (normally, a microscope objective lens) and a charge-coupled-device (CCD) camera. The objective lens would be mounted on a servomotor-driven translation stage, which would be capable of moving the lens in precisely controlled increments, relative to the camera, parallel to the focal-plane scan axis. The output of the CCD camera would be digitized and fed to a frame grabber in a computer. The computer would store the frame-grabber output for subsequent viewing and/or processing of images. The computer would contain a position-control interface board, through which it would control the servomotor. There are several versions of the invention. An essential feature common to all versions is that the stationary optical subassembly containing the camera would also contain a spatial window, at the focal plane of the objective lens, that would pass only a selected portion of the image. In one version

  15. Active Mask Segmentation of Fluorescence Microscope Images

    OpenAIRE

    Srinivasa, Gowri; Fickus, Matthew C.; Guo, Yusong; Linstedt, Adam D.; Kovačević, Jelena

    2009-01-01

    We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the “contour” to that of “inside and outside”, or, masks, allowing for easy mul...

  16. Atomic Force Microscope for Imaging and Spectroscopy

    Science.gov (United States)

    Pike, W. T.; Hecht, M. H.; Anderson, M. S.; Akiyama, T.; Gautsch, S.; deRooij, N. F.; Staufer, U.; Niedermann, Ph.; Howald, L.; Mueller, D.

    2000-01-01

    We have developed, built, and tested an atomic force microscope (AFM) for extraterrestrial applications incorporating a micromachined tip array to allow for probe replacement. It is part of a microscopy station originally intended for NASA's 2001 Mars lander to identify the size, distribution, and shape of Martian dust and soil particles. As well as imaging topographically down to nanometer resolution, this instrument can be used to reveal chemical information and perform infrared and Raman spectroscopy at unprecedented resolution.

  17. Interactions of heavy ions with biomolecules: a dynamical microscopic approach

    International Nuclear Information System (INIS)

    Zhang Fengshou; Beijing Radiation Center, Beijing; National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou

    2006-01-01

    The status of studying biology system therapy with X-rays, γ-rays, neutron, proton, and heavy ions is reviewed. The depth dose profile, called Bragg profile, makes heavy ion an ideal tool for radiotherapy. The physical process of therapy with heavy ions is analyzed and a 3-step interaction processes of heavy ions with biomolecules is proposed, that is, nuclear fragmentation in nuclear interaction, electron excitation in Coulomb interaction, and the biomolecules relaxation in surroundings, finally leads to a new structure of biomolecule. Since this physical process is the base of the following chemical process and biological process, a dynamical microscopic approach is strongly demanded to be built. (authors)

  18. Imaging and relative quantification of 127I in human thyroid follicles by analytical ion microscope: Characterization of benign thyroid epithelial tumors

    International Nuclear Information System (INIS)

    Fragu, P.; Briancon, C.; Noel, M.; Halpern, S.

    1989-01-01

    Analytical ion microscopy (AIM) can be used for imaging and relative quantification of chemical elements in tissue sections. We used this technique to assess the changes in 127I mapping within thyroid follicular cells and follicular lumina in benign thyroid epithelial abnormalities from 17 patients and in macroscopically normal perinodular tissue surrounding solitary cold nodules from 8 patients. Among the 17 patients, 9 had simple goiters, 5 had toxic nodular goiters, and 3 had hypofunctioning (cold) nodules. The tissue samples were fixed chemically and embedded in methacrylate resin to ensure preservation of organified iodine, and thin sections were analyzed by AIM. 127I was found in the follicular lumina and follicular epithelial cells of most specimens. The local concentration of 127I, which is proportional to the ratio of the two secondary ion beam currents of iodine and carbon, was evaluated in 30 follicular lumina and 30 follicular epithelial cells of each specimen. In normal tissue, the relative 127I concentration within follicular cells (mean, 0.72; range 0.01-8.30) was much lower than that in follicular lumina (mean, 4.63; range, 0.18-36.74). In simple goiter tissue, follicular lumen (mean, 0.57; range, 0.00-5.76), and cell (mean, 0.17; range, 0.002-1.82) relative 127I concentrations were below normal, but both distributions remained different. On the contrary, in toxic nodular goiter tissue the follicular cell relative 127I concentration (mean, 0.96; range, 0.003-27.3) largely overlapped that of the follicular lumina (mean, 2.1; range, 0.001-36.5). The cold nodules had the lowest relative follicular lumina 127I concentration (mean, 0.008; range, undetectable-0.07), and the relative cellular 127I concentrations were undetectable in 67%. These results demonstrate the capacity of AIM to characterize the functional activity of thyroid tissue without prior administration of radio-iodine

  19. Facilities for in situ ion beam studies in transmission electron microscopes

    International Nuclear Information System (INIS)

    Allen, C.W.; Ohnuki, S.; Takahashi, H.

    1993-08-01

    Interfacing an ion accelerator to a transmission electron microscope (TEM) allows the analytical functions of TEM imaging and electron diffraction from very small regions to be employed during ion-irradiation effects studies. At present there are ten such installations in Japan, one in France and one in the USA. General specifications of facilities which are operational in 1993 are summarized, and additional facilities which are planned or being proposed are briefly described

  20. Mass spectrometry imaging: Towards a lipid microscope?

    Science.gov (United States)

    Touboul, David; Brunelle, Alain; Laprévote, Olivier

    2011-01-01

    Biological imaging techniques are the most efficient way to locally measure the variation of different parameters on tissue sections. These analyses are gaining increasing interest since 20 years and allow observing extremely complex biological phenomena at lower and lower time and resolution scale. Nevertheless, most of them only target very few compounds of interest, which are chosen a priori, due to their low resolution power and sensitivity. New chemical imaging technique has to be introduced in order to overcome these limitations, leading to more informative and sensitive analyses for biologists and physicians. Two major mass spectrometry methods can be efficiently used to generate the distribution of biological compounds over a tissue section. Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry (MALDI-MS) needs the co-crystallization of the sample with a matrix before to be irradiated by a laser, whereas the analyte is directly desorbed by a primary ion bombardment for Secondary Ion Mass Spectrometry (SIMS) experiments. In both cases, energy used for desorption/ionization is locally deposited -some tens of microns for the laser and some hundreds of nanometers for the ion beam- meaning that small areas over the surface sample can be separately analyzed. Step by step analysis allows spectrum acquisitions over the tissue sections and the data are treated by modern informatics software in order to create ion density maps, i.e., the intensity plot of one specific ion versus the (x,y) position. Main advantages of SIMS and MALDI compared to other chemical imaging techniques lie in the simultaneous acquisition of a large number of biological compounds in mixture with an excellent sensitivity obtained by Time-of-Flight (ToF) mass analyzer. Moreover, data treatment is done a posteriori, due to the fact that no compound is selectively marked, and let us access to the localization of different lipid classes in only one complete acquisition. Copyright © 2010

  1. Active mask segmentation of fluorescence microscope images.

    Science.gov (United States)

    Srinivasa, Gowri; Fickus, Matthew C; Guo, Yusong; Linstedt, Adam D; Kovacević, Jelena

    2009-08-01

    We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the "contour" to that of "inside and outside," or masks, allowing for easy multidimensional segmentation. It adapts to the topology of the image through the use of multiple masks. The algorithm is almost invariant under initialization, allowing for random initialization, and uses a few easily tunable parameters. Experiments show that the active mask algorithm matches the ground truth well and outperforms the algorithm widely used in fluorescence microscopy, seeded watershed, both qualitatively, as well as quantitatively.

  2. The Digital Microscope and Its Image Processing Utility

    Directory of Open Access Journals (Sweden)

    Tri Wahyu Supardi

    2011-12-01

    Full Text Available Many institutions, including high schools, own a large number of analog or ordinary microscopes. These microscopes are used to observe small objects. Unfortunately, object observations on the ordinary microscope require precision and visual acuity of the user. This paper discusses the development of a high-resolution digital microscope from an analog microscope, including the image processing utility, which allows the digital microscope users to capture, store and process the digital images of the object being observed. The proposed microscope is constructed from hardware components that can be easily found in Indonesia. The image processing software is capable of performing brightness adjustment, contrast enhancement, histogram equalization, scaling and cropping. The proposed digital microscope has a maximum magnification of 1600x, and image resolution can be varied from 320x240 pixels up to 2592x1944 pixels. The microscope was tested with various objects with a variety of magnification, and image processing was carried out on the image of the object. The results showed that the digital microscope and its image processing system were capable of enhancing the observed object and other operations in accordance with the user need. The digital microscope has eliminated the need for direct observation by human eye as with the traditional microscope.

  3. Performance evaluation of image segmentation algorithms on microscopic image data

    Czech Academy of Sciences Publication Activity Database

    Beneš, Miroslav; Zitová, Barbara

    2015-01-01

    Roč. 275, č. 1 (2015), s. 65-85 ISSN 0022-2720 R&D Projects: GA ČR GAP103/12/2211 Institutional support: RVO:67985556 Keywords : image segmentation * performance evaluation * microscopic images Subject RIV: JC - Computer Hardware ; Software Impact factor: 2.136, year: 2015 http://library.utia.cas.cz/separaty/2014/ZOI/zitova-0434809-DOI.pdf

  4. In situ ion etching in a scanning electron microscope

    International Nuclear Information System (INIS)

    Dhariwal, R.S.; Fitch, R.K.

    1977-01-01

    A facility for ion etching in a scanning electron microscope is described which incorporates a new type of electrostatic ion source and viewing of the specimen is possible within about 30 sec after terminating the ion bombardment. Artefacts produced during etching have been studied and cone formation has been followed during its growth. The instrument has provided useful structural information on metals, alloys, and sinters. However, although insulating materials, such as plastics, glass and resins, have been successfully etched, interpretation of the resultant micrographs is more difficult. Ion etching of soft biological tissues, such as the rat duodenum was found to be of considerable interest. The observed structural features arise from the selective intake of the heavy fixation elements by different parts of the tissue. Hard biological materials, such as dental tissues and restorative materials, have also been studied and the prismatic structure of the enamel and the form and distribution of the dentinal tubules have been revealed. (author)

  5. Quantitative methods for the analysis of electron microscope images

    DEFF Research Database (Denmark)

    Skands, Peter Ulrik Vallø

    1996-01-01

    The topic of this thesis is an general introduction to quantitative methods for the analysis of digital microscope images. The images presented are primarily been acquired from Scanning Electron Microscopes (SEM) and interfermeter microscopes (IFM). The topic is approached though several examples...... foundation of the thesis fall in the areas of: 1) Mathematical Morphology; 2) Distance transforms and applications; and 3) Fractal geometry. Image analysis opens in general the possibility of a quantitative and statistical well founded measurement of digital microscope images. Herein lies also the conditions...

  6. Utilizing Neon Ion Microscope for GaSb nanopatterning studies: Nanostructure formation and comparison with low energy nanopatterning

    International Nuclear Information System (INIS)

    El-Atwani, Osman; Huynh, Chuong; Norris, Scott

    2016-01-01

    Graphical abstract: - Highlights: • Carl Zeiss-neon ion microscope was used to irradiated GaSb surfaces with 5 keV neon. • In-situ imaging using helium beam and ex-situ imaging using an electron beam were performed. • Differences in imaging output between the helium and the electron beam were observed. • Transition occurred in the nanostructure type and formation mechanism as the energy is changed from 2 to 5 keV. • Collision cascade simulations suggested a transition toward bulk-driven mechanisms. - Abstract: Low energy irradiation of GaSb surfaces has been shown to lead to nanopillar formation. Being performed ex-situ, controlling the parameters of the ion beam for controlled nanopattern formation is challenging. While mainly utilized for imaging and cutting purposes, the development of multibeam (helium/neon) ion microscopes has opened the path towards the use of these microscopes for in-situ ion irradiation and nanopatterning studies. In this study, in-situ irradiation (neon ions)/imaging (helium ions) of GaSb surfaces is performed using Carl Zeiss-neon ion microscope at low energies (5 and 10 keV). Imaging with helium ions, nanodots were shown to form at particular fluences after which are smoothed. Ex-situ imaging with SEM showed nanopore formation of size controlled by the ion energy and fluence. Compared to lower energy ex-situ neon ion irradiation at similar fluxes, where nanopillars are formed, the results demonstrated a transition in the nanostructure type and formation mechanism as the energy is changed from 2 to 5 keV. Simulations show an increase in the ballistic diffusion and a decrease in the strength of phase separation as a function of ion energy in agreement with the suppression of nanopillar formation at higher energies. Collision cascade simulations suggest a transition toward bulk-driven mechanisms.

  7. Utilizing Neon Ion Microscope for GaSb nanopatterning studies: Nanostructure formation and comparison with low energy nanopatterning

    Energy Technology Data Exchange (ETDEWEB)

    El-Atwani, Osman, E-mail: oelatwan25@gmail.com [School of Nuclear Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Huynh, Chuong [Carl Zeiss Microscopy, LLC, One Corporation Way, Peabody, MA 01960 (United States); Norris, Scott [Department of Mathematics, Southern Methodist University, Dallas, TX 75275 (United States)

    2016-05-01

    Graphical abstract: - Highlights: • Carl Zeiss-neon ion microscope was used to irradiated GaSb surfaces with 5 keV neon. • In-situ imaging using helium beam and ex-situ imaging using an electron beam were performed. • Differences in imaging output between the helium and the electron beam were observed. • Transition occurred in the nanostructure type and formation mechanism as the energy is changed from 2 to 5 keV. • Collision cascade simulations suggested a transition toward bulk-driven mechanisms. - Abstract: Low energy irradiation of GaSb surfaces has been shown to lead to nanopillar formation. Being performed ex-situ, controlling the parameters of the ion beam for controlled nanopattern formation is challenging. While mainly utilized for imaging and cutting purposes, the development of multibeam (helium/neon) ion microscopes has opened the path towards the use of these microscopes for in-situ ion irradiation and nanopatterning studies. In this study, in-situ irradiation (neon ions)/imaging (helium ions) of GaSb surfaces is performed using Carl Zeiss-neon ion microscope at low energies (5 and 10 keV). Imaging with helium ions, nanodots were shown to form at particular fluences after which are smoothed. Ex-situ imaging with SEM showed nanopore formation of size controlled by the ion energy and fluence. Compared to lower energy ex-situ neon ion irradiation at similar fluxes, where nanopillars are formed, the results demonstrated a transition in the nanostructure type and formation mechanism as the energy is changed from 2 to 5 keV. Simulations show an increase in the ballistic diffusion and a decrease in the strength of phase separation as a function of ion energy in agreement with the suppression of nanopillar formation at higher energies. Collision cascade simulations suggest a transition toward bulk-driven mechanisms.

  8. Adaptive optical microscope for brain imaging in vivo

    Science.gov (United States)

    Wang, Kai

    2017-04-01

    The optical heterogeneity of biological tissue imposes a major limitation to acquire detailed structural and functional information deep in the biological specimens using conventional microscopes. To restore optimal imaging performance, we developed an adaptive optical microscope based on direct wavefront sensing technique. This microscope can reliably measure and correct biological samples induced aberration. We demonstrated its performance and application in structural and functional brain imaging in various animal models, including fruit fly, zebrafish and mouse.

  9. Remote Histology Learning from Static versus Dynamic Microscopic Images

    Science.gov (United States)

    Mione, Sylvia; Valcke, Martin; Cornelissen, Maria

    2016-01-01

    Histology is the study of microscopic structures in normal tissue sections. Curriculum redesign in medicine has led to a decrease in the use of optical microscopes during practical classes. Other imaging solutions have been implemented to facilitate remote learning. With advancements in imaging technologies, learning material can now be digitized.…

  10. A method for fast automated microscope image stitching.

    Science.gov (United States)

    Yang, Fan; Deng, Zhen-Sheng; Fan, Qiu-Hong

    2013-05-01

    Image stitching is an important technology to produce a panorama or larger image by combining several images with overlapped areas. In many biomedical researches, image stitching is highly desirable to acquire a panoramic image which represents large areas of certain structures or whole sections, while retaining microscopic resolution. In this study, we develop a fast normal light microscope image stitching algorithm based on feature extraction. At first, an algorithm of scale-space reconstruction of speeded-up robust features (SURF) was proposed to extract features from the images to be stitched with a short time and higher repeatability. Then, the histogram equalization (HE) method was employed to preprocess the images to enhance their contrast for extracting more features. Thirdly, the rough overlapping zones of the images preprocessed were calculated by phase correlation, and the improved SURF was used to extract the image features in the rough overlapping areas. Fourthly, the features were corresponded by matching algorithm and the transformation parameters were estimated, then the images were blended seamlessly. Finally, this procedure was applied to stitch normal light microscope images to verify its validity. Our experimental results demonstrate that the improved SURF algorithm is very robust to viewpoint, illumination, blur, rotation and zoom of the images and our method is able to stitch microscope images automatically with high precision and high speed. Also, the method proposed in this paper is applicable to registration and stitching of common images as well as stitching the microscope images in the field of virtual microscope for the purpose of observing, exchanging, saving, and establishing a database of microscope images. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Early skin tumor detection from microscopic images through image processing

    International Nuclear Information System (INIS)

    Siddiqi, A.A.; Narejo, G.B.; Khan, A.M.

    2017-01-01

    The research is done to provide appropriate detection technique for skin tumor detection. The work is done by using the image processing toolbox of MATLAB. Skin tumors are unwanted skin growth with different causes and varying extent of malignant cells. It is a syndrome in which skin cells mislay the ability to divide and grow normally. Early detection of tumor is the most important factor affecting the endurance of a patient. Studying the pattern of the skin cells is the fundamental problem in medical image analysis. The study of skin tumor has been of great interest to the researchers. DIP (Digital Image Processing) allows the use of much more complex algorithms for image processing, and hence, can offer both more sophisticated performance at simple task, and the implementation of methods which would be impossibly by analog means. It allows much wider range of algorithms to be applied to the input data and can avoid problems such as build up of noise and signal distortion during processing. The study shows that few works has been done on cellular scale for the images of skin. This research allows few checks for the early detection of skin tumor using microscopic images after testing and observing various algorithms. After analytical evaluation the result has been observed that the proposed checks are time efficient techniques and appropriate for the tumor detection. The algorithm applied provides promising results in lesser time with accuracy. The GUI (Graphical User Interface) that is generated for the algorithm makes the system user friendly. (author)

  12. The optics of microscope image formation.

    Science.gov (United States)

    Wolf, David E

    2013-01-01

    Although geometric optics gives a good understanding of how the microscope works, it fails in one critical area, which is explaining the origin of microscope resolution. To accomplish this, one must consider the microscope from the viewpoint of physical optics. This chapter describes the theory of the microscope-relating resolution to the highest spatial frequency that a microscope can collect. The chapter illustrates how Huygens' principle or construction can be used to explain the propagation of a plane wave. It is shown that this limit increases with increasing numerical aperture (NA). As a corollary to this, resolution increases with decreasing wavelength because of how NA depends on wavelength. The resolution is higher for blue light than red light. Resolution is dependent on contrast, and the higher the contrast, the higher the resolution. This last point relates to issues of signal-to-noise and dynamic range. The use of video and new digital cameras has necessitated redefining classical limits such as those of Rayleigh's criterion. Copyright © 2007 Elsevier Inc. All rights reserved.

  13. Hydrogen and oxygen behaviors on Porous-Si surfaces observed using a scanning ESD ion microscope

    International Nuclear Information System (INIS)

    Itoh, Yuki; Ueda, Kazuyuki

    2004-01-01

    A scanning electron-stimulated desorption (ESD) ion microscope (SESDIM) measured the 2-D images of hydrogen and oxygen distribution on solid surfaces. A primary electron beam at 600 eV, with a pulse width of 220 ns, resulted in ion yields of H + and O + . This SESDIM is applied to the surface analysis of Porous-Si (Po-Si) partially covered with SiN films. During the heating of a specimen of the Po-Si at 800 deg. C under ultra-high-vacuum (UHV) conditions, the components of the surface materials were moved or diffused by thermal decomposition accompanied by a redistribution of hydrogen and oxygen. After cyclic heating of above 800 deg. C, the dynamic behaviors of H + and O + accompanied by the movements of the SiN layers were observed as images of H + and O + . This was because the H + and O + ions have been identified as composite materials by their kinetic energies

  14. Stitching Grid-wise Atomic Force Microscope Images

    DEFF Research Database (Denmark)

    Vestergaard, Mathias Zacho; Bengtson, Stefan Hein; Pedersen, Malte

    2016-01-01

    Atomic Force Microscopes (AFM) are able to capture images with a resolution in the nano metre scale. Due to this high resolution, the covered area per image is relatively small, which can be problematic when surveying a sample. A system able to stitch AFM images has been developed to solve this p...

  15. Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics.

    Science.gov (United States)

    Hayashi, Shinichi; Okada, Yasushi

    2015-05-01

    Most current superresolution (SR) microscope techniques surpass the diffraction limit at the expense of temporal resolution, compromising their applications to live-cell imaging. Here we describe a new SR fluorescence microscope based on confocal microscope optics, which we name the spinning disk superresolution microscope (SDSRM). Theoretically, the SDSRM is equivalent to a structured illumination microscope (SIM) and achieves a spatial resolution of 120 nm, double that of the diffraction limit of wide-field fluorescence microscopy. However, the SDSRM is 10 times faster than a conventional SIM because SR signals are recovered by optical demodulation through the stripe pattern of the disk. Therefore a single SR image requires only a single averaged image through the rotating disk. On the basis of this theory, we modified a commercial spinning disk confocal microscope. The improved resolution around 120 nm was confirmed with biological samples. The rapid dynamics of micro-tubules, mitochondria, lysosomes, and endosomes were observed with temporal resolutions of 30-100 frames/s. Because our method requires only small optical modifications, it will enable an easy upgrade from an existing spinning disk confocal to a SR microscope for live-cell imaging. © 2015 Hayashi and Okada. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  16. Characteristics of different frequency ranges in scanning electron microscope images

    International Nuclear Information System (INIS)

    Sim, K. S.; Nia, M. E.; Tan, T. L.; Tso, C. P.; Ee, C. S.

    2015-01-01

    We demonstrate a new approach to characterize the frequency range in general scanning electron microscope (SEM) images. First, pure frequency images are generated from low frequency to high frequency, and then, the magnification of each type of frequency image is implemented. By comparing the edge percentage of the SEM image to the self-generated frequency images, we can define the frequency ranges of the SEM images. Characterization of frequency ranges of SEM images benefits further processing and analysis of those SEM images, such as in noise filtering and contrast enhancement

  17. Characteristics of different frequency ranges in scanning electron microscope images

    Energy Technology Data Exchange (ETDEWEB)

    Sim, K. S., E-mail: kssim@mmu.edu.my; Nia, M. E.; Tan, T. L.; Tso, C. P.; Ee, C. S. [Faculty of Engineering and Technology, Multimedia University, 75450 Melaka (Malaysia)

    2015-07-22

    We demonstrate a new approach to characterize the frequency range in general scanning electron microscope (SEM) images. First, pure frequency images are generated from low frequency to high frequency, and then, the magnification of each type of frequency image is implemented. By comparing the edge percentage of the SEM image to the self-generated frequency images, we can define the frequency ranges of the SEM images. Characterization of frequency ranges of SEM images benefits further processing and analysis of those SEM images, such as in noise filtering and contrast enhancement.

  18. Microscopic imaging through turbid media Monte Carlo modeling and applications

    CERN Document Server

    Gu, Min; Deng, Xiaoyuan

    2015-01-01

    This book provides a systematic introduction to the principles of microscopic imaging through tissue-like turbid media in terms of Monte-Carlo simulation. It describes various gating mechanisms based on the physical differences between the unscattered and scattered photons and method for microscopic image reconstruction, using the concept of the effective point spread function. Imaging an object embedded in a turbid medium is a challenging problem in physics as well as in biophotonics. A turbid medium surrounding an object under inspection causes multiple scattering, which degrades the contrast, resolution and signal-to-noise ratio. Biological tissues are typically turbid media. Microscopic imaging through a tissue-like turbid medium can provide higher resolution than transillumination imaging in which no objective is used. This book serves as a valuable reference for engineers and scientists working on microscopy of tissue turbid media.

  19. Biomedical image retrieval using microscopic configuration with ...

    Indian Academy of Sciences (India)

    G DEEP

    2018-03-10

    Mar 10, 2018 ... The selection of feature descriptors affects the image .... Example of obtaining LBP for 3 9 3 neighbourhoods (adopted from Ojala et al [9]). 20 Page 2 of 13 ...... Directional binary wavelet patterns for biomedical image indexing ...

  20. A New Multichannel Spectral Imaging Laser Scanning Confocal Microscope

    Directory of Open Access Journals (Sweden)

    Yunhai Zhang

    2013-01-01

    Full Text Available We have developed a new multichannel spectral imaging laser scanning confocal microscope for effective detection of multiple fluorescent labeling in the research of biological tissues. In this paper, the design and key technologies of the system are introduced. Representative results on confocal imaging, 3-dimensional sectioning imaging, and spectral imaging are demonstrated. The results indicated that the system is applicable to multiple fluorescent labeling in biological experiments.

  1. Atom-probe field-ion-microscope mass spectrometer

    International Nuclear Information System (INIS)

    Nishikawa, Osamu

    1983-01-01

    The titled analyzer, called simply atom-probe, has been developed by combining a field ion microscope (FIM) and a mass spectrometer, and is divided into the time-of-flight type, magnetic sector type, and quadrupole type depending on the types of mass spectrometers. In this paper, the author first describes on the principle and construction of a high resolution, time-of-flight atom-probe developed and fabricated in his laboratory. The feature of the atom-probe lies in the analysis of atoms and molecules in hyper-fine structure region one by one utilizing the high resolution of FIM. It also has the advantages of directly determining the composition by a ratio of the numbers of respective ions because of a constant detection sensitivity regardless of mass numbers, of the resolution as high as single atom layer in depth direction, and of detecting the positional relationship among detected ions by the order of detection in a sample. To determine the composition in a hyperfine structure region, the limited small number of atoms and molecules in the region must be identified distinctly one by one. In the analyzed result of Ni-silicide formed by heating Si evaporated on a Ni tip at 1000 K for 5 minutes, each isotope was not only clearly separated, but also their abundance ratio was very close to the natural abundance ratio. The second half of the paper reports on the analysis of TiC promising for a cold cathode material, adsorption of CO and alcohol, and the composition and structure of silicides, as a few application examples. (Wakatsuki, Y.)

  2. Demonstration of Cold 40Ca+ Ions Confined in a Microscopic Surface-Electrode Ion Trap

    International Nuclear Information System (INIS)

    Chen Liang; Wan Wei; Xie Yi; Wu Hao-Yu; Zhou Fei; Feng Mang

    2013-01-01

    40 Ca + ions are successfully confined, under the cooling of a red-detuned laser, in a home-built microscopic surface-electrode (MSE) trap. With all electrodes deposited on a low-rf-loss substrate, our 500-μm-scale MSE trap is designed involving three potential wells and manufactured by the standard technique of the printed circuit board. Both linear and two-dimensional crystals of 40 Ca + are observed in the trap after preliminary micromotion compensation is carried out. The development of the MSE trap aims at large-scale trapped-ion quantum information processing

  3. In vivo cellular imaging with microscopes enabled by MEMS scanners

    Science.gov (United States)

    Ra, Hyejun

    High-resolution optical imaging plays an important role in medical diagnosis and biomedical research. Confocal microscopy is a widely used imaging method for obtaining cellular and sub-cellular images of biological tissue in reflectance and fluorescence modes. Its characteristic optical sectioning capability also enables three-dimensional (3-D) image reconstruction. However, its use has mostly been limited to excised tissues due to the requirement of high numerical aperture (NA) lenses for cellular resolution. Microscope miniaturization can enable in vivo imaging to make possible early cancer diagnosis and biological studies in the innate environment. In this dissertation, microscope miniaturization for in vivo cellular imaging is presented. The dual-axes confocal (DAC) architecture overcomes limitations of the conventional single-axis confocal (SAC) architecture to allow for miniaturization with high resolution. A microelectromechanical systems (MEMS) scanner is the central imaging component that is key in miniaturization of the DAC architecture. The design, fabrication, and characterization of the two-dimensional (2-D) MEMS scanner are presented. The gimbaled MEMS scanner is fabricated on a double silicon-on-insulator (SOI) wafer and is actuated by self-aligned vertical electrostatic combdrives. The imaging performance of the MEMS scanner in a DAC configuration is shown in a breadboard microscope setup, where reflectance and fluorescence imaging is demonstrated. Then, the MEMS scanner is integrated into a miniature DAC microscope. The whole imaging system is integrated into a portable unit for research in small animal models of human biology and disease. In vivo 3-D imaging is demonstrated on mouse skin models showing gene transfer and siRNA silencing. The siRNA silencing process is sequentially imaged in one mouse over time.

  4. Single-cell magnetic imaging using a quantum diamond microscope.

    Science.gov (United States)

    Glenn, D R; Lee, K; Park, H; Weissleder, R; Yacoby, A; Lukin, M D; Lee, H; Walsworth, R L; Connolly, C B

    2015-08-01

    We apply a quantum diamond microscope for detection and imaging of immunomagnetically labeled cells. This instrument uses nitrogen-vacancy (NV) centers in diamond for correlated magnetic and fluorescence imaging. Our device provides single-cell resolution and a field of view (∼1 mm(2)) two orders of magnitude larger than that of previous NV imaging technologies, enabling practical applications. To illustrate, we quantified cancer biomarkers expressed by rare tumor cells in a large population of healthy cells.

  5. Laser speckle contrast imaging using light field microscope approach

    Science.gov (United States)

    Ma, Xiaohui; Wang, Anting; Ma, Fenghua; Wang, Zi; Ming, Hai

    2018-01-01

    In this paper, a laser speckle contrast imaging (LSCI) system using light field (LF) microscope approach is proposed. As far as we known, it is first time to combine LSCI with LF. To verify this idea, a prototype consists of a modified LF microscope imaging system and an experimental device was built. A commercially used Lytro camera was modified for microscope imaging. Hollow glass tubes with different depth fixed in glass dish were used to simulate the vessels in brain and test the performance of the system. Compared with conventional LSCI, three new functions can be realized by using our system, which include refocusing, extending the depth of field (DOF) and gathering 3D information. Experiments show that the principle is feasible and the proposed system works well.

  6. 3D widefield light microscope image reconstruction without dyes

    Science.gov (United States)

    Larkin, S.; Larson, J.; Holmes, C.; Vaicik, M.; Turturro, M.; Jurkevich, A.; Sinha, S.; Ezashi, T.; Papavasiliou, G.; Brey, E.; Holmes, T.

    2015-03-01

    3D image reconstruction using light microscope modalities without exogenous contrast agents is proposed and investigated as an approach to produce 3D images of biological samples for live imaging applications. Multimodality and multispectral imaging, used in concert with this 3D optical sectioning approach is also proposed as a way to further produce contrast that could be specific to components in the sample. The methods avoid usage of contrast agents. Contrast agents, such as fluorescent or absorbing dyes, can be toxic to cells or alter cell behavior. Current modes of producing 3D image sets from a light microscope, such as 3D deconvolution algorithms and confocal microscopy generally require contrast agents. Zernike phase contrast (ZPC), transmitted light brightfield (TLB), darkfield microscopy and others can produce contrast without dyes. Some of these modalities have not previously benefitted from 3D image reconstruction algorithms, however. The 3D image reconstruction algorithm is based on an underlying physical model of scattering potential, expressed as the sample's 3D absorption and phase quantities. The algorithm is based upon optimizing an objective function - the I-divergence - while solving for the 3D absorption and phase quantities. Unlike typical deconvolution algorithms, each microscope modality, such as ZPC or TLB, produces two output image sets instead of one. Contrast in the displayed image and 3D renderings is further enabled by treating the multispectral/multimodal data as a feature set in a mathematical formulation that uses the principal component method of statistics.

  7. Chemical imaging of structured SAMs with a novel SFG microscope

    Science.gov (United States)

    Hoffmann, Dominik M. P.; Kuhnke, Klaus; Kern, Klaus

    2002-11-01

    We present a newly developed microscope for sum frequency generation (SFG) imaging of opaque and reflecting interfaces. The sample is viewed at an angle of 60° with respect to the surface normal in order to increase the collected SFG intensity. Our setup is designed to keep the whole field of view (FOV) in focus and to compensate for the distortion usually related to oblique imaging by means of a blazed grating. The separation of the SFG intensity and the reflected visible beam is accomplished by a suitable combination of spectral filters. The sum frequency microscope (SFM) is capable of in-situ chemically selective imaging by tuning the IR-beam to vibrational transitions of the respective molecules. The SFM is applied to imaging of structured self-assembled monolayers (SAM) of thiol molecules on a gold surface.

  8. Structure Identification in High-Resolution Transmission Electron Microscopic Images

    DEFF Research Database (Denmark)

    Vestergaard, Jacob Schack; Kling, Jens; Dahl, Anders Bjorholm

    2014-01-01

    A connection between microscopic structure and macroscopic properties is expected for almost all material systems. High-resolution transmission electron microscopy is a technique offering insight into the atomic structure, but the analysis of large image series can be time consuming. The present ...

  9. Scanning tunneling microscope for magneto-optical imaging

    NARCIS (Netherlands)

    Prins, M.W.J.; Groeneveld, R.H.M.; Abraham, D.L.; Schad, R.; Kempen, van H.; Kesteren, van H.W.

    1996-01-01

    Images of magnetic bits written in a Pt/Co multilayer are presented. Using photosensitive semiconducting tips in a scanning tunneling microscope the surface topography as well as the polarization-dependent optical transmission are measured. Magnetic contrast is achieved by detection of the Faraday

  10. The Reaction Microscope: Imaging and Pulse Shaping Control in Photodynamics

    NARCIS (Netherlands)

    Vredenborg, A.; Lehmann, C.S.; Irimia, D.; Roeterdink, W.; Janssen, M.H.M.

    2011-01-01

    Herein, we review the current capabilities and potential of advanced single-particle imaging techniques to study photodynamics in isolated molecules. These reaction microscopes are able to measure the full three-dimensional energy and angular distribution of (correlated) particles such as electrons

  11. Computer processing of microscopic images of bacteria : morphometry and fluorimetry

    NARCIS (Netherlands)

    Wilkinson, Michael H.F.; Jansen, Gijsbert J.; Waaij, Dirk van der

    1994-01-01

    Several techniques that use computer analysis of microscopic images have been developed to study the complicated microbial flora in the human intestine, including measuring the shape and fluorescence intensity of bacteria. These techniques allow rapid assessment of changes in the intestinal flora

  12. The Digital Image Processing And Quantitative Analysis In Microscopic Image Characterization

    International Nuclear Information System (INIS)

    Ardisasmita, M. Syamsa

    2000-01-01

    Many electron microscopes although have produced digital images, but not all of them are equipped with a supporting unit to process and analyse image data quantitatively. Generally the analysis of image has to be made visually and the measurement is realized manually. The development of mathematical method for geometric analysis and pattern recognition, allows automatic microscopic image analysis with computer. Image processing program can be used for image texture and structure periodic analysis by the application of Fourier transform. Because the development of composite materials. Fourier analysis in frequency domain become important for measure the crystallography orientation. The periodic structure analysis and crystal orientation are the key to understand many material properties like mechanical strength. stress, heat conductivity, resistance, capacitance and other material electric and magnetic properties. In this paper will be shown the application of digital image processing in microscopic image characterization and analysis in microscopic image

  13. Tissue imaging with a stigmatic mass microscope using laser desorption/ionization

    Science.gov (United States)

    Awazu, Kunio; Hazama, Hisanao; Hamanaka, Tomonori; Aoki, Jun; Toyoda, Michisato; Naito, Yasuhide

    2012-03-01

    A novel stigmatic mass microscope using laser desorption/ionization and a multi-turn time-of-flight mass spectrometer, MULTUM-IMG, has been developed. Stigmatic ion images of crystal violet masked by a fine square mesh grid with a 12.7 μm pitch were clearly observed, and the estimated spatial resolution was about 3 μm in the linear mode with a 20-fold ion optical magnification. Tissue sections of a brain and eyes of a mouse stained with crystal violet and methylene blue were observed in the linear mode, and the stigmatic total ion images of crystal violet and methylene blue agreed well with the optical photomicrograph of the same sections. Especially, the fine structure in the cornea tissue was clearly observed with a spatial resolution in the range of micrometers. Although the total measurement time of the stigmatic ion image for the whole-eye section was about 59 minutes using a laser with a 10 Hz repetition rate, the measurement time could be reduced to about 35 s using a laser with a 1 kHz repetition rate and automation of measurements. The stigmatic mass microscope developed in this research should be suitable for high-spatial resolution and high-throughput imaging mass spectrometry for pathology, pharmacokinetics, and so on.

  14. Microscopic oxygen imaging based on fluorescein bleaching efficiency measurements

    DEFF Research Database (Denmark)

    Beutler, Martin; Heisterkamp, Ines M.; Piltz, Bastian

    2014-01-01

    by a charge-coupled-device (ccd) camera mounted on a fluorescence microscope allowed a pixelwise estimation of the ratio function in a microscopic image. Use of a microsensor and oxygen-consuming bacteria in a sample chamber enabled the calibration of the system for quantification of absolute oxygen......Photobleaching of the fluorophore fluorescein in an aqueous solution is dependent on the oxygen concentration. Therefore, the time-dependent bleaching behavior can be used to measure of dissolved oxygen concentrations. The method can be combined with epi-fluorescence microscopy. The molecular...... states of the fluorophore can be expressed by a three-state energy model. This leads to a set of differential equations which describe the photobleaching behavior of fluorescein. The numerical solution of these equations shows that in a conventional wide-field fluorescence microscope, the fluorescence...

  15. Foucault imaging by using non-dedicated transmission electron microscope

    International Nuclear Information System (INIS)

    Taniguchi, Yoshifumi; Matsumoto, Hiroaki; Harada, Ken

    2012-01-01

    An electron optical system for observing Foucault images was constructed using a conventional transmission electron microscope without any special equipment for Lorentz microscopy. The objective lens was switched off and an electron beam was converged by a condenser optical system to the crossover on the selected area aperture plane. The selected area aperture was used as an objective aperture to select the deflected beam for Foucault mode, and the successive image-forming lenses were controlled for observation of the specimen images. The irradiation area on the specimen was controlled by selecting the appropriate diameter of the condenser aperture.

  16. Foucault imaging by using non-dedicated transmission electron microscope

    Science.gov (United States)

    Taniguchi, Yoshifumi; Matsumoto, Hiroaki; Harada, Ken

    2012-08-01

    An electron optical system for observing Foucault images was constructed using a conventional transmission electron microscope without any special equipment for Lorentz microscopy. The objective lens was switched off and an electron beam was converged by a condenser optical system to the crossover on the selected area aperture plane. The selected area aperture was used as an objective aperture to select the deflected beam for Foucault mode, and the successive image-forming lenses were controlled for observation of the specimen images. The irradiation area on the specimen was controlled by selecting the appropriate diameter of the condenser aperture.

  17. Foucault imaging by using non-dedicated transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Taniguchi, Yoshifumi [Science and Medical Systems Business Group, Hitachi High-Technologies Corp., Ichige, Hitachinaka, Ibaraki 312-8504 (Japan); Matsumoto, Hiroaki [Corporate Manufacturing Strategy Group, Hitachi High-Technologies Corp., Ishikawa-cho, Hitachinaka, Ibaraki 312-1991 (Japan); Harada, Ken [Central Research Laboratory, Hitachi Ltd., Hatoyama, Saitama 350-0395 (Japan)

    2012-08-27

    An electron optical system for observing Foucault images was constructed using a conventional transmission electron microscope without any special equipment for Lorentz microscopy. The objective lens was switched off and an electron beam was converged by a condenser optical system to the crossover on the selected area aperture plane. The selected area aperture was used as an objective aperture to select the deflected beam for Foucault mode, and the successive image-forming lenses were controlled for observation of the specimen images. The irradiation area on the specimen was controlled by selecting the appropriate diameter of the condenser aperture.

  18. Electric field effects in scanning tunneling microscope imaging

    DEFF Research Database (Denmark)

    Stokbro, Kurt; Quaade, Ulrich; Grey, Francois

    1998-01-01

    We present a high-voltage extension of the Tersoff-Hamann theory of scanning tunneling microscope (STM) images, which includes the effect of the electric field between the tip and the sample. The theoretical model is based on first-principles electronic structure calculations and has no adjustable...... parameters. We use the method to calculate theoretical STM images of the monohydrate Si(100)-H(2x1) surface with missing hydrogen defects at -2V and find an enhanced corrugation due to the electric field, in good agreement with experimental images....

  19. Assessing microscope image focus quality with deep learning.

    Science.gov (United States)

    Yang, Samuel J; Berndl, Marc; Michael Ando, D; Barch, Mariya; Narayanaswamy, Arunachalam; Christiansen, Eric; Hoyer, Stephan; Roat, Chris; Hung, Jane; Rueden, Curtis T; Shankar, Asim; Finkbeiner, Steven; Nelson, Philip

    2018-03-15

    Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using automated image analysis with high accuracy is important for obtaining a clean, unbiased image dataset. Complicating this task is the fact that image focus quality is only well-defined in foreground regions of images, and as a result, most previous approaches only enable a computation of the relative difference in quality between two or more images, rather than an absolute measure of quality. We present a deep neural network model capable of predicting an absolute measure of image focus on a single image in isolation, without any user-specified parameters. The model operates at the image-patch level, and also outputs a measure of prediction certainty, enabling interpretable predictions. The model was trained on only 384 in-focus Hoechst (nuclei) stain images of U2OS cells, which were synthetically defocused to one of 11 absolute defocus levels during training. The trained model can generalize on previously unseen real Hoechst stain images, identifying the absolute image focus to within one defocus level (approximately 3 pixel blur diameter difference) with 95% accuracy. On a simpler binary in/out-of-focus classification task, the trained model outperforms previous approaches on both Hoechst and Phalloidin (actin) stain images (F-scores of 0.89 and 0.86, respectively over 0.84 and 0.83), despite only having been presented Hoechst stain images during training. Lastly, we observe qualitatively that the model generalizes to two additional stains, Hoechst and Tubulin, of an unseen cell type (Human MCF-7) acquired on a different instrument. Our deep neural network enables classification of out-of-focus microscope images with both higher accuracy and greater precision than previous approaches via interpretable patch-level focus and certainty predictions. The use of

  20. Sensing of Streptococcus mutans by microscopic imaging ellipsometry

    Science.gov (United States)

    Khaleel, Mai Ibrahim; Chen, Yu-Da; Chien, Ching-Hang; Chang, Yia-Chung

    2017-05-01

    Microscopic imaging ellipsometry is an optical technique that uses an objective and sensing procedure to measure the ellipsometric parameters Ψ and Δ in the form of microscopic maps. This technique is well known for being noninvasive and label-free. Therefore, it can be used to detect and characterize biological species without any impact. Microscopic imaging ellipsometry was used to measure the optical response of dried Streptococcus mutans cells on a glass substrate. The ellipsometric Ψ and Δ maps were obtained with the Optrel Multiskop system for specular reflection in the visible range (λ=450 to 750 nm). The Ψ and Δ images at 500, 600, and 700 nm were analyzed using three different theoretical models with single-bounce, two-bounce, and multibounce light paths to obtain the optical constants and height distribution. The obtained images of the optical constants show different aspects when comparing the single-bounce analysis with the two-bounce or multibounce analysis in detecting S. mutans samples. Furthermore, the height distributions estimated by two-bounce and multibounce analyses of S. mutans samples were in agreement with the thickness values measured by AFM, which implies that the two-bounce and multibounce analyses can provide information complementary to that obtained by a single-bounce light path.

  1. Teaching SIMS fundamentals using the FIB ion microscope

    International Nuclear Information System (INIS)

    Chater, Richard J.; McPhail, David S.

    2008-01-01

    The use of liquid metal source ion beams for microscopy and ion milling applications has increased dramatically in recent years. This paper explores the teaching of ion-solid sputtering and ionization phenomena without the facility to mass analyse the ionised yield available in dedicated SIMS instrumentation. Fundamental parameters can be demonstrated during the limited period of an undergraduate laboratory teaching session

  2. A new clustering algorithm for scanning electron microscope images

    Science.gov (United States)

    Yousef, Amr; Duraisamy, Prakash; Karim, Mohammad

    2016-04-01

    A scanning electron microscope (SEM) is a type of electron microscope that produces images of a sample by scanning it with a focused beam of electrons. The electrons interact with the sample atoms, producing various signals that are collected by detectors. The gathered signals contain information about the sample's surface topography and composition. The electron beam is generally scanned in a raster scan pattern, and the beam's position is combined with the detected signal to produce an image. The most common configuration for an SEM produces a single value per pixel, with the results usually rendered as grayscale images. The captured images may be produced with insufficient brightness, anomalous contrast, jagged edges, and poor quality due to low signal-to-noise ratio, grained topography and poor surface details. The segmentation of the SEM images is a tackling problems in the presence of the previously mentioned distortions. In this paper, we are stressing on the clustering of these type of images. In that sense, we evaluate the performance of the well-known unsupervised clustering and classification techniques such as connectivity based clustering (hierarchical clustering), centroid-based clustering, distribution-based clustering and density-based clustering. Furthermore, we propose a new spatial fuzzy clustering technique that works efficiently on this type of images and compare its results against these regular techniques in terms of clustering validation metrics.

  3. Hard X-ray Microscopic Imaging Of Human Breast Tissues

    Science.gov (United States)

    Park, Sung H.; Kim, Hong T.; Kim, Jong K.; Jheon, Sang H.; Youn, Hwa S.

    2007-01-01

    X-ray microscopy with synchrotron radiation will be a useful tool for innovation of x-ray imaging in clinical and laboratory settings. It helps us observe detailed internal structure of material samples non-invasively in air. And, it also has the potential to solve some tough problems of conventional breast imaging if it could evaluate various conditions of breast tissue effectively. A new hard x-ray microscope with a spatial resolution better than 100 nm was installed at Pohang Light Source, a third generation synchrotron radiation facility in Pohang, Korea. The x-ray energy was set at 6.95 keV, and the x-ray beam was monochromatized by W/B4C monochromator. Condenser and objective zone plates were used as x-ray lenses. Zernike phase plate next to condenser zone plate was introduced for improved contrast imaging. The image of a sample was magnified 30 times by objective zone plate and 20 times by microscope objective, respectively. After additional 10 times digital magnification, the total magnifying power was up to 6000 times in the end. Phase contrast synchrotron images of 10-μm-thick female breast tissue of the normal, fibroadenoma, fibrocystic change and carcinoma cases were obtained. By phase contrast imaging, hard x-rays enable us to observe many structures of breast tissue without sample preparations such as staining or fixation.

  4. Hard X-ray Microscopic Imaging Of Human Breast Tissues

    International Nuclear Information System (INIS)

    Park, Sung H.; Kim, Hong T.; Kim, Jong K.; Jheon, Sang H.; Youn, Hwa S.

    2007-01-01

    X-ray microscopy with synchrotron radiation will be a useful tool for innovation of x-ray imaging in clinical and laboratory settings. It helps us observe detailed internal structure of material samples non-invasively in air. And, it also has the potential to solve some tough problems of conventional breast imaging if it could evaluate various conditions of breast tissue effectively. A new hard x-ray microscope with a spatial resolution better than 100 nm was installed at Pohang Light Source, a third generation synchrotron radiation facility in Pohang, Korea. The x-ray energy was set at 6.95 keV, and the x-ray beam was monochromatized by W/B4C monochromator. Condenser and objective zone plates were used as x-ray lenses. Zernike phase plate next to condenser zone plate was introduced for improved contrast imaging. The image of a sample was magnified 30 times by objective zone plate and 20 times by microscope objective, respectively. After additional 10 times digital magnification, the total magnifying power was up to 6000 times in the end. Phase contrast synchrotron images of 10-μm-thick female breast tissue of the normal, fibroadenoma, fibrocystic change and carcinoma cases were obtained. By phase contrast imaging, hard x-rays enable us to observe many structures of breast tissue without sample preparations such as staining or fixation

  5. Microscopic validation of whole mouse micro-metastatic tumor imaging agents using cryo-imaging and sliding organ image registration

    OpenAIRE

    Liu, Yiqiao; Zhou, Bo; Qutaish, Mohammed; Wilson, David L.

    2016-01-01

    We created a metastasis imaging, analysis platform consisting of software and multi-spectral cryo-imaging system suitable for evaluating emerging imaging agents targeting micro-metastatic tumor. We analyzed CREKA-Gd in MRI, followed by cryo-imaging which repeatedly sectioned and tiled microscope images of the tissue block face, providing anatomical bright field and molecular fluorescence, enabling 3D microscopic imaging of the entire mouse with single metastatic cell sensitivity. To register ...

  6. Morphometric Evaluation of Preeclamptic Placenta Using Light Microscopic Images

    Directory of Open Access Journals (Sweden)

    Rashmi Mukherjee

    2014-01-01

    Full Text Available Deficient trophoblast invasion and anomalies in placental development generally lead to preeclampsia (PE but the inter-relationship between placental function and morphology in PE still remains unknown. The aim of this study was to evaluate the morphometric features of placental villi and capillaries in preeclamptic and normal placentae. The study included light microscopic images of placental tissue sections of 40 preeclamptic and 35 normotensive pregnant women. Preprocessing and segmentation of these images were performed to characterize the villi and capillaries. Fisher’s linear discriminant analysis (FLDA, hierarchical cluster analysis (HCA, and principal component analysis (PCA were applied to identify the most significant placental (morphometric features from microscopic images. A total of 10 morphometric features were extracted, of which the villous parameters were significantly altered in PE. FLDA identified 5 highly significant morphometric features (>90% overall discrimination accuracy. Two large subclusters were clearly visible in HCA based dendrogram. PCA returned three most significant principal components cumulatively explaining 98.4% of the total variance based on these 5 significant features. Hence, quantitative microscopic evaluation revealed that placental morphometry plays an important role in characterizing PE, where the villous is the major component that is affected.

  7. A portable fluorescence microscopic imaging system for cholecystectomy

    Science.gov (United States)

    Ye, Jian; Yang, Chaoyu; Gan, Qi; Ma, Rong; Zhang, Zeshu; Chang, Shufang; Shao, Pengfei; Zhang, Shiwu; Liu, Chenhai; Xu, Ronald

    2016-03-01

    In this paper we proposed a portable fluorescence microscopic imaging system to prevent iatrogenic biliary injuries from occurring during cholecystectomy due to misidentification of the cystic structures. The system consisted of a light source module, a CMOS camera, a Raspberry Pi computer and a 5 inch HDMI LCD. Specifically, the light source module was composed of 690 nm and 850 nm LEDs, allowing the CMOS camera to simultaneously acquire both fluorescence and background images. The system was controlled by Raspberry Pi using Python programming with the OpenCV library under Linux. We chose Indocyanine green(ICG) as a fluorescent contrast agent and then tested fluorescence intensities of the ICG aqueous solution at different concentration levels by our fluorescence microscopic system compared with the commercial Xenogen IVIS system. The spatial resolution of the proposed fluorescence microscopic imaging system was measured by a 1951 USAF resolution target and the dynamic response was evaluated quantitatively with an automatic displacement platform. Finally, we verified the technical feasibility of the proposed system in mouse models of bile duct, performing both correct and incorrect gallbladder resection. Our experiments showed that the proposed system can provide clear visualization of the confluence between the cystic duct and common bile duct or common hepatic duct, suggesting that this is a potential method for guiding cholecystectomy. The proposed portable system only cost a total of $300, potentially promoting its use in resource-limited settings.

  8. Nanoscale X-Ray Microscopic Imaging of Mammalian Mineralized Tissue

    OpenAIRE

    Andrews, Joy C.; Almeida, Eduardo; van der Meulen, Marjolein C.H.; Alwood, Joshua S.; Lee, Chialing; Liu, Yijin; Chen, Jie; Meirer, Florian; Feser, Michael; Gelb, Jeff; Rudati, Juana; Tkachuk, Andrei; Yun, Wenbing; Pianetta, Piero

    2010-01-01

    A novel hard transmission X-ray microscope (TXM) at the Stanford Synchrotron Radiation Light-source operating from 5 to 15 keV X-ray energy with 14 to 30 µm2 field of view has been used for high-resolution (30–40 nm) imaging and density quantification of mineralized tissue. TXM is uniquely suited for imaging of internal cellular structures and networks in mammalian mineralized tissues using relatively thick (50 µm), untreated samples that preserve tissue micro- and nanostructure. To test this...

  9. Evaluating EUV mask pattern imaging with two EUV microscopes

    International Nuclear Information System (INIS)

    Goldberg, Kenneth A.; Takase, Kei; Naulleau, Patrick P.; Han, Hakseung; Barty, Anton; Kinoshita, Hiroo; Hamamoto, Kazuhiro

    2008-01-01

    Aerial image measurement plays a key role in the development of patterned reticles for each generation of lithography. Studying the field transmitted (reflected) from EUV masks provides detailed information about potential disruptions caused by mask defects, and the performance of defect repair strategies, without the complications of photoresist imaging. Furthermore, by measuring the continuously varying intensity distribution instead of a thresholded, binary resist image, aerial image measurement can be used as feedback to improve mask and lithography system modeling methods. Interest in EUV, at-wavelength, aerial image measurement lead to the creation of several research tools worldwide. These tools are used in advanced mask development work, and in the evaluation of the need for commercial at-wavelength inspection tools. They describe performance measurements of two such tools, inspecting the same EUV mask in a series of benchmarking tests that includes brightfield and darkfield patterns. One tool is the SEMATECH Berkeley Actinic Inspection Tool (AIT) operating on a bending magnet beamline at Lawrence Berkeley National Laboratory's Advanced Light Source. The AIT features an EUV Fresnel zoneplate microscope that emulates the numerical aperture of a 0.25-NA stepper, and projects the aerial image directly onto a CCD camera, with 700x magnification. The second tool is an EUV microscope (EUVM) operating at the NewSUBARU synchrotron in Hyogo, Japan. The NewSUBARU tool projects the aerial image using a reflective, 30x Schwarzschild objective lens, followed by a 10-200x x-ray zooming tube. The illumination conditions and the imaging etendue are different for the two tools. The benchmarking measurements were used to determine many imaging and performance properties of the tools, including resolution, modulation transfer function (MTF), aberration magnitude, aberration field-dependence (including focal-plane tilt), illumination uniformity, line-edge roughness, and flare

  10. Thermal diffusivity imaging with the thermal lens microscope.

    Science.gov (United States)

    Dada, Oluwatosin O; Feist, Peter E; Dovichi, Norman J

    2011-12-01

    A coaxial thermal lens microscope was used to generate images based on both the absorbance and thermal diffusivity of histological samples. A pump beam was modulated at frequencies ranging from 50 kHz to 5 MHz using an acousto-optic modulator. The pump and a CW probe beam were combined with a dichroic mirror, directed into an inverted microscope, and focused onto the specimen. The change in the transmitted probe beam's center intensity was detected with a photodiode. The photodiode's signal and a reference signal from the modulator were sent to a high-speed lock-in amplifier. The in-phase and quadrature signals were recorded as a sample was translated through the focused beams and used to generate images based on the amplitude and phase of the lock-in amplifier's signal. The amplitude is related to the absorbance and the phase is related to the thermal diffusivity of the sample. Thin sections of stained liver and bone tissues were imaged; the contrast and signal-to-noise ratio of the phase image was highest at frequencies from 0.1-1 MHz and dropped at higher frequencies. The spatial resolution was 2.5 μm for both amplitude and phase images, limited by the pump beam spot size. © 2011 Optical Society of America

  11. Development of the water window imaging x-ray microscope

    International Nuclear Information System (INIS)

    Hoover, R.B.; Shealy, D.L.; Baker, P.C.; Barbee, T.W. Jr.; Walker, A.B.C. Jr.

    1991-01-01

    This paper reports on the Water Window Imaging X-ray Microscopy which is currently being developed by a consortium from the Marshall Space Flight Center, the University of Alabama at Birmingham, Baker Consulting, the Lawrence Livermore National Laboratory, and Stanford University. The high quality solar images achieved during the Stanford/MSFC/LLNL Rocket X-ray Spectroheliograph flight conclusively established that excellent imaging could be obtained with doubly reflecting multilayer optical systems. Theoretical studies carried out as part of the MSFC X-ray Microscopy Program, demonstrated that high quality, high resolution multilayer x-ray imaging microscopes could be achieved with spherical optics in the Schwarzschild configuration and with Aspherical optical systems. Advanced Flow Polishing methods have been used to fabricate substrates for multilayer optics. On hemlite grade Sapphire, the authors have achieved microscopy mirror substrates on concave and convex spherical surfaces with 0.5 Angstrom rms surface smoothness, as measured by the Zygo profilometer. In this paper the authors report on the current status of fabrication and testing of the optical and mechanical subsystems for the Water Window Imaging X-ray Microscope

  12. High-speed atomic force microscope imaging: Adaptive multiloop mode

    Science.gov (United States)

    Ren, Juan; Zou, Qingze; Li, Bo; Lin, Zhiqun

    2014-07-01

    In this paper, an imaging mode (called the adaptive multiloop mode) of atomic force microscope (AFM) is proposed to substantially increase the speed of tapping mode (TM) imaging while preserving the advantages of TM imaging over contact mode (CM) imaging. Due to its superior image quality and less sample disturbances over CM imaging, particularly for soft materials such as polymers, TM imaging is currently the most widely used imaging technique. The speed of TM imaging, however, is substantially (over an order of magnitude) lower than that of CM imaging, becoming the major bottleneck of this technique. Increasing the speed of TM imaging is challenging as a stable probe tapping on the sample surface must be maintained to preserve the image quality, whereas the probe tapping is rather sensitive to the sample topography variation. As a result, the increase of imaging speed can quickly lead to loss of the probe-sample contact and/or annihilation of the probe tapping, resulting in image distortion and/or sample deformation. The proposed adaptive multiloop mode (AMLM) imaging overcomes these limitations of TM imaging through the following three efforts integrated together: First, it is proposed to account for the variation of the TM deflection when quantifying the sample topography; second, an inner-outer feedback control loop to regulate the TM deflection is added on top of the tapping-feedback control loop to improve the sample topography tracking; and, third, an online iterative feedforward controller is augmented to the whole control system to further enhance the topography tracking, where the next-line sample topography is predicted and utilized to reduce the tracking error. The added feedback regulation of the TM deflection ensures the probe-sample interaction force remains near the minimum for maintaining a stable probe-sample interaction. The proposed AMLM imaging is tested and demonstrated by imaging a poly(tert-butyl acrylate) sample in experiments. The

  13. Simulation study of secondary electron images in scanning ion microscopy

    CERN Document Server

    Ohya, K

    2003-01-01

    The target atomic number, Z sub 2 , dependence of secondary electron yield is simulated by applying a Monte Carlo code for 17 species of metals bombarded by Ga ions and electrons in order to study the contrast difference between scanning ion microscopes (SIM) and scanning electron microscopes (SEM). In addition to the remarkable reversal of the Z sub 2 dependence between the Ga ion and electron bombardment, a fine structure, which is correlated to the density of the conduction band electrons in the metal, is calculated for both. The brightness changes of the secondary electron images in SIM and SEM are simulated using Au and Al surfaces adjacent to each other. The results indicate that the image contrast in SIM is much more sensitive to the material species and is clearer than that for SEM. The origin of the difference between SIM and SEM comes from the difference in the lateral distribution of secondary electrons excited within the escape depth.

  14. Modulus design multiwavelength polarization microscope for transmission Mueller matrix imaging.

    Science.gov (United States)

    Zhou, Jialing; He, Honghui; Chen, Zhenhua; Wang, Ye; Ma, Hui

    2018-01-01

    We have developed a polarization microscope based on a commercial transmission microscope. We replace the halogen light source by a collimated LED light source module of six different colors. We use achromatic polarized optical elements that can cover the six different wavelength ranges in the polarization state generator (PSG) and polarization state analyzer (PSA) modules. The dual-rotating wave plate method is used to measure the Mueller matrix of samples, which requires the simultaneous rotation of the two quarter-wave plates in both PSG and PSA at certain angular steps. A scientific CCD detector is used as the image receiving module. A LabView-based software is developed to control the rotation angels of the wave plates and the exposure time of the detector to allow the system to run fully automatically in preprogrammed schedules. Standard samples, such as air, polarizers, and quarter-wave plates, are used to calibrate the intrinsic Mueller matrix of optical components, such as the objectives, using the eigenvalue calibration method. Errors due to the images walk-off in the PSA are studied. Errors in the Mueller matrices are below 0.01 using air and polarizer as standard samples. Data analysis based on Mueller matrix transformation and Mueller matrix polarization decomposition is used to demonstrate the potential application of this microscope in pathological diagnosis. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  15. Magnetoacoustic microscopic imaging of conductive objects and nanoparticles distribution

    Science.gov (United States)

    Liu, Siyu; Zhang, Ruochong; Luo, Yunqi; Zheng, Yuanjin

    2017-09-01

    Magnetoacoustic tomography has been demonstrated as a powerful and low-cost multi-wave imaging modality. However, due to limited spatial resolution and detection efficiency of magnetoacoustic signal, full potential of the magnetoacoustic imaging remains to be tapped. Here we report a high-resolution magnetoacoustic microscopy method, where magnetic stimulation is provided by a compact solenoid resonance coil connected with a matching network, and acoustic reception is realized by using a high-frequency focused ultrasound transducer. Scanning the magnetoacoustic microscopy system perpendicularly to the acoustic axis of the focused transducer would generate a two-dimensional microscopic image with acoustically determined lateral resolution. It is analyzed theoretically and demonstrated experimentally that magnetoacoustic generation in this microscopic system depends on the conductivity profile of conductive objects and localized distribution of superparamagnetic iron magnetic nanoparticles, based on two different but related implementations. The lateral resolution is characterized. Directional nature of magnetoacoustic vibration and imaging sensitivity for mapping magnetic nanoparticles are also discussed. The proposed microscopy system offers a high-resolution method that could potentially map intrinsic conductivity distribution in biological tissue and extraneous magnetic nanoparticles.

  16. A super-oscillatory lens optical microscope for subwavelength imaging.

    Science.gov (United States)

    Rogers, Edward T F; Lindberg, Jari; Roy, Tapashree; Savo, Salvatore; Chad, John E; Dennis, Mark R; Zheludev, Nikolay I

    2012-03-25

    The past decade has seen an intensive effort to achieve optical imaging resolution beyond the diffraction limit. Apart from the Pendry-Veselago negative index superlens, implementation of which in optics faces challenges of losses and as yet unattainable fabrication finesse, other super-resolution approaches necessitate the lens either to be in the near proximity of the object or manufactured on it, or work only for a narrow class of samples, such as intensely luminescent or sparse objects. Here we report a new super-resolution microscope for optical imaging that beats the diffraction limit of conventional instruments and the recently demonstrated near-field optical superlens and hyperlens. This non-invasive subwavelength imaging paradigm uses a binary amplitude mask for direct focusing of laser light into a subwavelength spot in the post-evanescent field by precisely tailoring the interference of a large number of beams diffracted from a nanostructured mask. The new technology, which--in principle--has no physical limits on resolution, could be universally used for imaging at any wavelength and does not depend on the luminescence of the object, which can be tens of micrometres away from the mask. It has been implemented as a straightforward modification of a conventional microscope showing resolution better than λ/6.

  17. Imaging properties and its improvements of scanning/imaging x-ray microscope

    International Nuclear Information System (INIS)

    Takeuchi, Akihisa; Uesugi, Kentaro; Suzuki, Yoshio

    2016-01-01

    A scanning / imaging X-ray microscope (SIXM) system has been developed at SPring-8. The SIXM consists of a scanning X-ray microscope with a one-dimensional (1D) X-ray focusing device and an imaging (full-field) X-ray microscope with a 1D X-ray objective. The motivation of the SIXM system is to realize a quantitative and highly-sensitive multimodal 3D X-ray tomography by taking advantages of both the scanning X-ray microscope using multi-pixel detector and the imaging X-ray microscope. Data acquisition process of a 2D image is completely different between in the horizontal direction and in the vertical direction; a 1D signal is obtained with the linear-scanning while the other dimensional signal is obtained with the imaging optics. Such condition have caused a serious problem on the imaging properties that the imaging quality in the vertical direction has been much worse than that in the horizontal direction. In this paper, two approaches to solve this problem will be presented. One is introducing a Fourier transform method for phase retrieval from one phase derivative image, and the other to develop and employ a 1D diffuser to produce an asymmetrical coherent illumination

  18. Red Blood Cell Count Automation Using Microscopic Hyperspectral Imaging Technology.

    Science.gov (United States)

    Li, Qingli; Zhou, Mei; Liu, Hongying; Wang, Yiting; Guo, Fangmin

    2015-12-01

    Red blood cell counts have been proven to be one of the most frequently performed blood tests and are valuable for early diagnosis of some diseases. This paper describes an automated red blood cell counting method based on microscopic hyperspectral imaging technology. Unlike the light microscopy-based red blood count methods, a combined spatial and spectral algorithm is proposed to identify red blood cells by integrating active contour models and automated two-dimensional k-means with spectral angle mapper algorithm. Experimental results show that the proposed algorithm has better performance than spatial based algorithm because the new algorithm can jointly use the spatial and spectral information of blood cells.

  19. Software for imaging phase-shift interference microscope

    Science.gov (United States)

    Malinovski, I.; França, R. S.; Couceiro, I. B.

    2018-03-01

    In recent years absolute interference microscope was created at National Metrology Institute of Brazil (INMETRO). The instrument by principle of operation is imaging phase-shifting interferometer (PSI) equipped with two stabilized lasers of different colour as traceable reference wavelength sources. We report here some progress in development of the software for this instrument. The status of undergoing internal validation and verification of the software is also reported. In contrast with standard PSI method, different methodology of phase evaluation is applied. Therefore, instrument specific procedures for software validation and verification are adapted and discussed.

  20. Backscattered Helium Spectroscopy in the Helium Ion Microscope: Principles, Resolution and Applications

    NARCIS (Netherlands)

    van Gastel, Raoul; Hlawacek, G.; Dutta, S.; Poelsema, Bene

    2015-01-01

    We demonstrate the possibilities and limitations for microstructure characterization using backscattered particles from a sharply focused helium ion beam. The interaction of helium ions with matter enables the imaging, spectroscopic characterization, as well as the nanometer scale modification of

  1. On the detection of early osteoarthritis by quantitative microscopic imaging

    Science.gov (United States)

    Mittelstaedt, Daniel John

    measurements. These studies demonstrate the ability to use two quantitative microscopic imaging techniques, microCT and microMRI, to detect microscopic changes in collagen and GAG from healthy, biochemically degraded, and early OA cartilage. The capability for microscopic imaging to detect alterations at the earliest stages of OA will ultimately improve the understanding of degradation and may help aid in the detection for the prevention of disease and repair of damaged cartilage.

  2. Adaptation of commercial microscopes for advanced imaging applications

    Science.gov (United States)

    Brideau, Craig; Poon, Kelvin; Stys, Peter

    2015-03-01

    Today's commercially available microscopes offer a wide array of options to accommodate common imaging experiments. Occasionally, an experimental goal will require an unusual light source, filter, or even irregular sample that is not compatible with existing equipment. In these situations the ability to modify an existing microscopy platform with custom accessories can greatly extend its utility and allow for experiments not possible with stock equipment. Light source conditioning/manipulation such as polarization, beam diameter or even custom source filtering can easily be added with bulk components. Custom and after-market detectors can be added to external ports using optical construction hardware and adapters. This paper will present various examples of modifications carried out on commercial microscopes to address both atypical imaging modalities and research needs. Violet and near-ultraviolet source adaptation, custom detection filtering, and laser beam conditioning and control modifications will be demonstrated. The availability of basic `building block' parts will be discussed with respect to user safety, construction strategies, and ease of use.

  3. Microscopic descriptions of high-energy heavy-ion collisions

    International Nuclear Information System (INIS)

    Bodmer, A.R.

    1977-01-01

    The essentials of the equation-of-motion (EOM) approach are given and some of its significant and interesting results are described. A framework for the theoretical description of high-energy heavy-ion (HE-HI) collisions is presented; specifically included are a critical assessment of various approaches--EOM calculations, Boltzmann equations/cascade calculations, and hydrodynamics--their relationships and their respective domains of applicability, if any, to HE-HI collisions. 11 figures, 3 tables

  4. Neural Network for Nanoscience Scanning Electron Microscope Image Recognition.

    Science.gov (United States)

    Modarres, Mohammad Hadi; Aversa, Rossella; Cozzini, Stefano; Ciancio, Regina; Leto, Angelo; Brandino, Giuseppe Piero

    2017-10-16

    In this paper we applied transfer learning techniques for image recognition, automatic categorization, and labeling of nanoscience images obtained by scanning electron microscope (SEM). Roughly 20,000 SEM images were manually classified into 10 categories to form a labeled training set, which can be used as a reference set for future applications of deep learning enhanced algorithms in the nanoscience domain. The categories chosen spanned the range of 0-Dimensional (0D) objects such as particles, 1D nanowires and fibres, 2D films and coated surfaces, and 3D patterned surfaces such as pillars. The training set was used to retrain on the SEM dataset and to compare many convolutional neural network models (Inception-v3, Inception-v4, ResNet). We obtained compatible results by performing a feature extraction of the different models on the same dataset. We performed additional analysis of the classifier on a second test set to further investigate the results both on particular cases and from a statistical point of view. Our algorithm was able to successfully classify around 90% of a test dataset consisting of SEM images, while reduced accuracy was found in the case of images at the boundary between two categories or containing elements of multiple categories. In these cases, the image classification did not identify a predominant category with a high score. We used the statistical outcomes from testing to deploy a semi-automatic workflow able to classify and label images generated by the SEM. Finally, a separate training was performed to determine the volume fraction of coherently aligned nanowires in SEM images. The results were compared with what was obtained using the Local Gradient Orientation method. This example demonstrates the versatility and the potential of transfer learning to address specific tasks of interest in nanoscience applications.

  5. A new approach to nuclear microscopy: The ion-electron emission microscope

    International Nuclear Information System (INIS)

    Doyle, B.L.; Vizkelethy, G.; Walsh, D.S.; Senftinger, B.; Mellon, M.

    1998-01-01

    A new multidimensional high lateral resolution ion beam analysis technique, Ion-Electron Emission Microscopy or IEEM is described. Using MeV energy ions, IEEM is shown to be capable of Ion Beam Induced Charge Collection (IBICC) measurements in semiconductors. IEEM should also be capable of microscopically and multidimensionally mapping the surface and bulk composition of solids. As such, IIEM has nearly identical capabilities as traditional nuclear microprobe analysis, with the advantage that the ion beam does not have to be focused. The technique is based on determining the position where an individual ion enters the surface of the sample by projection secondary electron emission microscopy. The x-y origination point of a secondary electron, and hence the impact coordinates of the corresponding incident ion, is recorded with a position sensitive detector connected to a standard photoemission electron microscope (PEEM). These signals are then used to establish coincidence with IBICC, atomic, or nuclear reaction induced ion beam analysis signals simultaneously caused by the incident ion

  6. Direct-write three-dimensional nanofabrication of nanopyramids and nanocones on Si by nanotumefaction using a helium ion microscope

    Science.gov (United States)

    Zhang, L.; Heinig, N. F.; Bazargan, S.; Abd-Ellah, M.; Moghimi, N.; Leung, K. T.

    2015-06-01

    The recently commercialized helium ion microscope (HIM) has already demonstrated its outstanding imaging capabilities in terms of resolution, surface sensitivity, depth of field and ease of charge compensation. Here, we show its exceptional patterning capabilities by fabricating dense lines and three-dimensional (3D) nanostructures on a Si substrate. Small focusing spot size and confined ion-Si interaction volume of a high-energy helium ion beam account for the high resolution in HIM patterning. We demonstrate that a set of resolvable parallel lines with a half pitch as small as 3.5 nm can be achieved. During helium ion bombardment of the Si surface, implantation outperforms milling due to the small mass of the helium ions, which produces tumefaction instead of depression in the Si surface. The Si surface tumefaction is the result of different kinetic processes including diffusion, coalescence and nanobubble formation of the implanted ions, and is found to be very stable structurally at room temperature. Under appropriate conditions, a linear dependence of the surface swollen height on the ion doses can be observed. This relation has enabled us to fabricate nanopyramids and nanocones, thus demonstrating that HIM patterning provides a new ‘bottom-up’ approach to fabricate 3D nanostructures. This surface tumefaction method is direct, both positioning and height accurate, and free of resist, etch, mode and precursor, and it promises new applications in nanoimprint mold fabrication and photomask clear defect reparation.

  7. Transmission electron microscope interfaced with ion accelerators and its application to materials science

    Energy Technology Data Exchange (ETDEWEB)

    Abe, Hiroaki; Naramoto, Hiroshi [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment; Hojou, Kiichi; Furuno, Shigemi; Tsukamoto, Tetsuo

    1997-03-01

    We have developed the transmission/analytical electron microscope interfaced with two sets of ion accelerators (TEM-Accelerators Facility) at JAERI-Takasaki. The facility is expected to provide quantitative insights into radiation effects, such as damage evolution, irradiation-induced phase transformation and their stability, through in-situ observation and analysis under ion and/or electron irradiation. The TEM-Accelerators Facility and its application to materials research are reviewed. (author)

  8. Imaging optical scattering of butterfly wing scales with a microscope.

    Science.gov (United States)

    Fu, Jinxin; Yoon, Beom-Jin; Park, Jung Ok; Srinivasarao, Mohan

    2017-08-06

    A new optical method is proposed to investigate the reflectance of structurally coloured objects, such as Morpho butterfly wing scales and cholesteric liquid crystals. Using a reflected-light microscope and a digital single-lens reflex (DSLR) camera, we have successfully measured the two-dimensional reflection pattern of individual wing scales of Morpho butterflies. We demonstrate that this method enables us to measure the bidirectional reflectance distribution function (BRDF). The scattering image observed in the back focal plane of the objective is projected onto the camera sensor by inserting a Bertrand lens in the optical path of the microscope. With monochromatic light illumination, we quantify the angle-dependent reflectance spectra from the wing scales of Morpho rhetenor by retrieving the raw signal from the digital camera sensor. We also demonstrate that the polarization-dependent reflection of individual wing scales is readily observed using this method, using the individual wing scales of Morpho cypris . In an effort to show the generality of the method, we used a chiral nematic fluid to illustrate the angle-dependent reflectance as seen by this method.

  9. Direct-write three-dimensional nanofabrication of nanopyramids and nanocones on Si by nanotumefaction using a helium ion microscope

    International Nuclear Information System (INIS)

    Zhang, L; Heinig, N F; Bazargan, S; Abd-Ellah, M; Moghimi, N; Leung, K T

    2015-01-01

    The recently commercialized helium ion microscope (HIM) has already demonstrated its outstanding imaging capabilities in terms of resolution, surface sensitivity, depth of field and ease of charge compensation. Here, we show its exceptional patterning capabilities by fabricating dense lines and three-dimensional (3D) nanostructures on a Si substrate. Small focusing spot size and confined ion–Si interaction volume of a high-energy helium ion beam account for the high resolution in HIM patterning. We demonstrate that a set of resolvable parallel lines with a half pitch as small as 3.5 nm can be achieved. During helium ion bombardment of the Si surface, implantation outperforms milling due to the small mass of the helium ions, which produces tumefaction instead of depression in the Si surface. The Si surface tumefaction is the result of different kinetic processes including diffusion, coalescence and nanobubble formation of the implanted ions, and is found to be very stable structurally at room temperature. Under appropriate conditions, a linear dependence of the surface swollen height on the ion doses can be observed. This relation has enabled us to fabricate nanopyramids and nanocones, thus demonstrating that HIM patterning provides a new ‘bottom-up’ approach to fabricate 3D nanostructures. This surface tumefaction method is direct, both positioning and height accurate, and free of resist, etch, mode and precursor, and it promises new applications in nanoimprint mold fabrication and photomask clear defect reparation. (paper)

  10. Live Imaging of Shoot Meristems on an Inverted Confocal Microscope Using an Objective Lens Inverter Attachment

    Science.gov (United States)

    Nimchuk, Zachary L.; Perdue, Tony D.

    2017-01-01

    Live imaging of above ground meristems can lead to new insights in plant development not possible from static imaging of fixed tissue. The use of an upright confocal microscope offers several technical and biological advantages for live imaging floral or shoot meristems. However, many departments and core facilities possess only inverted confocal microscopes and lack the funding for an additional upright confocal microscope. Here we show that imaging of living apical meristems can be performed on existing inverted confocal microscopes with the use of an affordable and detachable InverterScope accessory. PMID:28579995

  11. Live Imaging of Shoot Meristems on an Inverted Confocal Microscope Using an Objective Lens Inverter Attachment.

    Science.gov (United States)

    Nimchuk, Zachary L; Perdue, Tony D

    2017-01-01

    Live imaging of above ground meristems can lead to new insights in plant development not possible from static imaging of fixed tissue. The use of an upright confocal microscope offers several technical and biological advantages for live imaging floral or shoot meristems. However, many departments and core facilities possess only inverted confocal microscopes and lack the funding for an additional upright confocal microscope. Here we show that imaging of living apical meristems can be performed on existing inverted confocal microscopes with the use of an affordable and detachable InverterScope accessory.

  12. In-Situ atomic force microscopic observation of ion beam bombarded plant cell envelopes

    International Nuclear Information System (INIS)

    Sangyuenyongpipat, S.; Yu, L.D.; Brown, I.G.; Seprom, C.; Vilaithong, T.

    2007-01-01

    A program in ion beam bioengineering has been established at Chiang Mai University (CMU), Thailand, and ion beam induced transfer of plasmid DNA molecules into bacterial cells (Escherichia coli) has been demonstrated. However, a good understanding of the fundamental physical processes involved is lacking. In parallel work, onion skin cells have been bombarded with Ar + ions at energy 25 keV and fluence1-2 x 10 15 ions/cm 2 , revealing the formation of microcrater-like structures on the cell wall that could serve as channels for the transfer of large macromolecules into the cell interior. An in-situ atomic force microscope (AFM) system has been designed and installed in the CMU bio-implantation facility as a tool for the observation of these microcraters during ion beam bombardment. Here we describe some of the features of the in-situ AFM and outline some of the related work

  13. Fractional Diffusion, Low Exponent Lévy Stable Laws, and 'Slow Motion' Denoising of Helium Ion Microscope Nanoscale Imagery.

    Science.gov (United States)

    Carasso, Alfred S; Vladár, András E

    2012-01-01

    Helium ion microscopes (HIM) are capable of acquiring images with better than 1 nm resolution, and HIM images are particularly rich in morphological surface details. However, such images are generally quite noisy. A major challenge is to denoise these images while preserving delicate surface information. This paper presents a powerful slow motion denoising technique, based on solving linear fractional diffusion equations forward in time. The method is easily implemented computationally, using fast Fourier transform (FFT) algorithms. When applied to actual HIM images, the method is found to reproduce the essential surface morphology of the sample with high fidelity. In contrast, such highly sophisticated methodologies as Curvelet Transform denoising, and Total Variation denoising using split Bregman iterations, are found to eliminate vital fine scale information, along with the noise. Image Lipschitz exponents are a useful image metrology tool for quantifying the fine structure content in an image. In this paper, this tool is applied to rank order the above three distinct denoising approaches, in terms of their texture preserving properties. In several denoising experiments on actual HIM images, it was found that fractional diffusion smoothing performed noticeably better than split Bregman TV, which in turn, performed slightly better than Curvelet denoising.

  14. Ion-beam Plasma Neutralization Interaction Images

    International Nuclear Information System (INIS)

    Igor D. Kaganovich; Edward Startsev; S. Klasky; Ronald C. Davidson

    2002-04-01

    Neutralization of the ion beam charge and current is an important scientific issue for many practical applications. The process of ion beam charge and current neutralization is complex because the excitation of nonlinear plasma waves may occur. Computer simulation images of plasma neutralization of the ion beam pulse are presented

  15. Ion-beam Plasma Neutralization Interaction Images

    Energy Technology Data Exchange (ETDEWEB)

    Igor D. Kaganovich; Edward Startsev; S. Klasky; Ronald C. Davidson

    2002-04-09

    Neutralization of the ion beam charge and current is an important scientific issue for many practical applications. The process of ion beam charge and current neutralization is complex because the excitation of nonlinear plasma waves may occur. Computer simulation images of plasma neutralization of the ion beam pulse are presented.

  16. Modeling secondary electron emission from nanostructured materials in helium ion microscope

    International Nuclear Information System (INIS)

    Ohya, K.; Yamanaka, T.

    2013-01-01

    Charging of a SiO 2 layer on a Si substrate during helium (He) beam irradiation is investigated at an energy range relevant to a He ion microscope (HIM). A self-consistent calculation is performed to model the transport of the ions and secondary electrons (SEs), the charge accumulation in the layer, and the electric field below and above the surface. The calculated results are compared with those for gallium (Ga) ions at the same energy and 1 keV electrons corresponding to a low-voltage scanning electron microscope (SEM). The charging of thin layers ( 2 step formed on a Si substrate, a sharp increase in the number of SEs is observed, irrespective of whether a material is charged or not. When the He ions are incident on the bottom of the step, the re-entrance of SEs emitted from the substrate into the sidewall is clearly observed, but it causes the sidewall to be charged negatively. At the positions on the SiO 2 layer away from the step edge, the charging voltage becomes positive with increasing number of Ga ions and electrons. However, He ions do not induce such a voltage due to strong relaxation of positive and negative charges in the Si substrate and their recombination in the SiO 2 layer

  17. A framed, 16-image Kirkpatrick-Baez x-ray microscope

    Science.gov (United States)

    Marshall, F. J.; Bahr, R. E.; Goncharov, V. N.; Glebov, V. Yu.; Peng, B.; Regan, S. P.; Sangster, T. C.; Stoeckl, C.

    2017-09-01

    A 16-image Kirkpatrick-Baez (KB)-type x-ray microscope consisting of compact KB mirrors [F. J. Marshall, Rev. Sci. Instrum. 83, 10E518 (2012)] has been assembled for the first time with mirrors aligned to allow it to be coupled to a high-speed framing camera. The high-speed framing camera has four independently gated strips whose emission sampling interval is ˜30 ps. Images are arranged four to a strip with ˜60-ps temporal spacing between frames on a strip. By spacing the timing of the strips, a frame spacing of ˜15 ps is achieved. A framed resolution of ˜6-μm is achieved with this combination in a 400-μm region of laser-plasma x-ray emission in the 2- to 8-keV energy range. A principal use of the microscope is to measure the evolution of the implosion stagnation region of cryogenic DT target implosions on the University of Rochester's OMEGA Laser System [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)]. The unprecedented time and spatial resolutions achieved with this framed, multi-image KB microscope have made it possible to accurately determine the cryogenic implosion core emission size and shape at the peak of stagnation. These core size measurements, taken in combination with those of ion temperature, neutron-production temporal width, and neutron yield allow for inference of core pressures, currently exceeding 50 Gbar in OMEGA cryogenic target implosions [Regan et al., Phys. Rev. Lett. 117, 025001 (2016)].

  18. Optical design and system characterization of an imaging microscope at 121.6 nm

    Science.gov (United States)

    Gao, Weichuan; Finan, Emily; Kim, Geon-Hee; Kim, Youngsik; Milster, Thomas D.

    2018-03-01

    We present the optical design and system characterization of an imaging microscope prototype at 121.6 nm. System engineering processes are demonstrated through the construction of a Schwarzschild microscope objective, including tolerance analysis, fabrication, alignment, and testing. Further improvements on the as-built system with a correction phase plate are proposed and analyzed. Finally, the microscope assembly and the imaging properties of the prototype are demonstrated.

  19. Hyperspectral microscope imaging methods to classify gram-positive and gram-negative foodborne pathogenic bacteria

    Science.gov (United States)

    An acousto-optic tunable filter-based hyperspectral microscope imaging method has potential for identification of foodborne pathogenic bacteria from microcolony rapidly with a single cell level. We have successfully developed the method to acquire quality hyperspectral microscopic images from variou...

  20. Microscopic observation of pattern attack by aggressive ions on finished surface of aluminium alloy sacrificial anode

    International Nuclear Information System (INIS)

    Zaifol Samsu; Muhammad Daud; Siti Radiah Mohd Kamarudin; Nur Ubaidah Saidin; Azali Muhammad; Mohd Shaari Ripin; Rusni Rejab; Mohd Shariff Sattar

    2010-01-01

    This paper presents the results of a microscopic observation on submerged finished surface of aluminium alloy sacrificial anode. Experimental tests were carried out on polished surface aluminium anode exposed to seawater containing aggressive ions in order to observe of pattern corrosion attack on corroding surface of anode. Results have shown, at least under the present testing condition, that surface of sacrificial anode were attack by an aggressive ion such as chloride along grain boundaries. In addition, results of microanalysis showed that the corrosion products on surface of aluminium alloy have Al, Zn and O element for all sample and within the pit was consists of Al, Zn, O and Cl element. (author)

  1. Microscopic approach to subthreshold pion production in heavy-ion collisions

    International Nuclear Information System (INIS)

    Tohyama, M.; Kaps, R.; Masak, D.; Mosel, U.

    1985-01-01

    A microscopic approach to subthreshold pion production in heavy-ion collisions is proposed, in which the wave function of the nucleon system is approximated in the time-dependent Hartree-Fock theory and an effective interaction for the pion-production process is taken from (p,π) reaction theories. The model is applied to pion production in 16 O + 16 O collisions. (orig.)

  2. Design and implementation of a cost-effective microscope for fabrication and imaging

    International Nuclear Information System (INIS)

    Trout, G; Basu, S

    2009-01-01

    The use of lasers and optical systems for advanced research and demonstrative purposes has traditionally been cost-prohibitive for many researchers. In this note, we present the design and optimization of a low-cost microscopy setup capable of imaging, fabrication or photopolymerization via multiphoton excitation of a photoactivator and the study of processes such as diffusion using fluorescence recovery after photobleaching (FRAP). The setup features a continuous wave (CW) Ar-ion laser, a pulsed Nd 3+ :YAG laser, an inverted microscope with a CCD camera and appropriate optics. The setup is cost-effective and puts a once-expensive setup within reach of more researchers interested in micron- and sub-micron-scale processes. (technical design note)

  3. A simple way to obtain backscattered electron images in a scanning transmission electron microscope.

    Science.gov (United States)

    Tsuruta, Hiroki; Tanaka, Shigeyasu; Tanji, Takayoshi; Morita, Chiaki

    2014-08-01

    We have fabricated a simple detector for backscattered electrons (BSEs) and incorporated the detector into a scanning transmission electron microscope (STEM) sample holder. Our detector was made from a 4-mm(2) Si chip. The fabrication procedure was easy, and similar to a standard transmission electron microscopy (TEM) sample thinning process based on ion milling. A TEM grid containing particle objects was fixed to the detector with a silver paste. Observations were carried out using samples of Au and latex particles at 75 and 200 kV. Such a detector provides an easy way to obtain BSE images in an STEM. © The Author 2014. 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.

  4. Microscopic hyperspectral imaging studies of normal and diabetic retina of rats

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A microscopic hyperspectral imager was developed based on the microscopic technology and the spectral imaging technology. Some microscopic hyperspectral images of retina sections of the normal, the diabetic, and the treated rats were collected by the new imager. Single-band images and pseudo-color images of each group were obtained and the typical transmittance spectrums were ex-tracted. The results showed that the transmittance of outer nuclear layer cells of the diabetic group was generally higher than that of the normal. A small absorption peak appeared near the 180th band in the spectrum of the diabetic group and this peak weakened or disappeared in the spectrum of the treated group. Our findings indicate that the microscopic hyperspectral images include wealthy information of retina sections which is helpful for the ophthalmologist to reveal the pathogenesis of diabetic reti-nopathy and explore the therapeutic effect of drugs.

  5. Polarization resolved imaging with a reflection near-field optical microscope

    DEFF Research Database (Denmark)

    Bozhevolnyi, Sergey I.; Xiao, Mufei; Hvam, Jørn Märcher

    1999-01-01

    Using a rigorous microscopic point-dipole description of probe-sample interactions, we study imaging with a reflection scanning near-field optical microscope. Optical content, topographical artifacts, sensitivity window-i.e., the scale on which near-field optical images represent mainly optical...... configuration is preferable to the cross-linear one, since it ensures more isotropic (in the surface plane) near-field imaging of surface features. The numerical results are supported with experimental near-field images obtained by using a reflection microscope with an uncoated fiber tip....

  6. A simple water-immersion condenser for imaging living brain slices on an inverted microscope.

    Science.gov (United States)

    Prusky, G T

    1997-09-05

    Due to some physical limitations of conventional condensers, inverted compound microscopes are not optimally suited for imaging living brain slices with transmitted light. Herein is described a simple device that converts an inverted microscope into an effective tool for this application by utilizing an objective as a condenser. The device is mounted on a microscope in place of the condenser, is threaded to accept a water immersion objective, and has a slot for a differential interference contrast (DIC) slider. When combined with infrared video techniques, this device allows an inverted microscope to effectively image living cells within thick brain slices in an open perfusion chamber.

  7. An image processing approach to analyze morphological features of microscopic images of muscle fibers.

    Science.gov (United States)

    Comin, Cesar Henrique; Xu, Xiaoyin; Wang, Yaming; Costa, Luciano da Fontoura; Yang, Zhong

    2014-12-01

    We present an image processing approach to automatically analyze duo-channel microscopic images of muscular fiber nuclei and cytoplasm. Nuclei and cytoplasm play a critical role in determining the health and functioning of muscular fibers as changes of nuclei and cytoplasm manifest in many diseases such as muscular dystrophy and hypertrophy. Quantitative evaluation of muscle fiber nuclei and cytoplasm thus is of great importance to researchers in musculoskeletal studies. The proposed computational approach consists of steps of image processing to segment and delineate cytoplasm and identify nuclei in two-channel images. Morphological operations like skeletonization is applied to extract the length of cytoplasm for quantification. We tested the approach on real images and found that it can achieve high accuracy, objectivity, and robustness. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. High-resolution, high-throughput imaging with a multibeam scanning electron microscope.

    Science.gov (United States)

    Eberle, A L; Mikula, S; Schalek, R; Lichtman, J; Knothe Tate, M L; Zeidler, D

    2015-08-01

    Electron-electron interactions and detector bandwidth limit the maximal imaging speed of single-beam scanning electron microscopes. We use multiple electron beams in a single column and detect secondary electrons in parallel to increase the imaging speed by close to two orders of magnitude and demonstrate imaging for a variety of samples ranging from biological brain tissue to semiconductor wafers. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  9. Image enhancement of x-ray microscope using frequency spectrum analysis

    International Nuclear Information System (INIS)

    Li Wenjie; Chen Jie; Tian Jinping; Zhang Xiaobo; Liu Gang; Tian Yangchao; Liu Yijin; Wu Ziyu

    2009-01-01

    We demonstrate a new method for x-ray microscope image enhancement using frequency spectrum analysis. Fine sample characteristics are well enhanced with homogeneous visibility and better contrast from single image. This method is easy to implement and really helps to improve the quality of image taken by our imaging system.

  10. Image enhancement of x-ray microscope using frequency spectrum analysis

    Energy Technology Data Exchange (ETDEWEB)

    Li Wenjie; Chen Jie; Tian Jinping; Zhang Xiaobo; Liu Gang; Tian Yangchao [National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029 (China); Liu Yijin; Wu Ziyu, E-mail: wuzy@ihep.ac.c, E-mail: ychtian@ustc.edu.c [Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049 (China)

    2009-09-01

    We demonstrate a new method for x-ray microscope image enhancement using frequency spectrum analysis. Fine sample characteristics are well enhanced with homogeneous visibility and better contrast from single image. This method is easy to implement and really helps to improve the quality of image taken by our imaging system.

  11. On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water

    Energy Technology Data Exchange (ETDEWEB)

    Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr [Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris (France); Charpentier, Thibault [CEA, IRAMIS, NIMBE, LSDRM, UMR CEA-CNRS 3685, F-91191 Gif-sur-Yvette Cedex (France)

    2015-11-21

    Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as {sup 7}Li{sup +}, {sup 23}Na{sup +}, {sup 25}Mg{sup 2+}, {sup 35}Cl{sup −}, {sup 39}K{sup +}, or {sup 133}Cs{sup +}. Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFG tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.

  12. Microscopic image processing system for measuring nonuniform film thickness profiles: Image scanning ellipsometry

    International Nuclear Information System (INIS)

    Liu, A.H.; Plawsky, J.L.; Wayner, P.C. Jr.

    1993-01-01

    The long-term objective of this research program is to determine the stability and heat transfer characteristics of evaporating thin films. The current objective is to develop and use a microscopic image-processing system (IPS) which has two parts: an image analyzing interferometer (IAI) and an image scanning ellipsometer (ISE). The primary purpose of this paper is to present the basic concept of ISE, which is a novel technique to measure the two dimensional thickness profile of a non-uniform, thin film, from several nm up to several μm, in a steady state as well as in a transient state. It is a full-field imaging technique which can study every point on the surface simultaneously with high spatial resolution and thickness sensitivity, i.e., it can measure and map the 2-D film thickness profile. The ISE was tested by measuring the thickness profile and the refractive index of a nonuniform solid film

  13. An image processing pipeline to detect and segment nuclei in muscle fiber microscopic images.

    Science.gov (United States)

    Guo, Yanen; Xu, Xiaoyin; Wang, Yuanyuan; Wang, Yaming; Xia, Shunren; Yang, Zhong

    2014-08-01

    Muscle fiber images play an important role in the medical diagnosis and treatment of many muscular diseases. The number of nuclei in skeletal muscle fiber images is a key bio-marker of the diagnosis of muscular dystrophy. In nuclei segmentation one primary challenge is to correctly separate the clustered nuclei. In this article, we developed an image processing pipeline to automatically detect, segment, and analyze nuclei in microscopic image of muscle fibers. The pipeline consists of image pre-processing, identification of isolated nuclei, identification and segmentation of clustered nuclei, and quantitative analysis. Nuclei are initially extracted from background by using local Otsu's threshold. Based on analysis of morphological features of the isolated nuclei, including their areas, compactness, and major axis lengths, a Bayesian network is trained and applied to identify isolated nuclei from clustered nuclei and artifacts in all the images. Then a two-step refined watershed algorithm is applied to segment clustered nuclei. After segmentation, the nuclei can be quantified for statistical analysis. Comparing the segmented results with those of manual analysis and an existing technique, we find that our proposed image processing pipeline achieves good performance with high accuracy and precision. The presented image processing pipeline can therefore help biologists increase their throughput and objectivity in analyzing large numbers of nuclei in muscle fiber images. © 2014 Wiley Periodicals, Inc.

  14. Design of a normal incidence multilayer imaging X-ray microscope

    Science.gov (United States)

    Shealy, David L.; Gabardi, David R.; Hoover, Richard B.; Walker, Arthur B. C., Jr.; Lindblom, Joakim F.

    Normal incidence multilayer Cassegrain X-ray telescopes were flown on the Stanford/MSFC Rocket X-ray Spectroheliograph. These instruments produced high spatial resolution images of the sun and conclusively demonstrated that doubly reflecting multilayer X-ray optical systems are feasible. The images indicated that aplanatic imaging soft X-ray/EUV microscopes should be achievable using multilayer optics technology. A doubly reflecting normal incidence multilayer imaging X-ray microscope based on the Schwarzschild configuration has been designed. The design of the microscope and the results of the optical system ray trace analysis are discussed. High resolution aplanatic imaging X-ray microscopes using normal incidence multilayer X-ray mirrors should have many important applications in advanced X-ray astronomical instrumentation, X-ray lithography, biological, biomedical, metallurgical, and laser fusion research.

  15. Field electron emission spectrometer combined with field ion/electron microscope as a field emission laboratory

    International Nuclear Information System (INIS)

    Shkuratov, S.I.; Ivanov, S.N.; Shilimanov, S.N.

    1996-01-01

    The facility, combining the field ion microscope, field electron emission microscope and field electron emission spectrometer, is described. Combination of three methodologies makes it possible to carry out the complete cycle of emission studies. Atom-plane and clean surface of the studied samples is prepared by means of field evaporation of the material atom layers without any thermal and radiation impact. This enables the study of atom and electron structure of clean surface of the wide range materials, the study whereof through the field emission methods was previously rather difficult. The temperature of the samples under study changes from 75 up to 2500 K. The energy resolution of the electron analyzer equals 30 MeV. 19 refs., 10 figs

  16. Three Dimensional Imaging of Cold Atoms in a Magneto Optical Trap with a Light Field Microscope

    Science.gov (United States)

    2017-09-14

    with a Light Field Microscope Gordon E. Lott Follow this and additional works at: https://scholar.afit.edu/etd Part of the Atomic, Molecular and......https://scholar.afit.edu/etd/774 THREE-DIMENSIONAL IMAGING OF COLD ATOMS IN A MAGNETO-OPTICAL TRAP WITH A LIGHT FIELD MICROSCOPE DISSERTATION Gordon E

  17. Interferometric and optical tests of water window imaging x ray microscopes

    Science.gov (United States)

    Johnson, R. Barry

    1993-01-01

    Interferometric tests of Schwarzchild X-ray Microscope are performed to evaluate the optical properties and alignment of the components. Photographic measurements of the spatial resolution, focal properties, and vignetting characteristics of the prototype Water Window Imaging X-ray Microscope are made and analyzed.

  18. Imaging properties of the mesooptical Fourier transform microscope for nuclear research emulsion

    International Nuclear Information System (INIS)

    Bencze, Gy.L.; Soroko, L.M.

    1987-01-01

    The optical signal transformation in the Mesooptical Fourier Transform Microscope (MFTM) for nuclear emulsion is treated in terms of Fourier Optics. A continuous conversion of the traditional optical microscope into the MFTM is followed. The images of dot-like and straight line objects given by the MFTM are discussed

  19. Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules

    OpenAIRE

    Elliott, Jonathan T.; Dsouza, Alisha V.; Marra, Kayla; Pogue, Brian W.; Roberts, David W.; Paulsen, Keith D.

    2016-01-01

    Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system spe...

  20. High contrast imaging and flexible photomanipulation for quantitative in vivo multiphoton imaging with polygon scanning microscope.

    Science.gov (United States)

    Li, Yongxiao; Montague, Samantha J; Brüstle, Anne; He, Xuefei; Gillespie, Cathy; Gaus, Katharina; Gardiner, Elizabeth E; Lee, Woei Ming

    2018-02-28

    In this study, we introduce two key improvements that overcome limitations of existing polygon scanning microscopes while maintaining high spatial and temporal imaging resolution over large field of view (FOV). First, we proposed a simple and straightforward means to control the scanning angle of the polygon mirror to carry out photomanipulation without resorting to high speed optical modulators. Second, we devised a flexible data sampling method directly leading to higher image contrast by over 2-fold and digital images with 100 megapixels (10 240 × 10 240) per frame at 0.25 Hz. This generates sub-diffraction limited pixels (60 nm per pixels over the FOV of 512 μm) which increases the degrees of freedom to extract signals computationally. The unique combined optical and digital control recorded fine fluorescence recovery after localized photobleaching (r ~10 μm) within fluorescent giant unilamellar vesicles and micro-vascular dynamics after laser-induced injury during thrombus formation in vivo. These new improvements expand the quantitative biological-imaging capacity of any polygon scanning microscope system. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Specimen preparation of irradiated materials for examination in the atom probe field ion microscope

    International Nuclear Information System (INIS)

    Russell, K.F.; Miller, M.K.

    1994-01-01

    The atom probe field ion microscope (APFIM) requires specimens in the form of ultrasharp needles. Basic protective measures used to reduce exposure druing specimen preparation are discussed. The low-level radioactive specimen blanks may be made using a two-stage electropolishing process using a thin layer of electrolyte floating on a denser inert liquid; this produces a necked region and eventually two specimens from each single blank. The amount of material handled may also be reduced using a micropolishing technique to repolish blunt or fractured specimens. Control of contamination and possible spills is discussed

  2. Spatio-temporal imaging of voltage pulses with an ultrafast scanning tunneling microscope

    DEFF Research Database (Denmark)

    Jensen, Jacob Riis; Keil, Ulrich Dieter Felix; Hvam, Jørn Märcher

    1997-01-01

    Measurements on an ultrafast scanning tunneling microscope with simultaneous spatial and temporal resolution are presented. We show images of picosecond pulses propagating on a coplanar waveguide and resolve their mode structures. The influence of transmission line discontinuities on the mode...

  3. Remote laboratory for phase-aided 3D microscopic imaging and metrology

    Science.gov (United States)

    Wang, Meng; Yin, Yongkai; Liu, Zeyi; He, Wenqi; Li, Boqun; Peng, Xiang

    2014-05-01

    In this paper, the establishment of a remote laboratory for phase-aided 3D microscopic imaging and metrology is presented. Proposed remote laboratory consists of three major components, including the network-based infrastructure for remote control and data management, the identity verification scheme for user authentication and management, and the local experimental system for phase-aided 3D microscopic imaging and metrology. The virtual network computer (VNC) is introduced to remotely control the 3D microscopic imaging system. Data storage and management are handled through the open source project eSciDoc. Considering the security of remote laboratory, the fingerprint is used for authentication with an optical joint transform correlation (JTC) system. The phase-aided fringe projection 3D microscope (FP-3DM), which can be remotely controlled, is employed to achieve the 3D imaging and metrology of micro objects.

  4. Combined transmission electron microscope and ion channeling study of metastable metal alloys formed by ion implantation

    International Nuclear Information System (INIS)

    Cullis, A.G.; Borders, J.A.; Hirvonen, J.K.; Poate, J.M.

    1977-01-01

    Recently, ion implantation has been used to produce metastable alloy layers with a range of structures from crystalline substitutional solid solutions to amorphous. The technique offers the possibility of producing metastable metal layers with unique physical properties. Its application in the formation of alloys exhibiting different although complementary types of metastability is described. The metal combinations chosen (Ag-Cu and Ta-Cu) show little mutual solubility under equilibrium conditions

  5. Image alignment for tomography reconstruction from synchrotron X-ray microscopic images.

    Directory of Open Access Journals (Sweden)

    Chang-Chieh Cheng

    Full Text Available A synchrotron X-ray microscope is a powerful imaging apparatus for taking high-resolution and high-contrast X-ray images of nanoscale objects. A sufficient number of X-ray projection images from different angles is required for constructing 3D volume images of an object. Because a synchrotron light source is immobile, a rotational object holder is required for tomography. At a resolution of 10 nm per pixel, the vibration of the holder caused by rotating the object cannot be disregarded if tomographic images are to be reconstructed accurately. This paper presents a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images. This alignment process involves two steps. The first step is to match the "projected feature points" in the sequence of images. The matched projected feature points in the x-θ plane should form a set of sine-shaped loci. The second step is to fit the loci to a set of sine waves to compute the parameters required for alignment. The experimental results show that the proposed method outperforms two previously proposed methods, Xradia and SPIDER. The developed software system can be downloaded from the URL, http://www.cs.nctu.edu.tw/~chengchc/SCTA or http://goo.gl/s4AMx.

  6. Image alignment for tomography reconstruction from synchrotron X-ray microscopic images.

    Science.gov (United States)

    Cheng, Chang-Chieh; Chien, Chia-Chi; Chen, Hsiang-Hsin; Hwu, Yeukuang; Ching, Yu-Tai

    2014-01-01

    A synchrotron X-ray microscope is a powerful imaging apparatus for taking high-resolution and high-contrast X-ray images of nanoscale objects. A sufficient number of X-ray projection images from different angles is required for constructing 3D volume images of an object. Because a synchrotron light source is immobile, a rotational object holder is required for tomography. At a resolution of 10 nm per pixel, the vibration of the holder caused by rotating the object cannot be disregarded if tomographic images are to be reconstructed accurately. This paper presents a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images. This alignment process involves two steps. The first step is to match the "projected feature points" in the sequence of images. The matched projected feature points in the x-θ plane should form a set of sine-shaped loci. The second step is to fit the loci to a set of sine waves to compute the parameters required for alignment. The experimental results show that the proposed method outperforms two previously proposed methods, Xradia and SPIDER. The developed software system can be downloaded from the URL, http://www.cs.nctu.edu.tw/~chengchc/SCTA or http://goo.gl/s4AMx.

  7. Lateral resolution testing of a novel developed confocal microscopic imaging system

    Science.gov (United States)

    Zhang, Xin; Zhang, Yunhai; Chang, Jian; Huang, Wei; Xue, Xiaojun; Xiao, Yun

    2015-10-01

    Laser scanning confocal microscope has been widely used in biology, medicine and material science owing to its advantages of high resolution and tomographic imaging. Based on a set of confirmatory experiments and system design, a novel confocal microscopic imaging system is developed. The system is composed of a conventional fluorescence microscope and a confocal scanning unit. In the scanning unit a laser beam coupling module provides four different wavelengths 405nm 488nm 561nm and 638nm which can excite a variety of dyes. The system works in spot-to-spot scanning mode with a two-dimensional galvanometer. A 50 microns pinhole is used to guarantee that stray light is blocked and only the fluorescence signal from the focal point can be received . The three-channel spectral splitter is used to perform fluorescence imaging at three different working wavelengths simultaneously. The rat kidney tissue slice is imaged using the developed confocal microscopic imaging system. Nucleues labeled by DAPI and kidney spherule curved pipe labeled by Alexa Fluor 488 can be imaged clearly and respectively, realizing the distinction between the different components of mouse kidney tissue. The three-dimensional tomographic imaging of mouse kidney tissue is reconstructed by several two-dimensional images obtained in different depths. At last the resolution of the confocal microscopic imaging system is tested quantitatively. The experimental result shows that the system can achieve lateral resolution priority to 230nm.

  8. Image-projection ion-beam lithography

    International Nuclear Information System (INIS)

    Miller, P.A.

    1989-01-01

    Image-projection ion-beam lithography is an attractive alternative for submicron patterning because it may provide high throughput; it uses demagnification to gain advantages in reticle fabrication, inspection, and lifetime; and it enjoys the precise deposition characteristics of ions which cause essentially no collateral damage. This lithographic option involves extracting low-mass ions (e.g., He + ) from a plasma source, transmitting the ions at low voltage through a stencil reticle, and then accelerating and focusing the ions electrostatically onto a resist-coated wafer. While the advantages of this technology have been demonstrated experimentally by the work of IMS (Austria), many difficulties still impede extension of the technology to the high-volume production of microelectronic devices. We report a computational study of a lithography system designed to address problem areas in field size, telecentricity, and chromatic and geometric aberration. We present a novel ion-column-design approach and conceptual ion-source and column designs which address these issues. We find that image-projection ion-beam technology should in principle meet high-volume-production requirements. The technical success of our present relatively compact-column design requires that a glow-discharge-based ion source (or equivalent cold source) be developed and that moderate further improvement in geometric aberration levels be obtained. Our system requires that image predistortion be employed during reticle fabrication to overcome distortion due to residual image nonlinearity and space-charge forces. This constitutes a software data preparation step, as do correcting for distortions in electron lithography columns and performing proximity-effect corrections. Areas needing further fundamental work are identified

  9. Confocal Microscope Alignment of Nanocrystals for Coherent Diffraction Imaging

    International Nuclear Information System (INIS)

    Beitra, Loren; Watari, Moyu; Matsuura, Takashi; Shimamoto, Naonobu; Harder, Ross; Robinson, Ian

    2010-01-01

    We have installed and tested an Olympus LEXT confocal microscope at the 34-ID-C beamline of the Advanced Photon Source (APS). The beamline is for Coherent X-ray Diffraction (CXD) experiments in which a nanometre-sized crystal is aligned inside a focussed X-ray beam. The microscope was required for three-dimensional (3D) sample alignment to get around sphere-of-confusion issues when locating Bragg peaks in reciprocal space. In this way, and by use of strategic sample preparations, we have succeeded in measuring six Bragg peaks from a single 200 nm gold crystal and obtained six projections of its internal displacement field. This enables the clear identification of stacking-fault bands within the crystal. The confocal alignment method will allow a full determination of the strain tensor provided three or more Bragg reflections from the same crystal are found.

  10. Ghost microscope imaging system from the perspective of coherent-mode representation

    Science.gov (United States)

    Shen, Qian; Bai, Yanfeng; Shi, Xiaohui; Nan, Suqin; Qu, Lijie; Li, Hengxing; Fu, Xiquan

    2018-03-01

    The coherent-mode representation theory of partially coherent fields is firstly used to analyze a two-arm ghost microscope imaging system. It is shown that imaging quality of the generated images depend crucially on the distribution of the decomposition coefficients of the object imaged when the light source is fixed. This theory is also suitable for demonstrating the effects from the distance the object is moved away from the original plane on imaging quality. Our results are verified theoretically and experimentally.

  11. An ion-sputtering gun to clean crystal surfaces in-situ in an ultra-high-vacuum electron microscope

    International Nuclear Information System (INIS)

    Morita, Etsuo; Takayanagi, Kunio; Kobayashi, Kunio; Yagi, Katsumichi; Honjo, Goro

    1980-01-01

    The design and performance of an ion-sputtering gun for cleaning crystal surfaces in-situ in an ultra-high-vacuum electron microscope are reported. The electron microscopic aspects of ion-bombardment damage to ionic magnesium oxide, covalent germanium and silicon, and metallic gold and copper crystals, and the effects of annealing after and during sputtering are described. The growth of various kinds of films deposited in-situ on crystals cleaned by ion-sputtering are described and discussed. (author)

  12. Angularly-selective transmission imaging in a scanning electron microscope.

    Science.gov (United States)

    Holm, Jason; Keller, Robert R

    2016-08-01

    This work presents recent advances in transmission scanning electron microscopy (t-SEM) imaging control capabilities. A modular aperture system and a cantilever-style sample holder that enable comprehensive angular selectivity of forward-scattered electrons are described. When combined with a commercially available solid-state transmission detector having only basic bright-field and dark-field imaging capabilities, the advances described here enable numerous transmission imaging modes. Several examples are provided that demonstrate how contrast arising from diffraction to mass-thickness can be obtained. Unanticipated image contrast at some imaging conditions is also observed and addressed. Published by Elsevier B.V.

  13. Real-time image processing and control interface for remote operation of a microscope

    Science.gov (United States)

    Leng, Hesong; Wilder, Joseph

    1999-08-01

    A real-time image processing and control interface for remote operation of a microscope is presented in this paper. The system has achieved real-time color image display for 640 X 480 pixel images. Multi-resolution image representation can be provided for efficient transmission through the network. Through the control interface the computer can communicate with the programmable microscope via the RS232 serial ports. By choosing one of three scanning patterns, a sequence of images can be saved as BMP or PGM files to record information on an entire microscope slide. The system will be used by medical and graduate students at the University of Medicine and Dentistry of New Jersey for distance learning. It can be used in many network-based telepathology applications.

  14. Atomic Force Microscope Image Contrast Mechanisms on Supported Lipid Bilayers

    OpenAIRE

    Schneider, James; Dufrêne, Yves F.; Barger Jr., William R.; Lee, Gil U.

    2000-01-01

    This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures o...

  15. Microscope self-calibration based on micro laser line imaging and soft computing algorithms

    Science.gov (United States)

    Apolinar Muñoz Rodríguez, J.

    2018-06-01

    A technique to perform microscope self-calibration via micro laser line and soft computing algorithms is presented. In this technique, the microscope vision parameters are computed by means of soft computing algorithms based on laser line projection. To implement the self-calibration, a microscope vision system is constructed by means of a CCD camera and a 38 μm laser line. From this arrangement, the microscope vision parameters are represented via Bezier approximation networks, which are accomplished through the laser line position. In this procedure, a genetic algorithm determines the microscope vision parameters by means of laser line imaging. Also, the approximation networks compute the three-dimensional vision by means of the laser line position. Additionally, the soft computing algorithms re-calibrate the vision parameters when the microscope vision system is modified during the vision task. The proposed self-calibration improves accuracy of the traditional microscope calibration, which is accomplished via external references to the microscope system. The capability of the self-calibration based on soft computing algorithms is determined by means of the calibration accuracy and the micro-scale measurement error. This contribution is corroborated by an evaluation based on the accuracy of the traditional microscope calibration.

  16. High-resolution imaging in the scanning transmission electron microscope

    International Nuclear Information System (INIS)

    Pennycook, S.J.; Jesson, D.E.

    1992-03-01

    The high-resolution imaging of crystalline materials in the scanning transmission electron microscopy (STEM) is reviewed with particular emphasis on the conditions under which an incoherent image can be obtained. It is shown that a high-angle annular detector can be used to break the coherence of the imaging process, in the transverse plane through the geometry of the detector, or in three dimensions if multiphonon diffuse scattering is detected. In the latter case, each atom can be treated as a highly independent source of high-angle scattering. The most effective fast electron states are therefore tightly bound s-type Bloch states. Furthermore, they add constructively for each incident angle in the coherent STEM probe, so that s states are responsible for practically the entire image contrast. Dynamical effects are largely removed, and almost perfect incoherent imaging is achieved. s states are relatively insensitive to neighboring strings, so that incoherent imaging is maintained for superlattice and interfaces, and supercell calculations are unnecessary. With an optimum probe profile, the incoherent image represents a direct image of the crystal projection, with compositional sensitivity built in through the strong dependence of the scattering cross sections on atomic number Z

  17. Multi-technology Integration Based on Low-contrast Microscopic Image Enhancement

    Directory of Open Access Journals (Sweden)

    Haoge Ma

    2014-01-01

    Full Text Available Microscopic image enhancement is an important issue of image processing technique, which is used to improve the visual quality of image. This paper describes a novel multi resolution image segmentation algorithm for low DOF images. The algorithm is designed to separate a sharply focused object of interest from other foreground or background objects. The algorithm is fully automatic in that all parameters are image in dependent. A multiscale-approach based on high frequency wavelet coefficients and their statistics is used to perform context dependent classification of individual blocks of the image. Compared with the state of the art algorithms, this new algorithm provides better accuracy at higher speed.

  18. The importance of radiographic imaging in the microscopic assessment of bone tumors

    International Nuclear Information System (INIS)

    Larousserie, F.; Kreshak, J.; Gambarotti, M.; Alberghini, M.; Vanel, D.

    2013-01-01

    Introduction: Primary bone tumors are rare and require a multidisciplinary approach. Diagnosis involves primarily the radiologist and the pathologist. Bone lesions are often heterogeneous and the microscopic diagnostic component(s) may be in the minority, especially on core needle biopsies. Reactive processes, benign, and malignant tumors may have similar microscopic aspects. For these challenging cases, the correlation of microscopic and radiologic information is critical, or diagnostic mistakes may be made with severe clinical consequences for the patient. The purpose of this article is to explain how pathologists can best use imaging studies to improve the diagnostic accuracy of bone lesions. Diagnosis: Many bone lesions are microscopically and/or radiographically heterogeneous, especially those with both lytic and matrix components. Final diagnosis may require specific microscopic diagnostic features that may be present in the lesion, but not the biopsy specimen. A review of the imaging helps assess if sampling was adequate. The existence of a pre-existing bone lesion, syndrome (such as Ollier disease or multiple hereditary exostosis), or oncologic history may be of crucial importance. Finally, imaging information is very useful for the pathologist to perform accurate local and regional staging during gross examination. Conclusion: Close teamwork between pathologists, radiologists, and clinicians is of utmost importance in the evaluation and management of bone tumors. These lesions can be very difficult to interpret microscopically; imaging studies therefore play a crucial role in their accurate diagnosis

  19. The importance of radiographic imaging in the microscopic assessment of bone tumors

    Energy Technology Data Exchange (ETDEWEB)

    Larousserie, F., E-mail: frederique.larousserie@cch.aphp.fr [Université Paris Descartes, Sorbonne Paris Cité, Paris (France); Department of pathology, Rizzoli Institute, Bologna (Italy); Kreshak, J.; Gambarotti, M.; Alberghini, M.; Vanel, D. [Department of pathology, Rizzoli Institute, Bologna (Italy)

    2013-12-01

    Introduction: Primary bone tumors are rare and require a multidisciplinary approach. Diagnosis involves primarily the radiologist and the pathologist. Bone lesions are often heterogeneous and the microscopic diagnostic component(s) may be in the minority, especially on core needle biopsies. Reactive processes, benign, and malignant tumors may have similar microscopic aspects. For these challenging cases, the correlation of microscopic and radiologic information is critical, or diagnostic mistakes may be made with severe clinical consequences for the patient. The purpose of this article is to explain how pathologists can best use imaging studies to improve the diagnostic accuracy of bone lesions. Diagnosis: Many bone lesions are microscopically and/or radiographically heterogeneous, especially those with both lytic and matrix components. Final diagnosis may require specific microscopic diagnostic features that may be present in the lesion, but not the biopsy specimen. A review of the imaging helps assess if sampling was adequate. The existence of a pre-existing bone lesion, syndrome (such as Ollier disease or multiple hereditary exostosis), or oncologic history may be of crucial importance. Finally, imaging information is very useful for the pathologist to perform accurate local and regional staging during gross examination. Conclusion: Close teamwork between pathologists, radiologists, and clinicians is of utmost importance in the evaluation and management of bone tumors. These lesions can be very difficult to interpret microscopically; imaging studies therefore play a crucial role in their accurate diagnosis.

  20. Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images.

    Science.gov (United States)

    Kimori, Yoshitaka; Baba, Norio; Morone, Nobuhiro

    2010-07-08

    A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells and tissues. Currently, automatic spot extraction and characterization in complex microscopic images poses many challenges to conventional image processing methods. A new method to extract closely located, small target spots from biological images is proposed. This method starts with a simple but practical operation based on the extended morphological top-hat transformation to subtract an uneven background. The core of our novel approach is the following: first, the original image is rotated in an arbitrary direction and each rotated image is opened with a single straight line-segment structuring element. Second, the opened images are unified and then subtracted from the original image. To evaluate these procedures, model images of simulated spots with closely located targets were created and the efficacy of our method was compared to that of conventional morphological filtering methods. The results showed the better performance of our method. The spots of real microscope images can be quantified to confirm that the method is applicable in a given practice. Our method achieved effective spot extraction under various image conditions, including aggregated target spots, poor signal-to-noise ratio, and large variations in the background intensity. Furthermore, it has no restrictions with respect to the shape of the extracted spots. The features of our method allow its broad application in biological and biomedical image information analysis.

  1. Microscopic validation of whole mouse micro-metastatic tumor imaging agents using cryo-imaging and sliding organ image registration

    Science.gov (United States)

    Liu, Yiqiao; Zhou, Bo; Qutaish, Mohammed; Wilson, David L.

    2016-03-01

    We created a metastasis imaging, analysis platform consisting of software and multi-spectral cryo-imaging system suitable for evaluating emerging imaging agents targeting micro-metastatic tumor. We analyzed CREKA-Gd in MRI, followed by cryo-imaging which repeatedly sectioned and tiled microscope images of the tissue block face, providing anatomical bright field and molecular fluorescence, enabling 3D microscopic imaging of the entire mouse with single metastatic cell sensitivity. To register MRI volumes to the cryo bright field reference, we used our standard mutual information, non-rigid registration which proceeded: preprocess --> affine --> B-spline non-rigid 3D registration. In this report, we created two modified approaches: mask where we registered locally over a smaller rectangular solid, and sliding organ. Briefly, in sliding organ, we segmented the organ, registered the organ and body volumes separately and combined results. Though sliding organ required manual annotation, it provided the best result as a standard to measure other registration methods. Regularization parameters for standard and mask methods were optimized in a grid search. Evaluations consisted of DICE, and visual scoring of a checkerboard display. Standard had accuracy of 2 voxels in all regions except near the kidney, where there were 5 voxels sliding. After mask and sliding organ correction, kidneys sliding were within 2 voxels, and Dice overlap increased 4%-10% in mask compared to standard. Mask generated comparable results with sliding organ and allowed a semi-automatic process.

  2. Automated Image Analysis of Lung Branching Morphogenesis from Microscopic Images of Fetal Rat Explants

    Science.gov (United States)

    Rodrigues, Pedro L.; Rodrigues, Nuno F.; Duque, Duarte; Granja, Sara; Correia-Pinto, Jorge; Vilaça, João L.

    2014-01-01

    Background. Regulating mechanisms of branching morphogenesis of fetal lung rat explants have been an essential tool for molecular research. This work presents a new methodology to accurately quantify the epithelial, outer contour, and peripheral airway buds of lung explants during cellular development from microscopic images. Methods. The outer contour was defined using an adaptive and multiscale threshold algorithm whose level was automatically calculated based on an entropy maximization criterion. The inner lung epithelium was defined by a clustering procedure that groups small image regions according to the minimum description length principle and local statistical properties. Finally, the number of peripheral buds was counted as the skeleton branched ends from a skeletonized image of the lung inner epithelia. Results. The time for lung branching morphometric analysis was reduced in 98% in contrast to the manual method. Best results were obtained in the first two days of cellular development, with lesser standard deviations. Nonsignificant differences were found between the automatic and manual results in all culture days. Conclusions. The proposed method introduces a series of advantages related to its intuitive use and accuracy, making the technique suitable to images with different lighting characteristics and allowing a reliable comparison between different researchers. PMID:25250057

  3. Automated Image Analysis of Lung Branching Morphogenesis from Microscopic Images of Fetal Rat Explants

    Directory of Open Access Journals (Sweden)

    Pedro L. Rodrigues

    2014-01-01

    Full Text Available Background. Regulating mechanisms of branching morphogenesis of fetal lung rat explants have been an essential tool for molecular research. This work presents a new methodology to accurately quantify the epithelial, outer contour, and peripheral airway buds of lung explants during cellular development from microscopic images. Methods. The outer contour was defined using an adaptive and multiscale threshold algorithm whose level was automatically calculated based on an entropy maximization criterion. The inner lung epithelium was defined by a clustering procedure that groups small image regions according to the minimum description length principle and local statistical properties. Finally, the number of peripheral buds was counted as the skeleton branched ends from a skeletonized image of the lung inner epithelia. Results. The time for lung branching morphometric analysis was reduced in 98% in contrast to the manual method. Best results were obtained in the first two days of cellular development, with lesser standard deviations. Nonsignificant differences were found between the automatic and manual results in all culture days. Conclusions. The proposed method introduces a series of advantages related to its intuitive use and accuracy, making the technique suitable to images with different lighting characteristics and allowing a reliable comparison between different researchers.

  4. Imaging cardiomyocytes in intact tissue with a remote focusing microscope

    Science.gov (United States)

    Corbett, A. D.; Burton, R. A. B.; Bub, G.; Wilson, T.

    2015-03-01

    In cardiac imaging, the spacing between sub-cellular sarcomere structures is of great importance to physiologists in understanding muscle design and performance. Making accurate measurements of the sarcomere length (SL) presents a significant imaging challenge owing to the size of the SL (~2μm) and its naturally low variability (pathological models of chronic hypertension. As well as improving measurement precision, the distribution of α across the field of view provides additional structural information which can be related to disease morphology. To validate this new imaging protocol, the value ofα calculated from the oblique planes provided the input to a rigid model cell which was used to predict the appearance of the cell in the conventional focal plane. The comparison of the model to the image data provided a confidence metric for our measurements. Finally, by considering the optical transfer function, the range of cell orientations for which the method is valid could be calculated.

  5. Automated Analysis of Microscopic Images of Isolated Pancreatic Islets

    Czech Academy of Sciences Publication Activity Database

    Habart, D.; Švihlík, J.; Schier, Jan; Cahová, M.; Girman, P.; Zacharovová, K.; Berková, Z.; Kříž, J.; Fabryová, E.; Kosinová, L.; Papáčková, Z.; Kybic, J.; Saudek, F.

    2016-01-01

    Roč. 25, č. 12 (2016), s. 2145-2156 ISSN 0963-6897 Grant - others:GA ČR(CZ) GA14-10440S Institutional support: RVO:67985556 Keywords : enumeration of islets * image processing * image segmentation * islet transplantation * machine-learning * quality control Subject RIV: IN - Informatics, Computer Science Impact factor: 3.006, year: 2016 http://library.utia.cas.cz/separaty/2016/ZOI/schier-0465945.pdf

  6. TRANSMISSION ION CHANNELING IMAGES OF CRYSTAL DEFECTS

    NARCIS (Netherlands)

    KING, PJC; BREESE, MBH; WILSHAW, PR; SMULDERS, PJM; GRIME, GW

    This paper demonstrates how images of crystal defects can be produced using ion channeling. A focused, scanned beam of MeV protons from the University of Oxford Nuclear Microprobe has been used. With the beam aligned with a channeling direction of the crystal, protons transmitted through the thinned

  7. Design of an imaging microscope for soft X-ray applications

    Science.gov (United States)

    Hoover, Richard B.; Shealy, David L.; Gabardi, David R.; Walker, Arthur B. C., Jr.; Lindblom, Joakim F.

    1988-01-01

    An imaging soft X-ray microscope with a spatial resolution of 0.1 micron and normal incidence multilayer optics is discussed. The microscope has a Schwarzschild configuration, which consists of two concentric spherical mirrors with radii of curvature which minimize third-order spherical aberration, coma, and astigmatism. The performance of the Stanford/MSFC Cassegrain X-ray telescope and its relevance to the present microscope are addressed. A ray tracing analysis of the optical system indicates that diffraction-limited performance can be expected for an object height of 0.2 mm.

  8. Dual-mode optical microscope based on single-pixel imaging

    OpenAIRE

    Rodríguez Jiménez, Angel David; Clemente Pesudo, Pedro Javier; Tajahuerce, Enrique; Lancis Sáez, Jesús

    2016-01-01

    We demonstrate an inverted microscope that can image specimens in both reflection and transmission modes simultaneously with a single light source. The microscope utilizes a digital micromirror device (DMD) for patterned illumination altogether with two single-pixel photosensors for efficient light detection. The system, a scan-less device with no moving parts, works by sequential projection of a set of binary intensity patterns onto the sample that are codified onto a modified commercial DMD...

  9. Automated and unsupervised detection of malarial parasites in microscopic images

    Directory of Open Access Journals (Sweden)

    Purwar Yashasvi

    2011-12-01

    Full Text Available Abstract Background Malaria is a serious infectious disease. According to the World Health Organization, it is responsible for nearly one million deaths each year. There are various techniques to diagnose malaria of which manual microscopy is considered to be the gold standard. However due to the number of steps required in manual assessment, this diagnostic method is time consuming (leading to late diagnosis and prone to human error (leading to erroneous diagnosis, even in experienced hands. The focus of this study is to develop a robust, unsupervised and sensitive malaria screening technique with low material cost and one that has an advantage over other techniques in that it minimizes human reliance and is, therefore, more consistent in applying diagnostic criteria. Method A method based on digital image processing of Giemsa-stained thin smear image is developed to facilitate the diagnostic process. The diagnosis procedure is divided into two parts; enumeration and identification. The image-based method presented here is designed to automate the process of enumeration and identification; with the main advantage being its ability to carry out the diagnosis in an unsupervised manner and yet have high sensitivity and thus reducing cases of false negatives. Results The image based method is tested over more than 500 images from two independent laboratories. The aim is to distinguish between positive and negative cases of malaria using thin smear blood slide images. Due to the unsupervised nature of method it requires minimal human intervention thus speeding up the whole process of diagnosis. Overall sensitivity to capture cases of malaria is 100% and specificity ranges from 50-88% for all species of malaria parasites. Conclusion Image based screening method will speed up the whole process of diagnosis and is more advantageous over laboratory procedures that are prone to errors and where pathological expertise is minimal. Further this method

  10. Microscopic approach in Inelastic Heavy-Ions Scattering with Excitation of Nuclear Collective States

    International Nuclear Information System (INIS)

    Lukyanov, K.V.; Zemlyanya, E.V.; Khtina, I.N.; Lukyanov, V.K; Metawe, Z.; Hanna, K.M.

    2008-01-01

    In the density distribution of a deformed target-nucleus,the spherical λ = 0 and the deformed λ = 2 parts were considered. On this basis, the corresponding potential parts U 0 and U i nt(2) of a double-folding microscopic nucleus-nucleus optical potential are obtained. Then, for these potentials and by using the coupled- channel technique (ECIS), the elastic and inelastic amplitudes are calculated for 17 O heavy ions scattering on 2 + collective excited stat of various target nuclei. Besides,the same cross-sections are calculated in the frame of an adiabatic approach of the eikonal approximation, where the inelastic amplitude is the linear function of U i nt (2).Both the obtained results are compared with the experimental data, and also discus their efficiency in predicting the deformation parameters of nuclei

  11. Atomic force microscope image contrast mechanisms on supported lipid bilayers.

    Science.gov (United States)

    Schneider, J; Dufrêne, Y F; Barger, W R; Lee, G U

    2000-08-01

    This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures onto a monolayer of DSPE show an abrupt breakthrough event at a repeatable, material-dependent force. The breakthrough force for DSPE and MGDG is sizable, whereas the breakthrough force for DOPE is too small to measure accurately. Contact-mode AFM images on 1:1 mixed monolayers of DSPE/DOPE and MGDG/DOPE have a high topographic contrast at loads between the breakthrough force of each phase, and a low topographic contrast at loads above the breakthrough force of both phases. Frictional contrast is inverted and magnified at loads above the breakthrough force of both phases. These results emphasize the important role that surface forces and mechanics can play in imaging multicomponent biomembranes with AFM.

  12. A review of transmission electron microscopes with in situ ion irradiation

    Science.gov (United States)

    Hinks, J. A.

    2009-12-01

    Transmission electron microscopy (TEM) with in situ ion irradiation is unique amongst experimental techniques in allowing the direct observation of the internal microstructure of materials on the nanoscale whilst they are being subjected to bombardment with energetic particles. Invaluable insights into the underlying atomistic processes at work can be gained through direct investigation of radiation induced and enhanced effects such as: phase changes and segregation; mechanical and structural changes; atomic/layer mixing and chemical disorder; compositional changes; chemical reactions; grain growth and shrinkage; precipitation and dissolution; defect/bubble formation, growth, motion, coalescence, removal and destruction; ionisation; diffusion; and collision cascades. The experimental results obtained can be used to validate the predictions of computational models which in turn can elucidate the mechanisms behind the phenomena seen in the microscope. It is 50 years since the first TEM observations of in situ ion irradiation were made by D.W. Pashley, A.E.B. Presland and J.W. Menter at the Tube Investment Laboratories in Cambridge, United Kingdom and 40 years since the first interfacing of an ion beam system with a TEM by P.A. Thackery, R.S. Nelson and H.C. Sansom at the Atomic Energy Research Establishment at Harwell, United Kingdom. In that time the field has grown with references in the literature to around thirty examples of such facilities. This paper gives an overview of the importance of the technique, especially with regard to the current challenges faced in understanding radiation damage in nuclear environments; a description of some of the important construction elements and design considerations of TEMs with in situ ion irradiation; a brief history of the development of this type of instrument; a summary of the facilities built around the world over the last half century; and finally a focus on the instruments in operation today.

  13. A universal fluid cell for the imaging of biological specimens in the atomic force microscope.

    Science.gov (United States)

    Kasas, Sandor; Radotic, Ksenja; Longo, Giovanni; Saha, Bashkar; Alonso-Sarduy, Livan; Dietler, Giovanni; Roduit, Charles

    2013-04-01

    Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set-up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Copyright © 2013 Wiley Periodicals, Inc.

  14. Soft X-ray imaging with axisymmetry microscope and electronic readout

    International Nuclear Information System (INIS)

    Sauneuf, A.; Cavailler, C.; Henry, Ph.; Launspach, J.; Mascureau, J. de; Rostaing, M.

    1984-11-01

    An axisymmetric microscope with 10 X magnification has been constructed; its resolution has been measured using severals grids, backlighted by an X-ray source and found to be near 25 μm. So it could be used to make images of laser driven plasmas in the soft X-ray region. In order to see rapidly those images we have associated it with a new detector. It is a small image converter tube with a soft X-ray photocathode and a P20 phosphor deposited on an optic fiber plate. The electronic image appearing on the screen is read by a CCD working in the spectral range. An electronic image readout chain, which is identical to those we use with streak cameras, then processes automatically and immediatly the images given by the microscope

  15. Microscopic imaging ellipsometry of submicron-scale bacterial cells

    African Journals Online (AJOL)

    MIE can detect very thin layers and measure their precise ... for future applications especially in the field of biological imaging since it ... a quarter-wave plate and rotates with the range of angles from 5º ... calibrated first by using a flat substrate like glass,. Si, or Au. .... more sensitive detection of the boundary of the structure ...

  16. Removal of Vesicle Structures from Transmission Electron Microscope Images

    DEFF Research Database (Denmark)

    Jensen, Katrine Hommelhoff; Sigworth, Fred; Brandt, Sami Sebastian

    2015-01-01

    In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruct...

  17. In situ atomic force microscope imaging of supported lipid bilayers

    DEFF Research Database (Denmark)

    Kaasgaard, Thomas; Leidy, Chad; Ipsen, John Hjorth

    2001-01-01

    In situ AFM images of phospholipase A/sub 2/ (PLA/sub 2/) hydrolysis of mica-supported one- and two-component lipid bilayers are presented. For one-component DPPC bilayers an enhanced enzymatic activity is observed towards preexisting defects in the bilayer. Phase separation is observed in two-co...

  18. 3D microscopic imaging and evaluation of tubular tissue architecture

    Czech Academy of Sciences Publication Activity Database

    Janáček, Jiří; Čapek, Martin; Michálek, Jan; Karen, Petr; Kubínová, Lucie

    2014-01-01

    Roč. 63, Suppl.1 (2014), S49-S55 ISSN 0862-8408 R&D Projects: GA MŠk(CZ) LH13028; GA ČR(CZ) GA13-12412S Institutional support: RVO:67985823 Keywords : confocal microscopy * capillaries * brain * skeletal muscle * image analysis Subject RIV: EA - Cell Biology Impact factor: 1.293, year: 2014

  19. Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules.

    Science.gov (United States)

    Elliott, Jonathan T; Dsouza, Alisha V; Marra, Kayla; Pogue, Brian W; Roberts, David W; Paulsen, Keith D

    2016-09-01

    Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system specifications are characterized, and in vivo efficacy of the system in detecting ABY-029 is evaluated in a rat orthotopic glioma model following microdose injections, showing the suitability of the device for microdose phase 0 clinical trials.

  20. Simulation of high-resolution X-ray microscopic images for improved alignment

    International Nuclear Information System (INIS)

    Song Xiangxia; Zhang Xiaobo; Liu Gang; Cheng Xianchao; Li Wenjie; Guan Yong; Liu Ying; Xiong Ying; Tian Yangchao

    2011-01-01

    The introduction of precision optical elements to X-ray microscopes necessitates fine realignment to achieve optimal high-resolution imaging. In this paper, we demonstrate a numerical method for simulating image formation that facilitates alignment of the source, condenser, objective lens, and CCD camera. This algorithm, based on ray-tracing and Rayleigh-Sommerfeld diffraction theory, is applied to simulate the X-ray microscope beamline U7A of National Synchrotron Radiation Laboratory (NSRL). The simulations and imaging experiments show that the algorithm is useful for guiding experimental adjustments. Our alignment simulation method is an essential tool for the transmission X-ray microscope (TXM) with optical elements and may also be useful for the alignment of optical components in other modes of microscopy.

  1. A multiphoton laser scanning microscope setup for transcranial in vivo brain imaging on mice

    Science.gov (United States)

    Nase, Gabriele; Helm, P. Johannes; Reppen, Trond; Ottersen, Ole Petter

    2005-12-01

    We describe a multiphoton laser scanning microscope setup for transcranial in vivo brain imaging in mice. The modular system is based on a modified industrial standard Confocal Scanning Laser Microscope (CSLM) and is assembled mainly from commercially available components. A special multifunctional stage, which is optimized for both laser scanning microscopic observation and preparative animal surgery, has been developed and built. The detection unit includes a highly efficient photomultiplier tube installed in a Peltier-cooled thermal box shielding the detector from changes in room temperature and from distortions caused by external electromagnetic fields. The images are recorded using a 12-bit analog-to-digital converter. Depending on the characteristics of the staining, individual nerve cells can be imaged down to at least 100μm below the intact cranium and down to at least 200μm below the opened cranium.

  2. NMR imaging: A 'chemical' microscope for coal analysis

    International Nuclear Information System (INIS)

    French, D.C.; Dieckman, S.L.; Gopalsami, N.; Botto, R.E.

    1991-01-01

    This paper presents a new three-dimensional (3-D) nuclear magnetic resonance (NMR) imaging technique for spatially mapping proton distributions in whole coals and solvent-swollen coal samples. The technique is based on a 3-D back-projection protocol for data acquisition, and a reconstruction technique based on 3-D Radon transform inversion. In principle, the 3-D methodology provides higher spatial resolution of solid materials than is possible with conventional slice-selection protocols. The applicability of 3-D NMR imaging has been demonstrated by mapping the maceral phases in Utah Blind Canyon (APCS number-sign 6) coal and the distribution of mobile phases in Utah coal swollen with deuterated and protic pyridine. 7 refs., 5 figs

  3. Automatic analysis of microscopic images of red blood cell aggregates

    Science.gov (United States)

    Menichini, Pablo A.; Larese, Mónica G.; Riquelme, Bibiana D.

    2015-06-01

    Red blood cell aggregation is one of the most important factors in blood viscosity at stasis or at very low rates of flow. The basic structure of aggregates is a linear array of cell commonly termed as rouleaux. Enhanced or abnormal aggregation is seen in clinical conditions, such as diabetes and hypertension, producing alterations in the microcirculation, some of which can be analyzed through the characterization of aggregated cells. Frequently, image processing and analysis for the characterization of RBC aggregation were done manually or semi-automatically using interactive tools. We propose a system that processes images of RBC aggregation and automatically obtains the characterization and quantification of the different types of RBC aggregates. Present technique could be interesting to perform the adaptation as a routine used in hemorheological and Clinical Biochemistry Laboratories because this automatic method is rapid, efficient and economical, and at the same time independent of the user performing the analysis (repeatability of the analysis).

  4. Precision crystal alignment for high-resolution electron microscope imaging

    International Nuclear Information System (INIS)

    Wood, G.J.; Beeching, M.J.

    1990-01-01

    One of the more difficult tasks involved in obtaining quality high-resolution electron micrographs is the precise alignment of a specimen into the required zone. The current accepted procedure, which involves changing to diffraction mode and searching for symmetric point diffraction pattern, is insensitive to small amounts of misalignment and at best qualitative. On-line analysis of the fourier space representation of the image, both for determining and correcting crystal tilt, is investigated. 8 refs., 42 figs

  5. Direct microscopic image and measurement of the atomization process of a port fuel injector

    International Nuclear Information System (INIS)

    Esmail, Mohamed; Kawahara, Nobuyuki; Tomita, Eiji; Sumida, Mamoru

    2010-01-01

    The main objective of this study is to observe and investigate the phenomena of atomization, i.e. the fuel break-up process very close to the nozzle exit of a practical port fuel injector (PFI). In order to achieve this objective, direct microscopic images of the atomization process were obtained using an ultra-high-speed video camera that could record 102 frames at rates of up to 1 Mfps, coupled with a long-distance microscope and Barlow lens. The experiments were carried out using a PFI in a closed chamber at atmospheric pressure. Time-series images of the spray behaviour were obtained with a high temporal resolution using backlighting. The direct microscopic images of a liquid column break-up were compared with experimental results from laser-induced exciplex fluorescence (LIEF), and the wavelength obtained from the experimental results compared with that predicated from the Kelvin–Helmholtz break-up model. The droplet size diameters from a ligament break-up were compared with results predicated from Weber's analysis. Furthermore, experimental results of the mean droplet diameter from a direct microscopic image were compared with the results obtained from phase Doppler anemometry (PDA) experimental results. Three conclusions were obtained from this study. The atomization processes and detailed characterizations of the break-up of a liquid column were identified; the direct microscopic image results were in good agreement with the results obtained from LIEF, experimental results of the wavelength were in good agreement with those from the Kelvin–Helmholtz break-up model. The break-up process of liquid ligaments into droplets was investigated, and Weber's analysis of the predicated droplet diameter from ligament break-up was found to be applicable only at larger wavelengths. Finally, the direct microscopic image method and PDA method give qualitatively similar trends for droplet size distribution and quantitatively similar values of Sauter mean diameter

  6. Direct microscopic image and measurement of the atomization process of a port fuel injector

    Science.gov (United States)

    Esmail, Mohamed; Kawahara, Nobuyuki; Tomita, Eiji; Sumida, Mamoru

    2010-07-01

    The main objective of this study is to observe and investigate the phenomena of atomization, i.e. the fuel break-up process very close to the nozzle exit of a practical port fuel injector (PFI). In order to achieve this objective, direct microscopic images of the atomization process were obtained using an ultra-high-speed video camera that could record 102 frames at rates of up to 1 Mfps, coupled with a long-distance microscope and Barlow lens. The experiments were carried out using a PFI in a closed chamber at atmospheric pressure. Time-series images of the spray behaviour were obtained with a high temporal resolution using backlighting. The direct microscopic images of a liquid column break-up were compared with experimental results from laser-induced exciplex fluorescence (LIEF), and the wavelength obtained from the experimental results compared with that predicated from the Kelvin-Helmholtz break-up model. The droplet size diameters from a ligament break-up were compared with results predicated from Weber's analysis. Furthermore, experimental results of the mean droplet diameter from a direct microscopic image were compared with the results obtained from phase Doppler anemometry (PDA) experimental results. Three conclusions were obtained from this study. The atomization processes and detailed characterizations of the break-up of a liquid column were identified; the direct microscopic image results were in good agreement with the results obtained from LIEF, experimental results of the wavelength were in good agreement with those from the Kelvin-Helmholtz break-up model. The break-up process of liquid ligaments into droplets was investigated, and Weber's analysis of the predicated droplet diameter from ligament break-up was found to be applicable only at larger wavelengths. Finally, the direct microscopic image method and PDA method give qualitatively similar trends for droplet size distribution and quantitatively similar values of Sauter mean diameter.

  7. Internal scanning method as unique imaging method of optical vortex scanning microscope

    Science.gov (United States)

    Popiołek-Masajada, Agnieszka; Masajada, Jan; Szatkowski, Mateusz

    2018-06-01

    The internal scanning method is specific for the optical vortex microscope. It allows to move the vortex point inside the focused vortex beam with nanometer resolution while the whole beam stays in place. Thus the sample illuminated by the focused vortex beam can be scanned just by the vortex point. We show that this method enables high resolution imaging. The paper presents the preliminary experimental results obtained with the first basic image recovery procedure. A prospect of developing more powerful tools for topography recovery with the optical vortex scanning microscope is discussed shortly.

  8. New method for thickness determination and microscopic imaging of graphene-like two-dimensional materials

    International Nuclear Information System (INIS)

    Qin Xudong; Chen Yonghai; Liu Yu; Zhu Laipan; Li Yuan; Wu Qing; Huang Wei

    2016-01-01

    We employed the microscopic reflectance difference spectroscopy (micro-RDS) to determine the layer-number and microscopically image the surface topography of graphene and MoS 2 samples. The contrast image shows the efficiency and reliability of this new clipping technique. As a low-cost, quantifiable, no-contact and non-destructive method, it is not concerned with the characteristic signal of certain materials and can be applied to arbitrary substrates. Therefore it is a perfect candidate for characterizing the thickness of graphene-like two-dimensional materials. (paper)

  9. A widefield fluorescence microscope with a linear image sensor for image cytometry of biospecimens: Considerations for image quality optimization

    Energy Technology Data Exchange (ETDEWEB)

    Hutcheson, Joshua A.; Majid, Aneeka A.; Powless, Amy J.; Muldoon, Timothy J., E-mail: tmuldoon@uark.edu [Department of Biomedical Engineering, University of Arkansas, 120 Engineering Hall, Fayetteville, Arkansas 72701 (United States)

    2015-09-15

    Linear image sensors have been widely used in numerous research and industry applications to provide continuous imaging of moving objects. Here, we present a widefield fluorescence microscope with a linear image sensor used to image translating objects for image cytometry. First, a calibration curve was characterized for a custom microfluidic chamber over a span of volumetric pump rates. Image data were also acquired using 15 μm fluorescent polystyrene spheres on a slide with a motorized translation stage in order to match linear translation speed with line exposure periods to preserve the image aspect ratio. Aspect ratios were then calculated after imaging to ensure quality control of image data. Fluorescent beads were imaged in suspension flowing through the microfluidics chamber being pumped by a mechanical syringe pump at 16 μl min{sup −1} with a line exposure period of 150 μs. The line period was selected to acquire images of fluorescent beads with a 40 dB signal-to-background ratio. A motorized translation stage was then used to transport conventional glass slides of stained cellular biospecimens. Whole blood collected from healthy volunteers was stained with 0.02% (w/v) proflavine hemisulfate was imaged to highlight leukocyte morphology with a 1.56 mm × 1.28 mm field of view (1540 ms total acquisition time). Oral squamous cells were also collected from healthy volunteers and stained with 0.01% (w/v) proflavine hemisulfate to demonstrate quantifiable subcellular features and an average nuclear to cytoplasmic ratio of 0.03 (n = 75), with a resolution of 0.31 μm pixels{sup −1}.

  10. New light on ion channel imaging by total internal reflection fluorescence (TIRF) microscopy.

    Science.gov (United States)

    Yamamura, Hisao; Suzuki, Yoshiaki; Imaizumi, Yuji

    2015-05-01

    Ion channels play pivotal roles in a wide variety of cellular functions; therefore, their physiological characteristics, pharmacological responses, and molecular structures have been extensively investigated. However, the mobility of an ion channel itself in the cell membrane has not been examined in as much detail. A total internal reflection fluorescence (TIRF) microscope allows fluorophores to be imaged in a restricted region within an evanescent field of less than 200 nm from the interface of the coverslip and plasma membrane in living cells. Thus the TIRF microscope is useful for selectively visualizing the plasmalemmal surface and subplasmalemmal zone. In this review, we focused on a single-molecule analysis of the dynamic movement of ion channels in the plasma membrane using TIRF microscopy. We also described two single-molecule imaging techniques under TIRF microscopy: fluorescence resonance energy transfer (FRET) for the identification of molecules that interact with ion channels, and subunit counting for the determination of subunit stoichiometry in a functional channel. TIRF imaging can also be used to analyze spatiotemporal Ca(2+) events in the subplasmalemma. Single-molecule analyses of ion channels and localized Ca(2+) signals based on TIRF imaging provide beneficial pharmacological and physiological information concerning the functions of ion channels. Copyright © 2015 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

  11. Imaging of a large collection of human embryo using a super-parallel MR microscope

    International Nuclear Information System (INIS)

    Matsuda, Yoshimasa; Ono, Shinya; Otake, Yosuke; Handa, Shinya; Kose, Katsumi; Haishi, Tomoyuki; Yamada, Shigeto; Uwabe, Chikako; Shiota, Kohei

    2007-01-01

    Using 4 and 8-channel super-parallel magnetic resonance (MR) microscopes with a horizontal bore 2.34T superconducting magnet developed for 3-dimensional MR microscopy of the large Kyoto Collection of Human Embryos, we acquired T 1 -weighted 3D images of 1204 embryos at a spatial resolution of (40 μm) 3 to (150 μm) 3 in about 2 years. Similarity of image contrast between the T 1 -weighted images and stained anatomical sections indicated that T 1 -weighted 3D images could be used for an anatomical 3D image database for human embryology. (author)

  12. Confocal multispot microscope for fast and deep imaging in semicleared tissues

    Science.gov (United States)

    Adam, Marie-Pierre; Müllenbroich, Marie Caroline; Di Giovanna, Antonino Paolo; Alfieri, Domenico; Silvestri, Ludovico; Sacconi, Leonardo; Pavone, Francesco Saverio

    2018-02-01

    Although perfectly transparent specimens are imaged faster with light-sheet microscopy, less transparent samples are often imaged with two-photon microscopy leveraging its robustness to scattering; however, at the price of increased acquisition times. Clearing methods that are capable of rendering strongly scattering samples such as brain tissue perfectly transparent specimens are often complex, costly, and time intensive, even though for many applications a slightly lower level of tissue transparency is sufficient and easily achieved with simpler and faster methods. Here, we present a microscope type that has been geared toward the imaging of semicleared tissue by combining multispot two-photon excitation with rolling shutter wide-field detection to image deep and fast inside semicleared mouse brain. We present a theoretical and experimental evaluation of the point spread function and contrast as a function of shutter size. Finally, we demonstrate microscope performance in fixed brain slices by imaging dendritic spines up to 400-μm deep.

  13. First images from the Stanford tabletop scanning soft x-ray microscope

    International Nuclear Information System (INIS)

    Trail, J.A.; Byer, R.L.

    1988-01-01

    The authors have constructed a scanning soft x-ray microscope which uses a laser-produced plasma as the soft x-ray source and normal incidence multilayer coated mirrors in a Schwarzschild configuration as the focusing optics. The microscope operates at a wavelength of 140 angstrom, has a spatial resolution of 0.5 μm, and has a soft x-ray photon flux through the focus of 10 4 s -1 when operated with only 170 mW of average laser power. The microscope is compact; the complete system, including the laser, fits on a single optical table. In this paper they describe the microscope and present images of metallic microstructures

  14. The plant virus microscope image registration method based on mismatches removing.

    Science.gov (United States)

    Wei, Lifang; Zhou, Shucheng; Dong, Heng; Mao, Qianzhuo; Lin, Jiaxiang; Chen, Riqing

    2016-01-01

    The electron microscopy is one of the major means to observe the virus. The view of virus microscope images is limited by making specimen and the size of the camera's view field. To solve this problem, the virus sample is produced into multi-slice for information fusion and image registration techniques are applied to obtain large field and whole sections. Image registration techniques have been developed in the past decades for increasing the camera's field of view. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Alternatively, the methods are conceived just to provide visually pleasant registration for high overlap ratio image sequence. This work presents a method for virus microscope image registration acquired with detailed visual information and subpixel accuracy, even when overlap ratio of image sequence is 10% or less. The method proposed focus on the correspondence set and interimage transformation. A mismatch removal strategy is proposed by the spatial consistency and the components of keypoint to enrich the correspondence set. And the translation model parameter as well as tonal inhomogeneities is corrected by the hierarchical estimation and model select. In the experiments performed, we tested different registration approaches and virus images, confirming that the translation model is not always stationary, despite the fact that the images of the sample come from the same sequence. The mismatch removal strategy makes building registration of virus microscope images at subpixel accuracy easier and optional parameters for building registration according to the hierarchical estimation and model select strategies make the proposed method high precision and reliable for low overlap ratio image sequence. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

    Science.gov (United States)

    Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

    2015-01-01

    Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

  16. Focal dynamics of multiple filaments: Microscopic imaging and reconstruction

    International Nuclear Information System (INIS)

    Kiran, P. Prem; Bagchi, Suman; Kumar, G. Ravindra; Krishnan, Siva Rama; Arnold, C. L.; Couairon, A.

    2010-01-01

    We observe the complete dynamics of the propagation of very intense, femtosecond laser pulses in air under tight focusing conditions via direct imaging of the entire interaction zone. The whole life history of the focused pulses is then reconstructed by means of numerical simulations. We show that beam breakup leads to a dual-rate increase in filament numbers with laser power. Linearly and circularly polarized pulses give rise to beam breakup and fusion governed by external focusing conditions. For tight focusing conditions, intensity saturation due to plasma generation and nonlinear losses does not limit the intensity growth, thereby giving access to a new propagation regime featured by an efficient laser energy deposition in fully ionized air and intense 10 15 W/cm 2 pulses at the focus.

  17. Improvements in low-cost label-free QPI microscope for live cell imaging

    Science.gov (United States)

    Seniya, C.; Towers, C. E.; Towers, D. P.

    2017-07-01

    This paper reports an improvement in the development of a low-cost QPI microscope offering new capabilities in term of phase measurement accuracy for label-free live samples in the longer term (i.e., hours to days). The spatially separated scattered and non-scattered image light fields are reshaped in the Fourier plane and modulated to form an interference image at a CCD camera. The apertures that enable these two beams to be generated have been optimised by means of laser-cut apertures placed on the mirrors of a Michelson interferometer and has improved the phase measuring and reconstruction capability of the QPI microscope. The microscope was tested with transparent onion cells as an object of interest.

  18. Fast processing of microscopic images using object-based extended depth of field.

    Science.gov (United States)

    Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Pannarut, Montri; Shaw, Philip J; Tongsima, Sissades

    2016-12-22

    Microscopic analysis requires that foreground objects of interest, e.g. cells, are in focus. In a typical microscopic specimen, the foreground objects may lie on different depths of field necessitating capture of multiple images taken at different focal planes. The extended depth of field (EDoF) technique is a computational method for merging images from different depths of field into a composite image with all foreground objects in focus. Composite images generated by EDoF can be applied in automated image processing and pattern recognition systems. However, current algorithms for EDoF are computationally intensive and impractical, especially for applications such as medical diagnosis where rapid sample turnaround is important. Since foreground objects typically constitute a minor part of an image, the EDoF technique could be made to work much faster if only foreground regions are processed to make the composite image. We propose a novel algorithm called object-based extended depths of field (OEDoF) to address this issue. The OEDoF algorithm consists of four major modules: 1) color conversion, 2) object region identification, 3) good contrast pixel identification and 4) detail merging. First, the algorithm employs color conversion to enhance contrast followed by identification of foreground pixels. A composite image is constructed using only these foreground pixels, which dramatically reduces the computational time. We used 250 images obtained from 45 specimens of confirmed malaria infections to test our proposed algorithm. The resulting composite images with all in-focus objects were produced using the proposed OEDoF algorithm. We measured the performance of OEDoF in terms of image clarity (quality) and processing time. The features of interest selected by the OEDoF algorithm are comparable in quality with equivalent regions in images processed by the state-of-the-art complex wavelet EDoF algorithm; however, OEDoF required four times less processing time. This

  19. Helium ion microscopy of graphene: beam damage, image quality and edge contrast

    International Nuclear Information System (INIS)

    Fox, D; Zhou, Y B; O’Neill, A; Wang, J J; Coleman, J N; Donegan, J F; Zhang, H Z; Kumar, S; Duesberg, G S

    2013-01-01

    A study to analyse beam damage, image quality and edge contrast in the helium ion microscope (HIM) has been undertaken. The sample investigated was graphene. Raman spectroscopy was used to quantify the disorder that can be introduced into the graphene as a function of helium ion dose. The effects of the dose on both freestanding and supported graphene were compared. These doses were then correlated directly to image quality by imaging graphene flakes at high magnification. It was found that a high magnification image with a good signal to noise ratio will introduce very significant sample damage. A safe imaging dose of the order of 10 13 He + cm −2 was established, with both graphene samples becoming highly defective at doses over 5 × 10 14 He + cm −2 . The edge contrast of a freestanding graphene flake imaged in the HIM was then compared with the contrast of the same flake observed in a scanning electron microscope and a transmission electron microscope. Very strong edge sensitivity was observed in the HIM. This enhanced edge sensitivity over the other techniques investigated makes the HIM a powerful nanoscale dimensional metrology tool, with the capability of both fabricating and imaging features with sub-nanometre resolution. (paper)

  20. Imaging of surface plasmon polariton interference using phase-sensitive scanning tunneling microscope

    NARCIS (Netherlands)

    Jose, J.; Segerink, Franciscus B.; Korterik, Jeroen P.; Herek, Jennifer Lynn; Offerhaus, Herman L.

    2011-01-01

    We report the surface plasmon polariton interference, generated via a ‘buried’ gold grating, and imaged using a phase-sensitive Photon Scanning Tunneling Microscope (PSTM). The phase-resolved PSTM measurement unravels the complex surface plasmon polariton interference fields at the gold-air

  1. Chemical imaging of cotton fibers using an infrared microscope and a focal-plane array detector

    Science.gov (United States)

    In this presentation, the chemical imaging of cotton fibers with an infrared microscope and a Focal-Plane Array (FPA) detector will be discussed. Infrared spectroscopy can provide us with information on the structure and quality of cotton fibers. In addition, FPA detectors allow for simultaneous spe...

  2. Classification of gram-positive and gram-negative foodborne pathogenic bacteria with hyperspectral microscope imaging

    Science.gov (United States)

    Optical method with hyperspectral microscope imaging (HMI) has potential for identification of foodborne pathogenic bacteria from microcolonies rapidly with a cell level. A HMI system that provides both spatial and spectral information could be an effective tool for analyzing spectral characteristic...

  3. Rapid identification of salmonella serotypes with stereo and hyperspectral microscope imaging Methods

    Science.gov (United States)

    The hyperspectral microscope imaging (HMI) method can reduce detection time within 8 hours including incubation process. The early and rapid detection with this method in conjunction with the high throughput capabilities makes HMI method a prime candidate for implementation for the food industry. Th...

  4. High resolution imaging of dielectric surfaces with an evanescent field optical microscope

    NARCIS (Netherlands)

    van Hulst, N.F.; Segerink, Franciscus B.; Bölger, B.

    1992-01-01

    An evanescent field optical microscope (EFOM) is presented which employs frustrated total internal reflection o­n a localized scale by scanning a dielectric tip in close proximity to a sample surface. High resolution images of dielectric gratings and spheres containing both topographic and

  5. Acousto-Optic Tunable Filter Hyperspectral Microscope Imaging Method for Characterizing Spectra from Foodborne Pathogens.

    Science.gov (United States)

    Hyperspectral microscope imaging (HMI) method, which provides both spatial and spectral characteristics of samples, can be effective for foodborne pathogen detection. The acousto-optic tunable filter (AOTF)-based HMI method can be used to characterize spectral properties of biofilms formed by Salmon...

  6. MRT letter: Guided filtering of image focus volume for 3D shape recovery of microscopic objects.

    Science.gov (United States)

    Mahmood, Muhammad Tariq

    2014-12-01

    In this letter, a shape from focus (SFF) method is proposed that utilizes the guided image filtering to enhance the image focus volume efficiently. First, image focus volume is computed using a conventional focus measure. Then each layer of image focus volume is filtered using guided filtering. In this work, the all-in-focus image, which can be obtained from the initial focus volume, is used as guidance image. Finally, improved depth map is obtained from the filtered image focus volume by maximizing the focus measure along the optical axis. The proposed SFF method is efficient and provides better depth maps. The improved performance is highlighted by conducting several experiments using image sequences of simulated and real microscopic objects. The comparative analysis demonstrates the effectiveness of the proposed SFF method. © 2014 Wiley Periodicals, Inc.

  7. Atomic imaging of an InSe single-crystal surface with atomic force microscope

    OpenAIRE

    Uosaki, Kohei; Koinuma, Michio

    1993-01-01

    The atomic force microscope was employed to observed in air the surface atomic structure of InSe, one of III-VI compound semiconductors with layered structures. Atomic arrangements were observed in both n-type and p-type materials. The observed structures are in good agreement with those expected from bulk crystal structures. The atomic images became less clear by repeating the imaging process. Wide area imaging after the imaging of small area clearly showed that a mound was created at the sp...

  8. SUPERVISED AUTOMATIC HISTOGRAM CLUSTERING AND WATERSHED SEGMENTATION. APPLICATION TO MICROSCOPIC MEDICAL COLOR IMAGES

    Directory of Open Access Journals (Sweden)

    Olivier Lezoray

    2011-05-01

    Full Text Available In this paper, an approach to the segmentation of microscopic color images is addressed, and applied to medical images. The approach combines a clustering method and a region growing method. Each color plane is segmented independently relying on a watershed based clustering of the plane histogram. The marginal segmentation maps intersect in a label concordance map. The latter map is simplified based on the assumption that the color planes are correlated. This produces a simplified label concordance map containing labeled and unlabeled pixels. The formers are used as an image of seeds for a color watershed. This fast and robust segmentation scheme is applied to several types of medical images.

  9. Inverted light-sheet microscope for imaging mouse pre-implantation development.

    Science.gov (United States)

    Strnad, Petr; Gunther, Stefan; Reichmann, Judith; Krzic, Uros; Balazs, Balint; de Medeiros, Gustavo; Norlin, Nils; Hiiragi, Takashi; Hufnagel, Lars; Ellenberg, Jan

    2016-02-01

    Despite its importance for understanding human infertility and congenital diseases, early mammalian development has remained inaccessible to in toto imaging. We developed an inverted light-sheet microscope that enabled us to image mouse embryos from zygote to blastocyst, computationally track all cells and reconstruct a complete lineage tree of mouse pre-implantation development. We used this unique data set to show that the first cell fate specification occurs at the 16-cell stage.

  10. Switched capacitor charge pump used for low-distortion imaging in atomic force microscope.

    Science.gov (United States)

    Zhang, Jie; Zhang, Lian Sheng; Feng, Zhi Hua

    2015-01-01

    The switched capacitor charge pump (SCCP) is an effective method of linearizing charges on piezoelectric actuators and therefore constitute a significant approach to nano-positioning. In this work, it was for the first time implemented in an atomic force microscope for low-distortion imaging. Experimental results showed that the image quality was improved evidently under the SCCP drive compared with that under traditional linear voltage drive. © Wiley Periodicals, Inc.

  11. Excitation-scanning hyperspectral imaging system for microscopic and endoscopic applications

    Science.gov (United States)

    Mayes, Sam A.; Leavesley, Silas J.; Rich, Thomas C.

    2016-04-01

    Current microscopic and endoscopic technologies for cancer screening utilize white-light illumination sources. Hyper-spectral imaging has been shown to improve sensitivity while retaining specificity when compared to white-light imaging in both microscopy and in vivo imaging. However, hyperspectral imaging methods have historically suffered from slow acquisition times due to the narrow bandwidth of spectral filters. Often minutes are required to gather a full image stack. We have developed a novel approach called excitation-scanning hyperspectral imaging that provides 2-3 orders of magnitude increased signal strength. This reduces acquisition times significantly, allowing for live video acquisition. Here, we describe a preliminary prototype excitation-scanning hyperspectral imaging system that can be coupled with endoscopes or microscopes for hyperspectral imaging of tissues and cells. Our system is comprised of three subsystems: illumination, transmission, and imaging. The illumination subsystem employs light-emitting diode arrays to illuminate at different wavelengths. The transmission subsystem utilizes a unique geometry of optics and a liquid light guide. Software controls allow us to interface with and control the subsystems and components. Digital and analog signals are used to coordinate wavelength intensity, cycling and camera triggering. Testing of the system shows it can cycle 16 wavelengths at as fast as 1 ms per cycle. Additionally, more than 18% of the light transmits through the system. Our setup should allow for hyperspectral imaging of tissue and cells in real time.

  12. Three-dimensional phase-contrast X-ray microtomography with scanning–imaging X-ray microscope optics

    International Nuclear Information System (INIS)

    Takeuchi, Akihisa; Uesugi, Kentaro; Suzuki, Yoshio

    2013-01-01

    A novel three-dimensional X-ray microtomographic micro-imaging system which enables simultaneous measurement of differential phase contrast and absorption contrast has been developed. The optical system consists of a scanning microscope with one-dimensional focusing device and an imaging microscope with one-dimensional objective. A three-dimensional (3D) X-ray tomographic micro-imaging system has been developed. The optical system is based on a scanning–imaging X-ray microscope (SIXM) optics, which is a hybrid system consisting of a scanning microscope optics with a one-dimensional (1D) focusing (line-focusing) device and an imaging microscope optics with a 1D objective. In the SIXM system, each 1D dataset of a two-dimensional (2D) image is recorded independently. An object is illuminated with a line-focused beam. Positional information of the region illuminated by the line-focused beam is recorded with the 1D imaging microscope optics as line-profile data. By scanning the object with the line focus, 2D image data are obtained. In the same manner as for a scanning microscope optics with a multi-pixel detector, imaging modes such as phase contrast and absorption contrast can be arbitrarily configured after the image data acquisition. By combining a tomographic scan method and the SIXM system, quantitative 3D imaging is performed. Results of a feasibility study of the SIXM for 3D imaging are shown

  13. Failure Analysis of Heavy-Ion-Irradiated Schottky Diodes

    Science.gov (United States)

    Casey, Megan C.; Lauenstein, Jean-Marie; Wilcox, Edward P.; Topper, Alyson D.; Campola, Michael J.; Label, Kenneth A.

    2017-01-01

    In this work, we use high- and low-magnitude optical microscope images, infrared camera images, and scanning electron microscope images to identify and describe the failure locations in heavy-ion-irradiated Schottky diodes.

  14. Use of an axisymmetric microscope with electronic readout for collecting soft X-ray images

    International Nuclear Information System (INIS)

    Cavailler, C.; Henry, P.; Launspach, J.; De Mascureau, J.; Millerioux, M.; Rostaing, M.; Sauneuf, R.

    1984-08-01

    The axisymmetric microscope, first discussed by Wolter, provides high resolution and sensitivity for investigating the soft X-ray emission of laser-driven plasmas. Such a device having a 10 X magnification has been constructed. We present a comparison between the images of laser-driven plasmas given by this microscope and by a 10 X pinhole camera. Until now these images were recorded on X-ray film. We have shown that film could be replaced by C.C.D. in a pinhole camera when the photon energy lies within the 1-10 keV range. Below 1 keV the quantum yield is too low so we have used an image converter tube made by RTC. It is a diode-inverter tube with a soft X-ray photocathode and a P20 phosphor deposited on an optic fiber plate. The electronic image appearing on the screen is read by a C.C.D. working in the visible spectral fields. An electronic image readout chain, which is identical to those associated with streak cameras, then processes automatically and immediately the images given by the microscope [fr

  15. Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection

    Science.gov (United States)

    Deng, Yunsheng; Huang, Qimeng; Zhao, Yue; Zhou, Daming; Ying, Cuifeng; Wang, Deqiang

    2017-01-01

    We report a scalable method to fabricate high-quality graphene nanopores for biomolecule detection using a helium ion microscope (HIM). HIM milling shows promising capabilities for precisely controlling the size and shape, and may allow for the potential production of nanopores at wafer scale. Nanopores could be fabricated at different sizes ranging from 5 to 30 nm in diameter in few minutes. Compared with the current solid-state nanopore fabrication techniques, e.g. transmission electron microscopy, HIM is fast. Furthermore, we investigated the exposure-time dependence of graphene nanopore formation: the rate of pore expansion did not follow a simple linear relationship with exposure time, but a fast expansion rate at short exposure time and a slow rate at long exposure time. In addition, we performed biomolecule detection with our patterned graphene nanopore. The ionic current signals induced by 20-base single-stranded DNA homopolymers could be used as a basis for homopolymer differentiation. However, the charge interaction of homopolymer chains with graphene nanopores, and the conformations of homopolymer chains need to be further considered to improve the accuracy of discrimination.

  16. Atom probe field ion microscope study of the range and diffusivity of helium in tungsten

    International Nuclear Information System (INIS)

    Wagner, A.

    1978-08-01

    A time-of-flight (TOF) atom-probe field-ion microscope (FIM) specifically designed for the study of defects in metals is described. With this automated system 600 TOF min -1 can be recorded and analyzed. Performance tests of the instrument demonstrated that (1) the seven isotopes of molybdenum and the five isotopes of tungsten can be clearly resolved; and (2) the concentration and spatial distribution of all constitutents present at levels greater than 0.05 at. % in a W--25 at. % Re, Mo--1.0 at. % Ti, Mo--1.0 at. % Ti--0.08 at. % Zr (TZM), a low swelling stainless steel (LS1A) and a metallic glass (Metglas 2826) can be measured. The effect of the rate of field evaporation on the quantitative atom probe analysis of a Mo--1.0 at. % Ti alloy and a Mo--1.0 at. % Ti--0.08 at. % Zr alloy was investigated. As the field evaporation rate increased the measured Ti concentration was found to also increase. A simple qualitative model was proposed to explain the observation. The spatial distribution of titanium in a fast neutron irradiated Mo--1.0 at. % Ti alloy has been investigated. No evidence of Ti segregation to the voids was detected nor has any evidence of significant resolution of Ti from the TiC precipitates been detected. A small amount of segregation of carbon to a void was detected

  17. Design of a cathodoluminescence image generator using a Raspberry Pi coupled to a scanning electron microscope

    Science.gov (United States)

    Benítez, Alfredo; Santiago, Ulises; Sanchez, John E.; Ponce, Arturo

    2018-01-01

    In this work, an innovative cathodoluminescence (CL) system is coupled to a scanning electron microscope and synchronized with a Raspberry Pi computer integrated with an innovative processing signal. The post-processing signal is based on a Python algorithm that correlates the CL and secondary electron (SE) images with a precise dwell time correction. For CL imaging, the emission signal is collected through an optical fiber and transduced to an electrical signal via a photomultiplier tube (PMT). CL Images are registered in a panchromatic mode and can be filtered using a monochromator connected between the optical fiber and the PMT to produce monochromatic CL images. The designed system has been employed to study ZnO samples prepared by electrical arc discharge and microwave methods. CL images are compared with SE images and chemical elemental mapping images to correlate the emission regions of the sample.

  18. Carbonation of wollastonite(001) competing hydration: microscopic insights from ion spectroscopy and density functional theory.

    Science.gov (United States)

    Longo, Roberto C; Cho, Kyeongjae; Brüner, Philipp; Welle, Alexander; Gerdes, Andreas; Thissen, Peter

    2015-03-04

    In this paper, we report about the influence of the chemical potential of water on the carbonation reaction of wollastonite (CaSiO3) as a model surface of cement and concrete. Total energy calculations based on density functional theory combined with kinetic barrier predictions based on nudge elastic band method show that the exposure of the water-free wollastonite surface to CO2 results in a barrier-less carbonation. CO2 reacts with the surface oxygen and forms carbonate (CO3(2-)) complexes together with a major reconstruction of the surface. The reaction comes to a standstill after one carbonate monolayer has been formed. In case one water monolayer is covering the wollastonite surface, the carbonation is no more barrier-less, yet ending in a localized monolayer. Covered with multilayers of water, the thermodynamic ground state of the wollastonite completely changes due to a metal-proton exchange reaction (also called early stage hydration) and Ca(2+) ions are partially removed from solid phase into the H2O/wollastonite interface. Mobile Ca(2+) reacts again with CO2 and forms carbonate complexes, ending in a delocalized layer. By means of high-resolution time-of-flight secondary-ion mass spectrometry images, we confirm that hydration can lead to a partially delocalization of Ca(2+) ions on wollastonite surfaces. Finally, we evaluate the impact of our model surface results by the meaning of low-energy ion-scattering spectroscopy combined with careful discussion about the competing reactions of carbonation vs hydration.

  19. Proceedings of the workshop on microscopic and phenomenological studies of the interactions between light-heavy ions

    International Nuclear Information System (INIS)

    Yamaguchi, S.

    1993-01-01

    The workshop 'Microscopic and Phenomenological Studies of the Interactions between Light-Heavy Ions' was held at Institute for Nuclear Study, University of Tokyo from Dec. 24 to Dec. 26, 1991. The workshop included 1) studies of the nucleus-nucleus interactions of the systems as 16 O- 16 O, 16 O- 15 N, etc., or the studies of the elastic and inelastic scatterings and the transfer reactions in such systems, 2) structure and reactions of neutron-rich nuclei, 3) microscopic derivation of the effective two-nucleon interactions, 4) development of the methods of techniques applied to the heavier systems. (author)

  20. Investigation of acoustic waves generated in an elastic solid by a pulsed ion beam and their application in a FIB based scanning ion acoustic microscope

    International Nuclear Information System (INIS)

    Akhmadaliev, C.

    2004-12-01

    The aim of this work is to investigate the acoustic wave generation by pulsed and periodically modulated ion beams in different solid materials depending on the beam parameters and to demonstrate the possibility to apply an intensity modulated focused ion beam (FIB) for acoustic emission and for nondestructive investigation of the internal structure of materials on a microscopic scale. The combination of a FIB and an ultrasound microscope in one device can provide the opportunity of nondestructive investigation, production and modification of micro- and nanostructures simultaneously. This work consists of the two main experimental parts. In the first part the process of elastic wave generation during the irradiation of metallic samples by a pulsed beam of energetic ions was investigated in an energy range from 1.5 to 10 MeV and pulse durations of 0.5-5 μs, applying ions with different masses, e.g. oxygen, silicon and gold, in charge states from 1 + to 4 + . The acoustic amplitude dependence on the ion beam parameters like the ion mass and energy, the ion charge state, the beam spot size and the pulse duration were of interest. This work deals with ultrasound transmitted in a solid, i.e. bulk waves, because of their importance for acoustic transmission microscopy and nondestructive inspection of internal structure of a sample. The second part of this work was carried out using the IMSA-100 FIB system operating in an energy range from 30 to 70 keV. The scanning ion acoustic microscope based on this FIB system was developed and tested. (orig.)

  1. Investigation of acoustic waves generated in an elastic solid by a pulsed ion beam and their application in a FIB based scanning ion acoustic microscope

    Energy Technology Data Exchange (ETDEWEB)

    Akhmadaliev, C.

    2004-12-01

    The aim of this work is to investigate the acoustic wave generation by pulsed and periodically modulated ion beams in different solid materials depending on the beam parameters and to demonstrate the possibility to apply an intensity modulated focused ion beam (FIB) for acoustic emission and for nondestructive investigation of the internal structure of materials on a microscopic scale. The combination of a FIB and an ultrasound microscope in one device can provide the opportunity of nondestructive investigation, production and modification of micro- and nanostructures simultaneously. This work consists of the two main experimental parts. In the first part the process of elastic wave generation during the irradiation of metallic samples by a pulsed beam of energetic ions was investigated in an energy range from 1.5 to 10 MeV and pulse durations of 0.5-5 {mu}s, applying ions with different masses, e.g. oxygen, silicon and gold, in charge states from 1{sup +} to 4{sup +}. The acoustic amplitude dependence on the ion beam parameters like the ion mass and energy, the ion charge state, the beam spot size and the pulse duration were of interest. This work deals with ultrasound transmitted in a solid, i.e. bulk waves, because of their importance for acoustic transmission microscopy and nondestructive inspection of internal structure of a sample. The second part of this work was carried out using the IMSA-100 FIB system operating in an energy range from 30 to 70 keV. The scanning ion acoustic microscope based on this FIB system was developed and tested. (orig.)

  2. Automatic segmentation of Leishmania parasite in microscopic images using a modified CV level set method

    Science.gov (United States)

    Farahi, Maria; Rabbani, Hossein; Talebi, Ardeshir; Sarrafzadeh, Omid; Ensafi, Shahab

    2015-12-01

    Visceral Leishmaniasis is a parasitic disease that affects liver, spleen and bone marrow. According to World Health Organization report, definitive diagnosis is possible just by direct observation of the Leishman body in the microscopic image taken from bone marrow samples. We utilize morphological and CV level set method to segment Leishman bodies in digital color microscopic images captured from bone marrow samples. Linear contrast stretching method is used for image enhancement and morphological method is applied to determine the parasite regions and wipe up unwanted objects. Modified global and local CV level set methods are proposed for segmentation and a shape based stopping factor is used to hasten the algorithm. Manual segmentation is considered as ground truth to evaluate the proposed method. This method is tested on 28 samples and achieved 10.90% mean of segmentation error for global model and 9.76% for local model.

  3. Imaging of soft and hard materials using a Boersch phase plate in a transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Alloyeau, D., E-mail: alloyeau.damien@gmail.com [National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS/72, Berkeley, CA 94720 (United States); Hsieh, W.K. [National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS/72, Berkeley, CA 94720 (United States); Anderson, E.H.; Hilken, L. [Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley CA 94720 (United States); Benner, G. [Carl Zeiss NTS GmbH, Oberkochen 73447 (Germany); Meng, X. [Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, CA 94720-1770 (United States); Chen, F.R. [Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan (China); Kisielowski, C. [National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS/72, Berkeley, CA 94720 (United States)

    2010-04-15

    Using two levels of electron beam lithography, vapor phase deposition techniques, and FIB etching, we have fabricated an electrostatic Boersch phase plate for contrast enhancement of weak phase objects in a transmission electron microscope. The phase plate has suitable dimensions for the imaging of small biological samples without compromising the high-resolution capabilities of the microscope. A micro-structured electrode allows for phase tuning of the unscattered electron beam, which enables the recording of contrast enhanced in-focus images and in-line holograms. We have demonstrated experimentally that our phase plate improves the contrast of carbon nanotubes while maintaining high-resolution imaging performance, which is demonstrated for the case of an AlGaAs heterostructure. The development opens a new way to study interfaces between soft and hard materials.

  4. Computer Aided Quantification of Pathological Features for Flexor Tendon Pulleys on Microscopic Images

    Directory of Open Access Journals (Sweden)

    Yung-Chun Liu

    2013-01-01

    Full Text Available Quantifying the pathological features of flexor tendon pulleys is essential for grading the trigger finger since it provides clinicians with objective evidence derived from microscopic images. Although manual grading is time consuming and dependent on the observer experience, there is a lack of image processing methods for automatically extracting pulley pathological features. In this paper, we design and develop a color-based image segmentation system to extract the color and shape features from pulley microscopic images. Two parameters which are the size ratio of abnormal tissue regions and the number ratio of abnormal nuclei are estimated as the pathological progression indices. The automatic quantification results show clear discrimination among different levels of diseased pulley specimens which are prone to misjudgments for human visual inspection. The proposed system provides a reliable and automatic way to obtain pathological parameters instead of manual evaluation which is with intra- and interoperator variability. Experiments with 290 microscopic images from 29 pulley specimens show good correspondence with pathologist expectations. Hence, the proposed system has great potential for assisting clinical experts in routine histopathological examinations.

  5. Automatic detection of the hippocampal region associated with Alzheimer's disease from microscopic images of mice brain

    Science.gov (United States)

    Albaidhani, Tahseen; Hawkes, Cheryl; Jassim, Sabah; Al-Assam, Hisham

    2016-05-01

    The hippocampus is the region of the brain that is primarily associated with memory and spatial navigation. It is one of the first brain regions to be damaged when a person suffers from Alzheimer's disease. Recent research in this field has focussed on the assessment of damage to different blood vessels within the hippocampal region from a high throughput brain microscopic images. The ultimate aim of our research is the creation of an automatic system to count and classify different blood vessels such as capillaries, veins, and arteries in the hippocampus region. This work should provide biologists with efficient and accurate tools in their investigation of the causes of Alzheimer's disease. Locating the boundary of the Region of Interest in the hippocampus from microscopic images of mice brain is the first essential stage towards developing such a system. This task benefits from the variation in colour channels and texture between the two sides of the hippocampus and the boundary region. Accordingly, the developed initial step of our research to locating the hippocampus edge uses a colour-based segmentation of the brain image followed by Hough transforms on the colour channel that isolate the hippocampus region. The output is then used to split the brain image into two sides of the detected section of the boundary: the inside region and the outside region. Experimental results on a sufficiently number of microscopic images demonstrate the effectiveness of the developed solution.

  6. Apertureless near-field/far-field CW two-photon microscope for biological and material imaging and spectroscopic applications.

    Science.gov (United States)

    Nowak, Derek B; Lawrence, A J; Sánchez, Erik J

    2010-12-10

    We present the development of a versatile spectroscopic imaging tool to allow for imaging with single-molecule sensitivity and high spatial resolution. The microscope allows for near-field and subdiffraction-limited far-field imaging by integrating a shear-force microscope on top of a custom inverted microscope design. The instrument has the ability to image in ambient conditions with optical resolutions on the order of tens of nanometers in the near field. A single low-cost computer controls the microscope with a field programmable gate array data acquisition card. High spatial resolution imaging is achieved with an inexpensive CW multiphoton excitation source, using an apertureless probe and simplified optical pathways. The high-resolution, combined with high collection efficiency and single-molecule sensitive optical capabilities of the microscope, are demonstrated with a low-cost CW laser source as well as a mode-locked laser source.

  7. Analytical electron microscope based on scanning transmission electron microscope with wavelength dispersive x-ray spectroscopy to realize highly sensitive elemental imaging especially for light elements

    International Nuclear Information System (INIS)

    Koguchi, Masanari; Tsuneta, Ruriko; Anan, Yoshihiro; Nakamae, Koji

    2017-01-01

    An analytical electron microscope based on the scanning transmission electron microscope with wavelength dispersive x-ray spectroscopy (STEM-WDX) to realize highly sensitive elemental imaging especially for light elements has been developed. In this study, a large-solid-angle multi-capillary x-rays lens with a focal length of 5 mm, long-time data acquisition (e.g. longer than 26 h), and a drift-free system made it possible to visualize boron-dopant images in a Si substrate at a detection limit of 0.2 atomic percent. (paper)

  8. Fermi surface contours obtained from scanning tunneling microscope images around surface point defects

    International Nuclear Information System (INIS)

    Khotkevych-Sanina, N V; Kolesnichenko, Yu A; Van Ruitenbeek, J M

    2013-01-01

    We present a theoretical analysis of the standing wave patterns in scanning tunneling microscope (STM) images, which occur around surface point defects. We consider arbitrary dispersion relations for the surface states and calculate the conductance for a system containing a small-size tunnel contact and a surface impurity. We find rigorous theoretical relations between the interference patterns in the real-space STM images, their Fourier transforms and the Fermi contours of two-dimensional electrons. We propose a new method for reconstructing Fermi contours of surface electron states, directly from the real-space STM images around isolated surface defects. (paper)

  9. New deconvolution method for microscopic images based on the continuous Gaussian radial basis function interpolation model.

    Science.gov (United States)

    Chen, Zhaoxue; Chen, Hao

    2014-01-01

    A deconvolution method based on the Gaussian radial basis function (GRBF) interpolation is proposed. Both the original image and Gaussian point spread function are expressed as the same continuous GRBF model, thus image degradation is simplified as convolution of two continuous Gaussian functions, and image deconvolution is converted to calculate the weighted coefficients of two-dimensional control points. Compared with Wiener filter and Lucy-Richardson algorithm, the GRBF method has an obvious advantage in the quality of restored images. In order to overcome such a defect of long-time computing, the method of graphic processing unit multithreading or increasing space interval of control points is adopted, respectively, to speed up the implementation of GRBF method. The experiments show that based on the continuous GRBF model, the image deconvolution can be efficiently implemented by the method, which also has a considerable reference value for the study of three-dimensional microscopic image deconvolution.

  10. A Low-Cost Digital Microscope with Real-Time Fluorescent Imaging Capability.

    Science.gov (United States)

    Hasan, Md Mehedi; Alam, Mohammad Wajih; Wahid, Khan A; Miah, Sayem; Lukong, Kiven Erique

    2016-01-01

    This paper describes the development of a prototype of a low-cost digital fluorescent microscope built from commercial off-the-shelf (COTS) components. The prototype was tested to detect malignant tumor cells taken from a living organism in a preclinical setting. This experiment was accomplished by using Alexa Fluor 488 conjugate dye attached to the cancer cells. Our prototype utilizes a torch along with an excitation filter as a light source for fluorophore excitation, a dichroic mirror to reflect the excitation and pass the emitted green light from the sample under test and a barrier filter to permit only appropriate wavelength. The system is designed out of a microscope using its optical zooming property and an assembly of exciter filter, dichroic mirror and transmitter filter. The microscope is connected to a computer or laptop through universal serial bus (USB) that allows real-time transmission of captured florescence images; this also offers real-time control of the microscope. The designed system has comparable features of high-end commercial fluorescent microscopes while reducing cost, power, weight and size.

  11. A Low-Cost Digital Microscope with Real-Time Fluorescent Imaging Capability.

    Directory of Open Access Journals (Sweden)

    Md Mehedi Hasan

    Full Text Available This paper describes the development of a prototype of a low-cost digital fluorescent microscope built from commercial off-the-shelf (COTS components. The prototype was tested to detect malignant tumor cells taken from a living organism in a preclinical setting. This experiment was accomplished by using Alexa Fluor 488 conjugate dye attached to the cancer cells. Our prototype utilizes a torch along with an excitation filter as a light source for fluorophore excitation, a dichroic mirror to reflect the excitation and pass the emitted green light from the sample under test and a barrier filter to permit only appropriate wavelength. The system is designed out of a microscope using its optical zooming property and an assembly of exciter filter, dichroic mirror and transmitter filter. The microscope is connected to a computer or laptop through universal serial bus (USB that allows real-time transmission of captured florescence images; this also offers real-time control of the microscope. The designed system has comparable features of high-end commercial fluorescent microscopes while reducing cost, power, weight and size.

  12. A Low-Cost Digital Microscope with Real-Time Fluorescent Imaging Capability

    Science.gov (United States)

    Hasan, Md. Mehedi; Wahid, Khan A.; Miah, Sayem; Lukong, Kiven Erique

    2016-01-01

    This paper describes the development of a prototype of a low-cost digital fluorescent microscope built from commercial off-the-shelf (COTS) components. The prototype was tested to detect malignant tumor cells taken from a living organism in a preclinical setting. This experiment was accomplished by using Alexa Fluor 488 conjugate dye attached to the cancer cells. Our prototype utilizes a torch along with an excitation filter as a light source for fluorophore excitation, a dichroic mirror to reflect the excitation and pass the emitted green light from the sample under test and a barrier filter to permit only appropriate wavelength. The system is designed out of a microscope using its optical zooming property and an assembly of exciter filter, dichroic mirror and transmitter filter. The microscope is connected to a computer or laptop through universal serial bus (USB) that allows real-time transmission of captured florescence images; this also offers real-time control of the microscope. The designed system has comparable features of high-end commercial fluorescent microscopes while reducing cost, power, weight and size. PMID:27977709

  13. Automated detection of analyzable metaphase chromosome cells depicted on scanned digital microscopic images

    Science.gov (United States)

    Qiu, Yuchen; Wang, Xingwei; Chen, Xiaodong; Li, Yuhua; Liu, Hong; Li, Shibo; Zheng, Bin

    2010-02-01

    Visually searching for analyzable metaphase chromosome cells under microscopes is quite time-consuming and difficult. To improve detection efficiency, consistency, and diagnostic accuracy, an automated microscopic image scanning system was developed and tested to directly acquire digital images with sufficient spatial resolution for clinical diagnosis. A computer-aided detection (CAD) scheme was also developed and integrated into the image scanning system to search for and detect the regions of interest (ROI) that contain analyzable metaphase chromosome cells in the large volume of scanned images acquired from one specimen. Thus, the cytogeneticists only need to observe and interpret the limited number of ROIs. In this study, the high-resolution microscopic image scanning and CAD performance was investigated and evaluated using nine sets of images scanned from either bone marrow (three) or blood (six) specimens for diagnosis of leukemia. The automated CAD-selection results were compared with the visual selection. In the experiment, the cytogeneticists first visually searched for the analyzable metaphase chromosome cells from specimens under microscopes. The specimens were also automated scanned and followed by applying the CAD scheme to detect and save ROIs containing analyzable cells while deleting the others. The automated selected ROIs were then examined by a panel of three cytogeneticists. From the scanned images, CAD selected more analyzable cells than initially visual examinations of the cytogeneticists in both blood and bone marrow specimens. In general, CAD had higher performance in analyzing blood specimens. Even in three bone marrow specimens, CAD selected 50, 22, 9 ROIs, respectively. Except matching with the initially visual selection of 9, 7, and 5 analyzable cells in these three specimens, the cytogeneticists also selected 41, 15 and 4 new analyzable cells, which were missed in initially visual searching. This experiment showed the feasibility of

  14. Comparison of multilayered nanowire imaging by SEM and Helium Ion Microscopy

    International Nuclear Information System (INIS)

    Inkson, B J; Peng, Y; Jepson, M A E; Rodenburg, C; Liu, X

    2010-01-01

    The helium ion microscope (HeIM) is capable of probe sizes smaller than SEM and, with intrinsically small ion/sample interaction volumes, may therefore potentially offer higher spatial resolution secondary electron (SE) imaging of nanostructures. Here 55 nm diameter CoPt/Pt multilayered nanowires have been imaged by HeIM, SEM and TEM. It is found that there is an increased resolution of nanowire surface topography in HeIM SE images compared to SEM, however there is a reduction of materials contrast of the alternating Pt and CoPt layers. This can be attributed to the increased contribution of surface contamination layers to the ion-induced SE signal, and carbon is also observed to grow on the nanowires under prolonged HeIM scanning.

  15. Ionic channels in Langmuir-Blodgett films imaged by a scanning tunneling microscope.

    Science.gov (United States)

    Kolomytkin, O V; Golubok, A O; Davydov, D N; Timofeev, V A; Vinogradova, S A; Tipisev SYa

    1991-01-01

    The molecular structure of channels formed by gramicidin A in a lipid membrane was imaged by a scanning tunneling microscope operating in air. The mono- and bimolecular films of lipid with gramicidin A were deposited onto a highly oriented pyrolitic graphite substrate by the Langmuir-Blodgett technique. It has been shown that under high concentration gramicidin A molecules can form in lipid films a quasi-regular, densely packed structure. Single gramicidin A molecules were imaged for the first time as well. The cavity of 0.4 +/- 0.05 nm in halfwidth was found on the scanning tunneling microscopy image of the gramicidin A molecule. The results of direct observation obtained by means of scanning tunneling microscope are in good agreement with the known molecular model of gramicidin A. It was shown that gramicidin A molecules can exist in a lipid monolayer as individual molecules or combined into clusters. The results demonstrate that scanning tunneling microscope can be used for high spatial resolution study of ionic channel structure. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 PMID:1712239

  16. Ion pair formation in the vacuum ultraviolet region of NO studied by negative ion imaging spectroscopy

    International Nuclear Information System (INIS)

    Hikosaka, Y.; Kaneyasu, T.; Shigemasa, E.

    2007-01-01

    The pair formation of positive and negative fragment ions has been studied in the vacuum ultraviolet region of NO, with negative ion imaging spectroscopy. The negative ion yield curve obtained in the photon energy region of 19-25 eV exhibits many structures which are absent from the photoabsorption spectrum in the same region. The partial yields and asymmetry parameters associated with the dissociations into individual ion pair limits have been extracted from the negative ion images observed. On the basis of these quantities, the assignments for the structures exhibited on the negative ion yield curve are given and the dynamical properties on the ion pair dissociation are discussed

  17. Dual-mode optical microscope based on single-pixel imaging

    Science.gov (United States)

    Rodríguez, A. D.; Clemente, P.; Tajahuerce, E.; Lancis, J.

    2016-07-01

    We demonstrate an inverted microscope that can image specimens in both reflection and transmission modes simultaneously with a single light source. The microscope utilizes a digital micromirror device (DMD) for patterned illumination altogether with two single-pixel photosensors for efficient light detection. The system, a scan-less device with no moving parts, works by sequential projection of a set of binary intensity patterns onto the sample that are codified onto a modified commercial DMD. Data to be displayed are geometrically transformed before written into a memory cell to cancel optical artifacts coming from the diamond-like shaped structure of the micromirror array. The 24-bit color depth of the display is fully exploited to increase the frame rate by a factor of 24, which makes the technique practicable for real samples. Our commercial DMD-based LED-illumination is cost effective and can be easily coupled as an add-on module for already existing inverted microscopes. The reflection and transmission information provided by our dual microscope complement each other and can be useful for imaging non-uniform samples and to prevent self-shadowing effects.

  18. Dynamics of water and ions in clays of type montmorillonite by microscopic simulation and quasi-elastic neutron scattering

    International Nuclear Information System (INIS)

    Malikova, N.

    2005-09-01

    Montmorillonite clays in low hydration states, with Na + and Cs + compensating counter ions, are investigated by a combination of microscopic simulation and quasi-elastic neutron scattering to obtain information on the local structure and dynamics of water and ions in the interlayer. At first predictions of simulation into the dynamics of water and ions at elevate temperatures are shown (0 deg C 80 deg C, pertinent for the radioactive waste disposal scenario) Marked difference is observed between the modes of diffusion of the Na + and C + counter ions. In water dynamics, a significant step towards bulk water behaviour is seen on transition from the mono- to bilayer states. Secondly, a detailed comparison between simulation and quasi-elastic neutron scattering (Neutron Spin Echo and Time-of-Flight) regarding ambient temperature water dynamics is presented. Overall, the approaches are found to be in good agreement with each other and limitations of each of the methods are clearly shown. (author)

  19. Live cell imaging at the Munich ion microbeam SNAKE – a status report

    International Nuclear Information System (INIS)

    Drexler, Guido A; Siebenwirth, Christian; Drexler, Sophie E; Girst, Stefanie; Greubel, Christoph; Dollinger, Günther; Friedl, Anna A

    2015-01-01

    Ion microbeams are important tools in radiobiological research. Still, the worldwide number of ion microbeam facilities where biological experiments can be performed is limited. Even fewer facilities combine ion microirradiation with live-cell imaging to allow microscopic observation of cellular response reactions starting very fast after irradiation and continuing for many hours. At SNAKE, the ion microbeam facility at the Munich 14 MV tandem accelerator, a large variety of biological experiments are performed on a regular basis. Here, recent developments and ongoing research projects at the ion microbeam SNAKE are presented with specific emphasis on live-cell imaging experiments. An overview of the technical details of the setup is given, including examples of suitable biological samples. By ion beam focusing to submicrometer beam spot size and single ion detection it is possible to target subcellular structures with defined numbers of ions. Focusing of high numbers of ions to single spots allows studying the influence of high local damage density on recruitment of damage response proteins. The online version of this article (doi:10.1186/s13014-015-0350-7) contains supplementary material, which is available to authorized users

  20. Live cell imaging at the Munich ion microbeam SNAKE - a status report.

    Science.gov (United States)

    Drexler, Guido A; Siebenwirth, Christian; Drexler, Sophie E; Girst, Stefanie; Greubel, Christoph; Dollinger, Günther; Friedl, Anna A

    2015-02-18

    Ion microbeams are important tools in radiobiological research. Still, the worldwide number of ion microbeam facilities where biological experiments can be performed is limited. Even fewer facilities combine ion microirradiation with live-cell imaging to allow microscopic observation of cellular response reactions starting very fast after irradiation and continuing for many hours. At SNAKE, the ion microbeam facility at the Munich 14 MV tandem accelerator, a large variety of biological experiments are performed on a regular basis. Here, recent developments and ongoing research projects at the ion microbeam SNAKE are presented with specific emphasis on live-cell imaging experiments. An overview of the technical details of the setup is given, including examples of suitable biological samples. By ion beam focusing to submicrometer beam spot size and single ion detection it is possible to target subcellular structures with defined numbers of ions. Focusing of high numbers of ions to single spots allows studying the influence of high local damage density on recruitment of damage response proteins.

  1. Intensity-based segmentation and visualization of cells in 3D microscopic images using the GPU

    Science.gov (United States)

    Kang, Mi-Sun; Lee, Jeong-Eom; Jeon, Woong-ki; Choi, Heung-Kook; Kim, Myoung-Hee

    2013-02-01

    3D microscopy images contain abundant astronomical data, rendering 3D microscopy image processing time-consuming and laborious on a central processing unit (CPU). To solve these problems, many people crop a region of interest (ROI) of the input image to a small size. Although this reduces cost and time, there are drawbacks at the image processing level, e.g., the selected ROI strongly depends on the user and there is a loss in original image information. To mitigate these problems, we developed a 3D microscopy image processing tool on a graphics processing unit (GPU). Our tool provides efficient and various automatic thresholding methods to achieve intensity-based segmentation of 3D microscopy images. Users can select the algorithm to be applied. Further, the image processing tool provides visualization of segmented volume data and can set the scale, transportation, etc. using a keyboard and mouse. However, the 3D objects visualized fast still need to be analyzed to obtain information for biologists. To analyze 3D microscopic images, we need quantitative data of the images. Therefore, we label the segmented 3D objects within all 3D microscopic images and obtain quantitative information on each labeled object. This information can use the classification feature. A user can select the object to be analyzed. Our tool allows the selected object to be displayed on a new window, and hence, more details of the object can be observed. Finally, we validate the effectiveness of our tool by comparing the CPU and GPU processing times by matching the specification and configuration.

  2. Investigations of reactions between pure refractory metals and light gases with the field ion microscope and atom probe

    International Nuclear Information System (INIS)

    Krautz, E.; Haiml, G.

    1989-01-01

    The initial stages of selected reactions of the refractory metals tungsten, niobium and tantalum with hydrogen, oxygen, nitrogen and methane have been studied with the field ion microscope in atomic resolution whereby the composition of single net planes converages and surface zones could absolutely be analyzed with the atom probe by using field desorption under defined conditions at low temperatures. 14 refs., 9 figs. (Author)

  3. Super-resolution for everybody: An image processing workflow to obtain high-resolution images with a standard confocal microscope.

    Science.gov (United States)

    Lam, France; Cladière, Damien; Guillaume, Cyndélia; Wassmann, Katja; Bolte, Susanne

    2017-02-15

    In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure. We validate our workflow by imaging sub resolution fluorescent beads and measuring the maximum lateral and axial resolution of the confocal system. Subsequently, we apply the parameters to the imaging and data restoration of fluorescently labelled meiotic spindles of mouse oocytes. We measure a resolution increase of approximately 2-fold in the lateral and 3-fold in the axial direction throughout a depth of 60μm. This demonstrates that with our optimized workflow we reach a resolution that is comparable to 3D-SIM-imaging, but with better depth penetration for confocal images of beads and the biological sample. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Biomarkers at the microscopic range : ToF-SIMS molecular imaging of Archaea-derived lipids in a microbial mat

    NARCIS (Netherlands)

    Thiel, V.; Heim, C.; Arp, G.; Hahmann, U.; Sjovall, P.; Lausmaa, J.

    2007-01-01

    Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) with a bismuth cluster primary ion source was used for analysing microbial lipid biomarkers in 10-mu m-thick microscopic cryosections of methanotrophic microbial mats from the Black Sea. Without further sample preparation, archaeal isopranyl

  5. Scanning tunneling microscopic images and scanning tunneling spectra for coupled rectangular quantum corrals

    International Nuclear Information System (INIS)

    Mitsuoka, Shigenori; Tamura, Akira

    2011-01-01

    Assuming that an electron confined by double δ-function barriers lies in a quasi-stationary state, we derived eigenstates and eigenenergies of the electron. Such an electron has a complex eigenenergy, and the imaginary part naturally leads to the lifetime of the electron associated with tunneling through barriers. We applied this point of view to the electron confined in a rectangular quantum corral (QC) on a noble metal surface, and obtained scanning tunneling microscopic images and a scanning tunneling spectrum consistent with experimental ones. We investigated the electron states confined in coupled QCs and obtained the coupled states constructed with bonding and anti-bonding states. Using those energy levels and wavefunctions we specified scanning tunneling microscope (STM) images and scanning tunneling spectra (STS) for the doubly and triply coupled QCs. In addition we pointed out the feature of resonant electron states associated with the same QCs at both ends of the triply coupled QCs.

  6. Spectro-refractometry of individual microscopic objects using swept-source quantitative phase imaging.

    Science.gov (United States)

    Jung, Jae-Hwang; Jang, Jaeduck; Park, Yongkeun

    2013-11-05

    We present a novel spectroscopic quantitative phase imaging technique with a wavelength swept-source, referred to as swept-source diffraction phase microscopy (ssDPM), for quantifying the optical dispersion of microscopic individual samples. Employing the swept-source and the principle of common-path interferometry, ssDPM measures the multispectral full-field quantitative phase imaging and spectroscopic microrefractometry of transparent microscopic samples in the visible spectrum with a wavelength range of 450-750 nm and a spectral resolution of less than 8 nm. With unprecedented precision and sensitivity, we demonstrate the quantitative spectroscopic microrefractometry of individual polystyrene beads, 30% bovine serum albumin solution, and healthy human red blood cells.

  7. Scanning electron microscope cathodoluminescence imaging of subgrain boundaries, twins and planar deformation features in quartz

    Science.gov (United States)

    Hamers, M. F.; Pennock, G. M.; Drury, M. R.

    2017-04-01

    The study of deformation features has been of great importance to determine deformation mechanisms in quartz. Relevant microstructures in both growth and deformation processes include dislocations, subgrains, subgrain boundaries, Brazil and Dauphiné twins and planar deformation features (PDFs). Dislocations and twin boundaries are most commonly imaged using a transmission electron microscope (TEM), because these cannot directly be observed using light microscopy, in contrast to PDFs. Here, we show that red-filtered cathodoluminescence imaging in a scanning electron microscope (SEM) is a useful method to visualise subgrain boundaries, Brazil and Dauphiné twin boundaries. Because standard petrographic thin sections can be studied in the SEM, the observed structures can be directly and easily correlated to light microscopy studies. In contrast to TEM preparation methods, SEM techniques are non-destructive to the area of interest on a petrographic thin section.

  8. Time-of-flight atom-probe field-ion microscope for the study of defects in metals. Report No. 2357

    International Nuclear Information System (INIS)

    Hall, T.M.; Wagner, A.; Berger, A.S.; Seidman, D.N.

    1975-06-01

    An ultra-high vacuum time-of-flight (TOF) atom-probe field ion microscope (FIM) specifically designed for the study of defects in metals is described. The variable magnification FIM image is viewed with the aid of an internal image intensification system based on a channel electron-multiplier array. The specimen is held in a liquid-helium-cooled goniometer stage, and the specimen is exchanged by means of a high-vacuum (less than 10 -6 torr) specimen exchange device. This stage allows the specimen to be maintained at a tip temperature anywhere in the range from 13 to 450 0 K. Specimens can also be irradiated in-situ with any low-energy (less than 1 keV) gas ion employing a specially constructed ion gun. The pulse-field evaporated ions are detected by a Chevron ion-detector located 2.22 m from the FIM specimen. The TOF of the ions are measured by a specially constructed eight-channel digital timer with a resolution of +-10 ns. The entire process of applying the evaporation pulse to the specimen, measuring the dc and pulse voltages, and analyzing the TOF data is controlled by a NOVA 1220 computer. The computer is also interfaced to a Tektronix graphics terminal which displays the data in the form of a histogram of the number of events versus the mass-to-charge ratio. An extensive set of computer programs to test and operate the atom-probe FIM have been developed. With this automated system we can presently record and analyze 10 TOF s -1 . In the performance tests reported here the instrument has resolved the seven stable isotopes of molybdenum, the five stable isotopes of tungsten, and the two stable isotopes of rhenium in a tungsten--25 at. percent rhenium alloy

  9. Preprocessing with Photoshop Software on Microscopic Images of A549 Cells in Epithelial-Mesenchymal Transition.

    Science.gov (United States)

    Ren, Zhou-Xin; Yu, Hai-Bin; Shen, Jun-Ling; Li, Ya; Li, Jian-Sheng

    2015-06-01

    To establish a preprocessing method for cell morphometry in microscopic images of A549 cells in epithelial-mesenchymal transition (EMT). Adobe Photoshop CS2 (Adobe Systems, Inc.) was used for preprocessing the images. First, all images were processed for size uniformity and high distinguishability between the cell and background area. Then, a blank image with the same size and grids was established and cross points of the grids were added into a distinct color. The blank image was merged into a processed image. In the merged images, the cells with 1 or more cross points were chosen, and then the cell areas were enclosed and were replaced in a distinct color. Except for chosen cellular areas, all areas were changed into a unique hue. Three observers quantified roundness of cells in images with the image preprocess (IPP) or without the method (Controls), respectively. Furthermore, 1 observer measured the roundness 3 times with the 2 methods, respectively. The results between IPPs and Controls were compared for repeatability and reproducibility. As compared with the Control method, among 3 observers, use of the IPP method resulted in a higher number and a higher percentage of same-chosen cells in an image. The relative average deviation values of roundness, either for 3 observers or 1 observer, were significantly higher in Controls than in IPPs (p Photoshop, a chosen cell from an image was more objective, regular, and accurate, creating an increase of reproducibility and repeatability on morphometry of A549 cells in epithelial to mesenchymal transition.

  10. Reducing charging effects in scanning electron microscope images by Rayleigh contrast stretching method (RCS).

    Science.gov (United States)

    Wan Ismail, W Z; Sim, K S; Tso, C P; Ting, H Y

    2011-01-01

    To reduce undesirable charging effects in scanning electron microscope images, Rayleigh contrast stretching is developed and employed. First, re-scaling is performed on the input image histograms with Rayleigh algorithm. Then, contrast stretching or contrast adjustment is implemented to improve the images while reducing the contrast charging artifacts. This technique has been compared to some existing histogram equalization (HE) extension techniques: recursive sub-image HE, contrast stretching dynamic HE, multipeak HE and recursive mean separate HE. Other post processing methods, such as wavelet approach, spatial filtering, and exponential contrast stretching, are compared as well. Overall, the proposed method produces better image compensation in reducing charging artifacts. Copyright © 2011 Wiley Periodicals, Inc.

  11. Noise removal in extended depth of field microscope images through nonlinear signal processing.

    Science.gov (United States)

    Zahreddine, Ramzi N; Cormack, Robert H; Cogswell, Carol J

    2013-04-01

    Extended depth of field (EDF) microscopy, achieved through computational optics, allows for real-time 3D imaging of live cell dynamics. EDF is achieved through a combination of point spread function engineering and digital image processing. A linear Wiener filter has been conventionally used to deconvolve the image, but it suffers from high frequency noise amplification and processing artifacts. A nonlinear processing scheme is proposed which extends the depth of field while minimizing background noise. The nonlinear filter is generated via a training algorithm and an iterative optimizer. Biological microscope images processed with the nonlinear filter show a significant improvement in image quality and signal-to-noise ratio over the conventional linear filter.

  12. Surface features on Sahara soil dust particles made visible by atomic force microscope (AFM) phase images

    OpenAIRE

    G. Helas; M. O. Andreae

    2008-01-01

    We show that atomic force microscopy (AFM) phase images can reveal surface features of soil dust particles, which are not evident using other microscopic methods. The non-contact AFM method is able to resolve topographical structures in the nanometer range as well as to uncover repulsive atomic forces and attractive van der Waals' forces, and thus gives insight to surface properties. Though the method does not allow quantitative assignment in terms of chemical compound description, it clearly...

  13. Pancam and microscopic imager observations of dust on the Spirit Rovers

    DEFF Research Database (Denmark)

    Vaughan....[], Alicia F.; Johnson, Jeffrey R.; Walter, Goetz

    2010-01-01

    This work describes dust deposits on the Spirit Rover over 2000 sols through examination of Pancam and Microscopic Imager observations of specific locations on the rover body, including portions of the solar array, Pancam and Mini-TES calibration targets, and the magnets. This data set reveals...... the three "cleaning events" experienced by Spirit to date, the spectral properties of dust, and the tendency of dust particles to form aggregates 100 um and larger...

  14. Algorithm for detection of overlapped red blood cells in microscopic images of blood smears

    OpenAIRE

    Romero-Rondón, Miguel Fabián; Sanabria-Rosas, Laura Melissa; Bautista-Rozo, Lola Xiomara; Mendoza-Castellanos, Alfonso

    2016-01-01

    The hemogram is one of the most requested medical tests as it presents details about the three cell series in the blood: red series, white series and platelet series. To make some diagnostics, the specialist must undertake the test manually, observing the blood cells under the microscope, which implies a great physical effort. In order to facilitate this work, different digital image processing techniques to detect and classify red blood cells have been proposed. However, a common problem is ...

  15. Fine-grained leukocyte classification with deep residual learning for microscopic images.

    Science.gov (United States)

    Qin, Feiwei; Gao, Nannan; Peng, Yong; Wu, Zizhao; Shen, Shuying; Grudtsin, Artur

    2018-08-01

    Leukocyte classification and cytometry have wide applications in medical domain, previous researches usually exploit machine learning techniques to classify leukocytes automatically. However, constrained by the past development of machine learning techniques, for example, extracting distinctive features from raw microscopic images are difficult, the widely used SVM classifier only has relative few parameters to tune, these methods cannot efficiently handle fine-grained classification cases when the white blood cells have up to 40 categories. Based on deep learning theory, a systematic study is conducted on finer leukocyte classification in this paper. A deep residual neural network based leukocyte classifier is constructed at first, which can imitate the domain expert's cell recognition process, and extract salient features robustly and automatically. Then the deep neural network classifier's topology is adjusted according to the prior knowledge of white blood cell test. After that the microscopic image dataset with almost one hundred thousand labeled leukocytes belonging to 40 categories is built, and combined training strategies are adopted to make the designed classifier has good generalization ability. The proposed deep residual neural network based classifier was tested on microscopic image dataset with 40 leukocyte categories. It achieves top-1 accuracy of 77.80%, top-5 accuracy of 98.75% during the training procedure. The average accuracy on the test set is nearly 76.84%. This paper presents a fine-grained leukocyte classification method for microscopic images, based on deep residual learning theory and medical domain knowledge. Experimental results validate the feasibility and effectiveness of our approach. Extended experiments support that the fine-grained leukocyte classifier could be used in real medical applications, assist doctors in diagnosing diseases, reduce human power significantly. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Microscope image based fully automated stomata detection and pore measurement method for grapevines

    Directory of Open Access Journals (Sweden)

    Hiranya Jayakody

    2017-11-01

    Full Text Available Abstract Background Stomatal behavior in grapevines has been identified as a good indicator of the water stress level and overall health of the plant. Microscope images are often used to analyze stomatal behavior in plants. However, most of the current approaches involve manual measurement of stomatal features. The main aim of this research is to develop a fully automated stomata detection and pore measurement method for grapevines, taking microscope images as the input. The proposed approach, which employs machine learning and image processing techniques, can outperform available manual and semi-automatic methods used to identify and estimate stomatal morphological features. Results First, a cascade object detection learning algorithm is developed to correctly identify multiple stomata in a large microscopic image. Once the regions of interest which contain stomata are identified and extracted, a combination of image processing techniques are applied to estimate the pore dimensions of the stomata. The stomata detection approach was compared with an existing fully automated template matching technique and a semi-automatic maximum stable extremal regions approach, with the proposed method clearly surpassing the performance of the existing techniques with a precision of 91.68% and an F1-score of 0.85. Next, the morphological features of the detected stomata were measured. Contrary to existing approaches, the proposed image segmentation and skeletonization method allows us to estimate the pore dimensions even in cases where the stomatal pore boundary is only partially visible in the microscope image. A test conducted using 1267 images of stomata showed that the segmentation and skeletonization approach was able to correctly identify the stoma opening 86.27% of the time. Further comparisons made with manually traced stoma openings indicated that the proposed method is able to estimate stomata morphological features with accuracies of 89.03% for area

  17. Towards native-state imaging in biological context in the electron microscope

    Science.gov (United States)

    Weston, Anne E.; Armer, Hannah E. J.

    2009-01-01

    Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context. PMID:19916039

  18. A hybrid scanning force and light microscope for surface imaging and three-dimensional optical sectioning in differential interference contrast.

    Science.gov (United States)

    Stemmer, A

    1995-04-01

    The design of a scanned-cantilever-type force microscope is presented which is fully integrated into an inverted high-resolution video-enhanced light microscope. This set-up allows us to acquire thin optical sections in differential interference contrast (DIC) or polarization while the force microscope is in place. Such a hybrid microscope provides a unique platform to study how cell surface properties determine, or are affected by, the three-dimensional dynamic organization inside the living cell. The hybrid microscope presented in this paper has proven reliable and versatile for biological applications. It is the only instrument that can image a specimen by force microscopy and high-power DIC without having either to translate the specimen or to remove the force microscope. Adaptation of the design features could greatly enhance the suitability of other force microscopes for biological work.

  19. Automatic analysis of digitized TV-images by a computer-driven optical microscope

    International Nuclear Information System (INIS)

    Rosa, G.; Di Bartolomeo, A.; Grella, G.; Romano, G.

    1997-01-01

    New methods of image analysis and three-dimensional pattern recognition were developed in order to perform the automatic scan of nuclear emulsion pellicles. An optical microscope, with a motorized stage, was equipped with a CCD camera and an image digitizer, and interfaced to a personal computer. Selected software routines inspired the design of a dedicated hardware processor. Fast operation, high efficiency and accuracy were achieved. First applications to high-energy physics experiments are reported. Further improvements are in progress, based on a high-resolution fast CCD camera and on programmable digital signal processors. Applications to other research fields are envisaged. (orig.)

  20. Computer Aided Solution for Automatic Segmenting and Measurements of Blood Leucocytes Using Static Microscope Images.

    Science.gov (United States)

    Abdulhay, Enas; Mohammed, Mazin Abed; Ibrahim, Dheyaa Ahmed; Arunkumar, N; Venkatraman, V

    2018-02-17

    Blood leucocytes segmentation in medical images is viewed as difficult process due to the variability of blood cells concerning their shape and size and the difficulty towards determining location of Blood Leucocytes. Physical analysis of blood tests to recognize leukocytes is tedious, time-consuming and liable to error because of the various morphological components of the cells. Segmentation of medical imagery has been considered as a difficult task because of complexity of images, and also due to the non-availability of leucocytes models which entirely captures the probable shapes in each structures and also incorporate cell overlapping, the expansive variety of the blood cells concerning their shape and size, various elements influencing the outer appearance of the blood leucocytes, and low Static Microscope Image disparity from extra issues outcoming about because of noise. We suggest a strategy towards segmentation of blood leucocytes using static microscope images which is a resultant of three prevailing systems of computer vision fiction: enhancing the image, Support vector machine for segmenting the image, and filtering out non ROI (region of interest) on the basis of Local binary patterns and texture features. Every one of these strategies are modified for blood leucocytes division issue, in this manner the subsequent techniques are very vigorous when compared with its individual segments. Eventually, we assess framework based by compare the outcome and manual division. The findings outcome from this study have shown a new approach that automatically segments the blood leucocytes and identify it from a static microscope images. Initially, the method uses a trainable segmentation procedure and trained support vector machine classifier to accurately identify the position of the ROI. After that, filtering out non ROI have proposed based on histogram analysis to avoid the non ROI and chose the right object. Finally, identify the blood leucocytes type using

  1. Cancer cell imaging by stable wet near-field scanning optical microscope with resonance tracking method

    International Nuclear Information System (INIS)

    Park, Kyoung-Duck; Park, Doo-Jae; Jeong, Mun-Seok; Choi, Geun-Chang; Lee, Seung-Gol; Byeon, Clare-Chisu; Choi, Soo-Bong

    2014-01-01

    We report on a successful topographical and optical imaging of various cancer cells in liquid and in air by using a stable wet near-field scanning optical microscope that utilizes a resonance tracking method. We observed a clear dehydration which gives rise to a decrease in the cell volume down to 51%. In addition, a micro-ball lens effect due to the round-shaped young cancer cells was observed from near-field imaging, where the refractive index of young cancer cells was deduced.

  2. Cancer cell imaging by stable wet near-field scanning optical microscope with resonance tracking method

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kyoung-Duck [Sungkyunkwan University, Suwon (Korea, Republic of); Inha University, Incheon (Korea, Republic of); Park, Doo-Jae; Jeong, Mun-Seok [Sungkyunkwan University, Suwon (Korea, Republic of); Choi, Geun-Chang [Seoul National University, Seoul (Korea, Republic of); Lee, Seung-Gol [Inha University, Incheon (Korea, Republic of); Byeon, Clare-Chisu [Kyungpook National University, Daegu (Korea, Republic of); Choi, Soo-Bong [Incheon National University, Incheon (Korea, Republic of)

    2014-05-15

    We report on a successful topographical and optical imaging of various cancer cells in liquid and in air by using a stable wet near-field scanning optical microscope that utilizes a resonance tracking method. We observed a clear dehydration which gives rise to a decrease in the cell volume down to 51%. In addition, a micro-ball lens effect due to the round-shaped young cancer cells was observed from near-field imaging, where the refractive index of young cancer cells was deduced.

  3. Adaptive and automatic red blood cell counting method based on microscopic hyperspectral imaging technology

    Science.gov (United States)

    Liu, Xi; Zhou, Mei; Qiu, Song; Sun, Li; Liu, Hongying; Li, Qingli; Wang, Yiting

    2017-12-01

    Red blood cell counting, as a routine examination, plays an important role in medical diagnoses. Although automated hematology analyzers are widely used, manual microscopic examination by a hematologist or pathologist is still unavoidable, which is time-consuming and error-prone. This paper proposes a full-automatic red blood cell counting method which is based on microscopic hyperspectral imaging of blood smears and combines spatial and spectral information to achieve high precision. The acquired hyperspectral image data of the blood smear in the visible and near-infrared spectral range are firstly preprocessed, and then a quadratic blind linear unmixing algorithm is used to get endmember abundance images. Based on mathematical morphological operation and an adaptive Otsu’s method, a binaryzation process is performed on the abundance images. Finally, the connected component labeling algorithm with magnification-based parameter setting is applied to automatically select the binary images of red blood cell cytoplasm. Experimental results show that the proposed method can perform well and has potential for clinical applications.

  4. Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation.

    Science.gov (United States)

    Werley, Christopher A; Chien, Miao-Ping; Cohen, Adam E

    2017-12-01

    The rapid increase in the number and quality of fluorescent reporters and optogenetic actuators has yielded a powerful set of tools for recording and controlling cellular state and function. To achieve the full benefit of these tools requires improved optical systems with high light collection efficiency, high spatial and temporal resolution, and patterned optical stimulation, in a wide field of view (FOV). Here we describe our 'Firefly' microscope, which achieves these goals in a Ø6 mm FOV. The Firefly optical system is optimized for simultaneous photostimulation and fluorescence imaging in cultured cells. All but one of the optical elements are commercially available, yet the microscope achieves 10-fold higher light collection efficiency at its design magnification than the comparable commercially available microscope using the same objective. The Firefly microscope enables all-optical electrophysiology ('Optopatch') in cultured neurons with a throughput and information content unmatched by other neuronal phenotyping systems. This capability opens possibilities in disease modeling and phenotypic drug screening. We also demonstrate applications of the system to voltage and calcium recordings in human induced pluripotent stem cell derived cardiomyocytes.

  5. The system of digital-image optical microscope in semiconductor particle detector development

    International Nuclear Information System (INIS)

    Han Lixiang; Li Zhankui; Jin Genming; Wang Zhusheng; Xiao Guoqing

    2009-01-01

    Optical microscopic detection is very important in the process of semiconductor particle detector development. A system of digital-image optical microscope has been constructed with rather low price, which performance is comparable with the moderate-level imports. The system mounts powerful dry objective, and a 2μm resolution could be achieved. Observations with bright and dark field, polarized light,and interference light can be carried out on it. The system have large area on-line monitor,and the photographic device can be controlled by PC. It can be used in the control of defects and contaminations, pattern test, identification of crystal backing, inspection of the smoothness and the flatness of the crystal surface. It can also be used in some precise procedures, such as test, assembly, packaging and repairing. The quality of the bond could be examined by observing the appearance of the bond point and the microscopic structure of the solder. The surface fluctuation can be precisely measured under the microscope with the technology of multi-beam interference. In the article, the application of this system for semiconductor particle detector development has been illustrated, and the construction information has been described in detail. (authors)

  6. Immobilization method of yeast cells for intermittent contact mode imaging using the atomic force microscope

    International Nuclear Information System (INIS)

    De, Tathagata; Chettoor, Antony M.; Agarwal, Pranav; Salapaka, Murti V.; Nettikadan, Saju

    2010-01-01

    The atomic force microscope (AFM) is widely used for studying the surface morphology and growth of live cells. There are relatively fewer reports on the AFM imaging of yeast cells (Kasas and Ikai, 1995), (Gad and Ikai, 1995). Yeasts have thick and mechanically strong cell walls and are therefore difficult to attach to a solid substrate. In this report, a new immobilization technique for the height mode imaging of living yeast cells in solid media using AFM is presented. The proposed technique allows the cell surface to be almost completely exposed to the environment and studied using AFM. Apart from the new immobilization protocol, for the first time, height mode imaging of live yeast cell surface in intermittent contact mode is presented in this report. Stable and reproducible imaging over a 10-h time span is observed. A significant improvement in operational stability will facilitate the investigation of growth patterns and surface patterns of yeast cells.

  7. Hyperspectral microscope for in vivo imaging of microstructures and cells in tissues

    Science.gov (United States)

    Demos,; Stavros, G [Livermore, CA

    2011-05-17

    An optical hyperspectral/multimodal imaging method and apparatus is utilized to provide high signal sensitivity for implementation of various optical imaging approaches. Such a system utilizes long working distance microscope objectives so as to enable off-axis illumination of predetermined tissue thereby allowing for excitation at any optical wavelength, simplifies design, reduces required optical elements, significantly reduces spectral noise from the optical elements and allows for fast image acquisition enabling high quality imaging in-vivo. Such a technology provides a means of detecting disease at the single cell level such as cancer, precancer, ischemic, traumatic or other type of injury, infection, or other diseases or conditions causing alterations in cells and tissue micro structures.

  8. Field-ion microscope studies of the defect structure of the primary state of damage of irradiated metals

    International Nuclear Information System (INIS)

    Seidman, D.N.

    1975-01-01

    A review is presented of field ion microscope applications in studies of point defect distribution in irradiated metals. FIM results on the primary state of radiation damage in neutron and ion-irradiated iridium and tungsten, at both room-temperature and 78 0 K, showed that it consists of: (1) isolated vacancies; (2) depleted zones; (3) compact vacancy clusters of voids; and (4) dislocation loops. The fraction of vacancies stored in the dislocation loops represented a small fraction of the total vacancy concentration; in the case of tungsten it was approximately 10 percent. These FIM observations provide a simple explanation of the low yield-factor, determined by transmission electron microscopy, for a number of ion-irradiated metals

  9. Nanosecond Time-Resolved Microscopic Gate-Modulation Imaging of Polycrystalline Organic Thin-Film Transistors

    Science.gov (United States)

    Matsuoka, Satoshi; Tsutsumi, Jun'ya; Matsui, Hiroyuki; Kamata, Toshihide; Hasegawa, Tatsuo

    2018-02-01

    We develop a time-resolved microscopic gate-modulation (μ GM ) imaging technique to investigate the temporal evolution of the channel current and accumulated charges in polycrystalline pentacene thin-film transistors (TFTs). A time resolution of as high as 50 ns is achieved by using a fast image-intensifier system that could amplify a series of instantaneous optical microscopic images acquired at various time intervals after the stepped gate bias is switched on. The differential images obtained by subtracting the gate-off image allows us to acquire a series of temporal μ GM images that clearly show the gradual propagation of both channel charges and leaked gate fields within the polycrystalline channel layers. The frontal positions for the propagations of both channel charges and leaked gate fields coincide at all the time intervals, demonstrating that the layered gate dielectric capacitors are successively transversely charged up along the direction of current propagation. The initial μ GM images also indicate that the electric field effect is originally concentrated around a limited area with a width of a few micrometers bordering the channel-electrode interface, and that the field intensity reaches a maximum after 200 ns and then decays. The time required for charge propagation over the whole channel region with a length of 100 μ m is estimated at about 900 ns, which is consistent with the measured field-effect mobility and the temporal-response model for organic TFTs. The effect of grain boundaries can be also visualized by comparison of the μ GM images for the transient and the steady states, which confirms that the potential barriers at the grain boundaries cause the transient shift in the accumulated charges or the transient accumulation of additional charges around the grain boundaries.

  10. A preliminary investigation: the impact of microscopic condenser on depth of field in cytogenetic imaging

    Science.gov (United States)

    Ren, Liqiang; Qiu, Yuchen; Li, Zheng; Li, Yuhua; Zheng, Bin; Li, Shibo; Chen, Wei R.; Liu, Hong

    2013-02-01

    As one of the important components of optical microscopes, the condenser has a considerable impact on system performance, especially on the depth of field (DOF). DOF is a critical technical feature in cytogenetic imaging that may affect the efficiency and accuracy of clinical diagnosis. The purpose of this study is to investigate the influence of microscopic condenser on DOF using a prototype of transmitted optical microscope, based on objective and subjective evaluations. After the description of the relationship between condenser and objective lens and the theoretical analysis of the condenser impact on system numerical aperture and DOF, a standard resolution pattern and several cytogenetic samples are adopted to assess the condenser impact on DOF, respectively. The experimental results of these objective and subjective evaluations are in agreement with the theoretical analysis and show that, under the specific intermediate range of condenser numerical aperture ( NAcond ), the DOF value decreases with the increase of NAcond . Although the above qualitative results are obtained under the experimental conditions with a specific prototype system, the methods presented in this preliminary investigation could offer useful guidelines for optimizing operational parameters in cytogenetic imaging.

  11. Adaptive Scanning Optical Microscope (ASOM): A multidisciplinary optical microscope design for large field of view and high resolution imaging

    NARCIS (Netherlands)

    Potsaid, B.; Bellouard, Y.J.; Wen, J.T.

    2005-01-01

    From micro-assembly to biological observation, the optical microscope remains one of the most important tools for observing below the threshold of the naked human eye. However, in its conventional form, it suffers from a trade-off between resolution and field of view. This paper presents a new

  12. Characterization of platelet adhesion under flow using microscopic image sequence analysis.

    Science.gov (United States)

    Machin, M; Santomaso, A; Cozzi, M R; Battiston, M; Mazzuccato, M; De Marco, L; Canu, P

    2005-07-01

    A method for quantitative analysis of platelet deposition under flow is discussed here. The model system is based upon perfusion of blood platelets over an adhesive substrate immobilized on a glass coverslip acting as the lower surface of a rectangular flow chamber. The perfusion apparatus is mounted onto an inverted microscope equipped with epifluorescent illumination and intensified CCD video camera. Characterization is based on information obtained from a specific image analysis method applied to continuous sequences of microscopical images. Platelet recognition across the sequence of images is based on a time-dependent, bidimensional, gaussian-like pdf. Once a platelet is located,the variation of its position and shape as a function of time (i.e., the platelet history) can be determined. Analyzing the history we can establish if the platelet is moving on the surface, the frequency of this movement and the distance traveled before its resumes the velocity of a non-interacting cell. Therefore, we can determine how long the adhesion would last which is correlated to the resistance of the platelet-substrate bond. This algorithm enables the dynamic quantification of trajectories, as well as residence times, arrest and release frequencies for a high numbers of platelets at the same time. Statistically significant conclusions on platelet-surface interactions can then be obtained. An image analysis tool of this kind can dramatically help the investigation and characterization of the thrombogenic properties of artificial surfaces such as those used in artificial organs and biomedical devices.

  13. Open-dish incubator for live cell imaging with an inverted microscope.

    Science.gov (United States)

    Heidemann, Steven R; Lamoureux, Phillip; Ngo, Kha; Reynolds, Matthew; Buxbaum, Robert E

    2003-10-01

    Here we describe the design and fabrication of an inexpensive cell culture incubator for the stage of an inverted light microscope for use in live cell imaging. This device maintains the temperature of the cell culture at 37 degrees C with great stability and, after reaching equilibrium, provides focal stability of an image for 20-25 min with oil-immersion lenses. We describe two versions of the incubator: one for use with standard 60-mm plastic culture dishes, and the other version for imaging of cells on glass coverslips. Either can be made for less than $400. Most components are widely available commercially, and it requires only simple wiring and 3 h to assemble. Although the device is generally useful for live cell imaging on an inverted microscope, it is particularly suitable for work in which instruments are introduced into the culture, such as electrophysiology or micromanipulation. The design is based on the principle that control performance is limited by the lag time between detection and response. The key element of the design is a heated, temperature-controlled aluminum ring serving as a mini-incubator surrounding the culture vessel. For this reason, we call our design a "ringcubator."

  14. Imaging C. elegans embryos using an epifluorescent microscope and open source software.

    Science.gov (United States)

    Verbrugghe, Koen J C; Chan, Raymond C

    2011-03-24

    Cellular processes, such as chromosome assembly, segregation and cytokinesis,are inherently dynamic. Time-lapse imaging of living cells, using fluorescent-labeled reporter proteins or differential interference contrast (DIC) microscopy, allows for the examination of the temporal progression of these dynamic events which is otherwise inferred from analysis of fixed samples(1,2). Moreover, the study of the developmental regulations of cellular processes necessitates conducting time-lapse experiments on an intact organism during development. The Caenorhabiditis elegans embryo is light-transparent and has a rapid, invariant developmental program with a known cell lineage(3), thus providing an ideal experiment model for studying questions in cell biology(4,5)and development(6-9). C. elegans is amendable to genetic manipulation by forward genetics (based on random mutagenesis(10,11)) and reverse genetics to target specific genes (based on RNAi-mediated interference and targeted mutagenesis(12-15)). In addition, transgenic animals can be readily created to express fluorescently tagged proteins or reporters(16,17). These traits combine to make it easy to identify the genetic pathways regulating fundamental cellular and developmental processes in vivo(18-21). In this protocol we present methods for live imaging of C. elegans embryos using DIC optics or GFP fluorescence on a compound epifluorescent microscope. We demonstrate the ease with which readily available microscopes, typically used for fixed sample imaging, can also be applied for time-lapse analysis using open-source software to automate the imaging process.

  15. The virtual microscopy database-sharing digital microscope images for research and education.

    Science.gov (United States)

    Lee, Lisa M J; Goldman, Haviva M; Hortsch, Michael

    2018-02-14

    Over the last 20 years, virtual microscopy has become the predominant modus of teaching the structural organization of cells, tissues, and organs, replacing the use of optical microscopes and glass slides in a traditional histology or pathology laboratory setting. Although virtual microscopy image files can easily be duplicated, creating them requires not only quality histological glass slides but also an expensive whole slide microscopic scanner and massive data storage devices. These resources are not available to all educators and researchers, especially at new institutions in developing countries. This leaves many schools without access to virtual microscopy resources. The Virtual Microscopy Database (VMD) is a new resource established to address this problem. It is a virtual image file-sharing website that allows researchers and educators easy access to a large repository of virtual histology and pathology image files. With the support from the American Association of Anatomists (Bethesda, MD) and MBF Bioscience Inc. (Williston, VT), registration and use of the VMD are currently free of charge. However, the VMD site is restricted to faculty and staff of research and educational institutions. Virtual Microscopy Database users can upload their own collection of virtual slide files, as well as view and download image files for their own non-profit educational and research purposes that have been deposited by other VMD clients. Anat Sci Educ. © 2018 American Association of Anatomists. © 2018 American Association of Anatomists.

  16. Performance limitations of imaging microscopes for soft x-ray applications

    International Nuclear Information System (INIS)

    Lewotsky, K.L.; Kotha, A.; Harvey, J.E.

    1993-01-01

    Recent advances in the fabrication of nanometer-scale multilayer structures have yielded high-reflectance mirrors operating at near-normal incidence for soft X-ray wavelengths. These developments have stimulated renewed interest in high-resolution soft X-ray microscopy. The design of a Schwarzschild imaging microscope for soft X-ray applications has been reported by Hoover and Shealy. Based upon a geometrical ray-trace analysis of the residual design errors, diffraction-limited performance at a wavelength of 100 angstrom was predicted over an object size (diameter) of 0.4 mm. In this paper the authors expand upon the previous analysis of the Schwarzschild X-ray microscope design by determining the total image degradation due to diffraction, geometrical aberrations, alignment errors, and realistic assumptions concerning optical fabrication errors. NASA's Optical Surface Analysis Code (OSAC) is used to model the image degradation effects of residual surface irregularities over the entire range of relevant spatial frequencies. This includes small angle scattering effects due to mid spatial frequency surface errors falling between the traditional figure and finish specifications. Performance predictions are presented parametrically to provide some insight into the optical fabrication and alignment tolerances necessary to meet a particular image quality requirement

  17. Imaging the p-n junction in a gallium nitride nanowire with a scanning microwave microscope

    Energy Technology Data Exchange (ETDEWEB)

    Imtiaz, Atif [Physical Measurement Laboratory, National Institute of Standards and Technology, Boulder, Colorado 80305 (United States); Department of Electrical, Computer, and Energy Engineering, University of Colorado, Boulder, Colorado 80309 (United States); Wallis, Thomas M.; Brubaker, Matt D.; Blanchard, Paul T.; Bertness, Kris A.; Sanford, Norman A.; Kabos, Pavel, E-mail: kabos@boulder.nist.gov [Physical Measurement Laboratory, National Institute of Standards and Technology, Boulder, Colorado 80305 (United States); Weber, Joel C. [Physical Measurement Laboratory, National Institute of Standards and Technology, Boulder, Colorado 80305 (United States); Department of Mechanical Engineering, University of Colorado, Boulder, Colorado 80309 (United States); Coakley, Kevin J. [Information Technology Laboratory, National Institute of Standards and Technology, Boulder, Colorado 80305 (United States)

    2014-06-30

    We used a broadband, atomic-force-microscope-based, scanning microwave microscope (SMM) to probe the axial dependence of the charge depletion in a p-n junction within a gallium nitride nanowire (NW). SMM enables the visualization of the p-n junction location without the need to make patterned electrical contacts to the NW. Spatially resolved measurements of S{sub 11}{sup ′}, which is the derivative of the RF reflection coefficient S{sub 11} with respect to voltage, varied strongly when probing axially along the NW and across the p-n junction. The axial variation in S{sub 11}{sup ′}  effectively mapped the asymmetric depletion arising from the doping concentrations on either side of the junction. Furthermore, variation of the probe tip voltage altered the apparent extent of features associated with the p-n junction in S{sub 11}{sup ′} images.

  18. Scanning Electron Microscope Calibration Using a Multi-Image Non-Linear Minimization Process

    Science.gov (United States)

    Cui, Le; Marchand, Éric

    2015-04-01

    A scanning electron microscope (SEM) calibrating approach based on non-linear minimization procedure is presented in this article. A part of this article has been published in IEEE International Conference on Robotics and Automation (ICRA), 2014. . Both the intrinsic parameters and the extrinsic parameters estimations are achieved simultaneously by minimizing the registration error. The proposed approach considers multi-images of a multi-scale calibration pattern view from different positions and orientations. Since the projection geometry of the scanning electron microscope is different from that of a classical optical sensor, the perspective projection model and the parallel projection model are considered and compared with distortion models. Experiments are realized by varying the position and the orientation of a multi-scale chessboard calibration pattern from 300× to 10,000×. The experimental results show the efficiency and the accuracy of this approach.

  19. Imaging of current density distributions with a Nb weak-link scanning nano-SQUID microscope

    Science.gov (United States)

    Shibata, Yusuke; Nomura, Shintaro; Kashiwaya, Hiromi; Kashiwaya, Satoshi; Ishiguro, Ryosuke; Takayanagi, Hideaki

    2015-10-01

    Superconducting quantum interference devices (SQUIDs) are accepted as one of the highest magnetic field sensitive probes. There are increasing demands to image local magnetic fields to explore spin properties and current density distributions in a two-dimensional layer of semiconductors or superconductors. Nano-SQUIDs have recently attracting much interest for high spatial resolution measurements in nanometer-scale samples. Whereas weak-link Dayem Josephson junction nano-SQUIDs are suitable to miniaturization, hysteresis in current-voltage (I-V) characteristics that is often observed in Dayem Josephson junction is not desirable for a scanning microscope. Here we report on our development of a weak-link nano-SQUIDs scanning microscope with small hysteresis in I-V curve and on reconstructions of two-dimensional current density vector in two-dimensional electron gas from measured magnetic field.

  20. Microscope-integrated optical coherence tomography for image-aided positioning of glaucoma surgery

    Science.gov (United States)

    Li, Xiqi; Wei, Ling; Dong, Xuechuan; Huang, Ping; Zhang, Chun; He, Yi; Shi, Guohua; Zhang, Yudong

    2015-07-01

    Most glaucoma surgeries involve creating new aqueous outflow pathways with the use of a small surgical instrument. This article reported a microscope-integrated, real-time, high-speed, swept-source optical coherence tomography system (SS-OCT) with a 1310-nm light source for glaucoma surgery. A special mechanism was designed to produce an adjustable system suitable for use in surgery. A two-graphic processing unit architecture was used to speed up the data processing and real-time volumetric rendering. The position of the surgical instrument can be monitored and measured using the microscope and a grid-inserted image of the SS-OCT. Finally, experiments were simulated to assess the effectiveness of this integrated system. Experimental results show that this system is a suitable positioning tool for glaucoma surgery.

  1. MIDAS - an atomic force microscope for in-situ imaging of cometary dust particles

    International Nuclear Information System (INIS)

    Fehringer, H.M.; Ruedenauer, F.G.; Steiger, W.

    1997-02-01

    Comets are interesting bodies, since they are considered to consist of matter remaining in essentially unchanged chemistry from the presolar nebula. Investigation of cometary matter therefore permits to draw conclusion s with respect to the composition of presolar matter. The atomic force microscope MIDAS will be the first instrument to analyze, within ESA's ROSETTA-mission priestine cometary matter in the form of dust particles emitted by comet WIRTANEN during its perihelion in 2013. Within this project, a dust model has been developed, permitting estimation of dust collection times required for statistically significant imaging of cometary particles. The dynamics of dust collection has been developed and experimental dust collection surfaces have been produced making use of modem nanostructuring techniques. Mechanical properties of 3-dimensional piezo-control elements, which are an essential part of the MIDAS microscope, have been determined. (author)

  2. Microscope-integrated optical coherence tomography for image-aided positioning of glaucoma surgery.

    Science.gov (United States)

    Li, Xiqi; Wei, Ling; Dong, Xuechuan; Huang, Ping; Zhang, Chun; He, Yi; Shi, Guohua; Zhang, Yudong

    2015-07-01

    Most glaucoma surgeries involve creating new aqueous outflow pathways with the use of a small surgical instrument. This article reported a microscope-integrated, real-time, high-speed, swept-source optical coherence tomography system (SS-OCT) with a 1310-nm light source for glaucoma surgery. A special mechanism was designed to produce an adjustable system suitable for use in surgery. A two-graphic processing unit architecture was used to speed up the data processing and real-time volumetric rendering. The position of the surgical instrument can be monitored and measured using the microscope and a grid-inserted image of the SS-OCT. Finally, experiments were simulated to assess the effectiveness of this integrated system. Experimental results show that this system is a suitable positioning tool for glaucoma surgery.

  3. Novel low-dose imaging technique for characterizing atomic structures through scanning transmission electron microscope

    Science.gov (United States)

    Su, Chia-Ping; Syu, Wei-Jhe; Hsiao, Chien-Nan; Lai, Ping-Shan; Chen, Chien-Chun

    2017-08-01

    To investigate dislocations or heterostructures across interfaces is now of great interest to condensed matter and materials scientists. With the advances in aberration-corrected electron optics, the scanning transmission electron microscope has demonstrated its excellent capability of characterizing atomic structures within nanomaterials, and well-resolved atomic-resolution images can be obtained through long-exposure data acquisition. However, the sample drifting, carbon contamination, and radiation damage hinder further analysis, such as deriving three-dimensional (3D) structures from a series of images. In this study, a method for obtaining atomic-resolution images with significantly reduced exposure time was developed, using which an original high-resolution image with approximately one tenth the electron dose can be obtained by combining a fast-scan high-magnification image and a slow-scan low-magnification image. The feasibility of obtaining 3D atomic structures using the proposed approach was demonstrated through multislice simulation. Finally, the feasibility and accuracy of image restoration were experimentally verified. This general method cannot only apply to electron microscopy but also benefit to image radiation-sensitive materials using various light sources.

  4. Atomic imaging using secondary electrons in a scanning transmission electron microscope: experimental observations and possible mechanisms.

    Science.gov (United States)

    Inada, H; Su, D; Egerton, R F; Konno, M; Wu, L; Ciston, J; Wall, J; Zhu, Y

    2011-06-01

    We report detailed investigation of high-resolution imaging using secondary electrons (SE) with a sub-nanometer probe in an aberration-corrected transmission electron microscope, Hitachi HD2700C. This instrument also allows us to acquire the corresponding annular dark-field (ADF) images both simultaneously and separately. We demonstrate that atomic SE imaging is achievable for a wide range of elements, from uranium to carbon. Using the ADF images as a reference, we studied the SE image intensity and contrast as functions of applied bias, atomic number, crystal tilt, and thickness to shed light on the origin of the unexpected ultrahigh resolution in SE imaging. We have also demonstrated that the SE signal is sensitive to the terminating species at a crystal surface. A possible mechanism for atomic-scale SE imaging is proposed. The ability to image both the surface and bulk of a sample at atomic-scale is unprecedented, and can have important applications in the field of electron microscopy and materials characterization. Copyright © 2010 Elsevier B.V. All rights reserved.

  5. Manipulation of inverted and direct opals by a focused ion beam scanning electron microscope (FIB SEM)

    International Nuclear Information System (INIS)

    Magni, S; Milani, M; Tatti, F; Savoia, C

    2008-01-01

    Focused ion beam (FIB) milling techniques are presented aiming at the manipulation of both tin dioxide (SnO 2 ) inverted opals and polystyrene (PS) direct opals. Different SnO 2 opals are considered in order to estimate the regularity of their bulk after the production. A SnO 2 mesoporous monolith is FIB micromachined to make it suitable for optical applications. PS direct opals are structured by FIB milling at different scales. Ordered arrays of PS opals are modified by selectively removing a single sphere. In performing this task, we discuss the effects on the FIB milling due to the gas-assisted enhanced etching and to the binding of the nearest neighbours. Techniques to achieve imaging of PS opals in absence of a conductive coating are also brought up. Furthermore, isolated PS spheres are drilled with or without enhanced etching in order to produce controlled defects on them. The FIB-assisted manipulations we show may find potential applications in the field of photonic crystals, (bio)sensors and lithography assisted by colloidal masks.

  6. Imaging process in field ion microscopy from the FEM to the atom-probe

    International Nuclear Information System (INIS)

    Mueller, E.W.

    1976-01-01

    The development of the technique and the interpretations of the imaging mechanism, which involve a number of complex phenomena, are traced from the invention of the field emission microscope and the discovery of field desorption to the first field ion microscope. Subsequent introduction of cryogenic operation and utilization of field evaporation led, prior to 1960, to the attainment of high-quality images with full resolution of the atomic lattice and to fundamental applications in the study of lattice defects and other phenomena of physical metallurgy. Extension to the lower-melting metals by imaging with neon was aided by the availability of image intensification technology. The invention of the atom-probe FIM in 1967, permitting surface analysis with ultimate single-atom sensitivity, also brought the discovery of unexpected effects, such as field adsorption of the noble images gases and the abundant formation of metal-noble gas molecular ions. These phenomena, together with recent results of field desorption microcopy, must be included in a refined interpretation of the imaging process. 16 figs., 115 references

  7. eSIP: A Novel Solution-Based Sectioned Image Property Approach for Microscope Calibration.

    Directory of Open Access Journals (Sweden)

    Malte Butzlaff

    Full Text Available Fluorescence confocal microscopy represents one of the central tools in modern sciences. Correspondingly, a growing amount of research relies on the development of novel microscopic methods. During the last decade numerous microscopic approaches were developed for the investigation of various scientific questions. Thereby, the former qualitative imaging methods became replaced by advanced quantitative methods to gain more and more information from a given sample. However, modern microscope systems being as complex as they are, require very precise and appropriate calibration routines, in particular when quantitative measurements should be compared over longer time scales or between different setups. Multispectral beads with sub-resolution size are often used to describe the point spread function and thus the optical properties of the microscope. More recently, a fluorescent layer was utilized to describe the axial profile for each pixel, which allows a spatially resolved characterization. However, fabrication of a thin fluorescent layer with matching refractive index is technically not solved yet. Therefore, we propose a novel type of calibration concept for sectioned image property (SIP measurements which is based on fluorescent solution and makes the calibration concept available for a broader number of users. Compared to the previous approach, additional information can be obtained by application of this extended SIP chart approach, including penetration depth, detected number of photons, and illumination profile shape. Furthermore, due to the fit of the complete profile, our method is less susceptible to noise. Generally, the extended SIP approach represents a simple and highly reproducible method, allowing setup independent calibration and alignment procedures, which is mandatory for advanced quantitative microscopy.

  8. Neurite density imaging versus imaging of microscopic anisotropy in diffusion MRI: A model comparison using spherical tensor encoding.

    Science.gov (United States)

    Lampinen, Björn; Szczepankiewicz, Filip; Mårtensson, Johan; van Westen, Danielle; Sundgren, Pia C; Nilsson, Markus

    2017-02-15

    In diffusion MRI (dMRI), microscopic diffusion anisotropy can be obscured by orientation dispersion. Separation of these properties is of high importance, since it could allow dMRI to non-invasively probe elongated structures such as neurites (axons and dendrites). However, conventional dMRI, based on single diffusion encoding (SDE), entangles microscopic anisotropy and orientation dispersion with intra-voxel variance in isotropic diffusivity. SDE-based methods for estimating microscopic anisotropy, such as the neurite orientation dispersion and density imaging (NODDI) method, must thus rely on model assumptions to disentangle these features. An alternative approach is to directly quantify microscopic anisotropy by the use of variable shape of the b-tensor. Along those lines, we here present the 'constrained diffusional variance decomposition' (CODIVIDE) method, which jointly analyzes data acquired with diffusion encoding applied in a single direction at a time (linear tensor encoding, LTE) and in all directions (spherical tensor encoding, STE). We then contrast the two approaches by comparing neurite density estimated using NODDI with microscopic anisotropy estimated using CODIVIDE. Data were acquired in healthy volunteers and in glioma patients. NODDI and CODIVIDE differed the most in gray matter and in gliomas, where NODDI detected a neurite fraction higher than expected from the level of microscopic diffusion anisotropy found with CODIVIDE. The discrepancies could be explained by the NODDI tortuosity assumption, which enforces a connection between the neurite density and the mean diffusivity of tissue. Our results suggest that this assumption is invalid, which leads to a NODDI neurite density that is inconsistent between LTE and STE data. Using simulations, we demonstrate that the NODDI assumptions result in parameter bias that precludes the use of NODDI to map neurite density. With CODIVIDE, we found high levels of microscopic anisotropy in white matter

  9. Development of Scanning-Imaging X-Ray Microscope for Quantitative Three-Dimensional Phase Contrast Microimaging

    International Nuclear Information System (INIS)

    Takeuchi, Akihisa; Suzuki, Yoshio; Uesugi, Kentaro

    2013-01-01

    A novel x-ray microscope system has been developed for the purpose of quantitative and sensitive three-dimensional (3D) phase-contrast x-ray microimaging. The optical system is a hybrid that consists of a scanning microscope optics with a one-dimensional (1D) focusing (line-focusing) device and an imaging microscope optics with a 1D objective. These two optics are orthogonally arranged regarding their common optical axis. Each is used for forming each dimension of two-dimensional (2D) image. The same data acquisition process as that of the scanning microscope system enables quantitative and sensitive x-ray imaging such as phase contrast and absorption contrast. Because a 2D image is measured with only 1D translation scan, much shorter measurement time than that of conventional scanning optics has been realized. By combining a computed tomography (CT) technique, some 3D CT application examples are demonstrated

  10. High-speed imaging upgrade for a standard sample scanning atomic force microscope using small cantilevers

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Jonathan D.; Nievergelt, Adrian; Erickson, Blake W.; Yang, Chen; Dukic, Maja; Fantner, Georg E., E-mail: georg.fantner@epfl.ch [Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland)

    2014-09-15

    We present an atomic force microscope (AFM) head for optical beam deflection on small cantilevers. Our AFM head is designed to be small in size, easily integrated into a commercial AFM system, and has a modular architecture facilitating exchange of the optical and electronic assemblies. We present two different designs for both the optical beam deflection and the electronic readout systems, and evaluate their performance. Using small cantilevers with our AFM head on an otherwise unmodified commercial AFM system, we are able to take tapping mode images approximately 5–10 times faster compared to the same AFM system using large cantilevers. By using additional scanner turnaround resonance compensation and a controller designed for high-speed AFM imaging, we show tapping mode imaging of lipid bilayers at line scan rates of 100–500 Hz for scan areas of several micrometers in size.

  11. Advances in imaging and electron physics the scanning transmission electron microscope

    CERN Document Server

    Hawkes, Peter W

    2009-01-01

    Advances in Imaging and Electron Physics merges two long-running serials--Advances in Electronics and Electron Physics and Advances in Optical and Electron Microscopy. This series features extended articles on the physics of electron devices (especially semiconductor devices), particle optics at high and low energies, microlithography, image science and digital image processing, electromagnetic wave propagation, electron microscopy, and the computing methods used in all these domains.  This particular volume presents several timely articles on the scanning transmission electron microscope. Updated with contributions from leading international scholars and industry experts Discusses hot topic areas and presents current and future research trends Provides an invaluable reference and guide for physicists, engineers and mathematicians.

  12. High-speed multi-frame dynamic transmission electron microscope image acquisition system with arbitrary timing

    Science.gov (United States)

    Reed, Bryan W.; DeHope, William J.; Huete, Glenn; LaGrange, Thomas B.; Shuttlesworth, Richard M.

    2016-02-23

    An electron microscope is disclosed which has a laser-driven photocathode and an arbitrary waveform generator (AWG) laser system ("laser"). The laser produces a train of temporally-shaped laser pulses each being of a programmable pulse duration, and directs the laser pulses to the laser-driven photocathode to produce a train of electron pulses. An image sensor is used along with a deflector subsystem. The deflector subsystem is arranged downstream of the target but upstream of the image sensor, and has a plurality of plates. A control system having a digital sequencer controls the laser and a plurality of switching components, synchronized with the laser, to independently control excitation of each one of the deflector plates. This allows each electron pulse to be directed to a different portion of the image sensor, as well as to enable programmable pulse durations and programmable inter-pulse spacings.

  13. High-speed multiframe dynamic transmission electron microscope image acquisition system with arbitrary timing

    Science.gov (United States)

    Reed, Bryan W.; DeHope, William J.; Huete, Glenn; LaGrange, Thomas B.; Shuttlesworth, Richard M.

    2015-10-20

    An electron microscope is disclosed which has a laser-driven photocathode and an arbitrary waveform generator (AWG) laser system ("laser"). The laser produces a train of temporally-shaped laser pulses of a predefined pulse duration and waveform, and directs the laser pulses to the laser-driven photocathode to produce a train of electron pulses. An image sensor is used along with a deflector subsystem. The deflector subsystem is arranged downstream of the target but upstream of the image sensor, and has two pairs of plates arranged perpendicular to one another. A control system controls the laser and a plurality of switching components synchronized with the laser, to independently control excitation of each one of the deflector plates. This allows each electron pulse to be directed to a different portion of the image sensor, as well as to be provided with an independently set duration and independently set inter-pulse spacings.

  14. Image processing of muscle striations below the resolution limit of the light microscope

    International Nuclear Information System (INIS)

    Burns, D.H.; Holdren, D.N.; Periasamy, A.; Everts, W.C.; Pollack, G.H.

    1985-01-01

    We describe the use of digital deconvolution in the study of muscle striations below the resolution imposed by the optical diffraction of our video light microscope. To use deconvolution procedures on muscle images, the transfer function of the optical system is first characterized. This is accomplished by imaging a step object and fitting the image with the combination of a first order Bessel and Guassian function using a non-linear least squares approach. Due to the ill-conditioned nature of deconvolution, however, ambiguity in the reconstruction is sometimes found. To allow better estimation of the true object, separate deconvolution approaches are used and the reconstructions compared. In this manner, the fine structure of muscle striations is determined

  15. First test model of the optical microscope which images the whole vertical particle tracks without any depth scanning

    International Nuclear Information System (INIS)

    Soroko, L.M.

    2001-01-01

    The first test model of the optical microscope which produces the in focus image of the whole vertical particle track without depth scanning is described. The in focus image of the object consisting of the linear array of the point-like elements was obtained. A comparison with primary out of focus image of such an object has been made

  16. In situ transmission electron microscope studies of ion irradiation-induced and irradiation-enhanced phase changes

    International Nuclear Information System (INIS)

    Allen, C.W.

    1992-01-01

    Motivated at least initially by materials needs for nuclear reactor development, extensive irradiation effects studies employing transmission electron microscopes (TEM) have been performed for several decades, involving irradiation-induced and irradiation-enhanced microstructural changes, including phase transformations such as precipitation, dissolution, crystallization, amorphization, and order-disorder phenomena. From the introduction of commercial high voltage electron microscopes (HVEM) in the mid-1960s, studies of electron irradiation effects have constituted a major aspect of HVEM application in materials science. For irradiation effects studies two additional developments have had particularly significant impact; the development of TEM specimen holder sin which specimen temperature can be controlled in the range 10-2200 K and the interfacing of ion accelerators which allows in situ TEM studies of irradiation effects and the ion beam modification of materials within this broad temperature range. This paper treats several aspects of in situ studies of electron and ion beam-induced and enhanced phase changes and presents two case studies involving in situ experiments performed in an HVEM to illustrate the strategies of such an approach of the materials research of irradiation effects

  17. In-situ field-ion microscope study of the recovery behavior of heavy metal ion-irradiated tungsten, tungsten (rhenium) alloys and molybdenum

    International Nuclear Information System (INIS)

    Nielsen, C.H.

    1977-06-01

    Three field ion microscope (FIM) experiments were carried out to study the annealing behavior of heavy ion irradiated tungsten, tungsten (rhenium) alloys and molybdenum. The first experiment dealt with the stage I long-range migration of tungsten self interstitial atoms (SIAs) in high purity tungsten of resistivity ratio, R = 24,000 (R = rho 300 /rho 4 . 2 , where rho 300 and rho 4 . 2 are the room temperature and 0 0 C resistivities). The FIM specimens were irradiated in situ at 18 K with 30 keV W + ions to an average dose of 5 x 10 12 ions cm -2 and subsequently examined by the pulsed-field evaporation technique. The second experiment dealt with the phenomenon of impurity atom trapping of SIAs during long-range migration. It was shown that rhenium atoms in a tungsten matrix tend to capture tungsten SIAs and remain bound up to temperatures as high as 390 K. The final experiment was concerned with the low temperature annealing kinetics of irradiated molybdenum. High purity molybdenum of resistivity ratio R = 5700 was irradiated at 10 K with 30 keV Mo + ions to a dose of approximately 5 x 10 12 ions cm -2 . The results indicated that the electric field has only a minimal effect on the SIA annealing kinetics. This tends to strengthen the contention that the molybdenum SIA becomes mobile at 32 K

  18. Nucleus and cytoplasm segmentation in microscopic images using K-means clustering and region growing.

    Science.gov (United States)

    Sarrafzadeh, Omid; Dehnavi, Alireza Mehri

    2015-01-01

    Segmentation of leukocytes acts as the foundation for all automated image-based hematological disease recognition systems. Most of the time, hematologists are interested in evaluation of white blood cells only. Digital image processing techniques can help them in their analysis and diagnosis. The main objective of this paper is to detect leukocytes from a blood smear microscopic image and segment them into their two dominant elements, nucleus and cytoplasm. The segmentation is conducted using two stages of applying K-means clustering. First, the nuclei are segmented using K-means clustering. Then, a proposed method based on region growing is applied to separate the connected nuclei. Next, the nuclei are subtracted from the original image. Finally, the cytoplasm is segmented using the second stage of K-means clustering. The results indicate that the proposed method is able to extract the nucleus and cytoplasm regions accurately and works well even though there is no significant contrast between the components in the image. In this paper, a method based on K-means clustering and region growing is proposed in order to detect leukocytes from a blood smear microscopic image and segment its components, the nucleus and the cytoplasm. As region growing step of the algorithm relies on the information of edges, it will not able to separate the connected nuclei more accurately in poor edges and it requires at least a weak edge to exist between the nuclei. The nucleus and cytoplasm segments of a leukocyte can be used for feature extraction and classification which leads to automated leukemia detection.

  19. Science applications of a multispectral microscopic imager for the astrobiological exploration of Mars.

    Science.gov (United States)

    Núñez, Jorge I; Farmer, Jack D; Sellar, R Glenn; Swayze, Gregg A; Blaney, Diana L

    2014-02-01

    Future astrobiological missions to Mars are likely to emphasize the use of rovers with in situ petrologic capabilities for selecting the best samples at a site for in situ analysis with onboard lab instruments or for caching for potential return to Earth. Such observations are central to an understanding of the potential for past habitable conditions at a site and for identifying samples most likely to harbor fossil biosignatures. The Multispectral Microscopic Imager (MMI) provides multispectral reflectance images of geological samples at the microscale, where each image pixel is composed of a visible/shortwave infrared spectrum ranging from 0.46 to 1.73 μm. This spectral range enables the discrimination of a wide variety of rock-forming minerals, especially Fe-bearing phases, and the detection of hydrated minerals. The MMI advances beyond the capabilities of current microimagers on Mars by extending the spectral range into the infrared and increasing the number of spectral bands. The design employs multispectral light-emitting diodes and an uncooled indium gallium arsenide focal plane array to achieve a very low mass and high reliability. To better understand and demonstrate the capabilities of the MMI for future surface missions to Mars, we analyzed samples from Mars-relevant analog environments with the MMI. Results indicate that the MMI images faithfully resolve the fine-scale microtextural features of samples and provide important information to help constrain mineral composition. The use of spectral endmember mapping reveals the distribution of Fe-bearing minerals (including silicates and oxides) with high fidelity, along with the presence of hydrated minerals. MMI-based petrogenetic interpretations compare favorably with laboratory-based analyses, revealing the value of the MMI for future in situ rover-mediated astrobiological exploration of Mars. Mars-Microscopic imager-Multispectral imaging-Spectroscopy-Habitability-Arm instrument.

  20. Garnet film rotator applied in polarizing microscope for domain image modulation (abstract)

    Science.gov (United States)

    Wakabayashi, K.; Numata, T.; Inokuchi, S.

    1991-04-01

    A garnet film polarization rotator placed before the analyzer in a polarizing microscope was investigated to obtain the difference image of a positive and a negative one of magnetic domain in real time along with an image processor. In the difference image, a nonmagnetic image can be reduced and hence the weak magnetic contrast enhanced. Theoretical calculation of S/N and contrast C of the domain image as a function of the rotation shows they take maxima at the rotation angle of 2.6° and 0.1°, respectively, with the extinction ratio of e=4×10-6 of a polarizing microscope. Thus, since the thickness of the garnet film required is 1 μm or so, the absorption by the garnet rotator does not bring a serious problem even in a visible region for the domain observation. The optimum rotation of the rotator for a high quality observation was obtained by a quantitative study of images obtained experimentally as well as by a visual evaluation. A magnetically unsaturated garnet film with perpendicular magnetization (i.e., multidomain) was employed as a rotator, in which the polarization rotation angle θm of the undeflected beam with respect to the light diffraction could be continuously varied by an applied magnetic field. The dependences of S/N and C on θm were measured, resulting in a well agreement between the measured and the calculated. The visually best image was obtained at θm=0.5° which made the product of S/N and C maximum. The domain image of the Kerr rotation angle of θk=0.22° was observed in S/N=47 dB and C=0.4 when Ar+ laser (λ=515 nm) of tenths of a watt was employed as a light source. Since the domain image with 47 dB S/N does not need an image summation for a noise reduction, a garnet film rotator makes it possible to invert the contrast of a domain image in a real time for an improved domain observation.

  1. High-resolution electron microscope image analysis approach for superconductor YBa2Cu3O7-x

    International Nuclear Information System (INIS)

    Xu, J.; Lu, F.; Jia, C.; Hua, Z.

    1991-01-01

    In this paper, an HREM (High-resolution electron microscope) image analysis approach has been developed. The image filtering, segmentation and particles extraction based on gray-scale mathematical morphological operations, are performed on the original HREM image. The final image is a pseudocolor image, with the background removed, relatively uniform brightness, filtered slanting elongation, regular shape for every kind of particle, and particle boundaries that no longer touch each other so that the superconducting material structure can be shown clearly

  2. In vivo microscopic imaging of the bronchial mucosa using an endo-cytoscopy system.

    Science.gov (United States)

    Shibuya, Kiyoshi; Fujiwara, Taiki; Yasufuku, Kazuhiro; Alaa, Mohamed; Chiyo, Masako; Nakajima, Takahiro; Hoshino, Hidehisa; Hiroshima, Kenzo; Nakatani, Yukio; Yoshino, Ichiro

    2011-05-01

    We investigated the capabilities of an endo-cytoscopy system (ECS) that enables microscopic imaging of the tracheobronchial tree during bronchoscopy, including normal bronchial epithelium, dysplastic mucosa and squamous cell carcinoma. The newly developed ECS has a 3.2 mm diameter that can be passed through the 4.2 mm working channel of a mother endoscope for insertion of the ECS. It has a high magnification of 570× on a 17 in. video monitor. Twenty-two patients (7 squamous cell carcinoma, 11 squamous dysplasia and 4 after PDT therapies) were underwent white light, NBI light and AFI bronchoscopy. Both abnormal areas of interest and normal bronchial mucosa were stained with 0.5% methylene blue and examined with ECS at high magnification (570×). Histological examinations using haematoxylin and eosin staining were made of biopsied specimens. Analyzed ECS images were compared with the corresponding histological examinations. In normal bronchial mucosa, ciliated columnar epithelial cells were visible. In bronchial squamous dysplasia, superficial cells with abundant cytoplasm were arranged regularly. In squamous cell carcinoma, large, polymorphic tumor cells showed increased cellular densities with irregular stratified patterns. These ECS images corresponded well with the light-microscopic examination of conventional histology. ECS was useful for the discrimination between normal bronchial epithelial cells and dysplastic cells or malignant cells during bronchoscopy in real time. This novel technology has an excellent potential to provide in vivo diagnosis during bronchoscopic examinations. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  3. Martian Microscope

    Science.gov (United States)

    2004-01-01

    The microscopic imager (circular device in center) is in clear view above the surface at Meridiani Planum, Mars, in this approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity. The image was taken on the 9th sol of the rover's journey. The microscopic imager is located on the rover's instrument deployment device, or arm. The arrow is pointing to the lens of the instrument. Note the dust cover, which flips out to the left of the lens, is open. This approximated color image was created using the camera's violet and infrared filters as blue and red.

  4. Scanning tunnelling microscope imaging of nanoscale electron density gradients on the surface of GaAs

    International Nuclear Information System (INIS)

    Hamilton, B; Jacobs, J; Missous, M

    2003-01-01

    This paper is concerned with the scanning tunnelling microscope tunnelling conditions needed to produce constant current images dominated either by surface topology or by electronic effects. A model experimental structure was produced by cleaving a GaAs multiδ-doped layer in UHV and so projecting a spatially varying electron gas density onto the (110) surface. This cross sectional electron density varies on a nanometre scale in the [100] growth direction. The electronic structure and tunnelling properties of this system were modelled, and the tunnelling conditions favouring sensitivity to the surface electron gas density determined

  5. Textures of the soils and rocks at Gusev crater from Spirit's Microscopic Imager

    DEFF Research Database (Denmark)

    Herkenhoff, K.E.; Squyres, S.W.; Arvidson, R.

    2004-01-01

    The Microscopic Imager on the Spirit rover analyzed the textures of the soil and rocks at Gusev crater on Mars at a resolution of 100 micrometers. Weakly bound agglomerates of dust are present in the soil near the Columbia Memorial Station. Some of the brushed or abraded rock surfaces show igneous...... textures and evidence for alteration rinds, coatings, and veins consistent with secondary mineralization. The rock textures are consistent with a volcanic origin and subsequent alteration and/or weathering by impact events, wind, and possibly water....

  6. Analysis of hydrogen distribution on Mg-Ni alloy surface by scanning electron-stimulated desorption ion microscope (SESDIM)

    International Nuclear Information System (INIS)

    Yamaga, Atsushi; Hibino, Kiyohide; Suzuki, Masanori; Yamada, Masaaki; Tanaka, Kazuhide; Ueda, Kazuyuki

    2008-01-01

    Hydrogen distribution and behavior on a Mg-Ni alloy surface are studied by using a time-of-flight electron-stimulated desorption (TOF-ESD) microscopy and a scanning electron microscope with energy dispersive X-ray spectroscopy (SEM-EDX). The desorbed hydrogen ions are energy-discriminated and distinguished into two characters in the adsorbed states, which belong to Mg 2 Ni grains and the other to oxygen-contaminated Mg phase at the grain boundaries. Adsorbed hydrogen is found to be stable up to 150 deg. C, but becomes thermally unstable around at 200 deg. C

  7. Atom-probe field-ion microscope for the study of the interaction of impurity atoms or alloying elements with defects

    International Nuclear Information System (INIS)

    Wagner, A.; Hall, T.M.; Seidman, D.N.

    1976-10-01

    A time-of-flight (TOF) atom-probe field-ion microscope (FIM) designed for the study of defects is described. This atom probe features: (1) a variable magnification internal-image-intensification system; (2) a liquid-helium goniometer stage; (3) a low-energy (less than or equal 3 keV) gas-ion gun for in-situ irradiations; (4) an ultra-high vacuum (approximately 3.10 -10 torr) chamber; (5) a high vacuum (approximately 10 -6 torr) specimen-exchange device; (6) a Chevron ion detector; and (7) an eight-channel digital timer with a +-10 nsec resolution for measuring the TOFs. The entire process of applying the evaporation pulse to the specimen, measuring the voltages, and analyzing the TOF data is controlled by a computer. With this system we can record and analyze 600 TOFmin. Results on unirradiated specimens of molybdenum, tungsten, W/25 at. % Re, Mo/1.0 at. % Ti, Mo/1.0 at. % Ti/0.08 at. % Zr and a special low swelling stainless steel alloy (LS1A) demonstrate the instrument's ability to quantitatively determine concentrations at the 5.10 -4 at fr level and to determine their spatial distribution with a resolution of a few angstroms

  8. Scanless nonlinear optical microscope for image reconstruction and space-time correlation analysis

    Science.gov (United States)

    Ceffa, N. G.; Radaelli, F.; Pozzi, P.; Collini, M.; Sironi, L.; D'alfonso, L.; Chirico, G.

    2017-06-01

    Optical Microscopy has been applied to life science from its birth and reached widespread application due to its major advantages: limited perturbation of the biological tissue and the easy accessibility of the light sources. However, as the spatial and time resolution requirements and the time stability of the microscopes increase, researchers are struggling against some of its limitations: limited transparency and the refractivity of the living tissue to light and the field perturbations induced by the path in the tissue. We have developed a compact stand-alone, completely scan-less, optical setup that allows to acquire non-linear excitation images and to measure the sample dynamics simultaneously on an ensemble of arbitrary chosen regions of interests. The image is obtained by shining a square array of spots on the sample obtained by a spatial light modulator and by shifting it (10 ms refresh time) on the sample. The final image is computed from the superposition of (100-1000) images. Filtering procedures can be applied to the raw images of the excitation array before building the image. We discuss results that show how this setup can be used for the correction of wave front aberrations induced by turbid samples (such as living tissues) and for the computation of space-time cross-correlations in complex networks.

  9. Micrometer-scale magnetic imaging of geological samples using a quantum diamond microscope

    Science.gov (United States)

    Glenn, D. R.; Fu, R. R.; Kehayias, P.; Le Sage, D.; Lima, E. A.; Weiss, B. P.; Walsworth, R. L.

    2017-08-01

    Remanent magnetization in geological samples may record the past intensity and direction of planetary magnetic fields. Traditionally, this magnetization is analyzed through measurements of the net magnetic moment of bulk millimeter to centimeter sized samples. However, geological samples are often mineralogically and texturally heterogeneous at submillimeter scales, with only a fraction of the ferromagnetic grains carrying the remanent magnetization of interest. Therefore, characterizing this magnetization in such cases requires a technique capable of imaging magnetic fields at fine spatial scales and with high sensitivity. To address this challenge, we developed a new instrument, based on nitrogen-vacancy centers in diamond, which enables direct imaging of magnetic fields due to both remanent and induced magnetization, as well as optical imaging, of room-temperature geological samples with spatial resolution approaching the optical diffraction limit. We describe the operating principles of this device, which we call the quantum diamond microscope (QDM), and report its optimized image-area-normalized magnetic field sensitivity (20 µTṡµm/Hz1/2), spatial resolution (5 µm), and field of view (4 mm), as well as trade-offs between these parameters. We also perform an absolute magnetic field calibration for the device in different modes of operation, including three-axis (vector) and single-axis (projective) magnetic field imaging. Finally, we use the QDM to obtain magnetic images of several terrestrial and meteoritic rock samples, demonstrating its ability to resolve spatially distinct populations of ferromagnetic carriers.

  10. Comparison of Electron Imaging Modes for Dimensional Measurements in the Scanning Electron Microscope.

    Science.gov (United States)

    Postek, Michael T; Vladár, András E; Villarrubia, John S; Muto, Atsushi

    2016-08-01

    Dimensional measurements from secondary electron (SE) images were compared with those from backscattered electron (BSE) and low-loss electron (LLE) images. With the commonly used 50% threshold criterion, the lines consistently appeared larger in the SE images. As the images were acquired simultaneously by an instrument with the capability to operate detectors for both signals at the same time, the differences cannot be explained by the assumption that contamination or drift between images affected the SE, BSE, or LLE images differently. Simulations with JMONSEL, an electron microscope simulator, indicate that the nanometer-scale differences observed on this sample can be explained by the different convolution effects of a beam with finite size on signals with different symmetry (the SE signal's characteristic peak versus the BSE or LLE signal's characteristic step). This effect is too small to explain the >100 nm discrepancies that were observed in earlier work on different samples. Additional modeling indicates that those discrepancies can be explained by the much larger sidewall angles of the earlier samples, coupled with the different response of SE versus BSE/LLE profiles to such wall angles.

  11. Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution

    Science.gov (United States)

    Joens, Matthew S.; Huynh, Chuong; Kasuboski, James M.; Ferranti, David; Sigal, Yury J.; Zeitvogel, Fabian; Obst, Martin; Burkhardt, Claus J.; Curran, Kevin P.; Chalasani, Sreekanth H.; Stern, Lewis A.; Goetze, Bernhard; Fitzpatrick, James A. J.

    2013-12-01

    Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.

  12. Imaging sequential dehydrogenation of methanol on Cu(110) with a scanning tunneling microscope.

    Science.gov (United States)

    Kitaguchi, Y; Shiotari, A; Okuyama, H; Hatta, S; Aruga, T

    2011-05-07

    Adsorption of methanol and its dehydrogenation on Cu(110) were studied by using a scanning tunneling microscope (STM). Upon adsorption at 12 K, methanol preferentially forms clusters on the surface. The STM could induce dehydrogenation of methanol sequentially to methoxy and formaldehyde. This enabled us to study the binding structures of these products in a single-molecule limit. Methoxy was imaged as a pair of protrusion and depression along the [001] direction. This feature is fully consistent with the previous result that it adsorbs on the short-bridge site with the C-O axis tilted along the [001] direction. The axis was induced to flip back and forth by vibrational excitations with the STM. Two configurations were observed for formaldehyde, whose structures were proposed based on their characteristic images and motions.

  13. Imaging instrument for positron emitting heavy ion beam injection

    International Nuclear Information System (INIS)

    Llacer, J.; Chatterjee, A.; Jackson, H.C.; Lin, J.C.; Zunzunegui, M.V.

    1978-10-01

    The design and performance of an instrument for the imaging of coincidence annihilation gamma rays emitted from the end point of the trajectories of radioactive high-energy heavy ions is described. The positron-emitting heavy ions are the result of nuclear fragmentation of accelerated heavy ions used in cancer therapy or diagnostic medicine. The instrument constructed is capable of locating the ion beam trajectory end point within 1 mm for an injected activity of 200 nanoCi in a measurement time of 1 sec in some favorable conditions. Limited imaging in three dimensions is also demonstrated

  14. Fourier transform infrared spectroscopy microscopic imaging classification based on spatial-spectral features

    Science.gov (United States)

    Liu, Lian; Yang, Xiukun; Zhong, Mingliang; Liu, Yao; Jing, Xiaojun; Yang, Qin

    2018-04-01

    The discrete fractional Brownian incremental random (DFBIR) field is used to describe the irregular, random, and highly complex shapes of natural objects such as coastlines and biological tissues, for which traditional Euclidean geometry cannot be used. In this paper, an anisotropic variable window (AVW) directional operator based on the DFBIR field model is proposed for extracting spatial characteristics of Fourier transform infrared spectroscopy (FTIR) microscopic imaging. Probabilistic principal component analysis first extracts spectral features, and then the spatial features of the proposed AVW directional operator are combined with the former to construct a spatial-spectral structure, which increases feature-related information and helps a support vector machine classifier to obtain more efficient distribution-related information. Compared to Haralick’s grey-level co-occurrence matrix, Gabor filters, and local binary patterns (e.g. uniform LBPs, rotation-invariant LBPs, uniform rotation-invariant LBPs), experiments on three FTIR spectroscopy microscopic imaging datasets show that the proposed AVW directional operator is more advantageous in terms of classification accuracy, particularly for low-dimensional spaces of spatial characteristics.

  15. Science Applications of a Multispectral Microscopic Imager for the Astrobiological Exploration of Mars

    Science.gov (United States)

    Farmer, Jack D.; Sellar, R. Glenn; Swayze, Gregg A.; Blaney, Diana L.

    2014-01-01

    Abstract Future astrobiological missions to Mars are likely to emphasize the use of rovers with in situ petrologic capabilities for selecting the best samples at a site for in situ analysis with onboard lab instruments or for caching for potential return to Earth. Such observations are central to an understanding of the potential for past habitable conditions at a site and for identifying samples most likely to harbor fossil biosignatures. The Multispectral Microscopic Imager (MMI) provides multispectral reflectance images of geological samples at the microscale, where each image pixel is composed of a visible/shortwave infrared spectrum ranging from 0.46 to 1.73 μm. This spectral range enables the discrimination of a wide variety of rock-forming minerals, especially Fe-bearing phases, and the detection of hydrated minerals. The MMI advances beyond the capabilities of current microimagers on Mars by extending the spectral range into the infrared and increasing the number of spectral bands. The design employs multispectral light-emitting diodes and an uncooled indium gallium arsenide focal plane array to achieve a very low mass and high reliability. To better understand and demonstrate the capabilities of the MMI for future surface missions to Mars, we analyzed samples from Mars-relevant analog environments with the MMI. Results indicate that the MMI images faithfully resolve the fine-scale microtextural features of samples and provide important information to help constrain mineral composition. The use of spectral endmember mapping reveals the distribution of Fe-bearing minerals (including silicates and oxides) with high fidelity, along with the presence of hydrated minerals. MMI-based petrogenetic interpretations compare favorably with laboratory-based analyses, revealing the value of the MMI for future in situ rover-mediated astrobiological exploration of Mars. Key Words: Mars—Microscopic imager—Multispectral imaging

  16. Tapping mode imaging and measurements with an inverted atomic force microscope.

    Science.gov (United States)

    Chan, Sandra S F; Green, John-Bruce D

    2006-07-18

    This report demonstrates the successful use of the inverted atomic force microscope (i-AFM) for tapping mode AFM imaging of cantilever-supported samples. i-AFM is a mode of AFM operation in which a sample supported on a tipless cantilever is imaged by one of many tips in a microfabricated tip array. Tapping mode is an intermittent contact mode whereby the cantilever is oscillated at or near its resonance frequency, and the amplitude and/or phase are used to image the sample. In the process of demonstrating that tapping mode images could be obtained in the i-AFM design, it was observed that the amplitude of the cantilever oscillation decreased markedly as the cantilever and tip array were approached. The source of this damping of the cantilever oscillations was identified to be the well-known "squeeze film damping", and the extent of damping was a direct consequence of the relatively shorter tip heights for the tip arrays, as compared to those of commercially available tapping mode cantilevers with integrated tips. The functional form for the distance dependence of the damping coefficient is in excellent agreement with previously published models for squeeze film damping, and the values for the fitting parameters make physical sense. Although the severe damping reduces the cantilever free amplitude substantially, we found that we were still able to access the low-amplitude regime of oscillation necessary for attractive tapping mode imaging of fragile molecules.

  17. Image transfer with spatial coherence for aberration corrected transmission electron microscopes

    International Nuclear Information System (INIS)

    Hosokawa, Fumio; Sawada, Hidetaka; Shinkawa, Takao; Sannomiya, Takumi

    2016-01-01

    The formula of spatial coherence involving an aberration up to six-fold astigmatism is derived for aberration-corrected transmission electron microscopy. Transfer functions for linear imaging are calculated using the newly derived formula with several residual aberrations. Depending on the symmetry and origin of an aberration, the calculated transfer function shows characteristic symmetries. The aberrations that originate from the field’s components, having uniformity along the z direction, namely, the n-fold astigmatism, show rotational symmetric damping of the coherence. The aberrations that originate from the field’s derivatives with respect to z, such as coma, star, and three lobe, show non-rotational symmetric damping. It is confirmed that the odd-symmetric wave aberrations have influences on the attenuation of an image via spatial coherence. Examples of image simulations of haemoglobin and Si [211] are shown by using the spatial coherence for an aberration-corrected electron microscope. - Highlights: • The formula of partial coherence for aberration corrected TEM is derived. • Transfer functions are calculated with several residual aberrations. • The calculated transfer function shows the characteristic damping. • The odd-symmetric wave aberrations can cause the attenuation of image via coherence. • The examples of aberration corrected TEM image simulations are shown.

  18. Simultaneous topography imaging and broadband nanomechanical mapping on atomic force microscope

    Science.gov (United States)

    Li, Tianwei; Zou, Qingze

    2017-12-01

    In this paper, an approach is proposed to achieve simultaneous imaging and broadband nanomechanical mapping of soft materials in air by using an atomic force microscope. Simultaneous imaging and nanomechanical mapping are needed, for example, to correlate the morphological and mechanical evolutions of the sample during dynamic phenomena such as the cell endocytosis process. Current techniques for nanomechanical mapping, however, are only capable of capturing static elasticity of the material, or the material viscoelasticity in a narrow frequency band around the resonant frequency(ies) of the cantilever used, not competent for broadband nanomechanical mapping, nor acquiring topography image of the sample simultaneously. These limitations are addressed in this work by enabling the augmentation of an excitation force stimuli of rich frequency spectrum for nanomechanical mapping in the imaging process. Kalman-filtering technique is exploited to decouple and split the mixed signals for imaging and mapping, respectively. Then the sample indentation generated is quantified online via a system-inversion method, and the effects of the indentation generated and the topography tracking error on the topography quantification are taken into account. Moreover, a data-driven feedforward-feedback control is utilized to track the sample topography. The proposed approach is illustrated through experimental implementation on a polydimethylsiloxane sample with a pre-fabricated pattern.

  19. Automated determination of size and morphology information from soot transmission electron microscope (TEM)-generated images

    International Nuclear Information System (INIS)

    Wang, Cheng; Chan, Qing N.; Zhang, Renlin; Kook, Sanghoon; Hawkes, Evatt R.; Yeoh, Guan H.; Medwell, Paul R.

    2016-01-01

    The thermophoretic sampling of particulates from hot media, coupled with transmission electron microscope (TEM) imaging, is a combined approach that is widely used to derive morphological information. The identification and the measurement of the particulates, however, can be complex when the TEM images are of low contrast, noisy, and have non-uniform background signal level. The image processing method can also be challenging and time consuming, when the samples collected have large variability in shape and size, or have some degree of overlapping. In this work, a three-stage image processing sequence is presented to facilitate time-efficient automated identification and measurement of particulates from the TEM grids. The proposed processing sequence is first applied to soot samples that were thermophoretically sampled from a laminar non-premixed ethylene-air flame. The parameter values that are required to be set to facilitate the automated process are identified, and sensitivity of the results to these parameters is assessed. The same analysis process is also applied to soot samples that were acquired from an externally irradiated laminar non-premixed ethylene-air flame, which have different geometrical characteristics, to assess the morphological dependence of the proposed image processing sequence. Using the optimized parameter values, statistical assessments of the automated results reveal that the largest discrepancies that are associated with the estimated values of primary particle diameter, fractal dimension, and prefactor values of the aggregates for the tested cases, are approximately 3, 1, and 10 %, respectively, when compared with the manual measurements.

  20. Automated determination of size and morphology information from soot transmission electron microscope (TEM)-generated images

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Cheng; Chan, Qing N., E-mail: qing.chan@unsw.edu.au; Zhang, Renlin; Kook, Sanghoon; Hawkes, Evatt R.; Yeoh, Guan H. [UNSW, School of Mechanical and Manufacturing Engineering (Australia); Medwell, Paul R. [The University of Adelaide, Centre for Energy Technology (Australia)

    2016-05-15

    The thermophoretic sampling of particulates from hot media, coupled with transmission electron microscope (TEM) imaging, is a combined approach that is widely used to derive morphological information. The identification and the measurement of the particulates, however, can be complex when the TEM images are of low contrast, noisy, and have non-uniform background signal level. The image processing method can also be challenging and time consuming, when the samples collected have large variability in shape and size, or have some degree of overlapping. In this work, a three-stage image processing sequence is presented to facilitate time-efficient automated identification and measurement of particulates from the TEM grids. The proposed processing sequence is first applied to soot samples that were thermophoretically sampled from a laminar non-premixed ethylene-air flame. The parameter values that are required to be set to facilitate the automated process are identified, and sensitivity of the results to these parameters is assessed. The same analysis process is also applied to soot samples that were acquired from an externally irradiated laminar non-premixed ethylene-air flame, which have different geometrical characteristics, to assess the morphological dependence of the proposed image processing sequence. Using the optimized parameter values, statistical assessments of the automated results reveal that the largest discrepancies that are associated with the estimated values of primary particle diameter, fractal dimension, and prefactor values of the aggregates for the tested cases, are approximately 3, 1, and 10 %, respectively, when compared with the manual measurements.

  1. On the Progress of Scanning Transmission Electron Microscopy (STEM) Imaging in a Scanning Electron Microscope.

    Science.gov (United States)

    Sun, Cheng; Müller, Erich; Meffert, Matthias; Gerthsen, Dagmar

    2018-04-01

    Transmission electron microscopy (TEM) with low-energy electrons has been recognized as an important addition to the family of electron microscopies as it may avoid knock-on damage and increase the contrast of weakly scattering objects. Scanning electron microscopes (SEMs) are well suited for low-energy electron microscopy with maximum electron energies of 30 keV, but they are mainly used for topography imaging of bulk samples. Implementation of a scanning transmission electron microscopy (STEM) detector and a charge-coupled-device camera for the acquisition of on-axis transmission electron diffraction (TED) patterns, in combination with recent resolution improvements, make SEMs highly interesting for structure analysis of some electron-transparent specimens which are traditionally investigated by TEM. A new aspect is correlative SEM, STEM, and TED imaging from the same specimen region in a SEM which leads to a wealth of information. Simultaneous image acquisition gives information on surface topography, inner structure including crystal defects and qualitative material contrast. Lattice-fringe resolution is obtained in bright-field STEM imaging. The benefits of correlative SEM/STEM/TED imaging in a SEM are exemplified by structure analyses from representative sample classes such as nanoparticulates and bulk materials.

  2. Image transfer with spatial coherence for aberration corrected transmission electron microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Hosokawa, Fumio, E-mail: hosokawa@bio-net.co.jp [BioNet Ltd., 2-3-28 Nishikityo, Tachikwa, Tokyo (Japan); Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8503 (Japan); Sawada, Hidetaka [JEOL (UK) Ltd., JEOL House, Silver Court, Watchmead, Welwyn Garden City, Herts AL7 1LT (United Kingdom); Shinkawa, Takao [BioNet Ltd., 2-3-28 Nishikityo, Tachikwa, Tokyo (Japan); Sannomiya, Takumi [Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8503 (Japan)

    2016-08-15

    The formula of spatial coherence involving an aberration up to six-fold astigmatism is derived for aberration-corrected transmission electron microscopy. Transfer functions for linear imaging are calculated using the newly derived formula with several residual aberrations. Depending on the symmetry and origin of an aberration, the calculated transfer function shows characteristic symmetries. The aberrations that originate from the field’s components, having uniformity along the z direction, namely, the n-fold astigmatism, show rotational symmetric damping of the coherence. The aberrations that originate from the field’s derivatives with respect to z, such as coma, star, and three lobe, show non-rotational symmetric damping. It is confirmed that the odd-symmetric wave aberrations have influences on the attenuation of an image via spatial coherence. Examples of image simulations of haemoglobin and Si [211] are shown by using the spatial coherence for an aberration-corrected electron microscope. - Highlights: • The formula of partial coherence for aberration corrected TEM is derived. • Transfer functions are calculated with several residual aberrations. • The calculated transfer function shows the characteristic damping. • The odd-symmetric wave aberrations can cause the attenuation of image via coherence. • The examples of aberration corrected TEM image simulations are shown.

  3. Relaxation phenomena in and microscopic transport theories of deeply inelastic collisions between heavy ions

    International Nuclear Information System (INIS)

    Noerenberg, W.

    1976-01-01

    Relaxation phenomena in deeply inelastic collisions are qualitatively discussed and compared with precompound reactions. Different approaches for describing these processes are reviewed, in particular the microscopic transport theories, which can be understood from a generalized master equation for macroscopic variables. The Markoff approximation and the classical limit for the relative motion lead to two coupled equations, the classical equation of relative motion with friction and a Pauli master equation for the internal degrees of freedom. The master equation approximated by the corresponding Fokker-Planck equation for mass transfer and energy dissipation is discussed in detail. Simple analytic expressions are derived for the transport coefficients as functions of excitation energy, total mass, mass fragmentation and relative angular momentum. Calculated transport coefficients are compared with experimental values. Problems and future developments in microscopic transport theories are outlined. (orig.) [de

  4. Distinction between amorphous and healed planar deformation features in shocked quartz using composite color scanning electron microscope cathodoluminescence (SEM-CL) imaging

    Science.gov (United States)

    Hamers, Maartje F.; Pennock, Gill M.; Herwegh, Marco; Drury, Martyn R.

    2016-10-01

    Planar deformation features (PDFs) in quartz are one of the most reliable and most widely used forms of evidence for hypervelocity impact. PDFs can be identified in scanning electron microscope cathodoluminescence (SEM-CL) images, but not all PDFs show the same CL behavior: there are nonluminescent and red luminescent PDFs. This study aims to explain the origin of the different CL emissions in PDFs. Focused ion beam (FIB) thin foils were prepared of specific sample locations selected in composite color SEM-CL images and were analyzed in a transmission electron microscope (TEM). The FIB preparation technique allowed a direct, often one-to-one correlation between the CL images and the defect structure observed in TEM. This correlation shows that composite color SEM-CL imaging allows distinction between amorphous PDFs on one hand and healed PDFs and basal Brazil twins on the other: nonluminescent PDFs are amorphous, while healed PDFs and basal Brazil twins are red luminescent, with a dominant emission peak at 650 nm. We suggest that the red luminescence is the result of preferential beam damage along dislocations, fluid inclusions, and twin boundaries. Furthermore, a high-pressure phase (possibly stishovite) in PDFs can be detected in color SEM-CL images by its blue luminescence.

  5. Biomaterial imaging with MeV-energy heavy ion beams

    International Nuclear Information System (INIS)

    Seki, Toshio; Wakamatsu, Yoshinobu; Nakagawa, Shunichiro; Aoki, Takaaki; Ishihara, Akihiko; Matsuo, Jiro

    2014-01-01

    The spatial distribution of several chemical compounds in biological tissues and cells can be obtained with mass spectrometry imaging (MSI). In conventional secondary ion mass spectrometry (SIMS) with keV-energy ion beams, elastic collisions occur between projectiles and atoms of constituent molecules. The collisions produce fragments, making the acquisition of molecular information difficult. In contrast, ion beams with MeV-energy excite near-surface electrons and enhance the ionization of high-mass molecules; hence, SIMS spectra of fragment-suppressed ionized molecules can be obtained with MeV-SIMS. To compare between MeV and conventional SIMS, we used the two methods based on MeV and Bi 3 -keV ions, respectively, to obtain molecular images of rat cerebellum. Conventional SIMS images of m/z 184 were clearly observed, but with the Bi 3 ion, the distribution of the molecule with m/z 772.5 could be observed with much difficulty. This effect was attributed to the low secondary ion yields and we could not get many signal counts with keV-energy beam. On the other hand, intact molecular ion distributions of lipids were clearly observed with MeV-SIMS, although the mass of all lipid molecules was higher than 500 Da. The peaks of intact molecular ions in MeV-SIMS spectra allowed us to assign the mass. The high secondary ion sensitivity with MeV-energy heavy ions is very useful in biomaterial analysis

  6. Non-scanning x-ray fluorescence microscope: application to real time micro-imaging

    International Nuclear Information System (INIS)

    Sakurai, K.; Eba, H.

    2000-01-01

    So far, x-ray fluorescence (XRF) micro-imaging has been performed by a 2D positional scan of a sample against a collimated beam. Obtaining information on specific elements in a nondestructive manner is an attractive prospect for many scientific applications. Furthermore, a synchrotron micro-beam can enhance the spatial resolution down to 0.1 μm. However, the total measuring time becomes quite long (a few hours to a half day), since one needs a number of scanning points in order to obtain a high-quality image. It is possible to obtain an x-ray image with 1 M pixels and with 20 μm resolution in a very short time of 20 sec - 3 min using a non-scanning XRF microscope, which is based on completely different concept. In the present report, we discuss the application of this technique to real time micro-imaging. The experiments were carried out at BL-4A, Photon Factory, Tsukuba, Japan. We employed a grazing-incidence arrangement to make primary x-rays illuminate the whole sample surface. We adopted parallel-beam optics and extremely-close-geometry in order to detect x-ray fluorescence with a CCD camera. The selective-excitation capability of tunable monochromatic synchrotron radiation is a feasible method for distinguishing the elements of interest. One can obtain an image of each element by differentiating the images obtained above and below the absorption edges of interest. The growth of metallic dendrites from a solution dropped on a substrate was studied successfully. Several different growth patterns, corresponding to concentration and other conditions for diffusion, were observed as x-ray images. Since the present technique requires only 40 sec for each shot, it is possible to record a growing process through repeated exposures like a movie. The authors would like to thank Prof. A. Iida (Photon Factory) for his valuable comments. (author)

  7. Visible-to-visible four-photon ultrahigh resolution microscopic imaging with 730-nm diode laser excited nanocrystals.

    Science.gov (United States)

    Wang, Baoju; Zhan, Qiuqiang; Zhao, Yuxiang; Wu, Ruitao; Liu, Jing; He, Sailing

    2016-01-25

    Further development of multiphoton microscopic imaging is confronted with a number of limitations, including high-cost, high complexity and relatively low spatial resolution due to the long excitation wavelength. To overcome these problems, for the first time, we propose visible-to-visible four-photon ultrahigh resolution microscopic imaging by using a common cost-effective 730-nm laser diode to excite the prepared Nd(3+)-sensitized upconversion nanoparticles (Nd(3+)-UCNPs). An ordinary multiphoton scanning microscope system was built using a visible CW diode laser and the lateral imaging resolution as high as 161-nm was achieved via the four-photon upconversion process. The demonstrated large saturation excitation power for Nd(3+)-UCNPs would be more practical and facilitate the four-photon imaging in the application. A sample with fine structure was imaged to demonstrate the advantages of visible-to-visible four-photon ultrahigh resolution microscopic imaging with 730-nm diode laser excited nanocrystals. Combining the uniqueness of UCNPs, the proposed visible-to-visible four-photon imaging would be highly promising and attractive in the field of multiphoton imaging.

  8. Reconstruction of an Non-Monochromatically Illuminated Object Imaged through an Electron Microscope with a Fluctuating Electromagnetic Field

    NARCIS (Netherlands)

    Hoenders, B.J.

    1975-01-01

    It is shown that a weak phase object imaged by an electron microscope within the presence of instabilities of the lense currents and the acceleration voltage, fluctuating electromagnetic field, can be reconstructed from the intensity distribution in the image plane. Perfectly incoherent illumination

  9. Single DNA imaging and length quantification through a mobile phone microscope

    Science.gov (United States)

    Wei, Qingshan; Luo, Wei; Chiang, Samuel; Kappel, Tara; Mejia, Crystal; Tseng, Derek; Chan, Raymond Yan L.; Yan, Eddie; Qi, Hangfei; Shabbir, Faizan; Ozkan, Haydar; Feng, Steve; Ozcan, Aydogan

    2016-03-01

    The development of sensitive optical microscopy methods for the detection of single DNA molecules has become an active research area which cultivates various promising applications including point-of-care (POC) genetic testing and diagnostics. Direct visualization of individual DNA molecules usually relies on sophisticated optical microscopes that are mostly available in well-equipped laboratories. For POC DNA testing/detection, there is an increasing need for the development of new single DNA imaging and sensing methods that are field-portable, cost-effective, and accessible for diagnostic applications in resource-limited or field-settings. For this aim, we developed a mobile-phone integrated fluorescence microscopy platform that allows imaging and sizing of single DNA molecules that are stretched on a chip. This handheld device contains an opto-mechanical attachment integrated onto a smartphone camera module, which creates a high signal-to-noise ratio dark-field imaging condition by using an oblique illumination/excitation configuration. Using this device, we demonstrated imaging of individual linearly stretched λ DNA molecules (48 kilobase-pair, kbp) over 2 mm2 field-of-view. We further developed a robust computational algorithm and a smartphone app that allowed the users to quickly quantify the length of each DNA fragment imaged using this mobile interface. The cellphone based device was tested by five different DNA samples (5, 10, 20, 40, and 48 kbp), and a sizing accuracy of <1 kbp was demonstrated for DNA strands longer than 10 kbp. This mobile DNA imaging and sizing platform can be very useful for various diagnostic applications including the detection of disease-specific genes and quantification of copy-number-variations at POC settings.

  10. Development of a SEM-based low-energy in-line electron holography microscope for individual particle imaging.

    Science.gov (United States)

    Adaniya, Hidehito; Cheung, Martin; Cassidy, Cathal; Yamashita, Masao; Shintake, Tsumoru

    2018-05-01

    A new SEM-based in-line electron holography microscope has been under development. The microscope utilizes conventional SEM and BF-STEM functionality to allow for rapid searching of the specimen of interest, seamless interchange between SEM, BF-STEM and holographic imaging modes, and makes use of coherent low-energy in-line electron holography to obtain low-dose, high-contrast images of light element materials. We report here an overview of the instrumentation and first experimental results on gold nano-particles and carbon nano-fibers for system performance tests. Reconstructed images obtained from the holographic imaging mode of the new microscope show substantial image contrast and resolution compared to those acquired by SEM and BF-STEM modes, demonstrating the feasibility of high-contrast imaging via low-energy in-line electron holography. The prospect of utilizing the new microscope to image purified biological specimens at the individual particle level is discussed and electron optical issues and challenges to further improve resolution and contrast are considered. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. A scanning Hall probe microscope for high resolution magnetic imaging down to 300 mK

    International Nuclear Information System (INIS)

    Khotkevych, V. V.; Bending, S. J.; Milosevic, M. V.

    2008-01-01

    We present the design, construction, and performance of a low-temperature scanning Hall probe microscope with submicron lateral resolution and a large scanning range. The detachable microscope head is mounted on the cold flange of a commercial 3 He-refrigerator (Oxford Instruments, Heliox VT-50) and operates between room temperature and 300 mK. It is fitted with a three-axis slip-stick nanopositioner that enables precise in situ adjustment of the probe location within a 6x6x7 mm 3 space. The local magnetic induction at the sample surface is mapped with an easily changeable microfabricated Hall probe [typically GsAs/AlGaAs or AlGaAs/InGaAs/GaAs Hall sensors with integrated scanning tunnel microscopy (STM) tunneling tips] and can achieve minimum detectable fields ≥10 mG/Hz 1/2 . The Hall probe is brought into very close proximity to the sample surface by sensing and controlling tunnel currents at the integrated STM tip. The instrument is capable of simultaneous tunneling and Hall signal acquisition in surface-tracking mode. We illustrate the potential of the system with images of superconducting vortices at the surface of a Nb thin film down to 372 mK, and also of labyrinth magnetic-domain patterns of an yttrium iron garnet film captured at room temperature.

  12. as-PSOCT: Volumetric microscopic imaging of human brain architecture and connectivity.

    Science.gov (United States)

    Wang, Hui; Magnain, Caroline; Wang, Ruopeng; Dubb, Jay; Varjabedian, Ani; Tirrell, Lee S; Stevens, Allison; Augustinack, Jean C; Konukoglu, Ender; Aganj, Iman; Frosch, Matthew P; Schmahmann, Jeremy D; Fischl, Bruce; Boas, David A

    2018-01-15

    Polarization sensitive optical coherence tomography (PSOCT) with serial sectioning has enabled the investigation of 3D structures in mouse and human brain tissue samples. By using intrinsic optical properties of back-scattering and birefringence, PSOCT reliably images cytoarchitecture, myeloarchitecture and fiber orientations. In this study, we developed a fully automatic serial sectioning polarization sensitive optical coherence tomography (as-PSOCT) system to enable volumetric reconstruction of human brain samples with unprecedented sample size and resolution. The 3.5 μm in-plane resolution and 50 μm through-plane voxel size allow inspection of cortical layers that are a single-cell in width, as well as small crossing fibers. We show the abilities of as-PSOCT in quantifying layer thicknesses of the cerebellar cortex and creating microscopic tractography of intricate fiber networks in the subcortical nuclei and internal capsule regions, all based on volumetric reconstructions. as-PSOCT provides a viable tool for studying quantitative cytoarchitecture and myeloarchitecture and mapping connectivity with microscopic resolution in the human brain. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Adapting a compact confocal microscope system to a two-photon excitation fluorescence imaging architecture.

    Science.gov (United States)

    Diaspro, A; Corosu, M; Ramoino, P; Robello, M

    1999-11-01

    Within the framework of a national National Institute of Physics of Matter (INFM) project, we have realised a two-photon excitation (TPE) fluorescence microscope based on a new generation commercial confocal scanning head. The core of the architecture is a mode-locked Ti:Sapphire laser (Tsunami 3960, Spectra Physics Inc., Mountain View, CA) pumped by a high-power (5 W, 532 nm) laser (Millennia V, Spectra Physics Inc.) and an ultracompact confocal scanning head, Nikon PCM2000 (Nikon Instruments, Florence, Italy) using a single-pinhole design. Three-dimensional point-spread function has been measured to define spatial resolution performances. The TPE microscope has been used with a wide range of excitable fluorescent molecules (DAPI, Fura-2, Indo-1, DiOC(6)(3), fluoresceine, Texas red) covering a single photon spectral range from UV to green. An example is reported on 3D imaging of the helical structure of the sperm head of the Octopus Eledone cirrhosa labelled with an UV excitable dye, i.e., DAPI. The system can be easily switched for operating both in conventional and two-photon mode. Copyright 1999 Wiley-Liss, Inc.

  14. High-resolution imaging of ultracold fermions in microscopically tailored optical potentials

    International Nuclear Information System (INIS)

    Zimmermann, B; Mueller, T; Meineke, J; Esslinger, T; Moritz, H

    2011-01-01

    We report on the local probing and preparation of an ultracold Fermi gas on the length scale of one micrometer, i.e. of the order of the Fermi wavelength. The essential tool of our experimental setup is a pair of identical, high-resolution microscope objectives. One of the microscope objectives allows local imaging of the trapped Fermi gas of 6 Li atoms with a maximum resolution of 660 nm, while the other enables the generation of arbitrary optical dipole potentials on the same length scale. Employing a two-dimensional (2D) acousto-optical deflector, we demonstrate the formation of several trapping geometries, including a tightly focused single optical dipole trap, a 4x4 site 2D optical lattice and an 8 site ring lattice configuration. Furthermore, we show the ability to load and detect a small number of atoms in these trapping potentials. A site separation down to one micrometer in combination with the low mass of 6 Li results in tunneling rates that are sufficiently large for the implementation of Hubbard models with the designed geometries.

  15. Annular dark field electron microscope images with better than 2 A resolution at 100 kV

    International Nuclear Information System (INIS)

    Shin, D.H.; Kirkland, E.J.; Silcox, J.

    1989-01-01

    High-resolution scanning transmission electron microscope (STEM) images in the annular dark field (ADF) imaging mode approaching the theoretical point-to-point resolution limit are presented. The ADF images were obtained from a high T c superconducting YBa 2 Cu 3 O 7-x thin-film specimen at 100 kV. The 1.9 A resolution lattice image, which is the smallest lattice spacing in the specimen, corresponds to the minimum resolvable spatial frequency with 5% contrast in the contrast transfer function for annular dark field, and is smaller than the resolution limit given by the Rayleigh criterion. This demonstrates that STEM ADF imaging can have a resolution approximately 40% better than that of the bright field conventional transmission electron microscope (CTEM) imaging at Scherzer condition

  16. Surface features on Sahara soil dust particles made visible by atomic force microscope (AFM phase images

    Directory of Open Access Journals (Sweden)

    M. O. Andreae

    2008-10-01

    Full Text Available We show that atomic force microscopy (AFM phase images can reveal surface features of soil dust particles, which are not evident using other microscopic methods. The non-contact AFM method is able to resolve topographical structures in the nanometer range as well as to uncover repulsive atomic forces and attractive van der Waals' forces, and thus gives insight to surface properties. Though the method does not allow quantitative assignment in terms of chemical compound description, it clearly shows deposits of distinguishable material on the surface. We apply this technique to dust aerosol particles from the Sahara collected over the Atlantic Ocean and describe micro-features on the surfaces of such particles.

  17. Benchtop and animal validation of a portable fluorescence microscopic imaging system for potential use in cholecystectomy

    Science.gov (United States)

    Ye, Jian; Liu, Guanghui; Liu, Peng; Zhang, Shiwu; Shao, Pengfei; Smith, Zachary J.; Liu, Chenhai; Xu, Ronald X.

    2018-02-01

    We propose a portable fluorescence microscopic imaging system (PFMS) for intraoperative display of biliary structure and prevention of iatrogenic injuries during cholecystectomy. The system consists of a light source module, a camera module, and a Raspberry Pi computer with an LCD. Indocyanine green (ICG) is used as a fluorescent contrast agent for experimental validation of the system. Fluorescence intensities of the ICG aqueous solution at different concentration levels are acquired by our PFMS and compared with those of a commercial Xenogen IVIS system. We study the fluorescence detection depth by superposing different thicknesses of chicken breast on an ICG-loaded agar phantom. We verify the technical feasibility for identifying potential iatrogenic injury in cholecystectomy using a rat model in vivo. The proposed PFMS system is portable, inexpensive, and suitable for deployment in resource-limited settings.

  18. Construction and performance of a dilution-refrigerator based spectroscopic-imaging scanning tunneling microscope.

    Science.gov (United States)

    Singh, U R; Enayat, M; White, S C; Wahl, P

    2013-01-01

    We report on the set-up and performance of a dilution-refrigerator based spectroscopic imaging scanning tunneling microscope. It operates at temperatures below 10 mK and in magnetic fields up to 14T. The system allows for sample transfer and in situ cleavage. We present first-results demonstrating atomic resolution and the multi-gap structure of the superconducting gap of NbSe(2) at base temperature. To determine the energy resolution of our system we have measured a normal metal/vacuum/superconductor tunneling junction consisting of an aluminum tip on a gold sample. Our system allows for continuous measurements at base temperature on time scales of up to ≈170 h.

  19. A multifunctional force microscope for soft matter with in situ imaging

    Science.gov (United States)

    Roberts, Paul; Pilkington, Georgia A.; Wang, Yumo; Frechette, Joelle

    2018-04-01

    We present the multifunctional force microscope (MFM), a normal and lateral force-measuring instrument with in situ imaging. In the MFM, forces are calculated from the normal and lateral deflection of a cantilever as measured via fiber optic sensors. The motion of the cantilever is controlled normally by a linear micro-translation stage and a piezoelectric actuator, while the lateral motion of the sample is controlled by another linear micro-translation stage. The micro-translation stages allow for travel distances that span 25 mm with a minimum step size of 50 nm, while the piezo has a minimum step size of 0.2 nm, but a 100 μm maximum range. Custom-designed cantilevers allow for the forces to be measured over 4 orders of magnitude (from 50 μN to 1 N). We perform probe tack, friction, and hydrodynamic drainage experiments to demonstrate the sensitivity, versatility, and measurable force range of the instrument.

  20. Laser based imaging of time depending microscopic scenes with strong light emission

    Science.gov (United States)

    Hahlweg, Cornelius; Wilhelm, Eugen; Rothe, Hendrik

    2011-10-01

    Investigating volume scatterometry methods based on short range LIDAR devices for non-static objects we achieved interesting results aside the intended micro-LIDAR: the high speed camera recording of the illuminated scene of an exploding wire -intended for Doppler LIDAR tests - delivered a very effective method of observing details of objects with extremely strong light emission. As a side effect a schlieren movie is gathered without any special effort. The fact that microscopic features of short time processes with high emission and material flow might be imaged without endangering valuable equipment makes this technique at least as interesting as the intended one. So we decided to present our results - including latest video and photo material - instead of a more theoretical paper on our progress concerning the primary goal.

  1. Scanning differential polarization microscope: Its use to image linear and circular differential scattering

    International Nuclear Information System (INIS)

    Mickols, W.; Maestre, M.F.

    1988-01-01

    A differential polarization microscope that couples the sensitivity of single-beam measurement of circular dichroism and circular differential scattering with the simultaneous measurement of linear dichroism and linear differential scattering has been developed. The microscope uses a scanning microscope stage and single-point illumination to give the very shallow depth of field found in confocal microscopy. This microscope can operate in the confocal mode as well as in the near confocal condition that can allow one to program the coherence and spatial resolution of the microscope. This microscope has been used to study the change in the structure of chromatin during the development of sperm in Drosophila

  2. Blood capillary length estimation from three-dimensional microscopic data by image analysis and stereology.

    Science.gov (United States)

    Kubínová, Lucie; Mao, Xiao Wen; Janáček, Jiří

    2013-08-01

    Studies of the capillary bed characterized by its length or length density are relevant in many biomedical studies. A reliable assessment of capillary length from two-dimensional (2D), thin histological sections is a rather difficult task as it requires physical cutting of such sections in randomized directions. This is often technically demanding, inefficient, or outright impossible. However, if 3D image data of the microscopic structure under investigation are available, methods of length estimation that do not require randomized physical cutting of sections may be applied. Two different rat brain regions were optically sliced by confocal microscopy and resulting 3D images processed by three types of capillary length estimation methods: (1) stereological methods based on a computer generation of isotropic uniform random virtual test probes in 3D, either in the form of spatial grids of virtual "slicer" planes or spherical probes; (2) automatic method employing a digital version of the Crofton relations using the Euler characteristic of planar sections of the binary image; and (3) interactive "tracer" method for length measurement based on a manual delineation in 3D of the axes of capillary segments. The presented methods were compared in terms of their practical applicability, efficiency, and precision.

  3. Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue.

    Science.gov (United States)

    Lihavainen, E; Kislin, M; Toptunov, D; Khiroug, L; Ribeiro, A S

    2015-12-01

    The morphology of mitochondria can inform about their functional state and, thus, about cell vitality. For example, fragmentation of the mitochondrial network is associated with many diseases. Recent advances in neuronal imaging have enabled the observation of mitochondria in live brains for long periods of time, enabling the study of their dynamics in animal models of diseases. To aid these studies, we developed an automatic method, based on supervised learning, for quantifying the degree of mitochondrial fragmentation in tissue images acquired via two-photon microscopy from transgenic mice, which exclusively express Enhanced cyan fluorescent protein (ECFP) under Thy1 promoter, targeted to the mitochondrial matrix in subpopulations of neurons. We tested the method on images prior to and after cardiac arrest, and found it to be sensitive to significant changes in mitochondrial morphology because of the arrest. We conclude that the method is useful in detecting morphological abnormalities in mitochondria and, likely, in other subcellular structures as well. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  4. Microscopic time-resolved imaging of singlet oxygen by delayed fluorescence in living cells.

    Science.gov (United States)

    Scholz, Marek; Dědic, Roman; Hála, Jan

    2017-11-08

    Singlet oxygen is a highly reactive species which is involved in a number of processes, including photodynamic therapy of cancer. Its very weak near-infrared emission makes imaging of singlet oxygen in biological systems a long-term challenge. We address this challenge by introducing Singlet Oxygen Feedback Delayed Fluorescence (SOFDF) as a novel modality for semi-direct microscopic time-resolved wide-field imaging of singlet oxygen in biological systems. SOFDF has been investigated in individual fibroblast cells incubated with a well-known photosensitizer aluminium phthalocyanine tetrasulfonate. The SOFDF emission from the cells is several orders of magnitude stronger and much more readily detectable than the very weak near-infrared phosphorescence of singlet oxygen. Moreover, the analysis of SOFDF kinetics enables us to estimate the lifetimes of the involved excited states. Real-time SOFDF images with micrometer spatial resolution and submicrosecond temporal-resolution have been recorded. Interestingly, a steep decrease in the SOFDF intensity after the photodynamically induced release of a photosensitizer from lysosomes has been demonstrated. This effect could be potentially employed as a valuable diagnostic tool for monitoring and dosimetry in photodynamic therapy.

  5. Miniature Variable Pressure Scanning Electron Microscope for In-Situ Imaging and Chemical Analysis

    Science.gov (United States)

    Gaskin, Jessica A.; Jerman, Gregory; Gregory, Don; Sampson, Allen R.

    2012-01-01

    NASA Marshall Space Flight Center (MSFC) is leading an effort to develop a Miniaturized Variable Pressure Scanning Electron Microscope (MVP-SEM) for in-situ imaging and chemical analysis of uncoated samples. This instrument development will be geared towards operation on Mars and builds on a previous MSFC design of a mini-SEM for the moon (funded through the NASA Planetary Instrument Definition and Development Program). Because Mars has a dramatically different environment than the moon, modifications to the MSFC lunar mini-SEM are necessary. Mainly, the higher atmospheric pressure calls for the use of an electron gun that can operate at High Vacuum, rather than Ultra-High Vacuum. The presence of a CO2-rich atmosphere also allows for the incorporation of a variable pressure system that enables the in-situ analysis of nonconductive geological specimens. Preliminary testing of Mars meteorites in a commercial Environmental SEM(Tradmark) (FEI) confirms the usefulness of lowcurrent/low-accelerating voltage imaging and highlights the advantages of using the Mars atmosphere for environmental imaging. The unique capabilities of the MVP-SEM make it an ideal tool for pursuing key scientific goals of NASA's Flagship Mission Max-C; to perform in-situ science and collect and cache samples in preparation for sample return from Mars.

  6. Imaging single atoms using secondary electrons with an aberration-corrected electron microscope.

    Science.gov (United States)

    Zhu, Y; Inada, H; Nakamura, K; Wall, J

    2009-10-01

    Aberration correction has embarked on a new frontier in electron microscopy by overcoming the limitations of conventional round lenses, providing sub-angstrom-sized probes. However, improvement of spatial resolution using aberration correction so far has been limited to the use of transmitted electrons both in scanning and stationary mode, with an improvement of 20-40% (refs 3-8). In contrast, advances in the spatial resolution of scanning electron microscopes (SEMs), which are by far the most widely used instrument for surface imaging at the micrometre-nanometre scale, have been stagnant, despite several recent efforts. Here, we report a new SEM, with aberration correction, able to image single atoms by detecting electrons emerging from its surface as a result of interaction with the small probe. The spatial resolution achieved represents a fourfold improvement over the best-reported resolution in any SEM (refs 10-12). Furthermore, we can simultaneously probe the sample through its entire thickness with transmitted electrons. This ability is significant because it permits the selective visualization of bulk atoms and surface ones, beyond a traditional two-dimensional projection in transmission electron microscopy. It has the potential to revolutionize the field of microscopy and imaging, thereby opening the door to a wide range of applications, especially when combined with simultaneous nanoprobe spectroscopy.

  7. Imaging of Interlayer Coupling in van der Waals Heterostructures Using a Bright-Field Optical Microscope.

    Science.gov (United States)

    Alexeev, Evgeny M; Catanzaro, Alessandro; Skrypka, Oleksandr V; Nayak, Pramoda K; Ahn, Seongjoon; Pak, Sangyeon; Lee, Juwon; Sohn, Jung Inn; Novoselov, Kostya S; Shin, Hyeon Suk; Tartakovskii, Alexander I

    2017-09-13

    Vertically stacked atomic layers from different layered crystals can be held together by van der Waals forces, which can be used for building novel heterostructures, offering a platform for developing a new generation of atomically thin, transparent, and flexible devices. The performance of these devices is critically dependent on the layer thickness and the interlayer electronic coupling, influencing the hybridization of the electronic states as well as charge and energy transfer between the layers. The electronic coupling is affected by the relative orientation of the layers as well as by the cleanliness of their interfaces. Here, we demonstrate an efficient method for monitoring interlayer coupling in heterostructures made from transition metal dichalcogenides using photoluminescence imaging in a bright-field optical microscope. The color and brightness in such images are used here to identify mono- and few-layer crystals and to track changes in the interlayer coupling and the emergence of interlayer excitons after thermal annealing in heterobilayers composed of mechanically exfoliated flakes and as a function of the twist angle in atomic layers grown by chemical vapor deposition. Material and crystal thickness sensitivity of the presented imaging technique makes it a powerful tool for characterization of van der Waals heterostructures assembled by a wide variety of methods, using combinations of materials obtained through mechanical or chemical exfoliation and crystal growth.

  8. Computer aided solution for segmenting the neuron line in hippocampal microscope images

    Science.gov (United States)

    Albaidhani, Tahseen; Jassim, Sabah; Al-Assam, Hisham

    2017-05-01

    The brain Hippocampus component is known to be responsible for memory and spatial navigation. Its functionality depends on the status of different blood vessels within the Hippocampus and is severely impaired by Alzheimer's disease as a result blockage of increasing number of blood vessels by accumulation of amyloid-beta (Aβ) protein. Accurate counting of blood vessels within the Hippocampus of mice brain, from microscopic images, is an active research area for the understanding of Alzheimer's disease. Here, we report our work on automatic detection of the Region of Interest, i.e. the region in which blood vessels are located. This area typically falls between the hippocampus edge and the line of neurons within the Hippocampus. This paper proposes a new method to detect and exclude the neuron line to improve the accuracy of blood vessel counting because some neurons on it might lead to false positive cases as they look like blood vessels. Our proposed solution is based on using trainable segmentation approach with morphological operations, taking into account variation in colour, intensity values, and image texture. Experiments on a sufficient number of microscopy images of mouse brain demonstrate the effectiveness of the developed solution in preparation for blood vessels counting.

  9. Modulated electron-multiplied fluorescence lifetime imaging microscope: all-solid-state camera for fluorescence lifetime imaging.

    Science.gov (United States)

    Zhao, Qiaole; Schelen, Ben; Schouten, Raymond; van den Oever, Rein; Leenen, René; van Kuijk, Harry; Peters, Inge; Polderdijk, Frank; Bosiers, Jan; Raspe, Marcel; Jalink, Kees; Geert Sander de Jong, Jan; van Geest, Bert; Stoop, Karel; Young, Ian Ted

    2012-12-01

    We have built an all-solid-state camera that is directly modulated at the pixel level for frequency-domain fluorescence lifetime imaging microscopy (FLIM) measurements. This novel camera eliminates the need for an image intensifier through the use of an application-specific charge coupled device design in a frequency-domain FLIM system. The first stage of evaluation for the camera has been carried out. Camera characteristics such as noise distribution, dark current influence, camera gain, sampling density, sensitivity, linearity of photometric response, and optical transfer function have been studied through experiments. We are able to do lifetime measurement using our modulated, electron-multiplied fluorescence lifetime imaging microscope (MEM-FLIM) camera for various objects, e.g., fluorescein solution, fixed green fluorescent protein (GFP) cells, and GFP-actin stained live cells. A detailed comparison of a conventional microchannel plate (MCP)-based FLIM system and the MEM-FLIM system is presented. The MEM-FLIM camera shows higher resolution and a better image quality. The MEM-FLIM camera provides a new opportunity for performing frequency-domain FLIM.

  10. A portable confocal hyperspectral microscope without any scan or tube lens and its application in fluorescence and Raman spectral imaging

    Science.gov (United States)

    Li, Jingwei; Cai, Fuhong; Dong, Yongjiang; Zhu, Zhenfeng; Sun, Xianhe; Zhang, Hequn; He, Sailing

    2017-06-01

    In this study, a portable confocal hyperspectral microscope is developed. In traditional confocal laser scanning microscopes, scan lens and tube lens are utilized to achieve a conjugate relationship between the galvanometer and the back focal plane of the objective, in order to achieve a better resolution. However, these lenses make it difficult to scale down the volume of the system. In our portable confocal hyperspectral microscope (PCHM), the objective is placed directly next to the galvomirror. Thus, scan lens and tube lens are not included in our system and the size of this system is greatly reduced. Furthermore, the resolution is also acceptable in many biomedical and food-safety applications. Through reducing the optical length of the system, the signal detection efficiency is enhanced. This is conducive to realizing both the fluorescence and Raman hyperspectral imaging. With a multimode fiber as a pinhole, an improved image contrast is also achieved. Fluorescent spectral images for HeLa cells/fingers and Raman spectral images of kumquat pericarp are present. The spectral resolution and spatial resolutions are about 0.4 nm and 2.19 μm, respectively. These results demonstrate that this portable hyperspectral microscope can be used in in-vivo fluorescence imaging and in situ Raman spectral imaging.

  11. Microscopic calculation of friction coefficients for use in heavy-ion reaction

    International Nuclear Information System (INIS)

    Iwamoto, A.; Harada, K.; Yoshida, S.

    1981-01-01

    A microscopic calculation has been done for the friction coefficient for use in the deep-inelastic collision of heavy nuclei. We adopted the formalism of the linear response theory as a basis and used the adiabatic base of the two-center shell model. Several reaction channels with the total mass numbers of 236 and 260 systems were investigated. The friction coefficients for the radial and deforming motions including the coupling term were calculated as a function of the distance between two nuclei and deformation of the two nuclei for each channel. The general feature of the friction coefficient, its strength and form factor, was clarified in this model and comparison with the results of other models were done. It was found that our model gives a physically plausible value for the friction coefficient as a whole. (orig.)

  12. Microscopic heavy-ion theory. Final technical report, June 1, 1993 - May 31, 1996

    International Nuclear Information System (INIS)

    Ernst, D.J.; Oberacker, V.E.; Umar, A.S.

    1998-01-01

    In this Final Technical Report, the authors summarize the research activities of the three Principal Investigators (Professors Ernst, Oberacker, and Umar) at Vanderbilt University since the last reporting period through the subject award expiration date (Dec. 31, 1996) under contract DE-FG05-87ER40376 with the Department of Energy. The research effort is divided between the following three areas: nuclear structure and astrophysics (microscopic nuclear structure studies and properties of exotic nuclei at HRIBF, supernovae calculations in connection with nuclear astrophysics, and nuclear viscosity studies via muon-induced fission at PSI); pion and kaon interactions with the nucleus at high energies (interaction of pions and kaons with nuclei from low energies to 1 GeV, propagation of excited hadrons in the nuclear medium as probed by pion and electron induced reactions); nuclear physics at high energies (dynamical string-parton model to study multi-particle production at RHIC, electromagnetic lepton pair production at RHIC)

  13. A microscopic calculation of potentials and inertia parameters for heavy-ion collisions

    International Nuclear Information System (INIS)

    Flocard, H.; Vautherin, D.; Heenen, P.H.

    1979-09-01

    Within the adiabatic time dependent Hartree-Fock formalism, the potential V(R) and the inertia parameter M(R) corresponding to the symmetric heavy-ion collisions 12 C+ 12 C and 16 O+ 16 O are computed. It is found that the mass M(R) exhibits very sharp peaks. These peaks are shown to provide a plausible mechanism to explain the occurrence of quasi-molecular resonances

  14. Computational chemical imaging for cardiovascular pathology: chemical microscopic imaging accurately determines cardiac transplant rejection.

    Directory of Open Access Journals (Sweden)

    Saumya Tiwari

    Full Text Available Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients' biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures.

  15. Ultrabright planar optodes for luminescence life-time based microscopic imaging of O2 dynamics in biofilms

    DEFF Research Database (Denmark)

    Staal, Marc Jaap; Borisov, S M; Rickelt, L F

    2011-01-01

    New transparent optodes for life-time based microscopic imaging of O2 were developed by spin-coating a µm-thin layer of a highly luminescent cyclometalated iridium(III) coumarin complex in polystyrene onto glass cover slips. Compared to similar thin-film O2 optodes based on a ruthenium(II) polypy......New transparent optodes for life-time based microscopic imaging of O2 were developed by spin-coating a µm-thin layer of a highly luminescent cyclometalated iridium(III) coumarin complex in polystyrene onto glass cover slips. Compared to similar thin-film O2 optodes based on a ruthenium...

  16. Interaction between short fatigue cracks and grain boundaries. Systematic experiments with focussed ion beam microscope and microstructural tomography; Ueber die Wechselwirkung kurzer Ermuedungsrisse mit Korngrenzen. Systematische Experimente mit Focussed Ion Beam Microscope und mikrostruktureller Tomographie

    Energy Technology Data Exchange (ETDEWEB)

    Schaef, Wolfgang

    2011-04-15

    Increasing the microstructural resistance of metallic materials to short fatigue crack growth is a major task of today's materials science. In this regard, grain boundaries and precipitates are well known to decelerate short cracks, but a quantitative understanding of the blocking effect is still missing. This is due to the fact that crack deceleration is influenced by many parameters: cyclic load, crack length, distance to obstacles, orientations of grains and obstacles. Even the examination of a huge number of short cracks would not be sufficient to identify the effect of these parameters independently, especially since fatigue crack growth is a 3D problem and investigations of the sub surface orientation of cracks and grain boundaries are scarce. The Focused Ion Beam Microscope (FIB) offers new methods for systematic experiments and 3D-investigation of short fatigue cracks that will help to quantify the microstructural impact on short fatigue crack growth. The ion beam is used to cut micro notches in selected grains on the surface of samples characterised by Electron Backscatter Diffraction (EBSD). Plane fatigue cracks initiate under cyclic loading in defined distances to the grain boundaries. By this technique it is possible for the first time to present quantitative data to describe the effect of grain boundaries on short fatigue cracks in nickel based superalloys (CMSX-4) as well as in mild steels.

  17. Science applications of a multispectral microscopic imager for the astrobiological exploration of Mars

    Science.gov (United States)

    Nunez, Jorge; Farmer, Jack; Sellar, R. Glenn; Swayze, Gregg A.; Blaney, Diana L.

    2014-01-01

    Future astrobiological missions to Mars are likely to emphasize the use of rovers with in situ petrologic capabilities for selecting the best samples at a site for in situ analysis with onboard lab instruments or for caching for potential return to Earth. Such observations are central to an understanding of the potential for past habitable conditions at a site and for identifying samples most likely to harbor fossil biosignatures. The Multispectral Microscopic Imager (MMI) provides multispectral reflectance images of geological samples at the microscale, where each image pixel is composed of a visible/shortwave infrared spectrum ranging from 0.46 to 1.73 μm. This spectral range enables the discrimination of a wide variety of rock-forming minerals, especially Fe-bearing phases, and the detection of hydrated minerals. The MMI advances beyond the capabilities of current microimagers on Mars by extending the spectral range into the infrared and increasing the number of spectral bands. The design employs multispectral light-emitting diodes and an uncooled indium gallium arsenide focal plane array to achieve a very low mass and high reliability. To better understand and demonstrate the capabilities of the MMI for future surface missions to Mars, we analyzed samples from Mars-relevant analog environments with the MMI. Results indicate that the MMI images faithfully resolve the fine-scale microtextural features of samples and provide important information to help constrain mineral composition. The use of spectral endmember mapping reveals the distribution of Fe-bearing minerals (including silicates and oxides) with high fidelity, along with the presence of hydrated minerals. MMI-based petrogenetic interpretations compare favorably with laboratory-based analyses, revealing the value of the MMI for future in situ rover-mediated astrobiological exploration of Mars.

  18. Heavy-<span class="hlt">Ion</span> <span class="hlt">Imaging</span> Applied To Medicine

    Energy Technology Data Exchange (ETDEWEB)

    Fabrikant, J. I.; Tobias, C. A.; Capp, M. P.; Benton, E. V.; Holley, W. R.; Gray, Joel E.; Hendee, William R.; Haus, Andrew G.; Properzio, William S.

    1980-08-18

    Heavy particle radiography is a newly developed noninvasive low dose imaging procedure with increased resolution of minute density differences in soft tissues of the body. The method utilizes accelerated high energy ions, primarily carbon and neon, at the BEVALAC accelerator at the Lawrence Berkeley Laboratory. The research program applied to medicine utilizes heavy-ion radiography for low dose mammography, for treatment planning for cancer patients, and for imaging and accurate densitometry of skeletal structures and brain and spinal neoplasms. The presentation will be illustrated with clinical cases under study. Discussion will include the potential of heavy-ion imaging, and particularly reconstruction tomography, as an adjunct to existing diagnostic imaging procedures in medicine, both for the applications to the diagnosis, management and treatment of clinical cancer in man, but also for the early detection of small soft tissue tumors at low radiation dose.

  19. An Intelligent Decision Support System for Leukaemia Diagnosis using Microscopic Blood Images

    Science.gov (United States)

    Chin Neoh, Siew; Srisukkham, Worawut; Zhang, Li; Todryk, Stephen; Greystoke, Brigit; Peng Lim, Chee; Alamgir Hossain, Mohammed; Aslam, Nauman

    2015-01-01

    This research proposes an intelligent decision support system for acute lymphoblastic leukaemia diagnosis from microscopic blood images. A novel clustering algorithm with stimulating discriminant measures (SDM) of both within- and between-cluster scatter variances is proposed to produce robust segmentation of nucleus and cytoplasm of lymphocytes/lymphoblasts. Specifically, the proposed between-cluster evaluation is formulated based on the trade-off of several between-cluster measures of well-known feature extraction methods. The SDM measures are used in conjuction with Genetic Algorithm for clustering nucleus, cytoplasm, and background regions. Subsequently, a total of eighty features consisting of shape, texture, and colour information of the nucleus and cytoplasm sub-images are extracted. A number of classifiers (multi-layer perceptron, Support Vector Machine (SVM) and Dempster-Shafer ensemble) are employed for lymphocyte/lymphoblast classification. Evaluated with the ALL-IDB2 database, the proposed SDM-based clustering overcomes the shortcomings of Fuzzy C-means which focuses purely on within-cluster scatter variance. It also outperforms Linear Discriminant Analysis and Fuzzy Compactness and Separation for nucleus-cytoplasm separation. The overall system achieves superior recognition rates of 96.72% and 96.67% accuracies using bootstrapping and 10-fold cross validation with Dempster-Shafer and SVM, respectively. The results also compare favourably with those reported in the literature, indicating the usefulness of the proposed SDM-based clustering method. PMID:26450665

  20. An ultrahigh vacuum fast-scanning and variable temperature scanning tunneling microscope for large scale imaging.

    Science.gov (United States)

    Diaconescu, Bogdan; Nenchev, Georgi; de la Figuera, Juan; Pohl, Karsten

    2007-10-01

    We describe the design and performance of a fast-scanning, variable temperature scanning tunneling microscope (STM) operating from 80 to 700 K in ultrahigh vacuum (UHV), which routinely achieves large scale atomically resolved imaging of compact metallic surfaces. An efficient in-vacuum vibration isolation and cryogenic system allows for no external vibration isolation of the UHV chamber. The design of the sample holder and STM head permits imaging of the same nanometer-size area of the sample before and after sample preparation outside the STM base. Refractory metal samples are frequently annealed up to 2000 K and their cooldown time from room temperature to 80 K is 15 min. The vertical resolution of the instrument was found to be about 2 pm at room temperature. The coarse motor design allows both translation and rotation of the scanner tube. The total scanning area is about 8 x 8 microm(2). The sample temperature can be adjusted by a few tens of degrees while scanning over the same sample area.

  1. Examination of Scanning Electron Microscope and Computed Tomography Images of PICA

    Science.gov (United States)

    Lawson, John W.; Stackpoole, Margaret M.; Shklover, Valery

    2010-01-01

    Micrographs of PICA (Phenolic Impregnated Carbon Ablator) taken using a Scanning Electron Microscope (SEM) and 3D images taken with a Computed Tomography (CT) system are examined. PICA is a carbon fiber based composite (Fiberform ) with a phenolic polymer matrix. The micrographs are taken at different surface depths and at different magnifications in a sample after arc jet testing and show different levels of oxidative removal of the charred matrix (Figs 1 though 13). CT scans, courtesy of Xradia, Inc. of Concord CA, were captured for samples of virgin PICA, charred PICA and raw Fiberform (Fig. 14). We use these images to calculate the thermal conductivity (TC) of these materials using correlation function (CF) methods. CF methods give a mathematical description of how one material is embedded in another and is thus ideally suited for modeling composites like PICA. We will evaluate how the TC of the materials changes as a function of surface depth. This work is in collaboration with ETH-Zurich, which has expertise in high temperature materials and TC modeling (including CF methods).

  2. Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

    Science.gov (United States)

    Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

    2011-01-01

    Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

  3. A scanning tunneling microscope capable of imaging specified micron-scale small samples.

    Science.gov (United States)

    Tao, Wei; Cao, Yufei; Wang, Huafeng; Wang, Kaiyou; Lu, Qingyou

    2012-12-01

    We present a home-built scanning tunneling microscope (STM) which allows us to precisely position the tip on any specified small sample or sample feature of micron scale. The core structure is a stand-alone soft junction mechanical loop (SJML), in which a small piezoelectric tube scanner is mounted on a sliding piece and a "U"-like soft spring strip has its one end fixed to the sliding piece and its opposite end holding the tip pointing to the sample on the scanner. Here, the tip can be precisely aligned to a specified small sample of micron scale by adjusting the position of the spring-clamped sample on the scanner in the field of view of an optical microscope. The aligned SJML can be transferred to a piezoelectric inertial motor for coarse approach, during which the U-spring is pushed towards the sample, causing the tip to approach the pre-aligned small sample. We have successfully approached a hand cut tip that was made from 0.1 mm thin Pt∕Ir wire to an isolated individual 32.5 × 32.5 μm(2) graphite flake. Good atomic resolution images and high quality tunneling current spectra for that specified tiny flake are obtained in ambient conditions with high repeatability within one month showing high and long term stability of the new STM structure. In addition, frequency spectra of the tunneling current signals do not show outstanding tip mount related resonant frequency (low frequency), which further confirms the stability of the STM structure.

  4. A scanning tunneling microscope capable of imaging specified micron-scale small samples

    Science.gov (United States)

    Tao, Wei; Cao, Yufei; Wang, Huafeng; Wang, Kaiyou; Lu, Qingyou

    2012-12-01

    We present a home-built scanning tunneling microscope (STM) which allows us to precisely position the tip on any specified small sample or sample feature of micron scale. The core structure is a stand-alone soft junction mechanical loop (SJML), in which a small piezoelectric tube scanner is mounted on a sliding piece and a "U"-like soft spring strip has its one end fixed to the sliding piece and its opposite end holding the tip pointing to the sample on the scanner. Here, the tip can be precisely aligned to a specified small sample of micron scale by adjusting the position of the spring-clamped sample on the scanner in the field of view of an optical microscope. The aligned SJML can be transferred to a piezoelectric inertial motor for coarse approach, during which the U-spring is pushed towards the sample, causing the tip to approach the pre-aligned small sample. We have successfully approached a hand cut tip that was made from 0.1 mm thin Pt/Ir wire to an isolated individual 32.5 × 32.5 μm2 graphite flake. Good atomic resolution images and high quality tunneling current spectra for that specified tiny flake are obtained in ambient conditions with high repeatability within one month showing high and long term stability of the new STM structure. In addition, frequency spectra of the tunneling current signals do not show outstanding tip mount related resonant frequency (low frequency), which further confirms the stability of the STM structure.

  5. Proceedings of study meeting on microscopic and phenomenological research of interaction for light heavy-ion systems

    International Nuclear Information System (INIS)

    1991-06-01

    The Research Center for Nuclear Physics study meeting 'Microscopic and phenomenological research of interaction for light heavy-ion systems was held on March 7-9, 1990 as the study meeting in the second half of 1990, and 25 researchers took part in it. As the background of holding this study meeting, the fact that recently the rainbow scattering due to nuclear force was discovered experimentally in 16 O- 16 O system, and phenomenologically it was explained only by deep inter-nucleus potential. This should be evaluated as an important foothold for the research on the interaction for light heavy-ion systems and nuclear reaction mechanism. Accordingly, most of the papers presented this time were those related to the inter-nucleus potential and nuclear reaction mechanism. Also the development of theoretical analysis method was carried out and reported. Further, recently the experimental study on the structure and reaction of the neutron rich nucleus has advanced, and the theoretical research related to this topic was reported. (K.I.)

  6. Biomaterial imaging with MeV-energy heavy ion beams

    Energy Technology Data Exchange (ETDEWEB)

    Seki, Toshio, E-mail: seki@sakura.nucleng.kyoto-u.ac.jp [Department of Nuclear Engineering, Kyoto Univ., Uji, Kyoto 611-0011 (Japan); CREST, Japan Science and Technology Agency (JST), Chiyoda, Tokyo 102-0075 (Japan); Wakamatsu, Yoshinobu; Nakagawa, Shunichiro [Department of Nuclear Engineering, Kyoto Univ., Uji, Kyoto 611-0011 (Japan); Aoki, Takaaki [Department of Electronic Science and Engineering, Kyoto Univ., Nishikyo, Kyoto 615-8510 (Japan); CREST, Japan Science and Technology Agency (JST), Chiyoda, Tokyo 102-0075 (Japan); Ishihara, Akihiko [Laboratory of Cell Biology and Life Science, Graduate School of Human and Environmental Studies, Kyoto Univ., Sakyo, Kyoto 606-8501 (Japan); Matsuo, Jiro [Quantum Science and Engineering Center, Kyoto Univ., Uji, Kyoto 611-0011 (Japan); CREST, Japan Science and Technology Agency (JST), Chiyoda, Tokyo 102-0075 (Japan)

    2014-08-01

    The spatial distribution of several chemical compounds in biological tissues and cells can be obtained with mass spectrometry imaging (MSI). In conventional secondary ion mass spectrometry (SIMS) with keV-energy ion beams, elastic collisions occur between projectiles and atoms of constituent molecules. The collisions produce fragments, making the acquisition of molecular information difficult. In contrast, ion beams with MeV-energy excite near-surface electrons and enhance the ionization of high-mass molecules; hence, SIMS spectra of fragment-suppressed ionized molecules can be obtained with MeV-SIMS. To compare between MeV and conventional SIMS, we used the two methods based on MeV and Bi{sub 3}-keV ions, respectively, to obtain molecular images of rat cerebellum. Conventional SIMS images of m/z 184 were clearly observed, but with the Bi{sub 3} ion, the distribution of the molecule with m/z 772.5 could be observed with much difficulty. This effect was attributed to the low secondary ion yields and we could not get many signal counts with keV-energy beam. On the other hand, intact molecular ion distributions of lipids were clearly observed with MeV-SIMS, although the mass of all lipid molecules was higher than 500 Da. The peaks of intact molecular ions in MeV-SIMS spectra allowed us to assign the mass. The high secondary ion sensitivity with MeV-energy heavy ions is very useful in biomaterial analysis.

  7. Microstructural characterization of irradiated PWR steels using the atom probe field-ion microscope

    International Nuclear Information System (INIS)

    Miller, M.K.; Burke, M.G.

    1987-08-01

    Atom probe field-ion microscopy has been used to characterize the microstructure of a neutron-irradiated A533B pressure vessel steel weld. The atomic spatial resolution of this technique permits a complete structural and chemical description of the ultra-fine features that control the mechanical properties to be made. A variety of fine scale features including roughly spherical copper precipitates and clusters, spherical and rod-shaped molybdenum carbide and disc-shaped molybdenum nitride precipitates were observed to be inhomogeneously distributed in the ferrite. The copper content of the ferrite was substantially reduced from the nominal level. A thin film of molybdenum carbides and nitrides was observed on grain boundaries in addition to a coarse copper-manganese precipitate. Substantial enrichment of manganese and nickel were detected at the copper-manganese precipitate-ferrite interface and this enrichment extended into the ferrite. Enrichment of nickel, manganese and phosphorus were also measured at grain boundaries

  8. Origin of transverse momentum in relativistic heavy-ion collisions: Microscopic study

    International Nuclear Information System (INIS)

    Blaettel, B.; Koch, V.; Lang, A.; Weber, K.; Cassing, W.; Mosel, U.

    1991-01-01

    We study the origin of the transverse momentum distribution in heavy-ion collisions within a relativistic transport approach. To achieve a better understanding of the reaction dynamics, we decompose the total p t distribution into a mean-field, N-N collision, and Fermi-momentum part. We find that the origin of the transverse momentum strongly depends on the rapidity region. Our investigation of the impact-parameter and mass dependence suggests that peripheral collisions may be useful to investigate the momentum dependence of the mean-field in the nucleus-nucleus case, whereas the mass dependence could give hints about the N-N-collision part. Only after these two issues are settled it may be possible to extract information about the density dependence in central collisions, which may, however, necessitate reactions at even higher energies than the 800 MeV/nucleon considered in this work

  9. Microscopic classical equations of motion calculations of high-energy heavy-ion collisions

    International Nuclear Information System (INIS)

    Panos, C.N.

    1979-01-01

    Classical microscopic nonrelativistic calculations are made for collisions between equal-mass-nuclei projectile and target with A/sub P/ = A/sub T/ = 20 for laboratory energies E/sub L/ = 117, 400, and 800 MeV/A/sub P/ and also between nuclei with A/sub P/ = A/sub T/ = 40 for E/sub L/ = 400 MeV/A/sub P/. For a given initial configuration of the projectile and target nucleons the trajectories of all nucleons are calculated classically with two-body forces between all pairs of nucleons. The implementation of the CEOM calculations is discussed in detail. More limited relativistic calculations for single initial configurations are also made. The configurations representing the initial nuclei are chosen to have a reasonable radius and kinetic energy; however, they do not saturate with the two-body potentials used. The trajectory information is analyzed to give a large number of position and momentum dependent quantities such as densities, rapidity distributions, inclusive double differential cross sections, etc. The results show that a central collision (b = 0) proceeds in three stages, an initial transparent stage, a strongly interacting stage where the dissipation is large, and finally an expansion stage for which there is considerable dissipation. Appreciable potential energy effects were found for b = 0; however, the final distributions were very similar for the scattering equivalent potentials. For lower energies (E/sub L/ approx. = 100 MeV) there is some evidence of fusion into large fragments. The thermal models for b = 0 are tested. Noncentral collisions show typical nonequilibrium and transparency features. The multiplicity distribution is obtained for A/sub P/ = A/sub T/ = 20 and E/sub L/ = 800 MeV. A comparison of the impact parameter-integrated inclusive double differential cross sections is made with the experimental data for A/sub P/ = A/sub T/ = 20, E/sub L/ = 800 MeV and shows fair agreement

  10. Acoustic, electrochemical and microscopic characterization of interaction of Arthrospira platensis biofilm and heavy metal ions

    OpenAIRE

    Tekaya , Nadèje; Gammoudi , Ibtissèm; Braiek , Mohamed; Tarbague , Hakim; Morote , Fabien; Raimbault , Vincent; Sakly , Nawfel; Rebière , Dominique; Ben Ouada , Hatem; Lagarde , Florence; Ben Ouada , Hafedh; Cohen-Bouhacina , Touria; Déjous , Corinne; Jaffrezic-Renault , Nicole

    2013-01-01

    International audience; This study examines a biofilm of Arthrospira platensis and its interactions with cadmium and mercury, using electrochemical admittance spectroscopy technique combined with highly sensitive Love wave platform for the real-time detection in liquid medium. Spirulina cells were immobilized via multilayers of polyelectrolyte (PEM) on Si/SiO2 surface of both transducers and characterized using atomic force microscopy (AFM). Scanning electron microscopy (SEM) cell images reve...

  11. Simple and versatile modifications allowing time gated spectral acquisition, imaging and lifetime profiling on conventional wide-field microscopes

    International Nuclear Information System (INIS)

    Pal, Robert; Beeby, Andrew

    2014-01-01

    An inverted microscope has been adapted to allow time-gated imaging and spectroscopy to be carried out on samples containing responsive lanthanide probes. The adaptation employs readily available components, including a pulsed light source, time-gated camera, spectrometer and photon counting detector, allowing imaging, emission spectroscopy and lifetime measurements. Each component is controlled by a suite of software written in LabVIEW and is powered via conventional USB ports. (technical note)

  12. An ion beam analysis software based on ImageJ

    International Nuclear Information System (INIS)

    Udalagama, C.; Chen, X.; Bettiol, A.A.; Watt, F.

    2013-01-01

    The suit of techniques (RBS, STIM, ERDS, PIXE, IL, IF,…) available in ion beam analysis yields a variety of rich information. Typically, after the initial challenge of acquiring data we are then faced with the task of having to extract relevant information or to present the data in a format with the greatest impact. This process sometimes requires developing new software tools. When faced with such situations the usual practice at the Centre for Ion Beam Applications (CIBA) in Singapore has been to use our computational expertise to develop ad hoc software tools as and when we need them. It then became apparent that the whole ion beam community can benefit from such tools; specifically from a common software toolset that can be developed and maintained by everyone with freedom to use and allowance to modify. In addition to the benefits of readymade tools and sharing the onus of development, this also opens up the possibility for collaborators to access and analyse ion beam data without having to depend on an ion beam lab. This has the virtue of making the ion beam techniques more accessible to a broader scientific community. We have identified ImageJ as an appropriate software base to develop such a common toolset. In addition to being in the public domain and been setup for collaborative tool development, ImageJ is accompanied by hundreds of modules (plugins) that allow great breadth in analysis. The present work is the first step towards integrating ion beam analysis into ImageJ. Some of the features of the current version of the ImageJ ‘ion beam’ plugin are: (1) reading list mode or event-by-event files, (2) energy gates/sorts, (3) sort stacks, (4) colour function, (5) real time map updating, (6) real time colour updating and (7) median and average map creation

  13. Digital pulse processor for ion beam microprobe imaging

    International Nuclear Information System (INIS)

    Bogovac, M.; Jaksic, M.; Wegrzynek, D.; Markowicz, A.

    2009-01-01

    Capabilities of spectroscopic ion beam analysis (IBA) techniques that are available in ion microprobe facilities can be greatly improved by the use of digital pulse processing. We report here development of a digital multi parameter data acquisition system suitable for IBA imaging applications. Input signals from charge sensitive preamplifier are conditioned by using a simple circuit and digitized with fast ADCs. The digitally converted signals are processed in real time using FPGA. Implementation of several components of the system is presented.

  14. An ion beam analysis software based on ImageJ

    Energy Technology Data Exchange (ETDEWEB)

    Udalagama, C., E-mail: chammika@nus.edu.sg [Centre for Ion Beam Applications (CIBA), Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117 542 (Singapore); Chen, X.; Bettiol, A.A.; Watt, F. [Centre for Ion Beam Applications (CIBA), Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117 542 (Singapore)

    2013-07-01

    The suit of techniques (RBS, STIM, ERDS, PIXE, IL, IF,…) available in ion beam analysis yields a variety of rich information. Typically, after the initial challenge of acquiring data we are then faced with the task of having to extract relevant information or to present the data in a format with the greatest impact. This process sometimes requires developing new software tools. When faced with such situations the usual practice at the Centre for Ion Beam Applications (CIBA) in Singapore has been to use our computational expertise to develop ad hoc software tools as and when we need them. It then became apparent that the whole ion beam community can benefit from such tools; specifically from a common software toolset that can be developed and maintained by everyone with freedom to use and allowance to modify. In addition to the benefits of readymade tools and sharing the onus of development, this also opens up the possibility for collaborators to access and analyse ion beam data without having to depend on an ion beam lab. This has the virtue of making the ion beam techniques more accessible to a broader scientific community. We have identified ImageJ as an appropriate software base to develop such a common toolset. In addition to being in the public domain and been setup for collaborative tool development, ImageJ is accompanied by hundreds of modules (plugins) that allow great breadth in analysis. The present work is the first step towards integrating ion beam analysis into ImageJ. Some of the features of the current version of the ImageJ ‘ion beam’ plugin are: (1) reading list mode or event-by-event files, (2) energy gates/sorts, (3) sort stacks, (4) colour function, (5) real time map updating, (6) real time colour updating and (7) median and average map creation.

  15. Interior tomography in microscopic CT with image reconstruction constrained by full field of view scan at low spatial resolution

    Science.gov (United States)

    Luo, Shouhua; Shen, Tao; Sun, Yi; Li, Jing; Li, Guang; Tang, Xiangyang

    2018-04-01

    In high resolution (microscopic) CT applications, the scan field of view should cover the entire specimen or sample to allow complete data acquisition and image reconstruction. However, truncation may occur in projection data and results in artifacts in reconstructed images. In this study, we propose a low resolution image constrained reconstruction algorithm (LRICR) for interior tomography in microscopic CT at high resolution. In general, the multi-resolution acquisition based methods can be employed to solve the data truncation problem if the project data acquired at low resolution are utilized to fill up the truncated projection data acquired at high resolution. However, most existing methods place quite strict restrictions on the data acquisition geometry, which greatly limits their utility in practice. In the proposed LRICR algorithm, full and partial data acquisition (scan) at low and high resolutions, respectively, are carried out. Using the image reconstructed from sparse projection data acquired at low resolution as the prior, a microscopic image at high resolution is reconstructed from the truncated projection data acquired at high resolution. Two synthesized digital phantoms, a raw bamboo culm and a specimen of mouse femur, were utilized to evaluate and verify performance of the proposed LRICR algorithm. Compared with the conventional TV minimization based algorithm and the multi-resolution scout-reconstruction algorithm, the proposed LRICR algorithm shows significant improvement in reduction of the artifacts caused by data truncation, providing a practical solution for high quality and reliable interior tomography in microscopic CT applications. The proposed LRICR algorithm outperforms the multi-resolution scout-reconstruction method and the TV minimization based reconstruction for interior tomography in microscopic CT.

  16. Collaborative Research and Development. Delivery Order 0006: Transmission Electron Microscope Image Modeling and Semiconductor Heterointerface Characterization

    National Research Council Canada - National Science Library

    Mahalingam, Krishnamurthy

    2006-01-01

    .... Transmission electron microscope (TEM) characterization studies were performed on a variety of novel III-V semiconductor heterostructures being developed for advanced optoelectronic device applications...

  17. Applying deep learning technology to automatically identify metaphase chromosomes using scanning microscopic images: an initial investigation

    Science.gov (United States)

    Qiu, Yuchen; Lu, Xianglan; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Li, Shibo; Liu, Hong; Zheng, Bin

    2016-03-01

    Automated high throughput scanning microscopy is a fast developing screening technology used in cytogenetic laboratories for the diagnosis of leukemia or other genetic diseases. However, one of the major challenges of using this new technology is how to efficiently detect the analyzable metaphase chromosomes during the scanning process. The purpose of this investigation is to develop a computer aided detection (CAD) scheme based on deep learning technology, which can identify the metaphase chromosomes with high accuracy. The CAD scheme includes an eight layer neural network. The first six layers compose of an automatic feature extraction module, which has an architecture of three convolution-max-pooling layer pairs. The 1st, 2nd and 3rd pair contains 30, 20, 20 feature maps, respectively. The seventh and eighth layers compose of a multiple layer perception (MLP) based classifier, which is used to identify the analyzable metaphase chromosomes. The performance of new CAD scheme was assessed by receiver operation characteristic (ROC) method. A number of 150 regions of interest (ROIs) were selected to test the performance of our new CAD scheme. Each ROI contains either interphase cell or metaphase chromosomes. The results indicate that new scheme is able to achieve an area under the ROC curve (AUC) of 0.886+/-0.043. This investigation demonstrates that applying a deep learning technique may enable to significantly improve the accuracy of the metaphase chromosome detection using a scanning microscopic imaging technology in the future.

  18. Time-resolved magnetic imaging in an aberration-corrected, energy-filtered photoemission electron microscope

    International Nuclear Information System (INIS)

    Nickel, F.; Gottlob, D.M.; Krug, I.P.; Doganay, H.; Cramm, S.; Kaiser, A.M.; Lin, G.; Makarov, D.; Schmidt, O.G.

    2013-01-01

    We report on the implementation and usage of a synchrotron-based time-resolving operation mode in an aberration-corrected, energy-filtered photoemission electron microscope. The setup consists of a new type of sample holder, which enables fast magnetization reversal of the sample by sub-ns pulses of up to 10 mT. Within the sample holder current pulses are generated by a fast avalanche photo diode and transformed into magnetic fields by means of a microstrip line. For more efficient use of the synchrotron time structure, we developed an electrostatic deflection gating mechanism capable of beam blanking within a few nanoseconds. This allows us to operate the setup in the hybrid bunch mode of the storage ring facility, selecting one or several bright singular light pulses which are temporally well-separated from the normal high-intensity multibunch pulse pattern. - Highlights: • A new time-resolving operation mode in photoemission electron microscopy is shown. • Our setup works within an energy-filtered, aberration-corrected PEEM. • A new gating system for bunch selection using synchrotron radiation is developed. • An alternative magnetic excitation system is developed. • First tr-imaging using an energy-filtered, aberration-corrected PEEM is shown

  19. SEGMENTATION OF MICROSCOPIC IMAGES OF BACTERIA IN BULGARIAN YOGHURT BY TEMPLATE MATCHING

    Directory of Open Access Journals (Sweden)

    Zlatin Zlatev

    2016-12-01

    Full Text Available The diagnosis of deviations in quality of yogurt is performed by approved methods set out in the Bulgarian national standard (BNS and its adjacent regulations. The basic method of evaluation of the microbiological quality of the product is the microscopic. The method is subjective and requires significant processing time of the samples. The precision of diagnosis is not high and depends on the qualifications of the expert. The systems for pattern recognition in the most natural way interpret this specific expert activity. The aim of this report is to assess the possibility of application of a method of processing and image analysis for determination of the microbiological quality of yogurt. Selected method is template matching. A comparative analysis is made of the methods for template matching. The comparative analysis of available algorithms showed that the known ones have certain disadvantages associated with their rapid-action, the use of simplified procedures, they are sensitive to rotation of the object in the template. It is developed algorithm that complement these known and overcome some of their disadvantages.

  20. Atomic Force Microscope Imaging of the Aggregation of Mouse Immunoglobulin G Molecules

    Directory of Open Access Journals (Sweden)

    Ke Xia

    2003-01-01

    Full Text Available Mouse immunoglobulin G (Ig G1 and the mixture of Ig G1 and Ig G2 deposited on mica were imaged with an atomic force microscope at room temperature and ambient pressure. At a concentration around 1.0mg/L, the molecules were well dispersed. 2~3 days after sample preparation, both Ig G1 and the mixture could self- assemble into different shapes and further form some types of local-ordered toroidal aggregations (monotoroidal, intercrossed toroidal, concentric toroidal, etc.. The number of monomers was not identical in the different toroidal aggregations but in a same circle, the shapes of polymer self-assembled by several monomolecules were found to be almost the same. There was difference between the aggregation behavior of Ig G1 and the mixture. The mechanism of Ig G molecule aggregation was ascribed to the “Y” shape and loops structure of Ig G molecule.

  1. High resolution 3D confocal microscope imaging of volcanic ash particles.

    Science.gov (United States)

    Wertheim, David; Gillmore, Gavin; Gill, Ian; Petford, Nick

    2017-07-15

    We present initial results from a novel high resolution confocal microscopy study of the 3D surface structure of volcanic ash particles from two recent explosive basaltic eruptions, Eyjafjallajökull (2010) and Grimsvötn (2011), in Iceland. The majority of particles imaged are less than 100μm in size and include PM 10 s, known to be harmful to humans if inhaled. Previous studies have mainly used 2D microscopy to examine volcanic particles. The aim of this study was to test the potential of 3D laser scanning confocal microscopy as a reliable analysis tool for these materials and if so to what degree high resolution surface and volume data could be obtained that would further aid in their classification. First results obtained using an Olympus LEXT scanning confocal microscope with a ×50 and ×100 objective lens are highly encouraging. They reveal a range of discrete particle types characterised by sharp or concave edges consistent with explosive formation and sudden rupture of magma. Initial surface area/volume ratios are given that may prove useful in subsequent modelling of damage to aircraft engines and human tissue where inhalation has occurred. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Many-beam effects in electron microscope images of lattice defects

    International Nuclear Information System (INIS)

    Izui, Kazuhiko; Nishida, Takahiko; Furuno, Shigemi; Otsu, Hitoshi

    1974-01-01

    Multi-beam effects in electron microscopic images were investigated. A computation program was developed on the basis of a matrix theory of the multi-beam effects. The matrix theory for a perfect crystal and an imperfect crystal is described, and expression for absorption coefficient is presented. The amplitude of electron wave penetrating through lattice defects is expressed by using scattering matrices which correspond to crystal slices. Calculation of extinction distance was performed, and compared with experimental results. In case of systematic reflection, the difference between two beams and from four to eight beams approximation was small, while a large effect was seen in case of accidental reflection. The intensity profile of bend contour was calculated for silicon and copper-aluminum alloy. Distance between submaxima becomes short with increase of thickness. The change in stacking fault fringes with diffraction condition was investigated. Samples were copper-aluminum alloy. Systematic behavior of the fringes was obtained, and the calculated results reproduced experimental ones. (Kato, T.)

  3. Ion-ion coincidence imaging at high event rate using an in-vacuum pixel detector

    Science.gov (United States)

    Long, Jingming; Furch, Federico J.; Durá, Judith; Tremsin, Anton S.; Vallerga, John; Schulz, Claus Peter; Rouzée, Arnaud; Vrakking, Marc J. J.

    2017-07-01

    A new ion-ion coincidence imaging spectrometer based on a pixelated complementary metal-oxide-semiconductor detector has been developed for the investigation of molecular ionization and fragmentation processes in strong laser fields. Used as a part of a velocity map imaging spectrometer, the detection system is comprised of a set of microchannel plates and a Timepix detector. A fast time-to-digital converter (TDC) is used to enhance the ion time-of-flight resolution by correlating timestamps registered separately by the Timepix detector and the TDC. In addition, sub-pixel spatial resolution (principle experiment on strong field dissociative double ionization of carbon dioxide molecules (CO2), using a 400 kHz repetition rate laser system. The experimental results demonstrate that the spectrometer can detect multiple ions in coincidence, making it a valuable tool for studying the fragmentation dynamics of molecules in strong laser fields.

  4. Microscopic gate-modulation imaging of charge and field distribution in polycrystalline organic transistors

    Science.gov (United States)

    Matsuoka, Satoshi; Tsutsumi, Jun'ya; Kamata, Toshihide; Hasegawa, Tatsuo

    2018-04-01

    In this work, a high-resolution microscopic gate-modulation imaging (μ-GMI) technique is successfully developed to visualize inhomogeneous charge and electric field distributions in operating organic thin-film transistors (TFTs). We conduct highly sensitive and diffraction-limit gate-modulation sensing for acquiring difference images of semiconducting channels between at gate-on and gate-off states that are biased at an alternate frequency of 15 Hz. As a result, we observe unexpectedly inhomogeneous distribution of positive and negative local gate-modulation (GM) signals at a probe photon energy of 1.85 eV in polycrystalline pentacene TFTs. Spectroscopic analyses based on a series of μ-GMI at various photon energies reveal that two distinct effects appear, simultaneously, within the polycrystalline pentacene channel layers: Negative GM signals at 1.85 eV originate from the second-derivative-like GM spectrum which is caused by the effect of charge accumulation, whereas positive GM signals originate from the first-derivative-like GM spectrum caused by the effect of leaked gate fields. Comparisons with polycrystalline morphologies indicate that grain centers are predominated by areas with high leaked gate fields due to the low charge density, whereas grain edges are predominantly high-charge-density areas with a certain spatial extension as associated with the concentrated carrier traps. Consequently, it is reasonably understood that larger grains lead to higher device mobility, but with greater inhomogeneity in charge distribution. These findings provide a clue to understand and improve device characteristics of polycrystalline TFTs.

  5. Atomic force microscopic neutron-induced alpha-autoradiography for boron imaging in detailed cellular histology

    International Nuclear Information System (INIS)

    Amemiya, K.; Takahashi, H.; Fujita, K.; Nakazawa, M.; Yanagie, H.; Eriguchi, M.; Nakagawa, Y.; Sakurai, Y.

    2006-01-01

    The information on subcellular microdistribution of 10 B compounds a cell is significant to evaluate the efficacy of boron neutron capture therapy (BNCT) because the damage brought by the released alpha/lithium particles is highly localized along their path, and radiation sensitivity is quite different among each cell organelles. In neutron-induced alpha-autoradiography (NIAR) technique, 10 B can be measured as tracks for the energetic charged particles from 10 B(n, alpha) 7 Li reactions in solid state track detectors. To perform the NIAR at intracellular structure level for research of 10 B uptake and/or microdosimetry in BNCT, we have developed high-resolution NIAR method with an atomic force microscope (AFM). AFM has been used for analyses of biological specimens such as proteins, DNAs and surface of living cells have, however, intracellular detailed histology of cells has been hardly resolved with AFM since flat surface of sectioned tissue has quite less topographical contrast among each organelle. In our new sample preparation method using UV processing, materials that absorb UV in a semi-thin section are selectively eroded and vaporized by UV exposure, and then fine relief for cellular organelles such as mitochondria, endoplasmic reticulum, filament structure and so on reveals on flat surface of the section, which can be observed with an AFM. The imaging resolution was comparable to TEM imaging of cells. This new method provides fast and cost-effective observation of histological sections with an AFM. Combining this method with NIAR technique, intracellular boron mapping would be possible. (author)

  6. X-ray generation by femtosecond laser pulses and its application to soft X-ray imaging microscope

    International Nuclear Information System (INIS)

    Ikeda, Kenichi; Kotaki, Hideyuki; Nakajima, Kazuhisa

    2002-01-01

    We have developed laser-produced plasma X-ray sources using femtosecond laser pulses at 10Hz repetition rate in a table-top size in order to investigate basic mechanism of X-ray emission from laser-matter interactions and its application to a X-ray microscope. In a soft X-ray region over 5 nm wavelength, laser-plasma X-ray emission from a solid target achieved an intense flux of photons of the order of 1011 photons/rad per pulse with duration of a few 100 ps, which is intense enough to make a clear imaging in a short time exposure. As an application of laser-produced plasma X-ray source, we have developed a soft X-ray imaging microscope operating in the wavelength range around 14 nm. The microscope consists of a cylindrically ellipsoidal condenser mirror and a Schwarzshird objective mirror with highly-reflective multilayers. We report preliminary results of performance tests of the soft X-ray imaging microscope with a compact laser-produced plasma X-ray source

  7. Reconstructing 3D profiles of flux distribution in array of unshunted Josephson junctions from 2D scanning SQUID microscope images

    International Nuclear Information System (INIS)

    Nascimento, F.M.; Sergeenkov, S.; Araujo-Moreira, F.M.

    2012-01-01

    By using a specially designed algorithm (based on utilizing the so-called Hierarchical Data Format), we report on successful reconstruction of 3D profiles of local flux distribution within artificially prepared arrays of unshunted Nb-AlO x -Nb Josephson junctions from 2D surface images obtained via the scanning SQUID microscope. The analysis of the obtained results suggest that for large sweep areas, the local flux distribution significantly deviates from the conventional picture and exhibits a more complicated avalanche-type behavior with a prominent dendritic structure. -- Highlights: ► The penetration of external magnetic field into an array of Nb-AlO x -Nb Josephson junctions is studied. ► Using Scanning SQUID Microscope, 2D images of local flux distribution within array are obtained. ► Using specially designed pattern recognition algorithm, 3D flux profiles are reconstructed from 2D images.

  8. Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images

    Science.gov (United States)

    Yothers, Mitchell P.; Browder, Aaron E.; Bumm, Lloyd A.

    2017-01-01

    We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform. Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as a model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.

  9. Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images.

    Science.gov (United States)

    Yothers, Mitchell P; Browder, Aaron E; Bumm, Lloyd A

    2017-01-01

    We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform. Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as a model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.

  10. The influence of microscopic disorder on electron paramagnetic resonance spectra of Eu2+ ions in Pb1-xGexTe

    International Nuclear Information System (INIS)

    Radzynski, T; Lusakowski, A; Swiatek, K; Story, T

    2009-01-01

    In mixed crystals, because of the different ionic radii of cations or anions and the randomness in the placement of ions of different kinds, the crystal lattice is locally deformed. Such local deformations have significant influence on the ground state splitting of magnetic ions. Because this ground state splitting is responsible for the position of the electron paramagnetic resonance (EPR) lines, microscopic disorder is one of the factors which lead to the broadening of the lines, and eventually to their disappearance. This paper is devoted to semi-quantitative analysis of the influence of microscopic disorder on EPR spectra. The theory is compared against measurements performed on mono-crystalline Pb 1-x Ge x Te epitaxial layers containing Eu 2+ ions for different germanium and europium contents. With increasing germanium content we observe gradual disappearance of the EPR lines, although macroscopically, on the basis of x-ray diffraction analysis, each layer might have been considered as a perfect crystal.

  11. MicrOmega IR: a new infrared hyperspectral imaging microscope or in situ analysis

    Science.gov (United States)

    Vaitua, Leroi; Bibring, Jean-Pierre; Berthé, Michel

    2017-11-01

    MicrOmega IR is an ultra miniaturized Near Infrared hyperspectral microscope for in situ analysis of samples. It is designed to be implemented on board space planetary vehicles (lander and/or rovers). It acquires images of samples typically some 5 mm in width with a spatial sampling of 20 μm. On each pixel, MicrOmega acquires the spectrum in the spectral range 0.9 - 2.6 μm, with a possibility to extend the sensibility up to 4 μm. The spectrum will be measured in up to 300 contiguous spectral channels (600 in the extended range): given the diagnostic spectral features present in this domain, it provides the composition of each spatially resolved constituent. MicrOmega has thus the potential to identify: minerals, such as pyroxene and olivine, ferric oxides, hydrated phases such as phyllosilicates, sulfates and carbonates, ices and organics. The composition of the various phases within a given sample is a critical record of its formation and evolution. Coupled to the mapping information, it provides unique clues to describe the history of the parent body. In particular, the capability to identify hydrated grains and to characterize their adjacent phases has a huge potential in the search for potential bio-relics in Martian samples. This purely non destructive characterization enables further analyses (e.g. through mass spectrometry) to be performed, and/or to contribute to sample selection to return to Earth. MicrOmega IR is coupled to a visible microscope: MicrOmega VIS. Thus, the MicrOmega instrument is developed by an international consortium: IAS (Orsay, France), LESIA (Meudon, France), CBM (Orléans, France), University Of Bern (Bern, Switzerland), IKI (Moscow, Russia). This instrument (MicrOmega IR, MicrOmega VIS and the electronics) is selected for the ESA Exomars mission (launch scheduled for 2013). MicrOmega IR will be used in a reduced spectral range (0.9 - 2.6 μm), due to power, mass and thermal constraints: however, most minerals and other

  12. A field ion microscope study of the surface reaction of tungsten with n-octanol under an applied positive voltage: reaction conditions for the 'splitting' of (110) plane

    International Nuclear Information System (INIS)

    Terao, T.; Iwatsu, F.; Morikawa, H.

    1993-01-01

    Field ion microscopy is a powerful tool for the study of surface phenomena on an atomic scale, especially when they are crystal plane dependent, because the microscope shows many crystal planes of the sample tip simultaneously. Although a large number of FIM studies on vapor deposition, surface diffusion and surface reactions at a metal-gas interface have been reported, those on reactions at a metal-liquid interface are few. The authors have studied the corrosion or tungsten with aqueous solutions and found that water corroded the tungsten tips very severely to reduce the radius of curvature of the tip cap drastically. The reaction was so severe that it was not possible to trace it back to the very initial stages. They adopted, as a weaker reagent, one of the higher alcohols, n-octanol(C 8 H 17 OH), and found that it reacted with tungsten tips when an electrical pulse with a positive voltage between 5 and 10V was applied to the tip, giving very interesting field ion images in which the central (110) plane was divided into two parts located side by side across the [001] zone line. This means that some anisotropic surface reaction occurred which made a groove along the [001] zone line going through the (110) plane, usually the most stable plane chemically for bcc metals. They named this phenomenon 'splitting'. This reaction was less severe than that with water and some results on the morphology of the groove and on the reaction sequence have been reported. In the present paper more detailed reaction conditions which give rise to the splitting are described

  13. Analysis of photon-scanning tunneling microscope images of inhomogeneous samples: Determination of the local refractive index of channel waveguides

    International Nuclear Information System (INIS)

    Bourillot, E.; Fornel, F. de.; Goudonnet, J.P.

    1995-01-01

    Channel waveguides are imaged by a photon-scanning tunneling microscope (PSTM). The polarization of the light and its orientation with respect to the guide aids are shown to be very important parameters in the analysis of the images of such samples. We simulated image formation for the plane of incidence parallel to the axis of the guide. Our theoretical results are qualitatively in agreement with our measurements. These results show the ability of the PSTM to give information about the local refractive-index variations of a sample. 21 refs., 14 figs

  14. Image timing and detector performance of a matrix ion-chamber electronic portal imaging device

    International Nuclear Information System (INIS)

    Greer, P.

    1996-01-01

    The Oncology Centre of Auckland Hospital recently purchased a Varian PortalVision TM electronic portal imaging device (EPID). Image acquisition times, input-output characteristics and contrast-detail curves of this matrix liquid ion-chamber EPID have been measured to examine the variation in imaging performance with acquisition mode. The variation in detector performance with acquisition mode has been examined. The HV cycle time can be increased to improve image quality. Consideration should be given to the acquisition mode and HV cycle time used when imaging to ensure adequate imaging performance with reasonable imaging time. (author)

  15. Imaging of Norway spruce early somatic embryos with the ESEM, Cryo-SEM and laser scanning microscope.

    Science.gov (United States)

    Neděla, Vilém; Hřib, Jiří; Havel, Ladislav; Hudec, Jiří; Runštuk, Jiří

    2016-05-01

    This article describes the surface structure of Norway spruce early somatic embryos (ESEs) as a typical culture with asynchronous development. The microstructure of extracellular matrix covering ESEs were observed using the environmental scanning electron microscope as a primary tool and using the scanning electron microscope with cryo attachment and laser electron microscope as a complementary tool allowing our results to be proven independently. The fresh samples were observed in conditions of the air environment of the environmental scanning electron microscope (ESEM) with the pressure from 550Pa to 690Pa and the low temperature of the sample from -18°C to -22°C. The samples were studied using two different types of detector to allow studying either the thin surface structure or material composition. The scanning electron microscope with cryo attachment was used for imaging frozen extracellular matrix microstructure with higher resolution. The combination of both electron microscopy methods was suitable for observation of "native" plant samples, allowing correct evaluation of our results, free of error and artifacts. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Identification and imaging of modern paints using Secondary Ion Mass Spectrometry with MeV ions

    DEFF Research Database (Denmark)

    Bogdanović Radović, Iva; Siketić, Zdravko; Jembrih-Simbürger, Dubravka

    2017-01-01

    Secondary Ion Mass Spectrometry using MeV ion excitation was applied to analyse modern paint materials containing synthetic organic pigments and binders. It was demonstrated that synthetic organic pigments and binder components with molecular masses in the m/z range from 1 to 1200 could be identi......Secondary Ion Mass Spectrometry using MeV ion excitation was applied to analyse modern paint materials containing synthetic organic pigments and binders. It was demonstrated that synthetic organic pigments and binder components with molecular masses in the m/z range from 1 to 1200 could...... be identified in different paint samples with a high efficiency and in a single measurement. Different ways of mounting of mostly insulating paint samples were tested prior to the analysis in order to achieve the highest possible yield of pigment main molecular ions. As Time-of-Flight mass spectrometer for Me......V Secondary Ion Mass Spectrometry is attached to the heavy ion microprobe, molecular imaging on cross-sections of small paint fragments was performed using focused ions. Due to the fact that molecules are extracted from the uppermost layer of the sample and to avoid surface contamination, the paint samples...

  17. Ion beam induced fluorescence imaging in biological systems

    International Nuclear Information System (INIS)

    Bettiol, Andrew A.; Mi, Zhaohong; Vanga, Sudheer Kumar; Chen, Ce-belle; Tao, Ye; Watt, Frank

    2015-01-01

    Imaging fluorescence generated by MeV ions in biological systems such as cells and tissue sections requires a high resolution beam (<100 nm), a sensitive detection system and a fluorescent probe that has a high quantum efficiency and low bleaching rate. For cutting edge applications in bioimaging, the fluorescence imaging technique needs to break the optical diffraction limit allowing for sub-cellular structure to be visualized, leading to a better understanding of cellular function. In a nuclear microprobe this resolution requirement can be readily achieved utilizing low beam current techniques such as Scanning Transmission Ion Microscopy (STIM). In recent times, we have been able to extend this capability to fluorescence imaging through the development of a new high efficiency fluorescence detection system, and through the use of new novel fluorescent probes that are resistant to ion beam damage (bleaching). In this paper we demonstrate ion beam induced fluorescence imaging in several biological samples, highlighting the advantages and challenges associated with using this technique

  18. Thermal imaging experiments on ANACONDA ion beam generator

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Weihua; Yatsui, Kiyoshi [Nagaoka University of Technology (Japan). Lab. of Beam Technology; Olson, C J; Davis, H A [Los Alamos National Laboratory, Los Alamos, NM (United States)

    1997-12-31

    The thermal imaging technique was used in two experimental measurements. First, the ion intensity distribution on the anode surface was observed from different angles by using a multi-pinhole camera. Second, the plume from a target intercepting the beam was visualized by observing the distribution of temperature increase on a thin plate hit by the plume. (author). 6 figs., 4 refs.

  19. A Review of Automatic Methods Based on Image Processing Techniques for Tuberculosis Detection from Microscopic Sputum Smear Images.

    Science.gov (United States)

    Panicker, Rani Oomman; Soman, Biju; Saini, Gagan; Rajan, Jeny

    2016-01-01

    Tuberculosis (TB) is an infectious disease caused by the bacteria Mycobacterium tuberculosis. It primarily affects the lungs, but it can also affect other parts of the body. TB remains one of the leading causes of death in developing countries, and its recent resurgences in both developed and developing countries warrant global attention. The number of deaths due to TB is very high (as per the WHO report, 1.5 million died in 2013), although most are preventable if diagnosed early and treated. There are many tools for TB detection, but the most widely used one is sputum smear microscopy. It is done manually and is often time consuming; a laboratory technician is expected to spend at least 15 min per slide, limiting the number of slides that can be screened. Many countries, including India, have a dearth of properly trained technicians, and they often fail to detect TB cases due to the stress of a heavy workload. Automatic methods are generally considered as a solution to this problem. Attempts have been made to develop automatic approaches to identify TB bacteria from microscopic sputum smear images. In this paper, we provide a review of automatic methods based on image processing techniques published between 1998 and 2014. The review shows that the accuracy of algorithms for the automatic detection of TB increased significantly over the years and gladly acknowledges that commercial products based on published works also started appearing in the market. This review could be useful to researchers and practitioners working in the field of TB automation, providing a comprehensive and accessible overview of methods of this field of research.

  20. The influence of the microscope lamp filament colour temperature on the process of digital images of histological slides acquisition standardization.

    Science.gov (United States)

    Korzynska, Anna; Roszkowiak, Lukasz; Pijanowska, Dorota; Kozlowski, Wojciech; Markiewicz, Tomasz

    2014-01-01

    The aim of this study is to compare the digital images of the tissue biopsy captured with optical microscope using bright field technique under various light conditions. The range of colour's variation in immunohistochemically stained with 3,3'-Diaminobenzidine and Haematoxylin tissue samples is immense and coming from various sources. One of them is inadequate setting of camera's white balance to microscope's light colour temperature. Although this type of error can be easily handled during the stage of image acquisition, it can be eliminated with use of colour adjustment algorithms. The examination of the dependence of colour variation from microscope's light temperature and settings of the camera is done as an introductory research to the process of automatic colour standardization. Six fields of view with empty space among the tissue samples have been selected for analysis. Each field of view has been acquired 225 times with various microscope light temperature and camera white balance settings. The fourteen randomly chosen images have been corrected and compared, with the reference image, by the following methods: Mean Square Error, Structural SIMilarity and visual assessment of viewer. For two types of backgrounds and two types of objects, the statistical image descriptors: range, median, mean and its standard deviation of chromaticity on a and b channels from CIELab colour space, and luminance L, and local colour variability for objects' specific area have been calculated. The results have been averaged for 6 images acquired in the same light conditions and camera settings for each sample. The analysis of the results leads to the following conclusions: (1) the images collected with white balance setting adjusted to light colour temperature clusters in certain area of chromatic space, (2) the process of white balance correction for images collected with white balance camera settings not matched to the light temperature moves image descriptors into proper

  1. Decontamination of digital image sensors and assessment of electron microscope performance in a BSL-3 containment

    Directory of Open Access Journals (Sweden)

    Michael B. Sherman

    2015-05-01

    Full Text Available A unique biological safety level (BSL-3 cryo-electron microscopy facility with a 200 keV high-end cryo-electron microscope has been commissioned at the University of Texas Medical Branch (UTMB to study the structure of viruses and bacteria classified as select agents. We developed a microscope decontamination protocol based on chlorine dioxide gas with a continuous flow system. In this paper we report on testing digital camera sensors (both CCD and CMOS direct detector in a BSL-3 environment, and microscope performance after chlorine dioxide (ClO2 decontamination cycles.

  2. Identification and imaging of modern paints using Secondary Ion Mass Spectrometry with MeV ions

    Science.gov (United States)

    Bogdanović Radović, Iva; Siketić, Zdravko; Jembrih-Simbürger, Dubravka; Marković, Nikola; Anghelone, Marta; Stoytschew, Valentin; Jakšić, Milko

    2017-09-01

    Secondary Ion Mass Spectrometry using MeV ion excitation was applied to analyse modern paint materials containing synthetic organic pigments and binders. It was demonstrated that synthetic organic pigments and binder components with molecular masses in the m/z range from 1 to 1200 could be identified in different paint samples with a high efficiency and in a single measurement. Different ways of mounting of mostly insulating paint samples were tested prior to the analysis in order to achieve the highest possible yield of pigment main molecular ions. As Time-of-Flight mass spectrometer for MeV Secondary Ion Mass Spectrometry is attached to the heavy ion microprobe, molecular imaging on cross-sections of small paint fragments was performed using focused ions. Due to the fact that molecules are extracted from the uppermost layer of the sample and to avoid surface contamination, the paint samples were not embedded in the resin as is usually done when imaging of paint samples using different techniques in the field of cultural heritage.

  3. Fundamental limits to imaging resolution for focused ion beams

    International Nuclear Information System (INIS)

    Orloff, J.; Swanson, L.W.; Utlaut, M.

    1996-01-01

    This article investigates the limitations on the formation of focused ion beam images from secondary electrons. We use the notion of the information content of an image to account for the effects of resolution, contrast, and signal-to-noise ratio and show that there is a competition between the rate at which small features are sputtered away by the primary beam and the rate of collection of secondary electrons. We find that for small features, sputtering is the limit to imaging resolution, and that for extended small features (e.g., layered structures), rearrangement, redeposition, and differential sputtering rates may limit the resolution in some cases. copyright 1996 American Vacuum Society

  4. Electron energy loss spectroscopy microanalysis and imaging in the transmission electron microscope: example of biological applications

    International Nuclear Information System (INIS)

    Diociaiuti, Marco

    2005-01-01

    This paper reports original results obtained in our laboratory over the past few years in the application of both electron energy loss spectroscopy (EELS) and electron spectroscopy imaging (ESI) to biological samples, performed in two transmission electron microscopes (TEM) equipped with high-resolution electron filters and spectrometers: a Gatan model 607 single magnetic sector double focusing EEL serial spectrometer attached to a Philips 430 TEM and a Zeiss EM902 Energy Filtering TEM. The primary interest was on the possibility offered by the combined application of these spectroscopic techniques with those offered by the TEM. In particular, the electron beam focusing available in a TEM allowed us to perform EELS and ESI on very small sample volumes, where high-resolution imaging and electron diffraction techniques can provide important structural information. I show that ESI was able to improve TEM performance, due to the reduced chromatic aberration and the possibility of avoiding the sample staining procedure. Finally, the analysis of the oscillating extended energy loss fine structure (EXELFS) beyond the ionization edges characterizing the EELS spectra allowed me, in a manner very similar to the extended X-ray absorption fine structure (EXAFS) analysis of the X-ray absorption spectra, to obtain short-range structural information for such light elements of biological interest as O or Fe. The Philips EM430 (250-300 keV) TEM was used to perform EELS microanalysis on Ca, P, O, Fe, Al and Si. The assessment of the detection limits of this method was obtained working with well-characterized samples containing Ca and P, and mimicking the actual cellular matrix. I applied EELS microanalysis to Ca detection in bone tissue during the mineralization process and to P detection in the cellular membrane of erythrocytes treated with an anti-tumoral drug, demonstrating that the cellular membrane is a drug target. I applied EELS microanalysis and selected area electron

  5. Assessing various Infrared (IR) microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains

    Science.gov (United States)

    Roider, Clemens; Ritsch-Marte, Monika; Pemberger, Nadin; Cemper-Kiesslich, Jan; Hatzer-Grubwieser, Petra; Parson, Walther; Pallua, Johannes Dominikus

    2017-01-01

    Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization) was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies) between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43−at 450 cm-1 and ν4PO43− from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio decreases with

  6. Assessing various Infrared (IR microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains.

    Directory of Open Access Journals (Sweden)

    Claudia Woess

    Full Text Available Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43-at 450 cm-1 and ν4PO43- from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio

  7. Assessing various Infrared (IR) microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains.

    Science.gov (United States)

    Woess, Claudia; Unterberger, Seraphin Hubert; Roider, Clemens; Ritsch-Marte, Monika; Pemberger, Nadin; Cemper-Kiesslich, Jan; Hatzer-Grubwieser, Petra; Parson, Walther; Pallua, Johannes Dominikus

    2017-01-01

    Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization) was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies) between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43-at 450 cm-1 and ν4PO43- from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio decreases with time

  8. A new self-made digital slide scanner and microscope for imaging and quantification of fluorescent microspheres

    DEFF Research Database (Denmark)

    Henning, William; Bjerglund Andersen, Julie; Højgaard, Liselotte

    2015-01-01

    Objective: A low-cost microscope slide scanner was constructed for the purpose of digital imaging of newborn piglet brain tissue and to quantify fluorescent microspheres in tissue. Methods: Using a standard digital single-lens reflex (DSLR) camera, fluorescent imaging of newborn piglet brain tissue......-field imaging was tested by adding light diffuser film. Results: Cost of the slide scanner was a fraction of the cost of a commercial slide scanner. The slide scanner was able to image a large number of tissue slides in a semiautomatic manner and provided a large field of view (FOV) of 101 mm2 combined...... and an automatic algorithm to detect fluorescent microspheres in tissue was developed and validated and showed an acceptable difference to “gold standard” manual counting. The slide scanner can be regarded as a low-cost alternative for researchers when digital slide imaging and quantification of fluorescent...

  9. [Getting an insight into the brain - new optical clearing techniques and imaging using light-sheet microscope].

    Science.gov (United States)

    Pawłowska, Monika; Legutko, Diana; Stefaniuk, Marzena

    2017-01-01

    One of the biggest challenges in neuroscience is to understand how brain operates. For this, it would be the best to image the whole brain with at least cellular resolution, preserving the three-dimensional structure in order to capture the connections between different areas. Most currently available high-resolution imaging techniques are based on preparing thin brain sections that are next photographed one by one and subsequently bigger structures are reconstructed. These techniques are laborious and create artifacts. Recent optical clearing methods allow to obtain literally transparent brains that can be imaged using light-sheet microscope. The present review summarizes the most popular optical clearing techniques, describing their different mechanisms and comparing advantages and disadvantages of different approaches, and presents the principle of light-sheet microscopy and its use in imaging. Finally, it gives examples of application of optical tissue clearing and light-sheet imaging in neuroscience and beyond it.

  10. Nanoscale imaging of the growth and division of bacterial cells on planar substrates with the atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Van Der Hofstadt, M. [Institut de Bioenginyeria de Catalunya (IBEC), C/ Baldiri i Reixac 11-15, 08028 Barcelona (Spain); Hüttener, M.; Juárez, A. [Institut de Bioenginyeria de Catalunya (IBEC), C/ Baldiri i Reixac 11-15, 08028 Barcelona (Spain); Departament de Microbiologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona (Spain); Gomila, G., E-mail: ggomila@ibecbarcelona.eu [Institut de Bioenginyeria de Catalunya (IBEC), C/ Baldiri i Reixac 11-15, 08028 Barcelona (Spain); Departament d' Electronica, Universitat de Barcelona, C/ Marti i Franqués 1, 08028 Barcelona (Spain)

    2015-07-15

    With the use of the atomic force microscope (AFM), the Nanomicrobiology field has advanced drastically. Due to the complexity of imaging living bacterial processes in their natural growing environments, improvements have come to a standstill. Here we show the in situ nanoscale imaging of the growth and division of single bacterial cells on planar substrates with the atomic force microscope. To achieve this, we minimized the lateral shear forces responsible for the detachment of weakly adsorbed bacteria on planar substrates with the use of the so called dynamic jumping mode with very soft cantilever probes. With this approach, gentle imaging conditions can be maintained for long periods of time, enabling the continuous imaging of the bacterial cell growth and division, even on planar substrates. Present results offer the possibility to observe living processes of untrapped bacteria weakly attached to planar substrates. - Highlights: • Gelatine coatings used to weakly attach bacterial cells onto planar substrates. • Use of the dynamic jumping mode as a non-perturbing bacterial imaging mode. • Nanoscale resolution imaging of unperturbed single living bacterial cells. • Growth and division of single bacteria cells on planar substrates observed.

  11. Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking

    Directory of Open Access Journals (Sweden)

    Hamahashi Shugo

    2005-05-01

    Full Text Available Abstract Background The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D Nomarski differential interference contrast (DIC microscope images of Caenorhabditis elegans embryos. However, the system needed laborious hand-tuning of its parameters every time a new image set was used. It could not detect nuclei in the process of cell division, and could detect nuclei only from the two- to eight-cell stages. Results We developed a system that automates the detection of nuclei in a set of 4D DIC microscope images of C. elegans embryos. Local image entropy is used to produce regions of the images that have the image texture of the nucleus. From these regions, those that actually detect nuclei are manually selected at the first and last time points of the image set, and an object-tracking algorithm then selects regions that detect nuclei in between the first and last time points. The use of local image entropy makes the system applicable to multiple image sets without the need to change its parameter values. The use of an object-tracking algorithm enables the system to detect nuclei in the process of cell division. The system detected nuclei with high sensitivity and specificity from the one- to 24-cell stages. Conclusion A combination of local image entropy and an object-tracking algorithm enabled highly objective and productive detection of nuclei in a set of 4D DIC microscope images of C. elegans embryos. The system will facilitate genomic and computational analyses of C. elegans embryos.

  12. Pancam and Microscopic Imager observations of dust on the Spirit Rover: Cleaning events, spectral properties, and aggregates

    Science.gov (United States)

    Vaughan, Alicia F.; Johnson, Jeffrey R.; Herkenhoff, Kenneth E.; Sullivan, Robert; Landis, Geoffrey A.; Goetz, Walter; Madsen, Morten B.

    2010-01-01

    This work describes dust deposits on the Spirit Rover over 2000 sols through examination of Pancam and Microscopic Imager observations of specific locations on the rover body, including portions of the solar array, Pancam and Mini-TES calibration targets, and the magnets. This data set reveals the three "cleaning events" experienced by Spirit to date, the spectral properties of dust, and the tendency of dust particles to form aggregates 100 um and larger.

  13. Liquid microdroplet as an optical component to achieve imaging of 100 nm nanostructures on a far-field microscope

    Science.gov (United States)

    Hou, Beibei; Zhang, Luning

    2018-05-01

    We demonstrate that placing liquid microdroplets on a sample surface enables probing of the evanescent wave, thus having super-resolution capability on a far-field optical microscope. A simple method to form diiodomethane (CH2I2) liquid microdroplets with diameters of 10–90 μm in water is proposed. These microdroplets can be used to image various nanostructured samples with a feature size of about 100 nm under white-light illumination.

  14. Analysis of Zebrafish Kidney Development with Time-lapse Imaging Using a Dissecting Microscope Equipped for Optical Sectioning.

    Science.gov (United States)

    Perner, Birgit; Schnerwitzki, Danny; Graf, Michael; Englert, Christoph

    2016-04-07

    In order to understand organogenesis, the spatial and temporal alterations that occur during development of tissues need to be recorded. The method described here allows time-lapse analysis of normal and impaired kidney development in zebrafish embryos by using a fluorescence dissecting microscope equipped for structured illumination and z-stack acquisition. To visualize nephrogenesis, transgenic zebrafish (Tg(wt1b:GFP)) with fluorescently labeled kidney structures were used. Renal defects were triggered by injection of an antisense morpholino oligonucleotide against the Wilms tumor gene wt1a, a factor known to be crucial for kidney development. The advantage of the experimental setup is the combination of a zoom microscope with simple strategies for re-adjusting movements in x, y or z direction without additional equipment. To circumvent focal drift that is induced by temperature variations and mechanical vibrations, an autofocus strategy was applied instead of utilizing a usually required environmental chamber. In order to re-adjust the positional changes due to a xy-drift, imaging chambers with imprinted relocation grids were employed. In comparison to more complex setups for time-lapse recording with optical sectioning such as confocal laser scanning or light sheet microscopes, a zoom microscope is easy to handle. Besides, it offers dissecting microscope-specific benefits such as high depth of field and an extended working distance. The method to study organogenesis presented here can also be used with fluorescence stereo microscopes not capable of optical sectioning. Although limited for high-throughput, this technique offers an alternative to more complex equipment that is normally used for time-lapse recording of developing tissues and organ dynamics.

  15. Field ion microscopy

    International Nuclear Information System (INIS)

    Ramanathan, D.

    1975-01-01

    The basic features of the Field-Ion Microscope (FIM) and the theory of image formation are explained. Design parameters of the FIM, factors limiting its resolution, interpretation of the image, etc are briefly outlined. Relative merits of the various imaging gases and the applications of the FIM are also covered. (K.B.)

  16. Chip-scale fluorescence microscope based on a silo-filter complementary metal-oxide semiconductor image sensor.

    Science.gov (United States)

    Ah Lee, Seung; Ou, Xiaoze; Lee, J Eugene; Yang, Changhuei

    2013-06-01

    We demonstrate a silo-filter (SF) complementary metal-oxide semiconductor (CMOS) image sensor for a chip-scale fluorescence microscope. The extruded pixel design with metal walls between neighboring pixels guides fluorescence emission through the thick absorptive filter to the photodiode of a pixel. Our prototype device achieves 13 μm resolution over a wide field of view (4.8 mm × 4.4 mm). We demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

  17. Sub-wavelength imaging by depolarization in a reflection near-field optical microscope using an uncoated fiber probe

    DEFF Research Database (Denmark)

    Madsen, Steen; Bozhevolnyi, Sergey I.; Hvam, Jørn Märcher

    1998-01-01

    We present a reflection scanning near-field optical microscope utilizing counter-directional light propagation in an uncoated fiber probe, cross-polarized detection and shear-force feedback. Topographical and near-field optical imaging with a scanning speed of up to 10 mu m/s and a lateral...... resolution better than 40 nm are demonstrated with a latex projection test sample. Determination of the optical resolution as well as correlation between topographical and near-field optical images are discussed. (C) 1998 Elsevier Science B.V....

  18. Enhanced depth-of-field of an integral imaging microscope using a bifocal holographic optical element-micro lens array.

    Science.gov (United States)

    Kwon, Ki-Chul; Lim, Young-Tae; Shin, Chang-Won; Erdenebat, Munkh-Uchral; Hwang, Jae-Moon; Kim, Nam

    2017-08-15

    We propose and implement an integral imaging microscope with extended depth-of-field (DoF) using a bifocal holographic micro lens array (MLA). The properties of the two MLAs are switched via peristrophic multiplexing, where different properties of the MLA are recorded onto the single holographic optical element (HOE). The recorded MLA properties are perpendicular to each other: after the first mode is recorded, the HOE is rotated by 90° clockwise, and the second mode is recorded. The experimental results confirm that the DoF of the integral imaging microscopy system is extended successfully by using the bifocal MLA.

  19. A method for automatic grain segmentation of multi-angle cross-polarized microscopic images of sandstone

    Science.gov (United States)

    Jiang, Feng; Gu, Qing; Hao, Huizhen; Li, Na; Wang, Bingqian; Hu, Xiumian

    2018-06-01

    Automatic grain segmentation of sandstone is to partition mineral grains into separate regions in the thin section, which is the first step for computer aided mineral identification and sandstone classification. The sandstone microscopic images contain a large number of mixed mineral grains where differences among adjacent grains, i.e., quartz, feldspar and lithic grains, are usually ambiguous, which make grain segmentation difficult. In this paper, we take advantage of multi-angle cross-polarized microscopic images and propose a method for grain segmentation with high accuracy. The method consists of two stages, in the first stage, we enhance the SLIC (Simple Linear Iterative Clustering) algorithm, named MSLIC, to make use of multi-angle images and segment the images as boundary adherent superpixels. In the second stage, we propose the region merging technique which combines the coarse merging and fine merging algorithms. The coarse merging merges the adjacent superpixels with less evident boundaries, and the fine merging merges the ambiguous superpixels using the spatial enhanced fuzzy clustering. Experiments are designed on 9 sets of multi-angle cross-polarized images taken from the three major types of sandstones. The results demonstrate both the effectiveness and potential of the proposed method, comparing to the available segmentation methods.

  20. Microscope-Integrated Intraoperative Ultrahigh-Speed Swept-Source Optical Coherence Tomography for Widefield Retinal and Anterior Segment Imaging.

    Science.gov (United States)

    Lu, Chen D; Waheed, Nadia K; Witkin, Andre; Baumal, Caroline R; Liu, Jonathan J; Potsaid, Benjamin; Joseph, Anthony; Jayaraman, Vijaysekhar; Cable, Alex; Chan, Kinpui; Duker, Jay S; Fujimoto, James G

    2018-02-01

    To demonstrate the feasibility of retinal and anterior segment intraoperative widefield imaging using an ultrahigh-speed, swept-source optical coherence tomography (SS-OCT) surgical microscope attachment. A prototype post-objective SS-OCT using a 1,050-nm wavelength, 400 kHz A-scan rate, vertical cavity surface-emitting laser (VCSEL) light source was integrated to a commercial ophthalmic surgical microscope after the objective. Each widefield OCT data set was acquired in 3 seconds (1,000 × 1,000 A-scans, 12 × 12 mm 2 for retina and 10 × 10 mm 2 for anterior segment). Intraoperative SS-OCT was performed in 20 eyes of 20 patients. In six of seven membrane peels and five of seven rhegmatogenous retinal detachment repair surgeries, widefield retinal imaging enabled evaluation pre- and postoperatively. In all seven cataract cases, anterior imaging evaluated the integrity of the posterior lens capsule. Ultrahigh-speed SS-OCT enables widefield intraoperative viewing in the posterior and anterior eye. Widefield imaging visualizes ocular structures and pathology without requiring OCT realignment. [Ophthalmic Surg Lasers Imaging Retina. 2018;49:94-102.]. Copyright 2018, SLACK Incorporated.

  1. Imaging the Microscopic Structure of Shear Thinning and Thickening Colloidal Suspensions

    KAUST Repository

    Cheng, X.

    2011-09-01

    The viscosity of colloidal suspensions varies with shear rate, an important effect encountered in many natural and industrial processes. Although this non-Newtonian behavior is believed to arise from the arrangement of suspended particles and their mutual interactions, microscopic particle dynamics are difficult to measure. By combining fast confocal microscopy with simultaneous force measurements, we systematically investigate a suspension\\'s structure as it transitions through regimes of different flow signatures. Our measurements of the microscopic single-particle dynamics show that shear thinning results from the decreased relative contribution of entropic forces and that shear thickening arises from particle clustering induced by hydrodynamic lubrication forces. This combination of techniques illustrates an approach that complements current methods for determining the microscopic origins of non-Newtonian flow behavior in complex fluids.

  2. Color capable sub-pixel resolving optofluidic microscope and its application to blood cell imaging for malaria diagnosis.

    Directory of Open Access Journals (Sweden)

    Seung Ah Lee

    Full Text Available Miniaturization of imaging systems can significantly benefit clinical diagnosis in challenging environments, where access to physicians and good equipment can be limited. Sub-pixel resolving optofluidic microscope (SROFM offers high-resolution imaging in the form of an on-chip device, with the combination of microfluidics and inexpensive CMOS image sensors. In this work, we report on the implementation of color SROFM prototypes with a demonstrated optical resolution of 0.66 µm at their highest acuity. We applied the prototypes to perform color imaging of red blood cells (RBCs infected with Plasmodium falciparum, a particularly harmful type of malaria parasites and one of the major causes of death in the developing world.

  3. Influence of microscopic mottle on the definition of small image details

    Energy Technology Data Exchange (ETDEWEB)

    Selin, K; Reichmann, S [Sahlgrenska Sjukhuset, Goeteborg (Sweden)

    1979-01-01

    By a special technique of enlarging films a microscopic mottle caused by quantum fluctuations was demonstrated. It was found to affect depiction of small details in such a way as to suggest that it would be of importance for determining resolution capacity, especially in high-speed radiography. Thus, the modulation transfer function appears not to be the only factor determining radiographic resolution. The resolution of high-speed screens may be improved if the film speed is reduced, which leads to a diminished microscopic mottle.

  4. Evaluation of an X-ray-excited optical microscope for chemical imaging of metal and other surfaces.

    Science.gov (United States)

    Sabbe, Pieter-Jan; Dowsett, Mark; Hand, Matthew; Grayburn, Rosie; Thompson, Paul; Bras, Wim; Adriaens, Annemie

    2014-12-02

    The application of a modular system for the nondestructive chemical imaging of metal and other surfaces is described using heritage metals as an example. The custom-built X-ray-excited optical luminescence (XEOL) microscope, XEOM 1, images the chemical state and short-range atomic order of the top 200 nm of both amorphous and crystalline surfaces. A broad X-ray beam is used to illuminate large areas (up to 4 mm(2)) of the sample, and the resulting XEOL emission is collected simultaneously for each pixel by a charge-coupled device sensor to form an image. The input X-ray energy is incremented across a range typical for the X-ray absorption near-edge structure (XANES) and an image collected for each increment. The use of large-footprint beams combined with parallel detection allows the power density to be kept low and facilitates complete nondestructive XANES mapping on a reasonable time scale. In this study the microscope was evaluated by imaging copper surfaces with well-defined patterns of different corrosion products (cuprite Cu2O and nantokite CuCl). The images obtained show chemical contrast, and filtering the XEOL light allowed different corrosion products to be imaged separately. Absorption spectra extracted from software-selected regions of interest exhibit characteristic XANES fingerprints for the compounds present. Moreover, when the X-ray absorption edge positions were extracted from each spectrum, an oxidation state map of the sample could be compiled. The results show that this method allows one to obtain nondestructive and noninvasive information at the micrometer scale while using full-field imaging.

  5. Nuclear Magnetic Resonance Imaging of Li-ion Battery

    Directory of Open Access Journals (Sweden)

    D. Ohno

    2010-12-01

    Full Text Available Nuclear magnetic resonance (NMR imaging has high sensitivity to proton (1H and lithium (7Li. It is a useful measurement for electrolyte in Li-ion battery. 1H NMR images of lithium ion battery which is composed of LiMn2O4 / LiClO4 + propylene carbonate (PC / Li-metal have been studied. 1H NMR images of electrolyte near cathode material (LiMn2O4 showed anomalous intensity distribution, which was quite inhomogeneous. From NMR images as a function of repetition time (TR, it was concluded that the anomalous intensity distribution was not due to change of relaxation time but an indirect (spatial para-magnetization effect from cathode material. The paramagnetization induced by high magnetic field distorts linearity of magnetic gradient field, leading to apparent intensity variance. This functional image is an easy diagnostic measurement for magnetization of cathode material, which allows the possibility to check uniformity of cathode material and change of magnetization under electrochemical process.

  6. Separation method of heavy-ion particle image from gamma-ray mixed images using an imaging plate

    CERN Document Server

    Yamadera, A; Ohuchi, H; Nakamura, T; Fukumura, A

    1999-01-01

    We have developed a separation method of alpha-ray and gamma-ray images using the imaging plate (IP). The IP from which the first image was read out by an image reader was annealed at 50 deg. C for 2 h in a drying oven and the second image was read out by the image reader. It was found out that an annealing ratio, k, which is defined as a ratio of the photo-stimulated luminescence (PSL) density at the first measurement to that at the second measurement, was different for alpha rays and gamma rays. By subtracting the second image multiplied by a factor of k from the first image, the alpha-ray image was separated from the alpha and gamma-ray mixed images. This method was applied to identify the images of helium, carbon and neon particles of high energies using the heavy-ion medical accelerator, HIMAC. (author)

  7. Preparation of theoretical scanning tunneling microscope images of adsorbed molecules: a theoretical study of benzene on the Cu(110) surface

    International Nuclear Information System (INIS)

    Shapter, J.G.; Rogers, B.L.; Ford, M.J.

    2003-01-01

    Full text: Since its development in 1982, the Scanning Tunneling Microscope (STM) has developed into a powerful tool for the study of surfaces and adsorbates. However, the utility of the technique can be further enhanced through the development of techniques for generating theoretical STM images. This is particularly true when studying molecules adsorbed on a substrate, as the results are often interpreted superficially due to an inadequate understanding of the orbital overlap probed in the experiment. A method of preparing theoretical scanning tunneling microscope (STM) images using comparatively inexpensive desktop computers and the commercially available CRYSTAL98 package is presented through a study of benzene adsorbed on the Cu(110) surface. Density Functional Theory (DFT) and Hartree-Fock (HF) methods are used to model clean Cu(110) slabs of various thicknesses and to simulate the adsorption of benzene onto these slabs. Eight possible orientations of benzene on the Cu(110) surface are proposed, and the optimum orientation according to the calculations is presented. Theoretical STM images of the Cu(110) surface and benzene adsorbed on the Cu(110) surface are compared with experimental STM images of the system from a published study. Significant differences are observed and are examined in detail

  8. Confocal laser microscopic imaging of conspicuous facial pores in vivo: relation between the appearance and the internal structure of skin.

    Science.gov (United States)

    Sugata, Keiichi; Nishijima, Takafumi; Kitahara, Takashi; Takema, Yoshinori

    2008-05-01

    Conspicuous facial pores are one of the more serious esthetic defects of most concern to women. Previous microscopic observations of the skin surface around conspicuous pores have discovered large hollows and uneven skin tone. In this study, the observation area was extended from the skin surface to deeper skin to find the characteristic features of conspicuous pores in a wider spectrum. First, a magnified surface image of the cheek skin was obtained using a video microscope. Second, replicas were collected from the same area. Third, the horizontal cross-sectioned images of the epidermis and papillary dermis in different depths were non-invasively obtained using in vivo confocal laser scanning microscopy. These images were compared with each other to find a correlation between features of the skin surface and those of deeper layers. In cross-sectioned images of conspicuous pores, a strongly undulated epidermal-dermal junction was commonly observed around a pore's opening. Areas with this feature correlated well to the areas with larger hollows and an uneven skin tone. Our results indicate that there is a positive correlation between the incidence of the characteristic feature at the epidermal-dermal junction and the visual appearance of a pore.

  9. Pore sub-features reproducibility in direct microscopic and Livescan images--their reliability in personal identification.

    Science.gov (United States)

    Gupta, Abhishek; Sutton, Raul

    2010-07-01

    Third level features have been reported to have equal discriminatory power as second level details in establishing personal identification. Pore area, as an extended set third level sub-feature, has been studied by minimizing possible factors that could affect pore size. The reproducibility of pore surface area has been studied using direct microscopic and 500 ppi Livescan images. Direct microscopic pore area measurements indicated that the day on which the pore area was measured had a significant impact on the measured pore area. Pore area measurement was shown to be difficult to estimate in 500 ppi Livescan measurements owing to lack of resolution. It is not possible to reliably use pore area as an identifying feature in fingerprint examination.

  10. The application of phase contrast X-ray techniques for imaging Li-ion battery electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Eastwood, D.S. [Manchester X-ray Imaging Facility, School of Materials, University of Manchester, Manchester M13 9PL (United Kingdom); Research Complex at Harwell, Didcot, Oxon OX11 0FA (United Kingdom); Bradley, R.S. [Manchester X-ray Imaging Facility, School of Materials, University of Manchester, Manchester M13 9PL (United Kingdom); Tariq, F.; Cooper, S.J. [Dept. Earth Science and Engineering, Imperial College London, London SW7 2AZ (United Kingdom); Taiwo, O.O. [Dept. Chemical Engineering, University College London, London WC1E 7JE (United Kingdom); Gelb, J.; Merkle, A. [Carl Zeiss X-ray Microscopy Inc., Pleasanton, CA 94588 (United States); Brett, D.J.L. [Dept. Chemical Engineering, University College London, London WC1E 7JE (United Kingdom); Brandon, N.P. [Dept. Earth Science and Engineering, Imperial College London, London SW7 2AZ (United Kingdom); Withers, P.J.; Lee, P.D. [Manchester X-ray Imaging Facility, School of Materials, University of Manchester, Manchester M13 9PL (United Kingdom); Research Complex at Harwell, Didcot, Oxon OX11 0FA (United Kingdom); Shearing, P.R., E-mail: p.shearing@ucl.ac.uk [Dept. Chemical Engineering, University College London, London WC1E 7JE (United Kingdom)

    2014-04-01

    In order to accelerate the commercialization of fuel cells and batteries across a range of applications, an understanding of the mechanisms by which they age and degrade at the microstructural level is required. Here, the most widely commercialized Li-ion batteries based on porous graphite based electrodes which de/intercalate Li{sup +} ions during charge/discharge are studied by two phase contrast enhanced X-ray imaging modes, namely in-line phase contrast and Zernike phase contrast at the micro (synchrotron) and nano (laboratory X-ray microscope) level, respectively. The rate of charge cycling is directly dependent on the nature of the electrode microstructure, which are typically complex multi-scale 3D geometries with significant microstructural heterogeneities. We have been able to characterise the porosity and the tortuosity by micro-CT as well as the morphology of 5 individual graphite particles by nano-tomography finding that while their volume varied significantly their sphericity was surprisingly similar. The volume specific surface areas of the individual grains measured by nano-CT are significantly larger than the total volume specific surface area of the electrode from the micro-CT imaging, which can be attributed to the greater particle surface area visible at higher resolution.

  11. The application of phase contrast X-ray techniques for imaging Li-ion battery electrodes

    Science.gov (United States)

    Eastwood, D. S.; Bradley, R. S.; Tariq, F.; Cooper, S. J.; Taiwo, O. O.; Gelb, J.; Merkle, A.; Brett, D. J. L.; Brandon, N. P.; Withers, P. J.; Lee, P. D.; Shearing, P. R.

    2014-04-01

    In order to accelerate the commercialization of fuel cells and batteries across a range of applications, an understanding of the mechanisms by which they age and degrade at the microstructural level is required. Here, the most widely commercialized Li-ion batteries based on porous graphite based electrodes which de/intercalate Li+ ions during charge/discharge are studied by two phase contrast enhanced X-ray imaging modes, namely in-line phase contrast and Zernike phase contrast at the micro (synchrotron) and nano (laboratory X-ray microscope) level, respectively. The rate of charge cycling is directly dependent on the nature of the electrode microstructure, which are typically complex multi-scale 3D geometries with significant microstructural heterogeneities. We have been able to characterise the porosity and the tortuosity by micro-CT as well as the morphology of 5 individual graphite particles by nano-tomography finding that while their volume varied significantly their sphericity was surprisingly similar. The volume specific surface areas of the individual grains measured by nano-CT are significantly larger than the total volume specific surface area of the electrode from the micro-CT imaging, which can be attributed to the greater particle surface area visible at higher resolution.

  12. The application of phase contrast X-ray techniques for imaging Li-ion battery electrodes

    International Nuclear Information System (INIS)

    Eastwood, D.S.; Bradley, R.S.; Tariq, F.; Cooper, S.J.; Taiwo, O.O.; Gelb, J.; Merkle, A.; Brett, D.J.L.; Brandon, N.P.; Withers, P.J.; Lee, P.D.; Shearing, P.R.

    2014-01-01

    In order to accelerate the commercialization of fuel cells and batteries across a range of applications, an understanding of the mechanisms by which they age and degrade at the microstructural level is required. Here, the most widely commercialized Li-ion batteries based on porous graphite based electrodes which de/intercalate Li + ions during charge/discharge are studied by two phase contrast enhanced X-ray imaging modes, namely in-line phase contrast and Zernike phase contrast at the micro (synchrotron) and nano (laboratory X-ray microscope) level, respectively. The rate of charge cycling is directly dependent on the nature of the electrode microstructure, which are typically complex multi-scale 3D geometries with significant microstructural heterogeneities. We have been able to characterise the porosity and the tortuosity by micro-CT as well as the morphology of 5 individual graphite particles by nano-tomography finding that while their volume varied significantly their sphericity was surprisingly similar. The volume specific surface areas of the individual grains measured by nano-CT are significantly larger than the total volume specific surface area of the electrode from the micro-CT imaging, which can be attributed to the greater particle surface area visible at higher resolution

  13. In vivo imaging of middle-ear and inner-ear microstructures of a mouse guided by SD-OCT combined with a surgical microscope

    Science.gov (United States)

    Cho, Nam Hyun; Jang, Jeong Hun; Jung, Woonggyu; Kim, Jeehyun

    2014-01-01

    We developed an augmented-reality system that combines optical coherence tomography (OCT) with a surgical microscope. By sharing the common optical path in the microscope and OCT, we could simultaneously acquire OCT and microscope views. The system was tested to identify the middle-ear and inner-ear microstructures of a mouse. Considering the probability of clinical application including otorhinolaryngology, diseases such as middle-ear effusion were visualized using in vivo mouse and OCT images simultaneously acquired through the eyepiece of the surgical microscope during surgical manipulation using the proposed system. This system is expected to realize a new practical area of OCT application. PMID:24787787

  14. Multiplex Mass Spectrometric Imaging with Polarity Switching for Concurrent Acquisition of Positive and Negative Ion Images

    Science.gov (United States)

    Korte, Andrew R.; Lee, Young Jin

    2013-06-01

    We have recently developed a multiplex mass spectrometry imaging (MSI) method which incorporates high mass resolution imaging and MS/MS and MS3 imaging of several compounds in a single data acquisition utilizing a hybrid linear ion trap-Orbitrap mass spectrometer (Perdian and Lee, Anal. Chem. 82, 9393-9400, 2010). Here we extend this capability to obtain positive and negative ion MS and MS/MS spectra in a single MS imaging experiment through polarity switching within spiral steps of each raster step. This methodology was demonstrated for the analysis of various lipid class compounds in a section of mouse brain. This allows for simultaneous imaging of compounds that are readily ionized in positive mode (e.g., phosphatidylcholines and sphingomyelins) and those that are readily ionized in negative mode (e.g., sulfatides, phosphatidylinositols and phosphatidylserines). MS/MS imaging was also performed for a few compounds in both positive and negative ion mode within the same experimental set-up. Insufficient stabilization time for the Orbitrap high voltage leads to slight deviations in observed masses, but these deviations are systematic and were easily corrected with a two-point calibration to background ions.

  15. Intrasurgical Human Retinal Imaging With Manual Instrument Tracking Using a Microscope-Integrated Spectral-Domain Optical Coherence Tomography Device.

    Science.gov (United States)

    Hahn, Paul; Carrasco-Zevallos, Oscar; Cunefare, David; Migacz, Justin; Farsiu, Sina; Izatt, Joseph A; Toth, Cynthia A

    2015-07-01

    To characterize the first in-human intraoperative imaging using a custom prototype spectral-domain microscope-integrated optical coherence tomography (MIOCT) device during vitreoretinal surgery with instruments in the eye. Under institutional review board approval for a prospective intraoperative study, MIOCT images were obtained at surgical pauses with instruments held static in the vitreous cavity and then concurrently with surgical maneuvers. Postoperatively, MIOCT images obtained at surgical pauses were compared with images obtained with a high-resolution handheld spectral-domain OCT (HHOCT) system with objective endpoints, including acquisition of images acceptable for analysis and identification of predefined macular morphologic or pathologic features. Human MIOCT images were successfully obtained before incision and during pauses in surgical maneuvers. MIOCT imaging confirmed preoperative diagnoses, such as epiretinal membrane, full-thickness macular hole, and vitreomacular traction and demonstrated successful achievement of surgical goals. MIOCT and HHOCT images obtained at surgical pauses in two cohorts of five patients were comparable with greater than or equal to 80% correlation in 80% of patients. Real-time video-imaging concurrent with surgical manipulations enabled, for the first time using this device, visualization of dynamic instrument-retina interaction with targeted OCT tracking. MIOCT is successful for imaging at surgical pauses and for real-time image guidance with implementation of targeted OCT tracking. Even faster acquisition speeds are currently being developed with incorporation of a swept-source MIOCT engine. Further refinements and investigations will be directed toward continued integration for real-time volumetric imaging of surgical maneuvers. Ongoing development of seamless MIOCT systems will likely transform surgical visualization, approaches, and decision-making.

  16. Quantification of synovistis by MRI: correlation between dynamic and static gadolinium-enhanced magnetic resonance imaging and microscopic and macroscopic signs of synovial inflammation

    DEFF Research Database (Denmark)

    Østergaard, Mikkel; Stoltenberg, M; Løvgreen-Nielsen, P

    1998-01-01

    Dynamic and static gadolinium-diethylenetriaminepentaacetic acid(Gd-DTPA)-enhanced magnetic resonance imaging (MRI) were evaluated as measures of joint inflammation in arthritis, by a comparison with macroscopic and microscopic signs of synovitis. Furthermore, the importance of the size...

  17. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

    Science.gov (United States)

    Wu, J.S.; Kim, A. M.; Bleher, R.; Myers, B.D.; Marvin, R. G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.; Woodruff, T. K.; O'Halloran, T. V.; Dravid, Vinayak P.

    2013-01-01

    A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room- and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. PMID:23500508

  18. A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout.

    Science.gov (United States)

    McConnell, Gail; Trägårdh, Johanna; Amor, Rumelo; Dempster, John; Reid, Es; Amos, William Bradshaw

    2016-09-23

    Current optical microscope objectives of low magnification have low numerical aperture and therefore have too little depth resolution and discrimination to perform well in confocal and nonlinear microscopy. This is a serious limitation in important areas, including the phenotypic screening of human genes in transgenic mice by study of embryos undergoing advanced organogenesis. We have built an optical lens system for 3D imaging of objects up to 6 mm wide and 3 mm thick with depth resolution of only a few microns instead of the tens of microns currently attained, allowing sub-cellular detail to be resolved throughout the volume. We present this lens, called the Mesolens, with performance data and images from biological specimens including confocal images of whole fixed and intact fluorescently-stained 12.5-day old mouse embryos.

  19. Adaptive striping watershed segmentation method for processing microscopic images of overlapping irregular-shaped and multicentre particles.

    Science.gov (United States)

    Xiao, X; Bai, B; Xu, N; Wu, K

    2015-04-01

    Oversegmentation is a major drawback of the morphological watershed algorithm. Here, we study and reveal that the oversegmentation is not only because of the irregular shapes of the particle images, which people are familiar with, but also because of some particles, such as ellipses, with more than one centre. A new parameter, the striping level, is introduced and the criterion for striping parameter is built to help find the right markers prior to segmentation. An adaptive striping watershed algorithm is established by applying a procedure, called the marker searching algorithm, to find the markers, which can effectively suppress the oversegmentation. The effectiveness of the proposed method is validated by analysing some typical particle images including the images of gold nanorod ensembles. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

  20. Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope

    OpenAIRE

    Guan, Zeyi; Lee, Juhyun; Jiang, Hao; Dong, Siyan; Jen, Nelson; Hsiai, Tzung; Ho, Chih-Ming; Fei, Peng

    2015-01-01

    We developed a compact plane illumination plugin (PIP) device which enabled plane illumination and light sheet fluorescence imaging on a conventional inverted microscope. The PIP device allowed the integration of microscope with tunable laser sheet profile, fast image acquisition, and 3-D scanning. The device is both compact, measuring approximately 15 by 5 by 5 cm, and cost-effective, since we employed consumer electronics and an inexpensive device molding method. We demonstrated that PIP pr...

  1. Automatic Recognition of Acute Myelogenous Leukemia in Blood Microscopic Images Using K-means Clustering and Support Vector Machine.

    Science.gov (United States)

    Kazemi, Fatemeh; Najafabadi, Tooraj Abbasian; Araabi, Babak Nadjar

    2016-01-01

    Acute myelogenous leukemia (AML) is a subtype of acute leukemia, which is characterized by the accumulation of myeloid blasts in the bone marrow. Careful microscopic examination of stained blood smear or bone marrow aspirate is still the most significant diagnostic methodology for initial AML screening and considered as the first step toward diagnosis. It is time-consuming and due to the elusive nature of the signs and symptoms of AML; wrong diagnosis may occur by pathologists. Therefore, the need for automation of leukemia detection has arisen. In this paper, an automatic technique for identification and detection of AML and its prevalent subtypes, i.e., M2-M5 is presented. At first, microscopic images are acquired from blood smears of patients with AML and normal cases. After applying image preprocessing, color segmentation strategy is applied for segmenting white blood cells from other blood components and then discriminative features, i.e., irregularity, nucleus-cytoplasm ratio, Hausdorff dimension, shape, color, and texture features are extracted from the entire nucleus in the whole images containing multiple nuclei. Images are classified to cancerous and noncancerous images by binary support vector machine (SVM) classifier with 10-fold cross validation technique. Classifier performance is evaluated by three parameters, i.e., sensitivity, specificity, and accuracy. Cancerous images are also classified into their prevalent subtypes by multi-SVM classifier. The results show that the proposed algorithm has achieved an acceptable performance for diagnosis of AML and its common subtypes. Therefore, it can be used as an assistant diagnostic tool for pathologists.

  2. Dynamic nano-imaging of label-free living cells using electron beam excitation-assisted optical microscope

    Science.gov (United States)

    Fukuta, Masahiro; Kanamori, Satoshi; Furukawa, Taichi; Nawa, Yasunori; Inami, Wataru; Lin, Sheng; Kawata, Yoshimasa; Terakawa, Susumu

    2015-01-01

    Optical microscopes are effective tools for cellular function analysis because biological cells can be observed non-destructively and non-invasively in the living state in either water or atmosphere condition. Label-free optical imaging technique such as phase-contrast microscopy has been analysed many cellular functions, and it is essential technology for bioscience field. However, the diffraction limit of light makes it is difficult to image nano-structures in a label-free living cell, for example the endoplasmic reticulum, the Golgi body and the localization of proteins. Here we demonstrate the dynamic imaging of a label-free cell with high spatial resolution by using an electron beam excitation-assisted optical (EXA) microscope. We observed the dynamic movement of the nucleus and nano-scale granules in living cells with better than 100 nm spatial resolution and a signal-to-noise ratio (SNR) around 10. Our results contribute to the development of cellular function analysis and open up new bioscience applications. PMID:26525841

  3. Dynamic nano-imaging of label-free living cells using electron beam excitation-assisted optical microscope.

    Science.gov (United States)

    Fukuta, Masahiro; Kanamori, Satoshi; Furukawa, Taichi; Nawa, Yasunori; Inami, Wataru; Lin, Sheng; Kawata, Yoshimasa; Terakawa, Susumu

    2015-11-03

    Optical microscopes are effective tools for cellular function analysis because biological cells can be observed non-destructively and non-invasively in the living state in either water or atmosphere condition. Label-free optical imaging technique such as phase-contrast microscopy has been analysed many cellular functions, and it is essential technology for bioscience field. However, the diffraction limit of light makes it is difficult to image nano-structures in a label-free living cell, for example the endoplasmic reticulum, the Golgi body and the localization of proteins. Here we demonstrate the dynamic imaging of a label-free cell with high spatial resolution by using an electron beam excitation-assisted optical (EXA) microscope. We observed the dynamic movement of the nucleus and nano-scale granules in living cells with better than 100 nm spatial resolution and a signal-to-noise ratio (SNR) around 10. Our results contribute to the development of cellular function analysis and open up new bioscience applications.

  4. Scanning ion images; analysis of pharmaceutical drugs at organelle levels

    Science.gov (United States)

    Larras-Regard, E.; Mony, M.-C.

    1995-05-01

    With the ion analyser IMS 4F used in microprobe mode, it is possible to obtain images of fields of 10 × 10 [mu]m2, corresponding to an effective magnification of 7000 with lateral resolution of 250 nm, technical characteristics that are appropriate for the size of cell organelles. It is possible to characterize organelles by their relative CN-, P- and S- intensities when the tissues are prepared by freeze fixation and freeze substitution. The recognition of organelles enables correlation of the tissue distribution of ebselen, a pharmaceutical drug containing selenium. The various metabolites characterized in plasma, bile and urine during biotransformation of ebselen all contain selenium, so the presence of the drug and its metabolites can be followed by images of Se. We were also able to detect the endogenous content of Se in tissue, due to the increased sensitivity of ion analysis in microprobe mode. Our results show a natural occurrence of Se in the border corresponding to the basal lamina of cells of proximal but not distal tubules of the kidney. After treatment of rats with ebselen, an additional site of Se is found in the lysosomes. We suggest that in addition to direct elimination of ebselen and its metabolites by glomerular filtration and urinary elimination, a second process of elimination may occur: Se compounds reaching the epithelial cells via the basal lamina accumulate in lysosomes prior to excretion into the tubular fluid. The technical developments of using the IMS 4F instrument in the microprobe mode and the improvement in preparation of samples by freeze fixation and substitution further extend the limit of ion analysis in biology. Direct imaging of trace elements and molecules marked with a tracer make it possible to determine their targets by comparison with images of subcellular structures. This is a promising advance in the study of pathways of compounds within tissues, cells and the whole organism.

  5. Cellscope Aquatic: a Lab Quality, Portable Cellphone-Based Microscope for On-Site Collection of Algae Images

    Science.gov (United States)

    Steinberg, S. J.; Howard, M. D.

    2016-02-01

    Collecting algae samples from the field presents issues of specimen damage or degradation caused by preservation methods, handling and transport to laboratory facilities for identification. Traditionally, in-field collection of high quality microscopic images has not been possible due to the size, weight and fragility of high quality instruments and training of field staff in species identification. Scientists at the Southern California Coastal Water Research Project (SCCWRP) in collaboration with the Fletcher Lab, University of California Berkeley, Department of Bioengineering, tested and translated Fletcher's original medical CellScope for use in environmental monitoring applications. Field tests conducted by SCCWRP in 2014 led to modifications of the clinical CellScope to one better suited to in-field microscopic imaging for aquatic organisms. SCCWRP subsequently developed a custom cell-phone application to acquire microscopic imagery using the "CellScope Aquatic "in combination with other cell-phone derived field data (e.g. GPS location, date, time and other field observations). Data and imagery collected in-field may be transmitted in real-time to a web-based data system for tele-taxonomy evaluation and assessment by experts in the office. These hardware and software tools was tested in field in a variety of conditions and settings by multiple algae experts during the spring and summer of 2015 to further test and refine the CellScope Aquatic platform. The CellScope Aquatic provides an easy-to-use, affordable, lightweight, professional quality, data collection platform for environmental monitoring. Our ongoing efforts will focus on development of real-time expert systems for data analysis and image processing, to provide onsite feedback to field scientists.

  6. Imaging the PCP site of the NMDA ion channel

    Energy Technology Data Exchange (ETDEWEB)

    Waterhouse, Rikki N. E-mail: rnw7@columbia.edu

    2003-11-01

    The N-methyl-D-aspartate (NMDA) ion channel plays a role in neuroprotection, neurodegeneration, long-term potentiation, memory, and cognition. It is implicated in the pathophysiology of several neurological and neuropsychiatric disorders including Parkinson's Disease, Huntington's Chorea, schizophrenia, alcoholism and stroke. The development of effective radiotracers for the study of NMDA receptors is critical for our understanding of their function, and their modulation by endogenousr substances or therapeutic drugs. Since the NMDA/PCP receptor lies within the channel, it is a unique target and is theoretically accessible only when the channel is in the active and 'open' state, but not when it is in the inactive or 'closed' state. The physical location of the NMDA/PCP receptor not only makes it an important imaging target but also complicates the development of suitable PET and SPECT radiotracers for this site. An intimate understanding of the biochemical, pharmacological, physiological and behavioral processes associated with the NMDA ion channel is essential to develop improved imaging agents. This review outlines progress made towards the development of radiolabeled agents for PCP sites of the NMDA ion channel. In addition, the animal and pharmacological models used for in vitro and in vivo assessment of NMDA receptor targeted agents are discussed.

  7. Imaging the PCP site of the NMDA ion channel

    International Nuclear Information System (INIS)

    Waterhouse, Rikki N.

    2003-01-01

    The N-methyl-D-aspartate (NMDA) ion channel plays a role in neuroprotection, neurodegeneration, long-term potentiation, memory, and cognition. It is implicated in the pathophysiology of several neurological and neuropsychiatric disorders including Parkinson's Disease, Huntington's Chorea, schizophrenia, alcoholism and stroke. The development of effective radiotracers for the study of NMDA receptors is critical for our understanding of their function, and their modulation by endogenousr substances or therapeutic drugs. Since the NMDA/PCP receptor lies within the channel, it is a unique target and is theoretically accessible only when the channel is in the active and 'open' state, but not when it is in the inactive or 'closed' state. The physical location of the NMDA/PCP receptor not only makes it an important imaging target but also complicates the development of suitable PET and SPECT radiotracers for this site. An intimate understanding of the biochemical, pharmacological, physiological and behavioral processes associated with the NMDA ion channel is essential to develop improved imaging agents. This review outlines progress made towards the development of radiolabeled agents for PCP sites of the NMDA ion channel. In addition, the animal and pharmacological models used for in vitro and in vivo assessment of NMDA receptor targeted agents are discussed

  8. Advanced imaging techniques II: using a compound microscope for photographing point-mount specimens

    Science.gov (United States)

    Digital imaging technology has revolutionized the practice photographing insects for scientific study. Herein described are lighting and mounting techniques designed for imaging micro Hymenoptera. Techniques described here are applicable to all small insects, as well as other invertebrates. The ke...

  9. Innovative parameters obtained for digital analysis of microscopic images to evaluate in vitro hemorheological action of anesthetics

    Science.gov (United States)

    Alet, Analía. I.; Basso, Sabrina; Delannoy, Marcela; Alet, Nicolás. A.; D'Arrigo, Mabel; Castellini, Horacio V.; Riquelme, Bibiana D.

    2015-06-01

    Drugs used during anesthesia could enhance microvascular flow disturbance, not only for their systemic cardiovascular actions but also by a direct effect on the microcirculation and in particular on hemorheology. This is particularly important in high-risk surgical patients such as those with vascular disease (diabetes, hypertension, etc.). Therefore, in this work we propose a set of innovative parameters obtained by digital analysis of microscopic images to study the in vitro hemorheological effect of propofol and vecuronium on red blood cell from type 2 diabetic patients compared to healthy donors. Obtained innovative parameters allow quantifying alterations in erythrocyte aggregation, which can increase the in vivo risk of microcapillary obstruction.

  10. NUCLEAR SEGMENTATION IN MICROSCOPE CELL IMAGES: A HAND-SEGMENTED DATASET AND COMPARISON OF ALGORITHMS

    OpenAIRE

    Coelho, Luís Pedro; Shariff, Aabid; Murphy, Robert F.

    2009-01-01

    Image segmentation is an essential step in many image analysis pipelines and many algorithms have been proposed to solve this problem. However, they are often evaluated subjectively or based on a small number of examples. To fill this gap, we hand-segmented a set of 97 fluorescence microscopy images (a total of 4009 cells) and objectively evaluated some previously proposed segmentation algorithms.

  11. Cryogenic immersion microscope

    Science.gov (United States)

    Le Gros, Mark; Larabell, Carolyn A.

    2010-12-14

    A cryogenic immersion microscope whose objective lens is at least partially in contact with a liquid reservoir of a cryogenic liquid, in which reservoir a sample of interest is immersed is disclosed. When the cryogenic liquid has an index of refraction that reduces refraction at interfaces between the lens and the sample, overall resolution and image quality are improved. A combination of an immersion microscope and x-ray microscope, suitable for imaging at cryogenic temperatures is also disclosed.

  12. Design and calibration of a digital Fourier holographic microscope for particle sizing via goniometry and optical scatter imaging in transmission.

    Science.gov (United States)

    Rossi, Vincent M; Jacques, Steven L

    2016-06-13

    Goniometry and optical scatter imaging have been used for optical determination of particle size based upon optical scattering. Polystyrene microspheres in suspension serve as a standard for system validation purposes. The design and calibration of a digital Fourier holographic microscope (DFHM) are reported. Of crucial importance is the appropriate scaling of scattering angle space in the conjugate Fourier plane. A detailed description of this calibration process is described. Spatial filtering of the acquired digital hologram to use photons scattered within a restricted angular range produces an image. A pair of images, one using photons narrowly scattered within 8 - 15° (LNA), and one using photons broadly scattered within 8 - 39° (HNA), are produced. An image based on the ratio of these two images, OSIR = HNA/LNA, following Boustany et al. (2002), yields a 2D Optical Scatter Image (OSI) whose contrast is based on the angular dependence of photon scattering and is sensitive to the microsphere size, especially in the 0.5-1.0µm range. Goniometric results are also given for polystyrene microspheres in suspension as additional proof of principle for particle sizing via the DFHM.

  13. Real-time scanning charged-particle microscope image composition with correction of drift.

    Science.gov (United States)

    Cizmar, Petr; Vladár, András E; Postek, Michael T

    2011-04-01

    In this article, a new scanning electron microscopy (SEM) image composition technique is described, which can significantly reduce drift related image corruptions. Drift distortion commonly causes blur and distortions in the SEM images. Such corruption ordinarily appears when conventional image-acquisition methods, i.e., "slow scan" and "fast scan," are applied. The damage is often very significant; it may render images unusable for metrology applications, especially where subnanometer accuracy is required. The described correction technique works with a large number of quickly taken frames, which are properly aligned and then composed into a single image. Such image contains much less noise than the individual frames, while the blur and deformation is minimized. This technique also provides useful information about changes of the sample position in time, which may be applied to investigate the drift properties of the instrument without a need of additional equipment.

  14. Spectroscopic properties of Fe2+ ions at tetragonal sites-Crystal field effects and microscopic modeling of spin Hamiltonian parameters for Fe2+ (S=2) ions in K2FeF4 and K2ZnF4

    International Nuclear Information System (INIS)

    Rudowicz, C.; Piwowarska, D.

    2011-01-01

    Magnetic and spectroscopic properties of the planar antiferromagnet K 2 FeF 4 are determined by the Fe 2+ ions at tetragonal sites. The two-dimensional easy-plane anisotropy exhibited by K 2 FeF 4 is due to the zero field splitting (ZFS) terms arising from the orbital singlet ground state of Fe 2+ ions with the spin S=2. To provide insight into the single-ion magnetic anisotropy of K 2 FeF 4 , the crystal field theory and the microscopic spin Hamiltonian (MSH) approach based on the tensor method is adopted. Survey of available experimental data on the crystal field energy levels and free-ion parameters for Fe 2+ ions in K 2 FeF 4 and related compounds is carried out to provide input for microscopic modeling of the ZFS parameters and the Zeeman electronic ones. The ZFS parameters are expressed in the extended Stevens notation and include contributions up to the fourth-order using as perturbation the spin-orbit and electronic spin-spin couplings within the tetragonal crystal field states of the ground 5 D multiplet. Modeling of the ZFS parameters and the Zeeman electronic ones is carried out. Variation of these parameters is studied taking into account reasonable ranges of the microscopic ones, i.e. the spin-orbit and spin-spin coupling constants, and the energy level splittings, suitable for Fe 2+ ions in K 2 FeF 4 and Fe 2+ :K 2 ZnF 4 . Conversions between the ZFS parameters in the extended Stevens notation and the conventional ones are considered to enable comparison with the data of others. Comparative analysis of the MSH formulas derived earlier and our more complete ones indicates the importance of terms omitted earlier as well as the fourth-order ZFS parameters and the spin-spin coupling related contributions. The results may be useful also for Fe 2+ ions at axial symmetry sites in related systems, i.e. Fe:K 2 MnF 4 , Rb 2 Co 1-x Fe x F 4 , Fe 2+ :Rb 2 CrCl 4 , and Fe 2+ :Rb 2 ZnCl 4 . - Highlights: → Truncated zero field splitting (ZFS) terms for Fe 2+ in K

  15. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    Directory of Open Access Journals (Sweden)

    J. Mejia

    2013-11-01

    Full Text Available The single photon emission microscope (SPEM is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD. Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s-1·MBq-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

  16. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    International Nuclear Information System (INIS)

    Mejia, J.; Reis, M.A.; Miranda, A.C.C.; Batista, I.R.; Barboza, M.R.F.; Shih, M.C.; Fu, G.; Chen, C.T.; Meng, L.J.; Bressan, R.A.; Amaro, E. Jr

    2013-01-01

    The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s -1 ·MBq -1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99m Tc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99m Tc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity

  17. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    Energy Technology Data Exchange (ETDEWEB)

    Mejia, J. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Reis, M.A. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Miranda, A.C.C. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Batista, I.R. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Barboza, M.R.F.; Shih, M.C. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Fu, G. [GE Global Research, Schenectady, NY (United States); Chen, C.T. [Department of Radiology, University of Chicago, Chicago, IL (United States); Meng, L.J. [Department of Nuclear, Plasma and Radiological Engineering, University of Illinois, Urbana-Champaign, IL (United States); Bressan, R.A. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Amaro, E. Jr [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil)

    2013-11-06

    The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s{sup -1}·MBq{sup -1} were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging {sup 99m}Tc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using {sup 99m}Tc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

  18. Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images

    Science.gov (United States)

    Yang, Zhengfan; Fang, Jia; Chittuluru, Johnathan; Asturias, Francisco J.; Penczek, Pawel A.

    2012-01-01

    SUMMARY Identification of homogeneous subsets of images in a macromolecular electron microscopy (EM) image data set is a critical step in single-particle analysis. The task is handled by iterative algorithms, whose performance is compromised by the compounded limitations of image alignment and K-means clustering. Here we describe an approach, iterative stable alignment and clustering (ISAC) that, relying on a new clustering method and on the concepts of stability and reproducibility, can extract validated, homogeneous subsets of images. ISAC requires only a small number of simple parameters and, with minimal human intervention, can eliminate bias from two-dimensional image clustering and maximize the quality of group averages that can be used for ab initio three-dimensional structural determination and analysis of macromolecular conformational variability. Repeated testing of the stability and reproducibility of a solution within ISAC eliminates heterogeneous or incorrect classes and introduces critical validation to the process of EM image clustering. PMID:22325773

  19. Computer experiments on the imaging of point defects with the conventional transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Krakow, W [Xerox Corp., Rochester, N.Y. (USA)

    1978-02-01

    To aid in the interpretation of high resolution electron micrographs of defect structures in crystals, computer-simulated dark-field electron micrographs have been obtained for a variety of point defects in metals. Interpretation of these images in terms of atomic positions and atom correlations becomes straightforward, and it is a simple matter to distinguish between real structural information and image artifacts produced by the phase contrast mechanism in the electron optical imaging process.

  20. A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability

    International Nuclear Information System (INIS)

    Wang, Qi; Wang, Junting; Lu, Qingyou; Hou, Yubin

    2013-01-01

    We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d 31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices

  1. A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability.

    Science.gov (United States)

    Wang, Qi; Hou, Yubin; Wang, Junting; Lu, Qingyou

    2013-11-01

    We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices.

  2. A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability

    Science.gov (United States)

    Wang, Qi; Hou, Yubin; Wang, Junting; Lu, Qingyou

    2013-11-01

    We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices.

  3. Automatic choroid cells segmentation and counting based on approximate convexity and concavity of chain code in fluorescence microscopic image

    Science.gov (United States)

    Lu, Weihua; Chen, Xinjian; Zhu, Weifang; Yang, Lei; Cao, Zhaoyuan; Chen, Haoyu

    2015-03-01

    In this paper, we proposed a method based on the Freeman chain code to segment and count rhesus choroid-retinal vascular endothelial cells (RF/6A) automatically for fluorescence microscopy images. The proposed method consists of four main steps. First, a threshold filter and morphological transform were applied to reduce the noise. Second, the boundary information was used to generate the Freeman chain codes. Third, the concave points were found based on the relationship between the difference of the chain code and the curvature. Finally, cells segmentation and counting were completed based on the characteristics of the number of the concave points, the area and shape of the cells. The proposed method was tested on 100 fluorescence microscopic cell images, and the average true positive rate (TPR) is 98.13% and the average false positive rate (FPR) is 4.47%, respectively. The preliminary results showed the feasibility and efficiency of the proposed method.

  4. On-line transmission electron microscopic image analysis of chromatin texture for differentiation of thyroid gland tumors.

    Science.gov (United States)

    Kriete, A; Schäffer, R; Harms, H; Aus, H M

    1987-06-01

    Nuclei of the cells from the thyroid gland were analyzed in a transmission electron microscope by direct TV scanning and on-line image processing. The method uses the advantages of a visual-perception model to detect structures in noisy and low-contrast images. The features analyzed include area, a form factor and texture parameters from the second derivative stage. Three tumor-free thyroid tissues, three follicular adenomas, three follicular carcinomas and three papillary carcinomas were studied. The computer-aided cytophotometric method showed that the most significant differences were the statistics of the chromatin texture features of homogeneity and regularity. These findings document the possibility of an automated differentiation of tumors at the ultrastructural level.

  5. Secondary electron images obtained with a standard photoelectron emission microscope set-up

    International Nuclear Information System (INIS)

    Benka, Oswald; Zeppenfeld, Peter

    2005-01-01

    The first results of secondary electron images excited by 3-4.3 keV electrons are presented. The images are obtained with a standard FOCUS-PEEM set-up equipped with an imaging energy filter (IEF). The electron gun was mounted on a standard PEEM entrance flange at an angle of 25 deg. with respect to the sample surface. A low extraction voltage of 500 V was used to minimize the deflection of the electron beam by the PEEM extraction electrode. The secondary electron images are compared to photoelectron images excited by a standard 4.9 eV UV lamp. In the case of a Cu pattern on a Si substrate it is found that the lateral resolution without the IEF is about the same for electron and photon excitation but that the relative electron emission intensities are very different. The use of the IEF reduces the lateral resolution. Images for secondary electron energies between eV 1 and eV 2 were obtained by setting the IEF to -V 1 and -V 2 ∼-(V 1 +5V) potentials and taking the difference of both images. Images up to 100 eV electron energies were recorded. The material contrast obtained in these difference images is discussed in terms of a secondary electron and photoelectron emission model and secondary electron energy spectra measured with a LEED-Auger spectrometer

  6. Imaging molecular interaction of NO on Cu(110) with a scanning tunneling microscope.

    Science.gov (United States)

    Okuyama, Hiroshi

    2014-10-01

    Molecular interaction on metal surfaces is one of the central issues of surface science for the microscopic understanding of heterogeneous catalysis. In this Personal Account, I review the recent studies on NO/Cu(110) employing a scanning tunneling microscope (STM) to probe and control the molecule-molecule interaction on the surface. An individual NO molecule was observed as a characteristic dumbbell-shaped protrusion, visualizing the 2π* orbital. By manipulating the intermolecular distance with the STM, the overlap of the 2π* orbital between two NO molecules was controlled. The interaction causes the formation of the bonding and antibonding orbitals below and above the Fermi level, respectively, as a function of the intermolecular distance. The 2π* orbital also plays a role in the reaction of NO with water molecules. A water molecule donates a H-bond to NO, giving rise to the down-shift of the 2π* level below the Fermi level. This causes electron transfer from the substrate to NO, weakening, and eventually rupturing, the N-O bond. The facile bond cleavage by water molecules has implications for the catalytic reduction of NO under ambient conditions. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. An optical super-microscope for far-field, real-time imaging beyond the diffraction limit.

    Science.gov (United States)

    Wong, Alex M H; Eleftheriades, George V

    2013-01-01

    Optical microscopy suffers from a fundamental resolution limitation arising from the diffractive nature of light. While current solutions to sub-diffraction optical microscopy involve combinations of near-field, non-linear and fine scanning operations, we hereby propose and demonstrate the optical super-microscope (OSM) - a superoscillation-based linear imaging system with far-field working and observation distances - which can image an object in real-time and with sub-diffraction resolution. With our proof-of-principle prototype we report a point spread function with a spot size clearly reduced from the diffraction limit, and demonstrate corresponding improvements in two-point resolution experiments. Harnessing a new understanding of superoscillations, based on antenna array theory, our OSM achieves far-field, sub-diffraction optical imaging of an object without the need for fine scanning, data post-processing or object pre-treatment. Hence the OSM can be used in a wide variety of imaging applications beyond the diffraction limit, including real-time imaging of moving objects.

  8. Camera, handlens, and microscope optical system for imaging and coupled optical spectroscopy

    Science.gov (United States)

    Mungas, Greg S. (Inventor); Boynton, John (Inventor); Sepulveda, Cesar A. (Inventor); Nunes de Sepulveda, legal representative, Alicia (Inventor); Gursel, Yekta (Inventor)

    2012-01-01

    An optical system comprising two lens cells, each lens cell comprising multiple lens elements, to provide imaging over a very wide image distance and within a wide range of magnification by changing the distance between the two lens cells. An embodiment also provides scannable laser spectroscopic measurements within the field-of-view of the instrument.

  9. Preclinical evaluation and intraoperative human retinal imaging with a high-resolution microscope-integrated spectral domain optical coherence tomography device.

    Science.gov (United States)

    Hahn, Paul; Migacz, Justin; O'Donnell, Rachelle; Day, Shelley; Lee, Annie; Lin, Phoebe; Vann, Robin; Kuo, Anthony; Fekrat, Sharon; Mruthyunjaya, Prithvi; Postel, Eric A; Izatt, Joseph A; Toth, Cynthia A

    2013-01-01

    The authors have recently developed a high-resolution microscope-integrated spectral domain optical coherence tomography (MIOCT) device designed to enable OCT acquisition simultaneous with surgical maneuvers. The purpose of this report is to describe translation of this device from preclinical testing into human intraoperative imaging. Before human imaging, surgical conditions were fully simulated for extensive preclinical MIOCT evaluation in a custom model eye system. Microscope-integrated spectral domain OCT images were then acquired in normal human volunteers and during vitreoretinal surgery in patients who consented to participate in a prospective institutional review board-approved study. Microscope-integrated spectral domain OCT images were obtained before and at pauses in surgical maneuvers and were compared based on predetermined diagnostic criteria to images obtained with a high-resolution spectral domain research handheld OCT system (HHOCT; Bioptigen, Inc) at the same time point. Cohorts of five consecutive patients were imaged. Successful end points were predefined, including ≥80% correlation in identification of pathology between MIOCT and HHOCT in ≥80% of the patients. Microscope-integrated spectral domain OCT was favorably evaluated by study surgeons and scrub nurses, all of whom responded that they would consider participating in human intraoperative imaging trials. The preclinical evaluation identified significant improvements that were made before MIOCT use during human surgery. The MIOCT transition into clinical human research was smooth. Microscope-integrated spectral domain OCT imaging in normal human volunteers demonstrated high resolution comparable to tabletop scanners. In the operating room, after an initial learning curve, surgeons successfully acquired human macular MIOCT images before and after surgical maneuvers. Microscope-integrated spectral domain OCT imaging confirmed preoperative diagnoses, such as full-thickness macular hole

  10. In situ scanning tunneling microscope tip treatment device for spin polarization imaging

    Science.gov (United States)

    Li, An-Ping [Oak Ridge, TN; Jianxing, Ma [Oak Ridge, TN; Shen, Jian [Knoxville, TN

    2008-04-22

    A tip treatment device for use in an ultrahigh vacuum in situ scanning tunneling microscope (STM). The device provides spin polarization functionality to new or existing variable temperature STM systems. The tip treatment device readily converts a conventional STM to a spin-polarized tip, and thereby converts a standard STM system into a spin-polarized STM system. The tip treatment device also has functions of tip cleaning and tip flashing a STM tip to high temperature (>2000.degree. C.) in an extremely localized fashion. Tip coating functions can also be carried out, providing the tip sharp end with monolayers of coating materials including magnetic films. The device is also fully compatible with ultrahigh vacuum sample transfer setups.

  11. Scanning magnetic tunnel junction microscope for high-resolution imaging of remanent magnetization fields

    International Nuclear Information System (INIS)

    Lima, E A; Weiss, B P; Bruno, A C; Carvalho, H R

    2014-01-01

    Scanning magnetic microscopy is a new methodology for mapping magnetic fields with high spatial resolution and field sensitivity. An important goal has been to develop high-performance instruments that do not require cryogenic technology due to its high cost, complexity, and limitation on sensor-to-sample distance. Here we report the development of a low-cost scanning magnetic microscope based on commercial room-temperature magnetic tunnel junction (MTJ) sensors that typically achieves spatial resolution better than 7 µm. By comparing different bias and detection schemes, optimal performance was obtained when biasing the MTJ sensor with a modulated current at 1.0 kHz in a Wheatstone bridge configuration while using a lock-in amplifier in conjunction with a low-noise custom-made preamplifier. A precision horizontal (x–y) scanning stage comprising two coupled nanopositioners controls the position of the sample and a linear actuator adjusts the sensor-to-sample distance. We obtained magnetic field sensitivities better than 150 nT/Hz 1/2 between 0.1 and 10 Hz, which is a critical frequency range for scanning magnetic microscopy. This corresponds to a magnetic moment sensitivity of 10 –14  A m 2 , a factor of 100 better than achievable with typical commercial superconducting moment magnetometers. It also represents an improvement in sensitivity by a factor between 10 and 30 compared to similar scanning MTJ microscopes based on conventional bias-detection schemes. To demonstrate the capabilities of the instrument, two polished thin sections of representative geological samples were scanned along with a synthetic sample containing magnetic microparticles. The instrument is usable for a diversity of applications that require mapping of samples at room temperature to preserve magnetic properties or viability, including paleomagnetism and rock magnetism, nondestructive evaluation of materials, and biological assays. (paper)

  12. Scanning magnetic tunnel junction microscope for high-resolution imaging of remanent magnetization fields

    Science.gov (United States)

    Lima, E. A.; Bruno, A. C.; Carvalho, H. R.; Weiss, B. P.

    2014-10-01

    Scanning magnetic microscopy is a new methodology for mapping magnetic fields with high spatial resolution and field sensitivity. An important goal has been to develop high-performance instruments that do not require cryogenic technology due to its high cost, complexity, and limitation on sensor-to-sample distance. Here we report the development of a low-cost scanning magnetic microscope based on commercial room-temperature magnetic tunnel junction (MTJ) sensors that typically achieves spatial resolution better than 7 µm. By comparing different bias and detection schemes, optimal performance was obtained when biasing the MTJ sensor with a modulated current at 1.0 kHz in a Wheatstone bridge configuration while using a lock-in amplifier in conjunction with a low-noise custom-made preamplifier. A precision horizontal (x-y) scanning stage comprising two coupled nanopositioners controls the position of the sample and a linear actuator adjusts the sensor-to-sample distance. We obtained magnetic field sensitivities better than 150 nT/Hz1/2 between 0.1 and 10 Hz, which is a critical frequency range for scanning magnetic microscopy. This corresponds to a magnetic moment sensitivity of 10-14 A m2, a factor of 100 better than achievable with typical commercial superconducting moment magnetometers. It also represents an improvement in sensitivity by a factor between 10 and 30 compared to similar scanning MTJ microscopes based on conventional bias-detection schemes. To demonstrate the capabilities of the instrument, two polished thin sections of representative geological samples were scanned along with a synthetic sample containing magnetic microparticles. The instrument is usable for a diversity of applications that require mapping of samples at room temperature to preserve magnetic properties or viability, including paleomagnetism and rock magnetism, nondestructive evaluation of materials, and biological assays.

  13. Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf.

    Science.gov (United States)

    Shi, Lingyan; Rodríguez-Contreras, Adrián; Budansky, Yury; Pu, Yang; Nguyen, Thien An; Alfano, Robert R

    2014-06-01

    Two-photon (2P) excitation of the second singlet (S₂) state was studied to achieve deep optical microscopic imaging in brain tissue when both the excitation (800 nm) and emission (685 nm) wavelengths lie in the "tissue optical window" (650 to 950 nm). S₂ state technique was used to investigate chlorophyll α (Chl α) fluorescence inside a spinach leaf under a thick layer of freshly sliced rat brain tissue in combination with 2P microscopic imaging. Strong emission at the peak wavelength of 685 nm under the 2P S₂ state of Chl α enabled the imaging depth up to 450 μm through rat brain tissue.

  14. Label-free cellular structure imaging with 82 nm lateral resolution using an electron-beam excitation-assisted optical microscope.

    Science.gov (United States)

    Fukuta, Masahiro; Masuda, Yuriko; Inami, Wataru; Kawata, Yoshimasa

    2016-07-25

    We present label-free and high spatial-resolution imaging for specific cellular structures using an electron-beam excitation-assisted optical microscope (EXA microscope). Images of the actin filament and mitochondria of stained HeLa cells, obtained by fluorescence and EXA microscopy, were compared to identify cellular structures. Based on these results, we demonstrated the feasibility of identifying label-free cellular structures at a spatial resolution of 82 nm. Using numerical analysis, we calculated the imaging depth region and determined the spot size of a cathodoluminescent (CL) light source to be 83 nm at the membrane surface.

  15. Capturing and displaying microscopic images used in medical diagnostics and forensic science using 4K video resolution – an application in higher education

    NARCIS (Netherlands)

    Jan Kuijten; Ajda Ortac; Hans Maier; Gert de Heer

    2015-01-01

    To analyze, interpret and evaluate microscopic images, used in medical diagnostics and forensic science, video images for educational purposes were made with a very high resolution of 4096 × 2160 pixels (4K), which is four times as many pixels as High-Definition Video (1920 × 1080 pixels).

  16. Design and implementation of a sensitive high-resolution nonlinear spectral imaging microscope

    NARCIS (Netherlands)

    Palero, Jonathan A.; Latouche, Gwendal; de Bruijn, Henriëtte S.; van der Ploeg van den Heuvel, Angélique; Sterenborg, Henricus J. C. M.; Gerritsen, Hans C.

    2008-01-01

    Live tissue nonlinear microscopy based on multiphoton autofluorescence and second harmonic emission originating from endogenous fluorophores and noncentrosymmetric-structured proteins is rapidly gaining interest in biomedical applications. The advantage of this technique includes high imaging

  17. Magnetic imaging with a Zernike-type phase plate in a transmission electron microscope

    DEFF Research Database (Denmark)

    Pollard, Shawn; Malac, Marek; Beleggia, Marco

    2013-01-01

    We demonstrate the use of a hole-free phase plate (HFPP) for magnetic imaging in transmission electron microscopy by mapping the domain structure in PrDyFeB samples. The HFPP, a Zernike-like imaging method, allows for detecting magnetic signals in-focus to correlate the sample crystal structure...... the reference wave distortion from long-range fields affecting electron holography....

  18. Imaging optical fields below metal films and metal-dielectric waveguides by a scanning microscope

    Science.gov (United States)

    Zhu, Liangfu; Wang, Yong; Zhang, Douguo; Wang, Ruxue; Qiu, Dong; Wang, Pei; Ming, Hai; Badugu, Ramachandram; Rosenfeld, Mary; Lakowicz, Joseph R.

    2017-09-01

    Laser scanning confocal fluorescence microscopy (LSCM) is now an important method for tissue and cell imaging when the samples are located on the surfaces of glass slides. In the past decade, there has been extensive development of nano-optical structures that display unique effects on incident and transmitted light, which will be used with novel configurations for medical and consumer products. For these applications, it is necessary to characterize the light distribution within short distances from the structures for efficient detection and elimination of bulky optical components. These devices will minimize or possibly eliminate the need for free-space light propagation outside of the device itself. We describe the use of the scanning function of a LSCM to obtain 3D images of the light intensities below the surface of nano-optical structures. More specifically, we image the spatial distributions inside the substrate of fluorescence emission coupled to waveguide modes after it leaks through thin metal films or dielectric-coated metal films. The observed spatial distribution were in general agreement with far-field calculations, but the scanning images also revealed light intensities at angles not observed with classical back focal plane imaging. Knowledge of the subsurface optical intensities will be crucial in the combination of nano-optical structures with rapidly evolving imaging detectors.

  19. Semiautomated confocal imaging of fungal pathogenesis on plants: Microscopic analysis of macroscopic specimens.

    Science.gov (United States)

    Minker, Katharine R; Biedrzycki, Meredith L; Kolagunda, Abhishek; Rhein, Stephen; Perina, Fabiano J; Jacobs, Samuel S; Moore, Michael; Jamann, Tiffany M; Yang, Qin; Nelson, Rebecca; Balint-Kurti, Peter; Kambhamettu, Chandra; Wisser, Randall J; Caplan, Jeffrey L

    2018-02-01

    The study of phenotypic variation in plant pathogenesis provides fundamental information about the nature of disease resistance. Cellular mechanisms that alter pathogenesis can be elucidated with confocal microscopy; however, systematic phenotyping platforms-from sample processing to image analysis-to investigate this do not exist. We have developed a platform for 3D phenotyping of cellular features underlying variation in disease development by fluorescence-specific resolution of host and pathogen interactions across time (4D). A confocal microscopy phenotyping platform compatible with different maize-fungal pathosystems (fungi: Setosphaeria turcica, Cochliobolus heterostrophus, and Cercospora zeae-maydis) was developed. Protocols and techniques were standardized for sample fixation, optical clearing, species-specific combinatorial fluorescence staining, multisample imaging, and image processing for investigation at the macroscale. The sample preparation methods presented here overcome challenges to fluorescence imaging such as specimen thickness and topography as well as physiological characteristics of the samples such as tissue autofluorescence and presence of cuticle. The resulting imaging techniques provide interesting qualitative and quantitative information not possible with conventional light or electron 2D imaging. Microsc. Res. Tech., 81:141-152, 2018. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Wu, J.S., E-mail: jinsong-wu@northwestern.edu [Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Kim, A.M. [Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Bleher, R. [Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Myers, B.D. [Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Marvin, R.G. [Department of Chemistry, Northwestern University, Evanston, IL 60208 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Inada, H.; Nakamura, K. [Hitachi High-Technologies Corporation, Ibaraki 312-8504 (Japan); Zhang, X.F. [Hitachi High Technologies America, Inc., 5960 Inglewood Drive, Pleasanton, California 94588 (United States); Roth, E. [Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Li, S.Y. [Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208 (United States); and others

    2013-05-15

    A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. - Highlights: ► Applications of STEM in characterization of biological samples are demonstrated. ► Elemental analyses are performed by dual EDS and EELS. ► Both the surface and internal structure of cells can be studied simultaneously. ► The imaging contrast in low-dose cryo-STEM has been analyzed.

  1. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

    International Nuclear Information System (INIS)

    Wu, J.S.; Kim, A.M.; Bleher, R.; Myers, B.D.; Marvin, R.G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.

    2013-01-01

    A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. - Highlights: ► Applications of STEM in characterization of biological samples are demonstrated. ► Elemental analyses are performed by dual EDS and EELS. ► Both the surface and internal structure of cells can be studied simultaneously. ► The imaging contrast in low-dose cryo-STEM has been analyzed

  2. Scanning ion microscopy with low energy lithium ions

    International Nuclear Information System (INIS)

    Twedt, Kevin A.; Chen, Lei; McClelland, Jabez J.

    2014-01-01

    Using an ion source based on photoionization of laser-cooled lithium atoms, we have developed a scanning ion microscope with probe sizes of a few tens of nanometers and beam energies from 500 eV to 5 keV. These beam energies are much lower than the typical operating energies of the helium ion microscope or gallium focused ion beam systems. We demonstrate how low energy can be advantageous in ion microscopy when detecting backscattered ions, due to a decreased interaction volume and the potential for surface sensitive composition analysis. As an example application that demonstrates these advantages, we non-destructively image the removal of a thin residual resist layer during plasma etching in a nano-imprint lithography process. - Highlights: • We use an ion source based on photoionization of laser-cooled lithium atoms. • The ion source makes possible a low energy (500 eV to 5 keV) scanning ion microscope. • Low energy is preferred for ion microscopy with backscattered ions. • We use the microscope to image a thin resist used in nano-imprint lithography

  3. Nanoscale imaging and optimization of a compact "water window" SXR microscope

    Science.gov (United States)

    Torrisi, Alfio; Wachulak, Przemyslaw; Nawaz, Fahad; Bartnik, Andrzej; Kostecki, Jerzy; Wegrzyński, Lukasz; Jarocki, Roman; Szczurek, Mirosław; Fiedorowicz, Henryk

    2015-05-01

    The wavelength diffraction limit, described by the Rayleigh criterion, can be overcome if short wavelength radiations are employed, thus it is possible to resolve smaller features by the use of radiation in the extreme ultraviolet (EUV) and soft X-ray (SXR) spectral ranges. In particular way, radiation from the "water window" spectral range, which extends between K-absorption edges of carbon and oxygen (280÷540 eV), could be used in order to obtain high-contrast biological imaging. Laser-plasma double stream gas puff target source is suitable for SXR microscopy in the "water window" spectral range, which recently allowed to develop a system, operating at He-like nitrogen spectral line λ=2.88 nm, which permits to obtain images with half-pitch spatial resolution of ˜ 60 nm, exposure time as low as a few seconds and represents an important alternative for high resolution imaging for biomedical applications, material science and nanotechnology using a very compact laser source. The goal of measurements, presented herein, is to show SXR images of various biological samples, proving high contrast in the "water window" and characterize in more detail such compact microscopy system, based on a laser plasma source with a double stream gas puff target and a Fresnel zone plate (FZP) objective. The influence of various acquisition parameters on the quality of the obtained SXR images, expressed in terms of a signal-to-noise (SNR) will be demonstrated. Moreover, because the measurements are performed on SXR images, similar measurements might be performed as a benchmark in order to characterize different imaging systems as well.

  4. Label-free imaging of arterial cells and extracellular matrix using a multimodal CARS microscope

    Science.gov (United States)

    Wang, Han-Wei; Le, Thuc T.; Cheng, Ji-Xin

    2008-04-01

    A multimodal nonlinear optical imaging system that integrates coherent anti-Stokes Raman scattering (CARS), sum-frequency generation (SFG), and two-photon excitation fluorescence (TPEF) on the same platform was developed and applied to visualize single cells and extracellular matrix in fresh carotid arteries. CARS signals arising from CH 2-rich membranes allowed visualization of endothelial cells and smooth muscle cells of the arterial wall. Additionally, CARS microscopy allowed vibrational imaging of elastin and collagen fibrils which are also rich in CH 2 bonds. The extracellular matrix organization was further confirmed by TPEF signals arising from elastin's autofluorescence and SFG signals arising from collagen fibrils' non-centrosymmetric structure. Label-free imaging of significant components of arterial tissues suggests the potential application of multimodal nonlinear optical microscopy to monitor onset and progression of arterial diseases.

  5. Super-resolution imaging of ciliary microdomains in isolated olfactory sensory neurons using a custom two-color stimulated emission depletion microscope

    Science.gov (United States)

    Meyer, Stephanie A.; Ozbay, Baris N.; Potcoava, Mariana; Salcedo, Ernesto; Restrepo, Diego; Gibson, Emily A.

    2016-06-01

    We performed stimulated emission depletion (STED) imaging of isolated olfactory sensory neurons (OSNs) using a custom-built microscope. The STED microscope uses a single pulsed laser to excite two separate fluorophores, Atto 590 and Atto 647N. A gated timing circuit combined with temporal interleaving of the different color excitation/STED laser pulses filters the two channel detection and greatly minimizes crosstalk. We quantified the instrument resolution to be ˜81 and ˜44 nm, for the Atto 590 and Atto 647N channels. The spatial separation between the two channels was measured to be under 10 nm, well below the resolution limit. The custom-STED microscope is incorporated onto a commercial research microscope allowing brightfield, differential interference contrast, and epifluorescence imaging on the same field of view. We performed immunolabeling of OSNs in mice to image localization of ciliary membrane proteins involved in olfactory transduction. We imaged Ca2+-permeable cyclic nucleotide gated (CNG) channel (Atto 594) and adenylyl cyclase type III (ACIII) (Atto 647N) in distinct cilia. STED imaging resolved well-separated subdiffraction limited clusters for each protein. We quantified the size of each cluster to have a mean value of 88±48 nm and 124±43 nm, for CNG and ACIII, respectively. STED imaging showed separated clusters that were not resolvable in confocal images.

  6. Photon event distribution sampling: an image formation technique for scanning microscopes that permits tracking of sub-diffraction particles with high spatial and temporal resolutions.

    Science.gov (United States)

    Larkin, J D; Publicover, N G; Sutko, J L

    2011-01-01

    In photon event distribution sampling, an image formation technique for scanning microscopes, the maximum likelihood position of origin of each detected photon is acquired as a data set rather than binning photons in pixels. Subsequently, an intensity-related probability density function describing the uncertainty associated with the photon position measurement is applied to each position and individual photon intensity distributions are summed to form an image. Compared to pixel-based images, photon event distribution sampling images exhibit increased signal-to-noise and comparable spatial resolution. Photon event distribution sampling is superior to pixel-based image formation in recognizing the presence of structured (non-random) photon distributions at low photon counts and permits use of non-raster scanning patterns. A photon event distribution sampling based method for localizing single particles derived from a multi-variate normal distribution is more precise than statistical (Gaussian) fitting to pixel-based images. Using the multi-variate normal distribution method, non-raster scanning and a typical confocal microscope, localizations with 8 nm precision were achieved at 10 ms sampling rates with acquisition of ~200 photons per frame. Single nanometre precision was obtained with a greater number of photons per frame. In summary, photon event distribution sampling provides an efficient way to form images when low numbers of photons are involved and permits particle tracking with confocal point-scanning microscopes with nanometre precision deep within specimens. © 2010 The Authors Journal of Microscopy © 2010 The Royal Microscopical Society.

  7. A full-field transmission x-ray microscope for time-resolved imaging of magnetic nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Ewald, J.; Nisius, T.; Abbati, G.; Baumbach, S.; Overbuschmann, J.; Wilhein, T. [Institute for X-Optics (IXO), Hochschule Koblenz, Joseph-Rovan-Allee 2, 53424 Remagen (Germany); Wessels, P.; Wieland, M.; Drescher, M. [The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Institut für Experimentalphysik, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Vogel, A. [Institut für Angewandte Physik, University of Hamburg, Jungiusstraße 11, 20355 Hamburg (Germany); Viefhaus, J. [Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg (Germany); Meier, G. [The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg (Germany)

    2016-01-28

    Sub-nanosecond magnetization dynamics of small permalloy (Ni{sub 80}Fe{sub 20}) elements has been investigated with a new full-field transmission microscope at the soft X-ray beamline P04 of the high brilliance synchrotron radiation source PETRA III. The soft X-ray microscope generates a flat-top illumination field of 20 μm diameter using a grating condenser. A tilted nanostructured magnetic sample can be excited by a picosecond electric current pulse via a coplanar waveguide. The transmitted light of the sample plane is directly imaged by a micro zone plate with < 65 nm resolution onto a 2D gateable X-ray detector to select one particular bunch in the storage ring that probes the time evolution of the dynamic information successively via XMCD spectromicroscopy in a pump-probe scheme. In the experiments it was possible to generate a homogeneously magnetized state in patterned magnetic layers by a strong magnetic Oersted field pulse of 200 ps duration and directly observe the recovery to the initial flux-closure vortex patterns.

  8. The primary cilium of telocytes in the vasculature: electron microscope imaging.

    Science.gov (United States)

    Cantarero, I; Luesma, M J; Junquera, C

    2011-12-01

    Blood vessels are highly organized and complex structure, which are far more than simple tubes conducting the blood to almost any tissue of the body. The fine structure of the wall of blood vessels has been studied previously using the electron microscope, but the presence the telocytes associated with vasculature, a specific new cellular entity, has not been studied in depth. Interestingly, telocytes have been recently found in the epicardium, myocardium, endocardium, human term placenta, duodenal lamina propria and pleura. We show the presence of telocytes located on the extracellular matrix of blood vessels (arterioles, venules and capillaries) by immunohistochemistry and transmission electron microscopy. Also, we demonstrated the first evidence of a primary cilium in telocytes. Several functions have been proposed for these cells. Here, the telocyte-blood vessels cell proximity, the relationship between telocytes, exosomes and nervous trunks may have a special significance. © 2011 The Authors Journal of Cellular and Molecular Medicine © 2011 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

  9. Imaging the effect of hemoglobin on properties of RBCs using common-path digital holographic microscope

    Science.gov (United States)

    Joglekar, M.; Shah, H.; Trivedi, V.; Mahajan, S.; Chhaniwal, V.; Leitgeb, R.; Javidi, B.; Anand, A.

    2017-07-01

    Adequate supply of oxygen to the body is the most essential requirement. In vertebrate species this function is performed by Hemoglobin contained in red blood cells. The mass concentration of the Hb determines the oxygen carrying capacity of the blood. Thus it becomes necessary to determine its concentration in the blood, which helps in monitoring the health of a person. If the amount of Hb crosses certain range, then it is considered critical. As the Hb constitutes upto 96% of red blood cells dry content, it would be interesting to examine various physical and mechanical parameters of RBCs which depends upon its concentration. Various diseases bring about significant variation in the amount of hemoglobin which may alter certain parameters of the RBC such as surface area, volume, membrane fluctuation etc. The study of the variations of these parameters may be helpful in determining Hb content which will reflect the state of health of a human body leading to disease diagnosis. Any increase or decrease in the amount of Hb will change the density and hence the optical thickness of the RBCs, which affects the cell membrane and thereby changing its mechanical and physical properties. Here we describe the use of lateral shearing digital holographic microscope for quantifying the cell parameters for studying the change in biophysical properties of cells due to variation in hemoglobin concentration.

  10. Comparison of Macroscopic Pathology Measurements With Magnetic Resonance Imaging and Assessment of Microscopic Pathology Extension for Colorectal Liver Metastases

    International Nuclear Information System (INIS)

    Méndez Romero, Alejandra; Verheij, Joanne; Dwarkasing, Roy S.; Seppenwoolde, Yvette; Redekop, William K.; Zondervan, Pieter E.; Nowak, Peter J.C.M.; Ijzermans, Jan N.M.; Levendag, Peter C.; Heijmen, Ben J.M.; Verhoef, Cornelis

    2012-01-01

    Purpose: To compare pathology macroscopic tumor dimensions with magnetic resonance imaging (MRI) measurements and to establish the microscopic tumor extension of colorectal liver metastases. Methods and Materials: In a prospective pilot study we included patients with colorectal liver metastases planned for surgery and eligible for MRI. A liver MRI was performed within 48 hours before surgery. Directly after surgery, an MRI of the specimen was acquired to measure the degree of tumor shrinkage. The specimen was fixed in formalin for 48 hours, and another MRI was performed to assess the specimen/tumor shrinkage. All MRI sequences were imported into our radiotherapy treatment planning system, where the tumor and the specimen were delineated. For the macroscopic pathology analyses, photographs of the sliced specimens were used to delineate and reconstruct the tumor and the specimen volumes. Microscopic pathology analyses were conducted to assess the infiltration depth of tumor cell nests. Results: Between February 2009 and January 2010 we included 13 patients for analysis with 21 colorectal liver metastases. Specimen and tumor shrinkage after resection and fixation was negligible. The best tumor volume correlations between MRI and pathology were found for T1-weighted (w) echo gradient sequence (r s = 0.99, slope = 1.06), and the T2-w fast spin echo (FSE) single-shot sequence (r s = 0.99, slope = 1.08), followed by the T2-w FSE fat saturation sequence (r s = 0.99, slope = 1.23), and the T1-w gadolinium-enhanced sequence (r s = 0.98, slope = 1.24). We observed 39 tumor cell nests beyond the tumor border in 12 metastases. Microscopic extension was found between 0.2 and 10 mm from the main tumor, with 90% of the cases within 6 mm. Conclusions: MRI tumor dimensions showed a good agreement with the macroscopic pathology suggesting that MRI can be used for accurate tumor delineation. However, microscopic extensions found beyond the tumor border indicate that caution is needed

  11. Imaging and detection of early stage dental caries with an all-optical photoacoustic microscope

    International Nuclear Information System (INIS)

    Hughes, D A; Kirk, K J; Sampathkumar, A; Longbottom, C

    2015-01-01

    Tooth decay, at its earliest stages, manifests itself as small, white, subsurface lesions in the enamel. Current methods for detection in the dental clinic are visual and tactile investigations, and bite-wing X-ray radiographs. These techniques suffer from poor sensitivity and specificity at the earliest (and reversible) stages of the disease due to the small size (<100μm) of the lesion. A fine-resolution (600 nm) ultra-broadband (200 MHz) all-optical photoacoustic microscopy system was is used to image the early signs of tooth decay. Ex-vivo tooth samples exhibiting white spot lesions were scanned and were found to generate a larger (one order of magnitude) photoacoustic (PA) signal in the lesion regions compared to healthy enamel. The high contrast in the PA images potentially allows lesions to be imaged and measured at a much earlier stage than current clinical techniques allow. PA images were cross referenced with histology photographs to validate our experimental results. Our PA system provides a noncontact method for early detection of white-spot lesions with a high detection bandwidth that offers advantages over previously demonstrated ultrasound methods. The technique provides the sensing depth of an ultrasound system, but with the spatial resolution of an optical system

  12. Multifractal spectra of scanning electron microscope images of SnO2 thin films prepared by pulsed laser deposition

    International Nuclear Information System (INIS)

    Chen, Z.W.; Lai, J.K.L.; Shek, C.H.

    2005-01-01

    The concept of fractal geometry has proved useful in describing structures and processes in experimental systems. In this Letter, the surface topographies of SnO 2 thin films prepared by pulsed laser deposition for various substrate temperatures were measured by scanning electron microscope (SEM). Multifractal spectra f(α) show that the higher the substrate temperature, the wider the spectrum, and the larger the Δf(Δf=f(α min )-f(α max )). It is apparent that the nonuniformity of the height distribution increases with the increasing substrate temperature, and the liquid droplets of SnO 2 thin films are formed on previous thin films. These results show that the SEM images can be characterized by the multifractal spectra

  13. Automated microscopic characterization of metallic ores with image analysis: a key to improve ore processing. I: test of the methodology

    International Nuclear Information System (INIS)

    Berrezueta, E.; Castroviejo, R.

    2007-01-01

    Ore microscopy has traditionally been an important support to control ore processing, but the volume of present day processes is beyond the reach of human operators. Automation is therefore compulsory, but its development through digital image analysis, DIA, is limited by various problems, such as the similarity in reflectance values of some important ores, their anisotropism, and the performance of instruments and methods. The results presented show that automated identification and quantification by DIA are possible through multiband (RGB) determinations with a research 3CCD video camera on reflected light microscope. These results were obtained by systematic measurement of selected ores accounting for most of the industrial applications. Polarized light is avoided, so the effects of anisotropism can be neglected. Quality control at various stages and statistical analysis are important, as is the application of complementary criteria (e.g. metallogenetic). The sequential methodology is described and shown through practical examples. (Author)

  14. A fourth order PDE based fuzzy c- means approach for segmentation of microscopic biopsy images in presence of Poisson noise for cancer detection.

    Science.gov (United States)

    Kumar, Rajesh; Srivastava, Subodh; Srivastava, Rajeev

    2017-07-01

    For cancer detection from microscopic biopsy images, image segmentation step used for segmentation of cells and nuclei play an important role. Accuracy of segmentation approach dominate the final results. Also the microscopic biopsy images have intrinsic Poisson noise and if it is present in the image the segmentation results may not be accurate. The objective is to propose an efficient fuzzy c-means based segmentation approach which can also handle the noise present in the image during the segmentation process itself i.e. noise removal and segmentation is combined in one step. To address the above issues, in this paper a fourth order partial differential equation (FPDE) based nonlinear filter adapted to Poisson noise with fuzzy c-means segmentation method is proposed. This approach is capable of effectively handling the segmentation problem of blocky artifacts while achieving good tradeoff between Poisson noise removals and edge preservation of the microscopic biopsy images during segmentation process for cancer detection from cells. The proposed approach is tested on breast cancer microscopic biopsy data set with region of interest (ROI) segmented ground truth images. The microscopic biopsy data set contains 31 benign and 27 malignant images of size 896 × 768. The region of interest selected ground truth of all 58 images are also available for this data set. Finally, the result obtained from proposed approach is compared with the results of popular segmentation algorithms; fuzzy c-means, color k-means, texture based segmentation, and total variation fuzzy c-means approaches. The experimental results shows that proposed approach is providing better results in terms of various performance measures such as Jaccard coefficient, dice index, Tanimoto coefficient, area under curve, accuracy, true positive rate, true negative rate, false positive rate, false negative rate, random index, global consistency error, and variance of information as compared to other

  15. Can X-ray spectrum imaging replace backscattered electrons for compositional contrast in the scanning electron microscope?

    Science.gov (United States)

    Newbury, Dale E; Ritchie, Nicholas W M

    2011-01-01

    The high throughput of the silicon drift detector energy dispersive X-ray spectrometer (SDD-EDS) enables X-ray spectrum imaging (XSI) in the scanning electron microscope to be performed in frame times of 10-100 s, the typical time needed to record a high-quality backscattered electron (BSE) image. These short-duration XSIs can reveal all elements, except H, He, and Li, present as major constituents, defined as 0.1 mass fraction (10 wt%) or higher, as well as minor constituents in the range 0.01-0.1 mass fraction, depending on the particular composition and possible interferences. Although BSEs have a greater abundance by a factor of 100 compared with characteristic X-rays, the strong compositional contrast in element-specific X-ray maps enables XSI mapping to compete with BSE imaging to reveal compositional features. Differences in the fraction of the interaction volume sampled by the BSE and X-ray signals lead to more delocalization of the X-ray signal at abrupt compositional boundaries, resulting in poorer spatial resolution. Improved resolution in X-ray elemental maps occurs for the case of a small feature composed of intermediate to high atomic number elements embedded in a matrix of lower atomic number elements. XSI imaging strongly complements BSE imaging, and the SDD-EDS technology enables an efficient combined BSE-XSI measurement strategy that maximizes the compositional information. If 10 s or more are available for the measurement of an area of interest, the analyst should always record the combined BSE-XSI information to gain the advantages of both measures of compositional contrast. Copyright © 2011 Wiley Periodicals, Inc.

  16. Comparison and Supervised Learning of Segmentation Methods Dedicated to Specular Microscope Images of Corneal Endothelium

    Directory of Open Access Journals (Sweden)

    Yann Gavet

    2014-01-01

    Full Text Available The cornea is the front of the eye. Its inner cell layer, called the endothelium, is important because it is closely related to the light transparency of the cornea. An in vivo observation of this layer is performed by using specular microscopy to evaluate the health of the cells: a high spatial density will result in a good transparency. Thus, the main criterion required by ophthalmologists is the cell density of the cornea endothelium, mainly obtained by an image segmentation process. Different methods can perform the image segmentation of these cells, and the three most performing methods are studied here. The question for the ophthalmologists is how to choose the best algorithm and to obtain the best possible results with it. This paper presents a methodology to compare these algorithms together. Moreover, by the way of geometric dissimilarity criteria, the algorithms are tuned up, and the best parameter values are thus proposed to the expert ophthalmologists.

  17. Blood Capillary Length Estimation from Three-Dimensional Microscopic Data by Image Analysis and Stereology

    Czech Academy of Sciences Publication Activity Database

    Kubínová, Lucie; Mao, X. W.; Janáček, Jiří

    2013-01-01

    Roč. 19, č. 4 (2013), s. 898-906 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) ME09010; GA MŠk(CZ) LH13028; GA ČR(CZ) GAP108/11/0794 Institutional research plan: CEZ:AV0Z5011922 Institutional support: RVO:67985823 Keywords : capillaries * confocal microscopy * image analysis * length * rat brain * stereology Subject RIV: EA - Cell Biology Impact factor: 1.757, year: 2013

  18. Imaging circulating tumor cells in freely moving awake small animals using a miniaturized intravital microscope.

    Directory of Open Access Journals (Sweden)

    Laura Sarah Sasportas

    Full Text Available Metastasis, the cause for 90% of cancer mortality, is a complex and poorly understood process involving the invasion of circulating tumor cells (CTCs into blood vessels. These cells have potential prognostic value as biomarkers for early metastatic risk. But their rarity and the lack of specificity and sensitivity in measuring them render their interrogation by current techniques very challenging. How and when these cells are circulating in the blood, on their way to potentially give rise to metastasis, is a question that remains largely unanswered. In order to provide an insight into this "black box" using non-invasive imaging, we developed a novel miniature intravital microscopy (mIVM strategy capable of real-time long-term monitoring of CTCs in awake small animals. We established an experimental 4T1-GL mouse model of metastatic breast cancer, in which tumor cells express both fluorescent and bioluminescent reporter genes to enable both single cell and whole body tumor imaging. Using mIVM, we monitored blood vessels of different diameters in awake mice in an experimental model of metastasis. Using an in-house software algorithm we developed, we demonstrated in vivo CTC enumeration and computation of CTC trajectory and speed. These data represent the first reported use we know of for a miniature mountable intravital microscopy setup for in vivo imaging of CTCs in awake animals.

  19. Imaging circulating tumor cells in freely moving awake small animals using a miniaturized intravital microscope.

    Science.gov (United States)

    Sasportas, Laura Sarah; Gambhir, Sanjiv Sam

    2014-01-01

    Metastasis, the cause for 90% of cancer mortality, is a complex and poorly understood process involving the invasion of circulating tumor cells (CTCs) into blood vessels. These cells have potential prognostic value as biomarkers for early metastatic risk. But their rarity and the lack of specificity and sensitivity in measuring them render their interrogation by current techniques very challenging. How and when these cells are circulating in the blood, on their way to potentially give rise to metastasis, is a question that remains largely unanswered. In order to provide an insight into this "black box" using non-invasive imaging, we developed a novel miniature intravital microscopy (mIVM) strategy capable of real-time long-term monitoring of CTCs in awake small animals. We established an experimental 4T1-GL mouse model of metastatic breast cancer, in which tumor cells express both fluorescent and bioluminescent reporter genes to enable both single cell and whole body tumor imaging. Using mIVM, we monitored blood vessels of different diameters in awake mice in an experimental model of metastasis. Using an in-house software algorithm we developed, we demonstrated in vivo CTC enumeration and computation of CTC trajectory and speed. These data represent the first reported use we know of for a miniature mountable intravital microscopy setup for in vivo imaging of CTCs in awake animals.

  20. Imaging and detection of early stage dental caries with an all-optical photoacoustic microscope

    Science.gov (United States)

    Hughes, D. A.; Sampathkumar, A.; Longbottom, C.; Kirk, K. J.

    2015-01-01

    Tooth decay, at its earliest stages, manifests itself as small, white, subsurface lesions in the enamel. Current methods for detection in the dental clinic are visual and tactile investigations, and bite-wing X-ray radiographs. These techniques suffer from poor sensitivity and specificity at the earliest (and reversible) stages of the disease due to the small size (tooth decay. Ex-vivo tooth samples exhibiting white spot lesions were scanned and were found to generate a larger (one order of magnitude) photoacoustic (PA) signal in the lesion regions compared to healthy enamel. The high contrast in the PA images potentially allows lesions to be imaged and measured at a much earlier stage than current clinical techniques allow. PA images were cross referenced with histology photographs to validate our experimental results. Our PA system provides a noncontact method for early detection of white-spot lesions with a high detection bandwidth that offers advantages over previously demonstrated ultrasound methods. The technique provides the sensing depth of an ultrasound system, but with the spatial resolution of an optical system.