WorldWideScience

Sample records for raman microscopic imaging

  1. 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.

  2. Towards Chemical Imaging of Living Cells: Design and Application of a Confocal Raman Microscope

    NARCIS (Netherlands)

    Sijtsema, N.M.

    1997-01-01

    Raman microspectroscopy is a technique that can be used to obtain information about the chemical composition of a very small measurement volume (0.5 fl) in a (biological) sample. Molecules present in the sample can be identified based on their scattering characteristics and no special treatment or

  3. Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis.

    Science.gov (United States)

    Milewski, Robert J; Kumagai, Yutaro; Fujita, Katsumasa; Standley, Daron M; Smith, Nicholas I

    2010-11-19

    Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Due to extremely low signal levels, however, Raman microscopy requires sophisticated image processing techniques for noise reduction and signal extraction. To date, efficient, automated algorithms for resolving sub-cellular features in noisy, multi-dimensional image sets have not been explored extensively. We show that hybrid z-score normalization and standard regression (Z-LSR) can highlight the spectral differences within the cell and provide image contrast dependent on spectral content. In contrast to typical Raman imaging processing methods using multivariate analysis, such as single value decomposition (SVD), our implementation of the Z-LSR method can operate nearly in real-time. In spite of its computational simplicity, Z-LSR can automatically remove background and bias in the signal, improve the resolution of spatially distributed spectral differences and enable sub-cellular features to be resolved in Raman microscopy images of mouse macrophage cells. Significantly, the Z-LSR processed images automatically exhibited subcellular architectures whereas SVD, in general, requires human assistance in selecting the components of interest. The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without

  4. Microscopic modeling of the Raman diffusion

    International Nuclear Information System (INIS)

    Benisti, D.; Morice, O.; Gremillet, L.; Strozzi, D.

    2010-01-01

    In the typical conditions of density and electronic temperature of the Laser Megajoule (LMJ), a quantitative assessment of the Raman reflectivity requires an accurate calculation of the non-linear movement of each electron submitted to the waves propagating in the plasma. The interaction of a laser beam with a plasma generates an electronic wave shifted in frequency (that can be back-scattered) and an electron plasma wave (OPE). The OPE can give to the electrons a strongly non-linear movement by trapping them in a potential well. This non-linearity of microscopic origin has an impact on the plasma electronic density. We have succeeded in computing this plasma electronic density in a very accurate way by combining the principles of a perturbative approach with those of an adiabatic theory. Results show that the Raman diffusion can grow on temperature and density ranges more important than expected. We have predicted the threshold and the behavior of the Raman diffusion above this threshold as accurately as we had done it with a Vlasov code but by being 10000 times more rapid. (A.C.)

  5. 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.

  6. Raman Imaging Techniques and Applications

    CERN Document Server

    2012-01-01

    Raman imaging has long been used to probe the chemical nature of a sample, providing information on molecular orientation, symmetry and structure with sub-micron spatial resolution. Recent technical developments have pushed the limits of micro-Raman microscopy, enabling the acquisition of Raman spectra with unprecedented speed, and opening a pathway to fast chemical imaging for many applications from material science and semiconductors to pharmaceutical drug development and cell biology, and even art and forensic science. The promise of tip-enhanced raman spectroscopy (TERS) and near-field techniques is pushing the envelope even further by breaking the limit of diffraction and enabling nano-Raman microscopy.

  7. Coherent anti-Stokes Raman scattering spectroscope/microscope based on a widely tunable laser source

    Science.gov (United States)

    Dementjev, A.; Gulbinas, V.; Serbenta, A.; Kaucikas, M.; Niaura, G.

    2010-03-01

    We present a coherent anti-Stokes Raman scattering (CARS) microscope based on a robust and simple laser source. A picosecond laser operating in a cavity dumping regime at the 1 MHz repetition rate was used to pump a traveling wave optical parametric generator, which serves as a two-color excitation light source for the CARS microscope. We demonstrate the ability of the presented CARS microscope to measure CARS spectra and images by using several detection schemes.

  8. 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.

  9. Imaging with extrinsic Raman labels

    NARCIS (Netherlands)

    Sijtsema, N M; Duindam, J J; Puppels, G J; Otto, C; Greve, J

    1996-01-01

    In two separate examples we demonstrate the use of extrinsic Raman scattering probes for imaging of biological samples. First, the distribution of cholesterol in a rat eye Lens is determined with the use of the Raman scattered light from filipin, a molecule which binds specifically to cholesterol.

  10. Enhanced optical coupling and Raman scattering via microscopic interface engineering

    Science.gov (United States)

    Thompson, Jonathan V.; Hokr, Brett H.; Kim, Wihan; Ballmann, Charles W.; Applegate, Brian E.; Jo, Javier A.; Yamilov, Alexey; Cao, Hui; Scully, Marlan O.; Yakovlev, Vladislav V.

    2017-11-01

    Spontaneous Raman scattering is an extremely powerful tool for the remote detection and identification of various chemical materials. However, when those materials are contained within strongly scattering or turbid media, as is the case in many biological and security related systems, the sensitivity and range of Raman signal generation and detection is severely limited. Here, we demonstrate that through microscopic engineering of the optical interface, the optical coupling of light into a turbid material can be substantially enhanced. This improved coupling facilitates the enhancement of the Raman scattering signal generated by molecules within the medium. In particular, we detect at least two-orders of magnitude more spontaneous Raman scattering from a sample when the pump laser light is focused into a microscopic hole in the surface of the sample. Because this approach enhances both the interaction time and interaction region of the laser light within the material, its use will greatly improve the range and sensitivity of many spectroscopic techniques, including Raman scattering and fluorescence emission detection, inside highly scattering environments.

  11. 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.

  12. Detection of latent prints by Raman imaging

    Science.gov (United States)

    Lewis, Linda Anne [Andersonville, TN; Connatser, Raynella Magdalene [Knoxville, TN; Lewis, Sr., Samuel Arthur

    2011-01-11

    The present invention relates to a method for detecting a print on a surface, the method comprising: (a) contacting the print with a Raman surface-enhancing agent to produce a Raman-enhanced print; and (b) detecting the Raman-enhanced print using a Raman spectroscopic method. The invention is particularly directed to the imaging of latent fingerprints.

  13. Raman chemical imaging technology for food and agricultural applications

    Science.gov (United States)

    This paper presents Raman chemical imaging technology for inspecting food and agricultural products. The paper puts emphasis on introducing and demonstrating Raman imaging techniques for practical uses in food analysis. The main topics include Raman scattering principles, Raman spectroscopy measurem...

  14. High Fidelity Raman Chemical Imaging of Materials

    Science.gov (United States)

    Bobba, Venkata Nagamalli Koteswara Rao

    The development of high fidelity Raman imaging systems is important for a number of application areas including material science, bio-imaging, bioscience and healthcare, pharmaceutical analysis, and semiconductor characterization. The use of Raman imaging as a characterization tool for detecting the amorphous and crystalline regions in the biopolymer poly-L-lactic acid (PLLA) is the precis of my thesis. In the first chapter, a brief insight about the basics of Raman spectroscopy, Raman chemical imaging, Raman mapping, and Raman imaging techniques has been provided. The second chapter contains details about the successful development of tailored sample of PLLA. Biodegradable polymers are used in areas of tissue engineering, agriculture, packaging, and in medical field for drug delivery, implant devices, and surgical sutures. Detailed information about the sample preparation and characterization of these cold-drawn PLLA polymer substrates has been provided. Wide-field Raman hyperspectral imaging using an acousto-optic tunable filter (AOTF) was demonstrated in the early 1990s. The AOTF contributed challenges such as image walk, distortion, and image blur. A wide-field AOTF Raman imaging system has been developed as part of my research and methods to overcome some of the challenges in performing AOTF wide-field Raman imaging are discussed in the third chapter. This imaging system has been used for studying the crystalline and amorphous regions on the cold-drawn sample of PLLA. Of all the different modalities that are available for performing Raman imaging, Raman point-mapping is the most extensively used method. The ease of obtaining the Raman hyperspectral cube dataset with a high spectral and spatial resolution is the main motive of performing this technique. As a part of my research, I have constructed a Raman point-mapping system and used it for obtaining Raman hyperspectral image data of various minerals, pharmaceuticals, and polymers. Chapter four offers

  15. High-speed Vibrational Imaging and Spectral Analysis of Lipid Bodies by Compound Raman Microscopy

    OpenAIRE

    Slipchenko, Mikhail N.; Le, Thuc T.; Chen, Hongtao; Cheng, Ji-Xin

    2009-01-01

    Cells store excess energy in the form of cytoplasmic lipid droplets. At present, it is unclear how different types of fatty acids contribute to the formation of lipid-droplets. We describe a compound Raman microscope capable of both high-speed chemical imaging and quantitative spectral analysis on the same platform. We use a picosecond laser source to perform coherent Raman scattering imaging of a biological sample and confocal Raman spectral analysis at points of interest. The potential of t...

  16. Combined Raman and continuous-wave-excited two-photon fluorescence cell imaging

    NARCIS (Netherlands)

    Uzunbajakava, N.; Otto, Cornelis

    2003-01-01

    We demonstrate a confocal optical microscope that combines cw two-photon-excited fluorescence microscopy with confocal Raman microscopy. With this microscope fast image acquisition with fluorescence imaging can be used to select areas of interest for subsequent chemical analysis with spontaneous

  17. Revealing organization of cellulose in wood cell walls by Raman imaging

    Science.gov (United States)

    Umesh P. Agarwal; Sally A. Ralph

    2007-01-01

    Anisotropy of cellulose organization in mature black spruce wood cell wall was investigated by Raman imaging using a 1 [mu]m lateral-resolution capable confocal Raman microscope. In these studies, wood cross sections (CS) and radial longitudinal sections (LS) that were partially delignified by acid chlorite treatment were used. In the case of CS where latewood cells...

  18. Multifocus confocal Raman microspectroscopy for fast multimode vibrational imaging of living cells.

    Science.gov (United States)

    Okuno, Masanari; Hamaguchi, Hiro-o

    2010-12-15

    We have developed a multifocus confocal Raman microspectroscopic system for the fast multimode vibrational imaging of living cells. It consists of an inverted microscope equipped with a microlens array, a pinhole array, a fiber bundle, and a multichannel Raman spectrometer. Forty-eight Raman spectra from 48 foci under the microscope are simultaneously obtained by using multifocus excitation and image-compression techniques. The multifocus confocal configuration suppresses the background generated from the cover glass and the cell culturing medium so that high-contrast images are obtainable with a short accumulation time. The system enables us to obtain multimode (10 different vibrational modes) vibrational images of living cells in tens of seconds with only 1 mW laser power at one focal point. This image acquisition time is more than 10 times faster than that in conventional single-focus Raman microspectroscopy.

  19. 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)

  20. Raman microscopic studies of PVD deposited hard ceramic coatings

    International Nuclear Information System (INIS)

    Constable, C.P.

    2000-01-01

    PVD hard ceramic coatings grown via the combined cathodic arc/unbalance magnetron deposition process were studied using Raman microscopy. Characteristic spectra from binary, multicomponent, multilayered and superlattice coatings were acquired to gain knowledge of the solid-state physics associated with Raman scattering from polycrystalline PVD coatings and to compile a comprehensive spectral database. Defect-induced first order scattering mechanisms were observed which gave rise to two pronounced groups of bands related to the acoustical (150- 300cm -1 ) and optical (400-7 50cm -1 ) parts of the phonon spectrum. Evidence was gathered to support the theory that the optic modes were mainly due to the vibrations of the lighter elements and the acoustic modes due to the vibrations of the heavier elements within the lattice. A study into the deformation and disordering on the Raman spectral bands of PVD coatings was performed. TiAIN and TiZrN coatings were intentionally damaged via scratching methods. These scratches were then analysed by Raman mapping, both across and along, and a detailed spectral interpretation performed. Band broadening occurred which was related to 'phonon relaxation mechanisms' as a direct result of the breaking up of coating grains resulting in a larger proportion of grain boundaries per-unit-volume. A direct correlation of the amount of damage with band width was observed. Band shifts were also found to occur which were due to the stresses caused by the scratching process. These shifts were found to be the largest at the edges of scratches. The Raman mapping of 'droplets', a defect inherent to PVD deposition processes, found that higher compressive stresses and large amounts of disorder occurred for coating growth onto droplets. Strategies designed to evaluate the ability of Raman microscopy to monitor the extent of real wear on cutting tools were evaluated. The removal of a coating layer and subsequent detection of a base layer proved

  1. 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

  2. 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

  3. 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...

  4. 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

  5. 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.

  6. 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.

  7. Rheo-optical Raman study of microscopic deformation in high-density polyethylene under hot drawing

    OpenAIRE

    Kida, Takumitsu; Hiejima, Yusuke; Nitta, Koh-hei

    2015-01-01

    In situ observation of the microscopic structural changes in high-density polyethylene during hot drawing was performed by incorporating a temperature-controlled tensile machine into a Raman spectroscopy apparatus. It was found that the load sharing and molecular orientation during elongation drastically changed at 50°C. The microscopic stress of the crystalline chains decreased with increasing temperature and diminished around 50°C. Moreover, the orientation of the crystalline chains was gre...

  8. Raman imaging using fixed bandpass filter

    Science.gov (United States)

    Landström, L.; Kullander, F.; Lundén, H.; Wästerby, P.

    2017-05-01

    By using fixed narrow band pass optical filtering and scanning the laser excitation wavelength, hyperspectral Raman imaging could be achieved. Experimental, proof-of-principle results from the Chemical Warfare Agent (CWA) tabun (GA) as well as the common CWA simulant tributyl phosphate (TBP) on different surfaces/substrates are presented and discussed.

  9. 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.

  10. Wide-Field Vibrational Phase Contrast Imaging Based on Coherent Anti-Stokes Raman Scattering Holography

    International Nuclear Information System (INIS)

    Lv Yong-Gang; Ji Zi-Heng; Dong Da-Shan; Gong Qi-Huang; Shi Ke-Bin

    2015-01-01

    We propose and implement a wide-field vibrational phase contrast detection to obtain imaging of imaginary components of third-order nonlinear susceptibility in a coherent anti-Stokes Raman scattering (CARS) microscope with full suppression of the non-resonant background. This technique is based on the unique ability of recovering the phase of the generated CARS signal based on holographic recording. By capturing the phase distributions of the generated CARS field from the sample and from the environment under resonant illumination, we demonstrate the retrieval of imaginary components in the CARS microscope and achieve background free coherent Raman imaging. (paper)

  11. Atomic force microscope with combined FTIR-Raman spectroscopy having a micro thermal analyzer

    Science.gov (United States)

    Fink, Samuel D [Aiken, SC; Fondeur, Fernando F [North Augusta, SC

    2011-10-18

    An atomic force microscope is provided that includes a micro thermal analyzer with a tip. The micro thermal analyzer is configured for obtaining topographical data from a sample. A raman spectrometer is included and is configured for use in obtaining chemical data from the sample.

  12. 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

  13. 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.

  14. High-speed vibrational imaging and spectral analysis of lipid bodies by compound Raman microscopy.

    Science.gov (United States)

    Slipchenko, Mikhail N; Le, Thuc T; Chen, Hongtao; Cheng, Ji-Xin

    2009-05-28

    Cells store excess energy in the form of cytoplasmic lipid droplets. At present, it is unclear how different types of fatty acids contribute to the formation of lipid droplets. We describe a compound Raman microscope capable of both high-speed chemical imaging and quantitative spectral analysis on the same platform. We used a picosecond laser source to perform coherent Raman scattering imaging of a biological sample and confocal Raman spectral analysis at points of interest. The potential of the compound Raman microscope was evaluated on lipid bodies of cultured cells and live animals. Our data indicate that the in vivo fat contains much more unsaturated fatty acids (FAs) than the fat formed via de novo synthesis in 3T3-L1 cells. Furthermore, in vivo analysis of subcutaneous adipocytes and glands revealed a dramatic difference not only in the unsaturation level but also in the thermodynamic state of FAs inside their lipid bodies. Additionally, the compound Raman microscope allows tracking of the cellular uptake of a specific fatty acid and its abundance in nascent cytoplasmic lipid droplets. The high-speed vibrational imaging and spectral analysis capability renders compound Raman microscopy an indispensible analytical tool for the study of lipid-droplet biology.

  15. Dielectrophoretic positioning of single nanoparticles on atomic force microscope tips for tip-enhanced Raman spectroscopy.

    Science.gov (United States)

    Leiterer, Christian; Deckert-Gaudig, Tanja; Singh, Prabha; Wirth, Janina; Deckert, Volker; Fritzsche, Wolfgang

    2015-05-01

    Tip-enhanced Raman spectroscopy, a combination of Raman spectroscopy and scanning probe microscopy, is a powerful technique to detect the vibrational fingerprint of molecules at the nanometer scale. A metal nanoparticle at the apex of an atomic force microscope tip leads to a large enhancement of the electromagnetic field when illuminated with an appropriate wavelength, resulting in an increased Raman signal. A controlled positioning of individual nanoparticles at the tip would improve the reproducibility of the probes and is quite demanding due to usually serial and labor-intensive approaches. In contrast to commonly used submicron manipulation techniques, dielectrophoresis allows a parallel and scalable production, and provides a novel approach toward reproducible and at the same time affordable tip-enhanced Raman spectroscopy tips. We demonstrate the successful positioning of an individual plasmonic nanoparticle on a commercial atomic force microscope tip by dielectrophoresis followed by experimental proof of the Raman signal enhancing capabilities of such tips. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 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

  17. Spectroscopy and Raman imaging of inhomogeneous materials

    International Nuclear Information System (INIS)

    Maslova, Olga

    2014-01-01

    This thesis is aimed at developing methodologies in Raman spectroscopy and imaging. After reviewing the statistical instruments which allow treating giant amount of data (multivariate analysis and classification), the study is applied to two families of well-known materials which are used as models for testing the limits of the implemented developments. The first family is a series of carbon materials pyrolyzed at various temperatures and exhibiting inhomogeneities at a nm scale which is suitable for Raman-X-ray diffraction combination. Another results concern the polishing effect on carbon structure. Since it is found to induce Raman artifacts leading to the overestimation of the local structural disorder, a method based on the use of the G band width is therefore proposed in order to evaluate the crystallite size in both unpolished and polished nano-graphites. The second class of materials presents inhomogeneities at higher (micrometric) scales by the example of uranium dioxide ceramics. Being well adapted in terms of spatial scale, Raman imaging is thus used for probing their surfaces. Data processing is implemented via an approach combining the multivariate (principal component) analysis and the classical fitting procedure with Lorentzian profiles. The interpretation of results is supported via electron backscattering diffraction (EBSD) analysis which enables us to distinguish the orientation effects of ceramic grains from other underlying contributions. The last ones are mainly localized at the grain boundaries, that is testified by the appearance of a specific Raman mode. Their origin seems to be caused by stoichiometric oxygen variations or impurities, as well as strain inhomogeneities. The perspectives of this work include both the implementation of other mathematical methods and in-depth analysis of UO 2 structure damaged by irradiation (anisotropic effects, role of grain boundaries). (author) [fr

  18. 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

  19. 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...

  20. Raman Imaging of Plant Cell Walls in Sections of Cucumis sativus.

    Science.gov (United States)

    Zeise, Ingrid; Heiner, Zsuzsanna; Holz, Sabine; Joester, Maike; Büttner, Carmen; Kneipp, Janina

    2018-01-25

    Raman microspectra combine information on chemical composition of plant tissues with spatial information. The contributions from the building blocks of the cell walls in the Raman spectra of plant tissues can vary in the microscopic sub-structures of the tissue. Here, we discuss the analysis of 55 Raman maps of root, stem, and leaf tissues of Cucumis sativus , using different spectral contributions from cellulose and lignin in both univariate and multivariate imaging methods. Imaging based on hierarchical cluster analysis (HCA) and principal component analysis (PCA) indicates different substructures in the xylem cell walls of the different tissues. Using specific signals from the cell wall spectra, analysis of the whole set of different tissue sections based on the Raman images reveals differences in xylem tissue morphology. Due to the specifics of excitation of the Raman spectra in the visible wavelength range (532 nm), which is, e.g., in resonance with carotenoid species, effects of photobleaching and the possibility of exploiting depletion difference spectra for molecular characterization in Raman imaging of plants are discussed. The reported results provide both, specific information on the molecular composition of cucumber tissue Raman spectra, and general directions for future imaging studies in plant tissues.

  1. 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.

  2. 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.

  3. Coherent Raman scattering: Applications in imaging and sensing

    Science.gov (United States)

    Cui, Meng

    In this thesis, I discuss the theory, implementation and applications of coherent Raman scattering to imaging and sensing. A time domain interferometric method has been developed to collect high resolution shot-noise-limited Raman spectra over the Raman fingerprint regime and completely remove the electronic background signal in coherent Raman scattering. Compared with other existing coherent Raman microscopy methods, this time domain approach is proved to be simpler and more robust in rejecting background signal. We apply this method to image polymers and biological samples and demonstrate that the same setup can be used to collect two photon fluorescence and self phase modulation signals. A signal to noise ratio analysis is performed to show that this time domain method has a comparable signal to noise ratio to spectral domain methods, which we confirm experimentally. The coherent Raman method is also compared with spontaneous Raman scattering. The conditions under which coherent methods provide signal enhancement are discussed and experiments are performed to compare coherent Raman scattering with spontaneous Raman scattering under typical biological imaging conditions. A critical power, above which coherent Raman scattering is more sensitive than spontaneous Raman scattering, is experimentally determined to be ˜1mW in samples of high molecule concentration with a 75MHz laser system. This finding is contrary to claims that coherent methods provide many orders of magnitude enhancement under comparable conditions. In addition to the far field applications, I also discuss the combination of our time domain coherent Raman method with near field enhancement to explore the possibility of sensing and near field imaging. We report the first direct time-resolved coherent Raman measurement performed on a nanostructured substrate for molecule sensing. The preliminary results demonstrate that sub 20 fs pulses can be used to obtain coherent Raman spectra from a small number

  4. 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.

  5. 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

  6. Label-Free Raman Hyperspectral Imaging of Single Cells Cultured on Polymer Substrates.

    Science.gov (United States)

    Sinjab, Faris; Sicilia, Giovanna; Shipp, Dustin W; Marlow, Maria; Notingher, Ioan

    2017-12-01

    While Raman hyperspectral imaging has been widely used for label-free mapping of biomolecules in cells, these measurements require the cells to be cultured on weakly Raman scattering substrates. However, many applications in biological sciences and engineering require the cells to be cultured on polymer substrates that often generate large Raman scattering signals. Here, we discuss the theoretical limits of the signal-to-noise ratio in the Raman spectra of cells in the presence of polymer signals and how optical aberrations may affect these measurements. We show that Raman spectra of cells cultured on polymer substrates can be obtained using automatic subtraction of the polymer signals and demonstrate the capabilities of these methods in two important applications: tissue engineering and in vitro toxicology screening of drugs. Apart from their scientific and technological importance, these applications are examples of the two most common measurement configurations: (1) cells cultured on an optically thick polymer substrate measured using an immersion/dipping objective; and (2) cells cultured on a transparent polymer substrate and measured using an inverted optical microscope. In these examples, we show that Raman hyperspectral data sets with sufficient quality can be successfully acquired to map the distribution of common biomolecules in cells, such as nucleic acids, proteins, and lipids, as well as detecting the early stages of apoptosis. We also discuss strategies for further improvements that could expand the application of Raman hyperspectral imaging on polymer substrates even further in biomedical sciences and engineering.

  7. 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...

  8. Probing Xylan-Specific Raman Bands for Label-Free Imaging Xylan in Plant Cell Wall

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Yining; Yarbrough, John M.; Mittal, Ashutosh; Tucker, Melvin P.; Vinzant, Todd; Himmel, Michael E.

    2015-06-15

    Xylan constitutes a significant portion of biomass (e.g. 22% in corn stover used in this study). Xylan is also an important source of carbohydrates, besides cellulose, for renewable and sustainable energy applications. Currently used method for the localization of xylan in biomass is to use fluorescence confocal microscope to image the fluorescent dye labeled monoclonal antibody that specifically binds to xylan. With the rapid adoption of the Raman-based label-free chemical imaging techniques in biology, identifying Raman bands that are unique to xylan would be critical for the implementation of the above label-free techniques for in situ xylan imaging. Unlike lignin and cellulose that have long be assigned fingerprint Raman bands, specific Raman bands for xylan remain unclear. The major challenge is the cellulose in plant cell wall, which has chemical units highly similar to that of xylan. Here we report using xylanase to specifically remove xylan from feedstock. Under various degree of xylan removal, with minimum impact to other major cell wall components, i.e. lignin and cellulose, we have identified Raman bands that could be further tested for chemical imaging of xylan in biomass in situ.

  9. [Bone Cell Biology Assessed by Microscopic Approach. Assessment of bone quality using Raman and infrared spectroscopy].

    Science.gov (United States)

    Suda, Hiromi Kimura

    2015-10-01

    Bone quality, which was defined as "the sum total of characteristics of the bone that influence the bone's resistance to fracture" at the National Institute of Health (NIH) conference in 2001, contributes to bone strength in combination with bone mass. Bone mass is often measured as bone mineral density (BMD) and, consequently, can be quantified easily. On the other hand, bone quality is composed of several factors such as bone structure, bone matrix, calcification degree, microdamage, and bone turnover, and it is not easy to obtain data for the various factors. Therefore, it is difficult to quantify bone quality. We are eager to develop new measurement methods for bone quality that make it possible to determine several factors associated with bone quality at the same time. Analytic methods based on Raman and FTIR spectroscopy have attracted a good deal of attention as they can provide a good deal of chemical information about hydroxyapatite and collagen, which are the main components of bone. A lot of studies on bone quality using Raman and FTIR imaging have been reported following the development of the two imaging systems. Thus, both Raman and FTIR imaging appear to be promising new bone morphometric techniques.

  10. 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.

  11. 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.

  12. 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.…

  13. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Brückner, Michael [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Becker, Katja [Justus Liebig University Giessen, Biochemistry and Molecular Biology, 35392 Giessen (Germany); Popp, Jürgen [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany); Frosch, Torsten, E-mail: torsten.frosch@uni-jena.de [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany)

    2015-09-24

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

  14. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

    International Nuclear Information System (INIS)

    Brückner, Michael; Becker, Katja; Popp, Jürgen; Frosch, Torsten

    2015-01-01

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

  15. Microscopic description of protein thermostabilization mechanisms with disaccharides from Raman spectroscopy investigations

    Energy Technology Data Exchange (ETDEWEB)

    Hedoux, A; Affouard, F; Descamps, M; Guinet, Y; Paccou, L [Laboratoire de Dynamique et Structure des Materiaux Moleculaires UMR CNRS 8024, Universite de Lille 1, UFR de Physique, Batiment P5, 59 655 Villeneuve d' Ascq Cedex (France)

    2007-05-23

    The mechanisms of protein thermostabilization by sugar were analysed for three disaccharides (maltose, sucrose and trehalose) characterized by the same chemical formula (C{sub 12}H{sub 22}O{sub 11}). Raman scattering investigations simultaneously carried out in the low-frequency range and in the amide I band region provide a microscopic description of the process of protein thermal denaturation. From this detailed description, the influence of sugar on this process was analysed. The principal effect of sugars is to stabilize the tertiary structure, in which the biomolecule preserves its native conformation, through a strengthening of O-H interactions. This study shows that the bioprotective properties of sugars are mainly based on interactions between water and sugar. The exceptional properties of trehalose to preserve the native state of lysozyme by heating can be associated with its capability to distort the tetra-bonded hydrogen bond network of water.

  16. 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.

  17. High vacuum tip-enhanced Raman spectroscope based on a scanning tunneling microscope.

    Science.gov (United States)

    Fang, Yurui; Zhang, Zhenglong; Sun, Mengtao

    2016-03-01

    In this paper, we present the construction of a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) system that allows in situ sample preparation and measurement. A detailed description of the prototype instrument is presented with experimental validation of its use and novel ex situ experimental results using the HV-TERS system. The HV-TERS system includes three chambers held under a 10(-7) Pa vacuum. The three chambers are an analysis chamber, a sample preparation chamber, and a fast loading chamber. The analysis chamber is the core chamber and contains a scanning tunneling microscope (STM) and a Raman detector coupled with a 50 × 0.5 numerical aperture objective. The sample preparation chamber is used to produce single-crystalline metal and sub-monolayer molecular films by molecular beam epitaxy. The fast loading chamber allows ex situ preparation of samples for HV-TERS analysis. Atomic resolution can be achieved by the STM on highly ordered pyrolytic graphite. We demonstrate the measurement of localized temperature using the Stokes and anti-Stokes TERS signals from a monolayer of 1,2-benzenedithiol on a gold film using a gold tip. Additionally, plasmonic catalysis can be monitored label-free at the nanoscale using our device. Moreover, the HV-TERS experiments show simultaneously activated infrared and Raman vibrational modes, Fermi resonance, and some other non-linear effects that are not observed in atmospheric TERS experiments. The high spatial and spectral resolution and pure environment of high vacuum are beneficial for basic surface studies.

  18. High vacuum tip-enhanced Raman spectroscope based on a scanning tunneling microscope

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Yurui [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603-146, Beijing 100190 (China); Bionanophotonics, Department of Applied Physics, Chalmers University of Technology, Göteborg, SE 41296 (Sweden); Zhang, Zhenglong [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603-146, Beijing 100190 (China); School of Physics and Information Technology, Shaanxi Normal University, 710062 Xi’an (China); Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena (Germany); Sun, Mengtao, E-mail: mtsun@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603-146, Beijing 100190 (China)

    2016-03-15

    In this paper, we present the construction of a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) system that allows in situ sample preparation and measurement. A detailed description of the prototype instrument is presented with experimental validation of its use and novel ex situ experimental results using the HV-TERS system. The HV-TERS system includes three chambers held under a 10{sup −7} Pa vacuum. The three chambers are an analysis chamber, a sample preparation chamber, and a fast loading chamber. The analysis chamber is the core chamber and contains a scanning tunneling microscope (STM) and a Raman detector coupled with a 50 × 0.5 numerical aperture objective. The sample preparation chamber is used to produce single-crystalline metal and sub-monolayer molecular films by molecular beam epitaxy. The fast loading chamber allows ex situ preparation of samples for HV-TERS analysis. Atomic resolution can be achieved by the STM on highly ordered pyrolytic graphite. We demonstrate the measurement of localized temperature using the Stokes and anti-Stokes TERS signals from a monolayer of 1,2-benzenedithiol on a gold film using a gold tip. Additionally, plasmonic catalysis can be monitored label-free at the nanoscale using our device. Moreover, the HV-TERS experiments show simultaneously activated infrared and Raman vibrational modes, Fermi resonance, and some other non-linear effects that are not observed in atmospheric TERS experiments. The high spatial and spectral resolution and pure environment of high vacuum are beneficial for basic surface studies.

  19. Microscopic theory of cavity-enhanced single-photon emission from optical two-photon Raman processes

    Science.gov (United States)

    Breddermann, Dominik; Praschan, Tom; Heinze, Dirk; Binder, Rolf; Schumacher, Stefan

    2018-03-01

    We consider cavity-enhanced single-photon generation from stimulated two-photon Raman processes in three-level systems. We compare four fundamental system configurations, one Λ -, one V-, and two ladder (Ξ -) configurations. These can be realized as subsystems of a single quantum dot or of quantum-dot molecules. For a new microscopic understanding of the Raman process, we analyze the Heisenberg equation of motion applying the cluster-expansion scheme. Within this formalism an exact and rigorous definition of a cavity-enhanced Raman photon via its corresponding Raman correlation is possible. This definition for example enables us to systematically investigate the on-demand potential of Raman-transition-based single-photon sources. The four system arrangements can be divided into two subclasses, Λ -type and V-type, which exhibit strongly different Raman-emission characteristics and Raman-emission probabilities. Moreover, our approach reveals whether the Raman path generates a single photon or just induces destructive quantum interference with other excitation paths. Based on our findings and as a first application, we gain a more detailed understanding of experimental data from the literature. Our analysis and results are also transferable to the case of atomic three-level-resonator systems and can be extended to more complicated multilevel schemes.

  20. Design of SERS nanoprobes for Raman imaging: materials, critical factors and architectures.

    Science.gov (United States)

    Li, Mingwang; Qiu, Yuanyuan; Fan, Chenchen; Cui, Kai; Zhang, Yongming; Xiao, Zeyu

    2018-05-01

    Raman imaging yields high specificity and sensitivity when compared to other imaging modalities, mainly due to its fingerprint signature. However, intrinsic Raman signals are weak, thus limiting medical applications of Raman imaging. By adsorbing Raman molecules onto specific nanostructures such as noble metals, Raman signals can be significantly enhanced, termed surface-enhanced Raman scattering (SERS). Recent years have witnessed great interest in the development of SERS nanoprobes for Raman imaging. Rationally designed SERS nanoprobes have greatly enhanced Raman signals by several orders of magnitude, thus showing great potential for biomedical applications. In this review we elaborate on recent progress in design strategies with emphasis on material properties, modifying factors, and structural parameters.

  1. 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)

  2. Time-lapse Raman imaging of osteoblast differentiation

    Science.gov (United States)

    Hashimoto, Aya; Yamaguchi, Yoshinori; Chiu, Liang-Da; Morimoto, Chiaki; Fujita, Katsumasa; Takedachi, Masahide; Kawata, Satoshi; Murakami, Shinya; Tamiya, Eiichi

    2015-07-01

    Osteoblastic mineralization occurs during the early stages of bone formation. During this mineralization, hydroxyapatite (HA), a major component of bone, is synthesized, generating hard tissue. Many of the mechanisms driving biomineralization remain unclear because the traditional biochemical assays used to investigate them are destructive techniques incompatible with viable cells. To determine the temporal changes in mineralization-related biomolecules at mineralization spots, we performed time-lapse Raman imaging of mouse osteoblasts at a subcellular resolution throughout the mineralization process. Raman imaging enabled us to analyze the dynamics of the related biomolecules at mineralization spots throughout the entire process of mineralization. Here, we stimulated KUSA-A1 cells to differentiate into osteoblasts and conducted time-lapse Raman imaging on them every 4 hours for 24 hours, beginning 5 days after the stimulation. The HA and cytochrome c Raman bands were used as markers for osteoblastic mineralization and apoptosis. From the Raman images successfully acquired throughout the mineralization process, we found that β-carotene acts as a biomarker that indicates the initiation of osteoblastic mineralization. A fluctuation of cytochrome c concentration, which indicates cell apoptosis, was also observed during mineralization. We expect time-lapse Raman imaging to help us to further elucidate osteoblastic mineralization mechanisms that have previously been unobservable.

  3. 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.

  4. Dynamic Raman imaging system with high spatial and temporal resolution

    Science.gov (United States)

    Wang, Lei; Dai, Yinzhen; He, Hao; Lv, Ruiqi; Zong, Cheng; Ren, Bin

    2017-09-01

    There is an increasing need to study dynamic changing systems with significantly high spatial and temporal resolutions. In this work, we integrated point-scanning, line-scanning, and wide-field Raman imaging techniques into a single system. By using an Electron Multiplying CCD (EMCCD) with a high gain and high frame rate, we significantly reduced the time required for wide-field imaging, making it possible to monitor the electrochemical reactions in situ. The highest frame rate of EMCDD was ˜50 fps, and the Raman images for a specific Raman peak can be obtained by passing the signal from the sample through the Liquid Crystal Tunable Filter. The spatial resolutions of scanning imaging and wide-field imaging with a 100× objective (NA = 0.9) are 0.5 × 0.5 μm2 and 0.36 × 0.36 μm2, respectively. The system was used to study the surface plasmon resonance of Au nanorods, the surface-enhanced Raman scattering signal distribution for Au Nanoparticle aggregates, and dynamic Raman imaging of an electrochemical reacting system.

  5. Dental caries imaging using hyperspectral stimulated Raman scattering microscopy

    Science.gov (United States)

    Wang, Zi; Zheng, Wei; Jian, Lin; Huang, Zhiwei

    2016-03-01

    We report the development of a polarization-resolved hyperspectral stimulated Raman scattering (SRS) imaging technique based on a picosecond (ps) laser-pumped optical parametric oscillator system for label-free imaging of dental caries. In our imaging system, hyperspectral SRS images (512×512 pixels) in both fingerprint region (800-1800 cm-1) and high-wavenumber region (2800-3600 cm-1) are acquired in minutes by scanning the wavelength of OPO output, which is a thousand times faster than conventional confocal micro Raman imaging. SRS spectra variations from normal enamel to caries obtained from the hyperspectral SRS images show the loss of phosphate and carbonate in the carious region. While polarization-resolved SRS images at 959 cm-1 demonstrate that the caries has higher depolarization ratio. Our results demonstrate that the polarization resolved-hyperspectral SRS imaging technique developed allows for rapid identification of the biochemical and structural changes of dental caries.

  6. 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...

  7. 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).

  8. Cell Imaging by Spontaneous and Amplified Raman Spectroscopies

    Directory of Open Access Journals (Sweden)

    Giulia Rusciano

    2017-01-01

    Full Text Available Raman spectroscopy (RS is a powerful, noninvasive optical technique able to detect vibrational modes of chemical bonds. The high chemical specificity due to its fingerprinting character and the minimal requests for sample preparation have rendered it nowadays very popular in the analysis of biosystems for diagnostic purposes. In this paper, we first discuss the main advantages of spontaneous RS by describing the study of a single protozoan (Acanthamoeba, which plays an important role in a severe ophthalmological disease (Acanthamoeba keratitis. Later on, we point out that the weak signals that originated from Raman scattering do not allow probing optically thin samples, such as cellular membrane. Experimental approaches able to overcome this drawback are based on the use of metallic nanostructures, which lead to a huge amplification of the Raman yields thanks to the excitation of localized surface plasmon resonances. Surface-enhanced Raman scattering (SERS and tip-enhanced Raman scattering (TERS are examples of such innovative techniques, in which metallic nanostructures are assembled on a flat surface or on the tip of a scanning probe microscope, respectively. Herein, we provide a couple of examples (red blood cells and bacterial spores aimed at studying cell membranes with these techniques.

  9. 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

  10. 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.

  11. Raman spectroscopy and imaging: applications in human breast cancer diagnosis.

    Science.gov (United States)

    Brozek-Pluska, Beata; Musial, Jacek; Kordek, Radzislaw; Bailo, Elena; Dieing, Thomas; Abramczyk, Halina

    2012-08-21

    The applications of spectroscopic methods in cancer detection open new possibilities in early stage diagnostics. Raman spectroscopy and Raman imaging represent novel and rapidly developing tools in cancer diagnosis. In the study described in this paper Raman spectroscopy has been employed to examine noncancerous and cancerous human breast tissues of the same patient. The most significant differences between noncancerous and cancerous tissues were found in regions characteristic for the vibrations of carotenoids, lipids and proteins. Particular attention was paid to the role played by unsaturated fatty acids in the differentiation between the noncancerous and the cancerous tissues. Comparison of Raman spectra of the noncancerous and the cancerous tissues with the spectra of oleic, linoleic, α-linolenic, γ-linolenic, docosahexaenoic and eicosapentaenoic acids has been presented. The role of sample preparation in the determination of cancer markers is also discussed in this study.

  12. Raman Microscopic Analysis of Internal Stress in Boron-Doped Diamond

    Directory of Open Access Journals (Sweden)

    Kevin E. Bennet

    2015-05-01

    Full Text Available Analysis of the induced stress on undoped and boron-doped diamond (BDD thin films by confocal Raman microscopy is performed in this study to investigate its correlation with sample chemical composition and the substrate used during fabrication. Knowledge of this nature is very important to the issue of long-term stability of BDD coated neurosurgical electrodes that will be used in fast-scan cyclic voltammetry, as potential occurrence of film delaminations and dislocations during their surgical implantation can have unwanted consequences for the reliability of BDD-based biosensing electrodes. To achieve a more uniform deposition of the films on cylindrically-shaped tungsten rods, substrate rotation was employed in a custom-built chemical vapor deposition reactor. In addition to visibly preferential boron incorporation into the diamond lattice and columnar growth, the results also reveal a direct correlation between regions of pure diamond and enhanced stress. Definite stress release throughout entire film thicknesses was found in the current Raman mapping images for higher amounts of boron addition. There is also a possible contribution to the high values of compressive stress from sp2 type carbon impurities, besides that of the expected lattice mismatch between film and substrate.

  13. 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.

  14. Label-Free Raman Imaging to Monitor Breast Tumor Signatures.

    Science.gov (United States)

    Manciu, Felicia S; Ciubuc, John D; Parra, Karla; Manciu, Marian; Bennet, Kevin E; Valenzuela, Paloma; Sundin, Emma M; Durrer, William G; Reza, Luis; Francia, Giulio

    2017-08-01

    Although not yet ready for clinical application, methods based on Raman spectroscopy have shown significant potential in identifying, characterizing, and discriminating between noncancerous and cancerous specimens. Real-time and accurate medical diagnosis achievable through this vibrational optical method largely benefits from improvements in current technological and software capabilities. Not only is the acquisition of spectral information now possible in milliseconds and analysis of hundreds of thousands of data points achieved in minutes, but Raman spectroscopy also allows simultaneous detection and monitoring of several biological components. Besides demonstrating a significant Raman signature distinction between nontumorigenic (MCF-10A) and tumorigenic (MCF-7) breast epithelial cells, our study demonstrates that Raman can be used as a label-free method to evaluate epidermal growth factor activity in tumor cells. Comparative Raman profiles and images of specimens in the presence or absence of epidermal growth factor show important differences in regions attributed to lipid, protein, and nucleic acid vibrations. The occurrence, which is dependent on the presence of epidermal growth factor, of new Raman features associated with the appearance of phosphothreonine and phosphoserine residues reflects a signal transduction from the membrane to the nucleus, with concomitant modification of DNA/RNA structural characteristics. Parallel Western blotting analysis reveals an epidermal growth factor induction of phosphorylated Akt protein, corroborating the Raman results. The analysis presented in this work is an important step toward Raman-based evaluation of biological activity of epidermal growth factor receptors on the surfaces of breast cancer cells. With the ultimate future goal of clinically implementing Raman-guided techniques for the diagnosis of breast tumors (e.g., with regard to specific receptor activity), the current results just lay the foundation for

  15. 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 ...

  16. 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.

  17. Towards eye-safe standoff Raman imaging systems

    Science.gov (United States)

    Glimtoft, Martin; Bââth, Petra; Saari, Heikki; Mäkynen, Jussi; Näsilä, Antti; Östmark, Henric

    2014-05-01

    Standoff Raman imaging systems have shown the ability to detect single explosives particles. However, in many cases, the laser intensities needed restrict the applications where they can be safely used. A new generation imaging Raman system has been developed based on a 355 nm UV laser that, in addition to eye safety, allows discrete and invisible measurements. Non-dangerous exposure levels for the eye are several orders of magnitude higher in UVA than in the visible range that previously has been used. The UV Raman system has been built based on an UV Fabry-Perot Interferometer (UV-FPI) developed by VTT. The design allows for precise selection of Raman shifts in combination with high out-of-band blocking. The stable operation of the UV-FPI module under varying environmental conditions is arranged by controlling the temperature of the module and using a closed loop control of the FPI air gap based on capacitive measurement. The system presented consists of a 3rd harmonics Nd:YAG laser with 1.5 W average output at 1000 Hz, a 200 mm Schmidt-Cassegrain telescope, UV-FPI filter and an ICCD camera for signal gating and detection. The design principal leads to a Raman spectrum in each image pixel. The system is designed for field use and easy manoeuvring. Preliminary results show that in measurements of <60 s on 10 m distance, single AN particles of <300 μm diameter can be identified.

  18. Microscope Raman scattering and X-ray diffraction study of near-stoichiometric Ti:LiNbO3 waveguides

    International Nuclear Information System (INIS)

    Zhang, De-Long; Siu, G.G.; Pun, E.Y.B.

    2005-01-01

    The crystalline phase within guiding layers of near-stoichiometric strip and planar Ti:LiNbO 3 wave-guides, prepared by the method of simultaneous work of vapour transport equilibration (VTE) treatment and indiffusion of Ti film, was studied by combined confocal microscope Raman scattering and X-ray powder diffraction. The results show that the strip and planar waveguide layers still retain the LiNbO 3 phase and no other non-LiNbO 3 phases can be identified within the guiding layer. Li/Nb ratios inside and outside the strip and planar waveguide layers were determined from the microscope Raman scattering results and compared to those obtained from the measured optical absorption edge. It is shown that the Li/Nb ratios are homogeneous within the waveguide layer and are close inside and outside the waveguide layer. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  19. Depth profile of strain and composition in Si/Ge dot multilayers by microscopic phonon Raman spectroscopy

    International Nuclear Information System (INIS)

    Tan, P.H.; Bougeard, D.; Abstreiter, G.; Brunner, K.

    2005-01-01

    We characterized strain and Ge content depending on depth in a self-assembled Si/Ge dot multilayer by scanning a microscopic Raman probe at a (110) cleavage plane. The multilayer structure was deposited by molecular-beam epitaxy on a (001) Si substrate and consisted of 80 periods, each of them composed by 25 nm Si spacers and 8 monolayer Ge forming laterally and vertically uncorrelated islands with a height of 2 nm and a lateral diameter of about 20 nm. An average biaxial strain of -3.5% within the core regions of islands is determined from the splitting of longitudinal and transversal optical Ge-Ge phonon modes observed in polarized Raman measurements. The absolute mode frequencies further enable analysis of a Ge content of 0.82. The analyzed strain and composition of islands are nearly independent from depths below the sample surface. This indicates well-controlled deposition parameters and negligible intermixing during deposition of subsequent layers. These Raman results are in agreement with x-ray diffraction data. Small, local Raman frequency shifts were observed and discussed with respect to partial elastic strain relaxation of the multilayer stack after cleavage, undefined Raman-scattering geometries at the sample edge, and local heating by the laser probe

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Raman characterization of high temperature materials using an imaging detector

    International Nuclear Information System (INIS)

    Rosenblatt, G.M.; Veirs, D.K.

    1989-03-01

    The characterization of materials by Raman spectroscopy has been advanced by recent technological developments in light detectors. Imaging photomultiplier-tube detectors are now available that impart position information in two dimensions while retaining photon-counting sensitivity, effectively greatly reducing noise. The combination of sensitivity and reduced noise allows smaller amounts of material to be analyzed. The ability to observe small amount of material when coupled with position information makes possible Raman characterization in which many spatial elements are analyzed simultaneously. Raman spectroscopy making use of these capabilities has been used, for instance, to analyze the phases present in carbon films and fibers and to map phase-transformed zones accompanying crack propagation in toughened zirconia ceramics. 16 refs., 6 figs., 2 tabs

  6. 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.

  7. 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 ...

  8. 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

  9. 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

  10. 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

  11. 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

  12. Raman molecular imaging of brain frozen tissue sections.

    Science.gov (United States)

    Kast, Rachel E; Auner, Gregory W; Rosenblum, Mark L; Mikkelsen, Tom; Yurgelevic, Sally M; Raghunathan, Aditya; Poisson, Laila M; Kalkanis, Steven N

    2014-10-01

    Raman spectroscopy provides a molecular signature of the region being studied. It is ideal for neurosurgical applications because it is non-destructive, label-free, not impacted by water concentration, and can map an entire region of tissue. The objective of this paper is to demonstrate the meaningful spatial molecular information provided by Raman spectroscopy for identification of regions of normal brain, necrosis, diffusely infiltrating glioma and solid glioblastoma (GBM). Five frozen section tissues (1 normal, 1 necrotic, 1 GBM, and 2 infiltrating glioma) were mapped in their entirety using a 300-µm-square step size. Smaller regions of interest were also mapped using a 25-µm step size. The relative concentrations of relevant biomolecules were mapped across all tissues and compared with adjacent hematoxylin and eosin-stained sections, allowing identification of normal, GBM, and necrotic regions. Raman peaks and peak ratios mapped included 1003, 1313, 1431, 1585, and 1659 cm(-1). Tissue maps identified boundaries of grey and white matter, necrosis, GBM, and infiltrating tumor. Complementary information, including relative concentration of lipids, protein, nucleic acid, and hemoglobin, was presented in a manner which can be easily adapted for in vivo tissue mapping. Raman spectroscopy can successfully provide label-free imaging of tissue characteristics with high accuracy. It can be translated to a surgical or laboratory tool for rapid, non-destructive imaging of tumor margins.

  13. Pulsed Raman fiber laser and multispectral imaging in three dimensions

    DEFF Research Database (Denmark)

    Andersen, Joachim F.; Busck, Jens; Heiselberg, Henning

    2006-01-01

    Raman scattering in single-mode optical fibers is exploited to generate multispectral light from a green nanolaser with high pulse repetition rate. Each pulse triggers a picosecond camera and measures the distance by time-of-flight in each of the 0.5 Mpixels. Three-dimensional images...... are then constructed with submillimeter accuracy for all visible colors. The generation of a series of Stokes peaks by Raman scattering in a Si fiber is discussed in detail and the laser radar technique is demonstrated. The data recording takes only a few seconds, and the high accuracy 3D color imaging works at ranges...... up to ∼200 m. Applications for optical tomography in highly scattering media such as water and human tissue are mentioned. © 2006 Optical Society of America....

  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. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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....

  2. Confocal Raman Microscopy

    CERN Document Server

    Dieing, Thomas; Toporski, Jan

    2011-01-01

    Confocal Raman Microscopy is a relatively new technique that allows chemical imaging without specific sample preparation. By integrating a sensitive Raman spectrometer within a state-of-the-art microscope, Raman microscopy with a spatial resolution down to 200nm laterally and 500nm vertically can be achieved using visible light excitation. Recent developments in detector and computer technology as well as optimized instrument design have reduced integration times of Raman spectra by orders of magnitude, so that complete images consisting of tens of thousands of Raman spectra can be acquired in seconds or minutes rather than hours, which used to be standard just one decade ago. The purpose of this book is to provide the reader a comprehensive overview of the rapidly developing field of Confocal Raman Microscopy and its applications.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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 ...

  9. 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.

  10. 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.

  11. 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...

  12. 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

  13. Conjugated Polymer with Intrinsic Alkyne Units for Synergistically Enhanced Raman Imaging in Living Cells.

    Science.gov (United States)

    Li, Shengliang; Chen, Tao; Wang, Yunxia; Liu, Libing; Lv, Fengting; Li, Zhiliang; Huang, Yanyi; Schanze, Kirk S; Wang, Shu

    2017-10-16

    Development of Raman-active materials with enhanced and distinctive Raman vibrations in the Raman-silent region (1800-2800 cm -1 ) is highly required for specific molecular imaging of living cells with high spatial resolution. Herein, water-soluble cationic conjugated polymers (CCPs), poly(phenylene ethynylene) (PPE) derivatives, are explored for use as alkyne-state-dependent Raman probes for living cell imaging due to synergetic enhancement effect of alkyne vibrations in Raman-silent region compared to alkyne-containing small molecules. The enhanced alkyne signals result from the integration of alkyne groups into the rigid backbone and the delocalized π-conjugated structure. PPE-based conjugated polymer nanoparticles (CPNs) were also prepared as Raman-responsive nanomaterials for distinct imaging application. This work opens a new way into the development of conjugated polymer materials for enhanced Raman imaging. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. 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

  15. 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

  16. Microscopic theoretical study of Raman spectra in charge and spin ordered cuprate systems

    International Nuclear Information System (INIS)

    Raj, B.K.; Panda, S.K.; Rout, G.C.

    2013-01-01

    Highlights: • The model calculation treats CDW interaction as pseudogap for cuprates. • The interplay of Raman active CDW-SDW mixed modes are investigated. • Independent CDW and SDW gap values can be determined from experimental data. -- Abstract: Raman scattering is one of the most powerful methods to investigate the electron as well as the phonon excitations in the systems. In this communication, we present a theoretical study of Raman scattering in the normal state of the high-T C systems in the under-doped region displaying the interplay of the spin-density-wave (SDW) and charge-density-wave (CDW) interactions. The SDW order arises from the repulsive Coulomb interaction of electrons, while the CDW order arises due to strong electron–phonon interaction giving rise to Fermi surface instability. We calculate phonon response function in order to examine the possibility of observing the SDW excitation mode in presence of the CDW interaction present in the same conduction band. The Raman scattering intensity is calculated from the imaginary part of the phonon Green’s function assigning an arbitrary spectral width. The spectral density function displays two mixed modes of excitation peaks at energies 2(Δ c ± Δ s ). The evolution of excitation peaks are investigated by varying CDW coupling, SDW coupling and the phonon momentum transfer energy

  17. Microscopic theoretical study of Raman spectra in charge and spin ordered cuprate systems

    Energy Technology Data Exchange (ETDEWEB)

    Raj, B. K. [Dept. of Physics, Govt. Autonomous College, Angul, Orissa (India); Panda, S. K. [KD Science College, Pochilima, Hinjilicut, 761 101 Ganjam, Orissa (India); Rout, G.C., E-mail: gcr@iopb.res.in [Condensed Matter Physics Group, PG Dept. of Applied Physics and Ballistics, FM University, Balasore 756 019 (India)

    2013-09-15

    Highlights: • The model calculation treats CDW interaction as pseudogap for cuprates. • The interplay of Raman active CDW-SDW mixed modes are investigated. • Independent CDW and SDW gap values can be determined from experimental data. -- Abstract: Raman scattering is one of the most powerful methods to investigate the electron as well as the phonon excitations in the systems. In this communication, we present a theoretical study of Raman scattering in the normal state of the high-T{sub C} systems in the under-doped region displaying the interplay of the spin-density-wave (SDW) and charge-density-wave (CDW) interactions. The SDW order arises from the repulsive Coulomb interaction of electrons, while the CDW order arises due to strong electron–phonon interaction giving rise to Fermi surface instability. We calculate phonon response function in order to examine the possibility of observing the SDW excitation mode in presence of the CDW interaction present in the same conduction band. The Raman scattering intensity is calculated from the imaginary part of the phonon Green’s function assigning an arbitrary spectral width. The spectral density function displays two mixed modes of excitation peaks at energies 2(Δ{sub c} ± Δ{sub s}). The evolution of excitation peaks are investigated by varying CDW coupling, SDW coupling and the phonon momentum transfer energy.

  18. 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

  19. The biocompatibility of carbon hydroxyapatite/β-glucan composite for bone tissue engineering studied with Raman and FTIR spectroscopic imaging.

    Science.gov (United States)

    Sroka-Bartnicka, Anna; Kimber, James A; Borkowski, Leszek; Pawlowska, Marta; Polkowska, Izabela; Kalisz, Grzegorz; Belcarz, Anna; Jozwiak, Krzysztof; Ginalska, Grazyna; Kazarian, Sergei G

    2015-10-01

    The spectroscopic approaches of FTIR imaging and Raman mapping were applied to the characterisation of a new carbon hydroxyapatite/β-glucan composite developed for bone tissue engineering. The composite is an artificial bone material with an apatite-forming ability for the bone repair process. Rabbit bone samples were tested with an implanted bioactive material for a period of several months. Using spectroscopic and chemometric methods, we were able to determine the presence of amides and phosphates and the distribution of lipid-rich domains in the bone tissue, providing an assessment of the composite's bioactivity. Samples were also imaged in transmission using an infrared microscope combined with a focal plane array detector. CaF2 lenses were also used on the infrared microscope to improve spectral quality by reducing scattering artefacts, improving chemometric analysis. The presence of collagen and lipids at the bone/composite interface confirmed biocompatibility and demonstrate the suitability of FTIR microscopic imaging with lenses in studying these samples. It confirmed that the composite is a very good background for collagen growth and increases collagen maturity with the time of the bone growth process. The results indicate the bioactive and biocompatible properties of this composite and demonstrate how Raman and FTIR spectroscopic imaging have been used as an effective tool for tissue characterisation.

  20. 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).

  1. 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.

  2. 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.

  3. Raman imaging from microscopy to macroscopy: Quality and safety control of biological materials

    Science.gov (United States)

    Raman imaging can analyze biological materials by generating detailed chemical images. Over the last decade, tremendous advancements in Raman imaging and data analysis techniques have overcome problems such as long data acquisition and analysis times and poor sensitivity. This review article introdu...

  4. Live-cell stimulated Raman scattering imaging of alkyne-tagged biomolecules.

    Science.gov (United States)

    Hong, Senlian; Chen, Tao; Zhu, Yuntao; Li, Ang; Huang, Yanyi; Chen, Xing

    2014-06-02

    Alkynes can be metabolically incorporated into biomolecules including nucleic acids, proteins, lipids, and glycans. In addition to the clickable chemical reactivity, alkynes possess a unique Raman scattering within the Raman-silent region of a cell. Coupling this spectroscopic signature with Raman microscopy yields a new imaging modality beyond fluorescence and label-free microscopies. The bioorthogonal Raman imaging of various biomolecules tagged with an alkyne by a state-of-the-art Raman imaging technique, stimulated Raman scattering (SRS) microscopy, is reported. This imaging method affords non-invasiveness, high sensitivity, and molecular specificity and therefore should find broad applications in live-cell imaging. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. 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

  6. 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.

  7. 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.

  8. SERS imaging of cell-surface biomolecules metabolically labeled with bioorthogonal Raman reporters.

    Science.gov (United States)

    Xiao, Ming; Lin, Liang; Li, Zefan; Liu, Jie; Hong, Senlian; Li, Yaya; Zheng, Meiling; Duan, Xuanming; Chen, Xing

    2014-08-01

    Live imaging of biomolecules with high specificity and sensitivity as well as minimal perturbation is essential for studying cellular processes. Here, we report the development of a bioorthogonal surface-enhanced Raman scattering (SERS) imaging approach that exploits small Raman reporters for visualizing cell-surface biomolecules. The cells were cultured and imaged by SERS microscopy on arrays of Raman-enhancing nanoparticles coated on silicon wafers or glass slides. The Raman reporters including azides, alkynes, and carbondeuterium bonds are small in size and spectroscopically bioorthogonal (background-free). We demonstrated that various cell-surface biomolecules including proteins, glycans, and lipids were metabolically incorporated with the corresponding precursors bearing a Raman reporter and visualized by SERS microscopy. The coupling of SERS microscopy with bioorthogonal Raman reporters expands the capabilities of live-cell microscopy beyond the modalities of fluorescence and label-free imaging. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Poster - 14: Batch Effect Reduction in in-vitro Raman Microscopic Radiosensitivity Study Using Ovarian Cancer Cells

    International Nuclear Information System (INIS)

    Moradi, Hamid; Murugkar, Sangeeta; Ahmad, Abrar; Shepherdson, Dean; Nyiri, Balazs; Vuong, Nhung; Niedbala, Gosia; Vanderhyden, Barbara; Eapen, Libni

    2016-01-01

    Purpose: To improve classification by reducing batch effect in samples from the ovarian carcinoma cell lines A2780s (parental wild type) and A2780cp (cisplatin cross-radio-resistant), before, right after, and 24 hours after irradiation to 10Gy. Methods: Spectra were acquired with a home built confocal Raman microscope in 3 distinct runs of six samples: unirradiated s&cp (control pair), then 0h and 24h after irradiation. The Raman spectra were noise reduced, then background subtracted with SMIRF algorithm. ∼35 cell spectra were collected from each sample in 1024 channels from 700cm-1 to 1618cm-1. The spectra were analyzed by regularized multiclass LDA. For feature reduction the spectra were grouped into 3 overlapping group pairs: s-cp, 0Gy–10Gy0h and 0Gy10–Gy24h. The three features, the three differences of the mean spectra were mapped to the analysis sub-space by the inverse regularized covariance matrix. The batch effect noticeably confounded the dose and time effect. Results: To remove the batch effect, the 2+2=4D subspace extended by the covariance matrix of the means of the 0Gy control groups was subtracted from the spectra of each sample. Repeating the analysis on the spectra with the control group variability removed, the batch effect was dramatically reduced in the dose and time directions enabling sharp linear discrimination. The cell type classification also improved. Conclusions: We identified a efficient batch effect removal technique crucial to the applicability of Raman microscopy to radiosensitivity studies both on cell cultures and potential clinical diagnostic applications.

  10. Poster - 14: Batch Effect Reduction in in-vitro Raman Microscopic Radiosensitivity Study Using Ovarian Cancer Cells

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Hamid; Murugkar, Sangeeta; Ahmad, Abrar; Shepherdson, Dean; Nyiri, Balazs; Vuong, Nhung; Niedbala, Gosia; Vanderhyden, Barbara; Eapen, Libni [Carleton University, Carleton University, Carleton University, Carleton University, The Ottawa Hospital Cancer Centre, University of Ottawa, The Ottawa Hospital Cancer Centre, University of Ottawa, The Ottawa Hospital Cancer Centre (Canada)

    2016-08-15

    Purpose: To improve classification by reducing batch effect in samples from the ovarian carcinoma cell lines A2780s (parental wild type) and A2780cp (cisplatin cross-radio-resistant), before, right after, and 24 hours after irradiation to 10Gy. Methods: Spectra were acquired with a home built confocal Raman microscope in 3 distinct runs of six samples: unirradiated s&cp (control pair), then 0h and 24h after irradiation. The Raman spectra were noise reduced, then background subtracted with SMIRF algorithm. ∼35 cell spectra were collected from each sample in 1024 channels from 700cm-1 to 1618cm-1. The spectra were analyzed by regularized multiclass LDA. For feature reduction the spectra were grouped into 3 overlapping group pairs: s-cp, 0Gy–10Gy0h and 0Gy10–Gy24h. The three features, the three differences of the mean spectra were mapped to the analysis sub-space by the inverse regularized covariance matrix. The batch effect noticeably confounded the dose and time effect. Results: To remove the batch effect, the 2+2=4D subspace extended by the covariance matrix of the means of the 0Gy control groups was subtracted from the spectra of each sample. Repeating the analysis on the spectra with the control group variability removed, the batch effect was dramatically reduced in the dose and time directions enabling sharp linear discrimination. The cell type classification also improved. Conclusions: We identified a efficient batch effect removal technique crucial to the applicability of Raman microscopy to radiosensitivity studies both on cell cultures and potential clinical diagnostic applications.

  11. Quantitative volumetric Raman imaging of three dimensional cell cultures

    KAUST Repository

    Kallepitis, Charalambos

    2017-03-22

    The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell–material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

  12. Quantitative volumetric Raman imaging of three dimensional cell cultures

    Science.gov (United States)

    Kallepitis, Charalambos; Bergholt, Mads S.; Mazo, Manuel M.; Leonardo, Vincent; Skaalure, Stacey C.; Maynard, Stephanie A.; Stevens, Molly M.

    2017-03-01

    The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

  13. 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.

  14. 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.

  15. Novel strategies of Raman imaging for brain tumor research.

    Science.gov (United States)

    Anna, Imiela; Bartosz, Polis; Lech, Polis; Halina, Abramczyk

    2017-10-17

    Raman diagnostics and imaging have been shown to be an effective tool for the analysis and discrimination of human brain tumors from normal structures. Raman spectroscopic methods have potential to be applied in clinical practice as they allow for identification of tumor margins during surgery. In this study, we investigate medulloblastoma (grade IV WHO) (n= 5), low-grade astrocytoma (grades I-II WHO) (n =4), ependymoma (n=3) and metastatic brain tumors (n= 1) and the tissue from the negative margins used as normal controls. We compare a high grade medulloblastoma, low grade astrocytoma and non-tumor samples from human central nervous system (CNS) tissue. Based on the properties of the Raman vibrational features and Raman images we provide a real-time feedback method that is label-free to monitor tumor metabolism that reveals reprogramming of biosynthesis of lipids, proteins, DNA and RNA. Our results indicate marked metabolic differences between low and high grade brain tumors. We discuss molecular mechanisms causing these metabolic changes, particularly lipid alterations in malignant medulloblastoma and low grade gliomas that may shed light on the mechanisms driving tumor recurrence thereby revealing new approaches for the treatment of malignant glioma. We have found that the high-grade tumors of central nervous system (medulloblastoma) exhibit enhanced level of β-sheet conformation and down-regulated level of α-helix conformation when comparing against normal tissue. We have found that almost all tumors studied in the paper have increased Raman signals of nucleic acids. This increase can be interpreted as increased DNA/RNA turnover in brain tumors. We have shown that the ratio of Raman intensities I 2930 /I 2845 at 2930 and 2845 cm -1 is a good source of information on the ratio of lipid and protein contents. We have found that the ratio reflects the different lipid and protein contents of cancerous brain tissue compared to the non-tumor tissue. We found that

  16. 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.

  17. Using Raman spectroscopic imaging for non-destructive analysis of filler distribution in chalk filled polypropylene

    DEFF Research Database (Denmark)

    Boros, Evelin; Porse, Peter Bak; Nielsen, Inga

    2016-01-01

    A feasibility study on using Raman spectral imaging for visualization and analysis of filler distribution in chalk filled poly-propylene samples has been carried out. The spectral images were acquired using a Raman spectrometer with 785 nm light source.Eight injection-molded samples with concentr...

  18. Ex vivo and in vivo coherent Raman imaging of the peripheral and central nervous system

    Science.gov (United States)

    Huff, Terry Brandon

    A hallmark of nervous system disorders is damage or degradation of the myelin sheath. Unraveling the mechanisms underlying myelin degeneration and repair represent one of the great challenges in medicine. This thesis work details the development and utilization of advanced optical imaging methods to gain insight into the structure and function of myelin in both healthy and diseased states in the in vivo environment. This first part of this thesis discusses ex vivo studies of the effects of high-frequency stimulation of spinal tissues on the structure of the node of Ranvier as investigated by coherent anti-Stokes Raman scattering (CARS) imaging (manuscript submitted to Journal of Neurosciece). Reversible paranodal myelin retraction at the nodes of Ranvier was observed during 200 Hz electrical stimulation, beginning minutes after the onset and continuing for up to 10 min after stimulation was ceased. A mechanistic study revealed a Ca2+ dependent pathway: high-frequency stimulation induced paranodal myelin retraction via pathologic calcium influx into axons, calpain activation, and cytoskeleton degradation through spectrin break-down. Also, the construction of dual-scanning CARS microscope for large area mapping of CNS tissues is detailed (Optics Express, 2008, 16:19396-193409). A confocal scanning head equipped with a rotating polygon mirror provides high speed, high resolution imaging and is coupled with a motorized sample stage to generate high-resolution large-area images of mouse brain coronal section and guinea pig spinal cord cross section. The polygon mirror decreases the mosaic acquisition time significantly without reducing the resolution of individual images. The ex vivo studies are then extended to in vivo imaging of mouse sciatic nerve tissue by CARS and second harmonic generation (SHG) imaging (Journal of Microscopy, 2007, 225: 175-182). Following a minimally invasive surgery to open the skin, CARS imaging of myelinated axons and SHG imaging of the

  19. 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.

  20. Application of Raman Microspectroscopic and Raman imaging techniques for cell biological studies

    NARCIS (Netherlands)

    Puppels, G.J.; Puppels, G.J.; Bakker schut, T.C.; Bakker Schut, T.C.; Sijtsema, N.M.; Grond, M.; Grond, M.; Maraboeuf, F.; de Grauw, C.J.; de Grauw, C.J.; Figdor, Carl; Greve, Jan

    1995-01-01

    Raman spectroscopy is being used to study biological molecules for some three decades now. Thanks to continuing advances in instrumentation more and more applications have become feasible in which molecules are studied in situ, and this has enabled Raman spectroscopy to enter the realms of

  1. Development and Application of Raman Microspectroscopic and Raman Imaging Techniques for Cell Biological Studies

    NARCIS (Netherlands)

    PUPPELS, G J; SCHUT, T C B; SIJTSEMA, N M; GROND, M; MARABOEUF, F; DEGRAUW, C G; FIGDOR, C G; GREVE, J

    1995-01-01

    Raman spectroscopy is being used to study biological molecules for some three decades now. Thanks to continuing advances in instrumentation more and more applications have become feasible in which molecules are studied in situ, and this has enabled Raman spectroscopy to enter the realms of

  2. Integrated femtosecond stimulated Raman scattering and two-photon fluorescence imaging of subcellular lipid and vesicular structures

    Science.gov (United States)

    Li, Xuesong; Lam, Wen Jiun; Cao, Zhe; Hao, Yan; Sun, Qiqi; He, Sicong; Mak, Ho Yi; Qu, Jianan Y.

    2015-11-01

    The primary goal of this study is to demonstrate that stimulated Raman scattering (SRS) as a new imaging modality can be integrated into a femtosecond (fs) nonlinear optical (NLO) microscope system. The fs sources of high pulse peak power are routinely used in multimodal nonlinear microscopy to enable efficient excitation of multiple NLO signals. However, with fs excitations, the SRS imaging of subcellular lipid and vesicular structures encounters significant interference from proteins due to poor spectral resolution and a lack of chemical specificity, respectively. We developed a unique NLO microscope of fs excitation that enables rapid acquisition of SRS and multiple two-photon excited fluorescence (TPEF) signals. In the in vivo imaging of transgenic C. elegans animals, we discovered that by cross-filtering false positive lipid signals based on the TPEF signals from tryptophan-bearing endogenous proteins and lysosome-related organelles, the imaging system produced highly accurate assignment of SRS signals to lipid. Furthermore, we demonstrated that the multimodal NLO microscope system could sequentially image lipid structure/content and organelles, such as mitochondria, lysosomes, and the endoplasmic reticulum, which are intricately linked to lipid metabolism.

  3. Purchase of a Raman and Photoluminescence Imaging System for Characterization of Advanced Electrochemical and Electronic Materials

    Science.gov (United States)

    2016-01-05

    SECURITY CLASSIFICATION OF: Funds were used to purchase a Renishaw inVia Reflex Spectrometer System for Raman and Photoluminescence spectral...Unlimited UU UU UU UU 05-01-2016 15-Aug-2014 14-Aug-2015 Final Report: Purchase of a Raman and Photoluminescence Imaging System for Characterization of...MONITORING AGENCY NAME(S) AND ADDRESS (ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Raman spectroscopy

  4. Raman Spectroscopic Imaging of the Whole Ciona intestinalis Embryo during Development

    Science.gov (United States)

    Nakamura, Mitsuru J.; Hotta, Kohji; Oka, Kotaro

    2013-01-01

    Intracellular composition and the distribution of bio-molecules play central roles in the specification of cell fates and morphogenesis during embryogenesis. Consequently, investigation of changes in the expression and distribution of bio-molecules, especially mRNAs and proteins, is an important challenge in developmental biology. Raman spectroscopic imaging, a non-invasive and label-free technique, allows simultaneous imaging of the intracellular composition and distribution of multiple bio-molecules. In this study, we explored the application of Raman spectroscopic imaging in the whole Ciona intestinalis embryo during development. Analysis of Raman spectra scattered from C. intestinalis embryos revealed a number of localized patterns of high Raman intensity within the embryo. Based on the observed distribution of bio-molecules, we succeeded in identifying the location and structure of differentiated muscle and endoderm within the whole embryo, up to the tailbud stage, in a label-free manner. Furthermore, during cell differentiation, we detected significant differences in cell state between muscle/endoderm daughter cells and daughter cells with other fates that had divided from the same mother cells; this was achieved by focusing on the Raman intensity of single Raman bands at 1002 or 1526 cm−1, respectively. This study reports the first application of Raman spectroscopic imaging to the study of identifying and characterizing differentiating tissues in a whole chordate embryo. Our results suggest that Raman spectroscopic imaging is a feasible label-free technique for investigating the developmental process of the whole embryo of C. intestinalis. PMID:23977129

  5. 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

  6. 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.

  7. Raman technique application for rubber blends characterization

    Directory of Open Access Journals (Sweden)

    Smitthipong, W.

    2007-11-01

    Full Text Available Raman spectroscopy has been employed in a number of studies to examine the morphological changes in a variety of materials. It is a non-destructive analysis method and an equally useful method for the investigation of material structure. Recently, Raman spectroscopy has been developed to employ as an imaging instrumentation. Sample surface scanning in X- and Y-axis and sample depth (Z-axis can be carried out by modifying the focus of the laser beam from the Raman microscope. Therefore, three-dimensional images can be thus built by using special software. The surface and bulk properties of immiscible rubber blend were investigated by Raman spectroscopy. The results obtained by Raman spectroscopy were in good agreement with those of Scanning Electron Microscope (SEM. The combination of Raman spectrometry and SEM clearly elucidates the identification of phases between the dispersed phase and the matrix (continuous phase of the immiscible rubber blends.

  8. Preclinical Evaluation of Raman Nanoparticle Biodistribution for their Potential Use in Clinical Endoscopy Imaging

    DEFF Research Database (Denmark)

    Zavaleta, Cristina L; Hartman, Keith B; Miao, Zheng

    2011-01-01

    Raman imaging offers unsurpassed sensitivity and multiplexing capabilities. However, its limited depth of light penetration makes direct clinical translation challenging. Therefore, a more suitable way to harness its attributes in a clinical setting would be to couple Raman spectroscopy with endo...

  9. Tip-enhanced near-field Raman spectroscopy with a scanning tunneling microscope and side-illumination optics.

    Science.gov (United States)

    Yi, K J; He, X N; Zhou, Y S; Xiong, W; Lu, Y F

    2008-07-01

    Conventional Raman spectroscopy (RS) suffers from low spatial resolution and low detection sensitivity due to the optical diffraction limit and small interaction cross sections. It has been reported that a highly localized and significantly enhanced electromagnetic field could be generated in the proximity of a metallic tip illuminated by a laser beam. In this study, a tip-enhanced RS system was developed to both improve the resolution and enhance the detection sensitivity using the tip-enhanced near-field effects. This instrument, by combining RS with a scanning tunneling microscope and side-illumination optics, demonstrated significant enhancement on both optical sensitivity and spatial resolution using either silver (Ag)-coated tungsten (W) tips or gold (Au) tips. The sensitivity improvement was verified by observing the enhancement effects on silicon (Si) substrates. Lateral resolution was verified to be below 100 nm by mapping Ag nanostructures. By deploying the depolarization technique, an apparent enhancement of 175% on Si substrates was achieved. Furthermore, the developed instrument features fast and reliable optical alignment, versatile sample adaptability, and effective suppression of far-field signals.

  10. Surface enhanced raman scattering on tardigrada - Towards monitoring and imaging molecular structures in live cryptobiotic organisms

    DEFF Research Database (Denmark)

    Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak

    2013-01-01

    Tardigrades are microscopic metazoans which are able to survive extreme physical and chemical conditions by entering a stress tolerant state called cryptobiosis. At present, the molecular mechanisms behind cryptobiosis are still poorly understood. We show that surface enhanced Raman scattering su...

  11. Calibration and testing of a Raman hyperspectral imaging system to reveal powdered food adulteration.

    Science.gov (United States)

    Lohumi, Santosh; Lee, Hoonsoo; Kim, Moon S; Qin, Jianwei; Kandpal, Lalit Mohan; Bae, Hyungjin; Rahman, Anisur; Cho, Byoung-Kwan

    2018-01-01

    The potential adulteration of foodstuffs has led to increasing concern regarding food safety and security, in particular for powdered food products where cheap ground materials or hazardous chemicals can be added to increase the quantity of powder or to obtain the desired aesthetic quality. Due to the resulting potential health threat to consumers, the development of a fast, label-free, and non-invasive technique for the detection of adulteration over a wide range of food products is necessary. We therefore report the development of a rapid Raman hyperspectral imaging technique for the detection of food adulteration and for authenticity analysis. The Raman hyperspectral imaging system comprises of a custom designed laser illumination system, sensing module, and a software interface. Laser illumination system generates a 785 nm laser line of high power, and the Gaussian like intensity distribution of laser beam is shaped by incorporating an engineered diffuser. The sensing module utilize Rayleigh filters, imaging spectrometer, and detector for collection of the Raman scattering signals along the laser line. A custom-built software to acquire Raman hyperspectral images which also facilitate the real time visualization of Raman chemical images of scanned samples. The developed system was employed for the simultaneous detection of Sudan dye and Congo red dye adulteration in paprika powder, and benzoyl peroxide and alloxan monohydrate adulteration in wheat flour at six different concentrations (w/w) from 0.05 to 1%. The collected Raman imaging data of the adulterated samples were analyzed to visualize and detect the adulterant concentrations by generating a binary image for each individual adulterant material. The results obtained based on the Raman chemical images of adulterants showed a strong correlation (R>0.98) between added and pixel based calculated concentration of adulterant materials. This developed Raman imaging system thus, can be considered as a powerful

  12. 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.

  13. Glioblastoma cells labeled by robust Raman tags for enhancing imaging contrast.

    Science.gov (United States)

    Huang, Li-Ching; Chang, Yung-Ching; Wu, Yi-Syuan; Sun, Wei-Lun; Liu, Chan-Chuan; Sze, Chun-I; Chen, Shiuan-Yeh

    2018-05-01

    Complete removal of a glioblastoma multiforme (GBM), a highly malignant brain tumor, is challenging due to its infiltrative characteristics. Therefore, utilizing imaging agents such as fluorophores to increase the contrast between GBM and normal cells can help neurosurgeons to locate residual cancer cells during image guided surgery. In this work, Raman tag based labeling and imaging for GBM cells in vitro is described and evaluated. The cell membrane of a GBM adsorbs a substantial amount of functionalized Raman tags through overexpression of the epidermal growth factor receptor (EGFR) and "broadcasts" stronger pre-defined Raman signals than normal cells. The average ratio between Raman signals from a GBM cell and autofluorescence from a normal cell can be up to 15. In addition, the intensity of these images is stable under laser illuminations without suffering from the severe photo-bleaching that usually occurs in fluorescent imaging. Our results show that labeling and imaging GBM cells via robust Raman tags is a viable alternative method to distinguish them from normal cells. This Raman tag based method can be used solely or integrated into an existing fluorescence system to improve the identification of infiltrative glial tumor cells around the boundary, which will further reduce GBM recurrence. In addition, it can also be applied/extended to other types of cancer to improve the effectiveness of image guided surgery.

  14. 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...

  15. Gap-enhanced Raman tags for high-contrast sentinel lymph node imaging.

    Science.gov (United States)

    Bao, Zhouzhou; Zhang, Yuqing; Tan, Ziyang; Yin, Xia; Di, Wen; Ye, Jian

    2018-05-01

    The sentinel lymph node (SLN) biopsy is gaining in popularity as a procedure to investigate the lymphatic metastasis of malignant tumors. The commonly used techniques to identify the SLNs in clinical practice are blue dyes-guided visualization, radioisotope-based detection and near-infrared fluorescence imaging. However, all these methods have not been found to perfectly fit the clinical criteria with issues such as short retention time in SLN, poor spatial resolution, autofluorescence, low photostability and high cost. In this study, we have reported a new type of nanoprobes, named, gap-enhanced Raman tags (GERTs) for the SLN Raman imaging. With the advantageous features including unique "fingerprint" Raman signal, strong Raman enhancement, high photostability, good biocompatibility and extra-long retention time, we have demonstrated that GERTs are greatly favorable for high-contrast and deep SLN Raman imaging, which meanwhile reveals the dynamic migration behavior of the probes entering the SLN. In addition, a quantitative volumetric Raman imaging (qVRI) data-processing method is employed to acquire a high-resolution 3-dimensional (3D) margin of SLN as well as the content variation of GERTs in the SLN. Moreover, SLN detection could be realized via a cost-effective commercial portable Raman scanner. Therefore, GERTs hold the great potential to be translated in clinical application for accurate and intraoperative location of the SLN. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Label-Free Raman Imaging to Monitor Breast Tumor Signatures

    Science.gov (United States)

    Ciubuc, John

    Methods built on Raman spectroscopy have shown major potential in describing and discriminating between malignant and benign specimens. Accurate, real-time medical diagnosis benefits in substantial improvements through this vibrational optical method. Not only is acquisition of data possible in milliseconds and analysis in minutes, Raman allows concurrent detection and monitoring of all biological components. Besides validating a significant Raman signature distinction between non-tumorigenic (MCF-10A) and tumorigenic (MCF-7) breast epithelial cells, this study reveals a label-free method to assess overexpression of epidermal growth factor receptors (EGFR) in tumor cells. EGFR overexpression sires Raman features associated with phosphorylated threonine and serine, and modifications of DNA/RNA characteristics. Investigations by gel electrophoresis reveal EGF induction of phosphorylated Akt, agreeing with the Raman results. The analysis presented is a vital step toward Raman-based evaluation of EGF receptors in breast cancer cells. With the goal of clinically applying Raman-guided methods for diagnosis of breast tumors, the current results lay the basis for proving label-free optical alternatives in making prognosis of the disease.

  17. 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.

  18. 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....

  19. Micro-Raman Imaging for Biology with Multivariate Spectral Analysis

    KAUST Repository

    Malvaso, Federica

    2015-01-01

    . The aim of the following thesis work is to analyze Raman maps related to three pairs of different cells, highlighting differences and similarities through multivariate algorithms. The first pair of analyzed cells are human embryonic stem cells (h

  20. Unveiling the Aggregation of Lycopene in Vitro and in Vivo: UV-Vis, Resonance Raman, and Raman Imaging Studies.

    Science.gov (United States)

    Ishigaki, Mika; Meksiarun, Phiranuphon; Kitahama, Yasutaka; Zhang, Leilei; Hashimoto, Hideki; Genkawa, Takuma; Ozaki, Yukihiro

    2017-08-31

    The present study investigates the structure of lycopene aggregates both in vitro and in vivo using ultraviolet-visible (UV-vis) and Raman spectroscopies. The electronic absorption bands of the J- and H-aggregates in vitro shift to lower and higher energies, respectively, compared to that of the lycopene monomer. Along with these results, the frequencies of the ν 1 Raman bands were shifted to lower and higher frequencies, respectively. By plotting the frequencies of the ν 1 Raman band against the S 0 → S 2 transition energy, a linear relationship between the data set with different aggregation conformations can be obtained. Therefore, the band positions depending on the different conformations can be explained based on the idea that the effective conjugated C═C chain lengths within lycopene molecules are different due to the environmental effect (site-shift effect) caused by the aggregation conformation. Applying this knowledge to the in vivo measurement of a tomato fruit sample, the relationship between the aggregation conformation of lycopene and the spectral patterns observed in the UV-vis as well as Raman spectra in different parts of tomato fruits was discussed in detail. The results showed that the concentration of lycopene (particularly that of the J-aggregate) specifically increased, whereas that of chlorophyll decreased, with ripening. Furthermore, Raman imaging indicated that lycopene with different aggregate conformations was distributed inhomogeneously, even within one sample. The layer formation in tomato tissues with high concentrations of J- and H-aggregates was successfully visualized. In this manner, the presence of lycopene distributions with different aggregate conformations was unveiled in vivo.

  1. 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.

  2. 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.

  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. 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.

  5. 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.

  6. 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.

  7. A novel non-imaging optics based Raman spectroscopy device for transdermal blood analyte measurement

    Directory of Open Access Journals (Sweden)

    Chae-Ryon Kong

    2011-09-01

    Full Text Available Due to its high chemical specificity, Raman spectroscopy has been considered to be a promising technique for non-invasive disease diagnosis. However, during Raman excitation, less than one out of a million photons undergo spontaneous Raman scattering and such weakness in Raman scattered light often require highly efficient collection of Raman scattered light for the analysis of biological tissues. We present a novel non-imaging optics based portable Raman spectroscopy instrument designed for enhanced light collection. While the instrument was demonstrated on transdermal blood glucose measurement, it can also be used for detection of other clinically relevant blood analytes such as creatinine, urea and cholesterol, as well as other tissue diagnosis applications. For enhanced light collection, a non-imaging optical element called compound hyperbolic concentrator (CHC converts the wide angular range of scattered photons (numerical aperture (NA of 1.0 from the tissue into a limited range of angles accommodated by the acceptance angles of the collection system (e.g., an optical fiber with NA of 0.22. A CHC enables collimation of scattered light directions to within extremely narrow range of angles while also maintaining practical physical dimensions. Such a design allows for the development of a very efficient and compact spectroscopy system for analyzing highly scattering biological tissues. Using the CHC-based portable Raman instrument in a clinical research setting, we demonstrate successful transdermal blood glucose predictions in human subjects undergoing oral glucose tolerance tests.

  8. 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

  9. 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.

  10. 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.

  11. Sparse-sampling with time-encoded (TICO) stimulated Raman scattering for fast image acquisition

    Science.gov (United States)

    Hakert, Hubertus; Eibl, Matthias; Karpf, Sebastian; Huber, Robert

    2017-07-01

    Modern biomedical imaging modalities aim to provide researchers a multimodal contrast for a deeper insight into a specimen under investigation. A very promising technique is stimulated Raman scattering (SRS) microscopy, which can unveil the chemical composition of a sample with a very high specificity. Although the signal intensities are enhanced manifold to achieve a faster acquisition of images if compared to standard Raman microscopy, there is a trade-off between specificity and acquisition speed. Commonly used SRS concepts either probe only very few Raman transitions as the tuning of the applied laser sources is complicated or record whole spectra with a spectrometer based setup. While the first approach is fast, it reduces the specificity and the spectrometer approach records whole spectra -with energy differences where no Raman information is present-, which limits the acquisition speed. Therefore, we present a new approach based on the TICO-Raman concept, which we call sparse-sampling. The TICO-sparse-sampling setup is fully electronically controllable and allows probing of only the characteristic peaks of a Raman spectrum instead of always acquiring a whole spectrum. By reducing the spectral points to the relevant peaks, the acquisition time can be greatly reduced compared to a uniformly, equidistantly sampled Raman spectrum while the specificity and the signal to noise ratio (SNR) are maintained. Furthermore, all laser sources are completely fiber based. The synchronized detection enables a full resolution of the Raman signal, whereas the analogue and digital balancing allows shot noise limited detection. First imaging results with polystyrene (PS) and polymethylmethacrylate (PMMA) beads confirm the advantages of TICO sparse-sampling. We achieved a pixel dwell time as low as 35 μs for an image differentiating both species. The mechanical properties of the applied voice coil stage for scanning the sample currently limits even faster acquisition.

  12. 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

  13. 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.

  14. 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

  15. 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...

  16. 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.

  17. Label-free cellular imaging by broadband coherent anti-Stokes Raman scattering microscopy.

    Science.gov (United States)

    Parekh, Sapun H; Lee, Young Jong; Aamer, Khaled A; Cicerone, Marcus T

    2010-10-20

    Raman microspectroscopy can provide the chemical contrast needed to characterize the complex intracellular environment and macromolecular organization in cells without exogenous labels. It has shown a remarkable ability to detect chemical changes underlying cell differentiation and pathology-related chemical changes in tissues but has not been widely adopted for imaging, largely due to low signal levels. Broadband coherent anti-Stokes Raman scattering (B-CARS) offers the same inherent chemical contrast as spontaneous Raman but with increased acquisition rates. To date, however, only spectrally resolved signals from the strong CH-related vibrations have been used for CARS imaging. Here, we obtain Raman spectral images of single cells with a spectral range of 600-3200 cm⁻¹, including signatures from weakly scattering modes as well as CH vibrations. We also show that B-CARS imaging can be used to measure spectral signatures of individual cells at least fivefold faster than spontaneous Raman microspectroscopy and can be used to generate maps of biochemical species in cells. This improved spectral range and signal intensity opens the door for more widespread use of vibrational spectroscopic imaging in biology and clinical diagnostics. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. Label-free imaging of mammalian cell nucleoli by Raman microspectroscopy.

    Science.gov (United States)

    Schulze, H Georg; Konorov, Stanislav O; Piret, James M; Blades, Michael W; Turner, Robin F B

    2013-06-21

    The nucleolus is a prominent subnuclear structure whose major function is the transcription and assembly of ribosome subunits. The size of the nucleolus varies with the cell cycle, proliferation rate and stress. Changes in nucleolar size, number, chemical composition, and shape can be used to characterize malignant cells. We used spontaneous Raman microscopy as a label-free technique to examine nucleolar spatial and chemical features. Raman images of the 1003 cm(-1) phenylalanine band revealed large, well-defined subnuclear protein structures in MFC-7 breast cancer cells. The 783 cm(-1) images showed that nucleic acids were similarly distributed, but varied more in intensity, forming observable high-intensity regions. High subnuclear RNA concentrations were observed within some of these regions as shown by 809 cm(-1) Raman band images. Principal component analyses of sub-images and library spectra validated the subnuclear presence of RNA. They also revealed that an actin-like protein covaried with DNA within the nucleolus, a combination that accounted for 64% or more of the spectral variance. Embryonic stem cells are another rapidly proliferating cell type, but their nucleoli were not as large or well defined. Estimating the size of the larger MCF-7 nucleolus was used to show the utility of Raman microscopy for morphometric analyses. It was concluded that imaging based on Raman microscopy provides a promising new method for the study of nucleolar function and organization, in the evaluation of drug and experimental effects on the nucleolus, and in clinical diagnostics and prognostics.

  19. Raman hyperspectral imaging and analysis of fat spreads

    NARCIS (Netherlands)

    Dalen, van G.; Velzen, van E.J.J.; Heussen, P.C.M.; Sovago, M.; Malssen, van K.F.; Duynhoven, van J.P.M.

    2017-01-01

    The microstructure of fat spreads is of fundamental importance to their sensorial properties such as texture, mouthfeel and spreadability. Fat spreads are water in oil emulsions,with a continuous phase supported by a fat crystal network. Confocal Raman microscopy offers the possibility for the

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Noninvasive imaging of intracellular lipid metabolism in macrophages by Raman microscopy in combination with stable isotopic labeling.

    Science.gov (United States)

    Matthäus, Christian; Krafft, Christoph; Dietzek, Benjamin; Brehm, Bernhard R; Lorkowski, Stefan; Popp, Jürgen

    2012-10-16

    Monocyte-derived macrophages play a key role in atherogenesis because their transformation into foam cells is responsible for deposition of lipids in plaques within arterial walls. The appearance of cytosolic lipid droplets is a hallmark of macrophage foam cell formation, and the molecular basics involved in this process are not well understood. Of particular interest is the intracellular fate of different individual lipid species, such as fatty acids or cholesterol. Here, we utilize Raman microscopy to image the metabolism of such lipids and to trace their subsequent storage patterns. The combination of microscopic information with Raman spectroscopy provides a powerful molecular imaging method, which allows visualization at the diffraction limit of the employed laser light and biochemical characterization through associated spectral information. In order to distinguish the molecules of interest from other naturally occurring lipids spectroscopically, deuterium labels were introduced. Intracellular distribution and metabolic changes were observed for serum albumin-complexed palmitic and oleic acid and cholesterol and quantitatively evaluated by monitoring the increase in CD scattering intensities at 0.5, 1, 3, 6, 24, 30, and 36 h. This approach may also allow for investigating the cellular trafficking of other molecules, such as nutrients, metabolites, and drugs.

  6. 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.

  7. 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.

  8. Graphene-enhanced Raman imaging of TiO2 nanoparticles

    International Nuclear Information System (INIS)

    Naumenko, Denys; Snitka, Valentinas; Snopok, Boris; Arpiainen, Sanna; Lipsanen, Harri

    2012-01-01

    The interaction of anatase titanium dioxide (TiO 2 ) nanoparticles with chemical vapour deposited graphene sheets transferred on glass substrates is investigated by using atomic force microscopy, Raman spectroscopy and imaging. Significant electronic interactions between the nanoparticles of TiO 2 and graphene were found. The changes in the graphene Raman peak positions and intensity ratios indicate that charge transfer between graphene and TiO 2 nanoparticles occurred, increasing the Raman signal of the TiO 2 nanoparticles up to five times. The normalized Raman intensity of TiO 2 nanoparticles per their volume increased with the disorder of the graphene structure. The complementary reason for the observed enhancement is that due to the higher density of states in the defect sites of graphene, a higher electron transfer occurs from the graphene to the anatase TiO 2 nanoparticles. (paper)

  9. 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.

  10. 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.

  11. 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...

  12. Selective isolation and noninvasive analysis of circulating cancer stem cells through Raman imaging.

    Science.gov (United States)

    Cho, Hyeon-Yeol; Hossain, Md Khaled; Lee, Jin-Ho; Han, Jiyou; Lee, Hun Joo; Kim, Kyeong-Jun; Kim, Jong-Hoon; Lee, Ki-Bum; Choi, Jeong-Woo

    2018-04-15

    Circulating cancer stem cells (CCSCs), a rare circulating tumor cell (CTC) type, recently arose as a useful resource for monitoring and characterizing both cancers and their metastatic derivatives. However, due to the scarcity of CCSCs among hematologic cells in the blood and the complexity of the phenotype confirmation process, CCSC research can be extremely challenging. Hence, we report a nanoparticle-mediated Raman imaging method for CCSC characterization which profiles CCSCs based on their surface marker expression phenotypes. We have developed an integrated combinatorial Raman-Active Nanoprobe (RAN) system combined with a microfluidic chip to successfully process complete blood samples. CCSCs and CTCs were detected (90% efficiency) and classified in accordance with their respective surface marker expression via completely distinct Raman signals of RANs. Selectively isolated CCSCs (93% accuracy) were employed for both in vitro and in vivo tumor phenotyping to identify the tumorigenicity of the CCSCs. We utilized our new method to predict metastasis by screening blood samples from xenograft models, showing that upon CCSC detection, all subjects exhibited liver metastasis. Having highly efficient detection and noninvasive isolation capabilities, we have demonstrated that our RAN-based Raman imaging method will be valuable for predicting cancer metastasis and relapse via CCSC detection. Moreover, the exclusion of peak overlapping in CCSC analysis with our Raman imaging method will allow to expand the RAN families for various cancer types, therefore, increasing therapeutic efficacy by providing detailed molecular features of tumor subtypes. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. Raman-based imaging uncovers the effects of alginate hydrogel implants in spinal cord injury

    Science.gov (United States)

    Galli, Roberta; Tamosaityte, Sandra; Koch, Maria; Sitoci-Ficici, Kerim H.; Later, Robert; Uckermann, Ortrud; Beiermeister, Rudolf; Gelinsky, Michael; Schackert, Gabriele; Kirsch, Matthias; Koch, Edmund; Steiner, Gerald

    2015-07-01

    The treatment of spinal cord injury by using implants that provide a permissive environment for axonal growth is in the focus of the research for regenerative therapies. Here, Raman-based label-free techniques were applied for the characterization of morphochemical properties of surgically induced spinal cord injury in the rat that received an implant of soft unfunctionalized alginate hydrogel. Raman microspectroscopy followed by chemometrics allowed mapping the different degenerative areas, while multimodal multiphoton microscopy (e.g. the combination of coherent anti-Stokes Raman scattering (CARS), endogenous two-photon fluorescence and second harmonic generation on the same platform) enabled to address the morphochemistry of the tissue at cellular level. The regions of injury, characterized by demyelination and scarring, were retrieved and the distribution of key tissue components was evaluated by Raman mapping. The alginate hydrogel was detected in the lesion up to six months after implantation and had positive effects on the nervous tissue. For instance, multimodal multiphoton microscopy complemented the results of Raman mapping, providing the micromorphology of lipid-rich tissue structures by CARS and enabling to discern lipid-rich regions that contained myelinated axons from degenerative regions characterized by myelin fragmentation and presence of foam cells. These findings demonstrate that Raman-based imaging methods provide useful information for the evaluation of alginate implant effects and have therefore the potential to contribute to new strategies for monitoring degenerative and regenerative processes induced in SCI, thereby improving the effectiveness of therapies.

  19. 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.

  20. Segmentation of confocal Raman microspectroscopic imaging data using edge-preserving denoising and clustering.

    Science.gov (United States)

    Alexandrov, Theodore; Lasch, Peter

    2013-06-18

    Over the past decade, confocal Raman microspectroscopic (CRM) imaging has matured into a useful analytical tool to obtain spatially resolved chemical information on the molecular composition of biological samples and has found its way into histopathology, cytology, and microbiology. A CRM imaging data set is a hyperspectral image in which Raman intensities are represented as a function of three coordinates: a spectral coordinate λ encoding the wavelength and two spatial coordinates x and y. Understanding CRM imaging data is challenging because of its complexity, size, and moderate signal-to-noise ratio. Spatial segmentation of CRM imaging data is a way to reveal regions of interest and is traditionally performed using nonsupervised clustering which relies on spectral domain-only information with the main drawback being the high sensitivity to noise. We present a new pipeline for spatial segmentation of CRM imaging data which combines preprocessing in the spectral and spatial domains with k-means clustering. Its core is the preprocessing routine in the spatial domain, edge-preserving denoising (EPD), which exploits the spatial relationships between Raman intensities acquired at neighboring pixels. Additionally, we propose to use both spatial correlation to identify Raman spectral features colocalized with defined spatial regions and confidence maps to assess the quality of spatial segmentation. For CRM data acquired from midsagittal Syrian hamster ( Mesocricetus auratus ) brain cryosections, we show how our pipeline benefits from the complex spatial-spectral relationships inherent in the CRM imaging data. EPD significantly improves the quality of spatial segmentation that allows us to extract the underlying structural and compositional information contained in the Raman microspectra.

  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. Micro-Raman Imaging for Biology with Multivariate Spectral Analysis

    KAUST Repository

    Malvaso, Federica

    2015-05-05

    Raman spectroscopy is a noninvasive technique that can provide complex information on the vibrational state of the molecules. It defines the unique fingerprint that allow the identification of the various chemical components within a given sample. The aim of the following thesis work is to analyze Raman maps related to three pairs of different cells, highlighting differences and similarities through multivariate algorithms. The first pair of analyzed cells are human embryonic stem cells (hESCs), while the other two pairs are induced pluripotent stem cells (iPSCs) derived from T lymphocytes and keratinocytes, respectively. Although two different multivariate techniques were employed, ie Principal Component Analysis and Cluster Analysis, the same results were achieved: the iPSCs derived from T-lymphocytes show a higher content of genetic material both compared with the iPSCs derived from keratinocytes and the hESCs . On the other side, equally evident, was that iPS cells derived from keratinocytes assume a molecular distribution very similar to hESCs.

  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. Line-scan macro-scale Raman chemical imaging for authentication of powdered foods and ingredients

    Science.gov (United States)

    Adulteration and fraud for powdered foods and ingredients are rising food safety risks that threaten consumers’ health. In this study, a newly developed line-scan macro-scale Raman imaging system using a 5 W 785 nm line laser as excitation source was used to authenticate the food powders. The system...

  11. Quantitative imaging through a spectrograph : 2. stoichiometry mapping by Raman scattering

    NARCIS (Netherlands)

    Tolboom, R.A.L.; Dam, N.J.; Meulen, ter J.J.

    2004-01-01

    The Bayesian deconvolution algorithm described in a preceding paper [Appl. Opt. 43, 5669–5681 (2004)] is applied to measurement of the two-dimensional stoichiometry field in a combustible methane-air mixture by Raman imaging through a spectrograph. Stoichiometry (fuel equivalence ratio) is derived

  12. Quantitative imaging through a spectrograph. 2. Stoichiometry mapping by Raman scattering.

    NARCIS (Netherlands)

    Tolboom, R.A.L.; Dam, N.J.; Meulen, J.J. ter

    2004-01-01

    The Bayesian deconvolution algorithm described in a preceding paper [Appl. Opt. 43, 5669-5681 (2004)] is applied to measurement of the two-dimensional stoichiometry field in a combustible methane-air mixture by Raman imaging through a spectrograph. Stoichiometry (fuel equivalence ratio) is derived

  13. Noninvasive imaging of protein metabolic labeling in single human cells using stable isotopes and Raman microscopy

    NARCIS (Netherlands)

    van Manen, H.J.; Lenferink, Aufrid T.M.; Otto, Cornelis

    2008-01-01

    We have combined nonresonant Raman microspectroscopy and spectral imaging with stable isotope labeling by amino acids in cell culture (SILAC) to selectively detect the incorporation of deuterium-labeled phenylalanine, tyrosine, and methionine into proteins in intact, single HeLa cells. The C−D

  14. Investigation of Raman chemical imaging for detection of Lycopene changes in tomatoes during postharvest ripening

    Science.gov (United States)

    Lycopene is a major carotenoid in tomatoes and detecting changes in lycopene content can be used to monitor the ripening of tomatoes. Raman chemical imaging is a new technique that shows promise for mapping constituents of interest in complex food matrices. In this study, a benchtop point-scanning...

  15. Atomic force and shear force based tip-enhanced Raman spectroscopy and imaging

    NARCIS (Netherlands)

    Kharintsev, S.S.; Hoffmann, G.G.; Dorozhkin, P.S.; With, de G.; Loos, J.

    2007-01-01

    Underlying near-field optibal effects on the nanoscale have stimulated the development of apertureless vibrational spectroscopy and imaging with ultrahigh spatial resolution. We demonstrate tip-enhanced Raman spectra of single-walled carbon nanotubes (SWCNTs), recorded with a scanning near-field

  16. 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.

  17. 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.

  18. 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

  19. 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 ...

  20. 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...

  1. 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...

  2. 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

  3. Fabrication of large area plasmonic nanoparticle grating structure on silver halide based transmission electron microscope film and its application as a surface enhanced Raman spectroscopy substrate

    International Nuclear Information System (INIS)

    Sudheer,; Tiwari, P.; Singh, M. N.; Sinha, A. K.; Rai, V. N.; Srivastava, A. K.; Bhartiya, S.; Mukherjee, C.

    2015-01-01

    The plasmonic responses of silver nanoparticle grating structures of different periods made on silver halide based electron microscope film are investigated. Raster scan of the conventional scanning electron microscope (SEM) is used to carry out electron beam lithography for fabricating the plasmonic nanoparticle grating (PNG) structures. Morphological characterization of the PNG structures, carried out by the SEM and the atomic force microscope, indicates that the depth of the groove decreases with a decrease in the grating period. Elemental characterization performed by the energy dispersive spectroscopy and the x-ray diffraction shows the presence of nanoparticles of silver in the PNG grating. The optical characterization of the gratings shows that the localized surface plasmon resonance peak shifts from 366 to 378 nm and broadens with a decrease in grating period from 10 to 2.5 μm. The surface enhanced Raman spectroscopy of the Rhodamine-6G dye coated PNG structure shows the maximum enhancement by two orders of magnitude in comparison to the randomly distributed silver nanoparticles having similar size and shape as the PNG structure

  4. 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.

  5. 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.

  6. 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.

  7. A multimodal microcharacterisation of trace-element zonation and crystallographic orientation in natural cassiterite by combining cathodoluminescence, EBSD, EPMA and contribution of confocal Raman-in-SEM imaging.

    Science.gov (United States)

    Wille, G; Lerouge, C; Schmidt, U

    2018-01-16

    In cassiterite, tin is associated with metals (titanium, niobium, tantalum, indium, tungsten, iron, manganese, mercury). Knowledge of mineral chemistry and trace-element distribution is essential for: the understanding of ore formation, the exploration phase, the feasibility of ore treatment, and disposal/treatment of tailings after the exploitation phase. However, the availability of analytical methods make these characterisations difficult. We present a multitechnical approach to chemical and structural data that includes scanning electron microscopy (SEM)-based imaging and microanalysis techniques such as: secondary and backscattered electrons, cathodoluminescence (CL), electron probe microanalyser (EPMA), electron backscattered diffraction (EBSD) and confocal Raman-imaging integrated in a SEM (RISE). The presented results show the complementarity of the used analytical techniques. SEM, CL, EBSD, EPMA provide information from the interaction of an electron beam with minerals, leading to atomistic information about their composition, whereas RISE, Raman spectroscopy and imaging completes the studies with information about molecular vibrations, which are sensitive to structural modifications of the minerals. The correlation of Raman bands with the presence/absence of Nb, Ta, Fe (heterovalent substitution) and Ti (homovalent substitution) is established at a submicrometric scale. Combination of the different techniques makes it possible to establish a direct link between chemical and crystallographic data of cassiterite. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

  8. 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

  9. 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).

  10. 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

  11. 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

  12. 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.

  13. Theranostic Gold Nanoantennas for Simultaneous Multiplexed Raman Imaging of Immunomarkers and Photothermal Therapy.

    Science.gov (United States)

    Webb, Joseph A; Ou, Yu-Chuan; Faley, Shannon; Paul, Eden P; Hittinger, Joseph P; Cutright, Camden C; Lin, Eugene C; Bellan, Leon M; Bardhan, Rizia

    2017-07-31

    In this study, we demonstrate the theranostic capability of actively targeted, site-specific multibranched gold nanoantennas (MGNs) in triple-negative breast cancer (TNBC) cells in vitro. By utilizing multiplexed surface-enhanced Raman scattering (SERS) imaging, enabled by the narrow peak widths of Raman signatures, we simultaneously targeted immune checkpoint receptor programmed death ligand 1 (PDL1) and the epidermal growth factor receptor (EGFR) overexpressed in TNBC cells. A 1:1 mixture of MGNs functionalized with anti-PDL1 antibodies and Raman tag 5,5-dithio-bis-(2-nitrobenzoic acid) (DTNB) and MGNs functionalized with anti-EGFR antibodies and Raman tag para -mercaptobenzoic acid ( p MBA) were incubated with the cells. SERS imaging revealed a cellular traffic map of MGN localization by surface binding and receptor-mediated endocytosis, enabling targeted diagnosis of both biomarkers. Furthermore, cells incubated with anti-EGFR- p MBA-MGNs and illuminated with an 808 nm laser for 15 min at 4.7 W/cm 2 exhibited photothermal cell death only within the laser spot (indicated by live/dead cell fluorescence assay). Therefore, this study not only provides an optical imaging platform that can track immunomarkers with spatiotemporal control but also demonstrates an externally controlled light-triggered therapeutic approach enabling receptor-specific treatment with biocompatible theranostic nanoprobes.

  14. Raman Hyperspectral Imaging for Detection of Watermelon Seeds Infected with Acidovorax citrulli.

    Science.gov (United States)

    Lee, Hoonsoo; Kim, Moon S; Qin, Jianwei; Park, Eunsoo; Song, Yu-Rim; Oh, Chang-Sik; Cho, Byoung-Kwan

    2017-09-23

    The bacterial infection of seeds is one of the most important quality factors affecting yield. Conventional detection methods for bacteria-infected seeds, such as biological, serological, and molecular tests, are not feasible since they require expensive equipment, and furthermore, the testing processes are also time-consuming. In this study, we use the Raman hyperspectral imaging technique to distinguish bacteria-infected seeds from healthy seeds as a rapid, accurate, and non-destructive detection tool. We utilize Raman hyperspectral imaging data in the spectral range of 400-1800 cm -1 to determine the optimal band-ratio for the discrimination of watermelon seeds infected by the bacteria Acidovorax citrulli using ANOVA. Two bands at 1076.8 cm -1 and 437 cm -1 are selected as the optimal Raman peaks for the detection of bacteria-infected seeds. The results demonstrate that the Raman hyperspectral imaging technique has a good potential for the detection of bacteria-infected watermelon seeds and that it could form a suitable alternative to conventional methods.

  15. Transmission electron microscopy, fluorescence microscopy, and confocal raman microscopic analysis of ultrastructural and compositional heterogeneity of Cornus alba L. wood cell wall.

    Science.gov (United States)

    Ma, Jianfeng; Ji, Zhe; Zhou, Xia; Zhang, Zhiheng; Xu, Feng

    2013-02-01

    Transmission electron microscopy (TEM), fluorescence microscopy, and confocal Raman microscopy can be used to characterize ultrastructural and compositional heterogeneity of plant cell walls. In this study, TEM observations revealed the ultrastructural characterization of Cornus alba L. fiber, vessel, axial parenchyma, ray parenchyma, and pit membrane between cells, notably with the ray parenchyma consisting of two well-defined layers. Fluorescence microscopy evidenced that cell corner middle lamella was more lignified than adjacent compound middle lamella and secondary wall with variation in lignification level from cell to cell. In situ Raman images showed that the inhomogeneity in cell wall components (cellulose and lignin) among different cells and within morphologically distinct cell wall layers. As the significant precursors of lignin biosynthesis, the pattern of coniferyl alcohol and aldehyde (joint abbreviation Lignin-CAA for both structures) distribution in fiber cell wall was also identified by Raman images, with higher concentration occurring in the fiber secondary wall where there was the highest cellulose concentration. Moreover, noteworthy was the observation that higher concentration of lignin and very minor amounts of cellulose were visualized in the pit membrane areas. These complementary microanalytical methods provide more accurate and complete information with regard to ultrastructural and compositional characterization of plant cell walls.

  16. 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.

  17. 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)

  18. 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}.

  19. 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)

  20. 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.

  1. 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

  2. Vibrational imaging of glucose uptake activity in live cells and tissues by stimulated Raman scattering microscopy (Conference Presentation)

    Science.gov (United States)

    Hu, Fanghao; Chen, Zhixing; Zhang, Luyuan; Shen, Yihui; Wei, Lu; Min, Wei

    2016-03-01

    Glucose is consumed as an energy source by virtually all living organisms, from bacteria to humans. Its uptake activity closely reflects the cellular metabolic status in various pathophysiological transformations, such as diabetes and cancer. Extensive efforts such as positron emission tomography, magnetic resonance imaging and fluorescence microscopy have been made to specifically image glucose uptake activity but all with technical limitations. Here, we report a new platform to visualize glucose uptake activity in live cells and tissues with subcellular resolution and minimal perturbation. A novel glucose analogue with a small alkyne tag (carbon-carbon triple bond) is developed to mimic natural glucose for cellular uptake, which can be imaged with high sensitivity and specificity by targeting the strong and characteristic alkyne vibration on stimulated Raman scattering (SRS) microscope to generate a quantitative three dimensional concentration map. Cancer cells with differing metabolic characteristics can be distinguished. Heterogeneous uptake patterns are observed in tumor xenograft tissues, neuronal culture and mouse brain tissues with clear cell-cell variations. Therefore, by offering the distinct advantage of optical resolution but without the undesirable influence of bulky fluorophores, our method of coupling SRS with alkyne labeled glucose will be an attractive tool to study energy demands of living systems at the single cell level.

  3. 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.

  4. 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.

  5. The high throughput virtual slit enables compact, inexpensive Raman spectral imagers

    Science.gov (United States)

    Gooding, Edward; Deutsch, Erik R.; Huehnerhoff, Joseph; Hajian, Arsen R.

    2018-02-01

    Raman spectral imaging is increasingly becoming the tool of choice for field-based applications such as threat, narcotics and hazmat detection; air, soil and water quality monitoring; and material ID. Conventional fiber-coupled point source Raman spectrometers effectively interrogate a small sample area and identify bulk samples via spectral library matching. However, these devices are very slow at mapping over macroscopic areas. In addition, the spatial averaging performed by instruments that collect binned spectra, particularly when used in combination with orbital raster scanning, tends to dilute the spectra of trace particles in a mixture. Our design, employing free space line illumination combined with area imaging, reveals both the spectral and spatial content of heterogeneous mixtures. This approach is well suited to applications such as detecting explosives and narcotics trace particle detection in fingerprints. The patented High Throughput Virtual Slit1 is an innovative optical design that enables compact, inexpensive handheld Raman spectral imagers. HTVS-based instruments achieve significantly higher spectral resolution than can be obtained with conventional designs of the same size. Alternatively, they can be used to build instruments with comparable resolution to large spectrometers, but substantially smaller size, weight and unit cost, all while maintaining high sensitivity. When used in combination with laser line imaging, this design eliminates sample photobleaching and unwanted photochemistry while greatly enhancing mapping speed, all with high selectivity and sensitivity. We will present spectral image data and discuss applications that are made possible by low cost HTVS-enabled instruments.

  6. 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.

  7. In Situ Characterization of Ni and Ni/Fe Thin Film Electrodes for Oxygen Evolution in Alkaline Media by a Raman-Coupled Scanning Electrochemical Microscope Setup.

    Science.gov (United States)

    Steimecke, Matthias; Seiffarth, Gerda; Bron, Michael

    2017-10-17

    We present a spectroelectrochemical setup, in which Raman microscopy is combined with scanning electrochemical microscopy (SECM) in order to provide both spectroscopic and electrochemical information on the very same location of an electrode at the same time. The setup is applied to a subject of high academic and practical interest, namely, the oxygen evolution reaction at Ni and Ni/Fe electrodes. It comprises a transparent substrate electrode, onto which Ni and Ni/Fe thin films are deposited. An ultramicroelectrode (UME) is placed closely above the substrate to obtain electrochemical information, while a Raman microscope probes the same sample spot from below. To obtain information on oxygen evolution activity and structural changes, increasingly positive potentials from 0.1 up to 0.7 V vs Hg|HgO|1 M KOH were applied to the Ni/Fe-electrodes in 0.1 M KOH solution. Evolved oxygen is detected by reduction at a Pt UME, allowing for the determination of onset potentials, while the substrate current, which is recorded in parallel, is due to both overlapping oxygen evolution and the oxidation of Ni(OH) 2 to NiOOH. An optimum of 15% Fe in Ni/Fe films with respect to oxygen evolution activity was determined. At the same time, the potential-dependent formation of γ-NiOOH characterized by the Raman double band at 475 and 557 cm -1 allows for the conclusion that a certain amount of disorder introduced by Fe atoms is necessary to obtain high oxygen evolution reaction (OER) activity.

  8. Internalization kinetics and cytoplasmic localization of functionalized diatomite nanoparticles in cancer cells by Raman imaging.

    Science.gov (United States)

    Managò, Stefano; Migliaccio, Nunzia; Terracciano, Monica; Napolitano, Michela; Martucci, Nicola M; De Stefano, Luca; Rendina, Ivo; De Luca, Anna Chiara; Lamberti, Annalisa; Rea, Ilaria

    2018-04-01

    Porous biosilica nanoparticles obtained from diatomites (DNPs) have been recently demonstrated to be non-toxic nanovectors of therapeutic agents in cancer cells. In this work, the internalization kinetics and intracellular spatial distribution of functionalized DNPs incubated with human lung epidermoid carcinoma cell line (H1355) up to 72 hours are investigated by Raman imaging. The label-free Raman results are compared with confocal fluorescence microscopy and photoluminescence (PL) data. Raman bands specifically assigned to DNPs and cellular components provide evidence that the nanovectors are internalized and co-localize with lipid environments. A considerable DNPs uptake in cells is observed within 6 hours, with equilibrium being achieved after 18 hours. The obtained data show the presence of DNPs up to 72 hours, without damage to cell viability or morphology. The PL measurements performed on DNPs not penetrating the cells at different incubation times are strongly correlated with the results obtained by Raman imaging and confocal microscopy analyses. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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.

  10. 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

  11. 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

  12. 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...

  13. 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...

  14. 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...

  15. 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

  16. 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...

  17. 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.

  18. 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...

  19. 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.

  20. Unveiling NIR Aza-Boron-Dipyrromethene (BODIPY) Dyes as Raman Probes: Surface-Enhanced Raman Scattering (SERS)-Guided Selective Detection and Imaging of Human Cancer Cells.

    Science.gov (United States)

    Adarsh, Nagappanpillai; Ramya, Adukkadan N; Maiti, Kaustabh Kumar; Ramaiah, Danaboyina

    2017-10-12

    The development of new Raman reporters has attracted immense attention in diagnostic research based on surface enhanced Raman scattering (SERS) techniques, which is a well established method for ultrasensitive detection through molecular fingerprinting and imaging. Herein, for the first time, we report the unique and efficient Raman active features of the selected aza-BODIPY dyes 1-6. These distinctive attributes could be extended at the molecular level to allow detection through SERS upon adsorption onto nano-roughened gold surface. Among the newly revealed Raman reporters, the amino substituted derivative 4 showed high signal intensity at very low concentrations (ca. 0.4 μm for 4-Au). Interestingly, an efficient nanoprobe has been constructed by using gold nanoparticles as SERS substrate, and 4 as the Raman reporter (4-Au@PEG), which unexpectedly showed efficient recognition of three human cancer cells (lung: A549, cervical: HeLa, Fibrosarcoma: HT-1080) without any specific surface marker. We observed well reflected and resolved Raman mapping and characteristic signature peaks whereas, such recognition was not observed in normal fibroblast (3T3L1) cells. To confirm these findings, a SERS nanoprobe was conjugated with a specific tumour targeting marker, EGFR (Epidermal Growth Factor Receptor), a well known targeted agent for Human Fibrosarcoma (HT1080). This nanoprobe efficiently targeted the surface marker of HT1080 cells, threreby demonstrating its use as an ultrasensitive Raman probe for detection and targeted imaging, leaving normal cells unaffected. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Stress measurements in a magnesium oxide single crystal under constant load using the R-line shifts in a ruby sphere on a Raman microscope

    International Nuclear Information System (INIS)

    Banini, G.K.

    2005-01-01

    Using a Renishaw Raman Microscope and a constructed mechanical apparatus, a novel method for determining the stress in the contact region between a ruby indenter and an MgO crystal under static contact lead is described. The experiment was performed under normal laboratory conditions at the Cavendish Laboratory, University of Cambridge, UK. Manual focusing using the white light on the microscope was made onto the ruby sphere and by replacing the light with a HeNe laser, luminescence frequency in the R-lines of chromium ions at the relaxed (unstressed) positions could be determined. The MgO crystal was then quasi-statically loaded by the ruby sphere, while in the mechanical loading apparatus, and placed on the Renishaw. Manual focusing onto the ruby sphere was made through the MgO and the shift in R-lines from the relaxed positions determined. Literature values of stress coefficients in ruby were used to convert the shifts determined in the R-lines into hydrostatic and non-hydrostatic stresses at precise intervals across the contact region. It was revealed that large stresses hydrostatic occur in the contact region during quasi-static loading and these can be quantified for transparent solids (au)

  6. 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

  7. Faster tissue interface analysis from Raman microscopy images using compressed factorisation

    Science.gov (United States)

    Palmer, Andrew D.; Bannerman, Alistair; Grover, Liam; Styles, Iain B.

    2013-06-01

    The structure of an artificial ligament was examined using Raman microscopy in combination with novel data analysis. Basis approximation and compressed principal component analysis are shown to provide efficient compression of confocal Raman microscopy images, alongside powerful methods for unsupervised analysis. This scheme allows the acceleration of data mining, such as principal component analysis, as they can be performed on the compressed data representation, providing a decrease in the factorisation time of a single image from five minutes to under a second. Using this workflow the interface region between a chemically engineered ligament construct and a bone-mimic anchor was examined. Natural ligament contains a striated interface between the bone and tissue that provides improved mechanical load tolerance, a similar interface was found in the ligament construct.

  8. Imaging phospholipid conformational disorder and packing in giant multilamellar liposome by confocal Raman microspectroscopy

    Science.gov (United States)

    Noothalapati, Hemanth; Iwasaki, Keita; Yoshimoto, Chikako; Yoshikiyo, Keisuke; Nishikawa, Tomoe; Ando, Masahiro; Hamaguchi, Hiro-o.; Yamamoto, Tatsuyuki

    2017-12-01

    Liposomes are closed phospholipid bilayer systems that have profound applications in fundamental cell biology, pharmaceutics and medicine. Depending on the composition (pure or mixture of phospholipids, presence of cholesterol) and preparation protocol, intra- and inter-chain molecular interactions vary leading to changes in the quality (order and packing) of liposomes. So far it is not possible to image conformational disorders and packing densities within a liposome in a straightforward manner. In this study, we utilized confocal Raman microspectroscopy to visualize structural disorders and packing efficiency within a giant multilamellar liposome model by focusing mainly on three regions in the vibrational spectrum (Csbnd C stretching, Csbnd H deformation and Csbnd H stretching). We estimated properties such as trans/gauche isomers and lateral packing probability. Interestingly, our Raman imaging studies revealed gel phase rich domains and heterogeneous lateral packing within the giant multilamellar liposome.

  9. X-ray Photoelectron Spectroscopic and Raman microscopic investigation of the variscite group minerals: Variscite, strengite, scorodite and mansfieldite

    Science.gov (United States)

    Kloprogge, J. Theo; Wood, Barry J.

    2017-10-01

    Several structurally related AsO4 and PO4 minerals, were studied with Raman microscopy and X-ray Photoelectron Spectroscopy (XPS). XPS revealed only Fe, As and O for scorodite. The Fe 2p, As 3d, and O 1s indicated one position for Fe2 +, while 2 different environments for O and As were observed. The O 1s at 530.3 eV and the As 3d 5/2 at 43.7 eV belonged to AsO4, while minor bands for O 1s at 531.3 eV and As 3d 5/2 at 44.8 eV were due to AsO4 groups exposed on the surface possibly forming OH-groups. Mansfieldite showed, besides Al, As and O, a trace of Co. The PO4 equivalent of mansfieldite is variscite. The change in crystal structure replacing As with P resulted in an increase in the binding energy (BE) of the Al 2p by 2.9 eV. The substitution of Fe3 + for Al3 + in the structure of strengite resulted in a Fe 2p at 710.8 eV. An increase in the Fe 2p BE of 4.8 eV was found between mansfieldite and strengite. The scorodite Raman OH-stretching region showed a sharp band at 3513 cm- 1 and a broad band around 3082 cm- 1. The spectrum of mansfieldite was like that of scorodite with a sharp band at 3536 cm- 1 and broader maxima at 3100 cm- 1 and 2888 cm- 1. Substituting Al in the arsenate structure instead of Fe resulted in a shift of the metal-OH-stretching mode by 23 cm- 1 towards higher wavenumbers due to a slightly longer H-bonding in mansfieldite compared to scorodite. The intense band for scorodite at 805 cm- 1 was ascribed to the symmetric stretching mode of the AsO4. The medium intensity bands at 890, 869, and 830 cm- 1 were ascribed to the internal modes. A significant shift towards higher wavenumbers was observed for mansfieldite. The strengite Raman spectrum in the 900-1150 cm- 1 shows a strong band at 981 cm- 1 accompanied by a series of less intense bands. The 981 cm- 1 band was assigned to the PO4 symmetric stretching mode, while the weak band at 1116 cm- 1 was the corresponding antisymmetric stretching mode. The remaining bands at 1009, 1023 and 1035 cm- 1

  10. Raman Hyperspectral Imaging for Detection of Watermelon Seeds Infected with Acidovorax citrulli

    OpenAIRE

    Lee, Hoonsoo; Kim, Moon S.; Qin, Jianwei; Park, Eunsoo; Song, Yu-Rim; Oh, Chang-Sik; Cho, Byoung-Kwan

    2017-01-01

    The bacterial infection of seeds is one of the most important quality factors affecting yield. Conventional detection methods for bacteria-infected seeds, such as biological, serological, and molecular tests, are not feasible since they require expensive equipment, and furthermore, the testing processes are also time-consuming. In this study, we use the Raman hyperspectral imaging technique to distinguish bacteria-infected seeds from healthy seeds as a rapid, accurate, and non-destructive det...

  11. 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.

  12. Development of Raman microspectroscopy for automated detection and imaging of basal cell carcinoma

    Science.gov (United States)

    Larraona-Puy, Marta; Ghita, Adrian; Zoladek, Alina; Perkins, William; Varma, Sandeep; Leach, Iain H.; Koloydenko, Alexey A.; Williams, Hywel; Notingher, Ioan

    2009-09-01

    We investigate the potential of Raman microspectroscopy (RMS) for automated evaluation of excised skin tissue during Mohs micrographic surgery (MMS). The main aim is to develop an automated method for imaging and diagnosis of basal cell carcinoma (BCC) regions. Selected Raman bands responsible for the largest spectral differences between BCC and normal skin regions and linear discriminant analysis (LDA) are used to build a multivariate supervised classification model. The model is based on 329 Raman spectra measured on skin tissue obtained from 20 patients. BCC is discriminated from healthy tissue with 90+/-9% sensitivity and 85+/-9% specificity in a 70% to 30% split cross-validation algorithm. This multivariate model is then applied on tissue sections from new patients to image tumor regions. The RMS images show excellent correlation with the gold standard of histopathology sections, BCC being detected in all positive sections. We demonstrate the potential of RMS as an automated objective method for tumor evaluation during MMS. The replacement of current histopathology during MMS by a ``generalization'' of the proposed technique may improve the feasibility and efficacy of MMS, leading to a wider use according to clinical need.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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)

  19. 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)

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Angiogenesis - a crucial step in breast cancer growth, progression and dissemination by Raman imaging

    Science.gov (United States)

    Kopeć, Monika; Abramczyk, Halina

    2018-06-01

    Combined micro-Raman imaging and AFM imaging are efficient methods for analyzing human tissue due to their high spatial and spectral resolution as well as sensitivity to subtle chemical, structural and topographical changes. The aim of this study was to determine biochemical composition and mechanical topography around blood vessels in the tumor mass of human breast tissue. Significant alterations of the chemical composition and structural architecture around the blood vessel were found compared to the normal breast tissue. A pronounced increase of collagen-fibroblast-glycocalyx network, as well as enhanced lactic acid, and glycogen activity in patients affected by breast cancer were reported.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. Cetuximab-conjugated nanodiamonds drug delivery system for enhanced targeting therapy and 3D Raman imaging.

    Science.gov (United States)

    Li, Dandan; Chen, Xin; Wang, Hong; Liu, Jie; Zheng, Meiling; Fu, Yang; Yu, Yuan; Zhi, Jinfang

    2017-12-01

    In this study, a multicomponent nanodiamonds (NDs)-based targeting drug delivery system, cetuximab-NDs-cisplatin bioconjugate, combining both specific targeting and enhanced therapeutic efficacy capabilities, is developed and characterized. The specific targeting ability of cetuximab-NDs-cisplatin system on human liver hepatocellular carcinoma (HepG2) cells is evaluated through epidermal growth factor receptor (EGFR) blocking experiments, since EGFR is over-expressed on HepG2 cell membrane. Besides, cytotoxic evaluation confirms that cetuximab-NDs-cisplatin system could significantly inhibit the growth of HepG2 cells, and the therapeutic activity of this system is proven to be better than that of both nonspecific NDs-cisplatin conjugate and specific EGF-NDs-cisplatin conjugate. Furthermore, a 3-dimensional (3D) Raman imaging technique is utilized to visualize the targeting efficacy and enhanced internalization of cetuximab-NDs-cisplatin system in HepG2 cells, using the NDs existing in the bioconjugate as Raman probes, based on the characteristic Raman signal of NDs at 1332 cm -1 . These advantageous properties of cetuximab-NDs-cisplatin system propose a prospective imaging and treatment tool for further diagnostic and therapeutic purposes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Coherent Raman scattering microscopy for label-free imaging of live amphioxus

    Science.gov (United States)

    Yu, Zhilong; Chen, Tao; Zhang, Xiannian; Shen, Jie; Chen, Junyuan; Huang, Yanyi

    2012-03-01

    The existence of notochord distinguishes chordates from other phyla. Amphioxus is the only animal that keeps notochord during the whole life. Notochord is a unique organ for amphioxus, with its vertically arranged muscular notochordal plates, which is different from notochords in embryos of other chordates. We use stimulated Raman scattering (SRS) microscopy as a non-invasive technique to image the chemical components in amphioxus notochord. SRS provides chemical specificity as spontaneous Raman does and offers a higher sensitivity for fast acquisition. Unlike coherent anti- Stokes Raman scattering (CARS) microscopy, SRS microscopy doesn't have non-resonant background and can better differentiate different components in the specimen. We verify that the notochord is a protein-rich organ, which agrees well with the result of conventional staining methods. Detailed structures in notochordal plates and notochordal sheath are revealed by SRS microscopy with diffraction limited resolution. Our experiment shows that SRS microscopy is an excellent imaging tool for biochemical research with its intrinsic chemical selectivity, high spatiotemporal resolution and native 3D optical sectioning ability.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Multimodal assessment of SERS nanoparticle biodistribution post ingestion reveals new potential for clinical translation of Raman imaging.

    Science.gov (United States)

    Campbell, Jos L; SoRelle, Elliott D; Ilovich, Ohad; Liba, Orly; James, Michelle L; Qiu, Zhen; Perez, Valerie; Chan, Carmel T; de la Zerda, Adam; Zavaleta, Cristina

    2017-08-01

    Despite extensive research and development, new nano-based diagnostic contrast agents have faced major barriers in gaining regulatory approval due to their potential systemic toxicity and prolonged retention in vital organs. Here we use five independent biodistribution techniques to demonstrate that oral ingestion of one such agent, gold-silica Raman nanoparticles, results in complete clearance with no systemic toxicity in living mice. The oral delivery mimics topical administration to the oral cavity and gastrointestinal (GI) tract as an alternative to intravenous injection. Biodistribution and clearance profiles of orally (OR) vs. intravenously (IV) administered Raman nanoparticles were assayed over the course of 48 h. Mice given either an IV or oral dose of Raman nanoparticles radiolabeled with approximately 100 μCi (3.7MBq) of 64 Cu were imaged with dynamic microPET immediately post nanoparticle administration. Static microPET images were also acquired at 2 h, 5 h, 24 h and 48 h. Mice were sacrificed post imaging and various analyses were performed on the excised organs to determine nanoparticle localization. The results from microPET imaging, gamma counting, Raman imaging, ICP-MS, and hyperspectral imaging of tissue sections all correlated to reveal no evidence of systemic distribution of Raman nanoparticles after oral administration and complete clearance from the GI tract within 24 h. Paired with the unique signals and multiplexing potential of Raman nanoparticles, this approach holds great promise for realizing targeted imaging of tumors and dysplastic tissues within the oral cavity and GI-tract. Moreover, these results suggest a viable path for the first translation of high-sensitivity Raman contrast imaging into clinical practice. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. 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.

  18. 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.

  19. 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.

  20. 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...

  1. 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...

  2. 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 ...

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.)

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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)

  14. Biological image construction by using Raman radiation and Pca: preliminary results

    International Nuclear Information System (INIS)

    Martinez E, J. C.; Cordova F, T.; Hugo R, V.

    2015-10-01

    Full text: In the last years, the Raman spectroscopy (Rs) technique has had some applications in the study and analysis of biological samples, due to it is able to detect concentrations or presence of certain organic and inorganic compounds of medical interest. In this work, raw data were obtained through measurements in selected points on a square regions in order to detect specific organic / inorganic compounds on biological samples. Gold nano stars samples were prepared and coated with membrane markers (CD 10+ and CD 19+) and diluted in leukemic B lymphocytes. Each data block was evaluated independently by the method of principal component analysis (Pca) in order to find representative dimensionless values (Cp) for each Raman spectrum in a specific coordinate. Each Cp was normalized in a range of 0-255 in order to generate a representative image of 8 bits of the region under study. Data acquisition was performed with Raman microscopy system Renishaw in Via in the range of 550 to 1700 cm-1 with a 785 nm laser source, with a power of 17 m W and 15 s of exposure time were used for each spectrum. In preliminary results could detect the presence of molecular markers CD 10+ and CD 19+ with gold nano stars and discrimination between both markers. The results suggest conducting studies with specific concentrations organic and inorganic materials. (Author)

  15. Biological image construction by using Raman radiation and Pca: preliminary results

    Energy Technology Data Exchange (ETDEWEB)

    Martinez E, J. C. [IPN, Unidad Profesional Interdisciplinaria de Ingenieria, Campus Guanajuato, Av. Mineral de Valenciana 200, Col. Fracc. Industrial Puerto Interior, 36275 Silao, Guanajuato (Mexico); Cordova F, T. [Universidad de Guanajuato, DIC, Departamento de Ingenieria Fisica, Loma del Bosque No. 103, Col. Lomas del Campestre, 37150 Leon, Guanajuato (Mexico); Hugo R, V., E-mail: jcmartineze@ipn.mx [Universidad de Guadalajara, Centro Universitario de Tonala, Morelos No. 180, 69584 Tonala, Jalisco (Mexico)

    2015-10-15

    Full text: In the last years, the Raman spectroscopy (Rs) technique has had some applications in the study and analysis of biological samples, due to it is able to detect concentrations or presence of certain organic and inorganic compounds of medical interest. In this work, raw data were obtained through measurements in selected points on a square regions in order to detect specific organic / inorganic compounds on biological samples. Gold nano stars samples were prepared and coated with membrane markers (CD 10+ and CD 19+) and diluted in leukemic B lymphocytes. Each data block was evaluated independently by the method of principal component analysis (Pca) in order to find representative dimensionless values (Cp) for each Raman spectrum in a specific coordinate. Each Cp was normalized in a range of 0-255 in order to generate a representative image of 8 bits of the region under study. Data acquisition was performed with Raman microscopy system Renishaw in Via in the range of 550 to 1700 cm-1 with a 785 nm laser source, with a power of 17 m W and 15 s of exposure time were used for each spectrum. In preliminary results could detect the presence of molecular markers CD 10+ and CD 19+ with gold nano stars and discrimination between both markers. The results suggest conducting studies with specific concentrations organic and inorganic materials. (Author)

  16. 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.

  17. 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.

  18. Surface-Enhanced Raman Scattering Nanoparticles as Optical Labels for Imaging Cell Surface Proteins

    Science.gov (United States)

    MacLaughlin, Christina M.

    Assaying the expression of cell surface proteins has widespread application for characterizing cell type, developmental stage, and monitoring disease transformation. Immunophenotyping is conducted by treating cells with labelled targeting moieties that have high affinity for relevant surface protein(s). The sensitivity and specificity of immunophenotyping is defined by the choice of contrast agent and therefore, the number of resolvable signals that can be used to simultaneously label cells. Narrow band width surface-enhanced Raman scattering (SERS) nanoparticles are proposed as optical labels for multiplexed immunophenotying. Two types of surface coatings were investigated to passivate the gold nanoparticles, incorporate SERS functionality, and to facilitate attachment of targeting antibodies. Thiolated poly(ethylene glycol) forms dative bonds with the gold surface and is compatible with multiple physisorbed Raman-active reporter molecules. Ternary lipid bilayers are used to encapsulate the gold nanoparticles particles, and incorporate three different classes of Raman reporters. TEM, UV-Visible absorbance spectroscopy, DLS, and electrophoretic light scattering were used characterize the particle coating. Colourimetric protein assay, and secondary antibody labelling were used to quantify the antibody conjugation. Three different in vitromodels were used to investigate the binding efficacy and specificity of SERS labels for their biomarker targets. Primary human CLL cells, LY10 B lymphoma, and A549 adenocarcinoma lines were targeted. Dark field imaging was used to visualize the colocalization of SERS labels with cells, and evidence of receptor clustering was obtained based on colour shifts of the particles' Rayleigh scattering. Widefield, and spatially-resolved Raman spectra were used to detect labels singly, and in combination from labelled cells. Fluorescence flow cytometry was used to test the particles' binding specificity, and SERS from labelled cells was also

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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."

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Vibrational imaging of newly synthesized proteins in live cells by stimulated Raman scattering microscopy

    Science.gov (United States)

    Wei, Lu; Yu, Yong; Shen, Yihui; Wang, Meng C.; Min, Wei

    2013-01-01

    Synthesis of new proteins, a key step in the central dogma of molecular biology, has been a major biological process by which cells respond rapidly to environmental cues in both physiological and pathological conditions. However, the selective visualization of a newly synthesized proteome in living systems with subcellular resolution has proven to be rather challenging, despite the extensive efforts along the lines of fluorescence staining, autoradiography, and mass spectrometry. Herein, we report an imaging technique to visualize nascent proteins by harnessing the emerging stimulated Raman scattering (SRS) microscopy coupled with metabolic incorporation of deuterium-labeled amino acids. As a first demonstration, we imaged newly synthesized proteins in live mammalian cells with high spatial–temporal resolution without fixation or staining. Subcellular compartments with fast protein turnover in HeLa and HEK293T cells, and newly grown neurites in differentiating neuron-like N2A cells, are clearly identified via this imaging technique. Technically, incorporation of deuterium-labeled amino acids is minimally perturbative to live cells, whereas SRS imaging of exogenous carbon–deuterium bonds (C–D) in the cell-silent Raman region is highly sensitive, specific, and compatible with living systems. Moreover, coupled with label-free SRS imaging of the total proteome, our method can readily generate spatial maps of the quantitative ratio between new and total proteomes. Thus, this technique of nonlinear vibrational imaging of stable isotope incorporation will be a valuable tool to advance our understanding of the complex spatial and temporal dynamics of newly synthesized proteome in vivo. PMID:23798434

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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)

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. Implementation of stimulated Raman scattering microscopy for single cell analysis

    Science.gov (United States)

    D'Arco, Annalisa; Ferrara, Maria Antonietta; Indolfi, Maurizio; Tufano, Vitaliano; Sirleto, Luigi

    2017-05-01

    In this work, we present successfully realization of a nonlinear microscope, not purchasable in commerce, based on stimulated Raman scattering. It is obtained by the integration of a femtosecond SRS spectroscopic setup with an inverted research microscope equipped with a scanning unit. Taking account of strength of vibrational contrast of SRS, it provides label-free imaging of single cell analysis. Validation tests on images of polystyrene beads are reported to demonstrate the feasibility of the approach. In order to test the microscope on biological structures, we report and discuss the label-free images of lipid droplets inside fixed adipocyte cells.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Vibrational imaging and microspectroscopies based on coherent anti-Stokes Raman scattering microscopy

    International Nuclear Information System (INIS)

    Volkmer, Andreas

    2005-01-01

    For noninvasive characterization of chemical species or biological components within a complex heterogeneous system, their intrinsic molecular vibrational properties can be used in contrast mechanisms in optical microscopy. A series of recent advances have made coherent anti-Stokes Raman scattering (CARS) microscopy a powerful technique that allows vibrational imaging with high sensitivity, high spectral resolution and three-dimensional sectioning capability. In this review, we discuss theoretical and experimental aspects of CARS microscopy in a collinear excitation beam geometry. Particular attention is given to the underlying physical principles behind the new features of CARS signal generation under tight focusing conditions. We provide a brief overview of the instrumentation of CARS microscopy and its experimental characterization by means of imaging of model systems and live unstained cells. CARS microscopy offers the possibility of spatially resolved vibrational spectroscopy, providing chemical and physical structure information of molecular specimens on the sub-micrometre length scale. We review multiplex CARS microspectroscopy allowing fast acquisition of frequency-resolved CARS spectra, time-resolved CARS microspectroscopy recording ultrafast Raman free induction decays and CARS correlation spectroscopy probing dynamical processes with chemical selectivity. (topical review)

  13. 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.

  14. 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)].

  15. 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.

  16. Visualization and Non-Destructive Quantification of Inkjet-Printed Pharmaceuticals on Different Substrates Using Raman Spectroscopy and Raman Chemical Imaging

    DEFF Research Database (Denmark)

    Edinger, Magnus; Bar-Shalom, Daniel; Rantanen, Jukka

    2017-01-01

    and ethanol was developed. Inkjet printing technology was used to apply haloperidol ink onto three different substrates. Custom-made inorganic compacts and dry foam, as well as marketed paracetamol tablets were used as the substrates. RESULTS: Therapeutic personalized doses were printed by using one to ten...... printing rounds on the substrates. The haloperidol content in the finished dosage forms were determined by high-performance liquid chromatography (HPLC). The distribution of the haloperidol on the dosage forms were visualized using Raman chemical imaging combined with principal components analysis (PCA...... prediction was observed for the paracetamol tablets. It was not possible to quantify haloperidol on the dry foam due to the low and varying density of the substrate. CONCLUSIONS: Raman spectroscopy is a useful tool for visualization and quality control of inkjet printed personalized medicine....

  17. 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

  18. 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....

  19. Note: A portable Raman analyzer for microfluidic chips based on a dichroic beam splitter for integration of imaging and signal collection light paths

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Yijia; Xu, Shuping; Xu, Weiqing, E-mail: xuwq@jlu.edu.cn [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); Chen, Lei [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); College of Physics, Jilin University, Changchun 130012 (China); Chen, Gang [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); College of Chemistry, Jilin University, Changchun 130012 (China); Bi, Wenbin [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun 130022 (China); Cui, Haining [College of Physics, Jilin University, Changchun 130012 (China)

    2015-05-15

    An integrated and portable Raman analyzer featuring an inverted probe fixed on a motor-driving adjustable optical module was designed for the combination of a microfluidic system. It possesses a micro-imaging function. The inverted configuration is advantageous to locate and focus microfluidic channels. Different from commercial micro-imaging Raman spectrometers using manual switchable light path, this analyzer adopts a dichroic beam splitter for both imaging and signal collection light paths, which avoids movable parts and improves the integration and stability of optics. Combined with surface-enhanced Raman scattering technique, this portable Raman micro-analyzer is promising as a powerful tool for microfluidic analytics.

  20. Real-time biochemical sensor based on Raman scattering with CMOS contact imaging.

    Science.gov (United States)

    Muyun Cao; Yuhua Li; Yadid-Pecht, Orly

    2015-08-01

    This work presents a biochemical sensor based on Raman scattering with Complementary metal-oxide-semiconductor (CMOS) contact imaging. This biochemical optical sensor is designed for detecting the concentration of solutions. The system is built with a laser diode, an optical filter, a sample holder and a commercial CMOS sensor. The output of the system is analyzed by an image processing program. The system provides instant measurements with a resolution of 0.2 to 0.4 Mol. This low cost and easy-operated small scale system is useful in chemical, biomedical and environmental labs for quantitative bio-chemical concentration detection with results reported comparable to a highly cost commercial spectrometer.

  1. 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.

  2. 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.

  3. 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.

  4. Simultaneous UV Imaging and Raman Spectroscopy for the Measurement of Solvent-Mediated Phase Transformations During Dissolution Testing

    DEFF Research Database (Denmark)

    Ostergaard, Jesper; Wu, Jian; Naelapää, Kaisa

    2014-01-01

    The current work reports the simultaneous use of UV imaging and Raman spectroscopy for detailed characterization of drug dissolution behavior including solid-state phase transformations during dissolution. The dissolution of drug substances from compacts of sodium naproxen in 0.1 HCl as well as t...... of UV imaging and Raman spectroscopy offers a detailed characterization of drug dissolution behavior in a time-effective and sample-sparing manner. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 103:1149-1156, 2014....

  5. Coherent anti-stokes Raman scattering (CARS) microscopy: a novel technique for imaging the retina.

    Science.gov (United States)

    Masihzadeh, Omid; Ammar, David A; Kahook, Malik Y; Lei, Tim C

    2013-05-01

    To image the cellular and noncellular structures of the retina in an intact mouse eye without the application of exogenous fluorescent labels using noninvasive, nondestructive techniques. Freshly enucleated mouse eyes were imaged using two nonlinear optical techniques: coherent anti-Stokes Raman scattering (CARS) and two-photon autofluorescence (TPAF). Cross sectional transverse sections and sequential flat (en face) sagittal sections were collected from a region of sclera approximately midway between the limbus and optic nerve. Imaging proceeded from the surface of the sclera to a depth of ∼60 μm. The fluorescent signal from collagen fibers within the sclera was evident in the TPAF channel; the scleral collagen fibers showed no organization and appeared randomly packed. The sclera contained regions lacking TPAF and CARS fluorescence of ∼3 to 15 μm in diameter that could represent small vessels or scleral fibroblasts. Intense punctate CARS signals from the retinal pigment epithelial layer were of a size and shape of retinyl storage esters. Rod outer segments could be identified by the CARS signal from their lipid-rich plasma membranes. CARS microscopy can be used to image the outer regions of the mammalian retina without the use of a fluorescent dye or exogenously expressed recombinant protein. With technical advancements, CARS/TPAF may represent a new avenue for noninvasively imaging the retina and might complement modalities currently used in clinical practice.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Aggregation of gold nanoparticles followed by methotrexate release enables Raman imaging of drug delivery into cancer cells

    International Nuclear Information System (INIS)

    Durgadas, C. V.; Sharma, C. P.; Paul, W.; Rekha, M. R.; Sreenivasan, K.

    2012-01-01

    This study refers an aqueous synthesis of methotrexate (MTX)-conjugated gold nanoparticles (GNPs), their interaction with HepG2 cells, and the use of Raman imaging to observe cellular internalization and drug delivery. GNPs of average size 3.5–5 nm were stabilized using the amine terminated bifunctional biocompatible copolymer and amended by conjugating MTX, an anticancer drug. The nanoparticles were released MTX at a faster rate in acidic pH and subsequently found to form aggregates. The Raman signals of cellular components were found to be enhanced by the aggregated particles enabling the mapping to visualize site-specific drug delivery. The methodology seems to have potential in optimizing the characteristics of nanodrug carriers for emptying the cargo precisely at specified sites.Graphical AbstractDrug release induced particle aggregation enhances Raman signals to aid in imaging.

  17. Development and characterization of a handheld hyperspectral Raman imaging probe system for molecular characterization of tissue on mesoscopic scales.

    Science.gov (United States)

    St-Arnaud, Karl; Aubertin, Kelly; Strupler, Mathias; Madore, Wendy-Julie; Grosset, Andrée-Anne; Petrecca, Kevin; Trudel, Dominique; Leblond, Frédéric

    2018-01-01

    Raman spectroscopy is a promising cancer detection technique for surgical guidance applications. It can provide quantitative information relating to global tissue properties associated with structural, metabolic, immunological, and genetic biochemical phenomena in terms of molecular species including amino acids, lipids, proteins, and nucleic acid (DNA). To date in vivo Raman spectroscopy systems mostly included probes and biopsy needles typically limited to single-point tissue interrogation over a scale between 100 and 500 microns. The development of wider field handheld systems could improve tumor localization for a range of open surgery applications including brain, ovarian, and skin cancers. Here we present a novel Raman spectroscopy implementation using a coherent imaging bundle of fibers to create a probe capable of reconstructing molecular images over mesoscopic fields of view. Detection is performed using linear scanning with a rotation mirror and an imaging spectrometer. Different slits widths were tested at the entrance of the spectrometer to optimize spatial and spectral resolution while preserving sufficient signal-to-noise ratios to detect the principal Raman tissue features. The nonbiological samples, calcite and polytetrafluoroethylene (PTFE), were used to characterize the performance of the system. The new wide-field probe was tested on ex vivo samples of calf brain and swine tissue. Raman spectral content of both tissue types were validated with data from the literature and compared with data acquired with a single-point Raman spectroscopy probe. The single-point probe was used as the gold standard against which the new instrument was benchmarked as it has already been thoroughly validated for biological tissue characterization. We have developed and characterized a practical noncontact handheld Raman imager providing tissue information at a spatial resolution of 115 microns over a field of view >14 mm 2 and a spectral resolution of 6 cm -1 over

  18. Transmission electron microscopy and Raman characterization of copper (I) oxide microspheres composed of nanoparticles

    International Nuclear Information System (INIS)

    Wang Wenzhong; Tu Ya; Wang Lijuan; Liang Yujie; Shi Honglong

    2013-01-01

    Highlights: ► Raman spectroscopy of copper (I) oxide microspheres were investigated. ► Infrared active mode is greatly activated in Raman scattering spectrum. ► Infrared active mode shows up in Raman spectrum of copper (I) oxide microspheres. ► The defects existed in spheres could be responsible for the observed Raman property. - Abstract: The high-resolution transmission electron microscope and Raman spectroscopy were used to investigate the microstructures and Raman scattering property of copper (I) oxide microspheres composed of nanoparticles. High-resolution transmission electron microscope images indicate that the copper (I) oxide microspheres are composed of nanoparticles with random growth direction, indicating that there are many defects in microspheres. The Raman spectrum shows that infrared active mode, which must be odd parity and is Raman forbidden for bulk crystal due to its inversion symmetry, is activated and shows up in Raman scattering spectrum. On the basis of investigations of the microstructure features of copper (I) oxide microspheres, we attribute the appearance of IR active mode in Raman scattering spectrum to the breakdown of the symmetry of the lattice due to the presence of defects in the prepared copper (I) oxide microspheres as observed in HRTEM images.

  19. 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)

  20. Design and technical evaluation of fibre-coupled Raman probes for the image-guided discrimination of cancerous skin

    International Nuclear Information System (INIS)

    Schleusener, J; Reble, C; Helfmann, J; Gersonde, I; Cappius, H-J; Glanert, M; Fluhr, J W; Meinke, M C

    2014-01-01

    Two different designs for fibre-coupled Raman probes are presented that are optimized for discriminating cancerous and normal skin by achieving high epithelial sensitivity to detect a major component of the Raman signal from the depth range of the epithelium. This is achieved by optimizing Raman spot diameters to the range of ≈200 µm, which distinguishes this approach from the common applications of either Raman microspectroscopy (1–5 µm) or measurements on larger sampling volume using spot sizes of a few mm. Video imaging with a depicted area in the order of a few cm, to allow comparing Raman measurements to the location of the histo-pathologic findings, is integrated in both designs. This is important due to the inhomogeneity of cancerous lesions. Video image acquisition is achieved using white light LED illumination, which avoids ambient light artefacts. The design requirements focus either on a compact light-weight configuration, for pen-like handling, or on a video-visible measurement spot to enable increased positioning accuracy. Both probes are evaluated with regard to spot size, Rayleigh suppression, background fluorescence, depth sensitivity, clinical handling and ambient light suppression. Ex vivo measurements on porcine ear skin correlates well with findings of other groups. (paper)

  1. 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.

  2. 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

  3. Surface-enhanced Raman imaging of cell membrane by a highly homogeneous and isotropic silver nanostructure

    Science.gov (United States)

    Zito, Gianluigi; Rusciano, Giulia; Pesce, Giuseppe; Dochshanov, Alden; Sasso, Antonio

    2015-04-01

    Label-free chemical imaging of live cell membranes can shed light on the molecular basis of cell membrane functionalities and their alterations under membrane-related diseases. In principle, this can be done by surface-enhanced Raman scattering (SERS) in confocal microscopy, but requires engineering plasmonic architectures with a spatially invariant SERS enhancement factor G(x, y) = G. To this end, we exploit a self-assembled isotropic nanostructure with characteristics of homogeneity typical of the so-called near-hyperuniform disorder. The resulting highly dense, homogeneous and isotropic random pattern consists of clusters of silver nanoparticles with limited size dispersion. This nanostructure brings together several advantages: very large hot spot density (~104 μm-2), superior spatial reproducibility (SD nanotoxicity issues. See DOI: 10.1039/c5nr01341k

  4. Imaging chemical interfaces perpendicular to the optical axis with focus-engineered coherent anti-Stokes Raman scattering microscopy

    International Nuclear Information System (INIS)

    Krishnamachari, Vishnu Vardhan; Potma, Eric Olaf

    2007-01-01

    In vibrational microscopy, it is often necessary to distinguish between chemically distinct microscopic objects and to highlight the 'chemical interfaces' present in the sample under investigation. Here we apply the concept of focus engineering to enhance the sensitivity of coherent anti-Stokes Raman scattering (CARS) microscopy to these interfaces. Based on detailed numerical simulations, we show that using a focused Stokes field with a sharp phase jump along the longitudinal direction leads to the suppression of the signal from bulk regions and improves the signal contrast from vibrational resonant interfaces oriented perpendicular to the axis of beam propagation. We also demonstrate that the CARS spectral response from chemical interfaces exhibits a clean, Raman-like band-shape with such a phase-shaped excitation. This phenomenon of interface highlighting is a consequence of the coherent nature of CARS signal generation and it involves a complex interplay of the spectral phase of the sample and the spatial phase of the excitation fields

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Detection of explosives on the surface of banknotes by Raman hyperspectral imaging and independent component analysis.

    Science.gov (United States)

    Almeida, Mariana R; Correa, Deleon N; Zacca, Jorge J; Logrado, Lucio Paulo Lima; Poppi, Ronei J

    2015-02-20

    The aim of this study was to develop a methodology using Raman hyperspectral imaging and chemometric methods for identification of pre- and post-blast explosive residues on banknote surfaces. The explosives studied were of military, commercial and propellant uses. After the acquisition of the hyperspectral imaging, independent component analysis (ICA) was applied to extract the pure spectra and the distribution of the corresponding image constituents. The performance of the methodology was evaluated by the explained variance and the lack of fit of the models, by comparing the ICA recovered spectra with the reference spectra using correlation coefficients and by the presence of rotational ambiguity in the ICA solutions. The methodology was applied to forensic samples to solve an automated teller machine explosion case. Independent component analysis proved to be a suitable method of resolving curves, achieving equivalent performance with the multivariate curve resolution with alternating least squares (MCR-ALS) method. At low concentrations, MCR-ALS presents some limitations, as it did not provide the correct solution. The detection limit of the methodology presented in this study was 50 μg cm(-2). Copyright © 2014 Elsevier B.V. All rights reserved.

  13. 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)

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  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. 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. Real-time molecular imaging throughout the entire cell cycle by targeted plasmonic-enhanced Rayleigh/Raman spectroscopy.

    Science.gov (United States)

    Kang, Bin; Austin, Lauren A; El-Sayed, Mostafa A

    2012-10-10

    Due to their strong enhancement of scattered light, plasmonic nanoparticles have been utilized for various biological and medical applications. Here, we describe a new technique, Targeted Plasmonic-Enhanced Single-Cell Rayleigh/Raman Spectroscopy, to monitor the molecular changes of any cell-component, such as the nucleus, during the different phases of its full cell cycle by simultaneously recording its Rayleigh images and Raman vibration spectra in real-time. The analysis of the observed Raman DNA and protein peaks allowed the different phases of the cell cycle to be identified. This technique could be used for disease diagnostics and potentially improve our understanding of the molecular mechanisms of cellular functions such as division, death, signaling, and drug action.

  11. 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.

  12. 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...

  13. 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.

  14. Raman spectra of long chain hydrocarbons: anharmonic calculations, experiment and implications for imaging of biomembranes.

    Science.gov (United States)

    Šebek, Jiří; Pele, Liat; Potma, Eric O; Gerber, R Benny

    2011-07-28

    First-principles anharmonic vibrational calculations are carried out for the Raman spectrum of the C-H stretching bands in dodecane, and for the C-D bands in the deuterated molecule. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with liquid-state experiments, after smoothing the isolated-molecule sharp-line computed spectra. Very good agreement between the computed and experimental results is found for the two systems. The combined theoretical and experimental results provide insights into the spectrum, elucidating the roles of symmetric and asymmetric CH(3) and CH(2) hydrogenic stretches. This is expected to be very useful for the interpretation of spectra of long-chain hydrocarbons. The results show that anharmonic effects on the spectrum are large. On the other hand, vibrational degeneracy effects seem to be rather modest at the resolution of the experiments. The degeneracy effects may have more pronounced manifestations in higher-resolution experiments. The results show that first-principles anharmonic vibrational calculations for hydrocarbons are feasible, in good agreement with experiment, opening the way for applications to many similar systems. The results may be useful for the analysis of CARS imaging of lipids, for which dodecane is a representative molecule. It is suggested that first-principles vibrational calculations may be useful also for CARS imaging of other systems. This journal is © the Owner Societies 2011

  15. 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

  16. 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.

  17. 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).

  18. 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

  19. In situ oxidation state profiling of nickel hexacyanoferrate derivatized electrodes using line-imaging Raman spectroscopy and multivariate calibration

    International Nuclear Information System (INIS)

    Haight, S.M.; Schwartz, D.T.

    1999-01-01

    Metal hexacyanoferrate compounds show promise as electrochemically switchable ion exchange materials for use in the cleanup of radioactive wastes such as those found in storage basins and underground tanks at the Department of Energy's Hanford Nuclear Reservation. Reported is the use of line-imaging Raman spectroscopy for the in situ determination of oxidation state profiles in nickel hexacyanoferrate derivatized electrodes under potential control in an electrochemical cell. Line-imaging Raman spectroscopy is used to collect 256 contiguous Raman spectra every ∼5 microm from thin films (ca. 80 nm) formed by electrochemical derivatization of nickel electrodes. The cyanide stretching region of the Raman spectrum of the film is shown to be sensitive to iron oxidation state and is modeled by both univariate and multivariate correlations. Although both correlations fit the calibration set well, the multivariate (principle component regression or PCR) model's predictions of oxidation state are less sensitive to noise in the spectrum, yielding a much smoother oxidation state profile than the univariate model. Oxidation state profiles with spatial resolution of approximately 5 microm are shown for a nickel hexacyanoferrate derivatized electrode in reduced, intermediate, and oxidized states. In situ oxidation state profiles indicate that the 647.1 nm laser illumination photo-oxidizes the derivatized electrodes. This observation is confirmed using photoelectrochemical methods

  20. 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.

  1. 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.

  2. Raman imaging to investigate ultrastructure and composition of plant cell walls : distribution of lignin and cellulose in black spruce wood (Picea mariana)

    Science.gov (United States)

    Umesh P. Agarwal

    2006-01-01

    A detailed understanding of the structural organization of the cell wall of vascular plants is important from both the perspectives of plant biology and chemistry and of commercial utilization. A state-of-the-art 633-nm laser-based confocal Raman microscope was used to determine the distribution of cell wall components in the cross section of black spruce wood in situ...

  3. Penetration of silver nanoparticles into porcine skin ex vivo using fluorescence lifetime imaging microscopy, Raman microscopy, and surface-enhanced Raman scattering microscopy.

    Science.gov (United States)

    Zhu, Yongjian; Choe, Chun-Sik; Ahlberg, Sebastian; Meinke, Martina C; Alexiev, Ulrike; Lademann, Juergen; Darvin, Maxim E

    2015-05-01

    In order to investigate the penetration depth of silver nanoparticles (Ag NPs) inside the skin, porcine ears treated with Ag NPs are measured by two-photon tomography with a fluorescence lifetime imaging microscopy (TPT-FLIM) technique, confocal Raman microscopy (CRM), and surface-enhanced Raman scattering (SERS) microscopy. Ag NPs are coated with poly-N-vinylpyrrolidone and dispersed in pure water solutions. After the application of Ag NPs, porcine ears are stored in the incubator for 24 h at a temperature of 37°C. The TPT-FLIM measurement results show a dramatic decrease of the Ag NPs' signal intensity from the skin surface to a depth of 4 μm. Below 4 μm, the Ag NPs' signal continues to decline, having completely disappeared at 12 to 14 μm depth. CRM shows that the penetration depth of Ag NPs is 11.1 ± 2.1 μm. The penetration depth measured with a highly sensitive SERS microscopy reaches 15.6 ± 8.3 μm. Several results obtained with SERS show that the penetration depth of Ag NPs can exceed the stratum corneum (SC) thickness, which can be explained by both penetration of trace amounts of Ag NPs through the SC barrier and by the measurements inside the hair follicle, which cannot be excluded in the experiment.

  4. Raman microscopy of individual living human embryonic stem cells

    Science.gov (United States)

    Novikov, S. M.; Beermann, J.; Bozhevolnyi, S. I.; Harkness, L. M.; Kassem, M.

    2010-04-01

    We demonstrate the possibility of mapping the distribution of different biomolecules in living human embryonic stem cells grown on glass substrates, without the need for fluorescent markers. In our work we improve the quality of measurements by finding a buffer that gives low fluorescence, growing cells on glass substrates (whose Raman signals are relatively weak compared to that of the cells) and having the backside covered with gold to improve the image contrast under direct white light illumination. The experimental setup used for Raman microscopy is the commercially available confocal scanning Raman microscope (Alpha300R) from Witec and sub-μm spatially resolved Raman images were obtained using a 532 nm excitation wavelength.

  5. Polarization Sensitive Coherent Raman Measurements of DCVJ

    Science.gov (United States)

    Anderson, Josiah; Cooper, Nathan; Lawhead, Carlos; Shiver, Tegan; Ujj, Laszlo

    2014-03-01

    Coherent Raman spectroscopy which recently developed into coherent Raman microscopy has been used to produce label free imaging of thin layers of material and find the spatial distributions of certain chemicals within samples, e.g. cancer cells.(1) Not all aspects of coherent scattering have been used for imaging. Among those for example are special polarization sensitive measurements. Therefore we have investigated the properties of polarization sensitive CARS spectra of a highly fluorescent molecule, DCVJ.(2) Spectra has been recorded by using parallel polarized and perpendicular polarized excitations. A special polarization arrangement was developed to suppress the non-resonant background scattering from the sample. These results can be used to improve the imaging properties of a coherent Raman microscope in the future. This is the first time coherent Raman polarization sensitive measurements have been used to characterize the vibrational modes of DCVJ. 1: K. I. Gutkowski, et al., ``Fluorescence of dicyanovinyl julolidine in a room temperature ionic liquid '' Chemical Physics Letters 426 (2006) 329 - 333 2: Fouad El-Diasty, ``Coherent anti-Stokes Raman scattering: Spectroscopy and microscopy'' Vibrational Spectroscopy 55 (2011) 1-37

  6. Combining deep learning and coherent anti-Stokes Raman scattering imaging for automated differential diagnosis of lung cancer

    Science.gov (United States)

    Weng, Sheng; Xu, Xiaoyun; Li, Jiasong; Wong, Stephen T. C.

    2017-10-01

    Lung cancer is the most prevalent type of cancer and the leading cause of cancer-related deaths worldwide. Coherent anti-Stokes Raman scattering (CARS) is capable of providing cellular-level images and resolving pathologically related features on human lung tissues. However, conventional means of analyzing CARS images requires extensive image processing, feature engineering, and human intervention. This study demonstrates the feasibility of applying a deep learning algorithm to automatically differentiate normal and cancerous lung tissue images acquired by CARS. We leverage the features learned by pretrained deep neural networks and retrain the model using CARS images as the input. We achieve 89.2% accuracy in classifying normal, small-cell carcinoma, adenocarcinoma, and squamous cell carcinoma lung images. This computational method is a step toward on-the-spot diagnosis of lung cancer and can be further strengthened by the efforts aimed at miniaturizing the CARS technique for fiber-based microendoscopic imaging.

  7. 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)

  8. Multiplex coherent anti-Stokes Raman scattering microspectroscopy of brain tissue with higher ranking data classification for biomedical imaging

    Science.gov (United States)

    Pohling, Christoph; Bocklitz, Thomas; Duarte, Alex S.; Emmanuello, Cinzia; Ishikawa, Mariana S.; Dietzeck, Benjamin; Buckup, Tiago; Uckermann, Ortrud; Schackert, Gabriele; Kirsch, Matthias; Schmitt, Michael; Popp, Jürgen; Motzkus, Marcus

    2017-06-01

    Multiplex coherent anti-Stokes Raman scattering (MCARS) microscopy was carried out to map a solid tumor in mouse brain tissue. The border between normal and tumor tissue was visualized using support vector machines (SVM) as a higher ranking type of data classification. Training data were collected separately in both tissue types, and the image contrast is based on class affiliation of the single spectra. Color coding in the image generated by SVM is then related to pathological information instead of single spectral intensities or spectral differences within the data set. The results show good agreement with the H&E stained reference and spontaneous Raman microscopy, proving the validity of the MCARS approach in combination with SVM.

  9. 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.

  10. Intracellular imaging of docosanol in living cells by coherent anti-Stokes Raman scattering microscopy

    Science.gov (United States)

    You, Sixian; Liu, Yuan; Arp, Zane; Zhao, Youbo; Chaney, Eric J.; Marjanovic, Marina; Boppart, Stephen A.

    2017-07-01

    Docosanol is an over-the-counter topical agent that has proved to be one of the most effective therapies for treating herpes simplex labialis. However, the mechanism by which docosanol suppresses lesion formation remains poorly understood. To elucidate its mechanism of action, we investigated the uptake of docosanol in living cells using coherent anti-Stokes Raman scattering microscopy. Based on direct visualization of the deuterated docosanol, we observed highly concentrated docosanol inside living cells 24 h after drug treatment. In addition, different spatial patterns of drug accumulation were observed in different cell lines. In keratinocytes, which are the targeted cells of docosanol, the drug molecules appeared to be docking at the periphery of the cell membrane. In contrast, the drug molecules in fibroblasts appeared to accumulate in densely packed punctate regions throughout the cytoplasm. These results suggest that this molecular imaging approach is suitable for the longitudinal tracking of drug molecules in living cells to identify cell-specific trafficking and may also have implications for elucidating the mechanism by which docosanol suppresses lesion formation.

  11. Raman spectroscopy imaging reveals interplay between atherosclerosis and medial calcification in the human aorta

    Science.gov (United States)

    You, Amanda Y. F.; Bergholt, Mads S.; St-Pierre, Jean-Philippe; Kit-Anan, Worrapong; Pence, Isaac J.; Chester, Adrian H.; Yacoub, Magdi H.; Bertazzo, Sergio; Stevens, Molly M.

    2017-01-01

    Medial calcification in the human aorta accumulates during aging and is known to be aggravated in several diseases. Atherosclerosis, another major cause of cardiovascular calcification, shares some common aggravators. However, the mechanisms of cardiovascular calcification remain poorly understood. To elucidate the relationship between medial aortic calcification and atherosclerosis, we characterized the cross-sectional distributions of the predominant minerals in aortic tissue, apatite and whitlockite, and the associated extracellular matrix. We also compared the cellular changes between atherosclerotic and nonatherosclerotic human aortic tissues. This was achieved through the development of Raman spectroscopy imaging methods that adapted algorithms to distinguish between the major biomolecules present within these tissues. We present a relationship between apatite, cholesterol, and triglyceride in atherosclerosis, with the relative amount of all molecules concurrently increased in the atherosclerotic plaque. Further, the increase in apatite was disproportionately large in relation to whitlockite in the aortic media directly underlying a plaque, indicating that apatite is more pathologically significant in atherosclerosis-aggravated medial calcification. We also discovered a reduction of β-carotene in the whole aortic intima, including a plaque in atherosclerotic aortic tissues compared to nonatherosclerotic tissues. This unprecedented biomolecular characterization of the aortic tissue furthers our understanding of pathological and physiological cardiovascular calcification events in humans. PMID:29226241

  12. Surface enhanced Raman scattering imaging of developed thin-layer chromatography plates.

    Science.gov (United States)

    Freye, Chris E; Crane, Nichole A; Kirchner, Teresa B; Sepaniak, Michael J

    2013-04-16

    A method for hyphenating surface enhanced Raman scattering (SERS) and thin-layer chromatography (TLC) is presented that employs silver-polymer nanocomposites as an interface. Through the process of conformal blotting, analytes are transferred from TLC plates to nanocomposite films before being imaged via SERS. A procedure leading to maximum blotting efficiency was established by investigating various parameters such as time, pressure, and type and amount of blotting solvent. Additionally, limits of detection were established for test analytes malachite green isothiocyanate, 4-aminothiophenol, and Rhodamine 6G (Rh6G) ranging from 10(-7) to 10(-6) M. Band broadening due to blotting was minimal (∼10%) as examined by comparing the spatial extent of TLC-spotted Rh6G via fluorescence and then the SERS-based spot size on the nanocomposite after the blotting process. Finally, a separation of the test analytes was carried out on a TLC plate followed by blotting and the acquisition of distance × wavenumber × intensity three-dimensional TLC-SERS plots.

  13. Coherent Raman Imaging of Live Muscle Sarcomeres Assisted by SFG Microscopy.

    Science.gov (United States)

    Kim, Hyunmin; Kim, Do-Young; Joo, Kyung-Il; Kim, Jung-Hye; Jeong, Soon Moon; Lee, Eun Seong; Hahm, Jeong-Hoon; Kim, Kyuhyung; Moon, Dae Woon

    2017-08-23

    In this study, we used spectrally focused coherent anti-Stokes Raman scattering (spCARS) microscopy assisted by sum-frequency generation (SFG) to monitor the variations in the structural morphology and molecular vibrations of a live muscle of Caenorhabditis elegans. The subunits of the muscle sarcomeres, such as the M-line, myosin, dense body, and α-actinin, were alternatively observed using spCARS microscopy for different sample orientations, with the guidance of a myosin positional marker captured by SFG microscopy. Interestingly enough, the beam polarization dependence of the spCARS contrasts for two parallel subunits (dense body and myosin) showed a ~90° phase difference. The chemically sensitive spCARS spectra induced by the time-varying overlap of two pulses allowed (after a robust subtraction of the non-resonant background using a modified Kramers-Krönig transformation method) high-fidelity detection of various genetically modified muscle sarcomeres tuned to the C-H vibration (2800-3100 cm -1 ). Conversely, SFG image mapping assisted by phase-retrieved spCARS spectra also facilitated label-free monitoring of the changes in the muscle content of C. elegans that are associated with aging, based on the hypothesis that the C-H vibrational modes could serve as qualitative chemical markers sensitive to the amount and/or structural modulation of the muscle.

  14. Lipids, hemoproteins and carotenoids in alive Rhodotorula mucilaginosa cells under pesticide decomposition - Raman imaging study.

    Science.gov (United States)

    Pacia, Marta Z; Pukalski, Jan; Turnau, Katarzyna; Baranska, Malgorzata; Kaczor, Agnieszka

    2016-12-01

    Various species of yeasts are gaining attention as producers of nutraceuticals and biofuels and due to their capacity to biodegrade chemical waste. Rhodotorula mucilaginosa is one of the most oleaginous species of yeast, an efficient de novo carotenoid producer and was reported to be capable of decomposing of organic pesticides. In this work we studied the influence of a toxic pesticide, diazinone, on production of storage (lipids) and protective (carotenoids, hemoproteins) compounds by Rh. mucilaginosa alive cells with the help of Raman imaging. It occurred that the yeast in non-oleaginous phase and aerobic environment was rich in carotenoids and their level increased significantly under incubation with diazinone, while anaerobic environment resulted in production of both carotenoids and hemoproteins and the level of the latter decreased under the influence of the pesticide. For yeasts in oleaginous phase, it was concluded that lipid production (via triggering of NAD + accumulation and increase of the NO level) resulted in nitrosative stress leading to flavohemoprotein synthesis and was associated with the increase of the mitochondrial activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. 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...

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.)

  2. Resonance Raman imaging as a tool to assess the atmospheric pollution level: carotenoids in Lecanoraceae lichens as bioindicators.

    Science.gov (United States)

    Ibarrondo, I; Prieto-Taboada, N; Martínez-Arkarazo, I; Madariaga, J M

    2016-04-01

    Raman spectroscopy differentiation of carotenoids has traditionally been based on the ν 1 position (C = C stretching vibrations in the polyene chain) in the 1500-1600 cm(-1) range, using a 785 nm excitation laser. However, when the number of conjugated double bonds is similar, as in the cases of zeaxanthin and β-carotene, this distinction is still ambiguous due to the closeness of the Raman bands. This work shows the Raman results, obtained in resonance conditions using a 514 mm laser, on Lecanora campestris and Lecanora atra species, which can be used to differentiate and consequently characterize carotenoids. The presence of the carotenoid found in Lecanoraceae lichens has been demonstrated to depend on the atmospheric pollution level of the environment they inhabit. Astaxanthin, a superb antioxidant, appears as the principal xanthophyll in highly polluted sites, usually together with the UV screening pigment scytonemin; zeaxanthin is the major carotenoid in medium polluted environments, while β-carotene is the major carotenoid in cleaner environments. Based on these observations, an indirect classification of the stress suffered in a given environment can be assessed by simply analysing the carotenoid content in the Lecanoraceae lichens by using resonance Raman imaging.

  3. 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.

  4. 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)

  5. 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

  6. 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.

  7. 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.

  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. 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

  10. Facile synthesis of terminal-alkyne bioorthogonal molecules for live -cell surface-enhanced Raman scattering imaging through Au-core and silver/dopamine-shell nanotags.

    Science.gov (United States)

    Chen, Meng; Zhang, Ling; Yang, Bo; Gao, Mingxia; Zhang, Xiangmin

    2018-03-01

    Alkyne is unique, specific and biocompatible in the Raman-silent region of the cell, but there still remains a challenge to achieve ultrasensitive detection in living systems due to its weak Raman scattering. Herein, a terminal alkyne ((E)-2-[4-(ethynylbenzylidene)amino]ethane-1-thiol (EBAE)) with surface-enhanced Raman scattering is synthesized. The EBAE molecule possesses S- and C-termini, which can be directly bonded to gold nanoparticles and dopamine/silver by forming the Au-S chemical bond and the carbon-metal bond, respectively. The distance between Raman reporter and AuNPs/AgNPs can be reduced, contributing to forming hot-spot-based SERS substrate. The alkyne functionalized nanoparticles are based on Au core and encapsulating polydopamine shell, defined as Au-core and dopamine/Ag-shell (ACDS). The bimetallic ACDS induce strong SERS signals for molecular imaging that arise from the strong electromagnetic field. Furthermore, the EBAE provides a distinct peak in the cellular Raman-silent region with nearly zero background interference. The EBAE Raman signals could be tremendously enhanced when the Raman reporter is located at the middle of the Au-core and dopamine/Ag-shell. Therefore, this work could have huge potential benefits for the highly sensitive detection of intercellular information delivery by connecting the recognition molecules in biomedical diagnostics. Graphical abstract Terminal-alkyne-functionalized Au-core and silver/dopamine-shell nanotags for live-cell surface-enhanced Raman scattering imaging.

  11. Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) with Raman Imaging Applied to Lunar Meteorites.

    Science.gov (United States)

    Smith, Joseph P; Smith, Frank C; Booksh, Karl S

    2018-03-01

    Lunar meteorites provide a more random sampling of the surface of the Moon than do the returned lunar samples, and they provide valuable information to help estimate the chemical composition of the lunar crust, the lunar mantle, and the bulk Moon. As of July 2014, ∼96 lunar meteorites had been documented and ten of these are unbrecciated mare basalts. Using Raman imaging with multivariate curve resolution-alternating least squares (MCR-ALS), we investigated portions of polished thin sections of paired, unbrecciated, mare-basalt lunar meteorites that had been collected from the LaPaz Icefield (LAP) of Antarctica-LAP 02205 and LAP 04841. Polarized light microscopy displays that both meteorites are heterogeneous and consist of polydispersed sized and shaped particles of varying chemical composition. For two distinct probed areas within each meteorite, the individual chemical species and associated chemical maps were elucidated using MCR-ALS applied to Raman hyperspectral images. For LAP 02205, spatially and spectrally resolved clinopyroxene, ilmenite, substrate-adhesive epoxy, and diamond polish were observed within the probed areas. Similarly, for LAP 04841, spatially resolved chemical images with corresponding resolved Raman spectra of clinopyroxene, troilite, a high-temperature polymorph of anorthite, substrate-adhesive epoxy, and diamond polish were generated. In both LAP 02205 and LAP 04841, substrate-adhesive epoxy and diamond polish were more readily observed within fractures/veinlet features. Spectrally diverse clinopyroxenes were resolved in LAP 04841. Factors that allow these resolved clinopyroxenes to be differentiated include crystal orientation, spatially distinct chemical zoning of pyroxene crystals, and/or chemical and molecular composition. The minerals identified using this analytical methodology-clinopyroxene, anorthite, ilmenite, and troilite-are consistent with the results of previous studies of the two meteorites using electron microprobe

  12. 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

  13. Book Review: Reiner Salzer and Heinz W. Siesler (Eds.): Infrared and Raman spectroscopic imaging, 2nd ed

    International Nuclear Information System (INIS)

    Moore, David Steven

    2015-01-01

    This second edition of 'Infrared and Raman Spectroscopic Imaging' propels practitioners in that wide-ranging field, as well as other readers, to the current state of the art in a well-produced and full-color, completely revised and updated, volume. This new edition chronicles the expanded application of vibrational spectroscopic imaging from yesterday's time-consuming point-by-point buildup of a hyperspectral image cube, through the improvements afforded by the addition of focal plane arrays and line scan imaging, to methods applicable beyond the diffraction limit, instructs the reader on the improved instrumentation and image and data analysis methods, and expounds on their application to fundamental biomedical knowledge, food and agricultural surveys, materials science, process and quality control, and many others

  14. 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.

  15. Integration of Correlative Raman microscopy in a dual beam FIB-SEM J. of Raman Spectroscopy

    NARCIS (Netherlands)

    Timmermans, Frank Jan; Liszka, B.; Lenferink, Aufrid T.M.; van Wolferen, Hendricus A.G.M.; Otto, Cornelis

    2016-01-01

    We present an integrated confocal Raman microscope in a focused ion beam scanning electron microscope (FIB SEM). The integrated system enables correlative Raman and electron microscopic analysis combined with focused ion beam sample modification on the same sample location. This provides new

  16. 3D confocal Raman imaging of oil-rich emulsion from enzyme-assisted aqueous extraction of extruded soybean powder.

    Science.gov (United States)

    Wu, Longkun; Wang, Limin; Qi, Baokun; Zhang, Xiaonan; Chen, Fusheng; Li, Yang; Sui, Xiaonan; Jiang, Lianzhou

    2018-05-30

    The understanding of the structure morphology of oil-rich emulsion from enzyme-assisted extraction processing (EAEP) was a critical step to break the oil-rich emulsion structure in order to recover oil. Albeit EAEP method has been applied as an alternative way to conventional solvent extraction method, the structure morphology of oil-rich emulsion was still unclear. The current study aimed to investigate the structure morphology of oil-rich emulsion from EAEP using 3D confocal Raman imaging technique. With increasing the enzymatic hydrolysis duration from 1 to 3 h, the stability of oil-rich emulsion was decreased as visualized in the 3D confocal Raman images that the protein and oil were mixed together. The subsequent Raman spectrum analysis further revealed that the decreased stability of oil-rich emulsion was due to the protein aggregations via SS bonds or protein-lipid interactions. The conformational transfer in protein indicated the formation of a compact structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. 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.

  18. Pseudo-HE images derived from CARS/TPEF/SHG multimodal imaging in combination with Raman-spectroscopy as a pathological screening tool

    International Nuclear Information System (INIS)

    Bocklitz, Thomas W.; Salah, Firas Subhi; Vogler, Nadine; Heuke, Sandro; Chernavskaia, Olga; Schmidt, Carsten; Waldner, Maximilian J.; Greten, Florian R.; Bräuer, Rolf; Schmitt, Michael; Stallmach, Andreas; Petersen, Iver; Popp, Jürgen

    2016-01-01

    Due to the steadily increasing number of cancer patients worldwide the early diagnosis and treatment of cancer is a major field of research. The diagnosis of cancer is mostly performed by an experienced pathologist via the visual inspection of histo-pathological stained tissue sections. To save valuable time, low quality cryosections are frequently analyzed with diagnostic accuracies that are below those of high quality embedded tissue sections. Thus, alternative means have to be found that enable for fast and accurate diagnosis as the basis of following clinical decision making. In this contribution we will show that the combination of the three label-free non-linear imaging modalities CARS (coherent anti-Stokes Raman-scattering), TPEF (two-photon excited autofluorescence) and SHG (second harmonic generation) yields information that can be translated into computational hematoxylin and eosin (HE) images by multivariate statistics. Thereby, a computational HE stain is generated resulting in pseudo-HE overview images that allow for identification of suspicious regions. The latter are analyzed further by Raman-spectroscopy retrieving the tissue’s molecular fingerprint. The results suggest that the combination of non-linear multimodal imaging and Raman-spectroscopy possesses the potential as a precise and fast tool in routine histopathology. As the key advantage, both optical methods are non-invasive enabling for further pathological investigations of the same tissue section, e.g. a direct comparison with the current pathological gold-standard

  19. 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

  20. 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.

  1. Uptake of Retinoic Acid-Modified PMMA Nanoparticles in LX-2 and Liver Tissue by Raman Imaging and Intravital Microscopy.

    Science.gov (United States)

    Yildirim, Turgay; Matthäus, Christian; Press, Adrian T; Schubert, Stephanie; Bauer, Michael; Popp, Jürgen; Schubert, Ulrich S

    2017-10-01

    A primary amino-functionalized methyl methacrylate-based statistical copolymer is covalently coupled with retinoic acid (RA) and a fluorescent dye (DY590) in order to investigate the feasibility of the RA containing polymeric nanoparticles for Raman imaging studies and to study the possible selectivity of RA for hepatic stellate cells via intravital microscopy. Cationic nanoparticles are prepared by utilizing the nanoprecipitation method using modified polymers. Raman studies show that RA functional nanoparticles can be detectable in all tested cells without any need of additional label. Moreover, intravital microscopy indicates that DY590 is eliminated through the hepatobiliary route but not if used as covalently attached tracing molecule for nanoparticles. However, it is a suitable probe for sensitive detection of polymeric nanoparticles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. 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

  3. 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...

  4. [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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Characterization of conductive nanobiomaterials derived from viral assemblies by low-voltage STEM imaging and Raman scattering

    International Nuclear Information System (INIS)

    Plascencia-Villa, Germán; Bahena, Daniel; José-Yacamán, Miguel; Carreño-Fuentes, Liliana; Palomares, Laura A; Ramírez, Octavio T

    2014-01-01

    New technologies require the development of novel nanomaterials that need to be fully characterized to achieve their potential. High-resolution low-voltage scanning transmission electron microscopy (STEM) has proven to be a very powerful technique in nanotechnology, but its use for the characterization of nanobiomaterials has been limited. Rotavirus VP6 self-assembles into nanotubular assemblies that possess an intrinsic affinity for Au ions. This property was exploited to produce hybrid nanobiomaterials by the in situ functionalization of recombinant VP6 nanotubes with gold nanoparticles. In this work, Raman spectroscopy and advanced analytical electron microscopy imaging with spherical aberration-corrected (Cs) STEM and nanodiffraction at low-voltage doses were employed to characterize nanobiomaterials. STEM imaging revealed the precise structure and arrangement of the protein templates, as well as the nanostructure and atomic arrangement of gold nanoparticles with high spatial sub-Angstrom resolution and avoided radiation damage. The imaging was coupled with backscattered electron imaging, ultra-high resolution scanning electron microscopy and x-ray spectroscopy. The hybrid nanobiomaterials that were obtained showed unique properties as bioelectronic conductive devices and showed enhanced Raman scattering by their precise arrangement into superlattices, displaying the utility of viral assemblies as functional integrative self-assembled nanomaterials for novel applications. (paper)

  10. 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.

  11. 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.

  12. 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....

  13. 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.

  14. Examining live cell cultures during apoptosis by digital holographic phase imaging and Raman spectroscopy

    Science.gov (United States)

    Khmaladze, Alexander

    2017-11-01

    Cellular apoptosis is a unique, organized series of events, leading to programmed cell death. In this work, we present a combined digital holography/Raman spectroscopy technique to study live cell cultures during apoptosis. Digital holographic microscopy measurements of live cell cultures yield information about cell shape and volume, changes to which are indicative of alterations in cell cycle and initiation of cell death mechanisms. Raman spectroscopic measurements provide complementary information about cells, such as protein, lipid and nucleic acid content, and the spectral signatures associated with structural changes in molecules. Our work indicates that the chemical changes in proteins, which were detected by Raman measurements, preceded morphological changes, which were seen with digital holographic microscopy.

  15. Relationship between β-relaxation and structural stability of lysozyme: Microscopic insight on thermostabilization mechanism by trehalose from Raman spectroscopy experiments

    Energy Technology Data Exchange (ETDEWEB)

    Hédoux, Alain, E-mail: alain.hedoux@univ-lille1.fr; Paccou, Laurent; Guinet, Yannick [Université Lille Nord de France, F-59000 Lille France, USTL UMET UMR 8207 F-59655 Villeneuve d’Ascq (France)

    2014-06-14

    Raman investigations were carried out in the low-frequency and amide I regions on lysozyme aqueous solutions in absence and presence of trehalose. Raman spectroscopy gives the unique opportunity to analyze the protein and solvent dynamics in the low-frequency range while monitoring the unfolding process by capturing the spectrum of the amide I band. From the analysis of the quasielastic intensity, a dynamic change is firstly observed in a highly hydrated protein, around 70 °C, and interpreted in relation with the denaturation mechanism of the protein. The use of heavy water and partly deuterated trehalose gives clear information on protein–trehalose interactions in the native state of lysozyme (at room temperature) and during the thermal denaturation process of lysozyme. At room temperature, it was found that trehalose is preferentially excluded from the protein surface, and has a main effect on the tetrahedral local order of water molecules corresponding to a stiffening of the H-bond network in the solvent. The consequence is a significant reduction of the amplitude of fast relaxational motions, inducing a less marked dynamic transition shifted toward the high temperatures. Upon heating, interaction between trehalose and lysozyme is detected during the solvent penetration within the protein, i.e., while the native globular state softens into a molten globule (MG) state. Addition of trehalose reduces the protein flexibility in the MG state, improving the structural stability of the protein, and inhibiting the protein aggregation.

  16. Overview of the use of theory to understand infrared and Raman spectra and images of biomolecules: colorectal cancer as an example

    DEFF Research Database (Denmark)

    Piva, J. A. A. C.; Silva, J. L. R.; Raniero, L.

    2011-01-01

    In this work, we present the state of the art in the use of theory (first principles, molecular dynamics, and statistical methods) for interpreting and understanding the infrared (vibrational) absorption and Raman scattering spectra. It is discussed how they can be used in combination with purely...... of biomolecules are very sensitive to their environment and aggregation state, the combined use of infrared and Raman spectroscopy and imaging and theoretical simulations are clearly fields, which can benefit from their joint and mutual development....

  17. 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.

  18. 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.

  19. Self-diffusion of polycrystalline ice Ih under confining pressure: Hydrogen isotope analysis using 2-D Raman imaging

    Science.gov (United States)

    Noguchi, Naoki; Kubo, Tomoaki; Durham, William B.; Kagi, Hiroyuki; Shimizu, Ichiko

    2016-08-01

    We have developed a high-resolution technique based on micro Raman spectroscopy to measure hydrogen isotope diffusion profiles in ice Ih. The calibration curve for quantitative analysis of deuterium in ice Ih was constructed using micro Raman spectroscopy. Diffusion experiments using diffusion couples composed of dense polycrystalline H2O and D2O ice were carried out under a gas confining pressure of 100 MPa (to suppress micro-fracturing and pore formation) at temperatures from 235 K to 245 K and diffusion times from 0.2 to 94 hours. Two-dimensional deuterium profiles across the diffusion couples were determined by Raman imaging. The location of small spots of frost from room air could be detected from the shapes of the Raman bands of OH and OD stretching modes, which change because of the effect of the molar ratio of deuterium on the molecular coupling interaction. We emphasize the validity for screening the impurities utilizing the coupling interaction. Some recrystallization and grain boundary migration occurred in recovered diffusion couples, but analysis of two-dimensional diffusion profiles of regions not affected by grain boundary migration allowed us to measure a volume diffusivity for ice at 100 MPa of (2.8 ± 0.4) ×10-3exp[ -57.0 ± 15.4kJ /mol RT ] m2 /s (R is the gas constant, T is temperature). Based on ambient pressure diffusivity measurements by others, this value indicates a high (negative) activation volume for volume diffusivity of -29.5 cm3/mol or more. We can also constrain the value of grain boundary diffusivity in ice at 100 MPa to be volume diffusivity.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. [Revealing the chemical changes of tea cell wall induced by anthracnose with confocal Raman microscopy].

    Science.gov (United States)

    Li, Xiao-li; Luo, Liu-bin; Hu, Xiao-qian; Lou, Bing-gan; He, Yong

    2014-06-01

    Healthy tea and tea infected by anthracnose were first studied by confocal Raman microscopy to illustrate chemical changes of cell wall in the present paper. Firstly, Raman spectra of both healthy and infected sample tissues were collected with spatial resolution at micron-level, and ultrastructure of healthy and infected tea cells was got from scanning electron microscope. These results showed that there were significant changes in Raman shift and Raman intensity between healthy and infected cell walls, indicating that great differences occurred in chemical compositions of cell walls between healthy and infected samples. In details, intensities at many Raman bands which were closely associated with cellulose, pectin, esters were reduced after infection, revealing that the content of chemical compounds such as cellulose, pectin, esters was decreased after infection. Subsequently, chemical imaging of both healthy and infected tea cell walls were realized based on Raman fingerprint spectra of cellulose and microscopic spatial structure. It was found that not only the content of cellulose was reduced greatly after infection, but also the ordered structure of cellulose was destroyed by anthracnose infection. Thus, confocal Raman microscopy was shown to be a powerful tool to detect the chemical changes in cell wall of tea caused by anthracnose without any chemical treatment or staining. This research firstly applied confocal Raman microscopy in phytopathology for the study of interactive relationship between host and pathogen, and it will also open a new way for intensive study of host-pathogen at cellular level.

  5. Imaging in living cells using νB-H Raman spectroscopy: monitoring COSAN uptake.

    Science.gov (United States)

    Tarrés, Màrius; Canetta, Elisabetta; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J

    2014-03-28

    The boron-rich cobaltabisdicarbollide (COSAN) and its 8,8'-I2 derivative (I2-COSAN), both of purely inorganic nature, are shown to accumulate within living cells, where they can be detected using νB-H Raman microspectroscopy. This demonstrates an alternative method for cell labelling and detection.

  6. 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

  7. 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.

  8. 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)

  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. 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

  11. 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.

  12. 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...

  13. Identification of regions of normal grey matter and white matter from pathologic glioblastoma and necrosis in frozen sections using Raman imaging.

    Science.gov (United States)

    Kast, Rachel; Auner, Gregory; Yurgelevic, Sally; Broadbent, Brandy; Raghunathan, Aditya; Poisson, Laila M; Mikkelsen, Tom; Rosenblum, Mark L; Kalkanis, Steven N

    2015-11-01

    In neurosurgical applications, a tool capable of distinguishing grey matter, white matter, and areas of tumor and/or necrosis in near-real time could greatly aid in tumor resection decision making. Raman spectroscopy is a non-destructive spectroscopic technique which provides molecular information about the tissue under examination based on the vibrational properties of the constituent molecules. With careful measurement and data processing, a spatial step and repeat acquisition of Raman spectra can be used to create Raman images. Forty frozen brain tissue sections were imaged in their entirety using a 300-µm-square measurement grid, and two or more regions of interest within each tissue were also imaged using a 25 µm-square step size. Molecular correlates for histologic features of interest were identified within the Raman spectra, and novel imaging algorithms were developed to compare molecular features across multiple tissues. In previous work, the relative concentration of individual biomolecules was imaged. Here, the relative concentrations of 1004, 1300:1344, and 1660 cm(-1), which correspond primarily to protein and lipid content, were simultaneously imaged across all tissues. This provided simple interpretation of boundaries between grey matter, white matter, and diseased tissue, and corresponded with findings from adjacent hematoxylin and eosin-stained sections. This novel, yet simple, multi-channel imaging technique allows clinically-relevant resolution with straightforward molecular interpretation of Raman images not possible by imaging any single peak. This method can be applied to either surgical or laboratory tools for rapid, non-destructive imaging of grey and white matter.

  14. 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

  15. 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.

  16. 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.

  17. 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...

  18. 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.

  19. 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

  20. 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.