WorldWideScience

Sample records for microscopic imaging progress

  1. Reflection Imaging X-Ray Laser Microscope (RIXRALM) and its biological applications. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Suckewer, S.

    1998-07-01

    The main stimulus for the development of the proposed microscope (RIXRALM) is the possibility to view the surface and near surface structure of biological materials, such as cell membranes at much higher resolution than an optical (confocal) microscope. Although the prediction resolution of RIXRALM was lower than a Scanning Electron Microscope (SEM), the possibility to obtain images of cells (membranes) in a more natural, hydrated state and, in many cases, without staining, made the idea of a reflection X-ray microscope very attractive. The specimen can be in an H{sub 2}O saturated He atmosphere at atmospheric pressure. As the image can be obtained quickly (nsec exposure, occurring within seconds of insertion into such an environment), the cell surface can be seen in a state which is very close to its natural condition. Besides, the short exposure time eliminates the effect of motional blurring on the images. Their X-ray reflection microscope fit well in the very large gap in the size of biological objects studied in light microscopy (sub-micron size) and electron microscope (down to a few nanometers size).

  2. Surface imaging microscope

    Science.gov (United States)

    Rogala, Eric W.; Bankman, Isaac N.

    2008-04-01

    The three-dimensional shapes of microscopic objects are becoming increasingly important for battlespace CBRNE sensing. Potential applications of microscopic 3D shape observations include characterization of biological weapon particles and manufacturing of micromechanical components. Aerosol signatures of stand-off lidar systems, using elastic backscatter or polarization, are dictated by the aerosol particle shapes and sizes that must be well characterized in the lab. A low-cost, fast instrument for 3D surface shape microscopy will be a valuable point sensor for biological particle sensing applications. Both the cost and imaging durations of traditional techniques such as confocal microscopes, atomic force microscopes, and electron scanning microscopes are too high. We investigated the feasibility of a low-cost, fast interferometric technique for imaging the 3D surface shape of microscopic objects at frame rates limited only by the camera in the system. The system operates at two laser wavelengths producing two fringe images collected simultaneously by a digital camera, and a specialized algorithm we developed reconstructs the surface map of the microscopic object. The current implementation assembled to test the concept and develop the new 3D reconstruction algorithm has 0.25 micron resolution in the x and y directions, and about 0.1 micron accuracy in the z direction, as tested on a microscopic glass test object manufactured with etching techniques. We describe the interferometric instrument, present the reconstruction algorithm, and discuss further development.

  3. Multiphoton microscopic imaging of esophagus during the early phase of tumor progression.

    Science.gov (United States)

    Xu, Jian; Kang, Deyong; Xu, Meifang; Zhuo, Shuangmu; Zhu, Xiaoqin; Chen, Jianxin

    2013-01-01

    Esophageal cancer is one of the most common cancer and leading cause of cancer death worldwide. Multiphoton microscopy (MPM) has become a novel optical tool of choice for imaging tissue architecture and cellular morphology based on two-photon excited fluorescence and second harmonic generation. In this study, we used MPM to image microstructure of human normal esophagus, carcinoma in situ, and early invasive carcinoma in order to investigate the morphological change of tissue structure during the early phase of tumor progression. The diagnostic features such as the appearance of cancerous cells, the absence of the basement membrane were extracted to distinguish between normal and cancerous esophagus tissue. The infiltration depth during tumor progression was determined by the appearance of cancerous cells. The significant change of layer structure between cancerous tissue and normal esophagus was described. We also quantitatively described the differences of morphology between normal and cancerous cells. These results correlated well with the corresponding histological findings. With the advancement of clinically miniaturized MPM and the multi-photon probe, combining MPM with standard endoscopy will therefore allow us to make a real-time in vivo diagnosis of early esophageal cancer at the cellular level. © Wiley Periodicals, Inc.

  4. Microscopic Halftone Image Segmentation

    Institute of Scientific and Technical Information of China (English)

    WANG Yong-gang; YANG Jie; DING Yong-sheng

    2004-01-01

    Microscopic halftone image recognition and analysis can provide quantitative evidence for printing quality control and fault diagnosis of printing devices, while halftone image segmentation is one of the significant steps during the procedure. Automatic segmentation on microscopic dots by the aid of the Fuzzy C-Means (FCM) method that takes account of the fuzziness of halftone image and utilizes its color information adequately is realized. Then some examples show the technique effective and simple with better performance of noise immunity than some usual methods. In addition, the segmentation results obtained by the FCM in different color spaces are compared, which indicates that the method using the FCM in the f1f2f3 color space is superior to the rest.

  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. Athena microscopic Imager investigation

    Science.gov (United States)

    Herkenhoff, K. E.; Squyres, S. W.; Bell, J.F.; Maki, J.N.; Arneson, H.M.; Bertelsen, P.; Brown, D.I.; Collins, S.A.; Dingizian, A.; Elliott, S.T.; Goetz, W.; Hagerott, E.C.; Hayes, A.G.; Johnson, M.J.; Kirk, R.L.; McLennan, S.; Morris, R.V.; Scherr, L.M.; Schwochert, M.A.; Shiraishi, L.R.; Smith, G.H.; Soderblom, L.A.; Sohl-Dickstein, J. N.; Wadsworth, M.V.

    2003-01-01

    The Athena science payload on the Mars Exploration Rovers (MER) includes the Microscopic Imager (MI). The MI is a fixed-focus camera mounted on the end of an extendable instrument arm, the Instrument Deployment Device (IDD). The MI was designed to acquire images at a spatial resolution of 30 microns/pixel over a broad spectral range (400-700 nm). The MI uses the same electronics design as the other MER cameras but has optics that yield a field of view of 31 ?? 31 mm across a 1024 ?? 1024 pixel CCD image. The MI acquires images using only solar or skylight illumination of the target surface. A contact sensor is used to place the MI slightly closer to the target surface than its best focus distance (about 66 mm), allowing concave surfaces to be imaged in good focus. Coarse focusing (???2 mm precision) is achieved by moving the IDD away from a rock target after the contact sensor has been activated. The MI optics are protected from the Martian environment by a retractable dust cover. The dust cover includes a Kapton window that is tinted orange to restrict the spectral bandpass to 500-700 nm, allowing color information to be obtained by taking images with the dust cover open and closed. MI data will be used to place other MER instrument data in context and to aid in petrologic and geologic interpretations of rocks and soils on Mars. Copyright 2003 by the American Geophysical Union.

  7. Compact Microscope Imaging System Developed

    Science.gov (United States)

    McDowell, Mark

    2001-01-01

    The Compact Microscope Imaging System (CMIS) is a diagnostic tool with intelligent controls for use in space, industrial, medical, and security applications. The CMIS can be used in situ with a minimum amount of user intervention. This system, which was developed at the NASA Glenn Research Center, can scan, find areas of interest, focus, and acquire images automatically. Large numbers of multiple cell experiments require microscopy for in situ observations; this is only feasible with compact microscope systems. CMIS is a miniature machine vision system that combines intelligent image processing with remote control capabilities. The software also has a user-friendly interface that can be used independently of the hardware for post-experiment analysis. CMIS has potential commercial uses in the automated online inspection of precision parts, medical imaging, security industry (examination of currency in automated teller machines and fingerprint identification in secure entry locks), environmental industry (automated examination of soil/water samples), biomedical field (automated blood/cell analysis), and microscopy community. CMIS will improve research in several ways: It will expand the capabilities of MSD experiments utilizing microscope technology. It may be used in lunar and Martian experiments (Rover Robot). Because of its reduced size, it will enable experiments that were not feasible previously. It may be incorporated into existing shuttle orbiter and space station experiments, including glove-box-sized experiments as well as ground-based experiments.

  8. Simulations of optical microscope images

    Science.gov (United States)

    Germer, Thomas A.; Marx, Egon

    2006-03-01

    The resolution of an optical microscope is limited by the optical wavelengths used. However, there is no fundamental limit to the sensitivity of a microscope to small differences in any of a feature's dimensions. That is, those limits are determined by such things as the sensitivity of the detector array, the quality of the optical system, and the stability of the light source. The potential for using this nearly unbounded sensitivity has sparked interest in extending optical microscopy to the characterization of sub-wavelength structures created by photolithography and using that characterization for process control. In this paper, an analysis of the imaging of a semiconductor grating structure with an optical microscope will be presented. The analysis includes the effects of partial coherence in the illumination system, aberrations of both the illumination and the collection optics, non-uniformities in the illumination, and polarization. It can thus model just about any illumination configuration imaginable, including Koehler illumination, focused (confocal) illumination, or dark-field illumination. By propagating Jones matrices throughout the system, polarization control at the back focal planes of both illumination and collection can be investigated. Given a detailed characterization of the microscope (including aberrations), images can be calculated and compared to real data, allowing details of the grating structure to be determined, in a manner similar to that found in scatterometry.

  9. Microscope Image of Scavenged Particles

    Science.gov (United States)

    2008-01-01

    This image from NASA's Phoenix Mars Lander's Optical Microscope shows a strongly magnetic surface which has scavenged particles from within the microscope enclosure before a sample delivery from the lander's Robotic Arm. The particles correspond to the larger grains seen in fine orange material that makes up most of the soil at the Phoenix site. They vary in color, but are of similar size, about one-tenth of a millimeter. As the microscope's sample wheel moved during operation, these particles also shifted, clearing a thin layer of the finer orange particles that have also been collected. Together with the previous image, this shows that the larger grains are much more magnetic than the fine orange particles with a much larger volume of the grains being collected by the magnet. The image is 2 milimeters across. It is speculated that the orange material particles are a weathering product from the larger grains, with the weathering process both causing a color change and a loss of magnetism. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by JPL, Pasadena, Calif. Spacecraft development was by Lockheed Martin Space Systems, Denver.

  10. The Athena Microscopic Imager Investigation

    Science.gov (United States)

    Herkenhoff, K. E.; Aquyres, S. W.; Bell, J. F., III; Maki, J. N.; Arneson, H. M.; Brown, D. I.; Collins, S. A.; Dingizian, A.; Elliot, S. T.; Geotz, W.

    2003-01-01

    The Athena science payload on the Mars Exploration Rovers (MER) includes the Microscopic Imager (MI) [1]. The MI is a fixed-focus camera mounted on the end of an extendable instrument arm, the Instrument Deployment Device (IDD; see Figure 1).The MI was designed to acquire images at a spatial resolution of 30 microns/pixel over a broad spectral range (400 - 700 nm; see Table 1). Technically, the microscopic imager is not a microscope: it has a fixed magnification of 0.4 and is intended to produce images that simulate a geologist s view through a common hand lens. In photographers parlance, the system makes use of a macro lens. The MI uses the same electronics design as the other MER cameras [2, 3] but has optics that yield a field of view of 31 31 mm across a 1024 1024 pixel CCD image (Figure 2). The MI acquires images using only solar or skylightillumination of the target surface. A contact sensor is used to place the MI slightly closer to the target surface than its best focus distance (about 66 mm), allowing concave surfaces to be imaged in good focus. Because the MI has a relatively small depth of field (3 mm), a single MI image of a rough surface will contain both focused and unfocused areas. Coarse focusing will be achieved by moving the IDD away from a rock target after the contact sensor is activated. Multiple images taken at various distances will be acquired to ensure good focus on all parts of rough surfaces. By combining a set of images acquired in this way, a completely focused image can be assembled. Stereoscopic observations can be obtained by moving the MI laterally relative to its boresight. Estimates of the position and orientation of the MI for each acquired image will be stored in the rover computer and returned to Earth with the image data. The MI optics will be protected from the Martian environment by a retractable dust cover. The dust cover includes a Kapton window that is tinted orange to restrict the spectral bandpass to 500-700 nm

  11. Stimulated Brillouin Scattering Microscopic Imaging.

    Science.gov (United States)

    Ballmann, Charles W; Thompson, Jonathan V; Traverso, Andrew J; Meng, Zhaokai; Scully, Marlan O; Yakovlev, Vladislav V

    2015-01-01

    Two-dimensional stimulated Brillouin scattering microscopy is demonstrated for the first time using low power continuous-wave lasers tunable around 780 nm. Spontaneous Brillouin spectroscopy has much potential for probing viscoelastic properties remotely and non-invasively on a microscopic scale. Nonlinear Brillouin scattering spectroscopy and microscopy may provide a way to tremendously accelerate the data aquisition and improve spatial resolution. This general imaging setup can be easily adapted for specific applications in biology and material science. The low power and optical wavelengths in the water transparency window used in this setup provide a powerful bioimaging technique for probing the mechanical properties of hard and soft tissue.

  12. Stimulated Brillouin Scattering Microscopic Imaging

    Science.gov (United States)

    Ballmann, Charles W.; Thompson, Jonathan V.; Traverso, Andrew J.; Meng, Zhaokai; Scully, Marlan O.; Yakovlev, Vladislav V.

    2015-12-01

    Two-dimensional stimulated Brillouin scattering microscopy is demonstrated for the first time using low power continuous-wave lasers tunable around 780 nm. Spontaneous Brillouin spectroscopy has much potential for probing viscoelastic properties remotely and non-invasively on a microscopic scale. Nonlinear Brillouin scattering spectroscopy and microscopy may provide a way to tremendously accelerate the data aquisition and improve spatial resolution. This general imaging setup can be easily adapted for specific applications in biology and material science. The low power and optical wavelengths in the water transparency window used in this setup provide a powerful bioimaging technique for probing the mechanical properties of hard and soft tissue.

  13. Progress in Diffraction Enhanced Imaging

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ In cooperation with the Topography Station of Beijing Synchrotron Radiation under CAS Institute of High Energy Physics, a research group from the CAS Shanghai Institute of Optics and Fine Mechanics (SIOM) has made encouraging progress in the diffraction enhanced imaging technology through phase-contrast microscope by hard X-rays.

  14. First Atomic Force Microscope Image from Mars

    Science.gov (United States)

    2008-01-01

    This calibration image presents three-dimensional data from the atomic force microscope on NASA's Phoenix Mars Lander, showing surface details of a substrate on the microscope station's sample wheel. It will be used as an aid for interpreting later images that will show shapes of minuscule Martian soil particles. The area imaged by the microscope is 40 microns by 40 microns, small enough to fit on an eyelash. The grooves in this substrate are 14 microns (0.00055 inch) apart, from center to center. The vertical dimension is exaggerated in the image to make surface details more visible. The grooves are 300 nanometers (0.00001 inch) deep. This is the first atomic force microscope image recorded on another planet. It was taken on July 9, 2008, during the 44th Martian day, or sol, of the Phoenix mission since landing. Phoenix's Swiss-made atomic force microscope builds an image of the surface shape of a particle by sensing it with a sharp tip at the end of a spring, all microfabricated out of a silicon wafer. A strain gauge records how far the spring flexes to follow the contour of the surface. It can provide details of soil-particle shapes smaller than one-hundredth the width of a human hair. This is about 20 times smaller than what can be resolved with Phoenix's optical microscope, which has provided much higher-magnification imaging than anything seen on Mars previously. Both microscopes are part of Phoenix's Microscopy, Electrochemistry and Conductivity Analyzer.

  15. Cluster SIMS Microscope Mode Mass Spectrometry Imaging

    CERN Document Server

    Kiss, András; Jungmann, Julia H; Heeren, Ron M A

    2013-01-01

    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 is 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 mass spectral and imaging performance of the system is tested with various benchmark samples and thin tissue sections. We show that the high secondary ion yield (with respect to traditional monatomic primary ion sources) of the C60 primary ion ...

  16. Recent Opportunity Microscopic Imager Results

    Science.gov (United States)

    Herkenhoff, K. E.; Arvidson, R. E.; Jolliff, B. L.; Yingst, R.; Team, A.

    2013-12-01

    Opportunity arrived at exposures of Endeavour crater rim rocks in August 2011, on a hill dubbed 'Cape York.' These rocks have been the goal of exploration by Opportunity for the past few years because spectral evidence for phyllosilicates was observed at this location in orbital remote sensing data. As Opportunity circum¬navigated Cape York, the Microscopic Imager (MI) was used to examine the fine-scale textures of various soils and rocky outcrops. As reported previously, Opportunity discovered multiple bright linear features along the western periphery of Cape York that have been interpreted as veins of Ca sulfate deposited in fractures within the bedrock of Cape York. Opportunity then explored the northern and eastern sides of Cape York, including the area around 'Matijevic Hill' that shows evidence for phyllosilicates in CRISM data acquired from the Mars Reconnaissance Orbiter. One of the first outcrops examined near Matijevic Hill, dubbed 'Kirkwood,' is dominated by millimeter-size spherules. Unlike the hematite-rich concretions observed by Opportunity on Meridiani Planum, the aggregated 'newberries' in the Kirkwood exposure display internal structure and resistant rims. Compositionally, the spherule-rich rock is very similar to a nearby spherule-poor outcrop dubbed 'Whitewater Lake.' Thus these spherules have a more basalt-like composition compared to the hematite-rich concretions of the Burns Formation. The origin of the Kirkwood outcrop is uncertain, but the setting on the rim of the 22-km diameter Endeavour crater suggests that perhaps impact melting was involved in lapilli formation, possibly followed by mobilization and sorting in the ejecta blanket. Alternatively, the newberries may be diagenetic iron oxide concretions that are less well cemented than the 'blueberries' of the younger sulfate-rich Burns Formation. The Whitewater Lake outcrops contain the phyllosilicate phases observed from orbit, and are the oldest materials yet investigated by

  17. Miniaturized 3D microscope imaging system

    Science.gov (United States)

    Lan, Yung-Sung; Chang, Chir-Weei; Sung, Hsin-Yueh; Wang, Yen-Chang; Chang, Cheng-Yi

    2015-05-01

    We designed and assembled a portable 3-D miniature microscopic image system with the size of 35x35x105 mm3 . By integrating a microlens array (MLA) into the optical train of a handheld microscope, the biological specimen's image will be captured for ease of use in a single shot. With the light field raw data and program, the focal plane can be changed digitally and the 3-D image can be reconstructed after the image was taken. To localize an object in a 3-D volume, an automated data analysis algorithm to precisely distinguish profundity position is needed. The ability to create focal stacks from a single image allows moving or specimens to be recorded. Applying light field microscope algorithm to these focal stacks, a set of cross sections will be produced, which can be visualized using 3-D rendering. Furthermore, we have developed a series of design rules in order to enhance the pixel using efficiency and reduce the crosstalk between each microlens for obtain good image quality. In this paper, we demonstrate a handheld light field microscope (HLFM) to distinguish two different color fluorescence particles separated by a cover glass in a 600um range, show its focal stacks, and 3-D position.

  18. 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.

  19. Compact Microscope Imaging System with Intelligent Controls

    Science.gov (United States)

    McDowell, Mark

    2004-01-01

    The figure presents selected views of a compact microscope imaging system (CMIS) that includes a miniature video microscope, a Cartesian robot (a computer- controlled three-dimensional translation stage), and machine-vision and control subsystems. The CMIS was built from commercial off-the-shelf instrumentation, computer hardware and software, and custom machine-vision software. The machine-vision and control subsystems include adaptive neural networks that afford a measure of artificial intelligence. The CMIS can perform several automated tasks with accuracy and repeatability . tasks that, heretofore, have required the full attention of human technicians using relatively bulky conventional microscopes. In addition, the automation and control capabilities of the system inherently include a capability for remote control. Unlike human technicians, the CMIS is not at risk of becoming fatigued or distracted: theoretically, it can perform continuously at the level of the best human technicians. In its capabilities for remote control and for relieving human technicians of tedious routine tasks, the CMIS is expected to be especially useful in biomedical research, materials science, inspection of parts on industrial production lines, and space science. The CMIS can automatically focus on and scan a microscope sample, find areas of interest, record the resulting images, and analyze images from multiple samples simultaneously. Automatic focusing is an iterative process: The translation stage is used to move the microscope along its optical axis in a succession of coarse, medium, and fine steps. A fast Fourier transform (FFT) of the image is computed at each step, and the FFT is analyzed for its spatial-frequency content. The microscope position that results in the greatest dispersal of FFT content toward high spatial frequencies (indicating that the image shows the greatest amount of detail) is deemed to be the focal position.

  20. 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

  1. 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.

  2. Optical and digital microscopic imaging techniques and applications in pathology.

    Science.gov (United States)

    Chen, Xiaodong; Zheng, Bin; Liu, Hong

    2011-01-01

    The conventional optical microscope has been the primary tool in assisting pathological examinations. The modern digital pathology combines the power of microscopy, electronic detection, and computerized analysis. It enables cellular-, molecular-, and genetic-imaging at high efficiency and accuracy to facilitate clinical screening and diagnosis. This paper first reviews the fundamental concepts of microscopic imaging and introduces the technical features and associated clinical applications of optical microscopes, electron microscopes, scanning tunnel microscopes, and fluorescence microscopes. The interface of microscopy with digital image acquisition methods is discussed. The recent developments and future perspectives of contemporary microscopic imaging techniques such as three-dimensional and in vivo imaging are analyzed for their clinical potentials.

  3. DHM (Digital Holography Microscope) for imaging cells

    Energy Technology Data Exchange (ETDEWEB)

    Emery, Yves [Lyncee Tec SA, PSE-A, 1015 Lausanne (Switzerland); Cuche, Etienne [Lyncee Tec SA, PSE-A, 1015 Lausanne (Switzerland); Colomb, Tristan [STI-IOA-EPFL, 1015 Lausanne (Switzerland); Depeursinge, Christian [STI-IOA-EPFL, 1015 Lausanne (Switzerland); Rappaz, Benjamin [SV-BM-EPFL, 1015 Lausanne (Switzerland); Marquet, Pierre [CNP-CHUV, Site de Cery, 1008 Prilly (Switzerland); Magistretti, Pierre [SV-BM-EPFL, 1015 Lausanne (Switzerland)

    2007-04-15

    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 {sup h}ologram{sup .} 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.

  4. Scanning Nanospin Ensemble Microscope for Nanoscale Magnetic and Thermal Imaging.

    Science.gov (United States)

    Tetienne, Jean-Philippe; Lombard, Alain; Simpson, David A; Ritchie, Cameron; Lu, Jianing; Mulvaney, Paul; Hollenberg, Lloyd C L

    2016-01-13

    Quantum sensors based on solid-state spins provide tremendous opportunities in a wide range of fields from basic physics and chemistry to biomedical imaging. However, integrating them into a scanning probe microscope to enable practical, nanoscale quantum imaging is a highly challenging task. Recently, the use of single spins in diamond in conjunction with atomic force microscopy techniques has allowed significant progress toward this goal, but generalization of this approach has so far been impeded by long acquisition times or by the absence of simultaneous topographic information. Here, we report on a scanning quantum probe microscope which solves both issues by employing a nanospin ensemble hosted in a nanodiamond. This approach provides up to an order of magnitude gain in acquisition time while preserving sub-100 nm spatial resolution both for the quantum sensor and topographic images. We demonstrate two applications of this microscope. We first image nanoscale clusters of maghemite particles through both spin resonance spectroscopy and spin relaxometry, under ambient conditions. Our images reveal fast magnetic field fluctuations in addition to a static component, indicating the presence of both superparamagnetic and ferromagnetic particles. We next demonstrate a new imaging modality where the nanospin ensemble is used as a thermometer. We use this technique to map the photoinduced heating generated by laser irradiation of a single gold nanoparticle in a fluid environment. This work paves the way toward new applications of quantum probe microscopy such as thermal/magnetic imaging of operating microelectronic devices and magnetic detection of ion channels in cell membranes.

  5. 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

  6. 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.

  7. Overview of Athena Microscopic Imager Results

    Science.gov (United States)

    Herkenhoff, K.; Squyres, S.; Arvidson, R.; Bass, D.; Bell, J., III; Bertelsen, P.; Cabrol, N.; Ehlmann, B.; Farrand, W.; Gaddis, L.

    2005-01-01

    The Athena science payload on the Mars Exploration Rovers (MER) includes the Microscopic Imager (MI). The MI is a fixed-focus camera mounted on an extendable arm, the Instrument Deployment Device (IDD). The MI acquires images at a spatial resolution of 31 microns/pixel over a broad spectral range (400 - 700 nm). The MI uses the same electronics design as the other MER cameras but its optics yield a field of view of 32 32 mm across a 1024 1024 pixel CCD image. The MI acquires images using only solar or skylight illumination of the target surface. The MI science objectives, instrument design and calibration, operation, and data processing were described by Herkenhoff et al. Initial results of the MI experiment on both MER rovers (Spirit and Opportunity) have been published previously. Highlights of these and more recent results are described.

  8. Multi-compartment microscopic diffusion imaging.

    Science.gov (United States)

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

    2016-10-01

    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 microscopic tissue structure. This technique can be immediately used in the clinic for the assessment of various neurological conditions, as it requires only a widely available off-the-shelf sequence with two b-shells and high-angular gradient resolution achievable within clinically feasible scan times. To demonstrate the developed method, we use high-quality diffusion data acquired with a bespoke scanner system from the Human Connectome Project. This study establishes the normative values of the new biomarkers for a large cohort of healthy young adults, which may then support clinical diagnostics in patients. Moreover, we show that the microscopic diffusion indices offer direct sensitivity to pathological tissue alterations, exemplified in a preclinical animal model of Tuberous Sclerosis Complex (TSC), a genetic multi-organ disorder which impacts brain microstructure and hence may lead to neurological manifestations such as autism, epilepsy and developmental delay. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Beneš, Miroslav; Zitová, Barbara

    2015-01-01

    In our paper, we present a performance evaluation of image segmentation algorithms on microscopic image data. In spite of the existence of many algorithms for image data partitioning, there is no universal and 'the best' method yet. Moreover, images of microscopic samples can be of various character and quality which can negatively influence the performance of image segmentation algorithms. Thus, the issue of selecting suitable method for a given set of image data is of big interest. We carried out a large number of experiments with a variety of segmentation methods to evaluate the behaviour of individual approaches on the testing set of microscopic images (cross-section images taken in three different modalities from the field of art restoration). The segmentation results were assessed by several indices used for measuring the output quality of image segmentation algorithms. In the end, the benefit of segmentation combination approach is studied and applicability of achieved results on another representatives of microscopic data category - biological samples - is shown.

  10. Analysis on enhanced depth of field for integral imaging microscope.

    Science.gov (United States)

    Lim, Young-Tae; Park, Jae-Hyeung; Kwon, Ki-Chul; Kim, Nam

    2012-10-08

    Depth of field of the integral imaging microscope is studied. In the integral imaging microscope, 3-D information is encoded as a form of elemental images Distance between intermediate plane and object point decides the number of elemental image and depth of field of integral imaging microscope. From the analysis, it is found that depth of field of the reconstructed depth plane image by computational integral imaging reconstruction is longer than depth of field of optical microscope. From analyzed relationship, experiment using integral imaging microscopy and conventional microscopy is also performed to confirm enhanced depth of field of integral imaging microscopy.

  11. Optical microscopic imaging based on VRML language

    Science.gov (United States)

    Zhang, Xuedian; Zhang, Zhenyi; Sun, Jun

    2009-11-01

    As so-called VRML (Virtual Reality Modeling Language), is a kind of language used to establish a model of the real world or a colorful world made by people. As in international standard, VRML is the main kind of program language based on the "www" net building, which is defined by ISO, the kind of MIME is x-world or x-VRML. The most important is that it has no relationship with the operating system. Otherwise, because of the birth of VRML 2.0, its ability of describing the dynamic condition gets better, and the interaction of the internet evolved too. The use of VRML will bring a revolutionary change of confocal microscope. For example, we could send different kinds of swatch in virtual 3D style to the net. On the other hand, scientists in different countries could use the same microscope in the same time to watch the same samples by the internet. The mode of sending original data in the model of text has many advantages, such as: the faster transporting, the fewer data, the more convenient updating and fewer errors. In the following words we shall discuss the basic elements of using VRML in the field of Optical Microscopic imaging.

  12. Polymerized LB Films Imaged with a Combined Atomic Force Microscope-Fluorescence Microscope

    NARCIS (Netherlands)

    Putman, C.A.J.; Putman, Constant A.J.; Hansma, Helen G.; Gaub, Hermann E.; Hansma, Paul K.

    1992-01-01

    The first results obtained with a new stand-alone atomic force microscope (AFM) integrated with a standard Zeiss optical fluorescence microscope are presented. The optical microscope allows location and selection of objects to be imaged with the high-resolution AFM. Furthermore, the combined

  13. Polymerized LB films imaged with a combined atomic force microscope-fluorescence microscope

    NARCIS (Netherlands)

    Putman, Constant A.J.; Hansma, Helen G.; Gaub, Hermann E.; Hansma, Paul K.

    1992-01-01

    The first results obtained with a new stand-alone atomic force microscope (AFM) integrated with a standard Zeiss optical fluorescence microscope are presented. The optical microscope allows location and selection of objects to be imaged with the high-resolution AFM. Furthermore, the combined microsc

  14. Technique of Hadamard transform microscope fluorescence image analysis

    Institute of Scientific and Technical Information of China (English)

    梅二文; 顾文芳; 曾晓斌; 陈观铨; 曾云鹗

    1995-01-01

    Hadamard transform spatial multiplexed imaging technique is combined with fluorescence microscope and an instrument of Hadamard transform microscope fluorescence image analysis is developed. Images acquired by this instrument can provide a lot of useful information simultaneously, including three-dimensional Hadamard transform microscope cell fluorescence image, the fluorescence intensity and fluorescence distribution of a cell, the background signal intensity and the signal/noise ratio, etc.

  15. Optical and Digital Microscopic Imaging Techniques and Applications in Pathology

    Directory of Open Access Journals (Sweden)

    Xiaodong Chen

    2011-01-01

    Full Text Available The conventional optical microscope has been the primary tool in assisting pathological examinations. The modern digital pathology combines the power of microscopy, electronic detection, and computerized analysis. It enables cellular-, molecular-, and genetic-imaging at high efficiency and accuracy to facilitate clinical screening and diagnosis. This paper first reviews the fundamental concepts of microscopic imaging and introduces the technical features and associated clinical applications of optical microscopes, electron microscopes, scanning tunnel microscopes, and fluorescence microscopes. The interface of microscopy with digital image acquisition methods is discussed. The recent developments and future perspectives of contemporary microscopic imaging techniques such as three-dimensional and in vivo imaging are analyzed for their clinical potentials.

  16. 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...

  17. Plenoptic microscope based on laser optical feedback imaging (LOFI)

    CERN Document Server

    Glastre, W; Jacquin, O; de Chatellus, H Guillet; Lacot, E

    2015-01-01

    We present an overview of the performances of a plenoptic microscope which combines the high sensitivity of a laser optical feedback imaging setup , the high resolution of optical synthetic aperture and a shot noise limited signal to noise ratio by using acoustic photon tagging. By using an adapted phase filtering, this microscope allows phase drift correction and numerical aberration compensation (defocusing, coma, astigmatism ...). This new kind of microscope seems to be well adapted to make deep imaging through scattering and heterogeneous media.

  18. 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.…

  19. 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.…

  20. Center of Excellence: Microlaser microscope. Annual progress technical report

    Energy Technology Data Exchange (ETDEWEB)

    Webb, R.H.

    1993-09-01

    This Center-of-Excellence grant has two components: Development of an imaging, system based on microlaser arrays forms a central project among a group of laser diagnostic and therapeutic efforts primarily funded outside the grant. In year 2 we have dealt with the slow delivery of new microlaser array approach to the idea of all-solid-state confocal microscopy. One solution was moderately successful, and another has produced the first microscope that is electronically switchable from confocal to non-confocal. We think this may be a useful alternative to the final design. This report thus discloses patentable material. We describe first the central Microlaser Microscope project, then we will tough briefly on the other projects of the Center. Publications are primarily those of the smaller projects, though no longer exclusively so. The appendix includes some of the publications.

  1. 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.

  2. Understanding oxide interfaces: From microscopic imaging to electronic phases

    Science.gov (United States)

    Ilani, Shahal

    2014-03-01

    In the last decade, the advent of complex oxide interfaces has unleashed a wealth of new possibilities to create materials with unexpected functionalities. A notable example is the two-dimensional electron system formed at the interface between LaAlO3 and SrTiO3 (LAO/STO), which exhibits ferromagnetism, superconductivity, and a wide range of unique magneto-transport properties. A key challenge is to find the microscopic mechanisms that underlie these emergent phenomena. While there is a growing understanding that these phenomena might reflect rich structures at the micro-scale, experimental progress toward microscopic imaging of this system has been so far rather limited due to the buried nature of its interface. In this talk I will discuss our experiments that study this system on microscopic and macroscopic scales. Using a newly-developed nanotube-based scanning electrometer we image on the nanoscale the electrostatics and mechanics of this buried interface. We reveal the dynamics of structural domains in STO, their role in generating the contested anomalous piezoelectricity of this substrate, and their direct effects on the physics of the interface electrons. Using macroscopic magneto-transport experiments we demonstrate that a universal Lifshitz transition between the population of d-orbitals with different symmetries underlies many of the transport phenomena observed to date. We further show that the interactions between the itinerant electrons and localized spins leads to an unusual, gate-tunable magnetic phase diagram. These measurements highlight the unique physical settings that can be realized within this new class of low dimensional systems.

  3. Faraday rotation imaging microscope with microsecond pulse magnet

    Energy Technology Data Exchange (ETDEWEB)

    Suwa, Masayori, E-mail: msuwa@chem.sci.osaka-u.ac.jp [Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 (Japan); Tsukahara, Satoshi [Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 (Japan); Watarai, Hitoshi, E-mail: watarai@chem.sci.osaka-u.ac.jp [Institute for NanoScience Design, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan)

    2015-11-01

    We have fabricated a high-performance Faraday rotation (FR) imaging microscope that uses a microsecond pulse magnet comprising an insulated gated bipolar transistor and a 2 μF capacitor. Our microscope produced images with greater stability and sensitivity than those of previous microscopes that used millisecond pulse magnet; these improvements are likely due to high repetition rate and negligible Joule heating effects. The mechanical vibrations in the magnet coil caused by the pulsed current were significantly reduced. The present FR microscope constructed an averaged image from 1000 FR images within 10 min under 1.7 T. Applications of the FR microscope to discriminating three benzene derivatives in micro-capillaries and oscillation-free imaging of spherical polystyrene and polymethyl methacrylate microparticles demonstrated its high performance. - Highlights: • A microsecond pulse magnet with high repetition rate of 10 Hz was fabricated. • Faraday rotation (FR) imaging microscope with the μs magnet was constructed. • Benzene derivatives in microcapillaries were distinguished with the FR microscope. • FR images of single polymer microspheres of 20 μm were correctly acquired. • Observed FR angles agreed quantitatively with those expected from Verdet constants.

  4. 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.

  5. 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...

  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...

  7. 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...

  8. Optical and digital microscopic imaging techniques and applications in pathology

    OpenAIRE

    Xiaodong Chen; Bin Zheng; Hong Liu

    2011-01-01

    The conventional optical microscope has been the primary tool in assisting pathological examinations. The modern digital pathology combines the power of microscopy, electronic detection, and computerized analysis. It enables cellular-, molecular-, and genetic-imaging at high efficiency and accuracy to facilitate clinical screening and diagnosis. This paper first reviews the fundamental concepts of microscopic imaging and introduces the technical features and associated clinical applications o...

  9. 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).

  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. Imaging properties of coherent anti-Stokes Raman scattering microscope

    Institute of Scientific and Technical Information of China (English)

    Yuan Jing-He; Xiao Fan-Rong; Wang Gui-Ying; Xu Zhi-Zhan

    2005-01-01

    The coherent anti-Stokes Raman scattering (CARS) microscope with the combination of confocal and CARS techniques is a remarkable alternative for imaging chemical or biological specimens that neither fluoresce nor tolerate labelling. CARS is a nonlinear optical process, the imaging properties of CARS microscopy will be very different from the conventional confocal microscope. In this paper, the intensity distribution and the polarization property of the optical field near the focus was calculated. By using the Green function, the precise analytic solution to the wave equation of a Hertzian dipole source was obtained. We found that the intensity distributions vary considerably with the different experimental configurations and the different specimen shapes. So the conventional description of microscope (e.g. the point spread function) will fail to describe the imaging properties of the CARS microscope.

  12. Parameter estimation method for blurred cell images from fluorescence microscope

    Science.gov (United States)

    He, Fuyun; Zhang, Zhisheng; Luo, Xiaoshu; Zhao, Shulin

    2016-10-01

    Microscopic cell image analysis is indispensable to cell biology. Images of cells can easily degrade due to optical diffraction or focus shift, as this results in low signal-to-noise ratio (SNR) and poor image quality, hence affecting the accuracy of cell analysis and identification. For a quantitative analysis of cell images, restoring blurred images to improve the SNR is the first step. A parameter estimation method for defocused microscopic cell images based on the power law properties of the power spectrum of cell images is proposed. The circular radon transform (CRT) is used to identify the zero-mode of the power spectrum. The parameter of the CRT curve is initially estimated by an improved differential evolution algorithm. Following this, the parameters are optimized through the gradient descent method. Using synthetic experiments, it was confirmed that the proposed method effectively increased the peak SNR (PSNR) of the recovered images with high accuracy. Furthermore, experimental results involving actual microscopic cell images verified that the superiority of the proposed parameter estimation method for blurred microscopic cell images other method in terms of qualitative visual sense as well as quantitative gradient and PSNR.

  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. Compressive microscopic imaging with "positive-negative" light modulation

    Science.gov (United States)

    Yu, Wen-Kai; Yao, Xu-Ri; Liu, Xue-Feng; Lan, Ruo-Ming; Wu, Ling-An; Zhai, Guang-Jie; Zhao, Qing

    2016-07-01

    An experiment on compressive microscopic imaging with single-pixel detector and single-arm has been performed on the basis of "positive-negative" (differential) light modulation of a digital micromirror device (DMD). A magnified image of micron-sized objects illuminated by the microscope's own incandescent lamp has been successfully acquired. The image quality is improved by one more orders of magnitude compared with that obtained by conventional single-pixel imaging scheme with normal modulation using the same sampling rate, and moreover, the system is robust against the instability of light source and may be applied to very weak light condition. Its nature and the analysis of noise sources is discussed deeply. The realization of this technique represents a big step to the practical applications of compressive microscopic imaging in the fields of biology and materials science.

  15. 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.

  16. Microscopic images dataset for automation of RBCs counting

    Directory of Open Access Journals (Sweden)

    Sherif Abbas

    2015-12-01

    Full Text Available A method for Red Blood Corpuscles (RBCs counting has been developed using RBCs light microscopic images and Matlab algorithm. The Dataset consists of Red Blood Corpuscles (RBCs images and there RBCs segmented images. A detailed description using flow chart is given in order to show how to produce RBCs mask. The RBCs mask was used to count the number of RBCs in the blood smear image.

  17. Microscopic images dataset for automation of RBCs counting.

    Science.gov (United States)

    Abbas, Sherif

    2015-12-01

    A method for Red Blood Corpuscles (RBCs) counting has been developed using RBCs light microscopic images and Matlab algorithm. The Dataset consists of Red Blood Corpuscles (RBCs) images and there RBCs segmented images. A detailed description using flow chart is given in order to show how to produce RBCs mask. The RBCs mask was used to count the number of RBCs in the blood smear image.

  18. Microscopic neural image registration based on the structure of mitochondria

    Science.gov (United States)

    Cao, Huiwen; Han, Hua; Rao, Qiang; Xiao, Chi; Chen, Xi

    2017-02-01

    Microscopic image registration is a key component of the neural structure reconstruction with serial sections of neural tissue. The goal of microscopic neural image registration is to recover the 3D continuity and geometrical properties of specimen. During image registration, various distortions need to be corrected, including image rotation, translation, tissue deformation et.al, which come from the procedure of sample cutting, staining and imaging. Furthermore, there is only certain similarity between adjacent sections, and the degree of similarity depends on local structure of the tissue and the thickness of the sections. These factors make the microscopic neural image registration a challenging problem. To tackle the difficulty of corresponding landmarks extraction, we introduce a novel image registration method for Scanning Electron Microscopy (SEM) images of serial neural tissue sections based on the structure of mitochondria. The ellipsoidal shape of mitochondria ensures that the same mitochondria has similar shape between adjacent sections, and its characteristic of broad distribution in the neural tissue guarantees that landmarks based on the mitochondria distributed widely in the image. The proposed image registration method contains three parts: landmarks extraction between adjacent sections, corresponding landmarks matching and image deformation based on the correspondences. We demonstrate the performance of our method with SEM images of drosophila brain.

  19. Lactiferous vessel detection from microscopic cross-sectional images

    Science.gov (United States)

    Jariyawatthananon, Jirapath; Cooharojananone, Nagul; Lipikorn, Rajalida

    2014-04-01

    This paper presents the methods to detect and segment lactiferous vessels or rubber latex vessels from gray scale microscopic cross-sectional images using polynomial curve-fitting with maximum and minimum stationary points. Polynomial curve-fitting is used to detect the location of lactiferous vessels from an image of a non-dyed cross-sectional slice which was taken by a digital camera through microscope lens. The lactiferous vessels are then segmented from an image using maximum and minimum stationary points with morphological closing operation. Two species of rubber trees of age between one to two years old are sampled namely, RRIM600 and RRIT251. Two data sets contain 30 microscopic cross-sectional images of one-year old rubber tree's stems from each species are used in the experiments and the results reveal that most of the lactiferous vessel areas can be segmented correctly.

  20. Evidence from Opportunity's microscopic imager for water on Meridiani Planum

    DEFF Research Database (Denmark)

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

    2004-01-01

    on a millimeter scale; image mosaics of cross-stratification suggest that some sediments were deposited by flowing water. Vugs in some outcrop faces are probably molds formed by dissolution of relatively soluble minerals during diagenesis. Microscopic images support the hypothesis that hematite-rich spherules...

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

    NARCIS (Netherlands)

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

    2013-01-01

    RATIONALE: 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

  2. Compact Video Microscope Imaging System Implemented in Colloid Studies

    Science.gov (United States)

    McDowell, Mark

    2002-01-01

    Long description Photographs showing fiber-optic light source, microscope and charge-coupled discharge (CCD) camera head connected to camera body, CCD camera body feeding data to image acquisition board in PC, and Cartesian robot controlled via PC board. The Compact Microscope Imaging System (CMIS) is a diagnostic tool with intelligent controls for use in space, industrial, medical, and security applications. CMIS can be used in situ with a minimum amount of user intervention. This system can scan, find areas of interest in, focus on, and acquire images automatically. Many multiple-cell experiments require microscopy for in situ observations; this is feasible only with compact microscope systems. CMIS is a miniature machine vision system that combines intelligent image processing with remote control. The software also has a user-friendly interface, which can be used independently of the hardware for further post-experiment analysis. CMIS has been successfully developed in the SML Laboratory at the NASA Glenn Research Center and adapted for use for colloid studies and is available for telescience experiments. The main innovations this year are an improved interface, optimized algorithms, and the ability to control conventional full-sized microscopes in addition to compact microscopes. The CMIS software-hardware interface is being integrated into our SML Analysis package, which will be a robust general-purpose image-processing package that can handle over 100 space and industrial applications.

  3. Microscopic Image of Martian Surface Material on a Silicone Substrate

    Science.gov (United States)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for larger version of Figure 1 This image taken by the Optical Microscope on NASA's Phoenix Mars Lander shows soil sprinkled from the lander's Robot Arm scoop onto a silicone substrate. The substrate was then rotated in front of the microscope. This is the first sample collected and delivered for instrumental analysis onboard a planetary lander since NASA's Viking Mars missions of the 1970s. It is also the highest resolution image yet seen of Martian soil. The image is dominated by fine particles close to the resolution of the microscope. These particles have formed clumps, which may be a smaller scale version of what has been observed by Phoenix during digging of the surface material. The microscope took this image during Phoenix's Sol 17 (June 11), or the 17th Martian day after landing. The scale bar is 1 millimeter (0.04 inch). Zooming in on the Martian Soil In figure 1, three zoomed-in portions are shown with an image of Martian soil particles taken by the Optical Microscope on NASA's Phoenix Mars Lander. The left zoom box shows a composite particle. The top of the particle has a green tinge, possibly indicating olivine. The bottom of the particle has been reimaged at a different focus position in black and white (middle zoom box), showing that this is a clump of finer particles. The right zoom box shows a rounded, glassy particle, similar to those which have also been seen in an earlier sample of airfall dust collected on a surface exposed during landing. The shadows at the bottom of image are of the beams of the Atomic Force Microscope. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  4. 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.

  5. Automatic phases recognition in pituitary surgeries by microscope images classification

    OpenAIRE

    Lalys, Florent; Riffaud, Laurent; Morandi, Xavier; Jannin, Pierre

    2010-01-01

    International audience; The segmentation of the surgical workflow might be helpful for providing context-sensitive user interfaces, or generating automatic report. Our approach focused on the automatic recognition of surgical phases by microscope image classification. Our workflow, including images features extraction, image database labelisation, Principal Component Analysis (PCA) transformation and 10-fold cross-validation studies was performed on a specific type of neurosurgical interventi...

  6. Organizing and accessing methods for massive medical microscopic image data

    Science.gov (United States)

    Deng, Yan; Tang, Lixin

    2007-12-01

    The development of electronic medical archives requests to mosaic the medical microscopic images to a whole one, and the stitching result is usually a massive file hard to be stored or accessed. The paper proposes a file format named Medical TIFF to organize the massive microscopic image data. The Medical TIFF organizes the massive image data in tiles, appends the thumbnail of the result image at the end of the file, and offers the way to add medical information into the image file. Then the paper designs a three-layer system to access the file: the Physical Layer gathers the Medical TIFF components dispersed over the file and organizes them hierarchically, the Logical Layer uses a two dimensional dynamic array to deal with the tiles, and the Application Layer provides the interfaces for the applications developed on the basis of the system.

  7. [Multiple transmission electron microscopic image stitching based on sift features].

    Science.gov (United States)

    Li, Mu; Lu, Yanmeng; Han, Shuaihu; Wu, Zhuobin; Chen, Jiajing; Liu, Zhexing; Cao, Lei

    2015-08-01

    We proposed a new stitching method based on sift features to obtain an enlarged view of transmission electron microscopic (TEM) images with a high resolution. The sift features were extracted from the images, which were then combined with fitted polynomial correction field to correct the images, followed by image alignment based on the sift features. The image seams at the junction were finally removed by Poisson image editing to achieve seamless stitching, which was validated on 60 local glomerular TEM images with an image alignment error of 62.5 to 187.5 nm. Compared with 3 other stitching methods, the proposed method could effectively reduce image deformation and avoid artifacts to facilitate renal biopsy pathological diagnosis.

  8. Edge Effects and Coupling Effects in Atomic Force Microscope Images

    Institute of Scientific and Technical Information of China (English)

    ZHANGXiang-jun; MENGYong-gang; WENShi-zhu

    2004-01-01

    The AFM images were obtained by an atomic force microscope (AFM) and transformed from the deformation of AFM micro cantilever probe. However, due to the surface topography and surface forces applied on the AFM tip of sample, the deformation of AFM probe results in obvious edge effects and coupling effects in the AFM images. The deformation of AFM probe was analyzed,the mechanism of the edge effects and the coupling effects was investigated, and their results in the AFM images were studied. It is demanstrated by the theoretical analysis and AFM experiments that the edge effects make lateral force images more clear than the topography images, also make extraction of frictional force force from lateral force images mare complex and difficult. While the coupling effects make the comparison between topography images and lateral force images mare advantage to acquire precise topography information by AFM.

  9. 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 ...

  10. 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.

  11. 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.

  12. Visualization and Analysis of 3D Microscopic Images

    Science.gov (United States)

    Long, Fuhui; Zhou, Jianlong; Peng, Hanchuan

    2012-01-01

    In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain. PMID:22719236

  13. 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....

  14. Simulation of scanning transmission electron microscope images on desktop computers

    Energy Technology Data Exchange (ETDEWEB)

    Dwyer, C., E-mail: christian.dwyer@mcem.monash.edu.au [Monash Centre for Electron Microscopy, Department of Materials Engineering, Monash University, Victoria 3800 (Australia)

    2010-02-15

    Two independent strategies are presented for reducing the computation time of multislice simulations of scanning transmission electron microscope (STEM) images: (1) optimal probe sampling, and (2) the use of desktop graphics processing units. The first strategy is applicable to STEM images generated by elastic and/or inelastic scattering, and requires minimal effort for its implementation. Used together, these two strategies can reduce typical computation times from days to hours, allowing practical simulation of STEM images of general atomic structures on a desktop computer.

  15. AOTF hyperspectral microscopic imaging for foodborne pathogenic bacteria detection

    Science.gov (United States)

    Park, Bosoon; Lee, Sangdae; Yoon, Seung-Chul; Sundaram, Jaya; Windham, William R.; Hinton, Arthur, Jr.; Lawrence, Kurt C.

    2011-06-01

    Hyperspectral microscope imaging (HMI) method which provides both spatial and spectral information can be effective for foodborne pathogen detection. The AOTF-based hyperspectral microscope imaging method can be used to characterize spectral properties of biofilm formed by Salmonella enteritidis as well as Escherichia coli. The intensity of spectral imagery and the pattern of spectral distribution varied with system parameters (integration time and gain) of HMI system. The preliminary results demonstrated determination of optimum parameter values of HMI system and the integration time must be no more than 250 ms for quality image acquisition from biofilm formed by S. enteritidis. Among the contiguous spectral imagery between 450 and 800 nm, the intensity of spectral images at 498, 522, 550 and 594 nm were distinctive for biofilm; whereas, the intensity of spectral images at 546 nm was distinctive for E. coli. For more accurate comparison of intensity from spectral images, a calibration protocol, using neutral density filters and multiple exposures, need to be developed to standardize image acquisition. For the identification or classification of unknown food pathogen samples, ground truth regions-of-interest pixels need to be selected for "spectrally pure fingerprints" for the Salmonella and E. coli species.

  16. Restoration of images from the scanning-tunneling microscope

    Science.gov (United States)

    Kokaram, A. C.; Persad, N.; Lasenby, J.; Fitzgerald, W. J.; McKinnon, A.; Welland, M.

    1995-08-01

    During the acquisition of an image from any probe microscope instrument, various noise sources cause distortion in the observed image. It is often the case that impulsive disturbances cause bright groups of pixels to replace the actual image data in these locations. Furthermore, the images from a probe microscope show some amount of blurring caused both by the instrument function and the material properties. In almost all image-processing applications it is important to remove any impulsive distortion that may be present before deblurring can be attempted. We give a technique for detecting these impulses and reconstructing the image. This technique is superior to the standard global application of median filters for the case considered. The reconstruction is limited only to the affected regions and therefore results in a much sharper and more meaningful image. With the assumption of Gaussian blur it is then possible to propose several different deblurring methodologies. We present a novel Wiener-filter deblurring implementation and compare it to both maximum-entropy and Richardson-Lucy deblurring.

  17. Progress in microscopic direct reaction modeling of nucleon induced reactions

    Energy Technology Data Exchange (ETDEWEB)

    Dupuis, M.; Bauge, E.; Hilaire, S.; Lechaftois, F.; Peru, S.; Pillet, N.; Robin, C. [CEA, DAM, DIF, Arpajon (France)

    2015-12-15

    A microscopic nuclear reaction model is applied to neutron elastic and direct inelastic scatterings, and pre-equilibrium reaction. The JLM folding model is used with nuclear structure information calculated within the quasi-particle random phase approximation implemented with the Gogny D1S interaction. The folding model for direct inelastic scattering is extended to include rearrangement corrections stemming from both isoscalar and isovector density variations occurring during a transition. The quality of the predicted (n,n), (n,n{sup '}), (n,xn) and (n,n{sup '}γ) cross sections, as well as the generality of the present microscopic approach, shows that it is a powerful tool that can help improving nuclear reactions data quality. Short- and long-term perspectives are drawn to extend the present approach to more systems, to include missing reactions mechanisms, and to consistently treat both structure and reaction problems. (orig.)

  18. Experiments on terahertz 3D scanning microscopic imaging

    Science.gov (United States)

    Zhou, Yi; Li, Qi

    2016-10-01

    Compared with the visible light and infrared, terahertz (THz) radiation can penetrate nonpolar and nonmetallic materials. There are many studies on the THz coaxial transmission confocal microscopy currently. But few researches on the THz dual-axis reflective confocal microscopy were reported. In this paper, we utilized a dual-axis reflective confocal scanning microscope working at 2.52 THz. In contrast with the THz coaxial transmission confocal microscope, the microscope adopted in this paper can attain higher axial resolution at the expense of reduced lateral resolution, revealing more satisfying 3D imaging capability. Objects such as Chinese characters "Zhong-Hua" written in paper with a pencil and a combined sheet metal which has three layers were scanned. The experimental results indicate that the system can extract two Chinese characters "Zhong," "Hua" or three layers of the combined sheet metal. It can be predicted that the microscope can be applied to biology, medicine and other fields in the future due to its favorable 3D imaging capability.

  19. Three-dimensional microscopic light field particle image velocimetry

    Science.gov (United States)

    Truscott, Tadd T.; Belden, Jesse; Ni, Rui; Pendlebury, Jonathon; McEwen, Bryce

    2017-03-01

    A microscopic particle image velocimetry (μ {PIV}) technique is developed based on light field microscopy and is applied to flow through a microchannel containing a backward-facing step. The only hardware difference from a conventional μPIV setup is the placement of a microlens array at the intermediate image plane of the microscope. The method combines this optical hardware alteration with post-capture computation to enable 3D reconstruction of particle fields. From these particle fields, we measure three-component velocity fields, but find that accurate velocity measurements are limited to the two in-plane components at discrete depths through the volume (i.e., 2C-3D). Results are compared with a computational fluid dynamics simulation.

  20. 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.

  1. Microscope Image of a Martian Soil Surface Sample

    Science.gov (United States)

    2008-01-01

    This is the closest view of the material underneath NASA's Phoenix Mars Lander. This sample was taken from the top centimeter of the Martian soil, and this image from the lander's Optical Microscope demonstrates its overall composition. The soil is mostly composed of fine orange particles, and also contains larger grains, about a tenth of a millimeter in diameter, and of various colors. The soil is sticky, keeping together as a slab of material on the supporting substrate even though the substrate is tilted to the vertical. The fine orange grains are at or below the resolution of the Optical Microscope. Mixed into the soil is a small amount&mdashabout 0.5 percent&mdashof white grains, possibly of a salt. The larger grains range from black to almost transparent in appearance. At the bottom of the image, the shadows of the Atomic Force Microscope (AFM) beams are visible. This image is 1 millimeter x 2 millimeters. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by JPL, Pasadena, Calif. Spacecraft development was by Lockheed Martin Space Systems, Denver.

  2. Root dentine and endodontic instrumentation: cutting edge microscopic imaging.

    Science.gov (United States)

    Atmeh, Amre R; Watson, Timothy F

    2016-06-06

    Cutting of the dental hard tissues is an integral part of restorative dentistry. Cutting of the root dentine is also needed in preparation prior to endodontic treatment, with significant commercial investment for the development of flexible cutting instruments based around nickel titanium (NiTi) alloys. This paper describes the evolution of endodontic cutting instruments, both in materials used, e.g. the transition from stainless steel to NiTi, and the design of the actual instruments themselves and their method of activation-by hand or motor driven. We have been examining tooth-cutting interactions microscopically for over 25 years using a variety of microscopic techniques; in particular, video-rate confocal microscopy. This has given a unique insight into how many of the procedures that we take for granted are achieved in clinical practice, by showing microscopic video images of the cutting as it occurs within the tooth. This technology has now been extended to allow imaging of the endodontic instrument and the root canal wall for the first time. We are able to image dentine distortion and crack propagation during endodontic filing of the root canal space. We are also able to visualize the often claimed, but seldom seen action of contemporary endodontic instruments.

  3. 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.

  4. 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.

  5. Image Degradation in Microscopic Images: Avoidance, Artifacts, and Solutions.

    Science.gov (United States)

    Roels, Joris; Aelterman, Jan; De Vylder, Jonas; Lippens, Saskia; Luong, Hiêp Q; Guérin, Christopher J; Philips, Wilfried

    2016-01-01

    The goal of modern microscopy is to acquire high-quality image based data sets. A typical microscopy workflow is set up in order to address a specific biological question and involves different steps. The first step is to precisely define the biological question, in order to properly come to an experimental design for sample preparation and image acquisition. A better object representation allows biological users to draw more reliable scientific conclusions. Image restoration can manipulate the acquired data in an effort to reduce the impact of artifacts (spurious results) due to physical and technical limitations, resulting in a better representation of the object of interest. However, precise usage of these algorithms is necessary so as to avoid further artifacts that might influence the data analysis and bias the conclusions. It is essential to understand image acquisition, and how it introduces artifacts and degradations in the acquired data, so that their effects on subsequent analysis can be minimized. This paper provides an overview of the fundamental artifacts and degradations that affect many micrographs. We describe why artifacts appear, in what sense they impact overall image quality, and how to mitigate them by first improving the acquisition parameters and then applying proper image restoration techniques.

  6. Computer aided quantification of pathological features for flexor tendon pulleys on microscopic images.

    Science.gov (United States)

    Liu, Yung-Chun; Chen, Hsin-Chen; Shih, Hui-Hsuan; Yang, Tai-Hua; Yang, Hsiao-Bai; Yang, Dee-Shan; Su, Fong-Chin; Sun, Yung-Nien

    2013-01-01

    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.

  7. 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.

  8. [A microscopic image mosaicing algorithm based on normalized moment of inertia].

    Science.gov (United States)

    Lu, Fang-jie; Xia, Shun-ren

    2007-11-01

    A fast microscopic image mosaicing method is proposed in this paper by making a study of the mosaic methods and the characteristics of microscopic images. In the paper, invariant local features based on normalized moment of inertia (NMI) are used to select the matching points and calculate the spatial translation. The experimental results demonstrate that this algorithm can achieve fast, effective microscopic image mosaicing.

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

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Akihisa, E-mail: take@spring8.or.jp; Uesugi, Kentaro; Suzuki, Yoshio [Japan Synchrotron Radiation Research Institute (JASRI / SPring-8), Sayo, Hyogo 679-5198 (Japan)

    2016-01-28

    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.

  10. Imaging using lateral bending modes of atomic force microscope cantilevers

    Science.gov (United States)

    Caron, A.; Rabe, U.; Reinstädtler, M.; Turner, J. A.; Arnold, W.

    2004-12-01

    Using scanning probe techniques, surface properties such as shear stiffness and friction can be measured with a resolution in the nanometer range. The torsional deflection or buckling of atomic force microscope cantilevers has previously been used in order to measure the lateral forces acting on the tip. This letter shows that the flexural vibration modes of cantilevers oscillating in their width direction parallel to the sample surface can also be used for imaging. These lateral cantilever modes exhibit vertical deflection amplitudes if the cantilever is asymmetric in thickness direction, e.g., by a trapezoidal cross section.

  11. A compact microscope setup for multimodal nonlinear imaging in clinics and its application to disease diagnostics.

    Science.gov (United States)

    Meyer, Tobias; Baumgartl, Martin; Gottschall, Thomas; Pascher, Torbjörn; Wuttig, Andreas; Matthäus, Christian; Romeike, Bernd F M; Brehm, Bernhard R; Limpert, Jens; Tünnermann, Andreas; Guntinas-Lichius, Orlando; Dietzek, Benjamin; Schmitt, Michael; Popp, Jürgen

    2013-07-21

    The past years have seen increasing interest in nonlinear optical microscopic imaging approaches for the investigation of diseases due to the method's unique capabilities of deep tissue penetration, 3D sectioning and molecular contrast. Its application in clinical routine diagnostics, however, is hampered by large and costly equipment requiring trained staff and regular maintenance, hence it has not yet matured to a reliable tool for application in clinics. In this contribution implementing a novel compact fiber laser system into a tailored designed laser scanning microscope results in a small footprint easy to use multimodal imaging platform enabling simultaneously highly efficient generation and acquisition of second harmonic generation (SHG), two-photon excited fluorescence (TPEF) as well as coherent anti-Stokes Raman scattering (CARS) signals with optimized CARS contrast for lipid imaging for label-free investigation of tissue samples. The instrument combining a laser source and a microscope features a unique combination of the highest NIR transmission and a fourfold enlarged field of view suited for investigating large tissue specimens. Despite its small size and turnkey operation rendering daily alignment dispensable the system provides the highest flexibility, an imaging speed of 1 megapixel per second and diffraction limited spatial resolution. This is illustrated by imaging samples of squamous cell carcinoma of the head and neck (HNSCC) and an animal model of atherosclerosis allowing for a complete characterization of the tissue composition and morphology, i.e. the tissue's morphochemistry. Highly valuable information for clinical diagnostics, e.g. monitoring the disease progression at the cellular level with molecular specificity, can be retrieved. Future combination with microscopic probes for in vivo imaging or even implementation in endoscopes will allow for in vivo grading of HNSCC and characterization of plaque deposits towards the detection of high

  12. Progression of radical reactions on microscopic scale in food emulsions

    DEFF Research Database (Denmark)

    Raudsepp, Piret

    Understanding the progression of lipid oxidation in oil-in-water emulsions from the aspect of the food quality and safety, consumer satisfaction and cleaner food label is of importance, because most of the food emulsions are oil-in-water emulsions. There is an increasing tendency in the food...... industry to incorporate unsaturated oils into food products, but that results in shortened shelf-life. Therefore, studying the factors and consequences of the oxidative instability provides beneficial insight into prolonging the antioxidative stage and inhibiting undergoing oxidation processes to improve...... the food quality and increase the shelflife of the food products. In the present work, lipid oxidation in oil-in-water emulsions was studied via conventional analytical and via novel state-of-the-art techniques. For the first time, the effect of mixing emulsions made of saturated medium-chain triglyceride...

  13. Progression of radical reactions on microscopic scale in food emulsions

    DEFF Research Database (Denmark)

    Raudsepp, Piret

    Understanding the progression of lipid oxidation in oil-in-water emulsions from the aspect of the food quality and safety, consumer satisfaction and cleaner food label is of importance, because most of the food emulsions are oil-in-water emulsions. There is an increasing tendency in the food...... the food quality and increase the shelflife of the food products. In the present work, lipid oxidation in oil-in-water emulsions was studied via conventional analytical and via novel state-of-the-art techniques. For the first time, the effect of mixing emulsions made of saturated medium-chain triglyceride...... industry to incorporate unsaturated oils into food products, but that results in shortened shelf-life. Therefore, studying the factors and consequences of the oxidative instability provides beneficial insight into prolonging the antioxidative stage and inhibiting undergoing oxidation processes to improve...

  14. First Results of the Athena Microscopic Imager Investigation

    Science.gov (United States)

    Herkenhoff, K.; Squyres, S.; Archinal, B.; Arvidson, R.; Bass, D.; Barrett, J.; Becker, K.; Becker, T.; Bell, J., III; Burr, D.

    2004-01-01

    The Athena science payload on the Mars Exploration Rovers (MER) includes the Microscopic Imager (MI). The MI is a fixed-focus camera mounted on an extendable arm, the Instrument Deployment Device (IDD). The MI acquires images at a spatial resolution of 30 microns/pixel over a broad spectral range (400 - 700 nm). The MI uses the same electronics design as the other MER cameras but its optics yield a field of view of 31 x 31 mm across a 1024 x 1024 pixel CCD image. The MI acquires images using only solar or skylight illumination of the target surface. A contact sensor is used to place the MI slightly closer to the target surface than its best focus distance (about 69 mm), allowing concave surfaces to be imaged in good focus. Coarse focusing (approx. 2 mm precision) is achieved by moving the IDD away from a rock target after contact is sensed. The MI optics are protected from the Martian environment by a retractable dust cover. This cover includes a Kapton window that is tinted orange to restrict the spectral bandpass to 500 - 700 nm, allowing crude color information to be obtained by acquiring images with the cover open and closed. The MI science objectives, instrument design and calibration, operation, and data processing were described by Herkenhoff et al. Initial results of the MI experiment on both MER rovers ('Spirit' and 'Opportunity') are described below.

  15. Imaging in primary progressive aphasia

    Energy Technology Data Exchange (ETDEWEB)

    Abe, K. [Department of Neurology, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565 (Japan); Ukita, H. [Rehabilitation Service, Osaka University Hospital, Osaka (Japan); Yanagihara, T. [Department of Neurology, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565 (Japan)

    1997-08-01

    Primary progressive aphasia (PPA) presents with aphasia, with or without other minor cognitive dysfunction. We report five patients with PPA to show the correlation between their clinical signs and imaging findings. The patients can be divided into those with nonfluent (group 1) and those with fluent (group 2) aphasia. The characteristic speech impairment was bradylalia in group 1 and word amnesia in group 2. Impairment of comprehension was common but mild in both groups. On MRI, patients in group 1 showed predominantly left frontal and perisylvian atrophy with reduced uptake in the same region on single photon emission computed tomography (SPECT) using technetium-99m hexamethyl propyleneamine oxime ({sup 99m}Tc HMPAO). Patients in group 2 showed left temporal atrophy involving the superior, middle and inferior temporal gyri, hippocampus and parahippocampal gyrus on MRI and reduced uptake in the same region on SPECT. These findings correlated well with the functional anatomy of speech impairment. (orig.). With 4 figs., 1 tab.

  16. EUV optical system for the reticle imaging microscope (RIM)

    Science.gov (United States)

    Glatzel, H.; Daniel, J.; Khajehnouri, K.; Mueller, U.; Roff, T.; Rosenbohm, J.; Sporer, S.

    2006-03-01

    The EUV optical system of the Reticle Imaging Microscope (RIM) for EUV mask inspection consists of a pinched Xeplasma source, a pupil-relayed Koehler-type illumination system and an equal-radii Cassegrain-type microscope with a 10x magnification1. The 3D surface topologies were characterized over spatial wavelengths ranging from the clear apertures down to a few nanometers by using a portfolio of instruments including contacting profilometry, phase-shifting interferometry at 633 nm at various magnifications and Atomic Force Microscopy. Measured 3D topography maps were Fourier analyzed and Power Spectral Densities (PSDs) are computed over spatial periods ranging from the critical aperture down to a few nm. Integrated RMS surface errors over typically reported spatial period ranges were computed. For a different optical system we improved our polishing process to reduce surface errors for spatial periods below 10 mm. PSDs and integrated RMS surface errors will be shown in comparison with typical RIM surfaces. All surfaces of the RIM optical system were coated with high-reflectivity coatings to maximize optical throughput. A description of the coatings and their performance had been published recently by Michael Kriese et al.2 The transmitted wavefront error (TWF) of the imager module was measured in a double pass configuration using a Fizeau-type Interferometer at 633 nm wavelength and a convex retrosphere. The measured TWF will be shown over the entire Numerical Aperture (NA = 0.0625) of the microscope. The integrated RMS of the TWF measured 0.79 nm.

  17. Automated pollen identification using microscopic imaging and texture analysis.

    Science.gov (United States)

    Marcos, J Víctor; Nava, Rodrigo; Cristóbal, Gabriel; Redondo, Rafael; Escalante-Ramírez, Boris; Bueno, Gloria; Déniz, Óscar; González-Porto, Amelia; Pardo, Cristina; Chung, François; Rodríguez, Tomás

    2015-01-01

    Pollen identification is required in different scenarios such as prevention of allergic reactions, climate analysis or apiculture. However, it is a time-consuming task since experts are required to recognize each pollen grain through the microscope. In this study, we performed an exhaustive assessment on the utility of texture analysis for automated characterisation of pollen samples. A database composed of 1800 brightfield microscopy images of pollen grains from 15 different taxa was used for this purpose. A pattern recognition-based methodology was adopted to perform pollen classification. Four different methods were evaluated for texture feature extraction from the pollen image: Haralick's gray-level co-occurrence matrices (GLCM), log-Gabor filters (LGF), local binary patterns (LBP) and discrete Tchebichef moments (DTM). Fisher's discriminant analysis and k-nearest neighbour were subsequently applied to perform dimensionality reduction and multivariate classification, respectively. Our results reveal that LGF and DTM, which are based on the spectral properties of the image, outperformed GLCM and LBP in the proposed classification problem. Furthermore, we found that the combination of all the texture features resulted in the highest performance, yielding an accuracy of 95%. Therefore, thorough texture characterisation could be considered in further implementations of automatic pollen recognition systems based on image processing techniques.

  18. Time-gated FLIM microscope for corneal metabolic imaging

    Science.gov (United States)

    Silva, Susana F.; Batista, Ana; Domingues, José Paulo; Quadrado, Maria João.; Morgado, António Miguel

    2016-03-01

    Detecting corneal cells metabolic alterations may prove a valuable tool in the early diagnosis of corneal diseases. Nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) are autofluorescent metabolic co-factors that allow the assessment of metabolic changes through non-invasive optical methods. These co-factors exhibit double-exponential fluorescence decays, with well-separated short and lifetime components, which are related to their protein-bound and free-states. Corneal metabolism can be assessed by measuring the relative contributions of these two components. For that purpose, we have developed a wide-field time-gated fluorescence lifetime microscope based on structured illumination and one-photon excitation to record FAD lifetime images from corneas. NADH imaging was not considered as its UV excitation peak is regarded as not safe for in vivo measurements. The microscope relies on a pulsed blue diode laser (λ=443 nm) as excitation source, an ultra-high speed gated image intensifier coupled to a CCD camera to acquire fluorescence signals and a Digital Micromirror Device (DMD) to implement the Structured Illumination technique. The system has a lateral resolution better than 2.4 μm, a field of view of 160 per 120 μm and an optical sectioning of 6.91 +/- 0.45 μm when used with a 40x, 0.75 NA, Water Immersion Objective. With this setup we were able to measure FAD contributions from ex-vivo chicken corneas collected from a local slaughterhouse..

  19. RECENT PROGRESS ON PARTICLE IMAGE VELOCIMETRY IN CHINA

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    An up-to-date review of recent progress on Particle Image Velocimetry (PIV) instrumentations was extensively presented in the paper. Around 80 literatures were referenced. Among various aspects of PIV advances, the present concern was mainly placed on progresses of advanced algorithms and microscopic PIV. Attention was specifically directed toward contributions of domestic researchers to these subjects, which were stressed throughout the discussion. In addition, diverse applications of PIV technology in China, e.g., turbulence measurement, hydrodynamics, rotating flows, two-phase flows, were specifically summarized.

  20. Automated morphological analysis approach for classifying colorectal microscopic images

    Science.gov (United States)

    Marghani, Khaled A.; Dlay, Satnam S.; Sharif, Bayan S.; Sims, Andrew J.

    2003-10-01

    Automated medical image diagnosis using quantitative measurements is extremely helpful for cancer prognosis to reach a high degree of accuracy and thus make reliable decisions. In this paper, six morphological features based on texture analysis were studied in order to categorize normal and cancer colon mucosa. They were derived after a series of pre-processing steps to generate a set of different shape measurements. Based on the shape and the size, six features known as Euler Number, Equivalent Diamater, Solidity, Extent, Elongation, and Shape Factor AR were extracted. Mathematical morphology is used firstly to remove background noise from segmented images and then to obtain different morphological measures to describe shape, size, and texture of colon glands. The automated system proposed is tested to classifying 102 microscopic samples of colorectal tissues, which consist of 44 normal color mucosa and 58 cancerous. The results were first statistically evaluated, using one-way ANOVA method in order to examine the significance of each feature extracted. Then significant features are selected in order to classify the dataset into two categories. Finally, using two discrimination methods; linear method and k-means clustering, important classification factors were estimated. In brief, this study demonstrates that abnormalities in low-level power tissue morphology can be distinguished using quantitative image analysis. This investigation shows the potential of an automated vision system in histopathology. Furthermore, it has the advantage of being objective, and more importantly a valuable diagnostic decision support tool.

  1. A fast and efficient segmentation scheme for cell microscopic image.

    Science.gov (United States)

    Lebrun, G; Charrier, C; Lezoray, O; Meurie, C; Cardot, H

    2007-04-27

    Microscopic cellular image segmentation schemes must be efficient for reliable analysis and fast to process huge quantity of images. Recent studies have focused on improving segmentation quality. Several segmentation schemes have good quality but processing time is too expensive to deal with a great number of images per day. For segmentation schemes based on pixel classification, the classifier design is crucial since it is the one which requires most of the processing time necessary to segment an image. The main contribution of this work is focused on how to reduce the complexity of decision functions produced by support vector machines (SVM) while preserving recognition rate. Vector quantization is used in order to reduce the inherent redundancy present in huge pixel databases (i.e. images with expert pixel segmentation). Hybrid color space design is also used in order to improve data set size reduction rate and recognition rate. A new decision function quality criterion is defined to select good trade-off between recognition rate and processing time of pixel decision function. The first results of this study show that fast and efficient pixel classification with SVM is possible. Moreover posterior class pixel probability estimation is easy to compute with Platt method. Then a new segmentation scheme using probabilistic pixel classification has been developed. This one has several free parameters and an automatic selection must dealt with, but criteria for evaluate segmentation quality are not well adapted for cell segmentation, especially when comparison with expert pixel segmentation must be achieved. Another important contribution in this paper is the definition of a new quality criterion for evaluation of cell segmentation. The results presented here show that the selection of free parameters of the segmentation scheme by optimisation of the new quality cell segmentation criterion produces efficient cell segmentation.

  2. Spatial Domain based Image Enhancement Techniques for Scanned Electron Microscope-SEM-images

    Directory of Open Access Journals (Sweden)

    Rakhi Chanana

    2011-07-01

    Full Text Available The growing need for efficiently processing and analyzing the information contained in digital images is a continuous challenge in order to apply image processing. Digital images are captured from different imaging media elements like cameras, scanned electron microscopes etc. While going through the imaging process, Images get distorted in various forms resulting in extreme dark or light areas. All these things lead to the loss of information. The goal in each case is to extract useful information. In that case, Image processing extracts useful information by applying various image enhancement and algorithms. In this paper, we have discussed a practical implementation of various enhancement methods for Scanned Electron Microscope (SEM images and their experimental results. SEM images lead to very dark and light areas in an image. While imaging the information in the front scene is not only the source of information but some scenes on the dark side can also have the useful information. Before processing any further we require to enhance such images and one of the enhancement techniques i.e. Histogram Statistics comes out to be an ideal approach.

  3. Identification of staphylococcus species with hyperspectral microscope imaging and classification algrorithms

    Science.gov (United States)

    Hyperspectral microscope imaging is presented as a rapid and efficient tool to classify foodborne bacteria species. The spectral data were obtained from five different species of Staphylococcus spp. with a hyperspectral microscope imaging system that provided a maximum of 89 contiguous spectral imag...

  4. 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

  5. A STED-FLIM microscope applied to imaging the natural killer cell immune synapse

    Science.gov (United States)

    Lenz, M. O.; Brown, A. C. N.; Auksorius, E.; Davis, D. M.; Dunsby, C.; Neil, M. A. A.; French, P. M. W.

    2011-03-01

    We present a stimulated emission depletion (STED) fluorescence lifetime imaging (FLIM) microscope, excited by a microstructured optical fibre supercontinuum source that is pumped by a femtosecond Ti:Sapphire-laser, which is also used for depletion. Implemented using a piezo-scanning stage on a laser scanning confocal fluorescence microscope system with FLIM realised using time correlated single photon counting (TCSPC), this provides convenient switching between confocal and STED-FLIM with spatial resolution down to below 60 nm. We will present our design considerations to make a robust instrument for biological applications including a comparison between fixed phase plate and spatial light modulator (SLM) approaches to shape the STED beam and the correlation of STED and confocal FLIM microscopy. Following our previous application of FLIM-FRET to study intercellular signalling at the immunological synapse (IS), we are employing STED microscopy to characterize the spatial distribution of cellular molecules with subdiffraction resolution at the IS. In particular, we are imaging cytoskeletal structure at the Natural Killer cell activated immune synapse. We will also present our progress towards multilabel STED microscopy to determine how relative spatial molecular organization, previously undetectable by conventional microscopy techniques, is important for NK cell cytotoxic function. Keywords: STED, Stimulated Emission Depletion Microscopy, Natural Killer (NK) cell, Fluorescence lifetime imaging, FLIM, Super resolution microscopy.

  6. Progressive Wavelet Correlation for Image Recognition

    OpenAIRE

    Stojanovic, Igor

    2013-01-01

    An algorithm for recognition and retrieval of image from image collection is developed. Basis of the algorithm is the progressive wavelet correlation. The final result is the recognition and retrieval of the wanted image, if it is in the image collection. Instructions for the choice of correlation threshold value for obtaining desired results are defined. The areas where the algorithm can be applied are also discussed. To increase efficiency is presented two phases solution. The first phase u...

  7. Progressive refinement for robust image registration

    Institute of Scientific and Technical Information of China (English)

    Li Song; Yuanhua Zhou; Jun Zhou

    2005-01-01

    @@ A new image registration algorithm with robust cost function and progressive refinement estimation is developed on the basis of direct method (DM). The robustness lies in M-estimation to avert larger local noise and outliers.

  8. Research Progress on Image Segmentation

    Science.gov (United States)

    1981-06-01

    AUTHOR. HANON A.R. AND RISEMAM E- 𔃻. TITLE G SE MENTATION OF NATURA’ CNIE PAGE 6 REFERENCES FOR< IMAGE...PUBLICAIION-DAIA : 1976 KEY-WORDS : IMAGE SEGMENTATION AU’ihOR I KRUGER K. P., THOMPSON W. B, AND TURNER A. F, TITLE COMPUTER DIAGNOSIS OF TNEUMOCONIOSIS

  9. 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...

  10. Tissue classification in microscope imaging based on a discrete-band spectroscopy

    OpenAIRE

    Yoon, Gilwon; Kim, Hyejeong

    2011-01-01

    Automatic classification of tissue types has a potential use in endoscopic or microscopic imaging. For this study, the microscope images from composite tissue samples were measured. Different shades of red meat such as beef and pork and bloodless tissues such as chicken breast and fat were chosen to provide with similar and contrasted colors. We applied a partial least squares discriminant analysis (PLS-DA) to classify the tissue type of the image pixels. With the RGB color images that are us...

  11. Building 3D aerial image in photoresist with reconstructed mask image acquired with optical microscope

    Science.gov (United States)

    Chou, C. S.; Tang, Y. P.; Chu, F. S.; Huang, W. C.; Liu, R. G.; Gau, T. S.

    2012-03-01

    Calibration of mask images on wafer becomes more important as features shrink. Two major types of metrology have been commonly adopted. One is to measure the mask image with scanning electron microscope (SEM) to obtain the contours on mask and then simulate the wafer image with optical simulator. The other is to use an optical imaging tool Aerial Image Measurement System (AIMSTM) to emulate the image on wafer. However, the SEM method is indirect. It just gathers planar contours on a mask with no consideration of optical characteristics such as 3D topography structures. Hence, the image on wafer is not predicted precisely. Though the AIMSTM method can be used to directly measure the intensity at the near field of a mask but the image measured this way is not quite the same as that on the wafer due to reflections and refractions in the films on wafer. Here, a new approach is proposed to emulate the image on wafer more precisely. The behavior of plane waves with different oblique angles is well known inside and between planar film stacks. In an optical microscope imaging system, plane waves can be extracted from the pupil plane with a coherent point source of illumination. Once plane waves with a specific coherent illumination are analyzed, the partially coherent component of waves could be reconstructed with a proper transfer function, which includes lens aberration, polarization, reflection and refraction in films. It is a new method that we can transfer near light field of a mask into an image on wafer without the disadvantages of indirect SEM measurement such as neglecting effects of mask topography, reflections and refractions in the wafer film stacks. Furthermore, with this precise latent image, a separated resist model also becomes more achievable.

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

    Institute of Scientific and Technical Information of China (English)

    LI QingLi; XUE YongQi; ZHANG JingFa; XIAO GongHai

    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 seotions 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.

  13. 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.

  14. 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....

  15. BIOLUMINESCENCE IMAGING: PROGRESS AND APPLICATIONS

    OpenAIRE

    Badr, Christian E.; Tannous, Bakhos A

    2011-01-01

    Application of bioluminescence imaging has grown tremendously in the past decade and has significantly contributed to the core conceptual advances in biomedical research. This technology provides valuable means for monitoring of different biological processes for immunology, oncology, virology and neuroscience. In this review, we will discuss current trends in bioluminescence and its application in different fields with emphasis on cancer research.

  16. Identification and Classification of Adenovirus Particles in Digital Microscopic Images using Active Contours

    Directory of Open Access Journals (Sweden)

    Manjunatha Hiremath

    2014-06-01

    Full Text Available Medical imaging is the technique and process used to create images of the human body or medical science. Digital image processing is the use of computer algorithms to perform image processing on digital images. Microscope image processing dates back a half century when it was realized that some of the techniques of image capture and manipulation, first developed for television, could also be applied to images captured through the microscope. This paper presents semi-automated segmentation and identification of adenovirus particles using active contour with multi grid segmentation model. The geometric features are employed to identify the adenovirus particles in digital microscopic image. The min-max, 3 rules are used for recognition of adenovirus particles. The results are compared with manual method obtained by microbiologist.

  17. Influence of slant of objective on image formation in optical microscopes

    Institute of Scientific and Technical Information of China (English)

    Jiangang Wang; Rainer Koning

    2008-01-01

    A microscope image formation model based on scalar diffraction and Fourier optics has been developed, which takes a slant angle between the optical axis and the observed surface into account. The theoretical investigations of the imaging of line structures using this model show that reflection type microscopes are much stronger influenced by the slant angle than transmission type microscopes. In addition, the slant angle changes the image contrast and the image shape of a line structure, especially its edge. The larger the slant angle, the stronger the decrease of the image contrast, and the less steep the edge slope in both types of microscopes. Furthermore, the larger the numerical aperture of the objective, the less the effect of the slant angle on the line image shape.

  18. A HYBRID METHOD FOR AUTOMATIC COUNTING OF MICROORGANISMS IN MICROSCOPIC IMAGES

    OpenAIRE

    2016-01-01

    Microscopic image analysis is an essential process to enable the automatic enumeration and quantitative analysis of microbial images. There are several system are available for numerating microbial growth. Some of the existing method may be inefficient to accurately count the overlapped microorganisms. Therefore, in this paper we proposed an efficient method for automatic segmentation and counting of microorganisms in microscopic images. This method uses a hybrid approach based on...

  19. Progressive Diagenetic Alteration of Macro- and Micro-Scopic Biosignatures in Ancient Springs and Spring-Fed Lacustrine Environments

    Science.gov (United States)

    Potter-McIntyre, S. L.; Williams, J.; Phillips-Landers, C.; O'Connell, L.

    2016-05-01

    Microscopic and macroscopic biosignatures in modern spring deposits are compared with the Quaternary and Jurassic examples to show how these features are progressively altered and preserved on geologic time scales.

  20. 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.

  1. Nicotiana Occidentalis Chloroplast Ultrastructure imaged with Transmission Electron Microscopes Working at Different Accelerating Voltages

    OpenAIRE

    SVIDENSKÁ, Silvie

    2010-01-01

    The main goal of this thesis is to study and compare electron microscopy images of Nicotiana Occidentalis chloroplasts, obtained from two types of transmission electron microscopes,which work with different accelerating voltage of 80kV and 5kV. The two instruments, TEM JEOL 1010 and low voltage electron microscope LVEM5 are employed for experiments. In the first theoretical part, principle of electron microscopy and chloroplast morphology is described. In experimental part, electron microscop...

  2. Study on microscope hyperspectral medical imaging method for biomedical quantitative analysis

    Institute of Scientific and Technical Information of China (English)

    LI QingLi; XUE YongQi; XIAO GongHai; ZHANG JingFa

    2008-01-01

    A microscopic pushbroom hyperspectral imaging system was developed based on the microscopic technology and spectral imaging technology according to the principle of spectral imager in remote sensing. The basic principle and key technologies of this system were presented and the system per-formance was also analyzed. Some methods and algorithms were proposed to preprocess and nor-malize the microscopic hyperspectral data and retrieve the transmittance spectrum of samples. As a case study, the microscopic hyperspectral imaging system was used to image the retina sections of different rats and get some significant results. Experiment results show that the system can be used for the quantitative assessment and evaluating the effect of medication in biomedical research.

  3. An image acquisition system built with a modular frame grabber for scanning electron microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, S. [The Enrico Fermi Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Kapp, O.H. [The Department of Radiology and The Enrico Fermi Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    1995-09-01

    We have built an image acquisition and processing system based on a modular frame grabber board (MFG) for use with scanning (or scanning transmission) electron microscopes. The variable-scan acquisition module of the grabber board provides compatibility with electron microscopes processing various scan speeds, e.g., the very slow scan rate of our mirror-type electron microscope. In addition to the acquisition function, the board provides many image processing capabilities. A special time-base unit was built to synchronize the acquisition system with the scanning system on the electron microscope. A Windows application has been built to operate the MFG as well as manage all functions of the electron microscope. Using this approach we have been able to greatly simplify the task of digital image acquisition as well as creating a powerful and seamless interface to our Windows-based environment. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  4. Erythrocyte Features for Malaria Parasite Detection in Microscopic Images of Thin Blood Smear: A Review

    Directory of Open Access Journals (Sweden)

    Salam Shuleenda Devi

    2016-12-01

    Full Text Available Microscopic image analysis of blood smear plays a very important role in characterization of erythrocytes in screening of malaria parasites. The characteristics feature of erythrocyte changes due to malaria parasite infection. The microscopic features of the erythrocyte include morphology, intensity and texture. In this paper, the different features used to differentiate the non- infected and malaria infected erythrocyte have been reviewed.

  5. Development of in vivo confocal microscope for reflection and fluorescence imaging simultaneously

    Science.gov (United States)

    Ahn, MyoungKi; Chun, ByungSeon; Song, Cheol; Gweon, DaeGab

    2010-02-01

    In-vivo confocal microscope technology can be applied to the medical imaging diagnosis and new drug development. We present an in-vivo confocal microscope that can acquire a reflection image and a fluorescence image simultaneously and independently. To obtain reflection confocal images, we used a linearly polarized diode laser with the wavelength of 830 nm. To acquire fluorescence confocal images, we used two diode lasers with the wavelength of 488 nm and 660 nm, respectively. Because of a broad wavelength bandwidth from visible (488 nm) to near-IR (830 nm), we designed and optimized the optical system to reduce various optical aberrations. With the developed in-vivo confocal microscope, we performed ex-vivo cell imaging and in-vivo imaging of the human skin.

  6. The Impact of the Condenser on Cytogenetic Image Quality in Digital Microscope System

    Directory of Open Access Journals (Sweden)

    Liqiang Ren

    2013-01-01

    Full Text Available Background: Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved.

  7. Towards a digital model for an electron-microscope image.

    Science.gov (United States)

    Burge, R E; Ali, S M

    1988-01-01

    An image model is defined based on the boundaries between image regions with different textures and series of descriptions of those textures. Six models of texture are studied under the categories of pixel-based and region-based models. Several techniques for the determination of the unit-cell of textures are presented. The model is applied to the consideration of (a) image correction, (b) the classification of image texture, (c) image enhancement including averaging of detail in periodic specimens, and (d) image data compression. A floating point format, which provides a significant simplification for the Huffman code, is also introduced.

  8. Direct imaging Raman microscope based on tunable wavelength excitation and narrow band emission detection

    NARCIS (Netherlands)

    Puppels, G.J.; Grond, M.; Greve, J.

    1993-01-01

    A new type of imaging Raman microscope is described. First the advantages and disadvantages of the two possible approaches to Raman microscopy based on signal detection by means of a charge-coupled-device camera (i.e., direct imaging and image reconstruction) are discussed. Arguments are given to sh

  9. The Primary Study of Microscopical Focus Problem in the Color Image of Pigmented Spots

    Institute of Scientific and Technical Information of China (English)

    WANG Li; JIANG Da-lin

    2006-01-01

    Pigmented spot is an important branch in the science of skin. But when processing those images, the microscopical focusing problem arises. It affects the image recognition later. In order to find the best method to solve it, comparison and analysis are given to various existing methods of image fusion in this paper.The conclusion is wavelet transform based on pixel -level.

  10. Novel Scanning Near-Field Microwave Microscopes Capable of Imaging Semiconductors and Metals

    Science.gov (United States)

    Imtiaz, Atif; Tselev, Alexander; Anlage, Steven

    2003-03-01

    To study novel physics in condensed matter and materials science, experimental techniques of probing the high frequency electrical properties of materials are limited in resolution to the wavelength of the incident electromagnetic wave. We report here a novel near-field microscope that is capable of operation at radio and microwave frequencies[1]. The spatial resolution is comparable to NSOM in the scanning capacitance mode of the microscope[2]. Our objective is to image materials contrast at microwave frequencies and improve the spatial resolution. The microscope is sensitive to losses in materials, and we will present evidence of sheet resistance contrast in a Boron-doped Silicon sample. These experiments are performed with two versions of the near-field microwave microscope: one has integrated STM-feedback for distance control and the second one maintains a constant frequency shift through Distance Following technique. We will discuss the data on these films in light of a transmission line and lumped element model of the microscope. The microscope is an attractive platform for measuring local losses and local nonlinear properties of a rich variety of semiconducting and correlated-electron materials. [1] D.E. Steinhauer, et.al, "Quantitative Imaging of Sheet Resistance with a Scanning Near-Field Microwave Microscope", Appl. Phys. Lett. 72, 861 (1998) [2] Atif Imtiaz and Steven M. Anlage, "A novel STM-assisted microwave microscope with capacitance and loss imaging capability", Ultramicroscopy (in press); cond-mat/0203540

  11. Multithreshold progressive image sharing with compact shadows

    Science.gov (United States)

    Chen, Lee Shu-Teng; Lin, Ja-Chen

    2010-01-01

    We propose a multithreshold progressive reconstruction method. The image is encoded three times using Joint Photographic Experts Group (JPEG): first with a low-quality factor, then with a medium-quality factor, and last with a high-quality factor. Huffman coding is employed to encode the difference between the important image and the high-quality JPEG decompressed image. The three JPEG codes and the Huffman code are shared, respectively, according to four prespecified thresholds. The n-generated equally important shadows can be stored or transmitted using n channels in parallel. Cooperation among these generated shadows can progressively reconstruct the important image. The reconstructed image is loss-free when the number of collected shadows reaches the largest threshold. Each shadow is very compact and so can be hidden successfully in the JPEG codes of cover images to reduce the probability of being attacked when transmitted in an unfriendly environment. Comparisons with other image sharing methods are made. The contributions, such as easiness to apply to scalable Moving Picture Experts Group (MPEG) video transmission or resistance to differential attack, are also included.

  12. Imaging of Tissue Micro-Structures using a Multi-Modal Microscope Design

    Energy Technology Data Exchange (ETDEWEB)

    Demos, S G; Lieber, C A; Lin, B; Ramsamooj, R

    2005-08-12

    We investigate a microscope design that offers high signal sensitivity and hyperspectral imaging capabilities and allows for implementation of various optical imaging approaches while its operational complexity is minimized. This system utilizes long working distance microscope objectives that enable for off-axis illumination of the tissue thereby allowing for excitation at any optical wavelength and nearly eliminating spectral noise from the optical elements. Preliminary studies using human and animal tissues demonstrate the feasibility of this approach for real-time imaging of intact tissue microstructures using autofluorescence and light scattering imaging methods.

  13. Imaging of Tissue Micro-Structures using a Multi-Modal Microscope Design

    Energy Technology Data Exchange (ETDEWEB)

    Demos, S G; Lieber, C A; Lin, B; Ramsamooj, R

    2005-08-12

    We investigate a microscope design that offers high signal sensitivity and hyperspectral imaging capabilities and allows for implementation of various optical imaging approaches while its operational complexity is minimized. This system utilizes long working distance microscope objectives that enable for off-axis illumination of the tissue thereby allowing for excitation at any optical wavelength and nearly eliminating spectral noise from the optical elements. Preliminary studies using human and animal tissues demonstrate the feasibility of this approach for real-time imaging of intact tissue microstructures using autofluorescence and light scattering imaging methods.

  14. Sub-diffuse structured light imaging provides macroscopic maps of microscopic tissue structure (Conference Presentation)

    Science.gov (United States)

    Kanick, Stephen C.

    2016-03-01

    The onset and progression of cancer introduces changes to the intra-cellular ultrastructural components and to the morphology of the extracellular matrix. While previous work has shown that localized scatter imaging is sensitive to pathology-induced differences in these aspects of tissue microstructure, wide adaptation this knowledge for surgical guidance is limited by two factors. First, the time required to image with confocal-level localization of the remission signal can be substantial. Second, localized (i.e. sub-diffuse) scatter remission intensity is influenced interchangeably by parameters that define scattering frequency and anisotropy. This similarity relationship must be carefully considered in order to obtain unique estimates of biomarkers that define either the scatter density or features that describe the distribution (e.g. shape, size, and orientation) of scatterers. This study presents a novel approach that uses structured light imaging to address both of these limitations. Monte Carlo data were used to model the reflectance intensity over a wide range of spatial frequencies, reduced scattering coefficients, absorption coefficients, and a metric of the scattering phase function that directly maps to the fractal dimension of scatter sizes. The approach is validated in tissue-simulating phantoms constructed with user-tuned scattering phase functions. The validation analysis shows that the phase function can be described in the presence of different scatter densities or background absorptions. Preliminary data from clinical tissue specimens show quantitative images of both the scatter density and the tissue fractal dimension for various tissue types and pathologies. These data represent a novel wide-field quantitative approach to mapping microscopic structural biomarkers that cannot be obtained with standard diffuse imaging. Implications for the use of this approach to assess surgical margins will be discussed.

  15. Calculation of confocal microscope images of cholesteric blue phases

    Science.gov (United States)

    Fukuda, Jun-ichi; Okumura, Yasushi; Kikuchi, Hirotsugu

    2016-03-01

    Real-space images of bulk cholesteric blue phases (BPs) have been successfully obtained by confocal microscopy observations using structural color without doping fluorescent dye. However, theoretical interpretation of these images (for example, the understanding of the relation between intensity distribution and the ordering of BPs) remains challenging because typical lattice spacing of BPs is of the order of the wavelength of visible light, and therefore geometrical optics is entirely useless. In this work, we present a numerical approach to calculate the confocal images of BPs by solving the Maxwell equations. Calculated confocal images are consistent with experimental observations in terms of in-plane symmetry.

  16. Common tasks in microscopic and ultrastructural image analysis using ImageJ.

    Science.gov (United States)

    Papadopulos, Francesca; Spinelli, Matthew; Valente, Sabrina; Foroni, Laura; Orrico, Catia; Alviano, Francesco; Pasquinelli, Gianandrea

    2007-01-01

    Cooperation between research communities and software-development teams has led to the creation of novel software. The purpose of this paper is to show an alternative work method based on the usage of ImageJ (http://rsb.info.nih.gov/ij/), which can be effectively employed in solving common microscopic and ultrastructural image analysis tasks. As an open-source software, ImageJ provides the possibility to work in a free-development/sharing world. Its very "friendly" graphical user interface helps users to manage and edit biomedical images. The on-line material such as handbooks, wikis, and plugins leads users through various functions, giving clues about potential new applications. ImageJ is not only a morphometric analysis software, it is sufficiently flexible to be adapted to the numerous requirements tasked in the laboratories as routine as well as research demands. Examples include area measurements on selectively stained tissue components, cell count and area measurements at single cell level, immunohistochemical antigen quantification, and immunoelectron microscopy gold particle count.

  17. Electron microscope studies. Progress report, June 1, 1992--November 1, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Crewe, A.V.; Kapp, O.H.

    1993-11-01

    During the past year we have continued our work on the mirror-corrected high resolution STEM. We have made significant progress in the design and fabrication of the various microscope sub-systems and have completed a new display system. Additional calculations and computer simulations have been performed to confirm the original theory of mirror correctors. In our biological work we have made a careful study of the structure of globins, vertebrate and invertebrate, using the accumulated information contained in the Brookhaven Data Bank (3D structures), the Protein Identification Resource (ID sequences) and the data we have obtained with the STEM. Statistical templates have been generated to predict various classes of globins.

  18. Progress in Circular SAR Imaging Technique

    Directory of Open Access Journals (Sweden)

    Hong Wen

    2012-06-01

    Full Text Available Circular SAR (CSAR is a newly developed all-directional high resolution 3D imaging mode in recent years, to satisfy the demand of finer observation. The National Key Laboratory of Science and Technology on Microwave Imaging, Institute of Electronics, Chinese Academy of Sciences (MITL, IECAS, had the first test flight experiment in Aug. 2011 with a P-band full polarization SAR system, and successfully obtained the all-directional high resolution circular SAR image. The initial results show that CSAR technique has the encouraging potential capability in the fields of high precision mapping, disaster evaluation, resource management and the other related applications. This paper firstly makes a detailed discussion on the progress of circular SAR imaging technique, which emphases on the several airborne experiments performed these years to show CSAR’s attractive features, then studies and illustrates the key techniques, and finally discusses the development trends.

  19. Effect of hydration film on scanning images of atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A standard calibration grating was used for image scanning to investigate the effect of hydration films on imaging resolution by Atomic Force Microscope (AFM). The results showed that the hydration films greatly affect the imaging resolution for the tapping mode, but no evident effect on the contact mode. The possible reasons for the effect of hydration films on scanning images of AFM are also brought forward here.

  20. Progress in millimeter-wave imaging

    Science.gov (United States)

    Wikner, David A.

    2011-03-01

    The field of millimeter-wave (MMW) imaging has progressed significantly over the last two decades. The most obvious evidence of this is the widespread use of MMW full-body scanners, now commonly found in airports. The path to this point has been the result of the work of a wide range of experts from many scientific and engineering disciplines. This article represents one perspective of this progress. The development of MMW imagers, and all their associated component technologies, image processing techniques, clever engineering, etc. has been driven by a relatively small number of interesting applications. It has been known for about 70 years that RF energy can be used to "see" through things like clouds and detect, for example, hostile aircraft. As the RF frequency goes up to 35, 100, or 340 GHz, it becomes possible to image through obscurants with much improved resolution. However, as frequency increases, attenuation increases as well, so selecting the right frequency for the application is an important point. The challenge of seeing through obscurants such as fog, smoke and dust drives one towards a MMW imaging solution. Typical applications include guiding aircraft through low visibility conditions, detecting nearby watercraft in the fog, and searching for concealed weapons. So, while these capabilities have been demonstrated numerous times over the years, the practical and affordable implementation of the systems to accomplish these goals is where the real story lies.

  1. Quantitatively characterizing the microstructural features of breast ductal carcinoma tissues in different progression stages by Mueller matrix microscope.

    Science.gov (United States)

    Dong, Yang; Qi, Ji; He, Honghui; He, Chao; Liu, Shaoxiong; Wu, Jian; Elson, Daniel S; Ma, Hui

    2017-08-01

    Polarization imaging has been recognized as a potentially powerful technique for probing the microstructural information and optical properties of complex biological specimens. Recently, we have reported a Mueller matrix microscope by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission-light microscope, and applied it to differentiate human liver and cervical cancerous tissues with fibrosis. In this paper, we apply the Mueller matrix microscope for quantitative detection of human breast ductal carcinoma samples at different stages. The Mueller matrix polar decomposition and transformation parameters of the breast ductal tissues in different regions and at different stages are calculated and analyzed. For more quantitative comparisons, several widely-used image texture feature parameters are also calculated to characterize the difference in the polarimetric images. The experimental results indicate that the Mueller matrix microscope and the polarization parameters can facilitate the quantitative detection of breast ductal carcinoma tissues at different stages.

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

    Science.gov (United States)

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

    2013-12-01

    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. 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. 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. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  3. 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.

  4. High contrast, depth-resolved thermoreflectance imaging using a Nipkow disk confocal microscope.

    Science.gov (United States)

    Summers, J A; Yang, T; Tuominen, M T; Hudgings, J A

    2010-01-01

    We have developed a depth-resolved confocal thermal imaging technique that is capable of measuring the temperature distribution of an encapsulated or semi-obstructed device. The technique employs lock-in charge coupled device-based thermoreflectance imaging via a Nipkow disk confocal microscope, which is used to eliminate extraneous reflections from above or below the imaging plane. We use the confocal microscope to predict the decrease in contrast and dynamic range due to an obstruction for widefield thermoreflectance, and we demonstrate the ability of confocal thermoreflectance to maintain a high contrast and thermal sensitivity in the presence of large reflecting obstructions in the optical path.

  5. A HYBRID METHOD FOR AUTOMATIC COUNTING OF MICROORGANISMS IN MICROSCOPIC IMAGES

    Directory of Open Access Journals (Sweden)

    P.Kalavathi

    2016-03-01

    Full Text Available Microscopic image analysis is an essential process to enable the automatic enumeration and quantitative analysis of microbial images. There are several system are available for numerating microbial growth. Some of the existing method may be inefficient to accurately count the overlapped microorganisms. Therefore, in this paper we proposed an efficient method for automatic segmentation and counting of microorganisms in microscopic images. This method uses a hybrid approach based on morphological operation, active contour model and counting by region labelling process. The colony count value obtained by this proposed method is compared with the manual count and the count value obtained from the existing method

  6. Deep Tissue Microscopic Imaging of the Kidney with a Gradient-Index Lens System.

    Science.gov (United States)

    Li, Xin; Yu, Weiming

    2008-04-01

    Intravital microscopy using two-photon excitation is proven to be a valuable tool for studying the kidney and associated disease processes. However, routine performance of intravital kidney imaging is limited by the fact that fluorescence signal is attenuated by the tissue and at certain tissue depth lost its strength completely. For most of the animal tissues, this finite imaging depth is limited to a few hundred microns. Currently it is not possible to non-invasively image the kidney beyond the superficial tissue layers of the cortex. This has imposed significant limitations on the animal models one can use for imaging since structure such the glomerulus is typically located below the superficial layer of the cortex that can not be imaged using a conventional fluorescence microscope. Here we report the use of a needle-like lens system based on gradient-index (GRIN) microlenses capable of transferring high quality fluorescence images of the tissue through a regular microscope objective for deep tissue imaging of the kidney. By combining this GRIN lens system with a Zeiss LSM 510 NLO microscope, we are able to extend the imaging depth for kidney tissues far beyond the few hundred microns limit. This GRIN lens imaging system provides an alternative microendoscopic imaging tool that will enhance current intravital kidney imaging techniques for studying structural and functional properties of local tissues at locations below the superficial layers of the kidney.

  7. Resolution criteria in double-slit microscopic imaging experiments

    Science.gov (United States)

    You, Shangting; Kuang, Cuifang; Zhang, Baile

    2016-09-01

    Double-slit imaging is widely used for verifying the resolution of high-resolution and super-resolution microscopies. However, due to the fabrication limits, the slit width is generally non-negligible, which can affect the claimed resolution. In this paper we theoretically calculate the electromagnetic field distribution inside and near the metallic double slit using waveguide mode expansion method, and acquire the far-field image by vectorial Fourier optics. We find that the slit width has minimal influence when the illuminating light is polarized parallel to the slits. In this case, the claimed resolution should be based on the center-to-center distance of the double-slit.

  8. Advanced characterization of microscopic kidney biopsies utilizing image analysis techniques.

    Science.gov (United States)

    Goudas, Theodosios; Doukas, Charalampos; Chatziioannou, Aristotle; Maglogiannis, Ilias

    2012-01-01

    Correct annotation and identification of salient regions in Kidney biopsy images can provide an estimation of pathogenesis in obstructive nephropathy. This paper presents a tool for the automatic or manual segmentation of such regions along with methodology for their characterization in terms of the exhibited pathology. The proposed implementation is based on custom code written in Java and the utilization of open source tools (i.e. RapidMiner, ImageJ). The corresponding implementation details along with the initial evaluation of the proposed integrated system are also presented in the paper.

  9. 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...

  10. Content Progressive Coding of Limited Bits/pixel Images

    DEFF Research Database (Denmark)

    Jensen, Ole Riis; Forchhammer, Søren

    1999-01-01

    A new lossless context based method for content progressive coding of limited bits/pixel images is proposed. Progressive coding is achieved by separating the image into contelnt layers. Digital maps are compressed up to 3 times better than GIF.......A new lossless context based method for content progressive coding of limited bits/pixel images is proposed. Progressive coding is achieved by separating the image into contelnt layers. Digital maps are compressed up to 3 times better than GIF....

  11. Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging.

    Science.gov (United States)

    Cui, Xiquan; Lee, Lap Man; Heng, Xin; Zhong, Weiwei; Sternberg, Paul W; Psaltis, Demetri; Yang, Changhuei

    2008-08-05

    Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (approximately 0.9 microm for the first and approximately 0.8 microm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as Caenorhabditis elegans; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different Caenorhabditis elegans mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications.

  12. Texture analysis of liver fibrosis microscopic images: a study on the effect of biomarkers

    Institute of Scientific and Technical Information of China (English)

    Amr Amin; Doaa Mahmoud-Ghoneim

    2011-01-01

    Chronic hepatic injury results in liver fibrosis with eventual progression to irreversible cirrhosis. Liver fibrogenesis involves the activation of the quiescent hepatic stellate cell into an activated myofibroblast that is characterized by α-smooth muscle actin (α-SMA) expression and the production of collagens (types Ⅰ and Ⅲ). In the present study,rats were randomly divided into three groups: (i) control group, where rats were only treated with a vehicle; (ii) fibrosis group, where rats were treated with carbon tetrachloride (CCl4) to induce liver fibrosis; and (iii) silymarin group,where rats were protected with silymarin during CCl4 treatment. Rats were sacrificed and sections of liver tissue were counterstained with hematoxylin and eosin and Masson's trichrome. Other sections were immunostained using collagens and α-SMA primary antibodies. Fibrosis was confirmed using serum marker measurements. Microscopic images of the stained sections were acquired and digitized.The Biomarker Index of Fibrosis (BIF) was calculated from the images by quantifying the percentage of stained fibers.Statistical methods of texture analysis (TA), namely cooccurrence and run-length matrices, were applied on the digital images followed by classification using agglomerative hierarchical clustering and linear discriminant analysis with cross validation. TA applied on different biomarkers was successful in discriminating between the groups,showing 100% sensitivity and specificity for classification between the control and fibrosis groups using any biomarker. Some classification attempts showed dependence on the biomarker used, especially for classification between the silymarin and fibrosis groups, which showed optimal results using Masson's trichrome. TA results were consistent with both BIF and serum marker measurements.

  13. Resolution criteria in double-slit microscopic imaging experiments

    Science.gov (United States)

    You, Shangting; Kuang, Cuifang; Zhang, Baile

    2016-01-01

    Double-slit imaging is widely used for verifying the resolution of high-resolution and super-resolution microscopies. However, due to the fabrication limits, the slit width is generally non-negligible, which can affect the claimed resolution. In this paper we theoretically calculate the electromagnetic field distribution inside and near the metallic double slit using waveguide mode expansion method, and acquire the far-field image by vectorial Fourier optics. We find that the slit width has minimal influence when the illuminating light is polarized parallel to the slits. In this case, the claimed resolution should be based on the center-to-center distance of the double-slit. PMID:27640808

  14. Microscopic and macroscopic models for the onset and progression of Alzheimer's disease

    Science.gov (United States)

    Bertsch, Michiel; Franchi, Bruno; Carla Tesi, Maria; Tosin, Andrea

    2017-10-01

    In the first part of this paper we review a mathematical model for the onset and progression of Alzheimer’s disease (AD) that was developed in subsequent steps over several years. The model is meant to describe the evolution of AD in vivo. In Achdou et al (2013 J. Math. Biol. 67 1369–92) we treated the problem at a microscopic scale, where the typical length scale is a multiple of the size of the soma of a single neuron. Subsequently, in Bertsch et al (2017 Math. Med. Biol. 34 193–214) we concentrated on the macroscopic scale, where brain neurons are regarded as a continuous medium, structured by their degree of malfunctioning. In the second part of the paper we consider the relation between the microscopic and the macroscopic models. In particular we show under which assumptions the kinetic transport equation, which in the macroscopic model governs the evolution of the probability measure for the degree of malfunctioning of neurons, can be derived from a particle-based setting. The models are based on aggregation and diffusion equations for β-Amyloid (Aβ from now on), a protein fragment that healthy brains regularly produce and eliminate. In case of dementia Aβ monomers are no longer properly washed out and begin to coalesce forming eventually plaques. Two different mechanisms are assumed to be relevant for the temporal evolution of the disease: (i) diffusion and agglomeration of soluble polymers of amyloid, produced by damaged neurons; (ii) neuron-to-neuron prion-like transmission. In the microscopic model we consider mechanism (i), modelling it by a system of Smoluchowski equations for the amyloid concentration (describing the agglomeration phenomenon), with the addition of a diffusion term as well as of a source term on the neuronal membrane. At the macroscopic level instead we model processes (i) and (ii) by a system of Smoluchowski equations for the amyloid concentration, coupled to a kinetic-type transport equation for the distribution function of

  15. Expert Segmentation for the Extraction of Biomedical Structures in Microscopical Images

    Science.gov (United States)

    Botto, A.; Casali, Anna Maria; Dellepiane, Silvana G.; Ghilino, G.; Vernazza, Gianni L.

    1989-05-01

    To overcome the typical difficulties for the extraction of biomedical structures in microscopical images, a knowledge-based system has been designed with the aim of performing a model-driven segmentation towards automatic structure recognition. The work deals with the characterization of cell populations in human embryonal and foetal organs, in particular blood vessels and nervous cells. By using a-priori known description (in linguistic form) about the structures to be detected, a thresholding segmentation is initially used for locating darker pixels (markers). Then gradient extraction, region-growing, or other techniques are invoked around the area bounding markers. The computation of some specific attributes of the analyzed areas drives the recognition process allowing to maintain regions where structures are detected, and discard regions where structure presence is not verified. The segmentation and recognition process is controlled by a production system whose rules are activated on the basis of the input data, the progressive results, and the information (provided by the user) about the structures to be localized. Some results are presented to the user, obtained by changing processing parameters. They correspond to recognized maps with different reliability factors.

  16. 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......-component DMPC-DSPC bilayers and a remarkable enhanced hydrolytic activity of the PLA/sub 2/-enzyme for the DMPC-rich phase is seen. Furthermore, in a supported double bilayer system a characteristic ripple structure, most likely related to the formation of the P/sub beta /-ripple phase is observed....

  17. [Application of data fusion of microscopic spectral imaging in reservoir characterization].

    Science.gov (United States)

    Li, Jing; Zha, Ming; Guo, Yuan-Ling; Chen, Yong

    2011-10-01

    In recent years, spectral imaging technique has been applied widely in mineralogy and petrology. The technique combines the spectral technique with imaging technique. The samples can be analyzed and recognized both in spectra and space by using the technique. However, the problem is how to acquire the needful information from a large number of data of spectral imaging, and how to enhance the needful information. In the present paper, the experimental data were processed by using the technique of data fusion of microscopic spectral imaging. The space distribution map of chemical composition and physical parameters of samples were obtained. The result showed that the distribution of different hydrocarbon in the reservoirs, pore connectivity, etc. were revealed well. The technique of data fusion of microscopic spectral imaging provided a new method for reservoir characterization.

  18. Cerenkov ring imaging detector development: Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Aston, D.; Bienz, T.; Bird, F.; Dasu, S.; Dunwoodie, W.; Hallewell, G.; Kawahara, H.; Kwon, Y.; Leith, D.; Ratcliff, B.

    1988-10-01

    We present recent progress on the construction and testing of the first drift boxes and single electron detectors as they come from the production line. These detectors will be used for particle identification using the Ring Imaging technique in the SLD experiment at SLAC. Various experimental results are presented, including single electron pulse height measurements as a function of gas gain, detector gating capability, uniformity of response across the wire plane, charge division performance of a single electron signal, average pulse shape and its comparison with predicted shape, and cross-talk. 14 refs., 11 figs.

  19. Automatic segmentation of trophectoderm in microscopic images of human blastocysts.

    Science.gov (United States)

    Singh, Amarjot; Au, Jason; Saeedi, Parvaneh; Havelock, Jon

    2015-01-01

    Accurate assessment of embryos viability is an extremely important task in the optimization of in vitro fertilization treatment outcome. One of the common ways of assessing the quality of a human embryo is grading it on its fifth day of development based on morphological quality of its three main components (Trophectoderm, Inner Cell Mass, and the level of expansion or the thickness of its Zona Pellucida). In this study, we propose a fully automatic method for segmentation and measurement of TE region of blastocysts (day-5 human embryos). Here, we eliminate the inhomogeneities of the blastocysts surface using the Retinex theory and further apply a level-set algorithm to segment the TE regions. We have tested our method on a dataset of 85 images and have been able to achieve a segmentation accuracy of 84.6% for grade A, 89.0% for grade B, and 91.7% for grade C embryos.

  20. Automated Assessment of Keratocyte Density in Stromal Images from the ConfoScan 4 Confocal Microscope

    Science.gov (United States)

    Bourne, William M.; Patel, Sanjay V.

    2010-01-01

    Purpose. To develop a program to determine cell densities in images from the ConfoScan 4 (Nidek, Inc., Freemont, CA) confocal microscope and compare the densities with those determined in images obtained by the Tandem Scanning confocal microscope (Tandem Scanning Corp., Reston, VA). Methods. A program was developed that used image-processing routines to identify stromal cell nuclei in images from the ConfoScan 4 confocal microscope. Cell selection parameters were set to match cell densities from the program with those determined manually in 15 normal corneas of 15 volunteers. The program was tested on scans from 16 other normal volunteers and 17 volunteers 3 years after LASIK. Cell densities were compared to densities determined by manual assessment and to those in scans by the Tandem Scanning confocal microscope in the same corneas. Results. The difference in cell density between the automatic and manual assessment was −539 ± 3005 cells/mm3 (mean ± SD, P = 0.11) in the 16 test corneas. Densities estimated from the ConfoScan 4 agreed with those from the Tandem Scanning confocal microscope in all regions of the stroma except in the anterior 10%, where the ConfoScan 4 indicated a 30% lower density. Conclusions. Differences in anterior stromal cell density between the ConfoScan 4 and the Tandem Scanning confocal microscope can be explained by the different optical designs. The lower spatial resolution of the ConfoScan 4 limits its ability to resolve thin layers. The adaptation of our earlier cell-counting program to the ConfoScan 4 provides a timesaving, objective, and reproducible means of determining stromal cell densities in images from the ConfoScan 4. PMID:19892869

  1. High-speed video imaging and digital analysis of microscopic features in contracting striated muscle cells

    Science.gov (United States)

    Roos, Kenneth P.; Taylor, Stuart R.

    1993-02-01

    The rapid motion of microscopic features such as the cross striations of single contracting muscle cells are difficult to capture with conventional optical microscopes, video systems, and image processing approaches. An integrated digital video imaging microscope system specifically designed to capture images from single contracting muscle cells at speeds of up to 240 Hz and to analyze images to extract features critical for the understanding of muscle contraction is described. This system consists of a brightfield microscope with immersion optics coupled to a high-speed charge-coupled device (CCD) video camera, super-VHS (S- VHS) and optical media disk video recording (OMDR) systems, and a semiautomated digital image analysis system. Components are modified to optimize spatial and temporal resolution to permit the evaluation of submicrometer features in real physiological time. This approach permits the critical evaluation of the magnitude, time course, and uniformity of contractile function throughout the volume of a single living cell with higher temporal and spatial resolutions than previously possible.

  2. 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.

  3. X-ray imaging with grazing-incidence microscopes developed for the LIL program.

    Science.gov (United States)

    Rosch, R; Boutin, J Y; le Breton, J P; Gontier, D; Jadaud, J P; Reverdin, C; Soullié, G; Lidove, G; Maroni, R

    2007-03-01

    This article describes x-ray imaging with grazing-incidence microscopes, developed for the experimental program carried out on the Ligne d'Integration Laser (LIL) facility [J. P. Le Breton et al., Inertial Fusion Sciences and Applications 2001 (Elsevier, Paris, 2002), pp. 856-862] (24 kJ, UV-0.35 nm). The design includes a large target-to-microscope (400-700 mm) distance required by the x-ray ablation issues anticipated on the Laser MégaJoule facility [P. A. Holstein et al., Laser Part. Beams 17, 403 (1999)] (1.8 MJ) which is under construction. Two eight-image Kirkpatrick-Baez microscopes [P. Kirkpatrick and A. V. Baez J. Opt. Soc. Am. 38, 766 (1948)] with different spectral wavelength ranges and with a 400 mm source-to-mirror distance image the target on a custom-built framing camera (time resolution of approximately 80 ps). The soft x-ray version microscope is sensitive below 1 keV and its spatial resolution is better than 30 microm over a 2-mm-diam region. The hard x-ray version microscope has a 10 microm resolution over an 800-microm-diam region and is sensitive in the 1-5 keV energy range. Two other x-ray microscopes based on an association of toroidal/spherical surfaces (T/S microscopes) produce an image on a streak camera with a spatial resolution better than 30 microm over a 3 mm field of view in the direction of the camera slit. Both microscopes have been designed to have, respectively, a maximum sensitivity in the 0.1-1 and 1-5 keV energy range. We present the original design of these four microscopes and their test on a dc x-ray tube in the laboratory. The diagnostics were successfully used on LIL first experiments early in 2005. Results of soft x-ray imaging of a radiative jet during conical shaped laser interaction are shown.

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

    Directory of Open Access Journals (Sweden)

    Kimori Yoshitaka

    2010-07-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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.

  5. Feature-point-extracting-based automatically mosaic for composite microscopic images

    Institute of Scientific and Technical Information of China (English)

    YIN YanSheng; ZHAO XiuYang; TIAN XiaoFeng; LI Jia

    2007-01-01

    Image mosaic is a crucial step in the three-dimensional reconstruction of composite materials to align the serial images. A novel method is adopted to mosaic two SiC/Al microscopic images with an amplification coefficient of 1000. The two images are denoised by Gaussian model, and feature points are then extracted by using Harris corner detector. The feature points are filtered through Canny edge detector. A 40x40 feature template is chosen by sowing a seed in an overlapped area of the reference image, and the homologous region in floating image is acquired automatically by the way of correlation analysis. The feature points in matched templates are used as feature point-sets. Using the transformational parameters acquired by SVD-ICP method, the two images are transformed into the universal coordinates and merged to the final mosaic image.

  6. Automatic Cell Detection in Bright-Field Microscope Images Using SIFT, Random Forests, and Hierarchical Clustering.

    Science.gov (United States)

    Mualla, Firas; Scholl, Simon; Sommerfeldt, Bjorn; Maier, Andreas; Hornegger, Joachim

    2013-12-01

    We present a novel machine learning-based system for unstained cell detection in bright-field microscope images. The system is fully automatic since it requires no manual parameter tuning. It is also highly invariant with respect to illumination conditions and to the size and orientation of cells. Images from two adherent cell lines and one suspension cell line were used in the evaluation for a total number of more than 3500 cells. Besides real images, simulated images were also used in the evaluation. The detection error was between approximately zero and 15.5% which is a significantly superior performance compared to baseline approaches.

  7. Opportunity Microscopic Imager Results from the Western Rim of Endeavour Crater

    Science.gov (United States)

    Herkenhoff, K. E.; Arvidson, R. E.; Mittlefehldt, D. W.; Sullivan, R. J.

    2016-01-01

    The Athena science payload on the Mars Exploration Rovers (MER Spirit and Opportunity) includes the Microscopic Imager (MI), a fixed focus close-up camera mounted on the instrument arm. The MI acquires images at a scale of 31 micrometers/pixel over a broad spectral range (400 to 700 nm) using only natural illumination of target surfaces. Radio signals from Spirit have not been received since March 2010, so attempts to communicate with that rover ceased in mid-2011. The Opportunity MI optics were contaminated by a global dust storm in 2007. That contamination continues to reduce the contrast of MI images, and is being monitored by occasionally imaging the sky.

  8. Note: A novel atomic force microscope fast imaging approach: Variable-speed scanning

    Science.gov (United States)

    Zhang, Yudong; Fang, Yongchun; Yu, Jie; Dong, Xiaokun

    2011-05-01

    Imaging speed is one of the key factors limiting atomic force microscope's (AFM) wide applications. To improve its performance, a variable-speed scanning (VSS) method is designed in this note for an AFM. Specifically, in the VSS mode, the scanning speed is tuned online according to the feedback information to properly distribute imaging time along sample surface. Furthermore, some practical mechanism is proposed to determine the best time of moving the AFM tip to the next scanned point. The contrast experiment results show that the VSS method speeds up the imaging rate while ensuring image quality.

  9. 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...

  10. 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...

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

    NARCIS (Netherlands)

    Hulst, van N.F.; Segerink, F.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 dielectri

  12. 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...

  13. Tracking of colloidal particles using microscopic image sequence analysis - Application to particulate microelectrophoresis and particle deposition

    NARCIS (Netherlands)

    Wit, PJ; Busscher, HJ

    1997-01-01

    A method for colloidal particle tracking in microscopic video image sequences is presented, based upon minimization of a matrix containing the distances between predicted and measured particle positions within a field of view. The software required for particle tracking can be easily implemented in

  14. 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...

  15. 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...

  16. 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 th...

  17. 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

  18. 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.

  19. Restoration of distorted colour microscopic images from transverse chromatic aberration of imperfect lenses.

    Science.gov (United States)

    Wu, H-S; Murray, J; Morgello, S; Fiel, M I; Schiano, T; Kalir, T; Deligdisch, L; Gil, J

    2011-02-01

    An algorithm is presented for restoration of colour microscopic images with distortions from imperfect microscope lenses having transverse chromatic aberrations, resulting in a magnification that slightly varies with wavelengths or colours. The differential of each colour component image is computed as the difference between the component image and its slightly magnified version. The absolute values in the differential component images are generally higher at the edges where greater discontinuities occur. The two cross-correlation functions of the absolute differentials between red and green colours and between red and blue colours are then computed. The maximum in the two cross-correlation functions were sought, respectively, and the cross-correlation delays were then calculated. The two cross-correlation delays were used to determine dispersions and to realign the three colour components. Results of real microscopic images are provided. The restored image and the original are compared both visually and quantitatively in terms of the estimated entropies measured for the degree of concentrations using vector distributions.

  20. Multispectral Microscopic Imager (MMI): Multispectral Imaging of Geological Materials at a Handlens Scale

    Science.gov (United States)

    Farmer, J. D.; Nunez, J. I.; Sellar, R. G.; Gardner, P. B.; Manatt, K. S.; Dingizian, A.; Dudik, M. J.; McDonnell, G.; Le, T.; Thomas, J. A.; Chu, K.

    2011-12-01

    The Multispectral Microscopic Imager (MMI) is a prototype instrument presently under development for future astrobiological missions to Mars. The MMI is designed to be a arm-mounted rover instrument for use in characterizing the microtexture and mineralogy of materials along geological traverses [1,2,3]. Such geological information is regarded as essential for interpreting petrogenesis and geological history, and when acquired in near real-time, can support hypothesis-driven exploration and optimize science return. Correlated microtexure and mineralogy also provides essential data for selecting samples for analysis with onboard lab instruments, and for prioritizing samples for potential Earth return. The MMI design employs multispectral light-emitting diodes (LEDs) and an uncooled focal plane array to achieve the low-mass (Robotic Arm Camera (RAC; 5) and the Mars Science Laboratory's Mars Hand Lens Imager (MAHLI; 6). In this report we will review the capabilities of the MMI by highlighting recent lab and field applications, including: 1) glove box deployments in the Astromaterials lab at Johnson Space Center to analyze Apollo lunar samples; 2) GeoLab glove box deployments during the 2011 Desert RATS field trials in northern AZ to characterize analog materials collected by astronauts during simulated EVAs; 3) field deployments on Mauna Kea Volcano, Hawaii, during NASA's 2010 ISRU field trials, to analyze materials at the primary feedstock mining site; 4) lab characterization of geological samples from a complex, volcanic-hydrothermal terrain in the Cady Mts., SE Mojave Desert, California. We will show how field and laboratory applications have helped drive the development and refinement of MMI capabilities, while identifying synergies with other potential payload instruments (e.g. X-ray Diffraction) for solving real geological problems.

  1. Mathematical Progress in Expressive Image Synthesis I

    CERN Document Server

    2014-01-01

    This book presents revised versions of the best papers selected from the symposium “Mathematical Progress in Expressive Image Synthesis” (MEIS2013) held in Fukuoka, Japan, in 2013. The topics cover various areas of computer graphics (CG), such as surface deformation/editing, character animation, visual simulation of fluids, texture and sound synthesis, and photorealistic rendering. From a mathematical point of view, the book also presents papers addressing discrete differential geometry, Lie theory, computational fluid dynamics, function interpolation, and learning theory. This book showcases the latest joint efforts between mathematicians, CG researchers, and practitioners exploring important issues in graphics and visual perception. The book provides a valuable resource for all computer graphics researchers seeking open problem areas, especially those now entering the field who have not yet selected a research direction.

  2. Secondary electron imaging of monolayer materials inside a transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Cretu, Ovidiu, E-mail: cretu.ovidiu@nims.go.jp; Lin, Yung-Chang; Suenaga, Kazutomo [National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565 (Japan)

    2015-08-10

    A scanning transmission electron microscope equipped with a backscattered and secondary electron detector is shown capable to image graphene and hexagonal boron nitride monolayers. Secondary electron contrasts of the two lightest monolayer materials are clearly distinguished from the vacuum level. A signal difference between these two materials is attributed to electronic structure differences, which will influence the escape probabilities of the secondary electrons. Our results show that the secondary electron signal can be used to distinguish between the electronic structures of materials with atomic layer sensitivity, enhancing its applicability as a complementary signal in the analytical microscope.

  3. X-ray Bragg magnifier microscope as a linear shift invariant imaging system: image formation and phase retrieval.

    Science.gov (United States)

    Vagovič, P; Svéda, L; Cecilia, A; Hamann, E; Pelliccia, D; Gimenez, E N; Korytár, D; Pavlov, K M; Zápražný, Z; Zuber, M; Koenig, T; Olbinado, M; Yashiro, W; Momose, A; Fiederle, M; Baumbach, T

    2014-09-01

    We present the theoretical description of the image formation with the in-line germanium Bragg Magnifier Microscope (BMM) and the first successful phase retrieval of X-ray holograms recorded with this imaging system. The conditions under which the BMM acts as a linear shift invariant system are theoretically explained and supported by the experiment. Such an approach simplifies the mathematical treatment of the image formation and reconstruction as complicated propagation of the wavefront onto inclined planes can be avoided. Quantitative phase retrieval is demonstrated using a test sample and a proof of concept phase imaging of a spider leg is also presented.

  4. Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images.

    Science.gov (United States)

    Handfield, Louis-François; Strome, Bob; Chong, Yolanda T; Moses, Alan M

    2015-03-15

    Quantifying variability in protein expression is a major goal of systems biology and cell-to-cell variability in subcellular localization pattern has not been systematically quantified. We define a local measure to quantify cell-to-cell variability in high-throughput microscope images and show that it allows comparable measures of variability for proteins with diverse subcellular localizations. We systematically estimate cell-to-cell variability in the yeast GFP collection and identify examples of proteins that show cell-to-cell variability in their subcellular localization. Automated image analysis methods can be used to quantify cell-to-cell variability in microscope images. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Detection and Classification of Cancer from Microscopic Biopsy Images Using Clinically Significant and Biologically Interpretable Features

    Science.gov (United States)

    Kumar, Rajesh; Srivastava, Subodh

    2015-01-01

    A framework for automated detection and classification of cancer from microscopic biopsy images using clinically significant and biologically interpretable features is proposed and examined. The various stages involved in the proposed methodology include enhancement of microscopic images, segmentation of background cells, features extraction, and finally the classification. An appropriate and efficient method is employed in each of the design steps of the proposed framework after making a comparative analysis of commonly used method in each category. For highlighting the details of the tissue and structures, the contrast limited adaptive histogram equalization approach is used. For the segmentation of background cells, k-means segmentation algorithm is used because it performs better in comparison to other commonly used segmentation methods. In feature extraction phase, it is proposed to extract various biologically interpretable and clinically significant shapes as well as morphology based features from the segmented images. These include gray level texture features, color based features, color gray level texture features, Law's Texture Energy based features, Tamura's features, and wavelet features. Finally, the K-nearest neighborhood method is used for classification of images into normal and cancerous categories because it is performing better in comparison to other commonly used methods for this application. The performance of the proposed framework is evaluated using well-known parameters for four fundamental tissues (connective, epithelial, muscular, and nervous) of randomly selected 1000 microscopic biopsy images. PMID:27006938

  6. 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.

  7. Image analyses of collagen types and thickness in oral sub mucous fibrosis stained with picrosirius red under polarizing microscope

    Directory of Open Access Journals (Sweden)

    Venkatesh V Kamath

    2013-01-01

    Full Text Available Context: Oral submucous fibrosis (OSF is a potentially malignant oral disorder leading to increased fibrosis in the sub-epithelial layer. The collagen in the condition has been a subject of intense scrutiny in an attempt to understand the pathogenesis of the disease. Aim: The present study aims to quantify and qualify the collagen fibers in different histological grades of OSF using picrosirius red stain under the polarizing microscope. The quantification of the fibrosis was carried out using image analysis software and the fibers were graded according to staining hue and intensity into their respective subtypes. Comparison was done with normal mucosa, scar/keloid tissue samples. Materials and Methods: The present study included OSF (n = 50 of differing histological grades, keloid/scar (n = 4 and normal mucosa (n = 6 as control cases. Histological assessment was performed on hematoxylin and eosin stained sections. Picrosirius red stained slides were observed under a polarizing microscope for assessment of collagen subtypes. Quantification of collagen was done under polarizing microscope and image parameters were analyzed using ProReg® Capture Pro 2.8.8 (Lawrence and Mayo India Pvt Ltd, 2011 image analysis software. Results: The epithelial thickness in OSF, scar and keloid is less than that of normal mucosa and progressive decrease in the epithelial thickness is seen in the successive stages of OSF. The fibrosis increases with increasing grades of OSF, was higher in scar and keloid and was highly statistically significant. Type I collagen was more predominant in all stages of OSF, in normal oral mucosa and scar/keloid tissue samples as compared with type III. Though quantitative analysis of the collagen types I and III is possible, with picrosirius red qualitative analysis is an arduous task. The specificity of detection of collagen subtypes was acceptable with the picrosirius red stain, but the sensitivity left a lot to be desired.

  8. A new subdivision technique for grating based on CMOS microscopic imaging

    Institute of Scientific and Technical Information of China (English)

    Bo Yuan; Huimin Yan; Xiangqun Cao; Bin Lin

    2007-01-01

    We propose a new subdivision technique directly subdividing the grating stripe by using complementary metal-oxide semiconductor (CMOS) microscopic imaging system combined with image processing. The corresponding optical system, subdivision principle, and image processing methods are illuminated. The relations of systemic resolution to subdivision number, grating period, magnifying power and tilt angle are theoretically discussed and experimentally checked on the Abbe comparator. The measurement precision for displacement of the proposed subdivision system is tested in the range of 5 mm and the maximum displacement error is less than 0.4μm. The factors contributing to the systemic error are also discussed.

  9. Ultrafast video imaging of cell division from zebrafish egg using multimodal microscopic system

    Science.gov (United States)

    Lee, Sung-Ho; Jang, Bumjoon; Kim, Dong Hee; Park, Chang Hyun; Bae, Gyuri; Park, Seung Woo; Park, Seung-Han

    2017-07-01

    Unlike those of other ordinary laser scanning microscopies in the past, nonlinear optical laser scanning microscopy (SHG, THG microscopy) applied ultrafast laser technology which has high peak powers with relatively inexpensive, low-average-power. It short pulse nature reduces the ionization damage in organic molecules. And it enables us to take bright label-free images. In this study, we measured cell division of zebrafish egg with ultrafast video images using multimodal nonlinear optical microscope. The result shows in-vivo cell division label-free imaging with sub-cellular resolution.

  10. Imaging and identification of waterborne parasites using a chip-scale microscope.

    Directory of Open Access Journals (Sweden)

    Seung Ah Lee

    Full Text Available We demonstrate a compact portable imaging system for the detection of waterborne parasites in resource-limited settings. The previously demonstrated sub-pixel sweeping microscopy (SPSM technique is a lens-less imaging scheme that can achieve high-resolution (<1 µm bright-field imaging over a large field-of-view (5.7 mm×4.3 mm. A chip-scale microscope system, based on the SPSM technique, can be used for automated and high-throughput imaging of protozoan parasite cysts for the effective diagnosis of waterborne enteric parasite infection. We successfully imaged and identified three major types of enteric parasite cysts, Giardia, Cryptosporidium, and Entamoeba, which can be found in fecal samples from infected patients. We believe that this compact imaging system can serve well as a diagnostic device in challenging environments, such as rural settings or emergency outbreaks.

  11. 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.

  12. 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

  13. The research progress of metrological 248nm deep ultraviolent microscope inspection device

    Science.gov (United States)

    Wang, Zhi-xin; Li, Qi; Gao, Si-tian; Shi, Yu-shu; Li, Wei; Li, Shi

    2016-01-01

    In lithography process, the precision of wafer pattern to a large extent depends on the geometric dimensioning and tolerance of photomasks when accuracy of lithography aligner is certain. Since the minimum linewidth (Critical Dimension) of the aligner exposing shrinks to a few tens of nanometers in size, one-tenth of tolerance errors in fabrication may lead to microchip function failure, so it is very important to calibrate these errors of photomasks. Among different error measurement instruments, deep ultraviolent (DUV) microscope because of its high resolution, as well as its advantages compared to scanning probe microscope restrained by measuring range and scanning electron microscope restrained by vacuum environment, makes itself the most suitable apparatus. But currently there is very few DUV microscope adopting 248nm optical system, means it can attain 80nm resolution; furthermore, there is almost no DUV microscope possessing traceable calibration capability. For these reason, the National Institute of Metrology, China is developing a metrological 248nm DUV microscope mainly consists of DUV microscopic components, PZT and air supporting stages as well as interferometer calibration framework. In DUV microscopic component, the Köhler high aperture transmit condenser, DUV splitting optical elements and PMT pinhole scanning elements are built. In PZT and air supporting stages, a novel PZT actuating flexural hinge stage nested separate X, Y direction kinematics and a friction wheel driving long range air supporting stage are researched. In interferometer framework, a heterodyne multi-pass interferometer measures XY axis translation and Z axis rotation through Zerodur mirror mounted on stage. It is expected the apparatus has the capability to calibrate one dimensional linewidths and two dimensional pitches ranging from 200nm to 50μm with expanded uncertainty below 20nm.

  14. 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.

  15. Microscope basics.

    Science.gov (United States)

    Sluder, Greenfield; Nordberg, Joshua J

    2013-01-01

    This chapter provides information on how microscopes work and discusses some of the microscope issues to be considered in using a video camera on the microscope. There are two types of microscopes in use today for research in cell biology-the older finite tube-length (typically 160mm mechanical tube length) microscopes and the infinity optics microscopes that are now produced. The objective lens forms a magnified, real image of the specimen at a specific distance from the objective known as the intermediate image plane. All objectives are designed to be used with the specimen at a defined distance from the front lens element of the objective (the working distance) so that the image formed is located at a specific location in the microscope. Infinity optics microscopes differ from the finite tube-length microscopes in that the objectives are designed to project the image of the specimen to infinity and do not, on their own, form a real image of the specimen. Three types of objectives are in common use today-plan achromats, plan apochromats, and plan fluorite lenses. The concept of mounting video cameras on the microscope is also presented in the chapter. Copyright © 2003 Elsevier Inc. All rights reserved.

  16. Error correction based on micro-scanning preprocessing for an optical micro-scanning thermal microscope imaging system

    Science.gov (United States)

    Gao, Meijing; Xu, Jie; Tan, Ailing; Zu, Zhenlong; Yang, Ming; Wang, Jingyuan

    2017-06-01

    In recent years, various thermal microscope imaging systems have been developed to meet the demands of micro-thermal analysis for large-scale integrated circuits, biomedical, science, and research fields. However, conventional thermal microscope imaging systems, which use cooled infrared detectors are heavy and expensive. In order to solve this problem, we developed a thermal microscope imaging system based on an uncooled infrared detector. However, the spatial resolution of the thermal microscope imaging system based on an uncooled infrared detector is low. With optical micro-scanning technology, the spatial resolution of the thermal microscope imaging system can be increased without increasing the detector dimension or reducing the detector unit size. In order to improve its spatial resolution, a micro-scanning system based on optical plate rotation was developed, and an optical microscanning thermal microscope imaging system was obtained after the integrated design. Due to environmental factors, mechanical vibration, alignment error and other factors, there is micro-scanning error in the designed micro-scanning thermal microscope imaging system. The four low-resolution images collected by micro-scanning thermal microscope imaging system are not standard down-sampled images. The quality of the image interpolated directly by four collected images is reduced and the performance of the micro-scanning system isn't fully exploited. Therefore, based on the proposed second-order oversampling reconstruction micro-scanning error correction algorithm and the new edge directed interpolation algorithm, a new micro-scanning error correction technique is proposed. Simulations and experiments show that the proposed technique can effectively reduce optical micro-scanning error, improve the systems spatial resolution and optimize the effect of the imaging system. It can be applied to other electro-optical imaging systems to improve their spatial resolution.

  17. Unsupervised segmentation of low-contrast multichannel images: discrimination of tissue components in microscopic images of unstained specimens

    Science.gov (United States)

    Kopriva, Ivica; Popović Hadžija, Marijana; Hadžija, Mirko; Aralica, Gorana

    2015-06-01

    Low-contrast images, such as color microscopic images of unstained histological specimens, are composed of objects with highly correlated spectral profiles. Such images are very hard to segment. Here, we present a method that nonlinearly maps low-contrast color image into an image with an increased number of non-physical channels and a decreased correlation between spectral profiles. The method is a proof-of-concept validated on the unsupervised segmentation of color images of unstained specimens, in which case the tissue components appear colorless when viewed under the light microscope. Specimens of human hepatocellular carcinoma, human liver with metastasis from colon and gastric cancer and mouse fatty liver were used for validation. The average correlation between the spectral profiles of the tissue components was greater than 0.9985, and the worst case correlation was greater than 0.9997. The proposed method can potentially be applied to the segmentation of low-contrast multichannel images with high spatial resolution that arise in other imaging modalities.

  18. 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.

    2016-11-01

    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.

  19. 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.

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

    Science.gov (United States)

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

    2015-05-10

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

  1. Electron microscope studies. Progress report, 1 July 1990--1 June 1991

    Energy Technology Data Exchange (ETDEWEB)

    Crewe, A.V.; Kapp, O.H.

    1991-06-01

    This year our laboratory has continued to make progress in the design of electron-optical systems, in the study of structure-function relationships of large multi-subunit proteins, in the development of new image processing software and in achieving a workable sub-angstrom STEM. We present an algebraic approach to the symmetrical Einzel (unipotential) lens wherein we simplify the analysis by specifying a field shape that meets some preferred set of boundary or other conditions and then calculate the fields. In a second study we generalize this approach to study of three element electrostatic lenses of which the symmetrical Einzel lens is a particular form. The purpose is to develop a method for assisting in the design of a lens for a particular purpose. In our biological work we study a stable and functional dodecameric complex of globin chains from the hemoglobin of Lumbricus terrestris. This is a complex lacking the ``linker`` subunit first imaged in this lab and required for maintenance of the native structure. In addition, we do a complete work-up on the hemoglobin of the marine polychaete Eudistylia vancouverii demonstrating the presence of a hierarchy of globin complexes. We demonstrate stable field-emission in the sub-angstrom STEM and the preliminary alignment of the beam. We continue our exploration of a algorithms for alignment of sequences of protein and DNA. Our computer facilities now include four second generation RISC workstations and we continue to take increasing advantage of the floating-point and graphical performance of these devices.

  2. What structural length scales can be detected by the spectral variance of a microscope image?

    OpenAIRE

    Cherkezyan, Lusik; Subramanian, Hariharan; Backman, Vadim

    2014-01-01

    A spectroscopic microscope, configured to detect interference spectra of backscattered light in the far zone, quantifies the statistics of refractive-index (RI) distribution via the spectral variance (Σ̃2) of the acquired bright-field image. Its sensitivity to subtle structural changes within weakly scattering, label-free media at subdiffraction scales shows great promise in fields from material science to medical diagnostics. We further investigate the length-scale sensitivity of Σ̃ and reve...

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

    OpenAIRE

    Andreae, M. O.; G. Helas

    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...

  4. Super-resolution imaging strategies for cell biologists using a spinning disk microscope.

    Science.gov (United States)

    Hosny, Neveen A; Song, Mingying; Connelly, John T; Ameer-Beg, Simon; Knight, Martin M; Wheeler, Ann P

    2013-01-01

    In this study we use a spinning disk confocal microscope (SD) to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM)/Stochastic Optical Reconstruction Microscopy (STORM) methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM) and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging.

  5. Super-resolution imaging strategies for cell biologists using a spinning disk microscope.

    Directory of Open Access Journals (Sweden)

    Neveen A Hosny

    Full Text Available In this study we use a spinning disk confocal microscope (SD to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM/Stochastic Optical Reconstruction Microscopy (STORM methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging.

  6. Super-Resolution Imaging Strategies for Cell Biologists Using a Spinning Disk Microscope

    Science.gov (United States)

    Hosny, Neveen A.; Song, Mingying; Connelly, John T.; Ameer-Beg, Simon; Knight, Martin M.; Wheeler, Ann P.

    2013-01-01

    In this study we use a spinning disk confocal microscope (SD) to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM)/Stochastic Optical Reconstruction Microscopy (STORM) methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM) and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging. PMID:24130668

  7. Imaging of trapped vortices in YBCO coated conductor by scanning SQUID microscope

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, M. [Department of EESE, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581 (Japan)]. E-mail: inoue@ees.kyushu-u.ac.jp; Kiss, T. [Department of EESE, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581 (Japan); Koyanagi, S. [Department of EESE, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581 (Japan); Imamura, K. [Department of EESE, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581 (Japan); Takeo, M. [Department of EESE, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581 (Japan); Iijima, Y. [Fujikura Ltd., Tokyo 135-8512 (Japan); Kakimoto, K. [Fujikura Ltd., Tokyo 135-8512 (Japan); Saitoh, T. [Fujikura Ltd., Tokyo 135-8512 (Japan); Matsuda, J. [Superconductivity Research Laboratory, Tokyo 130-0062 (Japan); Tokunaga, Y. [Superconductivity Research Laboratory, Tokyo 130-0062 (Japan); Izumi, T. [Superconductivity Research Laboratory, Tokyo 130-0062 (Japan); Shiohara, Y. [Superconductivity Research Laboratory, Tokyo 130-0062 (Japan)

    2005-10-01

    We investigated trapped vortices in Y{sub 1}Ba{sub 2}Cu{sub 3}O{sub 7-{delta}} (YBCO) coated conductor by using a scanning SQUID microscope (SSM). Several peculiar properties of the vortices were observed such as a large bundle of vortices at a certain position and a coexistence of positive- and negative-sign vortices. Comparing the SSM images with that of low temperature scanning laser microscopy (LTSLM) and SEM, we identified the relationship between local dissipation and position of current blocking defect. Furthermore, regular vortex images were also observed by the SSM in the region where higher J {sub c} has been identified by the LTSLM.

  8. Boosting accuracy of automated classification of fluorescence microscope images for location proteomics

    Directory of Open Access Journals (Sweden)

    Huang Kai

    2004-06-01

    Full Text Available Abstract Background Detailed knowledge of the subcellular location of each expressed protein is critical to a full understanding of its function. Fluorescence microscopy, in combination with methods for fluorescent tagging, is the most suitable current method for proteome-wide determination of subcellular location. Previous work has shown that neural network classifiers can distinguish all major protein subcellular location patterns in both 2D and 3D fluorescence microscope images. Building on these results, we evaluate here new classifiers and features to improve the recognition of protein subcellular location patterns in both 2D and 3D fluorescence microscope images. Results We report here a thorough comparison of the performance on this problem of eight different state-of-the-art classification methods, including neural networks, support vector machines with linear, polynomial, radial basis, and exponential radial basis kernel functions, and ensemble methods such as AdaBoost, Bagging, and Mixtures-of-Experts. Ten-fold cross validation was used to evaluate each classifier with various parameters on different Subcellular Location Feature sets representing both 2D and 3D fluorescence microscope images, including new feature sets incorporating features derived from Gabor and Daubechies wavelet transforms. After optimal parameters were chosen for each of the eight classifiers, optimal majority-voting ensemble classifiers were formed for each feature set. Comparison of results for each image for all eight classifiers permits estimation of the lower bound classification error rate for each subcellular pattern, which we interpret to reflect the fraction of cells whose patterns are distorted by mitosis, cell death or acquisition errors. Overall, we obtained statistically significant improvements in classification accuracy over the best previously published results, with the overall error rate being reduced by one-third to one-half and with the average

  9. Progressive Coding of Palette Images and Digital Maps

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Salinas, J. Martin

    2002-01-01

    for the images with more colors. For street maps the 2D PPM is slightly better. The PPM based resolution progressive coding provides a better result than coding the resolution layers as individual images. Compared to GIF the resolution progressive 2D PPM's coding efficiency is significantly better. An example...

  10. Separation of image-distortion sources and magnetic-field measurement in scanning electron microscope (SEM).

    Science.gov (United States)

    Płuska, Mariusz; Czerwinski, Andrzej; Ratajczak, Jacek; Katcki, Jerzy; Oskwarek, Lukasz; Rak, Remigiusz

    2009-01-01

    The electron-microscope image distortion generated by electromagnetic interference (EMI) is an important problem for accurate imaging in scanning electron microscopy (SEM). Available commercial solutions to this problem utilize sophisticated hardware for EMI detection and compensation. Their efficiency depends on the complexity of distortions influence on SEM system. Selection of a proper method for reduction of the distortions is crucial. The current investigations allowed for a separation of the distortions impact on several components of SEM system. A sum of signals from distortion sources causes wavy deformations of specimen shapes in SEM images. The separation of various reasons of the distortion is based on measurements of the periodic deformations of the images for different electron beam energies and working distances between the microscope final aperture and the specimen. Using the SEM images, a direct influence of alternating magnetic field on the electron beam was distinguished. Distortions of electric signals in the scanning block of SEM were also separated. The presented method separates the direct magnetic field influence on the electron beam below the SEM final aperture (in the chamber) from its influence above this aperture (in the electron column). It also allows for the measurement of magnetic field present inside the SEM chamber. The current investigations gave practical guidelines for selecting the most efficient solution for reduction of the distortions.

  11. A transfer learning method for automatic identification of sandstone microscopic images

    Science.gov (United States)

    Li, Na; Hao, Huizhen; Gu, Qing; Wang, Danru; Hu, Xiumian

    2017-06-01

    Classification of sandstone microscopic images is an essential task in geology, and the classical method is either subjective or time-consuming. Computer aided automatic classification has been proved useful, but it seldom considers the situation where sandstone images are collected from separated regions. In this paper, we provide a method called Festra, which uses transfer learning to handle the problem of interregional sandstone microscopic image classification. The method contains two parts: one is feature selection, which aims to screen out features having great difference between the regions, the other is instance transfer using an enhanced TrAdaBoost, whose object is to mitigate the difference among thin section images collected from the regions. Experiments are conducted based on the sandstone images taken from four regions in Tibet to study the performance of Festra. The experimental results have proved both effectiveness and validity of Festra, which provides competitive prediction performance on all the four regions, with few target instances labeled suitable for the field use.

  12. Electron microscope studies. Progress report, 1 July 1964--1 June 1992

    Energy Technology Data Exchange (ETDEWEB)

    Crewe, A.V.; Kapp, O.H.

    1992-07-01

    This is a report covering the research performed in the Crewe laboratory between 1964 and 1992. Because of limitations of space we have provided relatively brief summaries of the major research directions of the facility during these years. A complete bibliography has been included and we have referenced groups of pertinent publications at the beginning of each section. This report summarizes our efforts to develop better electron microscopes and chronicles many of the experimental programs, in materials science and biology, that acted both as a stimulus to better microscope design and also as a testing ground for many instrumental innovations.

  13. 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.

  14. Imaging and identifying defects in nitride semiconductor thin films using a scanning electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Naresh-Kumar, G.; Hourahine, B.; Trager-Cowan, C. [Department of Physics, SUPA, University of Strathclyde, Glasgow (United Kingdom); Vilalta-Clemente, A.; Ruterana, P. [CIMAP UMR 6252 CNRS-ENSICAEN-CEA-UCBN, 6, Caen (France); Gamarra, P.; Lacam, C.; Tordjman, M.; Di Forte-Poisson, M.A. [Thales Research and Technology, III-V Lab, Marcoussis (France); Parbrook, P.J. [Department of Electrical and Electronic Engineering, University of Sheffield (United Kingdom); Day, A.P. [Aunt Daisy Scientific Ltd., Claremont House, High St, Lydney (United Kingdom); England, G. [K. E. Developments Ltd., Cambridge (United Kingdom)

    2012-03-15

    We describe the use of electron channelling contrast imaging (ECCI) - in a field emission scanning electron microscope (SEM) - to reveal and identify defects in nitride semiconductor thin films. In ECCI changes in crystallographic orientation, or changes in lattice constant due to local strain, are revealed by changes in grey scale in an image constructed by monitoring the intensity of backscattered electrons (BSEs) as an electron beam is scanned over a suitably oriented sample. Extremely small orientation changes are detectable, enabling small angle tilt and rotation boundaries and dislocations to be imaged. Images with a resolution of tens of nanometres are obtainable with ECCI. In this paper, we describe the use of ECCI with TEM to determine threading dislocation densities and types in InAlN/GaN heterostructures grown on SiC and sapphire substrates. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  15. Rapid imaging of mammalian brain slices with a compact light sheet fluorescent microscope

    Science.gov (United States)

    Yang, Zhengyi; Haslehurst, Peter; Scott, Suzanne; Emptage, Nigel; Dholakia, Kishan

    2017-02-01

    Light sheet fluorescent microscopy is able to provide high acquisition speed and high contrast images, as well as the low photo-bleaching and photo-damage brought to the sample. Here we describe a compact setup design optimized for applications in neuroscience, in particular fast imaging of sub-neuronal structures in mammalian brain slices. We report this prototype instrument is capable of rapid imaging wide area of the dendritic or axonal arbor of a dye-filled neuron in hippocampal slice. We also show several applications of this compact light sheet fluorescent microscope, to demonstrate that our approach offers a powerful functionality to the neuroscience community that is not achievable with traditional imaging methods.

  16. Efficient elastic imaging of single atoms on ultrathin supports in a scanning transmission electron microscope.

    Science.gov (United States)

    Hovden, Robert; Muller, David A

    2012-12-01

    Mono-atomic-layer membranes such as graphene offer new opportunities for imaging and detecting individual light atoms in transmission electron microscopes (TEM). For such applications where multiple scattering and diffraction effects are weak, we evaluate the detection efficiency and interpretability of single atom images for the most common detector geometries using quantitative quantum mechanical simulations. For well-resolved and atomically-thin specimens, the low angle annular dark field (LAADF) detector can provide a significant increase in signal-to-noise over other common detector geometries including annular bright field and incoherent bright field. This dramatically improves the visibility of organic specimens on atomic-layer membranes. Simulations of Adenosine Triphosphate (ATP) imaged under ideal conditions indicate the minimal dose requirements for elastic imaging by STEM or conventional TEM still exceed previously reported dose limits. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. 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.

  18. A Novel Scanning Near-Field Microwave Microscope Capable of High Resolution Loss Imaging

    Science.gov (United States)

    Imtiaz, Atif

    2005-03-01

    To study novel physics in condensed matter and materials science, experimental techniques need to be pushed for better sensitivity and higher spatial resolution. Classical techniques of probing the high frequency electrical properties of materials are limited in resolution to the wavelength of the incident electromagnetic wave. We report here a novel near-field microwave microscope to image materials contrast, with 2.5 nm spatial resolution in capacitance. Our objective is to improve the spatial resolution in local loss imaging. We will present evidence of sheet resistance contrast in a Boron-doped Silicon sample on sub- micron length scales. We will present quantitative analysis of the data on the Boron-doped Silicon sample in light of evanescent wave model of the microscope that we have developed. In addition, the probe to sample interaction on nanometer length scales will be discussed [1]. This work has been supported by an NSF IMR Grant DMR-9802756, and the University of Maryland/Rutgers NSF-MRSEC through the Near Field Microwave Microscope Shared Experimental Facility Grant DMR-00-80008. [1] Atif Imtiaz, Marc Pollak, Steven M. Anlage, John D. Barry and John Melngailis, ``Near-Field Microwave Microscopy on nanometer length scales'', to be published in J. Appl. Phys. (Feb. 1, 2005).

  19. Progress on PEEM3 — An Aberration Corrected X-Ray Photoemission Electron Microscope at the ALS

    Science.gov (United States)

    MacDowell, A. A.; Feng, J.; DeMello, A.; Doran, A.; Duarte, R.; Forest, E.; Kelez, N.; Marcus, M. A.; Miller, T.; Padmore, H. A.; Raoux, S.; Robin, D.; Scholl, A.; Schlueter, R.; Schmid, P.; Stöhr, J.; Wan, W.; Wei, D. H.; Wu, Y.

    2007-01-01

    A new ultrahigh-resolution photoemission electron microscope called PEEM3 is being developed and built at the Advanced Light Source (ALS). An electron mirror combined with a much-simplified magnetic dipole separator is to be used to provide simultaneous correction of spherical and chromatic aberrations. It is installed on an elliptically polarized undulator (EPU) beamline, and will be operated with very high spatial resolution and high flux to study the composition, structure, electric and magnetic properties of complex materials. The instrument has been designed and is described. The instrumental hardware is being deployed in 2 phases. The first phase is the deployment of a standard PEEM type microscope consisting of the standard linear array of electrostatic electron lenses. The second phase will be the installation of the aberration corrected upgrade to improve resolution and throughput. This paper describes progress as the instrument enters the commissioning part of the first phase.

  20. Determining optimum red filter slide distance on creating 3D electron microscope images using anaglyph method

    Science.gov (United States)

    Tresna, W. P.; Isnaeni

    2017-04-01

    Scanning Electron Microscope (SEM) is a proven instrument for analyzing material in which a 2D image of an object is produced. However, the optimization of a 3D image in the SEM system is usually difficult and costly. There is a simple method to produce a 3D image by using two light sources with a red and a blue filter combined in a certain angle. In this experiment, the authors conducted a simulation of the 3D image formation using anaglyph method by finding the optimum point of shifting the red and blue filters in an SEM image. The method used in this experiment was an image processing that employed a digital manipulation on a certain deviation distance of the central point of the main object. The simulation result of an SEM image with a magnification of 5000 times showed an optimal 3D effect that was achieved when the red filter was shifted by 1 μm to the right and the blue filter was shifted by 1 µm to the left from the central position. The result of this simulation can be used to understand better the viewing angle and the optimal position of the two light sources, i.e. red and blue filter pairs. The produced 3D image can be clearly seen using 3D glasses.

  1. Graphene-based Hall Sensors for direct magnetic imaging by using Scanning Hall Probe Microscope

    Science.gov (United States)

    Sonusen, Selda; Aksoy, Seda; Dede, Munir; Oral, Ahmet

    2013-03-01

    Graphene has been attracting great interest due to its unique electronic and mechanical properties for both fundamental and experimental studies since 2004. Graphene is a promising material for many applications in high speed electronic and spintronic devices as well as sensors. Its high mobility makes graphene a good candidate for magnetic imaging in Scanning Hall Probe Microscope (SHPM). Hall probes are used to scan the magnetic samples to image magnetic domains in SHPM. In this work, single layer graphene produced by chemical vapor deposition technique is used to fabricate Hall sensors by optical and the e-beam lithography with sizes from 500 nm to a few micrometers. The Hall crosses are characterized by Raman mapping to make sure that they are made of a single layer graphene. The Graphene Hall Sensors noise spectra is measured as a function of different bias currents and carrier concentrations at 300 K, 77 K and 4.24K. The imaging performance of the Hall sensor will be demonstrated at different temperatures by imaging a garnet crystal using a Low Temperature Scanning Hall Probe Microscope (LT-SHPM).

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

    Science.gov (United States)

    Takeuchi, Akihisa; Uesugi, Kentaro; Suzuki, Yoshio

    2013-09-01

    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.

  3. 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.

  4. 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.

  5. 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

  6. Electron microscope studies: Progress report for the period July 1, 1987 to June 30, 1988

    Energy Technology Data Exchange (ETDEWEB)

    Crewe, A.V.; Kapp, O.H.

    1988-08-01

    The work in our laboratory for the past year can be characterized as having had considerable success in our work on theoretical electron optics and in the biological use of our existing microscopes, but, on the other hand, we have encountered considerable frustration in our attempts to complete the construction of the Sub Angstrom STEM. With regard to theoretical electron optics, we have continued to pursue lines of inquiry which were opened up to us as a result of our previous work on the correction of third order aberrations. While the experimental proof of the sextupole concept is still some distance away, the number of theoretical investigations we have conducted on the system indicate that it should be possible to make it work. The logical outcome of this is the realization that we ought to begin investigating other remaining limitations to the resolution of a STEM. These considerations led to some work that was done on the correction of the fifth order aberrations. Another study of equal importance was the investigation we made on the use of a sextupole corrector in a transmission microscope of conventional design and the results here look quite promising. Other theoretical studies include some work which has recently been started on methods of characterization of electron beams. The reason for this study is that under normal circumstances when an electron beam is generated in a canning microscope the resolution is atrocious and the shape of the focused spot of electrons is very poor. Further work has been done on three dimensional reconstruction with the general aim of improving the precision of reconstruction and also being able to do so in spite of the existence of noise. Biological work on the existing microscope has proceeded apace and a large number of investigations have been done. Although the principle effort has remained towards investigations of giant hemoglobins, other molecules have also been studied.

  7. Computer control of a scanning electron microscope for digital image processing of thermal-wave images

    Science.gov (United States)

    Gilbert, Percy; Jones, Robert E.; Kramarchuk, Ihor; Williams, Wallace D.; Pouch, John J.

    1987-01-01

    Using a recently developed technology called thermal-wave microscopy, NASA Lewis Research Center has developed a computer controlled submicron thermal-wave microscope for the purpose of investigating III-V compound semiconductor devices and materials. This paper describes the system's design and configuration and discusses the hardware and software capabilities. Knowledge of the Concurrent 3200 series computers is needed for a complete understanding of the material presented. However, concepts and procedures are of general interest.

  8. 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.

  9. Nanocrystal Phase Identification by Lattice Fringe Fingerprinting from High Resolution Transmission Electron Microscope Images

    Science.gov (United States)

    Bjorge, Ruben; Seipel, Bjoern; Moeck, Peter; Fraundorf, Philip

    2006-05-01

    Lattice fringe fingerprinting is a novel and powerful method of identifying and characterizing nanocrystalline structures or materials based on images from direct space high-resolution transmission electron microscopy (HRTEM). We examine Fourier transformed HRTEM images of nanocrystals in certain orientations (i.e. lattice fringes and cross fringes) in order to obtain a lattice fringe fingerprint plot. Such plots are used to identify a crystalline nanoparticle by comparing the experimental data with data that are derived from a comprehensive database. A lattice fringe fingerprint plot is similar to a classical X-ray powder diffractogram, but an important advantage is that the intersection angles of lattice fringes give us additional information. When transmission electron microscope image acquisition and data interpretation are automated and connected to a comprehensive database (such as our Nano-Crystallography Database, http://nanocrystallography.research.pdx.edu/), fringe fingerprinting will be able to compete with powder X-ray diffraction in identifying unknown nanocrystals on a routine basis.

  10. 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

    2016-06-21

    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.

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

    CERN Document Server

    Hawkes, Peter W

    2009-01-01

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

  12. Cellular replication and atomic force microscope imaging using a UV-Bioimprint technique.

    Science.gov (United States)

    Muys, J J; Alkaisi, M M; Evans, J J

    2006-09-01

    Replication and fixation techniques have been of considerable interest for imaging and analysis of biological cells since the introduction of electron and scanning probe microscopy. Although such tools as the atomic force microscope (AFM) permit in situ morphological studies at a magnitude of resolution beyond traditional optical microscopy, they are difficult to operate and their resolution capabilities are rarely realized. We used a UV-Bioimprint replication technique to imprint a polymer layer onto cells attached to a substrate and rapidly cure to create an impression of cell topography. Replicas of chemically fixed and untreated cells analyzed by atomic force microscopy demonstrate nanometer resolution in the transfer of replicated features. UV-Bioimprint presents an improvement over techniques using heat-curable polymers as well as an alternative technique to the direct imaging of cells. The motivation for UV-Bioimprint is to effectively integrate scanning probe microscopy tools for imaging of cellular ultrastructure.

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

    Science.gov (United States)

    Hosokawa, Fumio; Sawada, Hidetaka; Shinkawa, Takao; Sannomiya, Takumi

    2016-08-01

    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.

  14. Hardware Segmentation on Digital Microscope Images for Acute Lymphoblastic Leukemia Diagnosis Using Xilinx System Generator

    Directory of Open Access Journals (Sweden)

    Prof. Kamal A. ElDahshan

    2014-09-01

    Full Text Available Image segmentation is considered the most critical step in image processing and helps to analyze, infer and make decisions especially in the medical field. Analyzing digital microscope images for earlier acute lymphoblastic leukemia diagnosis and treatment require sophisticated software and hardware systems. These systems must provide both highly accurate and extremely fast processing of large amounts of image data. In this work, the hardware segmentation framework for Acute Lymphoblastic Leukemia (ALL images based color histogram of Hue channel of HSV color space is proposed to segment each leukemia image into blasts and background using Field Programmable Gate Array (FPGA. The main purpose of this work is to implement image segmentation framework in a FPGA with minimum hardware resources and low execution time to be suitable enough for medical applications. Hardware framework of segmentation is designed using Xilinx System Generator (XSG as DSP design tool that enables the use of Simulink models, implemented in VHDL and synthesized for Xilinx SPARTAN-3E Starter kit (XC3S500E-FG320 FPGA.

  15. The formation and interpretation of defect images from crystalline materials in a scanning transmission electron microscope.

    Science.gov (United States)

    Maher, D M; Joy, D C

    1976-06-01

    The technique of scanning transmission electron microscopy (STEM) has been employed usefully in studies of amorphous materials, and the theory of image formation and interpretation in this case has been well developed. Less attention has been given to the practical and theoretical problems associated with the use of STEM for the examination of crystalline materials. In this case the contrast mechanisms are dominated by Bragg diffraction and so they are quite different from those occurring in amorphous substances. In this paper practical techniques for the observation and interpretation of contrast from defects in crystalline materials are discussed. It is shown that whilst images of defects are obtained readily under all typical STEM operating conditions, the form of the image and the information it contains varies with the angle subtended at the specimen by the detector. If this angle is too large significant image modifications relative to the "conventional" transmission electron microscope case may occur and the resolution of the image may degrade. If this angle is too small, then signal to noise considerations make an interpretation of the image difficult. In this paper we indicate how the detector angle may be chosen correctly, and also present techniques for setting up a STEM instrument for imaging a crystalline material containing lattice defects.

  16. [Progress of research in retinal image registration].

    Science.gov (United States)

    Yu, Lun; Wei, Lifang; Pan, Lin

    2011-10-01

    The retinal image registration has important applications in the processes of auxiliary diagnosis and treatment for a variety of diseases. The retinal image registration can be used to measure the disease process and the therapeutic effect. A variety of retinal image registration techniques have been studied extensively in recent years. However, there are still many problems existing and there are numerous research possibilities. Based on extensive investigation of existing literatures, the present paper analyzes the feature of retinal image and current challenges of retinal image registration, and reviews the transformation models of the retinal image registration technology and the main research algorithms in current retinal image registration, and analyzes the advantages and disadvantages of various types of algorithms. Some research challenges and future developing trends are also discussed.

  17. A photoelastic modulator-based birefringence imaging microscope for measuring biological specimens

    Science.gov (United States)

    Freudenthal, John; Leadbetter, Andy; Wolf, Jacob; Wang, Baoliang; Segal, Solomon

    2014-11-01

    The photoelastic modulator (PEM) has been applied to a variety of polarimetric measurements. However, nearly all such applications use point-measurements where each point (spot) on the sample is measured one at a time. The main challenge for employing the PEM in a camera-based imaging instrument is that the PEM modulates too fast for typical cameras. The PEM modulates at tens of KHz. To capture the specific polarization information that is carried on the modulation frequency of the PEM, the camera needs to be at least ten times faster. However, the typical frame rates of common cameras are only in the tens or hundreds frames per second. In this paper, we report a PEM-camera birefringence imaging microscope. We use the so-called stroboscopic illumination method to overcome the incompatibility of the high frequency of the PEM to the relatively slow frame rate of a camera. We trigger the LED light source using a field-programmable gate array (FPGA) in synchrony with the modulation of the PEM. We show the measurement results of several standard birefringent samples as a part of the instrument calibration. Furthermore, we show results observed in two birefringent biological specimens, a human skin tissue that contains collagen and a slice of mouse brain that contains bundles of myelinated axonal fibers. Novel applications of this PEM-based birefringence imaging microscope to both research communities and industrial applications are being tested.

  18. Magnetic Permeability Imaging of Metals with a Scanning Near-Field Microwave Microscope

    Science.gov (United States)

    Lee, Sheng-Chiang; Vlahacos, C. P.; Feenstra, B. J.; Schwartz, Andrew; Steinhauer, David; Wellstood, Fredrick; Anlage, Steven

    2001-03-01

    We extended the use of our scanning near-field microwave microscope to measure the local magnetic properties of metallic samples in a spatially-resolved manner. We use a small loop probe to detect magnetic perturbations in thin film and bulk samples. We demonstrate qualitative and quantitative understanding of permeability imaging through spatially-resolved ferromagnetic resonance experiments on a single crystal of the colossal magneto-resistive material La_0.8Sr_0.2MnO_3. The experimental results are well described by a simple model of the system. We also modified this microscope to image the ferromagnetic resonance field over a ferromagnetic sample in the presence of external magnetic field. The spatial resolution is on the order of the size of the loop, currently 200 μ m. Results demonstrating FMR imaging on La_0.8Sr_0.2MnO3 and amorphous magnetic tapes will be presented. Reference: S.C. Lee, C P. Vlahacos, B. J. Feenstra, Andrew Schwartz, D. E. Steinhauer, F. C. Wellstood, and Steve M. Anlage, Appl. Phys. Lett., December 18 (2000)

  19. Microscope-based imaging platform for large-scale analysis of oral biofilms.

    Science.gov (United States)

    Karygianni, L; Follo, M; Hellwig, E; Burghardt, D; Wolkewitz, M; Anderson, A; Al-Ahmad, A

    2012-12-01

    A microscopic method for noninvasively monitoring oral biofilms at the macroscale was developed to describe the spatial distribution of biofilms of different bacterial composition on bovine enamel surfaces (BES). For this purpose, oral biofilm was grown in situ on BES that were fixed at approximal sites of individual upper jaw acrylic devices worn by a volunteer for 3 or 5 days. Eubacteria, Streptococcus spp., and Fusobacterium nucleatum were stained using specific fluorescence in situ hybridization (FISH) probes. The resulting fluorescence signals were subsequently tested by confocal laser scanning microscopy (CLSM) and monitored by an automated wide-field microscope-based imaging platform (Scan∧R). Automated image processing and data analysis were conducted by microscope-associated software and followed by statistical evaluation of the results. The full segmentation of biofilm images revealed a random distribution of bacteria across the entire area of the enamel surfaces examined. Significant differences in the composition of the microflora were recorded across individual as well as between different enamel surfaces varying from sparsely colonized (47.26%) after 3 days to almost full surface coverage (84.45%) after 5 days. The enamel plates that were positioned at the back or in the middle of the oral cavity were found to be more suitable for the examination of biofilms up to 3 days old. In conclusion, automated microscopy combined with the use of FISH can enable the efficient visualization and meaningful quantification of bacterial composition over the entire sample surface. Due to the possibility of automation, Scan∧R overcomes the technical limitations of conventional CLSM.

  20. Methyl green and nitrotetrazolium blue chloride co-expression in colon tissue: A hyperspectral microscopic imaging analysis

    Science.gov (United States)

    Li, Qingli; Liu, Hongying; Wang, Yiting; Sun, Zhen; Guo, Fangmin; Zhu, Jianzhong

    2014-12-01

    Histological observation of dual-stained colon sections is usually performed by visual observation under a light microscope, or by viewing on a computer screen with the assistance of image processing software in both research and clinical settings. These traditional methods are usually not sufficient to reliably differentiate spatially overlapping chromogens generated by different dyes. Hyperspectral microscopic imaging technology offers a solution for these constraints as the hyperspectral microscopic images contain information that allows differentiation between spatially co-located chromogens with similar but different spectra. In this paper, a hyperspectral microscopic imaging (HMI) system is used to identify methyl green and nitrotetrazolium blue chloride in dual-stained colon sections. Hyperspectral microscopic images are captured and the normalized score algorithm is proposed to identify the stains and generate the co-expression results. Experimental results show that the proposed normalized score algorithm can generate more accurate co-localization results than the spectral angle mapper algorithm. The hyperspectral microscopic imaging technology can enhance the visualization of dual-stained colon sections, improve the contrast and legibility of each stain using their spectral signatures, which is helpful for pathologist performing histological analyses.

  1. Validation of a fiber-based confocal microscope for interventional image-guided procedures: correlation with multispectral optical imaging

    Science.gov (United States)

    Herzka, Daniel; Quijano, Jade; Xie, Jianwu; Krueger, Sascha; Weiss, Steffen; Abrat, Benjamin; Osdoit, Anne; Cavé, Charlotte; Burnett, Christopher; Danthi, S. Narasimhan; Li, King

    2006-03-01

    The concept of the biopsy is ubiquitous in current medical diagnosis of cancer and other diseases. The standard biopsy consists of removing a sample of tissue for evaluation and diagnosis, primarily to ascertain the presence of cancer cells by (histo)pathological analyses. However, the advent of new optical imaging modalities and targeted or "smart" agents, that have affinity for a select target, suggests the possibility of performing in vivo tissue characterization without the need for sample removal or the wait for histopathologic processing. Here we present work testing and validating a fiber-based confocal fluorescence microscopic imaging system intended for combination with a larger scale imaging modality (i.e. MRI or CT) to be used in image-guided in vivo tissue characterization. Fiber-based confocal fluorescence microscopic imaging experiments were performed (Cellvizio, Mauna Kea Technologies, Paris, France) in vivo in two mouse models including: 1) EGFP-expressing mouse melanoma model and 2) M21 mouse melanoma model. Both models are known to express integrin α νβ 3, a cell-surface receptor protein. We also performed an experiment in ex vivo chicken muscle tissue labelled with a fluorescein isothiocyanate-lectin targeted compound. In the mouse models, contrast agents that targeted the integrin were injected and the contrast agent localization in tumor was verified by a whole-body multispectral imager. The fiber-based tool was sensitive enough to detect and image the tissue of interest in all different experiments, and was found appropriate for use in interventional catheter-based procedures.

  2. Magnetic field imaging of a tungsten carbide film by scanning nano-SQUID microscope

    Science.gov (United States)

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

    2016-10-01

    We present the results of magnetic field imaging by scanning nano-superconducting quantum interference device (SQUID) microscopy on a tungsten carbide (W-C) film fabricated using focused-ion-beam chemical vapor deposition. We have investigated magnetic field change by a W-C film in an external magnetic field using a scanning nano-SQUID microscope system. We have found that the reduction of the magnetic field above the W-C film was 0.9%, indicating the penetration of vortices in the W-C at an external magnetic field of 0.171 mT.

  3. Second harmonic microscopic imaging and spectroscopic characterization in prostate pathological tissue.

    Science.gov (United States)

    Huang, Yanyue; Zhuang, Zhengfei

    2014-01-01

    Second harmonic microscopic imaging and spectroscopy technology has become a powerful tool for biomedical studies, especially in cancer research. In this paper, second harmonic generation in benign prostatic hyperplasia (BPH) and prostate cancer (PC) tissues in mouse model (C57BL6) have been reported. Excitated samples with different wavelength near-infrared laser from 780 to 850 nm we found that second harmonic signals from BPH nuclei stronger than that from PC, and a wavelength sensitivity was also observed in this experiment. Providing useful help for prostate malignancy diagnosis and identifying tissue components on clinic. © 2013 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    Helas, G.; Andreae, M. O.

    2008-10-01

    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 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.

  5. 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.

  6. 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.

  7. Nanoscale imaging of whole cells using a liquid enclosure and a scanning transmission electron microscope.

    Directory of Open Access Journals (Sweden)

    Diana B Peckys

    Full Text Available Nanoscale imaging techniques are needed to investigate cellular function at the level of individual proteins and to study the interaction of nanomaterials with biological systems. We imaged whole fixed cells in liquid state with a scanning transmission electron microscope (STEM using a micrometer-sized liquid enclosure with electron transparent windows providing a wet specimen environment. Wet-STEM images were obtained of fixed E. coli bacteria labeled with gold nanoparticles attached to surface membrane proteins. Mammalian cells (COS7 were incubated with gold-tagged epidermal growth factor and fixed. STEM imaging of these cells resulted in a resolution of 3 nm for the gold nanoparticles. The wet-STEM method has several advantages over conventional imaging techniques. Most important is the capability to image whole fixed cells in a wet environment with nanometer resolution, which can be used, e.g., to map individual protein distributions in/on whole cells. The sample preparation is compatible with that used for fluorescent microscopy on fixed cells for experiments involving nanoparticles. Thirdly, the system is rather simple and involves only minimal new equipment in an electron microscopy (EM laboratory.

  8. Offset-sparsity decomposition for automated enhancement of color microscopic image of stained specimen in histopathology

    Science.gov (United States)

    Kopriva, Ivica; Hadžija, Marijana Popović; Hadžija, Mirko; Aralica, Gorana

    2015-07-01

    We propose an offset-sparsity decomposition method for the enhancement of a color microscopic image of a stained specimen. The method decomposes vectorized spectral images into offset terms and sparse terms. A sparse term represents an enhanced image, and an offset term represents a "shadow." The related optimization problem is solved by computational improvement of the accelerated proximal gradient method used initially to solve the related rank-sparsity decomposition problem. Removal of an image-adapted color offset yields an enhanced image with improved colorimetric differences among the histological structures. This is verified by a no-reference colorfulness measure estimated from 35 specimens of the human liver, 1 specimen of the mouse liver stained with hematoxylin and eosin, 6 specimens of the mouse liver stained with Sudan III, and 3 specimens of the human liver stained with the anti-CD34 monoclonal antibody. The colorimetric difference improves on average by 43.86% with a 99% confidence interval (CI) of [35.35%, 51.62%]. Furthermore, according to the mean opinion score, estimated on the basis of the evaluations of five pathologists, images enhanced by the proposed method exhibit an average quality improvement of 16.60% with a 99% CI of [10.46%, 22.73%].

  9. Progress with the LOFAR Imaging Pipeline

    CERN Document Server

    Heald, George; Pizzo, Roberto; van Diepen, Ger; van Zwieten, Joris E; van Weeren, Reinout J; Rafferty, David; van der Tol, Sebastiaan; Birzan, Laura; Shulevski, Aleksandar; Swinbank, John; Orru, Emanuela; De Gasperin, Francesco; Ker, Louise; Bonafede, Annalisa; Macario, Giulia; Ferrari, Chiara

    2010-01-01

    One of the science drivers of the new Low Frequency Array (LOFAR) is large-area surveys of the low-frequency radio sky. Realizing this goal requires automated processing of the interferometric data, such that fully calibrated images are produced by the system during survey operations. The LOFAR Imaging Pipeline is the tool intended for this purpose, and is now undergoing significant commissioning work. The pipeline is now functional as an automated processing chain. Here we present several recent LOFAR images that have been produced during the still ongoing commissioning period. These early LOFAR images are representative of some of the science goals of the commissioning team members.

  10. Effects of Corneal Collagen Crosslinking on Confocal Microscopic Findings and Tear Indices in Patients with Progressive Keratoconus

    Science.gov (United States)

    Zare, Mohammad Ali; Mazloumi, Mehdi; Farajipour, Hasan; Hoseini, Bagher; Fallah, Mohammad R.; Mahrjerdi, Hadi Z.; Abtahi, Mohammad-Ali; Abtahi, Seyed-Hossein

    2016-01-01

    Background: To evaluate any change in tear indices and confocal microscopic findings after corneal collagen crosslinking (CXL) in patients with progressive keratoconus. Methods: Thirty-two consecutive eyes from 23 patients having progressive keratoconus were enrolled in this prospective, interventional cohort study. The standard crosslinking surgery was performed for all patients. Visual, refractive, and topographic evaluations were done before and at 6 months after surgery. Tear function tests and confocal microscopic examination were performed before and at 1 month and 6 months after the procedure. Results: There was no significant change in Schirmer-1 test results and tear osmolarity at 1 month and 6 months after CXL. Using confocal microscopy, all eyes showed reduced or absent subepithelial nerve plexus. Differences in basal epithelial cell density, epithelial mean cell area, and keratocyte density in anterior and middle stroma and endothelial cell pleomorphism were all significant at 1 month and 6 months after CXL (P < 0.05). No significant change was noted in endothelial cell count and their polymegathism at 6 months follow-up. Significant improvement was noted in uncorrected visual acuity, best corrected visual acuity, flattest corneal meridian (K2), and maximum keratometry in Pentacam (Kmax) after 6 months of the procedure. Conclusions: While CXL would have no effect on tear indices and endothelial cell count, it can cause a significant reduction in subepithelial nerve plexus and significant alterations in epithelial cell density in the anterior and middle stroma. PMID:28123695

  11. Progress with the LOFAR Imaging Pipeline

    NARCIS (Netherlands)

    G. Heald; J. McKean; R. Pizzo; G. van Diepen; J.E. van Zwieten; R.J. van Weeren; D. Rafferty; S. van der Tol; L. Birzan; A. Shulevski; J. Swinbank; E. Orrù; F. de Gasperin; L. Ker; A. Bonafede; G. Macario; C. Ferrari

    2010-01-01

    One of the science drivers of the new Low Frequency Array (LOFAR) is large-area surveys of the low-frequency radio sky. Realizing this goal requires automated processing of the interferometric data, such that fully calibrated images are produced by the system during survey operations. The LOFAR Imag

  12. A collaborative biomedical image mining framework: application on the image analysis of microscopic kidney biopsies.

    Science.gov (United States)

    Goudas, T; Doukas, C; Chatziioannou, A; Maglogiannis, I

    2013-01-01

    The analysis and characterization of biomedical image data is a complex procedure involving several processing phases, like data acquisition, preprocessing, segmentation, feature extraction and classification. The proper combination and parameterization of the utilized methods are heavily relying on the given image data set and experiment type. They may thus necessitate advanced image processing and classification knowledge and skills from the side of the biomedical expert. In this work, an application, exploiting web services and applying ontological modeling, is presented, to enable the intelligent creation of image mining workflows. The described tool can be directly integrated to the RapidMiner, Taverna or similar workflow management platforms. A case study dealing with the creation of a sample workflow for the analysis of kidney biopsy microscopy images is presented to demonstrate the functionality of the proposed framework.

  13. Musculoskeletal imaging in progress: the EOS imaging system.

    Science.gov (United States)

    Wybier, Marc; Bossard, Philippe

    2013-05-01

    The EOS 2D/3D radio-imaging device (Biospace med, France) can disclose a digital radiographic image of bones with a very low radiation dose. This in turn allows in obtaining a single image of a large field of view, as wide as the full skeleton. The simultaneous capturing of spatially paired AP and lateral X-ray images is also a specificity of EOS imaging, which further provides secondary 3D (volumic) reformation of skeletal images. The main indications of this new imaging technology are assessment and follow-up of balance disorders of the spine and of the lower limbs.

  14. Imaging living cells with a combined high-resolution multi-photon-acoustic microscope

    Science.gov (United States)

    Schenkl, Selma; Weiss, Eike; Stark, Martin; Stracke, Frank; Riemann, Iris; Lemor, Robert; König, Karsten

    2007-02-01

    With increasing demand for in-vivo observation of living cells, microscope techniques that do not need staining become more and more important. In this talk we present a combined multi-photon-acoustic microscope with the possibility to measure synchronously properties addressed by ultrasound and two-photon fluorescence. Ultrasound probes the local mechanical properties of a cell, while the high resolution image of the two-photon fluorescence delivers insight in cell morphology and activity. In the acoustic part of the microscope an ultrasound wave, with a frequency of GHz, is focused by an acoustic sapphire lens and detected by a piezo electric transducer assembled to the lens. The achieved lateral resolution is in the range of 1μm. Contrast in the images arises mainly from the local absorption of sound in the cells, related to properties, such as mass density, stiffness and viscose damping. Additionally acoustic microscopy can access the cell shape and the state of the cell membrane as it is a intrinsic volume scanning technique.The optical part bases on the emission of fluorescent biomolecules naturally present in cells (e.g. NAD(P)H, protophorphyrin IX, lipofuscin, melanin). The nonlinear effect of two-photon absorption provides a high lateral and axial resolution without the need of confocal detection. In addition, in the near-IR cell damages are drastically reduced in comparison to direct excitation in the visible or UV. Both methods can be considered as minimal invasive, as they relay on intrinsic contrast mechanisms and dispense with the need of staining. First results on living cells are presented and discussed.

  15. Scanning transmission electron microscopic tomography of cortical bone using Z-contrast imaging.

    Science.gov (United States)

    McNally, Elizabeth; Nan, Feihong; Botton, Gianluigi A; Schwarcz, Henry P

    2013-06-01

    Previously we presented (McNally et al., 2012) a model for the ultrastructure of bone showing that the mineral resides principally outside collagen fibrils in the form of 5 nm thick mineral structures hundreds of nanometers long oriented parallel to the fibrils. Here we use high-angle annular dark-field electron tomography in the scanning transmission electron microscope to confirm this model and further elucidate the composite structure. Views of a section cut parallel to the fibril axes show bundles of mineral structures extending parallel to the fibrils and encircling them. The mineral density inside the fibrils is too low to be visualized in these tomographic images. A section cut perpendicular to the fibril axes, shows quasi-circular walls composed of mineral structures, wrapping around apparently empty holes marking the sites of fibrils. These images confirm our original model that the majority of mineral in bone resides outside the collagen fibrils.

  16. Self-referencing digital holographic microscope for dynamic imaging of living cells

    Science.gov (United States)

    Anand, Arun; Chhaniwal, Vani; Mahajan, Swapnil; Trivedi, Vismay; Singh, Amardeep; Leitgeb, Rainer; Javidi, Bahram

    2014-06-01

    Digital holographic microscope is an ideal tool for quantitative phase contrast imaging of living cells. It yields the thickness distribution of the object under investigation from a single hologram. From a series of holograms the dynamics of the cell under investigation can be obtained. But two-beam digital holographic microscopes has low temporal stability due to uncorrelated phase changes occurring in the reference and object arms. One way to overcome is to use common path techniques, in which, the reference beam is derived from the object beam itself. Both the beams travel along the same path, increasing the temporal stability of the setup. In self-referencing techniques a portion of the object beam is converted into reference beam. It could be achieved by example, using a glass plate to create two laterally sheared versions of the object beam at the sensor, which interfere to produce the holograms/interferograms. This created a common path setup, leading to high temporal stability (~0.6nm). This technique could be used to map cell membrane fluctuations with high temporal stability. Here we provide an overview of our work on the development of temporally stable quantitative phase contrast techniques for dynamic imaging of micro-objects and biological specimen including red blood cells.

  17. Atomic force microscope controlled topographical imaging and proximal probe thermal desorption/ionization mass spectrometry imaging.

    Science.gov (United States)

    Ovchinnikova, Olga S; Kjoller, Kevin; Hurst, Gregory B; Pelletier, Dale A; Van Berkel, Gary J

    2014-01-21

    This paper reports on the development of a hybrid atmospheric pressure atomic force microscopy/mass spectrometry imaging system utilizing nanothermal analysis probes for thermal desorption surface sampling with subsequent atmospheric pressure chemical ionization and mass analysis. The basic instrumental setup and the general operation of the system were discussed, and optimized performance metrics were presented. The ability to correlate topographic images of a surface with atomic force microscopy and a mass spectral chemical image of the same surface, utilizing the same probe without moving the sample from the system, was demonstrated. Co-registered mass spectral chemical images and atomic force microscopy topographical images were obtained from inked patterns on paper as well as from a living bacterial colony on an agar gel. Spatial resolution of the topography images based on pixel size (0.2 μm × 0.8 μm) was better than the resolution of the mass spectral images (2.5 μm × 2.0 μm), which were limited by current mass spectral data acquisition rate and system detection levels.

  18. Imaging and analyzing the elasticity of vascular smooth muscle cells by atomic force acoustic microscope.

    Science.gov (United States)

    Zhang, Bo; Cheng, Qian; Chen, Ming; Yao, Wengang; Qian, Menglu; Hu, Bing

    2012-08-01

    Vascular smooth muscle cells (VSMCs) play an important role in the good performance of the vasculature. To study the surface, intracellular structure and elasticity of VSMCs, atomic force acoustic microscope (AFAM) was used for imaging VSMCs from A7r5 rat aorta arteries. The topography images of VSMCs were obtained in contact mode and the acoustic images were obtained by AFAM in sample vibration mode. Then, the force curve measurement derived using Young's modulus of the interested areas was used for evaluating elasticity properties. The acoustic images were found in higher resolution with more information than the topography images. The force curves showed the difference in Young's modulus of the different parts of VSMC. These findings demonstrate that AFAM is useful for displaying the surface, structure and elasticity property of VSMCs clearly, with short scanning time, negligible harm or damage to cell and nanometer-level resolution. Copyright © 2012 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  19. Imaging and analysis of subsurface Cu interconnects by detecting backscattered electrons in the scanning electron microscope

    Science.gov (United States)

    Gignac, L. M.; Kawasaki, M.; Boettcher, S. H.; Wells, O. C.

    2005-06-01

    Cu -SiO2-SiNx interconnects that were located 0.65-2.7-μm below the surface of silicon-integrated circuits were imaged in a scanning electron microscope and a transmission electron microscope with a scanning attachment by detecting backscattered electrons (BSEs) with an incident electron-beam energy (Eo) in the range of 30-400keV. BSE images could be used to detect voids in subsurface Cu interconnects, even in regions covered with upper level Cu lines or vias. As Eo was increased from 30to400keV, structures could be seen as a result of atomic number (Z) contrast farther below the surface while structures closer to the surface had reduced Z contrast. The subsurface beam diameter was measured from BSE images as a function of Eo and depth below the surface. For all Eo, the subsurface beam diameter initially rapidly increased with SiO2 overlayer thickness but, for 150keV, a leveling off in the beam spread was seen for depths >1.7μm. Beam broadening affected whether the TaN /Ta liners that surrounded the Cu conductors could be seen at the edges of the lines; this contrast was observed only when the subsurface beam diameter was ⩽1.5× the liner thickness. The BSE information depth for imaging 0.2-μm-sized voids in subsurface Cu -SiO2-SiNx interconnect structures at 30 and 150keV was estimated to be 0.65 and 3μm, respectively.

  20. A two-angle far-field microscope imaging technique for spray flows

    Science.gov (United States)

    Kourmatzis, Agisilaos; Pham, Phuong X.; Masri, Assaad R.

    2017-03-01

    Backlight imaging is frequently used for the visualization of multiphase flows, where with appropriate microscope lenses, quantitative information on the spray structure can be attained. However, a key issue resides in the nature of the measurement which relies on a single viewing angle, hence preventing imaging of all liquid structures and features, such as those located behind other fragments. This paper presents results from an extensive experimental study aimed as a step forward towards resolving this problem by using a pair of high speed cameras oriented at 90 degrees to each other, and synchronized to two high-speed diode lasers. Both cameras are used with long distance microscope lenses. The images are processed as pairs allowing for identification and classification of the same liquid structure from two perspectives at high temporal (5 kHz) and spatial resolution (∼3 μm). Using a controlled mono-disperse spray, simultaneous, time-resolved visualization of the same spherical object being focused on one plane while de-focused on the other plane 90 degrees to the first has allowed for a quantification of shot-to-shot defocused size measurement error. An extensive error analysis is performed for spheroidal structures imaged from two angles and the dual angle technique is extended to measure the volume of non-spherical fragments for the first time, by ‘discretising’ a fragment into a number of constituent ellipses. Error analysis is performed based on measuring the known volumes of solid arbitrary shapes, and volume estimates were found to be within  ∼11% of the real volume for representative ‘ligament-like’ shapes. The contribution concludes by applying the ellipsoidal method to a real spray consisting of multiple non-spherical fragments. This extended approach clearly demonstrates potential to yield novel volume weighted quantities of non-spherical objects in turbulent multiphase flow applications.

  1. Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method

    Science.gov (United States)

    Huynh, Toan; Daddysman, Matthew K.; Bao, Ying; Selewa, Alan; Kuznetsov, Andrey; Philipson, Louis H.; Scherer, Norbert F.

    2017-05-01

    Imaging specific regions of interest (ROIs) of nanomaterials or biological samples with different imaging modalities (e.g., light and electron microscopy) or at subsequent time points (e.g., before and after off-microscope procedures) requires relocating the ROIs. Unfortunately, relocation is typically difficult and very time consuming to achieve. Previously developed techniques involve the fabrication of arrays of features, the procedures for which are complex, and the added features can interfere with imaging the ROIs. We report the Fast and Accurate Relocation of Microscopic Experimental Regions (FARMER) method, which only requires determining the coordinates of 3 (or more) conspicuous reference points (REFs) and employs an algorithm based on geometric operators to relocate ROIs in subsequent imaging sessions. The 3 REFs can be quickly added to various regions of a sample using simple tools (e.g., permanent markers or conductive pens) and do not interfere with the ROIs. The coordinates of the REFs and the ROIs are obtained in the first imaging session (on a particular microscope platform) using an accurate and precise encoded motorized stage. In subsequent imaging sessions, the FARMER algorithm finds the new coordinates of the ROIs (on the same or different platforms), using the coordinates of the manually located REFs and the previously recorded coordinates. FARMER is convenient, fast (3-15 min/session, at least 10-fold faster than manual searches), accurate (4.4 μm average error on a microscope with a 100x objective), and precise (almost all errors are diverse set of samples and imaging methods: live mammalian cells at different time points; fixed bacterial cells on two microscopes with different imaging modalities; and nanostructures on optical and electron microscopes. FARMER can be readily adapted to any imaging system with an encoded motorized stage and can facilitate multi-session and multi-platform imaging experiments in biology, materials science

  2. Progress in spondylarthritis. Spondyloarthritis: lessons from imaging

    OpenAIRE

    2009-01-01

    The advent of magnetic resonance imaging (MRI) and advanced sonographic techniques has led to a resurgence of interest in the role of imaging in the evaluation and management of spondyloarthritis. Radiography remains the cornerstone of diagnosis although MRI is more sensitive in early stages of the disease. Inflammatory changes in the sacroiliac joints and spine can now be reliably quantified and can also predict the subsequent development of radiographic changes in the corresponding location...

  3. Eight-channel Kirkpatrick-Baez microscope for multiframe x-ray imaging diagnostics in laser plasma experiments.

    Science.gov (United States)

    Yi, Shengzhen; Zhang, Zhe; Huang, Qiushi; Zhang, Zhong; Mu, Baozhong; Wang, Zhanshan; Fang, Zhiheng; Wang, Wei; Fu, Sizu

    2016-10-01

    Because grazing-incidence Kirkpatrick-Baez (KB) microscopes have better resolution and collection efficiency than pinhole cameras, they have been widely used for x-ray imaging diagnostics of laser inertial confinement fusion. The assembly and adjustment of a multichannel KB microscope must meet stringent requirements for image resolution and reproducible alignment. In the present study, an eight-channel KB microscope was developed for diagnostics by imaging self-emission x-rays with a framing camera at the Shenguang-II Update (SGII-Update) laser facility. A consistent object field of view is ensured in the eight channels using an assembly method based on conical reference cones, which also allow the intervals between the eight images to be tuned to couple with the microstrips of the x-ray framing camera. The eight-channel KB microscope was adjusted via real-time x-ray imaging experiments in the laboratory. This paper describes the details of the eight-channel KB microscope, its optical and multilayer design, the assembly and alignment methods, and results of imaging in the laboratory and at the SGII-Update.

  4. Eight-channel Kirkpatrick-Baez microscope for multiframe x-ray imaging diagnostics in laser plasma experiments

    Science.gov (United States)

    Yi, Shengzhen; Zhang, Zhe; Huang, Qiushi; Zhang, Zhong; Mu, Baozhong; Wang, Zhanshan; Fang, Zhiheng; Wang, Wei; Fu, Sizu

    2016-10-01

    Because grazing-incidence Kirkpatrick-Baez (KB) microscopes have better resolution and collection efficiency than pinhole cameras, they have been widely used for x-ray imaging diagnostics of laser inertial confinement fusion. The assembly and adjustment of a multichannel KB microscope must meet stringent requirements for image resolution and reproducible alignment. In the present study, an eight-channel KB microscope was developed for diagnostics by imaging self-emission x-rays with a framing camera at the Shenguang-II Update (SGII-Update) laser facility. A consistent object field of view is ensured in the eight channels using an assembly method based on conical reference cones, which also allow the intervals between the eight images to be tuned to couple with the microstrips of the x-ray framing camera. The eight-channel KB microscope was adjusted via real-time x-ray imaging experiments in the laboratory. This paper describes the details of the eight-channel KB microscope, its optical and multilayer design, the assembly and alignment methods, and results of imaging in the laboratory and at the SGII-Update.

  5. Imaging of disease progression in a case of idiopathic moyamoya

    Directory of Open Access Journals (Sweden)

    A. Chacko

    2013-08-01

    Full Text Available Moyamoya is a rare cerebrovascular disease characterised by progressive stenosis of the terminal portion of the internal carotid artery and its main branches. We report on the progression of the disease in a 3-year-old boy, confirmed to have idiopathic Moyamoya disease, over 6 ensuing years, using serial magnetic resonance imaging with MR angiography. Comparison is also made with conventional angiography at the last visit. Characteristic imaging appearances of asymmetric narrowing of the internal carotid arteries (especially the supra-clinoid portion with numerous collateral vessels around the brainstem especially within the ambient and quadrigeminal plate cisterns are demonstrated with progression.

  6. Clinical features and confocal microscopic imaging characteristics of 466 cases with infectious keratitis

    Directory of Open Access Journals (Sweden)

    Hui Xiao

    2014-10-01

    Full Text Available AIM: To observe the role of confocal microscopy in infectious keratitis management. METHODS:Totally 466 patients(467 eyesdiagnosed as infectious keratitis from January 2010 to December 2013 were retrospectively studied. the corneas were examined early by in vivo confocal microscopy. The characteristics of their images and clinical features were studied and summarized.RESULTS:All patients were recorded, the average age was 54.4±13.0 years, in which 264 cases(56.7%were male, and 202 cases(43.3%were female. In the 466 patients, 190(40.8%were fungal keratitis, 148(31.8%were viral keratitis, 125(26.8%were bacterial keratitis and 3(0.6%were acanthamoeba keratitis. There were fungal hyphae in the images of fungal keratitis. Amebic cysts were found in acanthamoeba keratitis. CONCLUSION:Confocal microscope can help the early diagnose and treatment of infectious keratitis. It is a noninvasive imaging technique that provides high resolution images of ocular structures at a cellular level and infectious keratitis represents one of its most important clinical uses.

  7. A light sheet confocal microscope for image cytometry with a variable linear slit detector

    Science.gov (United States)

    Hutcheson, Joshua A.; Khan, Foysal Z.; Powless, Amy J.; Benson, Devin; Hunter, Courtney; Fritsch, Ingrid; Muldoon, Timothy J.

    2016-03-01

    We present a light sheet confocal microscope (LSCM) capable of high-resolution imaging of cell suspensions in a microfluidic environment. In lieu of conventional pressure-driven flow or mechanical translation of the samples, we have employed a novel method of fluid transport, redox-magnetohydrodynamics (redox-MHD). This method achieves fluid motion by inducing a small current into the suspension in the presence of a magnetic field via electrodes patterned onto a silicon chip. This on-chip transportation requires no moving parts, and is coupled to the remainder of the imaging system. The microscopy system comprises a 450 nm diode 20 mW laser coupled to a single mode fiber and a cylindrical lens that converges the light sheet into the back aperture of a 10x, 0.3 NA objective lens in an epi-illumination configuration. The emission pathway contains a 150 mm tube lens that focuses the light onto the linear sensor at the conjugate image plane. The linear sensor (ELiiXA+ 8k/4k) has three lateral binning modes which enables variable detection aperture widths between 5, 10, or 20 μm, which can be used to vary axial resolution. We have demonstrated redox-MHD-enabled light sheet microscopy in suspension of fluorescent polystyrene beads. This approach has potential as a high-throughput image cytometer with myriad cellular diagnostic applications.

  8. A new self-made digital slide scanner and microscope for imaging and quantification of fluorescent microspheres

    DEFF Research Database (Denmark)

    Henning, William; Bjerglund Andersen, Julie; Højgaard, Liselotte;

    2015-01-01

    Objective: A low-cost microscope slide scanner was constructed for the purpose of digital imaging of newborn piglet brain tissue and to quantify fluorescent microspheres in tissue. Methods: Using a standard digital single-lens reflex (DSLR) camera, fluorescent imaging of newborn piglet brain tissue...

  9. Automatic Recognition of Human Parasite Cysts on Microscopic Stools Images using Principal Component Analysis and Probabilistic Neural Network

    Directory of Open Access Journals (Sweden)

    Beaudelaire Saha Tchinda

    2015-09-01

    Full Text Available Parasites live in a host and get its food from or at the expensive of that host. Cysts represent a form of resistance and spread of parasites. The manual diagnosis of microscopic stools images is time-consuming and depends on the human expert. In this paper, we propose an automatic recognition system that can be used to identify various intestinal parasite cysts from their microscopic digital images. We employ image pixel feature to train the probabilistic neural networks (PNN. Probabilistic neural networks are suitable for classification problems. The main novelty is the use of features vectors extracted directly from the image pixel. For this goal, microscopic images are previously segmented to separate the parasite image from the background. The extracted parasite is then resized to 12x12 image features vector. For dimensionality reduction, the principal component analysis basis projection has been used. 12x12 extracted features were orthogonalized into two principal components variables that consist the input vector of the PNN. The PNN is trained using 540 microscopic images of the parasite. The proposed approach was tested successfully on 540 samples of protozoan cysts obtained from 9 kinds of intestinal parasites.

  10. Automatic cell object extraction of red tide algae in microscopic images

    Science.gov (United States)

    Yu, Kun; Ji, Guangrong; Zheng, Haiyong

    2017-03-01

    Extracting the cell objects of red tide algae is the most important step in the construction of an automatic microscopic image recognition system for harmful algal blooms. This paper describes a set of composite methods for the automatic segmentation of cells of red tide algae from microscopic images. Depending on the existence of setae, we classify the common marine red tide algae into non-setae algae species and Chaetoceros, and design segmentation strategies for these two categories according to their morphological characteristics. In view of the varied forms and fuzzy edges of non-setae algae, we propose a new multi-scale detection algorithm for algal cell regions based on border- correlation, and further combine this with morphological operations and an improved GrabCut algorithm to segment single-cell and multicell objects. In this process, similarity detection is introduced to eliminate the pseudo cellular regions. For Chaetoceros, owing to the weak grayscale information of their setae and the low contrast between the setae and background, we propose a cell extraction method based on a gray surface orientation angle model. This method constructs a gray surface vector model, and executes the gray mapping of the orientation angles. The obtained gray values are then reconstructed and linearly stretched. Finally, appropriate morphological processing is conducted to preserve the orientation information and tiny features of the setae. Experimental results demonstrate that the proposed methods can effectively remove noise and accurately extract both categories of algae cell objects possessing a complete shape, regular contour, and clear edge. Compared with other advanced segmentation techniques, our methods are more robust when considering images with different appearances and achieve more satisfactory segmentation effects.

  11. Neutron imaging — Detector options in progress

    Science.gov (United States)

    Lehmann, E. H.; Tremsin, A.; Grünzweig, C.; Johnson, I.; Boillat, P.; Josic, L.

    2011-01-01

    Neutron imaging is a non-invasive method for material research on the macroscopic level. It is carried out at laboratories equipped with powerful neutron sources, suitable neutron beam lines and neutron detection systems. Decades ago neutron radiography began capturing images with film techniques. These techniques yielded excellent spatial resolution even over large fields of view. In the recent years, improvements in the detection techniques and their digitization have been the main forces driving successes in neutron imaging. Several detector options have been developed, implemented and used in practical applications in order to achieve digital information from the neutron transmission process which is needed for a quantitative evaluation of image data by sophisticated methods like neutron tomography, phase contrast imaging, neutron interferometry and time dependent studies. The most common approach in digital neutron imaging is a conversion of the neutron field information into visible light by a scintillation process, where a neutron converter is needed because neutrons do not excite directly due to their neutral charge. Low level light signals can be observed either with sensitive camera systems or by using amorphous silicon based semiconductor plate devices. However, these now established detection techniques are still limited in respect to spatial and time resolution. The best possible spatial resolution which can be achieved today is available by a system built at PSI with about 10 μm pixel size. Recently, it was upgraded with a tilted option for an increased resolution by a factor of 4 in one direction. Scintillator based techniques are limited by the dissipation of the secondary particles. This limitation has motivated the search for new detector options. One approach is a pixilated system where the readout per incoming neutron can be used to calculate precisely the position of its impact. Such devices are realized as the TIMEPIX system already. The

  12. Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens

    Science.gov (United States)

    Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

    2013-11-01

    This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10-2 Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

  13. Research progress of magnetic resonance imaging contrast agents

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Magnetic resonance imaging (MRI) is a clinical diagnostic modality, which has become popular in hospitals around the world. Approximately 30% of MRI exams include the use of contrast agents. The research progress of the paramagnetic resonance imaging contrast agents was described briefly. Three important approaches in the soluble paramagnetic resonance imaging contrast agents design including nonionic, tissue-specific and macromolecular contrast agents were investigated. In addition, the problems in the research and development in future were discussed.

  14. Research Progress of Melanoma Imaging with Radionuclide Agents

    Directory of Open Access Journals (Sweden)

    YOU Qiang

    2015-11-01

    Full Text Available In comparison with CT, ultrasonography, MRI et al, scintigraphic imaging have the advantages of high specificity and recognizes lesions and structure-function of the receptor and metabolism in molecular level, which could diagnose melanoma and its metastasis earlier. With the emergence of more new imaging agents, this unique advantage was more obviously. This article discussed the latest research progress of melanoma imaging with radionuclide agents from aspects of single photon and positron.

  15. Microscopic method in processed animal proteins identification in feed: applications of image analysis

    Directory of Open Access Journals (Sweden)

    Savoini G

    2004-01-01

    Full Text Available Processed animal proteins (PAP detection and identification in feedstuffs can be difficult in distinguishing among land animals, i.e. poultry and mammals. Thus, the aim of this study was to evaluate the potential application of image analysis in PAP identification. For this purpose four reference samples containing poultry meals and four reference samples containing mammalian meat and bone meals were used. Each sample was analyzed using the microscopic method (98/88/EC. Bone fragments are characterized by similar morphological features (colours, shape, lacunae shape, lacunae distribution, etc. that make it diff i c u l t to distinguish between poultry and mammals. Through a digital camera and an image analysis software a total of 30 bone fragment lacunae images at X400 were obtained. For each image 29 geometric parameters related to the lacunae and 3 geometric parameters related to the canaliculae of lacunae, were measured using the image analysis software obtaining 960 observations. Of the 32 descriptors used two, the area of the lacunae and their perimeter, were able to explain 96.15% of the total variability of the data, even though their contribution was different (83.97% vs. 12.18%, respectively. Through these two descriptors it was possible to distinguish between mammalian and poultry lacunae, except in two cases (6.6%, in which poultry lacunae were wrongly classified as mammalian. This latter can be related with higher variability in the lacunae area recorded for mammals compared to poultry. On the basis of the present study, it can be concluded that image analysis represents a promising potential tool in PAP identification, that may provide accurate and reliable results in feedstuffs characterisation, analysis and control.

  16. 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 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.

  17. High definition infrared chemical imaging of colorectal tissue using a Spero QCL microscope.

    Science.gov (United States)

    Bird, B; Rowlette, J

    2017-04-10

    Mid-infrared microscopy has become a key technique in the field of biomedical science and spectroscopy. This label-free, non-destructive technique permits the visualisation of a wide range of intrinsic biochemical markers in tissues, cells and biofluids by detection of the vibrational modes of the constituent molecules. Together, infrared microscopy and chemometrics is a widely accepted method that can distinguish healthy and diseased states with high accuracy. However, despite the exponential growth of the field and its research world-wide, several barriers currently exist for its full translation into the clinical sphere, namely sample throughput and data management. The advent and incorporation of quantum cascade lasers (QCLs) into infrared microscopes could help propel the field over these remaining hurdles. Such systems offer several advantages over their FT-IR counterparts, a simpler instrument architecture, improved photon flux, use of room temperature camera systems, and the flexibility of a tunable illumination source. In this current study we explore the use of a QCL infrared microscope to produce high definition, high throughput chemical images useful for the screening of biopsied colorectal tissue.

  18. Automated plasmodia recognition in microscopic images for diagnosis of malaria using convolutional neural networks

    Science.gov (United States)

    Krappe, Sebastian; Benz, Michaela; Gryanik, Alexander; Tannich, Egbert; Wegner, Christine; Stamminger, Marc; Wittenberg, Thomas; Münzenmayer, Chrisitan

    2017-03-01

    Malaria is one of the world's most common and serious tropical diseases, caused by parasites of the genus plasmodia that are transmitted by Anopheles mosquitoes. Various parts of Asia and Latin America are affected but highest malaria incidence is found in Sub-Saharan Africa. Standard diagnosis of malaria comprises microscopic detection of parasites in stained thick and thin blood films. As the process of slide reading under the microscope is an error-prone and tedious issue we are developing computer-assisted microscopy systems to support detection and diagnosis of malaria. In this paper we focus on a deep learning (DL) approach for the detection of plasmodia and the evaluation of the proposed approach in comparison with two reference approaches. The proposed classification schemes have been evaluated with more than 180,000 automatically detected and manually classified plasmodia candidate objects from so-called thick smears. Automated solutions for the morphological analysis of malaria blood films could apply such a classifier to detect plasmodia in the highly complex image data of thick smears and thereby shortening the examination time. With such a system diagnosis of malaria infections should become a less tedious, more reliable and reproducible and thus a more objective process. Better quality assurance, improved documentation and global data availability are additional benefits.

  19. Super-resolution imaging of ciliary microdomains in isolated olfactory sensory neurons using a custom STED microscope

    Science.gov (United States)

    Meyer, Stephanie A.; Ozbay, Baris; Restrepo, Diego; Gibson, Emily A.

    2014-03-01

    We performed super-resolution imaging of isolated olfactory sensory neurons (OSNs) using a custom-built Stimulated Emission Depletion (STED) microscope. The design for the STED microscope is based on the system developed in the laboratory of Dr. Stefan Hell1. Our system is capable of imaging with sub-diffraction limited resolution simultaneously in two color channels (at Atto 590/Atto 647N wavelengths). A single, pulsed laser source (ALP; Fianium, Inc.) generates all four laser beams, two excitation and two STED. The two STED beams are coupled into one polarization maintaining (PM) fiber and the two excitation beams into another. They are then collimated and both STED beams pass through a vortex phase plate (RPC Photonics) to allow shaping into a donut at the focus of the objective lens. The beams are then combined and sent into an inverted research microscope (IX-71; Olympus Inc.) allowing widefield epifluorescence, brightfield and DIC imaging on the same field of view as STED imaging. A fast piezo stage scans the sample during STED and confocal imaging. The fluorescent signals from the two color channels are detected with two avalanche photodiodes (APD) after appropriate spectral filtering. The resolution of the system was characterized by imaging 40 nm fluorescent beads as ~60 nm (Atto 590) and ~50 nm (Atto 647N). We performed STED imaging on immunolabeled isolated OSNs tagged at the CNGA2 and ANO2 proteins. The STED microscope allows us to resolve ciliary CNGA2 microdomains of ~54 nm that were blurred in confocal.

  20. Progress in spondylarthritis. Spondyloarthritis: lessons from imaging.

    Science.gov (United States)

    Maksymowych, Walter P

    2009-01-01

    The advent of magnetic resonance imaging (MRI) and advanced sonographic techniques has led to a resurgence of interest in the role of imaging in the evaluation and management of spondyloarthritis. Radiography remains the cornerstone of diagnosis although MRI is more sensitive in early stages of the disease. Inflammatory changes in the sacroiliac joints and spine can now be reliably quantified and can also predict the subsequent development of radiographic changes in the corresponding locations. MRI-based scoring systems for inflammation are highly responsive, facilitating proof-of-concept studies of new therapies for spondyloarthritis. Assessment of chronic changes is much less reliable using MRI, while assessment using radiography lacks sensitivity to change. Assessment of disease modification therefore remains a principle challenge in the development of new therapies for ankylosing spondylitis. Ultrasound may be the preferred approach to the assessment of peripheral inflammation, especially enthesitis. Scintigraphy and computed tomography offer few advantages over MRI.

  1. 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 were 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.

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    G. Helas

    2008-08-01

    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.

  4. Three-dimensional microscopic tomographic imagings of the cataract in a human lens in vivo.

    Science.gov (United States)

    Masters, B

    1998-10-26

    The problem of three-dimensional visualization of a human lens in vivo has been solved by a technique of volume rendering a transformed series of 60 rotated Scheimpflug (a dual slit reflected light microscope) digital images. The data set was obtained by rotating the Scheimpflug camera about the optic axis of the lens in 3 degree increments. The transformed set of optical sections were first aligned to correct for small eye movements, and then rendered into a volume reconstruction with volume rendering computer graphics techniques. To help visualize the distribution of lens opacities (cataracts) in the living, human lens the intensity of light scattering was pseudocolor coded and the cataract opacities were displayed as a movie.

  5. Dual Raman-Brillouin Microscope for Chemical and Mechanical Characterization and Imaging.

    Science.gov (United States)

    Traverso, Andrew J; Thompson, Jonathan V; Steelman, Zachary A; Meng, Zhaokai; Scully, Marlan O; Yakovlev, Vladislav V

    2015-08-01

    We present a unique confocal microscope capable of measuring the Raman and Brillouin spectra simultaneously from a single spatial location. Raman and Brillouin scattering offer complementary information about a material's chemical and mechanical structure, respectively, and concurrent monitoring of both of these spectra would set a new standard for material characterization. We achieve this by applying recent innovations in Brillouin spectroscopy that reduce the necessary acquisition times to durations comparable to conventional Raman spectroscopy while attaining a high level of spectral accuracy. To demonstrate the potential of the system, we map the Raman and Brillouin spectra of a molded poly(ethylene glycol) diacrylate (PEGDA) hydrogel sample in cyclohexane to create two-dimensional images with high contrast at microscale resolutions. This powerful tool has the potential for very diverse analytical applications in basic science, industry, and medicine.

  6. 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.

  7. A high-pressure atomic force microscope for imaging in supercritical carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Lea, A. S.; Higgins, S. R.; Knauss, K. G.; Rosso, K. M.

    2011-01-01

    A high-pressure atomic force microscope(AFM) that enables in situ, atomic scale measurements of topography of solid surfaces in contact with supercritical CO2 (scCO2) fluids has been developed. This apparatus overcomes the pressure limitations of the hydrothermal AFM and is designed to handle pressures up to 100 atm at temperatures up to ~350 K. A standard optically-based cantilever deflection detection system was chosen. When imaging in compressible supercritical fluids such as scCO2, precise control of pressure and temperature in the fluid cell is the primary technical challenge. Noise levels and imaging resolution depend on minimization of fluid density fluctuations that change the fluidrefractive index and hence the laser path. We demonstrate with our apparatus in situ atomic scale imaging of a calcite (CaCO3) mineral surface in scCO2; both single, monatomic steps and dynamic processes occurring on the (101¯4) surface are presented. Finally, this new AFM provides unprecedented in situ access to interfacial phenomena at solid–fluid interfaces under pressure.

  8. Measurement of RBC agglutination with microscopic cell image analysis in a microchannel chip.

    Science.gov (United States)

    Cho, Chi Hyun; Kim, Ju Yeon; Nyeck, Agnes E; Lim, Chae Seung; Hur, Dae Sung; Chung, Chanil; Chang, Jun Keun; An, Seong Soo A; Shin, Sehyun

    2014-01-01

    Since Landsteiner's discovery of ABO blood groups, RBC agglutination has been one of the most important immunohematologic techniques for ABO and RhD blood groupings. The conventional RBC agglutination grading system for RhD blood typings relies on macroscopic reading, followed by the assignment of a grade ranging from (-) to (4+) to the degree of red blood cells clumping. However, with the new scoring method introduced in this report, microscopically captured cell images of agglutinated RBCs, placed in a microchannel chip, are used for analysis. Indeed, the cell images' pixel number first allows the differentiation of agglutinated and non-agglutinated red blood cells. Finally, the ratio of agglutinated RBCs per total RBC counts (CRAT) from 90 captured images is then calculated. During the trial, it was observed that the agglutinated group's CRAT was significantly higher (3.77-0.003) than that of the normal control (0). Based on these facts, it was established that the microchannel method was more suitable for the discrimination between agglutinated RBCs and non-agglutinated RhD negative, and thus more reliable for the grading of RBCs agglutination than the conventional method.

  9. Non-rigid Registration for Large Sets of Microscopic Images on Graphics Processors.

    Science.gov (United States)

    Ruiz, Antonio; Ujaldon, Manuel; Cooper, Lee; Huang, Kun

    2009-04-01

    Microscopic imaging is an important tool for characterizing tissue morphology and pathology. 3D reconstruction and visualization of large sample tissue structure requires registration of large sets of high-resolution images. However, the scale of this problem presents a challenge for automatic registration methods. In this paper we present a novel method for efficient automatic registration using graphics processing units (GPUs) and parallel programming. Comparing a C++ CPU implementation with Compute Unified Device Architecture (CUDA) libraries and pthreads running on GPU we achieve a speed-up factor of up to 4.11× with a single GPU and 6.68× with a GPU pair. We present execution times for a benchmark composed of two sets of large-scale images: mouse placenta (16K × 16K pixels) and breast cancer tumors (23K × 62K pixels). It takes more than 12 hours for the genetic case in C++ to register a typical sample composed of 500 consecutive slides, which was reduced to less than 2 hours using two GPUs, in addition to a very promising scalability for extending those gains easily on a large number of GPUs in a distributed system.

  10. 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.

  11. 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.

  12. Classification of Salmonella enterica serotypes with selective bands using visible/NIR hyperspectral microscope images.

    Science.gov (United States)

    Eady, M; Park, B

    2016-07-01

    Optical detection of foodborne bacteria such as Salmonella classifies bacteria by analysing spectral data, and has potential for rapid detection. In this experiment hyperspectral microscopy is explored as a means for classifying five Salmonella serotypes. Initially, the microscope collects 89 spectral measurements between 450 and 800 nm. Here, the objective was to develop correct classification of five serotypes with optimal spectral bands selected through multivariate data analysis (MVDA), thus reducing the data processing and storage requirement necessary for practical application in the food industry. An upright digital microscope is equipped with an acousto-optical tuneable filter, electron multiplying charge-coupled device, and metal halide lighting source. Images for each of the five serotypes were collected, and informative bands were identified through a principal component analysis, for four abbreviated spectral ranges containing 3, 7, 12 and 20 spectral bands. The experiment was repeated with an independent repetition and images were collected at each of the reduced band sets, identified by the first repetition. A support vector machine (SVM) was used to classify serotypes. Results showed that with the first repetition, classification accuracy decreased from 99.5% (89 bands) to 84.5% (3 bands), whereas the second repetition showed classification accuracies of 100%, possibly due to a reduction in spectral noise. The support vector machine regression (SVMR) was applied with cross-validation, and had R(2) calibration and validation values >0.922. Although classification accuracies through SVM classification showed that as little as 3 bands were able to classify 100% of the samples, the SVMR shows that the smallest root-mean squared-error values were 0.001 and 0.002 for 20 and 12 bands, respectively, suggesting that the 12 band range collected between 586 and 630 nm is optimal for classifying bacterial serotypes, with only the informative HMI bands selected.

  13. Fluorescence liftime imaging (FLIM) using ps-pulsed diode lasers in laser scanning microscopes

    Science.gov (United States)

    Ruck, Angelika C.; Dolp, Frank; Happ, Claudia; Steiner, Rudolf; Beil, Michael

    2003-06-01

    A setup consisting on a laser scanning microscope equipped with appropriate detection units was developed for time-resolved intracellular fluorescence spectroscopy and fluorescence lifetime imaging (FLIM) for on-line detection of structural changes of various biomolecules. Short-pulsed excitation was performed with a diode laser which emits pulses at 398 nm with 70 ps duration. The laser was coupled to the laser scanning microscope. For time resolved spectroscopy a setup consisting of an Czerny Turner spectrometer and a MCP-gated and -intensified CCD camera was used. Time-gated spectra within the cells were acquired by placing the laser beam in "spot scan" mode. In addition, a time-correlated single photon counting module was used to determine the fluorescence lifetime from single spots and to record lifetime images (τ-mapping). The time-resolved fluorescence characteristics of 5-ALA (5-aminolevulinic-acid), as well as 5-ALAhe (5-aminolevulinic-acid-hexylester)- induced protoporphyrine IX (PPIX) were investigated before and during PDT with subcellular resolution. For cells which were incubated with 5-ALA, a component with a fluorescence lifetime of about 7 ns was correlated with a structured fluorescence, which probably coincides with mitochondria, whereas a shorter lifetime was found in the cytoplasm. In the case of 5-ALAhe the lifetime of PPIX was longer, which could be due to different localization. During PDT the component with the longer lifetime completely vanished, whereas the shorter liftime was retained. It seems that FLIM is a valuable method to selectively identify and localize the photodynamically active photosensitizer.

  14. Computational Chemical Imaging for Cardiovascular Pathology: Chemical Microscopic Imaging Accurately Determines Cardiac Transplant Rejection

    Science.gov (United States)

    Tiwari, Saumya; Reddy, Vijaya B.; Bhargava, Rohit; Raman, Jaishankar

    2015-01-01

    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. PMID:25932912

  15. 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.

  16. 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.

  17. Progress in 3D imaging and display by integral imaging

    Science.gov (United States)

    Martinez-Cuenca, R.; Saavedra, G.; Martinez-Corral, M.; Pons, A.; Javidi, B.

    2009-05-01

    Three-dimensionality is currently considered an important added value in imaging devices, and therefore the search for an optimum 3D imaging and display technique is a hot topic that is attracting important research efforts. As main value, 3D monitors should provide the observers with different perspectives of a 3D scene by simply varying the head position. Three-dimensional imaging techniques have the potential to establish a future mass-market in the fields of entertainment and communications. Integral imaging (InI), which can capture true 3D color images, has been seen as the right technology to 3D viewing to audiences of more than one person. Due to the advanced degree of development, InI technology could be ready for commercialization in the coming years. This development is the result of a strong research effort performed along the past few years by many groups. Since Integral Imaging is still an emerging technology, the first aim of the "3D Imaging and Display Laboratory" at the University of Valencia, has been the realization of a thorough study of the principles that govern its operation. Is remarkable that some of these principles have been recognized and characterized by our group. Other contributions of our research have been addressed to overcome some of the classical limitations of InI systems, like the limited depth of field (in pickup and in display), the poor axial and lateral resolution, the pseudoscopic-to-orthoscopic conversion, the production of 3D images with continuous relief, or the limited range of viewing angles of InI monitors.

  18. 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.

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

    Science.gov (United States)

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

    2014-02-01

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

  20. Characterization of Lunar Soils Using a Thermal Infrared Microscopic Spectral Imaging System

    Science.gov (United States)

    Crites, S. T.; Lucey, P. G.

    2010-12-01

    Lunar Reconnaissance Orbiter's Diviner radiometer has provided the planetary science community with a large amount of thermal infrared spectral data. This data set offers rich opportunities for lunar science, but interpretation of the data is complicated by the limited data on lunar materials. While spectra of pure terrestrial minerals have been used effectively for Mars applications, lunar minerals and glasses have been affected by space weathering processes that may alter their spectral properties in important ways. For example, mineral grains acquire vapor deposited coatings, and agglutinate glass contains abundant nanophase iron as a result of exposure to the space environment. Producing mineral separates in sufficient quantities (at least tens of mg) for spectral characterization is painstaking, time consuming and labor intensive; as an alternative we have altered an infrared hyperspectral imaging system developed for remote sensing under funding from the Planetary Instrument Definition and Development program (PIDDP) to enable resolved microscopic spectral imaging. The concept is to characterize the spectral properties of individual grains in lunar soils, enabling a wide range of spectral behaviors of components to be measured rapidly. The instrument, sensitive from 8 to 15 microns at 15 wavenumber resolution, images a field of view of 8 millimeters at 30 micron resolution and scans at a rate of about 1 mm/second enabling relatively large areas to be scanned rapidly. Our experiments thus far use a wet-sieved 90-150 um size fraction with the samples arrayed on a heated substrate in a single layer in order to prevent spectral interactions between grains. We have begun with pure mineral separates, and unsurprisingly we find that the individual mineral grain emission spectra of a wide range of silicates are very similar to spectra of coarse grained powders. We have begun to obtain preliminary data on lunar soils as well. We plan to continue imaging of lunar soils

  1. Application of the progressive wavelet correlation for image recognition and retrieval from the collection of images

    OpenAIRE

    Stojanovic, Igor; Markovski, Smile; Martinovska, Cveta; Mileva, Aleksandra

    2012-01-01

    An algorithm for recognition and retrieval of image from image collection is developed. Basis of the algorithm is the progressive wavelet correlation. The final result is the recognition and retrieval of the wanted image, if it is in the image collection. Instructions for the choice of correlation threshold value for obtaining desired results are defined. To increase efficiency is presented two phases solution. The first phase uses well known methods of image retrieving by descriptors based o...

  2. 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).

  3. Multiphoton microscopic imaging of fibrotic focus in invasive ductal carcinoma of the breast

    Science.gov (United States)

    Chen, Sijia; Nie, Yuting; Lian, Yuane; Wu, Yan; Fu, Fangmeng; Wang, Chuan; Zhuo, Shuangmu; Chen, Jianxin

    2014-11-01

    During the proliferation of breast cancer, the desmoplastic can evoke a fibrosis response by invading healthy tissue. Fibrotic focus (FF) in invasive ductal carcinoma (IDC) of the breast had been reported to be associated with significantly poorer survival rate than IDC without FF. As an important prognosis indicator, it's difficult to obtain the exact fibrotic information from traditional detection method such as mammography. Multiphoton imaging based on two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) has been recently employed for microscopic examination of unstained tissue. In this study, multiphoton microscopy (MPM) was used to image the fibrotic focus in invasive ductal carcinoma tissue. The morphology and distribution of collagen in fibrotic focus can be demonstrated by the SHG signal. Variation of collagen between IDC with and without FF will be examined and further characterized, which may be greatly related to the metastasis of breast cancer. Our result suggested that the MPM can be efficient in identifying and locating the fibrotic focus in IDC. Combining with the pathology analysis and other detecting methods, MPM owns potential in becoming an advanced histological tool for detecting the fibrotic focus in IDC and collecting prognosis information, which may guide the subsequent surgery option and therapy procedure for patients.

  4. Automatic layer segmentation of H&E microscopic images of mice skin

    Science.gov (United States)

    Hussein, Saif; Selway, Joanne; Jassim, Sabah; Al-Assam, Hisham

    2016-05-01

    Mammalian skin is a complex organ composed of a variety of cells and tissue types. The automatic detection and quantification of changes in skin structures has a wide range of applications for biological research. To accurately segment and quantify nuclei, sebaceous gland, hair follicles, and other skin structures, there is a need for a reliable segmentation of different skin layers. This paper presents an efficient segmentation algorithm to segment the three main layers of mice skin, namely epidermis, dermis, and subcutaneous layers. It also segments the epidermis layer into two sub layers, basal and cornified layers. The proposed algorithm uses adaptive colour deconvolution technique on H&E stain images to separate different tissue structures, inter-modes and Otsu thresholding techniques were effectively combined to segment the layers. It then uses a set of morphological and logical operations on each layer to removing unwanted objects. A dataset of 7000 H&E microscopic images of mutant and wild type mice were used to evaluate the effectiveness of the algorithm. Experimental results examined by domain experts have confirmed the viability of the proposed algorithms.

  5. Non-destructive on-chip cell sorting system with real-time microscopic image processing

    Directory of Open Access Journals (Sweden)

    Ichiki Takanori

    2004-06-01

    Full Text Available Abstract Studying cell functions for cellomics studies often requires the use of purified individual cells from mixtures of various kinds of cells. We have developed a new non-destructive on-chip cell sorting system for single cell based cultivation, by exploiting the advantage of microfluidics and electrostatic force. The system consists of the following two parts: a cell sorting chip made of poly-dimethylsiloxane (PDMS on a 0.2-mm-thick glass slide, and an image analysis system with a phase-contrast/fluorescence microscope. The unique features of our system include (i identification of a target from sample cells is achieved by comparison of the 0.2-μm-resolution phase-contrast and fluorescence images of cells in the microchannel every 1/30 s; (ii non-destructive sorting of target cells in a laminar flow by application of electrostatic repulsion force for removing unrequited cells from the one laminar flow to the other; (iii the use of agar gel for electrodes in order to minimize the effect on cells by electrochemical reactions of electrodes, and (iv pre-filter, which was fabricated within the channel for removal of dust contained in a sample solution from tissue extracts. The sorting chip is capable of continuous operation and we have purified more than ten thousand cells for cultivation without damaging them. Our design has proved to be very efficient and suitable for the routine use in cell purification experiments.

  6. Design and commissioning of a directly coupled in-vivo multiphoton microscope for skin imaging in humans and large animals

    Science.gov (United States)

    Mulholland, William J.; Kendall, Mark A.

    2004-02-01

    The application of near infrared multiphoton excitation to the laser-scanning microscope was first conceived by Denk, Strickler and Webb in 1990. Since then, advances in design have seen the multiphoton laser scanning microscope (MPLSM) applied to a wide range of biological research areas, including skin imaging and vaccine delivery. The technique has the attributes of low phototoxicity, high-resolution functional imaging to depths in scattered tissues. These characteristics have encouraged engineers and scientists to develop in-vivo imaging systems. For these applications, laser excitation pulses can be delivered to the sample through optical fibers. Although this solution provides a number of advantages relating to movement and flexibility of the site of interest relative to the laser source, the peak powers that can be delivered down the fiber are limited. We report on the design and commissioning of a directly coupled in-vivo MPM system, optimised for the imaging of epidermal vaccines delivered to a range of biological models and humans. Specifically, we seek to apply the system to visualise in-vivo, the influence of hand-held, helium powered needle-free systems on skin cells. A standard Nikon E600FN microscope, dissected above the optical plane was cantilevered from a vibration isolated table using rigid support arms. The modified microscope was coupled to an infrared optimised Bio-Rad Radiance 2100MP, multiphoton dedicated laser scanning control and image acquisition system. Femtosecond laser pulses were provided by a 10W Verdi pumped Mira Ti:Sapphire laser, from Coherent Inc. The microscope was modified such that the transmission half may be selectively attached for conventional imaging with ex-vivo and cell culture samples, or removed for in-vivo imaging of skin sites on the body of humans and large animals. Optical performance of the system, and aspects of its design and commissioning are discussed in this paper.

  7. Automatic detection of mitochondria from electron microscope tomography images: a curve fitting approach

    Science.gov (United States)

    Tasel, Serdar F.; Hassanpour, Reza; Mumcuoglu, Erkan U.; Perkins, Guy C.; Martone, Maryann

    2014-03-01

    Mitochondria are sub-cellular components which are mainly responsible for synthesis of adenosine tri-phosphate (ATP) and involved in the regulation of several cellular activities such as apoptosis. The relation between some common diseases of aging and morphological structure of mitochondria is gaining strength by an increasing number of studies. Electron microscope tomography (EMT) provides high-resolution images of the 3D structure and internal arrangement of mitochondria. Studies that aim to reveal the correlation between mitochondrial structure and its function require the aid of special software tools for manual segmentation of mitochondria from EMT images. Automated detection and segmentation of mitochondria is a challenging problem due to the variety of mitochondrial structures, the presence of noise, artifacts and other sub-cellular structures. Segmentation methods reported in the literature require human interaction to initialize the algorithms. In our previous study, we focused on 2D detection and segmentation of mitochondria using an ellipse detection method. In this study, we propose a new approach for automatic detection of mitochondria from EMT images. First, a preprocessing step was applied in order to reduce the effect of nonmitochondrial sub-cellular structures. Then, a curve fitting approach was presented using a Hessian-based ridge detector to extract membrane-like structures and a curve-growing scheme. Finally, an automatic algorithm was employed to detect mitochondria which are represented by a subset of the detected curves. The results show that the proposed method is more robust in detection of mitochondria in consecutive EMT slices as compared with our previous automatic method.

  8. Optical scatter imaging: a microscopic modality for the rapid morphological assay of living cells

    Science.gov (United States)

    Boustany, Nada N.

    2007-02-01

    Tumors derived from epithelial cells comprise the majority of human tumors and their growth results from the accumulation of multiple mutations affecting cellular processes critical for tissue homeostasis, including cell proliferation and cell death. To understand these processes and address the complexity of cancer cell function, multiple cellular responses to different experimental conditions and specific genetic mutations must be analyzed. Fundamental to this endeavor is the development of rapid cellular assays in genetically defined cells, and in particular, the development of optical imaging methods that allow dynamic observation and real-time monitoring of cellular processes. In this context, we are developing an optical scatter imaging technology that is intended to bridge the gap between light and electron microscopy by rapidly providing morphometric information about the relative size and shape of non-spherical organelles, with sub-wavelength resolution. Our goal is to complement current microscopy techniques used to study cells in-vitro, especially in long-term time-lapse studies of living cells, where exogenous labels can be toxic, and electron microscopy will destroy the sample. The optical measurements are based on Fourier spatial filtering in a standard microscope, and could ultimately be incorporated into existing high-throughput diagnostic platforms for cancer cell research and histopathology of neoplastic tissue arrays. Using an engineered epithelial cell model of tumor formation, we are currently studying how organelle structure and function are altered by defined genetic mutations affecting the propensity for cell death and oncogenic potential, and by environmental conditions promoting tumor growth. This talk will describe our optical scatter imaging technology and present results from our studies on apoptosis, and the function of BCL-2 family proteins.

  9. Cell type classifiers for breast cancer microscopic images based on fractal dimension texture analysis of image color layers.

    Science.gov (United States)

    Jitaree, Sirinapa; Phinyomark, Angkoon; Boonyaphiphat, Pleumjit; Phukpattaranont, Pornchai

    2015-01-01

    Having a classifier of cell types in a breast cancer microscopic image (BCMI), obtained with immunohistochemical staining, is required as part of a computer-aided system that counts the cancer cells in such BCMI. Such quantitation by cell counting is very useful in supporting decisions and planning of the medical treatment of breast cancer. This study proposes and evaluates features based on texture analysis by fractal dimension (FD), for the classification of histological structures in a BCMI into either cancer cells or non-cancer cells. The cancer cells include positive cells (PC) and negative cells (NC), while the normal cells comprise stromal cells (SC) and lymphocyte cells (LC). The FD feature values were calculated with the box-counting method from binarized images, obtained by automatic thresholding with Otsu's method of the grayscale images for various color channels. A total of 12 color channels from four color spaces (RGB, CIE-L*a*b*, HSV, and YCbCr) were investigated, and the FD feature values from them were used with decision tree classifiers. The BCMI data consisted of 1,400, 1,200, and 800 images with pixel resolutions 128 × 128, 192 × 192, and 256 × 256, respectively. The best cross-validated classification accuracy was 93.87%, for distinguishing between cancer and non-cancer cells, obtained using the Cr color channel with window size 256. The results indicate that the proposed algorithm, based on fractal dimension features extracted from a color channel, performs well in the automatic classification of the histology in a BCMI. This might support accurate automatic cell counting in a computer-assisted system for breast cancer diagnosis.

  10. Rapid detection of parasite in muscle fibers of fishes using a portable microscope imaging technique (Conference Presentation)

    Science.gov (United States)

    Lee, Jayoung; Lee, Hoonsoo; Kim, Moon S.; Cho, Byoungkwan

    2017-05-01

    Fishes are a widely used food material in the world. Recently about 4% of the fishes are infected with Kudoa thyrsites in Asian ocean. Kudoa thyrsites is a parasite that is found within the muscle fibers of fishes. The infected fishes can be a reason of food poisoning, which should be sorted out before distribution and consumption. Although Kudoa thyrsites is visible to the naked eye, it could be easily overlooked due to the micro-scale size and similar color with fish tissue. In addition, the visual inspection is labor intensive works resulting in loss of money and time. In this study, a portable microscopic camera was utilized to obtain images of raw fish slices. The optimized image processing techniques with polarized transmittance images provided reliable performance. The result shows that the portable microscopic imaging method can be used to detect parasites rapidly and non-destructively, which could be an alternative to manual inspections.

  11. Reflected-light, photoluminescence and OBIC imaging of solar cells using a confocal scanning laser MACROscope/microscope

    Energy Technology Data Exchange (ETDEWEB)

    Ribes, A.C.; Damaskinos, S.; Tiedje, H.F.; Dixon, A.E.; Brodie, D.E. [Guelph-Waterloo Program for Graduate Work in Physics, Waterloo Campus, University of Waterloo, Waterloo, ON (Canada)

    1996-11-27

    This paper describes a confocal scanning beam MACROscope/Microscope which can image specimens up to 7x7 cm in size using reflected light, photoluminescence and optical beam induced current. The MACROscope provides a 10{mu}m spot size at various wavelengths and generates 512x512 pixel images in less than 5 s. When used in combination with a conventional confocal scanning laser microscope sub-micron spot sizes become possible providing resolutions as high as 0.25{mu}m laterally and 0.5{mu}m axially in reflected light. The main function of this imaging system is to spatially resolve any defects within solar cells and similar devices. Several reflected-light, photoluminescence and OBIC images of CdS/CuInSe{sub 2} and CdZnS/CuInSe{sub 2} thin film solar cells are presented

  12. Proliferating cell nuclear antigen (PCNA) allows the automatic identification of follicles in microscopic images of human ovarian tissue

    CERN Document Server

    Kelsey, Thomas W; Castillo, Luis; Wallace, W Hamish B; Gonzálvez, Francisco Cóppola; 10.2147/PLMI.S11116

    2010-01-01

    Human ovarian reserve is defined by the population of nongrowing follicles (NGFs) in the ovary. Direct estimation of ovarian reserve involves the identification of NGFs in prepared ovarian tissue. Previous studies involving human tissue have used hematoxylin and eosin (HE) stain, with NGF populations estimated by human examination either of tissue under a microscope, or of images taken of this tissue. In this study we replaced HE with proliferating cell nuclear antigen (PCNA), and automated the identification and enumeration of NGFs that appear in the resulting microscopic images. We compared the automated estimates to those obtained by human experts, with the "gold standard" taken to be the average of the conservative and liberal estimates by three human experts. The automated estimates were within 10% of the "gold standard", for images at both 100x and 200x magnifications. Automated analysis took longer than human analysis for several hundred images, not allowing for breaks from analysis needed by humans. O...

  13. A three-photon microscope with adaptive optics for deep-tissue in vivo structural and functional brain imaging

    Science.gov (United States)

    Tao, Xiaodong; Lu, Ju; Lam, Tuwin; Rodriguez, Ramiro; Zuo, Yi; Kubby, Joel

    2017-02-01

    We developed a three-photon adaptive optics add-on to a commercial two-photon laser scanning microscope. We demonstrated its capability for structural and functional imaging of neurons labeled with genetically encoded red fluorescent proteins or calcium indicators deep in the living mouse brain with cellular and subcellular resolution.

  14. 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...

  15. Ultrabright planar optodes for luminescence life-time based microscopic imaging of O2 dynamics in biofilms

    DEFF Research Database (Denmark)

    Staal, Marc Jaap; Borisov, S M; Rickelt, L F

    2011-01-01

    New transparent optodes for life-time based microscopic imaging of O2 were developed by spin-coating a µm-thin layer of a highly luminescent cyclometalated iridium(III) coumarin complex in polystyrene onto glass cover slips. Compared to similar thin-film O2 optodes based on a ruthenium(II) polypy...

  16. A real-time pseudocolor encoding technique for the phase rate-of-change in the imaging system of microscope

    Science.gov (United States)

    Chen, Guanying; Duan, Wenshan

    1999-05-01

    A real-time white light stereo pseudocolor encoding technique for the phase rate-of-change in the imaging system of microscope is presented. It is analyzed by the theory of partially coherent light. The analytic results showed that the information about phase rate-of-change of the input object function is reflected in the output stereo pseudocolor image under given conditions and illuminated by incoherent source.

  17. Applying deep learning technology to automatically identify metaphase chromosomes using scanning microscopic images: an initial investigation

    Science.gov (United States)

    Qiu, Yuchen; Lu, Xianglan; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Li, Shibo; Liu, Hong; Zheng, Bin

    2016-03-01

    Automated high throughput scanning microscopy is a fast developing screening technology used in cytogenetic laboratories for the diagnosis of leukemia or other genetic diseases. However, one of the major challenges of using this new technology is how to efficiently detect the analyzable metaphase chromosomes during the scanning process. The purpose of this investigation is to develop a computer aided detection (CAD) scheme based on deep learning technology, which can identify the metaphase chromosomes with high accuracy. The CAD scheme includes an eight layer neural network. The first six layers compose of an automatic feature extraction module, which has an architecture of three convolution-max-pooling layer pairs. The 1st, 2nd and 3rd pair contains 30, 20, 20 feature maps, respectively. The seventh and eighth layers compose of a multiple layer perception (MLP) based classifier, which is used to identify the analyzable metaphase chromosomes. The performance of new CAD scheme was assessed by receiver operation characteristic (ROC) method. A number of 150 regions of interest (ROIs) were selected to test the performance of our new CAD scheme. Each ROI contains either interphase cell or metaphase chromosomes. The results indicate that new scheme is able to achieve an area under the ROC curve (AUC) of 0.886+/-0.043. This investigation demonstrates that applying a deep learning technique may enable to significantly improve the accuracy of the metaphase chromosome detection using a scanning microscopic imaging technology in the future.

  18. Continuous-Wave Stimulated Emission Depletion Microscope for Imaging Actin Cytoskeleton in Fixed and Live Cells

    Directory of Open Access Journals (Sweden)

    Bhanu Neupane

    2015-09-01

    Full Text Available Stimulated emission depletion (STED microscopy provides a new opportunity to study fine sub-cellular structures and highly dynamic cellular processes, which are challenging to observe using conventional optical microscopy. Using actin as an example, we explored the feasibility of using a continuous wave (CW-STED microscope to study the fine structure and dynamics in fixed and live cells. Actin plays an important role in cellular processes, whose functioning involves dynamic formation and reorganization of fine structures of actin filaments. Frequently used confocal fluorescence and STED microscopy dyes were employed to image fixed PC-12 cells (dyed with phalloidin- fluorescein isothiocyante and live rat chondrosarcoma cells (RCS transfected with actin-green fluorescent protein (GFP. Compared to conventional confocal fluorescence microscopy, CW-STED microscopy shows improved spatial resolution in both fixed and live cells. We were able to monitor cell morphology changes continuously; however, the number of repetitive analyses were limited primarily by the dyes used in these experiments and could be improved with the use of dyes less susceptible to photobleaching. In conclusion, CW-STED may disclose new information for biological systems with a proper characteristic length scale. The challenges of using CW-STED microscopy to study cell structures are discussed.

  19. SEGMENTATION OF MICROSCOPIC IMAGES OF BACTERIA IN BULGARIAN YOGHURT BY TEMPLATE MATCHING

    Directory of Open Access Journals (Sweden)

    Zlatin Zlatev

    2016-12-01

    Full Text Available The diagnosis of deviations in quality of yogurt is performed by approved methods set out in the Bulgarian national standard (BNS and its adjacent regulations. The basic method of evaluation of the microbiological quality of the product is the microscopic. The method is subjective and requires significant processing time of the samples. The precision of diagnosis is not high and depends on the qualifications of the expert. The systems for pattern recognition in the most natural way interpret this specific expert activity. The aim of this report is to assess the possibility of application of a method of processing and image analysis for determination of the microbiological quality of yogurt. Selected method is template matching. A comparative analysis is made of the methods for template matching. The comparative analysis of available algorithms showed that the known ones have certain disadvantages associated with their rapid-action, the use of simplified procedures, they are sensitive to rotation of the object in the template. It is developed algorithm that complement these known and overcome some of their disadvantages.

  20. 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 PM10s, 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. 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.

  2. Time-resolved magnetic imaging in an aberration-corrected, energy-filtered photoemission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Nickel, F., E-mail: fl.nickel@fz-juelich.de [Peter Grünberg Institut PGI-6 “Electronic Properties”, Research Center Jülich, 52425 Jülich (Germany); Gottlob, D.M. [Peter Grünberg Institut PGI-6 “Electronic Properties”, Research Center Jülich, 52425 Jülich (Germany); Fakultät für Physik und Center for Nanointegration Duisburg-Essen (CeNIDE), Universität Duisburg-Essen, 47048 Duisburg (Germany); Krug, I.P.; Doganay, H.; Cramm, S. [Peter Grünberg Institut PGI-6 “Electronic Properties”, Research Center Jülich, 52425 Jülich (Germany); Kaiser, A.M. [SPECS Surface Nano Analysis GmbH, Voltastraße 5, 13355 Berlin (Germany); Lin, G. [Institute for Integrative Nanosciences, IFW Dresden, Helmholtzstraße 20, 01069 Dresden (Germany); Material Systems for Nanoelectronics, Chemnitz University of Technology, Reichenhainer Strasse 70, 09107 Chemnitz (Germany); Makarov, D.; Schmidt, O.G. [Institute for Integrative Nanosciences, IFW Dresden, Helmholtzstraße 20, 01069 Dresden (Germany); and others

    2013-07-15

    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.

  3. Compact, common path quantitative phase microscopic techniques for imaging cell dynamics

    Indian Academy of Sciences (India)

    A Anand; P Vora; S Mahajan; V Trivedi; V Chhaniwal; A Singh; R Leitgeb; B Javidi

    2014-01-01

    Microscopy using visible electromagnetic radiation can be used to investigate living cells in various environments. But bright field microscopy only provides two-dimensional (2D) intensity distribution at a single object plane. One of the ways to retrieve object height/thickness information is to employ quantitative phase microscopic (QPM) techniques. Interferometric QPM techniques are widely used for this. Digital holographic microscopy (DHM) is one of the stateof-the-art methods for quantitative three-dimensional (3D) imaging. Usually it is implemented in two-beam geometry, which is prone to mechanical vibrations. But to study dynamics of objects like red blood cells, one needs temporal stability much better than the fluctuations of the object, which the two-beam geometry fails to deliver. One way to overcome this hurdle is to use selfreferencing techniques, in which a portion of the object beam will act as the reference beam. Here the development of self-referencing QPM techniques is described along with the results.

  4. The application of pattern recognition in the automatic classification of microscopic rock images

    Science.gov (United States)

    Młynarczuk, Mariusz; Górszczyk, Andrzej; Ślipek, Bartłomiej

    2013-10-01

    The classification of rocks is an inherent part of modern geology. The manual identification of rock samples is a time-consuming process, and-due to the subjective nature of human judgement-burdened with risk. In the course of the study discussed in the present paper, the authors investigated the possibility of automating this process. During the study, nine different rock samples were used. Their digital images were obtained from thin sections, with a polarizing microscope. These photographs were subsequently classified in an automatic manner, by means of four pattern recognition methods: the nearest neighbor algorithm, the K-nearest neighbor, the nearest mode algorithm, and the method of optimal spherical neighborhoods. The effectiveness of these methods was tested in four different color spaces: RGB, CIELab, YIQ, and HSV. The results of the study show that the automatic recognition of the discussed rock types is possible. The study also revealed that, if the CIELab color space and the nearest neighbor classification method are used, the rock samples in question are classified correctly, with the recognition levels of 99.8%.

  5. Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images

    CERN Document Server

    Yothers, Mitchell P; Bumm, Lloyd A

    2016-01-01

    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 (NNs) 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 (DHCT). Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional re...

  6. Mapping Atomic Orbitals with the Transmission Electron Microscope: Images of Defective Graphene Predicted from First-Principles Theory.

    Science.gov (United States)

    Pardini, Lorenzo; Löffler, Stefan; Biddau, Giulio; Hambach, Ralf; Kaiser, Ute; Draxl, Claudia; Schattschneider, Peter

    2016-07-15

    Transmission electron microscopy has been a promising candidate for mapping atomic orbitals for a long time. Here, we explore its capabilities by a first-principles approach. For the example of defected graphene, exhibiting either an isolated vacancy or a substitutional nitrogen atom, we show that three different kinds of images are to be expected, depending on the orbital character. To judge the feasibility of visualizing orbitals in a real microscope, the effect of the optics' aberrations is simulated. We demonstrate that, by making use of energy filtering, it should indeed be possible to map atomic orbitals in a state-of-the-art transmission electron microscope.

  7. Optimal microscopic systems for long-term imaging of intracellular calcium using a ratiometric genetically-encoded calcium indicator.

    Science.gov (United States)

    Miyamoto, Akitoshi; Bannai, Hiroko; Michikawa, Takayuki; Mikoshiba, Katsuhiko

    2013-05-03

    Monitoring the pattern of intracellular Ca(2+) signals that control many diverse cellular processes is essential for understanding regulatory mechanisms of cellular functions. Various genetically encoded Ca(2+) indicators (GECIs) are used for monitoring intracellular Ca(2+) changes under several types of microscope systems. However, it has not yet been explored which microscopic system is ideal for long-term imaging of the spatiotemporal patterns of Ca(2+) signals using GECIs. We here compared the Ca(2+) signals reported by a fluorescence resonance energy transfer (FRET)-based ratiometric GECI, yellow cameleon 3.60 (YC3.60), stably expressed in DT40 B lymphocytes, using three different imaging systems. These systems included a wide-field fluorescent microscope, a multipoint scanning confocal system, and a single-point scanning confocal system. The degree of photobleaching and the signal-to-noise ratio of YC3.60 in DT40 cells were highly dependent on the fluorescence excitation method, although the total illumination energy was maintained at a constant level within each of the imaging systems. More strikingly, the Ca(2+) responses evoked by B-cell antigen receptor stimulation in YC3.60-expressing DT40 cells were different among the imaging systems, and markedly affected by the illumination power used. Our results suggest that optimization of the imaging system, including illumination and acquisition conditions, is crucial for accurate visualization of intracellular Ca(2+) signals.

  8. Progress Update on Iterative Reconstruction of Neutron Tomographic Images

    Energy Technology Data Exchange (ETDEWEB)

    Hausladen, Paul [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Gregor, Jens [Univ. of Tennessee, Knoxville, TN (United States)

    2016-09-15

    This report satisfies the fiscal year 2016 technical deliverable to report on progress in development of fast iterative reconstruction algorithms for project OR16-3DTomography-PD2Jb, "3D Tomography and Image Processing Using Fast Neutrons." This project has two overall goals. The first of these goals is to extend associated-particle fast neutron transmission and, particularly, induced-reaction tomographic imaging algorithms to three dimensions. The second of these goals is to automatically segment the resultant tomographic images into constituent parts, and then extract information about the parts, such as the class of shape and potentially shape parameters. This report addresses of the component of the project concerned with three-dimensional (3D) image reconstruction.

  9. Offset-sparsity decomposition for enhancement of color microscopic image of stained specimen in histopathology: further results

    Science.gov (United States)

    Kopriva, Ivica; Popović Hadžija, Marijana; Hadžija, Mirko; Aralica, Gorana

    2016-03-01

    Recently, novel data-driven offset-sparsity decomposition (OSD) method was proposed by us to increase colorimetric difference between tissue-structures present in the color microscopic image of stained specimen in histopathology. The OSD method performs additive decomposition of vectorized spectral images into image-adapted offset term and sparse term. Thereby, the sparse term represents an enhanced image. The method was tested on images of the histological slides of human liver stained with hematoxylin and eosin, anti-CD34 monoclonal antibody and Sudan III. Herein, we present further results related to increase of colorimetric difference between tissue structures present in the images of human liver specimens with pancreatic carcinoma metastasis stained with Gomori, CK7, CDX2 and LCA, and with colon carcinoma metastasis stained with Gomori, CK20 and PAN CK. Obtained relative increase of colorimetric difference is in the range [19.36%, 103.94%].

  10. A New Efficient Hybrid Coding For Progressive Transmission Of Images

    Science.gov (United States)

    Akansu, Ali N.; Haddad, Richard A.

    1988-10-01

    The hybrid coding technique developed here involves a function of two concepts: progressive interactive image transmission coupled with transform differential coding. There are two notable features in this approach. First, a local average of an mxm (typically 5 x 5) pixel array is formed, quantized and transmitted to the receiver for a preliminary display. This initial pass provides a crude but recognizable image before any further processing or encoding. Upon request from the receiver, the technique then switches to an iterative transform differential encoding scheme. Each iteration progressively provides more image detail at the receiver as requested. Secondly, this hybrid coding technique uses a computationally efficient, real, orthogonal transform, called the Modified Hermite Transform(MHT) [1], to encode the difference image. This MHT is then compared with the Discrete Cosine Transform(DCT) [2] for the same hybrid algorithm. For the standard images tested, we found that the progressive differential coding method per-forms comparably to the well-known direct transform coding methods. The DCT was used as the standard in this traditional approach. This hybrid technique was within 5% of SNR peak-to-peak for the "LENA" image. Comparisons between MHT and DCT as the transform vehicle for the hybrid technique were also conducted. For a transform block size N=8, the DCT requires 50% more multiplications than the MHT. The price paid for this efficiency is modest. For the example tested ("LENA"), the DCT performance gain was 4.2 dB while the MHT was 3.8 dB.

  11. 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.

  12. Subsurface imaging of metal lines embedded in a dielectric with a scanning microwave microscope

    Science.gov (United States)

    You, Lin; Ahn, Jung-Joon; Obeng, Yaw S.; Kopanski, Joseph J.

    2016-02-01

    We demonstrate the ability of the scanning microwave microscope (SMM) to detect subsurface metal lines embedded in a dielectric film with sub-micrometer resolution. The SMM was used to image 1.2 μm-wide Al-Si-Cu metal lines encapsulated with either 800 nm or 2300 nm of plasma deposited silicon dioxide. Both the reflected microwave (S 11) amplitude and phase shifted near resonance frequency while the tip scanned across these buried lines. The shallower line edge could be resolved within 900 nm  ±  70 nm, while the deeper line was resolved within 1200 nm  ±  260 nm. The spatial resolution obtained in this work is substantially better that the 50 μm previously reported in the literature. Our observations agree very well with the calculated change in peak frequency and phase using a simple lumped element model for an SMM with a resonant transmission line. By conducting experiments at various eigenmodes, different contrast levels and signal-to-noise ratios have been compared. With detailed sensitivity studies, centered around 9.3 GHz, it has been revealed that the highest amplitude contrast is obtained when the probe microwave frequency matches the exact resonance frequency of the experimental setup. By RLC equivalent circuit modeling of the tip-sample system, two competing effects have been identified to account for the positive and negative S 11 amplitude and phase contrasts, which can be leveraged to further improve the contrast and resolution. Official contribution of the National Institute of Standards and Technology; not subject to copyright in the United States.

  13. Early prognosis of metastasis risk in inflammatory breast cancer by texture analysis of tumour microscopic images.

    Science.gov (United States)

    Kolarevic, Daniela; Tomasevic, Zorica; Dzodic, Radan; Kanjer, Ksenija; Vukosavljevic, Dragica Nikolic; Radulovic, Marko

    2015-10-01

    Inflammatory breast cancer (IBC) is a rare and aggressive type of locally advanced breast cancer. The purpose of this study was to determine the value of microscopic tumour histomorphology texture for prognosis of local and systemic recurrence at the time of initial IBC diagnosis. This retrospective study included a group of 52 patients selected on the basis of non-metastatic IBC diagnosis, stage IIIB. Gray-Level-Co-Occurrence-Matrix (GLCM) texture analysis was performed on digital images of primary tumour tissue sections stained with haematoxylin/eosin. Obtained values were categorized by use of both data- and outcome-based methods. All five acquired GLCM texture features significantly associated with metastasis outcome. By accuracies of 69-81% and AUCs of 0.71-0.81, prognostic performance of GLCM parameters exceeded that of standard major IBC clinical prognosticators such as tumour grade and response to induction chemotherapy. Furthermore, a composite score consisting of tumour grade, contrast and correlation as independent features resulted in further enhancement of prognostic performance by accuracy of 89%, discrimination efficiency by AUC of 0.93 and an outstanding hazard ratio of 71.6 (95%CI, 41.7-148.4). Internal validation was successfully performed by bootstrap and split-sample cross-validation, suggesting that the model is generalizable. This study indicates for the first time the potential use of primary breast tumour histology texture as a highly accurate, simple and cost-effective prognostic indicator of metastasis risk in IBC. Clinical relevance of the obtained results rests on the role of prognosis in decisions on induction chemotherapy and the resulting impact on quality of life and survival.

  14. 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.

  15. Recent Opportunity Microscopic Imager Results from the Western Rim of Endeavour Crater

    Science.gov (United States)

    Herkenhoff, K. E.; Arvidson, R. E.; Jolliff, B. L.; Mittlefehldt, D. W.; Sullivan, R. J., Jr.; Gellert, R.; Sims, M. H.

    2016-12-01

    The Athena science payload on the Mars Exploration Rover Oppor­tunity includes the Microscopic Imager (MI), a fixed-focus close-up camera mounted on the instrument arm. The MI acquires images at a scale of 31 µm/pixel over a broad spectral range (400 to 700 nm) using only natural illumination of target surfaces. Opportunity has been exploring exposures of Noachian-age rocks along the rim of Endeavour crater since August 2011, moti­vated by orbital spectral evidence for phyllosilicates at multiple locations along the crater's rim. Because Opportunity can no longer directly sense phyllosilicate mineralogy with the MiniTES or Mössbauer spectrometers, the rover mis­sion is focusing on characterizing outcrop multispectral reflectance with Pancam, elemental chemistry with the Alpha Particle X-ray Spectrometer (APXS) and microtexture with the MI of potential phyllosilicate host rocks. In addition, the Rock Abrasion Tool (RAT) gives an indication of rock hardness. After traversing more than 42 km (26 miles) since landing in 2004, the rover entered "Marathon Valley" to investigate rock exposures in which phyllosili­cates were detected by the CRISM instrument on the Mars Reconnaissance Orbiter. Where clastic textures are resolved, the outcrop pavement in Marathon Valley consists of poorly-sorted dark, sub-rounded to sub-angular clasts in a soft (based on RAT grind data), fine-grained, brighter matrix (see Figure showing 5x5 cm post-grind MI mosaic of "Pierre Pinaut3," acquired on Sol 4373 when target was fully shadowed). These observations are consistent with high-energy emplacement due to impact cratering. The soft, recessive, altered appearance of the matrix material suggests that it is the likely host of phyllosilicate alteration in these rocks. The bedrock appears to have been aqueously altered, but APXS measurements of major elements indicate that the alteration was isochemical, unlike in other Endeavour rim rocks. Also, MI views of a small patch of dark sand

  16. A fiber-optic fluorescence microscope using a consumer-grade digital camera for in vivo cellular imaging.

    Directory of Open Access Journals (Sweden)

    Dongsuk Shin

    Full Text Available BACKGROUND: Early detection is an essential component of cancer management. Unfortunately, visual examination can often be unreliable, and many settings lack the financial capital and infrastructure to operate PET, CT, and MRI systems. Moreover, the infrastructure and expense associated with surgical biopsy and microscopy are a challenge to establishing cancer screening/early detection programs in low-resource settings. Improvements in performance and declining costs have led to the availability of optoelectronic components, which can be used to develop low-cost diagnostic imaging devices for use at the point-of-care. Here, we demonstrate a fiber-optic fluorescence microscope using a consumer-grade camera for in vivo cellular imaging. METHODS: The fiber-optic fluorescence microscope includes an LED light, an objective lens, a fiber-optic bundle, and a consumer-grade digital camera. The system was used to image an oral cancer cell line labeled with 0.01% proflavine. A human tissue specimen was imaged following surgical resection, enabling dysplastic and cancerous regions to be evaluated. The oral mucosa of a healthy human subject was imaged in vivo, following topical application of 0.01% proflavine. FINDINGS: The fiber-optic microscope resolved individual nuclei in all specimens and tissues imaged. This capability allowed qualitative and quantitative differences between normal and precancerous or cancerous tissues to be identified. The optical efficiency of the system permitted imaging of the human oral mucosa in real time. CONCLUSION: Our results indicate this device as a useful tool to assist in the identification of early neoplastic changes in epithelial tissues. This portable, inexpensive unit may be particularly appropriate for use at the point-of-care in low-resource settings.

  17. A fiber-optic fluorescence microscope using a consumer-grade digital camera for in vivo cellular imaging.

    Science.gov (United States)

    Shin, Dongsuk; Pierce, Mark C; Gillenwater, Ann M; Williams, Michelle D; Richards-Kortum, Rebecca R

    2010-06-23

    Early detection is an essential component of cancer management. Unfortunately, visual examination can often be unreliable, and many settings lack the financial capital and infrastructure to operate PET, CT, and MRI systems. Moreover, the infrastructure and expense associated with surgical biopsy and microscopy are a challenge to establishing cancer screening/early detection programs in low-resource settings. Improvements in performance and declining costs have led to the availability of optoelectronic components, which can be used to develop low-cost diagnostic imaging devices for use at the point-of-care. Here, we demonstrate a fiber-optic fluorescence microscope using a consumer-grade camera for in vivo cellular imaging. The fiber-optic fluorescence microscope includes an LED light, an objective lens, a fiber-optic bundle, and a consumer-grade digital camera. The system was used to image an oral cancer cell line labeled with 0.01% proflavine. A human tissue specimen was imaged following surgical resection, enabling dysplastic and cancerous regions to be evaluated. The oral mucosa of a healthy human subject was imaged in vivo, following topical application of 0.01% proflavine. The fiber-optic microscope resolved individual nuclei in all specimens and tissues imaged. This capability allowed qualitative and quantitative differences between normal and precancerous or cancerous tissues to be identified. The optical efficiency of the system permitted imaging of the human oral mucosa in real time. Our results indicate this device as a useful tool to assist in the identification of early neoplastic changes in epithelial tissues. This portable, inexpensive unit may be particularly appropriate for use at the point-of-care in low-resource settings.

  18. 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

  19. 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

  20. Tomographic imaging of transparent biological samples using the pyramid phase microscope.

    Science.gov (United States)

    Iglesias, Ignacio

    2016-08-01

    We show how a pyramid phase microscope can be used to obtain tomographic information of the spatial variation of refractive index in biological samples using the Radon transform. A method that uses the information provided by the phase microscope for axial and lateral repositioning of the sample when it rotates is also described. Its application to the reconstruction of mouse embryos in the blastocyst stage is demonstrated.

  1. Three-dimensional Orientation Sensors by Defocused Imaging of Gold Nanorods through an Ordinary Wide-Field Microscope

    CERN Document Server

    Li, Tao; Chen, Xiao-Jun; Xu, Yi; Dai, Qiaofeng; Liu, Hai-Ying; Lan, Sheng; Wu, Li-Jun

    2011-01-01

    Gold (Au) nanoparticles particularly nanorods are actively exploited as imaging probes because of their special nonblinking and nonbleaching absorption, scattering and emitting properties that arise from the excitation of surface plasmons. Herein, we report a novel orientation sensor at nanoscale by defocused imaging of single Au nanorods (AuNRs) through an ordinary wide-field optical microscope. By simultaneously recording defocused images and two-photon luminescence intensities for a large number of single AuNRs, we correlate their defocused images with their three-dimensional spatial orientations. As many AuNRs can be monitored in parallel, defocused imaging of single AuNRs is a high throughput sensing technique that allows us to obtain their spatial orientations within one frame in situ and real-time. The probe size can be down to several nanometers, which is highly desirable in order to minimize any potential interference from the probe itself. Furthermore, the sensing property is insensitive to the exci...

  2. 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.

  3. 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.

  4. Role of phantoms in progress of medical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Tanada, Shuji [National Inst. of Radiological Sciences, Chiba (Japan)

    1998-09-01

    Importance of phantoms in medical imaging was discussed from the aspect of quality control/assurance which consisting of accuracy management and performance assessment of the imaging apparatuses. Phantoms have played significant roles in progress of nuclear medicine. Medical images would be classified in the two: morphological ones as represented by X-ray CT and MRI and functional ones by PET and SPECT. The roles of phantoms played are those for evaluation of organ/tissue exposure dose due to the administered radiopharmaceuticals, for evaluation of accuracy management and performance assessment of apparatuses (I.e., homogeneity and stability of the sensitivity, linearity between measured value and radioactivity and assessment of spacial resolution in the reconstructed images), for evaluation of reconstructed images as quantitatively-assessed functional ones, for evaluation of cross calibration among multiple apparatuses and for validation of tracer kinetic model analysis. In summary, phantoms in medical imaging are useful in the assessment of accurate performance, in the assurance of reliability of results, in the comparison of quantitative repeated or inter-individual examination results and in the quantitative evaluation of the function of small structures like the basal ganglia and thalamus. (K.H.)

  5. Progress of MEMS Scanning Micromirrors for Optical Bio-Imaging

    Directory of Open Access Journals (Sweden)

    Lih Y. Lin

    2015-11-01

    Full Text Available Microelectromechanical systems (MEMS have an unmatched ability to incorporate numerous functionalities into ultra-compact devices, and due to their versatility and miniaturization, MEMS have become an important cornerstone in biomedical and endoscopic imaging research. To incorporate MEMS into such applications, it is critical to understand underlying architectures involving choices in actuation mechanism, including the more common electrothermal, electrostatic, electromagnetic, and piezoelectric approaches, reviewed in this paper. Each has benefits and tradeoffs and is better suited for particular applications or imaging schemes due to achievable scan ranges, power requirements, speed, and size. Many of these characteristics are fabrication-process dependent, and this paper discusses various fabrication flows developed to integrate additional optical functionality beyond simple lateral scanning, enabling dynamic control of the focus or mirror surface. Out of this provided MEMS flexibility arises some challenges when obtaining high resolution images: due to scanning non-linearities, calibration of MEMS scanners may become critical, and inherent image artifacts or distortions during scanning can degrade image quality. Several reviewed methods and algorithms have been proposed to address these complications from MEMS scanning. Given their impact and promise, great effort and progress have been made toward integrating MEMS and biomedical imaging.

  6. 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.

  7. Pulse-modulated second harmonic imaging microscope quantitatively demonstrates marked increase of collagen in tumor after chemotherapy

    Science.gov (United States)

    Raja, Anju M.; Xu, Shuoyu; Sun, Wanxin; Zhou, Jianbiao; Tai, Dean C. S.; Chen, Chien-Shing; Rajapakse, Jagath C.; So, Peter T. C.; Yu, Hanry

    2010-09-01

    Pulse-modulated second harmonic imaging microscopes (PM-SHIMs) exhibit improved signal-to-noise ratio (SNR) over conventional SHIMs on sensitive imaging and quantification of weak collagen signals inside tissues. We quantify the spatial distribution of sparse collagen inside a xenograft model of human acute myeloid leukemia (AML) tumor specimens treated with a new drug against receptor tyrosine kinase (ABT-869), and observe a significant increase in collagen area percentage, collagen fiber length, fiber width, and fiber number after chemotherapy. This finding reveals new insights into tumor responses to chemotherapy and suggests caution in developing new drugs and therapeutic regimens against cancers.

  8. Progressive image data compression with adaptive scale-space quantization

    Science.gov (United States)

    Przelaskowski, Artur

    1999-12-01

    Some improvements of embedded zerotree wavelet algorithm are considere. Compression methods tested here are based on dyadic wavelet image decomposition, scalar quantization and coding in progressive fashion. Profitable coders with embedded form of code and rate fixing abilities like Shapiro EZW and Said nad Pearlman SPIHT are modified to improve compression efficiency. We explore the modifications of the initial threshold value, reconstruction levels and quantization scheme in SPIHT algorithm. Additionally, we present the result of the best filter bank selection. The most efficient biorthogonal filter banks are tested. Significant efficiency improvement of SPIHT coder was finally noticed even up to 0.9dB of PSNR in some cases. Because of the problems with optimization of quantization scheme in embedded coder we propose another solution: adaptive threshold selection of wavelet coefficients in progressive coding scheme. Two versions of this coder are tested: progressive in quality and resolution. As a result, improved compression effectiveness is achieved - close to 1.3 dB in comparison to SPIHT for image Barbara. All proposed algorithms are optimized automatically and are not time-consuming. But sometimes the most efficient solution must be found in iterative way. Final results are competitive across the most efficient wavelet coders.

  9. Time course of pH change in plant epidermis using microscopic pH imaging system

    Science.gov (United States)

    Dan, Risako; Shimizu, Megumi; Kazama, Haruko; Sakaue, Hirotaka

    2010-11-01

    We established a microscopic pH imaging system to track the time course of pH change in plant epidermis in vivo. In the previous research, we have found out that anthocyanin containing cells have higher pH. However, it was not clear whether the anthocyanin increased the pH or anthocyanin was synthesized result from the higher pH. Therefore, we further investigated the relationship between anthocyanin and pH change. To track the time course of pH change in plant epidermis, we established a system using luminescent imaging technique. We used HPTS (8-Hydroxypyrene-1,3,6-Trisulfonate) as pH indicator and applied excitation ratio imaging method. Luminescent image was converted to a pH distribution by obtained in vitro calibration using known pH solution. Cellular level observation was enabled by merging microscopic color picture of the same region to the pH change image. The established system was applied to epidermal cells of red-tip leaf lettuce, Lactuca Sativa L. and the time course was tracked in the growth process. We would discuss about the relationship between anthocyanin and pH change in plant epidermis.

  10. 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.

  11. Centimeter-deep tissue fluorescence microscopic imaging with high signal-to-noise ratio and picomole sensitivity

    CERN Document Server

    Cheng, Bingbing; Wei, Ming-Yuan; Pei, Yanbo; DSouza, Francis; Nguyen, Kytai T; Hong, Yi; Tang, Liping; Yuan, Baohong

    2015-01-01

    Fluorescence microscopic imaging in centimeter-deep tissue has been highly sought-after for many years because much interesting in vivo micro-information, such as microcirculation, tumor angiogenesis, and metastasis, may deeply locate in tissue. In this study, for the first time this goal has been achieved in 3-centimeter deep tissue with high signal-to-noise ratio (SNR) and picomole sensitivity under radiation safety thresholds. These results are demonstrated not only in tissue-mimic phantoms but also in actual tissues, such as porcine muscle, ex vivo mouse liver, ex vivo spleen, and in vivo mouse tissue. These results are achieved based on three unique technologies: excellent near infrared ultrasound-switchable fluorescence (USF) contrast agents, a sensitive USF imaging system, and an effective correlation method. Multiplex USF fluorescence imaging is also achieved. It is useful to simultaneously image multiple targets and observe their interactions. This work opens the door for future studies of centimeter...

  12. Temporal trajectory and progression score estimation from voxelwise longitudinal imaging measures: Application to amyloid imaging

    Science.gov (United States)

    Bilgel, Murat; Jedynak, Bruno; Wong, Dean F.; Resnick, Susan M.; Prince, Jerry L.

    2015-01-01

    Cortical β-amyloid deposition begins in Alzheimer’s disease (AD) years before the onset of any clinical symptoms. It is therefore important to determine the temporal trajectories of amyloid deposition in these earliest stages in order to better understand their associations with progression to AD. A method for estimating the temporal trajectories of voxelwise amyloid as measured using longitudinal positron emission tomography (PET) imaging is presented. The method involves the estimation of a score for each subject visit based on the PET data that reflects their amyloid progression. This amyloid progression score allows subjects with similar progressions to be aligned and analyzed together. The estimation of the progression scores and the amyloid trajectory parameters are performed using an expectation-maximization algorithm. The correlations among the voxel measures of amyloid are modeled to reflect the spatial nature of PET images. Simulation results show that model parameters are captured well at a variety of noise and spatial correlation levels. The method is applied to longitudinal amyloid imaging data considering each cerebral hemisphere separately. The results are consistent across the hemispheres and agree with a global index of brain amyloid known as mean cortical DVR. Unlike mean cortical DVR, which depends on a priori defined regions, the progression score extracted by the method is data-driven and does not make assumptions about regional longitudinal changes. Compared to regressing on age at each voxel, the longitudinal trajectory slopes estimated using the proposed method show better localized longitudinal changes. PMID:26221692

  13. A Progressive Image Compression Method Based on EZW Algorithm

    Science.gov (United States)

    Du, Ke; Lu, Jianming; Yahagi, Takashi

    A simple method based on the EZW algorithm is presented for improving image compression performance. Recent success in wavelet image coding is mainly attributed to recognition of the importance of data organization and representation. There have been several very competitive wavelet coders developed, namely, Shapiro's EZW(Embedded Zerotree Wavelets)(1), Said and Pearlman's SPIHT(Set Partitioning In Hierarchical Trees)(2), and Bing-Bing Chai's SLCCA(Significance-Linked Connected Component Analysis for Wavelet Image Coding)(3). The EZW algorithm is based on five key concepts: (1) a DWT(Discrete Wavelet Transform) or hierarchical subband decomposition, (2) prediction of the absence of significant information across scales by exploiting self-similarity inherent in images, (3) entropy-coded successive-approximation quantization, (4) universal lossless data compression which is achieved via adaptive arithmetic coding. and (5) DWT coefficients' degeneration from high scale subbands to low scale subbands. In this paper, we have improved the self-similarity statistical characteristic in concept (5) and present a progressive image compression method.

  14. 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.

  15. Tomographic incoherent phase imaging, a diffraction tomography alternative for any white-light microscope

    Science.gov (United States)

    Bon, Pierre; Aknoun, Shérazade; Savatier, Julien; Wattellier, Benoit; Monneret, Serge

    2013-02-01

    In this paper, we discuss the possibility of making tomographic reconstruction of the refractive index of a microscopic sample using a quadriwave lateral shearing interferometer, under incoherent illumination. A Z-stack is performed and the acquired incoherent elecromagnetic fields are deconvoluted before to retrieve in a quantitative manner the refractive index. The results are presented on polystyrene beads and can easily be expanded to biological samples. This technique is suitable to any white-light microscope equipped with nanometric Z-stack module.

  16. A role for susceptibility weighted imaging in progressive multifocal leukoencephalopathy

    LENUS (Irish Health Repository)

    Yap, SM

    2017-04-01

    We report a radiologic finding on magnetic resonance imaging (MRI) of the brain of two cases of progressive multifocal leukoencephalopathy (PML) of hypointense signal of subcortical U-fibres on susceptibility weighted (SW) sequence. The first case is a 50-year-old man recently treated with chemotherapy including rituximab for non-Hodgkin\\'s lymphoma. The second case is a 64-year-old woman with human immunodeficiency virus (HIV) infection. Iron deposition is a likely causative factor. We propose that SWI may be especially useful in the assessment of indeterminate cases to reduce the likelihood of a missed diagnosis of PML

  17. Multiparameter breast cancer cell image analysis for objective estimation of nuclear grade: comparison with light microscopic observational data

    Science.gov (United States)

    Berzins, Juris; Sneiders, Uldis; Plegere, Daina; Freivalds, Talivaldis; Grigalinovica, Romalda

    2000-04-01

    We performed a multi parameter image analysis assessment of breast cancer cell population nuclear grade (NG), which is regarded as one of the main prognostic factors for treatment efficacy and survival of the patients and compared it with light microscopic estimation of NG. Cytological imprint slides from 20 ductal carcinomas were stained according to Leischmann-AzureII-eosine method, and NG was estimated by light microscopic observation according to Black in Fisher's modification. Simultaneously, using specially elaborated software, in each patient 100 cancer cells were analyzed for nuclear perimeter, diameter, area, nucleolar area, and average intensity of staining. The chromatin structure was assessed using mean diameter of chromatin grains and relatively chromatic are within the nucleus. Light microscopic estimation revealed 4/15 grade 2 and 7/15 grade 3 tumors out of 15 filtrating ductal carcinomas, with 4/15 classified as intermediate between grade 2-3. Multifactoral linear correlation coefficient r equals 0.39, p < 0.001 for ductal cancer, higher NG comes with increasing nucleolar area, nuclear roundness factor, nuclear are, and chromatin area within the cell nucleus. Image analysis may yield precise information on NG as a prognostic factor in breast cancer patients.

  18. Cellular level nanomanipulation using atomic force microscope aided with superresolution imaging

    Science.gov (United States)

    Chacko, Jenu Varghese; Harke, Benjamin; Canale, Claudio; Diaspro, Alberto

    2014-10-01

    Atomic force microscopes (AFM) provide topographical and mechanical information of the sample with very good axial resolution, but are limited in terms of chemical specificity and operation time-scale. An optical microscope coupled to an AFM can recognize and target an area of interest using specific identification markers like fluorescence tags. A high resolution fluorescence microscope can visualize fluorescence structures or molecules below the classical optical diffraction limit and reach nanometer scale resolution. A stimulated emission depletion (STED) microscopy superresolution (SR) microscope coupled to an AFM is an example in which the AFM tip gains nanoscale manipulation capabilities. The SR targeting and visualization ability help in fast and specific identification of subdiffraction-sized cellular structures and manoeuvring the AFM tip onto the target. We demonstrate how to build a STED AFM and use it for biological nanomanipulation aided with fast visualization. The STED AFM based bionanomanipulation is presented for the first time in this article. This study points to future nanosurgeries performable at single-cell level and a physical targeted manipulation of cellular features as it is currently used in research domains like nanomedicine and nanorobotics.

  19. Prevention of electron beam transmittance for biological cell imaging using electron beam excitation-assisted optical microscope

    Science.gov (United States)

    Fukuta, Masahiro; Nawa, Yasunori; Inami, Wataru; Kawata, Yoshimasa

    2017-04-01

    We demonstrated the high-spatial-resolution imaging of label-free biological cells using an electron beam excitation-assisted optical (EXA) microscope without irradiation damage by the electron beam. An EXA microscope can be used to observe a specimen with a nanometric light source excited in the Si3N4 membrane by an electron beam. The incident electron beam penetrates the Si3N4 membrane and damages the specimen. To suppress the irradiation damage of the specimen, we prevented the transmittance of the electron beam by coating the Si3N4 membrane with a gold thin film. To obtain an electron beam transmittance through the Si3N4 of 0%, a gold film of 15 nm thickness was required. By adding the gold layer, a label-free cellular structure was observed with 135-nm spatial resolution.

  20. 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.

  1. Imaging in Colorectal Cancer: Progress and Challenges for the Clinicians

    Directory of Open Access Journals (Sweden)

    Eric Van Cutsem

    2016-08-01

    Full Text Available The use of imaging in colorectal cancer (CRC has significantly evolved over the last twenty years, establishing important roles in surveillance, diagnosis, staging, treatment selection and follow up. The range of modalities has broadened with the development of novel tracer and contrast agents, and the fusion of technologies such as positron emission tomography (PET and computed tomography (CT. Traditionally, the most widely used modality for assessing treatment response in metastasised colon and rectal tumours is CT, combined with use of the RECIST guidelines. However, a growing body of evidence suggests that tumour size does not always adequately correlate with clinical outcomes. Magnetic resonance imaging (MRI is a more versatile technique and dynamic contrast-enhanced (DCE-MRI and diffusion-weighted (DW-MRI may be used to evaluate biological and functional effects of treatment. Integrated fluorodeoxyglucose (FDG-PET/CT combines metabolic and anatomical imaging to improve sensitivity and specificity of tumour detection, and a number of studies have demonstrated improved diagnostic accuracy of this modality in a variety of tumour types, including CRC. These developments have enabled the progression of treatment strategies in rectal cancer and improved the detection of hepatic metastatic disease, yet are not without their limitations. These include technical, economical and logistical challenges, along with a lack of robust evidence for standardisation and formal guidance. In order to successfully apply these novel imaging techniques and utilise their benefit to provide truly personalised cancer care, advances need to be clinically realised in a routine and robust manner.

  2. DISC: Deep Image Saliency Computing via Progressive Representation Learning.

    Science.gov (United States)

    Chen, Tianshui; Lin, Liang; Liu, Lingbo; Luo, Xiaonan; Li, Xuelong

    2016-06-01

    Salient object detection increasingly receives attention as an important component or step in several pattern recognition and image processing tasks. Although a variety of powerful saliency models have been intensively proposed, they usually involve heavy feature (or model) engineering based on priors (or assumptions) about the properties of objects and backgrounds. Inspired by the effectiveness of recently developed feature learning, we provide a novel deep image saliency computing (DISC) framework for fine-grained image saliency computing. In particular, we model the image saliency from both the coarse-and fine-level observations, and utilize the deep convolutional neural network (CNN) to learn the saliency representation in a progressive manner. In particular, our saliency model is built upon two stacked CNNs. The first CNN generates a coarse-level saliency map by taking the overall image as the input, roughly identifying saliency regions in the global context. Furthermore, we integrate superpixel-based local context information in the first CNN to refine the coarse-level saliency map. Guided by the coarse saliency map, the second CNN focuses on the local context to produce fine-grained and accurate saliency map while preserving object details. For a testing image, the two CNNs collaboratively conduct the saliency computing in one shot. Our DISC framework is capable of uniformly highlighting the objects of interest from complex background while preserving well object details. Extensive experiments on several standard benchmarks suggest that DISC outperforms other state-of-the-art methods and it also generalizes well across data sets without additional training. The executable version of DISC is available online: http://vision.sysu.edu.cn/projects/DISC.

  3. Microscopic Polyangiitis

    Science.gov (United States)

    ... are here: Home / Types of Vasculitis / Microscopic Polyangiitis Microscopic Polyangiitis First Description Who gets Microscopic Polyangiitis (the “ ... differences as to justify separate classifications. Who gets Microscopic Polyangiitis? A typical patient MPA can affect individuals ...

  4. 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

  5. Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging

    CERN Document Server

    Afik, Eldad

    2013-01-01

    Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, cellular trafficking, bacteria taxis, fluid dynamics in microfluidics devices. The 3d position of a fluorescent particle can be determined using 2d imaging alone, by measuring the diffraction rings generated by an out-of-focus particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from particles vicinity. It is capable of real time analysis thanks to its high performance and low memory footprint. Many of the algorithmic concepts introduced can be advantageous in other cases, particularly for sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. The image analysis algorithm, which is an offspring of the full 3d circle Hough transform, addresses the need to efficiently trace the trajectories of several particles concurrent...

  6. 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

  7. Diagnostics of hemangioma by the methods of correlation and fractal analysis of laser microscopic images of blood plasma

    Science.gov (United States)

    Boychuk, T. M.; Bodnar, B. M.; Vatamanesku, L. I.

    2012-01-01

    For the first time the complex correlation and fractal analysis was used for the investigation of microscopic images of both tissue images and hemangioma liquids. It was proposed a physical model of description of phase distributions formation of coherent radiation, which was transformed by optical anisotropic biological structures. The phase maps of laser radiation in the boundary diffraction zone were used as the main information parameter. The results of investigating the interrelation between the values of correlation (correlation area, asymmetry coefficient and autocorrelation function excess) and fractal (dispersion of logarithmic dependencies of power spectra) parameters are presented. They characterize the coordinate distributions of phase shifts in the points of laser images of histological sections of hemangioma, hemangioma blood smears and blood plasma with vascular system pathologies. The diagnostic criteria of hemangioma nascency are determined.

  8. Local dynamic range compensation for scanning electron microscope imaging system by sub-blocking multiple peak HE with convolution.

    Science.gov (United States)

    Sim, K S; Teh, V; Tey, Y C; Kho, T K

    2016-11-01

    This paper introduces new development technique to improve the Scanning Electron Microscope (SEM) image quality and we name it as sub-blocking multiple peak histogram equalization (SUB-B-MPHE) with convolution operator. By using this new proposed technique, it shows that the new modified MPHE performs better than original MPHE. In addition, the sub-blocking method consists of convolution operator which can help to remove the blocking effect for SEM images after applying this new developed technique. Hence, by using the convolution operator, it effectively removes the blocking effect by properly distributing the suitable pixel value for the whole image. Overall, the SUB-B-MPHE with convolution outperforms the rest of methods. SCANNING 38:492-501, 2016. © 2015 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

  9. Computer aided measurement of melanoma depth of invasion in microscopic images.

    Science.gov (United States)

    Mokhtari, Mojgan; Rezaeian, Mahdie; Gharibzadeh, Shahriar; Malekian, Vahid

    2014-06-01

    This paper presents a novel computer aided technique for measurement of melanoma depth of invasion. Melanoma is the deadliest form of skin cancer with worldwide increasing incidences. For a conclusive diagnosis of melanoma, skin biopsies should be examined under a microscope. Visual inspection of microscopic samples is often subjective, time-consuming, cumbersome and prone to human errors. This fact demonstrates the necessity of developing an automated method which assists pathologists in evaluating histopathological samples more accurately in the busy clinical environment. To the best of our knowledge, this is the first time that a computer-assisted diagnosis algorithm has been applied in measurement of melanoma invasion depth. The proposed method uses a clustering algorithm for granular layer extraction and a pre-trained SVM classifier for detection of malignant melanocytes. The experimental results with average error of 3.9μm demonstrate that the proposed method is reliable and effective. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Progress on retinal image analysis for age related macular degeneration.

    Science.gov (United States)

    Kanagasingam, Yogesan; Bhuiyan, Alauddin; Abràmoff, Michael D; Smith, R Theodore; Goldschmidt, Leonard; Wong, Tien Y

    2014-01-01

    Age-related macular degeneration (AMD) is the leading cause of vision loss in those over the age of 50 years in the developed countries. The number is expected to increase by ∼1.5 fold over the next ten years due to an increase in aging population. One of the main measures of AMD severity is the analysis of drusen, pigmentary abnormalities, geographic atrophy (GA) and choroidal neovascularization (CNV) from imaging based on color fundus photograph, optical coherence tomography (OCT) and other imaging modalities. Each of these imaging modalities has strengths and weaknesses for extracting individual AMD pathology and different imaging techniques are used in combination for capturing and/or quantification of different pathologies. Current dry AMD treatments cannot cure or reverse vision loss. However, the Age-Related Eye Disease Study (AREDS) showed that specific anti-oxidant vitamin supplementation reduces the risk of progression from intermediate stages (defined as the presence of either many medium-sized drusen or one or more large drusen) to late AMD which allows for preventative strategies in properly identified patients. Thus identification of people with early stage AMD is important to design and implement preventative strategies for late AMD, and determine their cost-effectiveness. A mass screening facility with teleophthalmology or telemedicine in combination with computer-aided analysis for large rural-based communities may identify more individuals suitable for early stage AMD prevention. In this review, we discuss different imaging modalities that are currently being considered or used for screening AMD. In addition, we look into various automated and semi-automated computer-aided grading systems and related retinal image analysis techniques for drusen, geographic atrophy and choroidal neovascularization detection and/or quantification for measurement of AMD severity using these imaging modalities. We also review the existing telemedicine studies which

  11. A scanning Hall probe microscope for high resolution, large area, variable height magnetic field imaging.

    Science.gov (United States)

    Shaw, Gorky; Kramer, R B G; Dempsey, N M; Hasselbach, K

    2016-11-01

    We present a scanning Hall probe microscope operating in ambient conditions. One of the unique features of this microscope is the use of the same stepper motors for both sample positioning as well as scanning, which makes it possible to have a large scan range (few mm) in the x and y directions, with a scan resolution of 0.1 μm. Protocols have been implemented to enable scanning at different heights from the sample surface. The z range is 35 mm. Microstructured Hall probes of size 1-5 μm have been developed. A minimum probe-sample distance <2 μm has been obtained by the combination of new Hall probes and probe-sample distance regulation using a tuning fork based force detection technique. The system is also capable of recording local B(z) profiles. We discuss the application of the microscope for the study of micro-magnet arrays being developed for applications in micro-systems.

  12. A novel STM-assisted microwave microscope with capacitance and loss imaging capability.

    Science.gov (United States)

    Imtiaz, Atif; Anlage, Steven M

    2003-04-01

    We report a new technique of scanning capacitance microscopy at microwave frequencies. A near field scanning microwave microscope probe is kept at a constant height of about 1 nm above the sample with the help of scanning tunneling microscope (STM) feedback. The microwaves are incident onto the sample through a coaxial resonator that is terminated at one end with a sharp tip (the same tip is used to conduct STM), and capacitively coupled to a feedback circuit and microwave source at the other end. The feedback circuit keeps the source locked onto the resonance frequency of the resonator and outputs the frequency shift and quality factor change due to property variations of the sample. The spatial resolution due to capacitance variations is congruent with 2.5 nm. The microwave microscope is sensitive to sample sheet resistance, as demonstrated through measurements on a doped silicon sample. We develop a quantitative transmission line model treating the tip to sample interaction as a series combination of capacitance and sheet resistance in the sample.

  13. 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

  14. Comparative analysis of microscopic images and XRF and EDS results of bricks from arheological sites Mediana and Naisus

    Directory of Open Access Journals (Sweden)

    Kalamković Snežana

    2014-01-01

    Full Text Available This paper describes the archaeological sites Mediana and Naisus during Late Antiquity. Microscopic images of bricks, and the results and analysis of XRF bricks from these archaeological sites are shown. Based on the results, it can be concluded that a similar brick exterior, and approximately the same chemical composition. One reason is, most likely, a similar chemical composition of the soil, because the archaeological sites are geographically close to each other. Another reason could be the same way bricks were producted, and that the same fuel was used in the kilns.

  15. Innovative parameters obtained for digital analysis of microscopic images to evaluate in vitro hemorheological action of anesthetics

    Science.gov (United States)

    Alet, Analía. I.; Basso, Sabrina; Delannoy, Marcela; Alet, Nicolás. A.; D'Arrigo, Mabel; Castellini, Horacio V.; Riquelme, Bibiana D.

    2015-06-01

    Drugs used during anesthesia could enhance microvascular flow disturbance, not only for their systemic cardiovascular actions but also by a direct effect on the microcirculation and in particular on hemorheology. This is particularly important in high-risk surgical patients such as those with vascular disease (diabetes, hypertension, etc.). Therefore, in this work we propose a set of innovative parameters obtained by digital analysis of microscopic images to study the in vitro hemorheological effect of propofol and vecuronium on red blood cell from type 2 diabetic patients compared to healthy donors. Obtained innovative parameters allow quantifying alterations in erythrocyte aggregation, which can increase the in vivo risk of microcapillary obstruction.

  16. Restoration of Scanning Tunneling Microscope Images by means of Two-Dimensional Maximum Entropy Method

    Science.gov (United States)

    Matsumoto, Hisanori; Tokiwano, Kazuo; Hosoi, Hirotaka; Sueoka, Kazuhisa; Mukasa, Koichi

    2002-05-01

    We present a new technique for the restoration of scanning tunneling microscopy (STM) images, which is a two-dimensional extension of a recently developed statistical approach based on the one-dimensional least-squares method (LSM). An STM image is regarded as a realization of a stochastic process and assumed to be a composition of an underlying image and noise. We express the underlying image in terms of a two-dimensional generalized trigonometric polynomial suitable for representing the atomic protrusions in STM images. The optimization of the polynomial is performed by the two-dimensional LSM combined with the power spectral density function estimated by means of the maximum entropy method (MEM) iterative algorithm for two-dimensional signals. The restored images are obtained as the optimum least-squares fitting polynomial which is a continuous surface. We apply this technique to modeled and actual STM data. Results show that the present method yields a reasonable restoration of STM images.

  17. Time-Lapse Observation of Electrolysis of Copper Sulfate with a Full-Field X-ray Fluorescence Imaging Microscope

    Science.gov (United States)

    Ohigashi, Takuji; Aota, Tatsuya; Watanabe, Norio; Takano, Hidekazu; Yokosuka, Hiroki; Aoki, Sadao

    2008-06-01

    The time-lapse observation of the electrodeposition of copper in copper sulfate solution was performed by imaging X-ray fluorescence from the copper deposition. The X-ray fluorescence was directly imaged with a full-field Wolter mirror microscope, which was constructed at the Photon Factory. Controlling the electric current in the solution from 0 to 71.7 µA, the deposition of copper on a Pt cathode was directly observed by imaging its X-ray fluorescence. One exposure time for obtaining an X-ray fluorescence image was 80 s. Then, it was 17 min later from the beginning of the electrolysis when the X-ray fluorescence image of the electrodeposition is observed for the first time. At this exposure time, the detection limit of the mass of copper was estimated to be 0.60 pg/image, which was calculated using test samples of 1.00×10-3-1.00 mol/l copper sulfate solutions.

  18. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    Directory of Open Access Journals (Sweden)

    J. Mejia

    2013-11-01

    Full Text Available The single photon emission microscope (SPEM is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD. Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s-1·MBq-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

  19. Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

    Energy Technology Data Exchange (ETDEWEB)

    Mejia, J. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Reis, M.A. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Miranda, A.C.C. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Batista, I.R. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Barboza, M.R.F.; Shih, M.C. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Fu, G. [GE Global Research, Schenectady, NY (United States); Chen, C.T. [Department of Radiology, University of Chicago, Chicago, IL (United States); Meng, L.J. [Department of Nuclear, Plasma and Radiological Engineering, University of Illinois, Urbana-Champaign, IL (United States); Bressan, R.A. [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil); Laboratório Interdisciplinar de Neurociências Clínicas, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Amaro, E. Jr [Hospital Israelita Albert Einstein, Instituto do Cérebro, São Paulo, SP (Brazil)

    2013-11-06

    The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s{sup -1}·MBq{sup -1} were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging {sup 99m}Tc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using {sup 99m}Tc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

  20. Sub-diffraction imaging on standard microscopes through photobleaching microscopy with non-linear processing.

    Science.gov (United States)

    Munck, Sebastian; Miskiewicz, Katarzyna; Sannerud, Ragna; Menchon, Silvia A; Jose, Liya; Heintzmann, Rainer; Verstreken, Patrik; Annaert, Wim

    2012-05-01

    Visualization of organelles and molecules at nanometer resolution is revolutionizing the biological sciences. However, such technology is still limited for many cell biologists. We present here a novel approach using photobleaching microscopy with non-linear processing (PiMP) for sub-diffraction imaging. Bleaching of fluorophores both within the single-molecule regime and beyond allows visualization of stochastic representations of sub-populations of fluorophores by imaging the same region over time. Our method is based on enhancing the probable positions of the fluorophores underlying the images. The random nature of the bleached fluorophores is assessed by calculating the deviation of the local actual bleached fluorescence intensity to the average bleach expectation as given by the overall decay of intensity. Subtracting measured from estimated decay images yields differential images. Non-linear enhancement of maxima in these diffraction-limited differential images approximates the positions of the underlying structure. Summing many such processed differential images yields a super-resolution PiMP image. PiMP allows multi-color, three-dimensional sub-diffraction imaging of cells and tissues using common fluorophores and can be implemented on standard wide-field or confocal systems.

  1. Research progress in nanographene oxide with tumor imaging and therapy

    Directory of Open Access Journals (Sweden)

    YOU Peihong

    2015-04-01

    Full Text Available Nanographene oxide,one of graphene oxide derivatives and a novel two-dimensional carbon nanomaterial,has become a popular research topic in nanomedicine due to its unique properties such as ultra-high surface-to-volume ratio and great photo-thermal effect.It contains a large amount of reactive chemical groups,including carboxy group,carbonyl group,hydroxyl group and epoxy group,which enable its easy biological and chemical functionalization and excellent biocompatibility.Therefore,it has potential applications in biomedical field.This paper briefly describes the preparation and functionalization of nanographeme oxide,and then mainly focuses on its application studies in the biomedical field,including in vitro and in vivo toxicity tests and advanced research progress of tumor imaging and treatment.

  2. 3rd International Symposium Mathematical Progress in Expressive Image Synthesis

    CERN Document Server

    Ochiai, Hiroyuki

    2016-01-01

    Progress in Expressive Image Synthesis” (MEIS2015), was held in Fukuoka, Japan, September 25–27, 2015. The aim of the symposium was to provide a unique venue where various issues in computer graphics (CG) application fields could be discussed by mathematicians, CG researchers, and practitioners. Through the previous symposiums MEIS2013 and MEIS2014, mathematicians as well as CG researchers have recognized that CG is a specific and practical activity derived from mathematical theories. Issues found in CG broaden the field of mathematics and vice versa, and CG visualizes mathematical theories in an aesthetic manner. In this volume, the editors aim to provoke interdisciplinary research projects through the peer-reviewed papers and poster presentations at the this year’s symposium. This book captures interactions among mathematicians, CG researchers, and practitioners sharing important, state-of-the-art issues in graphics and visual perception. The book is suitable for all CG researchers seeking open pro...

  3. Cryogenic immersion microscope

    Science.gov (United States)

    Le Gros, Mark; Larabell, Carolyn A.

    2010-12-14

    A cryogenic immersion microscope whose objective lens is at least partially in contact with a liquid reservoir of a cryogenic liquid, in which reservoir a sample of interest is immersed is disclosed. When the cryogenic liquid has an index of refraction that reduces refraction at interfaces between the lens and the sample, overall resolution and image quality are improved. A combination of an immersion microscope and x-ray microscope, suitable for imaging at cryogenic temperatures is also disclosed.

  4. 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...... was performed. A computer algorithm available for download was created to detect fluorescent microspheres in the brain tissue slides and to calculate regional cerebral blood flow (rCBF). The precision of the algorithm was tested by comparing with manual counting of the fluorescent microspheres. Finally, bright...... with a resolution of 2.9 µm. The mean difference (SD) between manual and automatic counts was in absolute numbers 0.32 (1.5) microspheres ranging from -5 to 5 microspheres per slide. The relative total difference between automatic and manual counts was -3.1%. Conclusions: A slide scanner was constructed...

  5. Automatic choroid cells segmentation and counting based on approximate convexity and concavity of chain code in fluorescence microscopic image

    Science.gov (United States)

    Lu, Weihua; Chen, Xinjian; Zhu, Weifang; Yang, Lei; Cao, Zhaoyuan; Chen, Haoyu

    2015-03-01

    In this paper, we proposed a method based on the Freeman chain code to segment and count rhesus choroid-retinal vascular endothelial cells (RF/6A) automatically for fluorescence microscopy images. The proposed method consists of four main steps. First, a threshold filter and morphological transform were applied to reduce the noise. Second, the boundary information was used to generate the Freeman chain codes. Third, the concave points were found based on the relationship between the difference of the chain code and the curvature. Finally, cells segmentation and counting were completed based on the characteristics of the number of the concave points, the area and shape of the cells. The proposed method was tested on 100 fluorescence microscopic cell images, and the average true positive rate (TPR) is 98.13% and the average false positive rate (FPR) is 4.47%, respectively. The preliminary results showed the feasibility and efficiency of the proposed method.

  6. A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability

    Science.gov (United States)

    Wang, Qi; Hou, Yubin; Wang, Junting; Lu, Qingyou

    2013-11-01

    We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices.

  7. High spatial resolution hard X-ray microscope using X-ray refractive lens and phase contrast imaging experiments

    CERN Document Server

    Kohmura, Y; Takeuchi, A; Takano, H; Suzuki, Y; Ishikawa, T; Ohigashi, T; Yokosuka, H

    2001-01-01

    A high spatial resolution X-ray microscope was constructed using an X-ray refractive lens as an objective. The spatial resolution was tested using 18 keV X-ray. A 0.4 mu m line and 0.4 mu m space tantalum test pattern was successfully resolved. Using the similar setup with the addition of a phase plate, a Zernike type phase-contrast microscopy experiment was carried out for the phase retrieval of the samples. Two-dimensional phase-contrast images were successfully taken for the first time in the hard X-ray region. Images of a gold mesh sample were analyzed and the validity of this method was indicated. An improvement of the lens, however, is required for the precise phase retrieval of the samples.

  8. Diffusion-weighted imaging in patients with progressive multifocal leukoencephalopathy

    Energy Technology Data Exchange (ETDEWEB)

    Cosottini, M. [University of Pisa, Department of Neuroscience, Pisa (Italy); Service of Neuroradiology AO, Pisa (Italy); Tavarelli, C.; De Cori, S.; Bartolozzi, C. [University of Pisa, Department of Radiology, Pisa (Italy); Del Bono, L.; Doria, G. [Unit of Infectious Diseases AO, Pisa (Italy); Giannelli, M. [Unit of Medical Physics, Pisa (Italy); Michelassi, M.C. [Service of Neuroradiology AO, Pisa (Italy); Murri, L. [University of Pisa, Department of Neuroscience, Pisa (Italy)

    2008-05-15

    Progressive multifocal leukoencephalopathy (PML) is a severe demyelinating disease of the central nervous system due to JC polyoma virus infection of oligodendrocytes. PML develops in patients with impaired T-cell function as occurs in HIV, malignancy or immunosuppressive drugs users. Until now no imaging methods have been reported to correlate with clinical status. Diffusion-weighted imaging (DWI) is a robust MRI tool in investigating white matter architecture and diseases. The aim of our work was to assess diffusion abnormalities in focal white matter lesions in patients with PML and to correlate the lesion load measured with conventional MRI and DWI to clinical variables. We evaluated eight patients with a biopsy or laboratory-supported diagnosis of PML. All patients underwent MRI including conventional sequences (fluid attenuated inversion recovery-FLAIR) and DWI. Mean diffusivity (MD) maps were used to quantify diffusion on white matter lesions. Global lesion load was calculated by manually tracing lesions on FLAIR images, while total, central core and peripheral lesion loads were calculated by manually tracing lesions on DWI images. Lesion load obtained with the conventional or DWI-based methods were correlated with clinical variables such as disease duration, disease severity and survival. White matter focal lesions are characterized by a central core with low signal on DWI images and high MD (1.853 x 10{sup -3} mm2/s), surrounded by a rim of high signal intensity on DWI and lower MD (1.1 x 10{sup -3} mm2/s). The MD value of normal-appearing white matter is higher although not statistically significant (0.783 x 10{sup -3} mm2/s) with respect to control subjects (0.750 x 10{sup -3} mm2/s). Inter-rater correlations of global lesion load between FLAIR (3.96%) and DWI (3.43%) was excellent (ICC =0.87). Global lesion load on FLAIR and DWI correlates with disease duration and severity (respectively, p = 0.037, p = 0.0272 with Karnofsky scale and p = 0.0338 with

  9. Perspectives for in situ Scanning Tunnel Microscopic Imaging of Proteins at HOPG surfaces

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov; Thuesen, Marianne Hallberg; Møller, Per

    1996-01-01

    potentials on in situ potentiostatic control and releases nm size HOPG scrap bits. These are clearly different in shape from the ex situ imaged molecular-size structures. Laccase could not, however, be imaged by in situ STM, most likely due to structural incompatibility between hydrophobic HOPG surface...

  10. Magnetic imaging with a Zernike-type phase plate in a transmission electron microscope

    DEFF Research Database (Denmark)

    Pollard, Shawn; Malac, Marek; Beleggia, Marco

    2013-01-01

    We demonstrate the use of a hole-free phase plate (HFPP) for magnetic imaging in transmission electron microscopy by mapping the domain structure in PrDyFeB samples. The HFPP, a Zernike-like imaging method, allows for detecting magnetic signals in-focus to correlate the sample crystal structure a...

  11. Measurement and correction of microscopic head motion during magnetic resonance imaging of the brain.

    Directory of Open Access Journals (Sweden)

    Julian Maclaren

    Full Text Available Magnetic resonance imaging (MRI is a widely used method for non-invasive study of the structure and function of the human brain. Increasing magnetic field strengths enable higher resolution imaging; however, long scan times and high motion sensitivity mean that image quality is often limited by the involuntary motion of the subject. Prospective motion correction is a technique that addresses this problem by tracking head motion and continuously updating the imaging pulse sequence, locking the imaging volume position and orientation relative to the moving brain. The accuracy and precision of current MR-compatible tracking systems and navigator methods allows the quantification and correction of large-scale motion, but not the correction of very small involuntary movements in six degrees of freedom. In this work, we present an MR-compatible tracking system comprising a single camera and a single 15 mm marker that provides tracking precision in the order of 10 m and 0.01 degrees. We show preliminary results, which indicate that when used for prospective motion correction, the system enables improvement in image quality at both 3 T and 7 T, even in experienced and cooperative subjects trained to remain motionless during imaging. We also report direct observation and quantification of the mechanical ballistocardiogram (BCG during simultaneous MR imaging. This is particularly apparent in the head-feet direction, with a peak-to-peak displacement of 140 m.

  12. Camera, handlens, and microscope optical system for imaging and coupled optical spectroscopy

    Science.gov (United States)

    Mungas, Greg S. (Inventor); Boynton, John (Inventor); Sepulveda, Cesar A. (Inventor); Nunes de Sepulveda, legal representative, Alicia (Inventor); Gursel, Yekta (Inventor)

    2012-01-01

    An optical system comprising two lens cells, each lens cell comprising multiple lens elements, to provide imaging over a very wide image distance and within a wide range of magnification by changing the distance between the two lens cells. An embodiment also provides scannable laser spectroscopic measurements within the field-of-view of the instrument.

  13. Multimodal optical setup for nonlinear and fluorescence lifetime imaging microscopies: improvement on a commercial confocal inverted microscope

    Science.gov (United States)

    Pelegati, V. B.; Adur, J.; de Thomaz, A. A.; Almeida, D. B.; Baratti, M. O.; Carvalho, H. F.; Cesar, C. L.

    2012-03-01

    In this work we proposed and built a multimodal optical setup that extends a commercially available confocal microscope (Olympus FV300) to include nonlinear optical (NLO) microscopy and fluorescence lifetime imaging microscopy (FLIM). The NLO microscopies included two-photon fluorescence (TPFE), Second Harmonic Generation (SHG) and Third Harmonic Generation (THG). The whole system, including FLIM, used only one laser source composed of an 80 MHz femtosecond laser. The commercial Ti:sapphire lasers can be tuned up to 690-1040 nm bringing the THG signal to the 350 nm region where most microscope optics do not work. However, the third harmonic is only generated at the sample, meaning that we only have to take care of the collection optics. To do that we used a remote photomultiplier to acquire the THG signal at the 310-350 nm wavelength window. After performing the tests to guarantee that we are observing actually SHG/THG signals we than used this system to acquire multimodal images of several biological samples, from epithelial cancer to vegetables. The ability to see the collagen network together with the cell nuclei proved to be important for cancer tissues diagnosis. Moreover, FLIM provides information about the cell metabolism, also very important for cancer cell processes.

  14. Widefield imaging of upconverting nanoparticles on epifluorescence microscopes adapted for laser illumination with top-hat profile

    Science.gov (United States)

    Mrazek, Jiri; Pospisilova, Martina; Svozil, Vit; Cadek, Ondrej; Nesporova, Kristina; Sulakova, Romana; Brandejsova, Martina; Vranova, Jana; Velebny, Vladimir

    2016-05-01

    We describe a modification of epifluorescence microscopes that allows quantitative widefield imaging of samples labeled by upconverting nanoparticles (UCNP). A top-hat illumination profile on the sample was achieved with a 980-nm laser diode by using tandem microlens arrays, a moving diffuser and a telescope, which adjusts the top-hat area to the field of view. Illumination homogeneity is a critical factor for imaging of UCNP since the intensity of their luminescence typically scales with the second power of the excitation intensity. Our illuminator is combined with the epifluorescence attachment of the microscope, allowing easy switching between observation of UCNP and traditional fluorescent dyes. Illumination profile homogeneity of about 98% was measured for objectives with magnification from 4× to 100×, and the top-hat profile was also obtained with phase contrast objectives. We demonstrate capability of the illuminator by evaluating in vitro uptake of UCNP encapsulated in oleyl-hyaluronan micelles into breast cancer cells. Micelles bearing the targeting peptide were about an order of magnitude more efficient than nontargeted micelles.

  15. Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.

    Science.gov (United States)

    Nakamura, Eiichi

    2013-01-02

    "The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Traceable measurement and imaging of the complex permittivity of a multiphase mineral specimen at micron scales using a microwave microscope.

    Science.gov (United States)

    Gregory, A P; Blackburn, J F; Hodgetts, T E; Clarke, R N; Lees, K; Plint, S; Dimitrakis, G A

    2017-01-01

    This paper describes traceable measurements of the dielectric permittivity and loss tangent of a multiphase material (particulate rock set in epoxy) at micron scales using a resonant Near-Field Scanning Microwave Microscope (NSMM) at 1.2GHz. Calibration and extraction of the permittivity and loss tangent is via an image charge analysis which has been modified by the use of the complex frequency to make it applicable for high loss materials. The results presented are obtained using a spherical probe tip, 0.1mm in diameter, and also a conical probe tip with a rounded end 0.01mm in diameter, which allows imaging with higher resolution (≈10µm). The microscope is calibrated using approach-curve data over a restricted range of gaps (typically between 1% and 10% of tip diameter) as this is found to give the best measurement accuracy. For both tips the uncertainty of scanned measurements of permittivity is estimated to be±10% (at coverage factor k=2) for permittivity ⪝10. Loss tangent can be resolved to approximately 0.001. Subject to this limit, the uncertainty of loss tangent measurements is estimated to be±20% (at k=2). The reported measurements inform studies of how microwave energy interacts with multiphase materials containing microwave absorbent phases.

  17. Raster image correlation spectroscopy (RICS) for measuring fast protein dynamics and concentrations with a commercial laser scanning confocal microscope.

    Science.gov (United States)

    Brown, C M; Dalal, R B; Hebert, B; Digman, M A; Horwitz, A R; Gratton, E

    2008-01-01

    Raster image correlation spectroscopy (RICS) is a new and novel technique for measuring molecular dynamics and concentrations from fluorescence confocal images. The RICS technique extracts information about molecular dynamics and concentrations from images of living cells taken on commercial confocal systems. Here we develop guidelines for performing the RICS analysis on an analogue commercial laser scanning confocal microscope. Guidelines for typical instrument settings, image acquisition settings and analogue detector characterization are presented. Using appropriate instrument/acquisition parameters, diffusion coefficients and concentrations can be determined, even for highly dynamic dye molecules in solution. Standard curves presented herein demonstrate the ability to detect protein concentrations as low as approximately 2 nM. Additionally, cellular measurements give accurate values for the diffusion of paxillin-enhanced-green fluorescent protein (EGFP), an adhesion adaptor molecule, in the cytosol of the cell and also show slower paxillin dynamics near adhesions where paxillin interacts with immobile adhesion components. Methods are presented to account for bright immobile structures within the cell that dominate spatial correlation functions; allowing the extraction of fast protein dynamics within and near these structures. A running average algorithm is also presented to address slow cellular movement or movement of cellular features such as adhesions. Finally, methods to determine protein concentration in the presence of immobile structures within the cell are presented. A table is presented giving guidelines for instrument and imaging setting when performing RICS on the Olympus FV300 confocal and these guidelines are a starting point for performing the analysis on other commercial confocal systems.

  18. In situ scanning tunneling microscope tip treatment device for spin polarization imaging

    Science.gov (United States)

    Li, An-Ping [Oak Ridge, TN; Jianxing, Ma [Oak Ridge, TN; Shen, Jian [Knoxville, TN

    2008-04-22

    A tip treatment device for use in an ultrahigh vacuum in situ scanning tunneling microscope (STM). The device provides spin polarization functionality to new or existing variable temperature STM systems. The tip treatment device readily converts a conventional STM to a spin-polarized tip, and thereby converts a standard STM system into a spin-polarized STM system. The tip treatment device also has functions of tip cleaning and tip flashing a STM tip to high temperature (>2000.degree. C.) in an extremely localized fashion. Tip coating functions can also be carried out, providing the tip sharp end with monolayers of coating materials including magnetic films. The device is also fully compatible with ultrahigh vacuum sample transfer setups.

  19. Prototype of annotation tools for microscopic digital images on Android devices

    Science.gov (United States)

    Muhimmah, I.; Nugraha, D. DC

    2016-01-01

    Reading a slide under a microscope manually is very complicated. An expert may spend 3-4 hours to read a single slide. Moreover, the intra- and inter-observer variability is known to be high. This prototype was developed to simplify the slide-reading process on Android devices in order to accelerate the reading process and generate more accurate information.The prototype allows users to annotate the boundaries of an object. Moreover, the proposed prototype has successfully reconstructed multiple object boundaries into simple closed curves from a limited amount of user input.Thecoordinates of the annotated objects are stored in a text file (*.txt) that can be usedfor further analysis.The prototype's performance with respect to time and memory usage are included.

  20. A segmentation method for 3D visualization of neurons imaged with a confocal laser scanning microscope

    Science.gov (United States)

    Anderson, Jeffrey R.; Barrett, Steven F.; Wilcox, Michael J.

    2005-04-01

    Our understanding of the world around us is based primarily on three-dimensional information because of the environment in which we live and interact. Medical or biological image information is often collected in the form of two-dimensional, serial section images. As such, it is difficult for the observer to mentally reconstruct the three dimensional features of each object. Although many image rendering software packages allow for 3D views of the serial sections, they lack the ability to segment, or isolate different objects in the data set. Segmentation is the key to creating 3D renderings of distinct objects from serial slice images, like separate pieces to a puzzle. This paper describes a segmentation method for objects recorded with serial section images. The user defines threshold levels and object labels on a single image of the data set that are subsequently used to automatically segment each object in the remaining images of the same data set, while maintaining boundaries between contacting objects. The performance of the algorithm is verified using mathematically defined shapes. It is then applied to the visual neurons of the housefly, Musca domestica. Knowledge of the fly"s visual system may lead to improved machine visions systems. This effort has provided the impetus to develop this segmentation algorithm. The described segmentation method can be applied to any high contrast serial slice data set that is well aligned and registered. The medical field alone has many applications for rapid generation of 3D segmented models from MRI and other medical imaging modalities.

  1. Imaging microscopic distribution of antifungal agents in dandruff treatments with stimulated Raman scattering microscopy

    Science.gov (United States)

    Garrett, Natalie L.; Singh, Bhumika; Jones, Andrew; Moger, Julian

    2017-06-01

    Treatment of dandruff condition usually involves use of antidandruff shampoos containing antifungal agents. Different antifungal agents show variable clinical efficacy based on their cutaneous distribution and bioavailability. Using stimulated Raman scattering (SRS), we mapped the distribution of unlabeled low-molecular weight antifungal compounds zinc pyrithione (ZnPT) and climbazole (CBZ) on the surface of intact porcine skin with cellular precision. SRS has sufficient chemical selectivity and sensitivity to detect the agents on the skin surface based on their unique chemical motifs that do not occur naturally in biological tissues. Moreover, SRS is able to correlate the distribution of the agents with the morphological features of the skin using the CH2 stretch mode, which is abundant in skin lipids. This is a significant strength of the technique since it allows the microscopic accumulation of the agents to be correlated with physiological features and their chemical environment without the use of counter stains. Our findings show that due to its lower solubility, ZnPT coats the surface of the skin with a sparse layer of crystals in the size range of 1 to 4 μm. This is consistent with the current understanding of the mode of action of ZnPT. In contrast, CBZ being more soluble and hydrophobic resulted in diffuse homogeneous distribution. It predominantly resided in microscopic lipid-rich crevasses and penetrated up to 60 μm into the infundibular spaces surrounding the hair shaft. The ability of the SRS to selectively map the distribution of agents on the skin's surface has the potential to provide insight into the mechanisms underpinning the topical application of antifungal or skin-active agents that could lead to the rational engineering of enhanced formulations.

  2. Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf.

    Science.gov (United States)

    Shi, Lingyan; Rodríguez-Contreras, Adrián; Budansky, Yury; Pu, Yang; Nguyen, Thien An; Alfano, Robert R

    2014-06-01

    Two-photon (2P) excitation of the second singlet (S₂) state was studied to achieve deep optical microscopic imaging in brain tissue when both the excitation (800 nm) and emission (685 nm) wavelengths lie in the "tissue optical window" (650 to 950 nm). S₂ state technique was used to investigate chlorophyll α (Chl α) fluorescence inside a spinach leaf under a thick layer of freshly sliced rat brain tissue in combination with 2P microscopic imaging. Strong emission at the peak wavelength of 685 nm under the 2P S₂ state of Chl α enabled the imaging depth up to 450 μm through rat brain tissue.

  3. Extreme ultraviolet mask defect inspection with a half pitch 16-nm node using simulated projection electron microscope images

    Science.gov (United States)

    Iida, Susumu; Amano, Tsuyoshi; Hirano, Ryoichi; Terasawa, Tsuneo; Watanabe, Hidehiro

    2013-04-01

    According to an International Technology Roadmap for Semiconductors (ITRS-2012) update, the sensitivity requirement for an extreme ultraviolet (EUV) mask pattern inspection system is to be less than 18 nm for half pitch (hp) 16-nm node devices. The inspection sensitivity of extrusion and intrusion defects on hp 64-nm line-and-space patterned EUV mask were investigated using simulated projection electron microscope (PEM) images. The obtained defect images showed that the optimization of current density and image processing techniques were essential for the detection of defects. Extrusion and intrusion defects 16 nm in size were detected on images formed by 3000 electrons per pixel. The landing energy also greatly influenced the defect detection efficiency. These influences were different for extrusion and intrusion defects. These results were in good agreement with experimentally obtained yield curves of the mask materials and the elevation angles of the defects. These results suggest that the PEM technique has a potential to detect 16-nm size defects on an hp 64-nm patterned EUV mask.

  4. Modulated electron-multiplied fluorescence lifetime imaging microscope: all-solid-state camera for fluorescence lifetime imaging

    NARCIS (Netherlands)

    Zhao, Q.; Schelen, B.; Schouten, R., et al.

    2012-01-01

    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 des

  5. Molecular imaging probes spy on the body's inner workings: miniaturized microscopes, microbubbles, 7- and 15-T scanners, diffusion-tensor MRI, and other molecular-imaging technologies are pushing molecular imaging into the future.

    Science.gov (United States)

    Mertz, Leslie

    2013-01-01

    Molecular imaging is one of the hot-button areas within medical imaging. This technology employs imaging techniques in concert with molecular probes, or biomarkers, that together noninvasively spy on cellular function and molecular processes. In some cases, this technology may be able to detect the very earliest stages of diseases and eliminate them on the spot. This paper discusses how miniaturized microscopes, microbubbles, 7T and 15T scanners, diffusion-tensor MRI and other molecular imaging technologies are pushing molecular imaging into the future.

  6. Multi-colour microscopic interferometry for optical metrology and imaging applications

    Science.gov (United States)

    Upputuri, Paul Kumar; Pramanik, Manojit; Nandigana, Krishna Mohan; Kothiyal, Mahendra Prasad

    2016-09-01

    Interferometry has been widely used for optical metrology and imaging applications because of their precision, reliability, and versatility. Although single-wavelength interferometery can provide high sensitivity and resolution, it has several drawbacks, namely, it fails to quantify large-discontinuities, large-deformations, and shape of unpolished surfaces. Multiple-wavelength techniques have been successfully used to overcome the drawbacks associated with single wavelength analysis. The use of colour CCD camera allows simultaneous acquisition of multiple interferograms. The advances in colour CCD cameras and image processing techniques have made the multi-colour interferometry a faster, simpler, and cost-effective tool for industrial applications. This article reviews the recent advances in multi-colour interferometric techniques and their demanding applications for characterization of micro-systems, non-destructive testing, and bio-imaging applications.

  7. Site-resolved imaging of single atoms with a Faraday quantum gas microscope

    CERN Document Server

    Yamamoto, Ryuta; Kato, Kohei; Kuno, Takuma; Sakura, Yuto; Takahashi, Yoshiro

    2016-01-01

    We successfully demonstrate a quantum gas microscopy using the Faraday effect which has an inherently non-destructive nature. The observed Faraday rotation angle reaches 3.0(2) degrees for a single atom. We reveal the non-destructive feature of this Faraday imaging method by comparing the detuning dependence of the Faraday signal strength with that of the photon scattering rate. We determine the atom distribution with deconvolution analysis. We also demonstrate the absorption and the dark field Faraday imaging, and reveal the different shapes of the point spread functions for these methods, which are fully explained by theoretical analysis. Our result is an important first step towards an ultimate quantum non-demolition site-resolved imaging and furthermore opens up the possibilities for quantum feedback control of a quantum many-body system with a single-site resolution.

  8. Automated Classification Of Scanning Electron Microscope Particle Images Using Morphological Analysis

    Science.gov (United States)

    Lamarche, B. L.; Lewis, R. R.; Girvin, D. C.; McKinley, J. P.

    2008-12-01

    We are developing a software tool that can automatically classify anthropogenic and natural aerosol particulates using morphological analysis. Our method was developed using SEM (background and secondary electron) images of single particles. Particle silhouettes are detected and converted into polygons using Intel's OpenCV image processing library. Our analysis then proceeds independently for the two kinds of images. Analysis of secondary images concerns itself solely with the silhouette and seeks to quantify its shape and roughness. Traversing the polygon with spline interpolation, we uniformly sample k(s), the signed curvature of the silhouette's path as a function of distance along the perimeter s. k(s) is invariant under rotation and translation. The power spectrum of k(s) qualitatively shows both shape and roughness: more power at low frequencies indicates variation in shape; more power at higher frequencies indicates a rougher silhouette. We present a series of filters (low-, band-, and high-pass) which we convolve with k(s) to yield a set of parameters that characterize the shape and roughness numerically. Analysis of backscatter images focuses on the (visual) texture, which is the result of both composition and geometry. Using the silhouette as a boundary, we compute the variogram, a statistical measure of inter-pixel covariance as a function of distance. Variograms take on characteristic curves, which we fit with a heuristic, asymptotic function that uses a small set of parameters. The combination of silhouette and variogram fit parameters forms the basis of a multidimensional classification space whose dimensionality we may reduce by principal component analysis and whose region boundaries allow us to classify new particles. This analysis is performed without a priori knowledge of other physical, chemical, or climatic properties. The method will be adapted to multi-particulate images.

  9. Meta-instrument: high speed positioning and tracking platform for near-field optical imaging microscopes

    CERN Document Server

    Bijster, R J F; Spierdijk, J P F; Dekker, A; Klop, W A; Kramer, G F IJ; Cheng, L K; Hagen, R A J; Sadeghian, H

    2016-01-01

    High resolution and high throughput imaging are typically mutually exclusive. The meta-instrument pairs high resolution optical concepts such as nano-antennas, superoscillatory lenses and hyperlenses with a miniaturized opto-mechatronic platform for precise and high speed positioning of the optical elements at lens-to-sample separations that are measured in tens of nanometers. Such platform is a necessary development for bringing near-field optical imaging techniques to their industrial application. Towards this purpose, we present two designs and proof-of-principle instruments that are aimed at realizing sub-nanometer positional precision with a 100 kHz bandwidth.

  10. Investigation of microscopic radiation damage in waste forms using ODNMR and AEM techniques. 1997 annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.

    1997-09-01

    'This project seeks to understand the microscopic effects of radiation damage in nuclear waste forms. The authors approach to this challenge encompasses studies in electron microscopy, laser spectroscopy, and computational modeling and simulation. During this first year of the project, efforts have focused on a-decay induced microscopic damage in crystalline orthophosphates (YPO{sub 4} and LuPO{sub 4}) that contain the short-lived a-emitting isotope {sup 244}Cm (t{sub 1/2} = 18.1 y). The samples that they studied were synthesized in 1980 and the initial {sup 244}Cm concentration was {approximately}1%. Studying these materials is of importance to nuclear waste management because of the opportunity to gain insight into accumulated radiation damage and the influence of aging on such damage. These factors are critical to the long-term performance of actual waste forms [1]. Lanthanide orthophosphates, including LuPO{sub 4} and YPO{sub 4}, have been suggested as waste forms for high level nuclear waste [2] and potential hosts for excess weapons plutonium [3,4]. The work is providing insight into the characteristics of these previously known radiation-resistant materials. They have observed loss of crystallinity (partial amorphization) as a direct consequence of prolonged exposure to intense alpha radiolysis in these materials. More importantly, the observation of microscopic cavities in these aged materials provides evidence of significant chemical decomposition that may be difficult to detect in the earlier stages of radiation damage. The preliminary results show that, in characterizing crystalline compounds as high level nuclear waste forms, chemical decomposition effects may be more important than lattice amorphization which has been the focus of many previous studies. More extensive studies, including in-situ analysis of the dynamics of thermal annealing of self-radiation induced amorphization and cavity formation, will be conducted on these aged {sup 244}Cm

  11. First-Principle Calculation for Scanning-Tunneling-Microscopic Images of a Monolayer Graphite Surface

    Institute of Scientific and Technical Information of China (English)

    陈向荣; 押山淳; 岡田晋; 芶清泉

    2003-01-01

    We have applied first-principle total-energy electronic structure calculations in the local density approximation to calculate the scanning tunnelling microscopy images of a monolayer graphite surface near the Fermi level. The results obtained agree well with the observation, which has not been interpreted before.

  12. High-speed microscopic imaging of flagella motility and swimming in Giardia lamblia trophozoites.

    Science.gov (United States)

    Lenaghan, Scott C; Davis, Corinne A; Henson, William R; Zhang, Zhili; Zhang, Mingjun

    2011-08-23

    We report, in this paper, several findings about the swimming and attachment mechanisms of Giardia lamblia trophozoites. These data were collected using a combination of a high-contrast CytoViva imaging system and a particle image velocimetry camera, which can capture images at speeds greater than 800 frames/s. Using this system, we discovered that, during rapid swimming of Giardia trophozoites, undulations of the caudal region contributed to forward propulsion combined with the beating of the flagella pairs. It was also discovered, in contrast to previous studies with 10 times slower image sampling technique, that the anterior and posterolateral flagella beat with a clearly defined power stroke and not symmetrical undulations. During the transition from free swimming to attachment, trophozoites modified their swimming behavior from a rapid rotating motion to a more stable planar swimming. While using this planar swimming motion, the trophozoites used the flagella for propulsion and directional control. In addition to examination of the posterolateral and anterior flagella, a model to describe the motion of the ventral flagella was derived, indicating that the ventral flagella beat in an expanding sine wave. In addition, the structure of the ventrocaudal groove creates boundary conditions that determine the form of beating of the ventral flagella. The results from this study indicate that Giardia is able to simultaneously generate both ciliary beating and typical eukaryotic flagellar beating using different pairs of flagella.

  13. Imaging and detection of early stage dental caries with an all-optical photoacoustic microscope

    Science.gov (United States)

    Hughes, D. A.; Sampathkumar, A.; Longbottom, C.; Kirk, K. J.

    2015-01-01

    Tooth decay, at its earliest stages, manifests itself as small, white, subsurface lesions in the enamel. Current methods for detection in the dental clinic are visual and tactile investigations, and bite-wing X-ray radiographs. These techniques suffer from poor sensitivity and specificity at the earliest (and reversible) stages of the disease due to the small size (<100μm) of the lesion. A fine-resolution (600 nm) ultra-broadband (200 MHz) all-optical photoacoustic microscopy system was is used to image the early signs of tooth decay. Ex-vivo tooth samples exhibiting white spot lesions were scanned and were found to generate a larger (one order of magnitude) photoacoustic (PA) signal in the lesion regions compared to healthy enamel. The high contrast in the PA images potentially allows lesions to be imaged and measured at a much earlier stage than current clinical techniques allow. PA images were cross referenced with histology photographs to validate our experimental results. Our PA system provides a noncontact method for early detection of white-spot lesions with a high detection bandwidth that offers advantages over previously demonstrated ultrasound methods. The technique provides the sensing depth of an ultrasound system, but with the spatial resolution of an optical system.

  14. Photoacoustic imaging of intestinal strictures: microscopic and macroscopic assessment in vivo (Conference Presentation)

    Science.gov (United States)

    Xu, Guan; Lei, Hao; Johnson, Laura A.; Moons, David S.; Ma, Teng; Zhou, Qifa; Rice, Michael D.; Ni, Jun; Wang, Xueding; Higgins, Peter D. R.

    2017-03-01

    The pathology of Crohn's disease (CD) is characterized by obstructing intestinal strictures because of inflammation (with high levels of hemoglobin), fibrosis (high levels of collagen), or a combination of both. Inflammatory strictures are medically treated. Fibrotic strictures have to be removed surgically. The accurate characterization of the strictures is therefore critical for the management of CD. Currently the comprehensive assessment of a stricture is difficult, as the standard diagnostic procedure, endoscopic biopsy, is superficial and with limited locations as well as depth. In our previous studies, photoacoustic imaging (PAI) has recovered the layered architectures and the relative content of the molecular components in human and animal tissues ex vivo. This study will investigate the capability of multispectral PAI in resolving the architecture and the molecular components of intestinal strictures in rats in vivo. PA images at 532, 1210 and 1310 nm targeting the strong optical absorption of hemoglobin, lipid and collagen were acquired using two approaches. A compact linear array, CL15-7, was used to transcutaneously acquire PA signals generated by the a fiber optics diffuser positioned within the inner lumen of the strictures. Another approach was to use an endoscopic capsule probe for acoustic resolution PA microscopy. The capsule probe is designed for human and therefore cannot fit into rat colon. The inner surface of the intestinal stricture was exposed and the probe was attached to the diseased location for imaging. The findings in PA images were confirmed by histology results.

  15. Semi-automated 3D leaf reconstruction and analysis of trichome patterning from light microscopic images.

    Directory of Open Access Journals (Sweden)

    Henrik Failmezger

    2013-04-01

    Full Text Available Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons.

  16. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo; Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-02-27

    The authors present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1 pm could successfully be resolved. In addition, lateral drifts rates of below 15 pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  17. Label-free imaging of intracellular motility by low-coherent quantitative phase microscope in reflection geometry

    Science.gov (United States)

    Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

    2011-11-01

    We demonstrate tomographic imaging of intracellular activity of living cells by a low-coherent quantitative phase microscope. The intracellular organelles, such as the nucleus, nucleolus, and mitochondria, are moving around inside living cells, driven by the cellular physiological activity. In order to visualize the intracellular motility in a label-free manner we have developed a reflection-type quantitative phase microscope which employs the phase shifting interferometric technique with a low-coherent light source. The phase shifting interferometry enables us to quantitatively measure the intensity and phase of the optical field, and the low-coherence interferometry makes it possible to selectively probe a specific sectioning plane in the cell volume. The results quantitatively revealed the depth-resolved fluctuations of intracellular surfaces so that the plasma membrane and the membranes of intracellular organelles were independently measured. The transversal and the vertical spatial resolutions were 0.56 μm and 0.93 μm, respectively, and the mechanical sensitivity of the phase measurement was 1.2 nanometers. The mean-squared displacement was applied as a statistical tool to analyze the temporal fluctuation of the intracellular organelles. To the best of our knowledge, our system visualized depth-resolved intracellular organelles motion for the first time in sub-micrometer resolution without contrast agents.

  18. A full-field transmission x-ray microscope for time-resolved imaging of magnetic nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Ewald, J.; Nisius, T.; Abbati, G.; Baumbach, S.; Overbuschmann, J.; Wilhein, T. [Institute for X-Optics (IXO), Hochschule Koblenz, Joseph-Rovan-Allee 2, 53424 Remagen (Germany); Wessels, P.; Wieland, M.; Drescher, M. [The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Institut für Experimentalphysik, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Vogel, A. [Institut für Angewandte Physik, University of Hamburg, Jungiusstraße 11, 20355 Hamburg (Germany); Viefhaus, J. [Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg (Germany); Meier, G. [The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg (Germany)

    2016-01-28

    Sub-nanosecond magnetization dynamics of small permalloy (Ni{sub 80}Fe{sub 20}) elements has been investigated with a new full-field transmission microscope at the soft X-ray beamline P04 of the high brilliance synchrotron radiation source PETRA III. The soft X-ray microscope generates a flat-top illumination field of 20 μm diameter using a grating condenser. A tilted nanostructured magnetic sample can be excited by a picosecond electric current pulse via a coplanar waveguide. The transmitted light of the sample plane is directly imaged by a micro zone plate with < 65 nm resolution onto a 2D gateable X-ray detector to select one particular bunch in the storage ring that probes the time evolution of the dynamic information successively via XMCD spectromicroscopy in a pump-probe scheme. In the experiments it was possible to generate a homogeneously magnetized state in patterned magnetic layers by a strong magnetic Oersted field pulse of 200 ps duration and directly observe the recovery to the initial flux-closure vortex patterns.

  19. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Science.gov (United States)

    Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-03-01

    We present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1pm could successfully be resolved. In addition, lateral drifts rates of below 15pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  20. Combined macroscopic and microscopic approach to the fracture of metals. Technical progress report, July 1976--June 1977

    Energy Technology Data Exchange (ETDEWEB)

    Gurland, J; Rice, J R; Asaro, R J; Needleman, A

    1977-07-01

    The work includes the completion of a comprehensive study of the contributions of dislocation substructures and local stresses at particle interfaces to the strain hardening of dispersion hardened steels, and the presentation of a model of segregant induced embrittlement of grain interfaces. Work was continued on crack initiation at inclusions and on the theory of plastic flow localization. These microscopic effects are discussed in relation to the mechanisms of brittle fracture and ductile rupture of metals and alloys. On a more macroscopic scale, the state of stress and strain associated with the large plastic deformation at a crack tip was further defined based on finite element and slip line calculations, and some preliminary results were obtained by finite element methods for stable crack growth under plane strain conditions. A new finite element method has been developed for fully plastic flow under plane strain conditions.

  1. Super-resolution imaging of ciliary microdomains in isolated olfactory sensory neurons using a custom two-color stimulated emission depletion microscope

    Science.gov (United States)

    Meyer, Stephanie A.; Ozbay, Baris N.; Potcoava, Mariana; Salcedo, Ernesto; Restrepo, Diego; Gibson, Emily A.

    2016-06-01

    We performed stimulated emission depletion (STED) imaging of isolated olfactory sensory neurons (OSNs) using a custom-built microscope. The STED microscope uses a single pulsed laser to excite two separate fluorophores, Atto 590 and Atto 647N. A gated timing circuit combined with temporal interleaving of the different color excitation/STED laser pulses filters the two channel detection and greatly minimizes crosstalk. We quantified the instrument resolution to be ˜81 and ˜44 nm, for the Atto 590 and Atto 647N channels. The spatial separation between the two channels was measured to be under 10 nm, well below the resolution limit. The custom-STED microscope is incorporated onto a commercial research microscope allowing brightfield, differential interference contrast, and epifluorescence imaging on the same field of view. We performed immunolabeling of OSNs in mice to image localization of ciliary membrane proteins involved in olfactory transduction. We imaged Ca2+-permeable cyclic nucleotide gated (CNG) channel (Atto 594) and adenylyl cyclase type III (ACIII) (Atto 647N) in distinct cilia. STED imaging resolved well-separated subdiffraction limited clusters for each protein. We quantified the size of each cluster to have a mean value of 88±48 nm and 124±43 nm, for CNG and ACIII, respectively. STED imaging showed separated clusters that were not resolvable in confocal images.

  2. Photon event distribution sampling: an image formation technique for scanning microscopes that permits tracking of sub-diffraction particles with high spatial and temporal resolutions.

    Science.gov (United States)

    Larkin, J D; Publicover, N G; Sutko, J L

    2011-01-01

    In photon event distribution sampling, an image formation technique for scanning microscopes, the maximum likelihood position of origin of each detected photon is acquired as a data set rather than binning photons in pixels. Subsequently, an intensity-related probability density function describing the uncertainty associated with the photon position measurement is applied to each position and individual photon intensity distributions are summed to form an image. Compared to pixel-based images, photon event distribution sampling images exhibit increased signal-to-noise and comparable spatial resolution. Photon event distribution sampling is superior to pixel-based image formation in recognizing the presence of structured (non-random) photon distributions at low photon counts and permits use of non-raster scanning patterns. A photon event distribution sampling based method for localizing single particles derived from a multi-variate normal distribution is more precise than statistical (Gaussian) fitting to pixel-based images. Using the multi-variate normal distribution method, non-raster scanning and a typical confocal microscope, localizations with 8 nm precision were achieved at 10 ms sampling rates with acquisition of ~200 photons per frame. Single nanometre precision was obtained with a greater number of photons per frame. In summary, photon event distribution sampling provides an efficient way to form images when low numbers of photons are involved and permits particle tracking with confocal point-scanning microscopes with nanometre precision deep within specimens. © 2010 The Authors Journal of Microscopy © 2010 The Royal Microscopical Society.

  3. Development of microscopic systems for high-speed dual-excitation ratiometric Ca2+ imaging.

    Science.gov (United States)

    Fukano, Takashi; Shimozono, Satoshi; Miyawaki, Atsushi

    2008-08-01

    For quantitative measurements of Ca(2+) concentration ([Ca(2+)]), ratiometric dyes are preferable, because the use of such dyes allows for correction of uneven loading or partitioning of dye within the cell as well as variations in cell thickness. Although dual-excitation ratiometric dyes for measuring [Ca(2+)], such as Fura-2, Fura-Red, and ratiometric-pericam, are widely used for a variety of applications, it has been difficult to use them for monitoring very fast Ca(2+) dynamics or Ca(2+) changes in highly motile cells. To overcome this problem, we have developed three new dual-excitation ratiometry systems. (1) A system in which two laser beams are alternated on every scanning line, allowing us to obtain confocal images using dual-excitation ratiometric dyes. This system increases the rate at which ratio measurements can be made to 200 Hz and provides confocal images at 1-10 Hz depending on the image size. (2) A truly simultaneous dual-excitation ratiometry system that used linearly polarized excitation light and polarization detection, allowing us to obtain ratiometric images without any time lag. This system, however, is based on statistical features of the fluorescence polarization and is limited to samples that contain a large number of fluorophores. In addition, this method requires complicated calculations. (3) An efficient, nearly simultaneous dual-excitation ratiometry system that allows us to rapidly switch between two synchronized excitation-detection components by employing two high-power light-emitting diodes (LEDs) and two high-speed liquid crystal shutters. The open/close operation of the two shutters is synchronized with the on/off switching of the two LEDs. This system increases the rate at which ratio measurements are made to 1 kHz, and provides ratio images at 10-100 Hz depending on the signal intensity.

  4. Time-resolved microspectrofluorometry and fluorescence lifetime imaging of photosensitizers using picosecond pulsed diode lasers in laser scanning microscopes.

    Science.gov (United States)

    Kress, Matthias; Meier, Thomas; Steiner, Rudolf; Dolp, Frank; Erdmann, Rainer; Ortmann, Uwe; Rück, Angelika

    2003-01-01

    This work describes the time-resolved fluorescence characteristics of two different photosensitizers in single cells, in detail mTHPC and 5-ALA induced PPIX, which are currently clinically used in photodynamic therapy. The fluorescence lifetime of the drugs was determined in the cells from time-gated spectra as well as single photon counting, using a picosecond pulsed diode laser for fluorescence excitation. The diode laser, which emits pulses at 398 nm with 70 ps full width at half maximum duration, was coupled to a confocal laser scanning microscope. For time-resolved spectroscopy a setup consisting of a Czerny Turner spectrometer and a MCP-gated and -intensified CCD camera was used. Time-gated spectra within the cells were acquired by placing the laser beam in "spot scan" mode. In addition, a time-correlated single photon counting module was used to determine the fluorescence lifetime from single spots and to record lifetime images. The fluorescence lifetime of mTHPC decreased from 7.5 to 5.5 ns during incubation from 1 to 6 h. This decrease was probably attributed to enhanced formation of aggregates during incubation. Fluorescence lifetime imaging showed that longer lifetimes were correlated with accumulation in the cytoplasm in the neighborhood of the cell nucleus, whereas shorter lifetimes were found in the outer cytoplasm. For cells that were incubated with 5-ALA, a fluorescence lifetime of 7.4 ns was found for PPIX; a shorter lifetime at 3.6 ns was probably attributed to photoproducts and aggregates of PPIX. In contrast from fluorescence intensity images alone, different fluorescence species could not be distinguished. However, in the lifetime image a structured fluorescence distribution in the cytoplasm was correlated with the longer lifetime and probably coincides with mitochondria. In conclusion, picosecond diode lasers coupled to a laser scanning microscope equipped with appropriate detection units allows time-resolved spectroscopy and lifetime imaging

  5. Wide-range length metrology by dual-imaging-unit atomic force microscope based on porous alumina.

    Science.gov (United States)

    Zhang, Dongxian; Zhang, Haijun; Lin, Xiaofeng

    2004-06-15

    A new dual-imaging-unit atomic force microscope (DIU-AFM) was developed for wide-range length metrology. In the DIU-AFM, two AFM units were combined, one as a reference unit, and the other a test one. Their probes with Z piezo elements and tips were horizontally set in parallel at the same height to reduce errors due to geometric asymmetry. An XY scanner was attached to an XY block that was able to move in the X direction with a step of about 500 nm. A standard porous alumina film was employed as the reference sample. Both reference sample and test sample were installed at the center of the XY scanner on the same surface and were simultaneously imaged. The two images had the same lateral size, and thus the length of the test sample image could be accurately measured by counting the number of periodic features of the reference one. The XY block together with the XY scanner were next moved in the X direction for about 1.5 microm and a second pair of reference and test images were obtained by activating the scanner. In this way, a series of pairs of images were acquired and could be spliced into two wide-range reference and test images, respectively. Again, the two spliced images were of the same size and the length of test image was measured based on the reference one. This article presents a discussion about the structure and control of the DIU-AFM system. Some experiments were carried out on the system to demonstrate the method of length calculation and measurement. Experiments show a satisfactory result of wide-range length metrology based on the hexagonal features of the porous alumina with a periodic length of several tens of nanometers. Using this method the DIU-AFM is capable of realizing nanometer-order accuracy length metrology when covering a wide range from micron to several hundreds of microns, or even up to millimeter order.

  6. Multifractal spectra of scanning electron microscope images of SnO2 thin films prepared by pulsed laser deposition

    Science.gov (United States)

    Chen, Z. W.; Lai, J. K. L.; Shek, C. H.

    2005-09-01

    The concept of fractal geometry has proved useful in describing structures and processes in experimental systems. In this Letter, the surface topographies of SnO2 thin films prepared by pulsed laser deposition for various substrate temperatures were measured by scanning electron microscope (SEM). Multifractal spectra f(α) show that the higher the substrate temperature, the wider the spectrum, and the larger the Δf(Δf=f(α)-f(α)). It is apparent that the nonuniformity of the height distribution increases with the increasing substrate temperature, and the liquid droplets of SnO2 thin films are formed on previous thin films. These results show that the SEM images can be characterized by the multifractal spectra.

  7. Multifractal spectra of scanning electron microscope images of SnO{sub 2} thin films prepared by pulsed laser deposition

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Z.W. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong (China)]. E-mail: cnzwchen@yahoo.com.cn; Lai, J.K.L. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong (China); Shek, C.H. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong (China)

    2005-09-26

    The concept of fractal geometry has proved useful in describing structures and processes in experimental systems. In this Letter, the surface topographies of SnO{sub 2} thin films prepared by pulsed laser deposition for various substrate temperatures were measured by scanning electron microscope (SEM). Multifractal spectra f({alpha}) show that the higher the substrate temperature, the wider the spectrum, and the larger the {delta}f({delta}f=f({alpha}{sub min})-f({alpha}{sub max})). It is apparent that the nonuniformity of the height distribution increases with the increasing substrate temperature, and the liquid droplets of SnO{sub 2} thin films are formed on previous thin films. These results show that the SEM images can be characterized by the multifractal spectra.

  8. Lab-on-DVD: standard DVD drives as a novel laser scanning microscope for image based point of care diagnostics.

    Science.gov (United States)

    Ramachandraiah, Harisha; Amasia, Mary; Cole, Jackie; Sheard, Paul; Pickhaver, Simon; Walker, Chris; Wirta, Valtteri; Lexow, Preben; Lione, Richard; Russom, Aman

    2013-04-21

    We present a novel "Lab-on-DVD" system and demonstrate its capability for rapid and low-cost HIV diagnostics by counting CD4+ cells isolated from whole blood. We show that a commercial DVD drive can, with certain modifications, be turned into an improved DVD-based laser scanning microscope (DVD-LSM). The system consists of a multi-layered disposable polymer disc and a modified commercial DVD reader with rotational control for sample handling, temperature control for optimized bioassay, a photodiode array for detection, and software for signal processing and user interface - all the necessary components required for a truly integrated lab-on-a-chip system, with the capability to deliver high-resolution images down to 1 μm in size. Using discs modified with antibodies, we specifically captured CD4+ cells from whole blood, demonstrating single cell resolution imaging. The novel integrated DVD platform with sub-micron image resolution brings, for the first time, affordable cellular diagnostic testing to the point-of-care and should be readily applicable at resource-limited settings.

  9. A method for sizing submicrometer particles in air collected on formvar films and imaged by scanning electron microscope

    Directory of Open Access Journals (Sweden)

    E. Hamacher-Barth

    2013-06-01

    Full Text Available Here we present a method to systematically investigate single aerosol particles collected on formvar film supported by a copper grid, with Scanning Electron Microscopy (SEM operating at low accelerating voltage. The method enabled us to observe the surface of the sample grid at high resolution. Subsequent processing of the images with digital image analysis provided a statistically and quantitative size resolved information on the particle population including their morphology on the film. The quality of the presented method was established using polystyrene nanospheres as standards in the size range expected for ambient aerosol particles over remote marine areas (20–900 nm in diameter. The sizing was found to be critically dependent on the contrasting properties of the particles towards the collection substrate. The relative standard deviation of the diameters of polystyrene nanospheres was better than 10% for sizes larger than 40 nm and 18% for 21 nm particles compared with the manufacturer's certificate. The size distributions derived from the microscope images of airborne aerosols collected during a research expedition to north of 80° N in the summer of 2008 were compared with simultaneously collected number particle size distributions seen by a Twin Differential Mobility Particle Sizer. We captured a representative fraction of the aerosol particles with SEM and were able to causally relate the determined morphological properties of the aerosol under investigation to aerosol transformation processes in air being advected from the marginal ice edge/open sea south of 80° N.

  10. Atomic Resolution Imaging at an Ultralow Accelerating Voltage by a Monochromatic Transmission Electron Microscope

    Science.gov (United States)

    Morishita, Shigeyuki; Mukai, Masaki; Suenaga, Kazu; Sawada, Hidetaka

    2016-10-01

    Transmission electron microscopy using low-energy electrons would be very useful for atomic resolution imaging of specimens that would be damaged at higher energies. However, the resolution at low voltages is degraded because of geometrical and chromatic aberrations. In the present study, we diminish the effect of these aberrations by using a delta-type corrector and a monochromator. The dominant residual aberration in a delta-type corrector, which is the sixth-order three-lobe aberration, is counterbalanced by other threefold aberrations. Defocus spread caused by chromatic aberration is reduced by using a monochromated beam with an energy spread of 0.05 eV. We obtain images of graphene and demonstrate atomic resolution at an ultralow accelerating voltage of 15 kV.

  11. Quantification of scar margin in keloid different from atrophic scar by multiphoton microscopic imaging.

    Science.gov (United States)

    Zhu, Xiaoqin; Zhuo, Shuangmu; Zheng, Liqin; Jiang, Xingshan; Chen, Jianxin; Lin, Bifang

    2011-01-01

    Multiphoton microscopy (MPM) was applied to examine the marginal region at dermis of keloid compared with atrophic scar. High-resolution large-area image showed an obvious boundary at the scar margin and different morphological patterns of elastin and collagen on the two sides, further visualized by the focused three-dimensional images. Content alteration of elastin or collagen between the two sides of boundary was quantified to show significant difference between keloid and atrophic scar. Owing to the raised property of keloid with overproduced collagen on the scar side, the content alteration was positive for elastin and negative for collagen. On the contrary, the content alteration was negative for elastin and positive for collagen in the atrophic scar case due to the atrophic collagen on the scar side. It indicated that examination of the scar margin by MPM may lead a new way to discriminate different types of scars and better understand the scarring mechanisms.

  12. Imaging and nanofabrication with the helium ion microscope of the Van Leeuwenhoek Laboratory in Delft.

    Science.gov (United States)

    Alkemade, Paul F A; Koster, Emma M; van Veldhoven, Emile; Maas, Diederik J

    2012-01-01

    Although helium ion microscopy (HIM) was introduced only a few years ago, many new application fields are emerging. The connecting factor between these novel applications is the unique interaction of the primary helium ion beam with the sample material at and just below its surface. In particular, the HIM secondary electron signal stems from an area that is extremely well localized around the point of incidence of the primary beam. This makes the HIM well suited for both high-resolution imaging and high-resolution nanofabrication. Another advantage in nanofabrication is the low ion backscattering fraction, which leads to a weak proximity effect. The subnanometer probe size and the unique beam-materials interactions have opened new areas of research. This review presents a selection of studies conducted on a single instrument. The selection encompasses applications ranging from imaging to nanofabrication and from fundamental academic research to applied industrial developments.

  13. A fourth order PDE based fuzzy c- means approach for segmentation of microscopic biopsy images in presence of Poisson noise for cancer detection.

    Science.gov (United States)

    Kumar, Rajesh; Srivastava, Subodh; Srivastava, Rajeev

    2017-07-01

    For cancer detection from microscopic biopsy images, image segmentation step used for segmentation of cells and nuclei play an important role. Accuracy of segmentation approach dominate the final results. Also the microscopic biopsy images have intrinsic Poisson noise and if it is present in the image the segmentation results may not be accurate. The objective is to propose an efficient fuzzy c-means based segmentation approach which can also handle the noise present in the image during the segmentation process itself i.e. noise removal and segmentation is combined in one step. To address the above issues, in this paper a fourth order partial differential equation (FPDE) based nonlinear filter adapted to Poisson noise with fuzzy c-means segmentation method is proposed. This approach is capable of effectively handling the segmentation problem of blocky artifacts while achieving good tradeoff between Poisson noise removals and edge preservation of the microscopic biopsy images during segmentation process for cancer detection from cells. The proposed approach is tested on breast cancer microscopic biopsy data set with region of interest (ROI) segmented ground truth images. The microscopic biopsy data set contains 31 benign and 27 malignant images of size 896 × 768. The region of interest selected ground truth of all 58 images are also available for this data set. Finally, the result obtained from proposed approach is compared with the results of popular segmentation algorithms; fuzzy c-means, color k-means, texture based segmentation, and total variation fuzzy c-means approaches. The experimental results shows that proposed approach is providing better results in terms of various performance measures such as Jaccard coefficient, dice index, Tanimoto coefficient, area under curve, accuracy, true positive rate, true negative rate, false positive rate, false negative rate, random index, global consistency error, and variance of information as compared to other

  14. Further analysis of assessments of the coefficient of variation of corneal endothelial cell areas from specular microscopic images.

    Science.gov (United States)

    Doughty, Michael J; Aakre, Bente Monica

    2008-09-01

    The aim of this study was to compare two methods of assessments of the coefficient of variation (COV) of endothelial cell area. A single image (Topcon SP-2000P specular microscope) was obtained from the central region of the corneal endothelium of 45 healthy white (Norwegian) individuals, aged from 24 to 43 years and without a history of major eye disease or surgery. The image file was printed to A3-size, the cell-cell boundaries marked manually and the areas of the cells measured with a digitiser pad. The same image file was independently processed by the semi-automated Topcon IMAGEnet system. From either method, the cell area data from 100 contiguous cells approximately in the middle portion of the images were used to calculate the average cell area (AVG), the coefficient of variation (COV) on the cell areas and the endothelial cell density (ECD). Both methods produced similar AVG and ECD values that were not statistically different (p >or= 0.180). The SD values on the cell areas increased in relation to the AVG values (Pearson's r >or= 0.557). The resultant COV values were only marginally higher with the manual method (27.8 versus. 26.3 per cent) but the limits of agreement (LoA) for the COV values were rather large at -4.9 to +7.9 per cent. A semi-automated image analysis system can be used to generate COV data for the corneal endothelium similar to those of a manual method. The limits of agreement between the methods are substantial and this probably reflects the extreme sensitivity of the COV calculation to even a few different cell area values. This poor agreement needs to be considered in any comparative studies.

  15. Microstructure Characterization and Imaging of Fine-Grained Steel by Microscopic Ultrasonic Techniques

    Science.gov (United States)

    Hirsekorn, S.; Rabe, U.; Batista, L.; Behl, L.

    2011-06-01

    An important task in materials science is the design of new steel grades with tailored microstructures for powerful mechanical properties aiming at a common optimization of contradicting properties such as weight reduction and formability versus high stiffness and strength. For this purpose techniques are required to image and characterize microstructures and probe local material properties in the micro- and nanoscale. This contribution reports on investigations of fine-grained steels by scanning acoustic microscopy (SAM) and atomic force acoustic microscopy (AFAM).

  16. Imaging circulating tumor cells in freely moving awake small animals using a miniaturized intravital microscope.

    Directory of Open Access Journals (Sweden)

    Laura Sarah Sasportas

    Full Text Available Metastasis, the cause for 90% of cancer mortality, is a complex and poorly understood process involving the invasion of circulating tumor cells (CTCs into blood vessels. These cells have potential prognostic value as biomarkers for early metastatic risk. But their rarity and the lack of specificity and sensitivity in measuring them render their interrogation by current techniques very challenging. How and when these cells are circulating in the blood, on their way to potentially give rise to metastasis, is a question that remains largely unanswered. In order to provide an insight into this "black box" using non-invasive imaging, we developed a novel miniature intravital microscopy (mIVM strategy capable of real-time long-term monitoring of CTCs in awake small animals. We established an experimental 4T1-GL mouse model of metastatic breast cancer, in which tumor cells express both fluorescent and bioluminescent reporter genes to enable both single cell and whole body tumor imaging. Using mIVM, we monitored blood vessels of different diameters in awake mice in an experimental model of metastasis. Using an in-house software algorithm we developed, we demonstrated in vivo CTC enumeration and computation of CTC trajectory and speed. These data represent the first reported use we know of for a miniature mountable intravital microscopy setup for in vivo imaging of CTCs in awake animals.

  17. High-speed broadband nanomechanical property quantification and imaging of life science materials using atomic force microscope

    Science.gov (United States)

    Ren, Juan

    Nanoscale morphological characterization and mechanical properties quantification of soft and biological materials play an important role in areas ranging from nano-composite material synthesis and characterization, cellular mechanics to drug design. Frontier studies in these areas demand the coordination between nanoscale morphological evolution and mechanical behavior variations through simultaneous measurement of these two aspects of properties. Atomic force microscope (AFM) is very promising in achieving such simultaneous measurements at high-speed and broadband owing to its unique capability in applying force stimuli and then, measuring the response at specific locations in a physiologically friendly environment with pico-newton force and nanometer spatial resolution. Challenges, however, arise as current AFM systems are unable to account for the complex and coupled dynamics of the measurement system and probe-sample interaction during high-speed imaging and broadband measurements. In this dissertation, the creation of a set of dynamics and control tools to probe-based high-speed imaging and rapid broadband nanomechanical spectroscopy of soft and biological materials are presented. Firstly, advanced control-based approaches are presented to improve the imaging performance of AFM imaging both in air and in liquid. An adaptive contact mode (ACM) imaging scheme is proposed to replace the traditional contact mode (CM) imaging by addressing the major concerns in both the speed and the force exerted to the sample. In this work, the image distortion caused by the topography tracking error is accounted for in the topography quantification and the quantified sample topography is utilized in a gradient-based optimization method to adjust the cantilever deflection set-point for each scanline closely around the minimal level needed for maintaining a stable probe-sample contact, and a data-driven iterative feedforward control that utilizes a prediction of the next

  18. Handheld nonlinear microscope system comprising a 2 MHz repetition rate, mode-locked Yb-fiber laser for in vivo biomedical imaging.

    Science.gov (United States)

    Krolopp, Ádám; Csákányi, Attila; Haluszka, Dóra; Csáti, Dániel; Vass, Lajos; Kolonics, Attila; Wikonkál, Norbert; Szipőcs, Róbert

    2016-09-01

    A novel, Yb-fiber laser based, handheld 2PEF/SHG microscope imaging system is introduced. It is suitable for in vivo imaging of murine skin at an average power level as low as 5 mW at 200 kHz sampling rate. Amplified and compressed laser pulses having a spectral bandwidth of 8 to 12 nm at around 1030 nm excite the biological samples at a ~1.89 MHz repetition rate, which explains how the high quality two-photon excitation fluorescence (2PEF) and second harmonic generation (SHG) images are obtained at the average power level of a laser pointer. The scanning, imaging and detection head, which comprises a conventional microscope objective for beam focusing, has a physical length of ~180 mm owing to the custom designed imaging telescope system between the laser scanner mirrors and the entrance aperture of the microscope objective. Operation of the all-fiber, all-normal dispersion Yb-fiber ring laser oscillator is electronically controlled by a two-channel polarization controller for Q-switching free mode-locked operation. The whole nonlinear microscope imaging system has the main advantages of the low price of the fs laser applied, fiber optics flexibility, a relatively small, light-weight scanning and detection head, and a very low risk of thermal or photochemical damage of the skin samples.

  19. Sparse sampling and reconstruction for electron and scanning probe microscope imaging

    Science.gov (United States)

    Anderson, Hyrum; Helms, Jovana; Wheeler, Jason W.; Larson, Kurt W.; Rohrer, Brandon R.

    2015-07-28

    Systems and methods for conducting electron or scanning probe microscopy are provided herein. In a general embodiment, the systems and methods for conducting electron or scanning probe microscopy with an undersampled data set include: driving an electron beam or probe to scan across a sample and visit a subset of pixel locations of the sample that are randomly or pseudo-randomly designated; determining actual pixel locations on the sample that are visited by the electron beam or probe; and processing data collected by detectors from the visits of the electron beam or probe at the actual pixel locations and recovering a reconstructed image of the sample.

  20. Sparse sampling and reconstruction for electron and scanning probe microscope imaging

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Hyrum; Helms, Jovana; Wheeler, Jason W.; Larson, Kurt W.; Rohrer, Brandon R.

    2015-07-28

    Systems and methods for conducting electron or scanning probe microscopy are provided herein. In a general embodiment, the systems and methods for conducting electron or scanning probe microscopy with an undersampled data set include: driving an electron beam or probe to scan across a sample and visit a subset of pixel locations of the sample that are randomly or pseudo-randomly designated; determining actual pixel locations on the sample that are visited by the electron beam or probe; and processing data collected by detectors from the visits of the electron beam or probe at the actual pixel locations and recovering a reconstructed image of the sample.

  1. Microscopic particle image velocimetry measurements of transition to turbulence in microscale capillaries

    Science.gov (United States)

    Natrajan, V. K.; Christensen, K. T.

    2007-07-01

    The character of transitional capillary flow is investigated using pressure-drop measurements and instantaneous velocity fields acquired by microscopic PIV in the streamwise wall-normal plane of a 536 μm capillary over the Reynolds-number range 1,800 ≤ Re ≤ 3,400 in increments of 100. The pressure-drop measurements reveal a deviation from laminar behavior at Re = 1,900 with the differences between the measured and the predicted laminar-flow pressure drop increasing with increasing Re. These observations are consistent with the characteristics of the mean velocity profiles which begin to deviate from the parabolic laminar profile at Re = 1,900, interpreted as the onset of transition, by becoming increasingly flatter and fuller with increasing Re. A fully-turbulent state is attained at Re ≅ 3,400 where the mean velocity profile collapses onto the mean profile of fully-developed turbulent pipe flow from an existing direct numerical simulation at Re = 5,300. Examination of the instantaneous velocity fields acquired by micro-PIV in the range 1,900 ≤ Re flows at the microscale are composed of a subset of velocity fields illustrating a purely laminar behavior and a subset of fields that capture significant departure from laminar behavior. The fraction of velocity fields displaying non-laminar behavior increases with increasing Re, consistent with past observations of a growing number of intermittent turbulent spots bounded by nominally laminar flow in macroscale pipe flow with increasing Re. Instantaneous velocity fields that are non-laminar in character consistently contain multiple spanwise vortices that appear to streamwise-align to form larger-scale interfaces that incline slightly away from the wall. The characteristics of these “trains” of vortices are reminiscent of the spatial features of hairpin-like vortices and hairpin vortex packets often observed in fully-turbulent wall-bounded flow at both the macro- and micro-scales. Finally, single

  2. 3D Segmentations of Neuronal Nuclei from Confocal Microscope Image Stacks

    Directory of Open Access Journals (Sweden)

    Antonio eLaTorre

    2013-12-01

    Full Text Available In this paper, we present an algorithm to create 3D segmentations of neuronal cells from stacks of previously segmented 2D images. The idea behind this proposal is to provide a general method to reconstruct 3D structures from 2D stacks, regardless of how these 2D stacks have been obtained. The algorithm not only reuses the information obtained in the 2D segmentation, but also attempts to correct some typical mistakes made by the 2D segmentation algorithms (for example, under segmentation of tightly-coupled clusters of cells. We have tested our algorithm in a real scenario --- the segmentation of the neuronal nuclei in different layers of the rat cerebral cortex. Several representative images from different layers of the cerebral cortex have been considered and several 2D segmentation algorithms have been compared. Furthermore, the algorithm has also been compared with the traditional 3D Watershed algorithm and the results obtained here show better performance in terms of correctly identified neuronal nuclei.

  3. Microscopic thin film optical anisotropy imaging at the solid-liquid interface

    Science.gov (United States)

    Miranda, Adelaide; De Beule, Pieter A. A.

    2016-04-01

    Optical anisotropy of thin films has been widely investigated through ellipsometry, whereby typically an optical signal is averaged over a ˜1 cm2 elliptical area that extends with increasing angle-of-incidence (AOI). Here, we report on spectroscopic imaging ellipsometry at the solid-liquid interface applied to a supported lipid bilayer (SLB). We detail how a differential spectrally resolved ellipsometry measurement, between samples with and without optically anisotropic thin film on an absorbing substrate, can be applied to recover in and out of plane refractive indices of the thin film with known film thickness, hence determining the thin film optical anisotropy. We also present how optimal wavelength and AOI settings can be determined ensuring low parameter cross correlation between the refractive indices to be determined from a differential measurement in Δ ellipsometry angle. Furthermore, we detail a Monte Carlo type analysis that allows one to determine the minimal required optical ellipsometry resolution to recover a given thin film anisotropy. We conclude by presenting a new setup for a spectroscopic imaging ellipsometry based on fiber supercontinuum laser technology, multi-wavelength diode system, and an improved liquid cell design, delivering a 5 ×-10 × ellipsometric noise reduction over state-of-the-art. We attribute this improvement to increased ellipsometer illumination power and a reduced light path in liquid through the use of a water dipping objective.

  4. Comparison of different approaches for modelling microscope images on the basis of rigorous diffraction calculation

    Science.gov (United States)

    Bodermann, Bernd; Ehret, Gerd

    2005-08-01

    High resolution optical microscopy is still an important instrument for dimensional characterisation of micro- und nanostructures. For precise measurements of dimensional quantities a highly accurate modelling of the optical imaging on the basis of rigorous diffraction calculation is essential, which accounts for both the polarisation effects and the 2D or 3D geometry of the structures. Some applications like for example the measurements of linewidths on photomasks demands for measurement uncertainties of few nm or less. For these requirements the numerical and the model induced uncertainty, respectively, may be limiting factors even for sophisticated modelling software. At PTB we use two different rigorous grating diffraction models for modelling of the intensity distribution in the image plane, the rigorous coupled wave analysis (RCWA) method and the finite elements (FEM) method. In order to evaluate the performance of both methods we performed comparative calculations on the basis of a test suite of binary chrome on glass gratings with different line widths reaching from 100nm to 10μm, and with different line/space ratios between 0.01 and 100. We present results of this comparison for TE, TM and unpolarised Koehler illumination of the grating. Residual deviations between both methods and the resulting measurement uncertainty and related to the corresponding time consumptions are considered.

  5. 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 of the ev......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...

  6. Microscopic imaging of glyceraldehyde-induced tissue glycation with intrinsic second harmonic generation and two-photon fluorescence contrasts

    Science.gov (United States)

    Hwang, Yu Jer; Granelli, Joseph; Tirumalasetty, Manasa; Lyubovitsky, Julia

    2013-02-01

    The bioinspired approaches to tissue strengthening and preservation rely on non-toxic cross-linking agents one of which is glyceraldehyde. In this study we used multiphoton microscopy that employs second harmonic generation (SHG) contrast to evaluate collagen microstructures and two-photon fluorescence (TPF) contrast to monitor progression of cross-linking upon treatment of tissues with glyceraldehyde. We examined collagen hydrogels assembled at 37 °C and 27 °C, bovine scleral and corneal tissues, skin as well as rat tail tendons. The results show a different effect of glyceraldehyde on collagen microstructures within the above tissues. This effect depends on the original microstructural assembly of collagen within a specific tissue. Our data suggests that epidermis (in skin and cornea) will protect collagen from cross-linking with glyceraldehyde. The work highlights benefits of monitoring progression of collagen cross-linking and effects of cross-linking on fiber microstructures as imaged with SHG and TPF signals.

  7. Capturing and displaying microscopic images used in medical diagnostics and forensic science using 4K video resolution - an application in higher education.

    Science.gov (United States)

    Maier, Hans; de Heer, Gert; Ortac, Ajda; Kuijten, Jan

    2015-11-01

    To analyze, interpret and evaluate microscopic images, used in medical diagnostics and forensic science, video images for educational purposes were made with a very high resolution of 4096 × 2160 pixels (4K), which is four times as many pixels as High-Definition Video (1920 × 1080 pixels). The unprecedented high resolution makes it possible to see details that remain invisible to any other video format. The images of the specimens (blood cells, tissue sections, hair, fibre, etc.) are recorded using a 4K video camera which is attached to a light microscope. After processing, this resulted in very sharp and highly detailed images. This material was then used in education for classroom discussion. Spoken explanation by experts in the field of medical diagnostics and forensic science was also added to the high-resolution video images to make it suitable for self-study.

  8. High-speed spiral imaging technique for an atomic force microscope using a linear quadratic Gaussian controller

    Science.gov (United States)

    Habibullah, H.; Pota, H. R.; Petersen, I. R.

    2014-03-01

    This paper demonstrates a high-speed spiral imaging technique for an atomic force microscope (AFM). As an alternative to traditional raster scanning, an approach of gradient pulsing using a spiral line is implemented and spirals are generated by applying single-frequency cosine and sine waves of slowly varying amplitudes to the X and Y-axes of the AFM's piezoelectric tube scanner (PTS). Due to these single-frequency sinusoidal input signals, the scanning process can be faster than that of conventional raster scanning. A linear quadratic Gaussian controller is designed to track the reference sinusoid and a vibration compensator is combined to damp the resonant mode of the PTS. An internal model of the reference sinusoidal signal is included in the plant model and an integrator for the system error is introduced in the proposed control scheme. As a result, the phase error between the input and output sinusoids from the X and Y-PTSs is reduced. The spirals produced have particularly narrow-band frequency measures which change slowly over time, thereby making it possible for the scanner to achieve improved tracking and continuous high-speed scanning rather than being restricted to the back and forth motion of raster scanning. As part of the post-processing of the experimental data, a fifth-order Butterworth filter is used to filter noises in the signals emanating from the position sensors and a Gaussian image filter is used to filter the images. A comparison of images scanned using the proposed controller (spiral) and the AFM PI controller (raster) shows improvement in the scanning rate using the proposed method.

  9. High-speed spiral imaging technique for an atomic force microscope using a linear quadratic Gaussian controller

    Energy Technology Data Exchange (ETDEWEB)

    Habibullah, H., E-mail: h.habib@student.adfa.edu.au; Pota, H. R., E-mail: h.pota@adfa.edu.au; Petersen, I. R., E-mail: i.petersen@adfa.edu.au [School of Engineering and Information Technology, University of New South Wales, Canberra, Australian Capital Territory 2612 (Australia)

    2014-03-15

    This paper demonstrates a high-speed spiral imaging technique for an atomic force microscope (AFM). As an alternative to traditional raster scanning, an approach of gradient pulsing using a spiral line is implemented and spirals are generated by applying single-frequency cosine and sine waves of slowly varying amplitudes to the X and Y-axes of the AFM’s piezoelectric tube scanner (PTS). Due to these single-frequency sinusoidal input signals, the scanning process can be faster than that of conventional raster scanning. A linear quadratic Gaussian controller is designed to track the reference sinusoid and a vibration compensator is combined to damp the resonant mode of the PTS. An internal model of the reference sinusoidal signal is included in the plant model and an integrator for the system error is introduced in the proposed control scheme. As a result, the phase error between the input and output sinusoids from the X and Y-PTSs is reduced. The spirals produced have particularly narrow-band frequency measures which change slowly over time, thereby making it possible for the scanner to achieve improved tracking and continuous high-speed scanning rather than being restricted to the back and forth motion of raster scanning. As part of the post-processing of the experimental data, a fifth-order Butterworth filter is used to filter noises in the signals emanating from the position sensors and a Gaussian image filter is used to filter the images. A comparison of images scanned using the proposed controller (spiral) and the AFM PI controller (raster) shows improvement in the scanning rate using the proposed method.

  10. High-speed spiral imaging technique for an atomic force microscope using a linear quadratic Gaussian controller.

    Science.gov (United States)

    Habibullah, H; Pota, H R; Petersen, I R

    2014-03-01

    This paper demonstrates a high-speed spiral imaging technique for an atomic force microscope (AFM). As an alternative to traditional raster scanning, an approach of gradient pulsing using a spiral line is implemented and spirals are generated by applying single-frequency cosine and sine waves of slowly varying amplitudes to the X and Y-axes of the AFM's piezoelectric tube scanner (PTS). Due to these single-frequency sinusoidal input signals, the scanning process can be faster than that of conventional raster scanning. A linear quadratic Gaussian controller is designed to track the reference sinusoid and a vibration compensator is combined to damp the resonant mode of the PTS. An internal model of the reference sinusoidal signal is included in the plant model and an integrator for the system error is introduced in the proposed control scheme. As a result, the phase error between the input and output sinusoids from the X and Y-PTSs is reduced. The spirals produced have particularly narrow-band frequency measures which change slowly over time, thereby making it possible for the scanner to achieve improved tracking and continuous high-speed scanning rather than being restricted to the back and forth motion of raster scanning. As part of the post-processing of the experimental data, a fifth-order Butterworth filter is used to filter noises in the signals emanating from the position sensors and a Gaussian image filter is used to filter the images. A comparison of images scanned using the proposed controller (spiral) and the AFM PI controller (raster) shows improvement in the scanning rate using the proposed method.

  11. Imaging bacteriorhodopsinlike molecules of claretmembranes from Tibet halobacteria xz515 by atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Halobacteria H. sp.xz 515 was isolated from a salt lake in Tibet. Although proton release-and-uptake across claret membrane is in reverse order compared to bacteriorhodopsin in purple membrane from Halobacterium Salinarum, and its efficiency of proton pump is much lower,AFM image shows that the molecules are still arranged in a two-dimensional hexagonal lattice of trimers. Primary structure of C- to G-helix of the archaerhodopsin shows that it has only 56% homology with bacteriorhodopsin. But the interactive amino acid residues at the interface between Band D-helixes are conserved. These amino acid residues are believed to play a significant role in the stability of protein oligomers.

  12. Characterizing primary refractory neuroblastoma: prediction of outcome by microscopic image analysis

    Science.gov (United States)

    Niazi, M. Khalid Khan; Weiser, Daniel A.; Pawel, Bruce R.; Gurcan, Metin N.

    2015-03-01

    Neuroblastoma is a childhood cancer that starts in very early forms of nerve cells found in an embryo or fetus. It is a highly lethal cancer of sympathetic nervous system that commonly affects children of age five or younger. It accounts for a disproportionate number of childhood cancer deaths and remains a difficult cancer to eradicate despite intensive treatment that includes chemotherapy, surgery, hematopoietic stem cell transplantation, radiation therapy and immunotherapy. A poorly characterized group of patients are the 15% with primary refractory neuroblastoma (PRN) which is uniformly lethal due to de novo chemotherapy resistance. The lack of response to therapy is currently assessed after multiple months of cytotoxic therapy, driving the critical need to develop pretreatment clinic-biological biomarkers that can guide precise and effective therapeutic strategies. Therefore, our guiding hypothesis is that PRN has distinct biological features present at diagnosis that can be identified for prediction modeling. During a visual analysis of PRN slides, stained with hematoxylin and eosin, we observed that patients who survived for less than three years contained large eosin-stained structures as compared to those who survived for greater than three years. So, our hypothesis is that the size of eosin stained structures can be used as a differentiating feature to characterize recurrence in neuroblastoma. To test this hypothesis, we developed an image analysis method that performs stain separation, followed by the detection of large structures stained with Eosin. On a set of 21 PRN slides, stained with hematoxylin and eosin, our image analysis method predicted the outcome with 85.7% accuracy.

  13. Quaternary and secondary structural imaging of a human hair by a VSFG-detected IR super-resolution microscope

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Makoto, E-mail: makotos@res.titech.ac.jp [Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503 (Japan); Kikuchi, Katsuya [Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503 (Japan); Fujii, Masaaki, E-mail: mfujii@res.titech.ac.jp [Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503 (Japan)

    2013-06-20

    Highlights: ► IR super-resolution image of cross section of a human black hair were measured. ► For the amide III band, human hair gave strong VSFG signals at the cortex area. ► Distribution of α-helix based quaternary structure of keratin proteins was observed. ► The VSFG signal disappeared completely when the amide I band was monitored. ► The α-helix of keratin proteins is well aligned along the axial direction in hair. - Abstract: IR super-resolution images of cross sections of a human black hair were measured by using a home-made vibrational sum-frequency generation (VSFG) detected IR microscope in the 6–9 μm region with a sub-micrometer spatial resolution. For the amide III band, the sample gave clear strong signals at the cortex area. This enabled us to measure the distribution of intermediate filaments, which have an α-helix based quaternary structure of keratin proteins in the hair. On the other hand, the VSFG signal disappeared completely when the amide I band was monitored by the same polarization of incident light. From the polarization dependence of VSFG, it is concluded that the α-helix of keratin proteins are well aligned along the axial direction in human hair.

  14. iSpectra: An Open Source Toolbox For The Analysis of Spectral Images Recorded on Scanning Electron Microscopes.

    Science.gov (United States)

    Liebske, Christian

    2015-08-01

    iSpectra is an open source and system-independent toolbox for the analysis of spectral images (SIs) recorded on energy-dispersive spectroscopy (EDS) systems attached to scanning electron microscopes (SEMs). The aim of iSpectra is to assign pixels with similar spectral content to phases, accompanied by cumulative phase spectra with superior counting statistics for quantification. Pixel-to-phase assignment starts with a threshold-based pre-sorting of spectra to create groups of pixels with identical elemental budgets, similar to a method described by van Hoek (2014). Subsequent merging of groups and re-assignments of pixels using elemental or principle component histogram plots enables the user to generate chemically and texturally plausible phase maps. A variety of standard image processing algorithms can be applied to groups of pixels to optimize pixel-to-phase assignments, such as morphology operations to account for overlapping excitation volumes over pixels located at phase boundaries. iSpectra supports batch processing and allows pixel-to-phase assignments to be applied to an unlimited amount of SIs, thus enabling phase mapping of large area samples like petrographic thin sections.

  15. Support Immersion Endoscopy in Post-Extraction Alveolar Bone Chambers: A New Window for Microscopic Bone Imaging In Vivo.

    Directory of Open Access Journals (Sweden)

    Wilfried Engelke

    Full Text Available Using an endoscopic approach, small intraoral bone chambers, which are routinely obtained during tooth extraction and implantation, provide visual in vivo access to internal bone structures. The aim of the present paper is to present a new method to quantify bone microstructure and vascularisation in vivo. Ten extraction sockets and 6 implant sites in 14 patients (6 men / 8 women were examined by support immersion endoscopy (SIE. After tooth extraction or implant site preparation, microscopic bone analysis (MBA was performed using short distance SIE video sequences of representative bone areas for off-line analysis with ImageJ. Quantitative assessment of the microstructure and vascularisation of the bone in dental extraction and implant sites in vivo was performed using ImageJ. MBA revealed bone morphology details such as unmineralised and mineralised areas, vascular canals and the presence of bleeding through vascular canals. Morphometric examination revealed that there was more unmineralised bone and less vascular canal area in the implant sites than in the extraction sockets.

  16. Study of corrosion in archaeological gilded irons by Raman imaging and a coupled scanning electron microscope-Raman system

    Science.gov (United States)

    Veneranda, Marco; Costantini, Ilaria; de Vallejuelo, Silvia Fdez-Ortiz; Garcia, Laura; García, Iñaki; Castro, Kepa; Azkarate, Agustín; Madariaga, Juan Manuel

    2016-12-01

    In this work, analytical and chemical imaging tools have been applied to the study of a gilded spur found in the medieval necropolis of Erenozar (Bizkaia, Spain). As a first step, a lot of portable equipment has been used to study the object in a non-invasive way. The hand-held energy-dispersive X-ray fluorescence equipment allowed us to characterize the artefact as a rare example of an iron matrix item decorated by means of a fire gilding technique. On the other hand, the use of a portable Raman system helped us to detect the main degradation compounds affecting the spur. Afterwards, further information was acquired in the laboratory by analysing detached fragments. The molecular images obtained using confocal Raman microscopy permitted us to characterize the stratigraphic succession of iron corrosions. Furthermore, the combined use of this technique with a scanning electron microscope (SEM) was achieved owing to the use of a structural and chemical analyser interface. In this way, the molecular characterization, enhanced by the magnification feature of the SEM, allowed us to identify several micrometric degradation compounds. Finally, the effectiveness of one of the most used desalination baths (NaOH) was evaluated by comparing its effects with those provided by a reference bath (MilliQ). The comparison proved that basic treatment avoided any side effects on the spur decorated by fire gilding, compensating for the lack of bibliographic documentation in this field. This article is part of the themed issue "Raman spectroscopy in art and archaeology".

  17. Application of the progressive wavelet correlation for image recognition and retrieval from the collection of images - Thesis

    OpenAIRE

    Stojanovic, Igor

    2011-01-01

    An algorithm for recognition and retrieval of image from image collection is developed. Basis of the algorithm is the progressive wavelet correlation. The final result is the recognition and retrieval of the wanted image, if it is in the image collection. Instructions for the choice of correlation threshold value for obtaining desired results are defined. The areas where the algorithm can be applied are also discussed. To increase efficiency is presented two phases solution. The first phase u...

  18. Surprises of electron microscopic imaging of proteins and polymers covering gold nanoparticles layer by layer.

    Science.gov (United States)

    Pyshnaya, Inna A; Razum, Kristina V; Dolodoev, Anton S; Shashkova, Valeriya V; Ryabchikova, Elena I

    2017-02-01

    Gold nanoparticles (GNPs) are used in complicated nanoconstructions, and their preparation implies careful analysis of the intermediate and resulting products, including visualisation of the NPs. Visualisation of protein and/or organic polymer covers on GNPs using electron microscopy (EM) was a goal of this study. We covered GNPs with human serum albumin or PEG, and then added a second layer of branched or linear polyethyleneimine. EM studies were supplemented with dynamic light scattering, spectrophotometry and gel electrophoresis, which confirmed the presence and integrity of a cover on GNPs in mixtures with uranylacetate (UA) or phosphotungstic acid (PTA). Covered GNPs were contrasted 'on a drop' or in suspension with UA (pH 4.5) or PTA (pH 0.5, 3.0, 5.0 and 7.0), and studied by transmission EM. A cover on GNPs becomes visible as the result of direct interaction of UA or PTA with the components of a layer. The same NPs could look 'naked' or demonstrate a distinct cover of average electron density. The most distinct images of the layers were obtained using PTA at pH 0.5. Thus, visualisation of protein and/or polymeric layers covering the GNPs by EM depends on the type of contrasting reagent and contrasting conditions, but does not depend on surface charge of the NPs and the chemical nature of a cover.

  19. A new method based on Adaptive Discrete Wavelet Entropy Energy and Neural Network Classifier (ADWEENN) for recognition of urine cells from microscopic images independent of rotation and scaling.

    Science.gov (United States)

    Avci, Derya; Leblebicioglu, Mehmet Kemal; Poyraz, Mustafa; Dogantekin, Esin

    2014-02-01

    So far, analysis and classification of urine cells number has become an important topic for medical diagnosis of some diseases. Therefore, in this study, we suggest a new technique based on Adaptive Discrete Wavelet Entropy Energy and Neural Network Classifier (ADWEENN) for Recognition of Urine Cells from Microscopic Images Independent of Rotation and Scaling. Some digital image processing methods such as noise reduction, contrast enhancement, segmentation, and morphological process are used for feature extraction stage of this ADWEENN in this study. Nowadays, the image processing and pattern recognition topics have come into prominence. The image processing concludes operation and design of systems that recognize patterns in data sets. In the past years, very difficulty in classification of microscopic images was the deficiency of enough methods to characterize. Lately, it is seen that, multi-resolution image analysis methods such as Gabor filters, discrete wavelet decompositions are superior to other classic methods for analysis of these microscopic images. In this study, the structure of the ADWEENN method composes of four stages. These are preprocessing stage, feature extraction stage, classification stage and testing stage. The Discrete Wavelet Transform (DWT) and adaptive wavelet entropy and energy is used for adaptive feature extraction in feature extraction stage to strengthen the premium features of the Artificial Neural Network (ANN) classifier in this study. Efficiency of the developed ADWEENN method was tested showing that an avarage of 97.58% recognition succes was obtained.

  20. Microscopic identification of Chinese medicinal materials based on X-ray phase contrast imaging: from qualitative to quantitative

    Science.gov (United States)

    Xue, Y.; Liang, Z.; Tan, H.; Ni, L.; Zhao, Z.; Xiao, T.; Xu, H.

    2016-07-01

    Although a variety of methods, ranging from simple morphological examination to physical and chemical analysis, and DNA molecular biology, exist for authenticating Chinese medicinal materials(CMMs), no methods can achieve both the source species identification and quality evaluation of CMMs simultaneously. Furthermore, the methods that are currently available for the identification of CMMs, including both optical and electronic microscopy, usually entail strict requirements for sample preparation or testing environment, such as the slicing of super-thin sections, or processing with specific chemical reagents. These treatments not only damage the CMMs but may also cause some of the original microstructures to be missed. Additionally, they may even yield false results. Owing to the unique penetrating character of X-rays, X-ray phase contrast imaging(XPCI) can be used to realize the inner microstructures of CMMs through nondestructive imaging. With the higher flux and luminance of the third generation of synchrotron radiation facility, XPCI can provides clearer and finer microstructures of CMMs, which are mainly composed of C, H, O, and N elements, with better spatial and density resolutions. For more than ten years, the X-ray imaging group at the Shanghai Institute of Applied Physics has investigated the microstructures of CMMs by XPCI and they have established and developed a quantitative X-ray phase contrast micro-CT for investigating the characteristic microstructures of CMMs. During this period, a variety of typical CMMs have been investigated, from two-dimensional (2D) radiography to three-dimensional (3D) micro-CT, from qualitative to quantitative. Taken together, these results verify that quantitative X-ray phase contrast micro-CT is a practical tool for the microscopic investigation of CMMs. Additionally, further efforts are being made to find the relationship between the microstructures' quantitative factors and active chemical components. At present

  1. Progress on Developing Adaptive Optics-Optical Coherence Tomography for In Vivo Retinal Imaging: Monitoring and Correction of Eye Motion Artifacts.

    Science.gov (United States)

    Zawadzki, Robert J; Capps, Arlie G; Kim, Dae Yu; Panorgias, Athanasios; Stevenson, Scott B; Hamann, Bernd; Werner, John S

    2014-03-01

    Recent progress in retinal image acquisition techniques, including optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO), combined with improved performance of adaptive optics (AO) instrumentation, has resulted in improvement in the quality of in vivo images of cellular structures in the human retina. Here, we present a short review of progress on developing AO-OCT instruments. Despite significant progress in imaging speed and resolution, eye movements present during acquisition of a retinal image with OCT introduce motion artifacts into the image, complicating analysis and registration. This effect is especially pronounced in high-resolution datasets acquired with AO-OCT instruments. Several retinal tracking systems have been introduced to correct retinal motion during data acquisition. We present a method for correcting motion artifacts in AO-OCT volume data after acquisition using simultaneously captured adaptive optics-scanning laser ophthalmoscope (AO-SLO) images. We extract transverse eye motion data from the AO-SLO images, assign a motion adjustment vector to each AO-OCT A-scan, and re-sample from the scattered data back onto a regular grid. The corrected volume data improve the accuracy of quantitative analyses of microscopic structures.

  2. Progress on Developing Adaptive Optics–Optical Coherence Tomography for In Vivo Retinal Imaging: Monitoring and Correction of Eye Motion Artifacts

    Science.gov (United States)

    Zawadzki, Robert J.; Capps, Arlie G.; Kim, Dae Yu; Panorgias, Athanasios; Stevenson, Scott B.; Hamann, Bernd; Werner, John S.

    2014-01-01

    Recent progress in retinal image acquisition techniques, including optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO), combined with improved performance of adaptive optics (AO) instrumentation, has resulted in improvement in the quality of in vivo images of cellular structures in the human retina. Here, we present a short review of progress on developing AO-OCT instruments. Despite significant progress in imaging speed and resolution, eye movements present during acquisition of a retinal image with OCT introduce motion artifacts into the image, complicating analysis and registration. This effect is especially pronounced in high-resolution datasets acquired with AO-OCT instruments. Several retinal tracking systems have been introduced to correct retinal motion during data acquisition. We present a method for correcting motion artifacts in AO-OCT volume data after acquisition using simultaneously captured adaptive optics-scanning laser ophthalmoscope (AO-SLO) images. We extract transverse eye motion data from the AO-SLO images, assign a motion adjustment vector to each AO-OCT A-scan, and re-sample from the scattered data back onto a regular grid. The corrected volume data improve the accuracy of quantitative analyses of microscopic structures. PMID:25544826

  3. Microscope on Mars

    Science.gov (United States)

    2004-01-01

    This image taken at Meridiani Planum, Mars by the panoramic camera on the Mars Exploration Rover Opportunity shows the rover's microscopic imager (circular device in center), located on its instrument deployment device, or 'arm.' The image was acquired on the ninth martian day or sol of the rover's mission.

  4. Microscope on Mars

    Science.gov (United States)

    2004-01-01

    This image taken at Meridiani Planum, Mars by the panoramic camera on the Mars Exploration Rover Opportunity shows the rover's microscopic imager (circular device in center), located on its instrument deployment device, or 'arm.' The image was acquired on the ninth martian day or sol of the rover's mission.

  5. 'Sub-atomic' resolution of non-contact atomic force microscope images induced by a heterogeneous tip structure: a density functional theory study.

    Science.gov (United States)

    Campbellová, Anna; Ondráček, Martin; Pou, Pablo; Pérez, Rubén; Klapetek, Petr; Jelínek, Pavel

    2011-07-22

    A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.

  6. Distinction between amorphous and healed planar deformation features in shocked quartz using composite color scanning electron microscope cathodoluminescence (SEM-CL) imaging

    NARCIS (Netherlands)

    Hamers, Maartje F.; Pennock, Gill M.; Herwegh, Marco; Drury, Martyn R.

    2016-01-01

    Planar deformation features (PDFs) in quartz are one of the most reliable and most widely used forms of evidence for hypervelocity impact. PDFs can be identified in scanning electron microscope cathodoluminescence (SEM-CL) images, but not all PDFs show the same CL behavior: there are nonluminescent

  7. Dark-field imaging based on post-processed electron backscatter diffraction patterns of bulk crystalline materials in a scanning electron microscope.

    Science.gov (United States)

    Brodusch, Nicolas; Demers, Hendrix; Gauvin, Raynald

    2015-01-01

    Dark-field (DF) images were acquired in the scanning electron microscope with an offline procedure based on electron backscatter diffraction (EBSD) patterns (EBSPs). These EBSD-DF images were generated by selecting a particular reflection on the electron backscatter diffraction pattern and by reporting the intensity of one or several pixels around this point at each pixel of the EBSD-DF image. Unlike previous studies, the diffraction information of the sample is the basis of the final image contrast with a pixel scale resolution at the EBSP providing DF imaging in the scanning electron microscope. The offline facility of this technique permits the selection of any diffraction condition available in the diffraction pattern and displaying the corresponding image. The high number of diffraction-based images available allows a better monitoring of deformation structures compared to electron channeling contrast imaging (ECCI) which is generally limited to a few images of the same area. This technique was applied to steel and iron specimens and showed its high capability in describing more rigorously the deformation structures around micro-hardness indents. Due to the offline relation between the reference EBSP and the EBSD-DF images, this new technique will undoubtedly greatly improve our knowledge of deformation mechanism and help to improve our understanding of the ECCI contrast mechanisms.

  8. Macroscopic and microscopic spatially-resolved analysis of food contaminants and constituents using laser-ablation electrospray ionization mass spectrometry imaging

    OpenAIRE

    Nielen, Michel W.F.; VAN BEEK, TERIS A.

    2014-01-01

    Laser-ablation electrospray ionization (LAESI) mass spectrometry imaging (MSI) does not require very flat surfaces, high-precision sample preparation, or the addition of matrix. Because of these features, LAESI-MSI may be the method of choice for spatially-resolved food analysis. In this work, LAESI time-of-flight MSI was investigated for macroscopic and microscopic imaging of pesticides, mycotoxins, and plant metabolites on rose leaves, orange and lemon fruit, ergot bodies, cherry tomatoes, ...

  9. Optical modeling of Fresnel zoneplate microscopes.

    Science.gov (United States)

    Naulleau, Patrick P; Mochi, Iacopo; Goldberg, Kenneth A

    2011-07-10

    Defect free masks remain one of the most significant challenges facing the commercialization of extreme ultraviolet (EUV) lithography. Progress on this front requires high-performance wavelength-specific metrology of EUV masks, including high-resolution and aerial-image microscopy performed near the 13.5 nm wavelength. Arguably the most cost-effective and rapid path to proliferating this capability is through the development of Fresnel zoneplate-based microscopes. Given the relative obscurity of such systems, however, modeling tools are not necessarily optimized to deal with them and their imaging properties are poorly understood. Here we present a modeling methodology to analyze zoneplate microscopes based on commercially available optical modeling software and use the technique to investigate the imaging performance of an off-axis EUV microscope design. The modeling predicts that superior performance can be achieved by tilting the zoneplate, making it perpendicular to the chief ray at the center of the field, while designing the zoneplate to explicitly work in that tilted plane. Although the examples presented here are in the realm of EUV mask inspection, the methods described and analysis results are broadly applicable to zoneplate microscopes in general, including full-field soft-x-ray microscopes routinely used in the synchrotron community.

  10. An ImageJ-based algorithm for a semi-automated method for microscopic image enhancement and DNA repair foci counting

    Energy Technology Data Exchange (ETDEWEB)

    Klokov, D., E-mail: dmitry.klokov@cnl.ca [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada); Suppiah, R. [Queen' s Univ., Dept. of Biomedical and Molecular Sciences, Kingston, Ontario (Canada)

    2015-06-15

    Proper evaluation of the health risks of low-dose ionizing radiation exposure heavily relies on the ability to accurately measure very low levels of DNA damage in cells. One of the most sensitive methods for measuring DNA damage levels is the quantification of DNA repair foci that consist of macromolecular aggregates of DNA repair proteins, such as γH2AX and 53BP1, forming around individual DNA double-strand breaks. They can be quantified using immunofluorescence microscopy and are widely used as markers of DNA double-strand breaks. However this quantification, if performed manually, may be very tedious and prone to inter-individual bias. Low-dose radiation studies are especially sensitive to this potential bias due to a very low magnitude of the effects anticipated. Therefore, we designed and validated an algorithm for the semi-automated processing of microscopic images and quantification of DNA repair foci. The algorithm uses ImageJ, a freely available image analysis software that is customizable to individual cellular properties or experimental conditions. We validated the algorithm using immunolabeled 53BP1 and γH2AX in normal human fibroblast AG01522 cells under both normal and irradiated conditions. This method is easy to learn, can be used by nontrained personnel, and can help avoiding discrepancies in inter-laboratory comparison studies examining the effects of low-dose radiation. (author)

  11. Modeling of cerebral oxygen transport based on in vivo microscopic imaging of microvascular network structure, blood flow and oxygenation

    Directory of Open Access Journals (Sweden)

    Louis Gagnon

    2016-08-01

    Full Text Available Oxygen is delivered to brain tissue by a dense network of microvessels, which actively control cerebral blood flow (CBF through vasodilation and contraction in response to changing levels of neural activity. Understanding these network-level processes is immediately relevant for (1 interpretation of functional Magnetic Resonance Imaging (fMRI signals, and (2 investigation of neurological diseases in which a deterioration of neurovascular and neuro-metabolic physiology contributes to motor and cognitive decline. Experimental data on the structure, flow and oxygen levels of microvascular networks are needed, together with theoretical methods to integrate this information and predict physiologically relevant properties that are not directly measurable. Recent progress in optical imaging technologies for high-resolution in vivo measurement of the cerebral microvascular architecture, blood flow, and oxygenation enables construction of detailed computational models of cerebral hemodynamics and oxygen transport based on realistic three-dimensional microvascular networks. In this article, we review state-of-the-art optical microscopy technologies for quantitative in vivo imaging of cerebral microvascular structure, blood flow and oxygenation, and theoretical methods that utilize such data to generate spatially resolved models for blood flow and oxygen transport. These bottom-up models are essential for the understanding of the processes governing brain oxygenation in normal and disease states and for eventual translation of the lessons learned from animal studies to humans.

  12. The Multispectral Microscopic Imager: Integrating Microimaging with Spectroscopy for the In-Situ Exploration of the Moon

    Science.gov (United States)

    Nunez, J. I.; Farmer, J. D.; Sellar, R. G.; Allen, Carlton C.

    2010-01-01

    To maximize the scientific return, future robotic and human missions to the Moon will need to have in-situ capabilities to enable the selection of the highest value samples for returning to Earth, or a lunar base for analysis. In order to accomplish this task efficiently, samples will need to be characterized using a suite of robotic instruments that can provide crucial information about elemental composition, mineralogy, volatiles and ices. Such spatially-correlated data sets, which place mineralogy into a microtextural context, are considered crucial for correct petrogenetic interpretations. . Combining microscopic imaging with visible= nearinfrared reflectance spectroscopy, provides a powerful in-situ approach for obtaining mineralogy within a microtextural context. The approach is non-destructive and requires minimal mechanical sample preparation. This approach provides data sets that are comparable to what geologists routinely acquire in the field, using a hand lens and in the lab using thin section petrography, and provide essential information for interpreting the primary formational processes in rocks and soils as well as the effects of secondary (diagenetic) alteration processes. Such observations lay a foundation for inferring geologic histories and provide "ground truth" for similar instruments on orbiting satellites; they support astronaut EVA activities and provide basic information about the physical properties of soils required for assessing associated health risks, and are basic tools in the exploration for in-situ resources to support human exploration of the Moon.

  13. Progresses in 3D integral imaging with optical processing

    Energy Technology Data Exchange (ETDEWEB)

    Martinez-Corral, Manuel; Martinez-Cuenca, Raul; Saavedra, Genaro; Navarro, Hector; Pons, Amparo [Department of Optics. University of Valencia. Calle Doctor Moliner 50, E46 100, Burjassot (Spain); Javidi, Bahram [Electrical and Computer Engineering Department, University of Connecticut, Storrs, CT 06269-1157 (United States)], E-mail: manuel.martinez@uv.es

    2008-11-01

    Integral imaging is a promising technique for the acquisition and auto-stereoscopic display of 3D scenes with full parallax and without the need of any additional devices like special glasses. First suggested by Lippmann in the beginning of the 20th century, integral imaging is based in the intersection of ray cones emitted by a collection of 2D elemental images which store the 3D information of the scene. This paper is devoted to the study, from the ray optics point of view, of the optical effects and interaction with the observer of integral imaging systems.

  14. Image interpolation for progressive transmission by using radial basis function networks.

    Science.gov (United States)

    Sigitani, T; Iiguni, Y; Maeda, H

    1999-01-01

    This paper investigates the application of a radial basis function network (RBFN) to a hierarchical image coding for progressive transmission. The RBFN is then used to generate an interpolated image from the subsampled version. An efficient method of computing the network parameters is developed for reduction in computational and memory requirements. The coding method does not suffer from problems of blocking effect and can produce the coarsest image quickly. Quantization error effects introduced at one stage are considered in decoding images at the following stages, thus allowing lossless progressive transmission.

  15. Images as drivers of progress in cardiac computational modelling.

    Science.gov (United States)

    Lamata, Pablo; Casero, Ramón; Carapella, Valentina; Niederer, Steve A; Bishop, Martin J; Schneider, Jürgen E; Kohl, Peter; Grau, Vicente

    2014-08-01

    Computational models have become a fundamental tool in cardiac research. Models are evolving to cover multiple scales and physical mechanisms. They are moving towards mechanistic descriptions of personalised structure and function, including effects of natural variability. These developments are underpinned to a large extent by advances in imaging technologies. This article reviews how novel imaging technologies, or the innovative use and extension of established ones, integrate with computational models and drive novel insights into cardiac biophysics. In terms of structural characterization, we discuss how imaging is allowing a wide range of scales to be considered, from cellular levels to whole organs. We analyse how the evolution from structural to functional imaging is opening new avenues for computational models, and in this respect we review methods for measurement of electrical activity, mechanics and flow. Finally, we consider ways in which combined imaging and modelling research is likely to continue advancing cardiac research, and identify some of the main challenges that remain to be solved.

  16. Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope

    Science.gov (United States)

    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 provided significant contrast and resolution enhancement to conventional microscopy through imaging different multi-cellular fluorescent structures, including 3-D branched cells in vitro and live zebrafish embryos. Imaging with the integration of PIP greatly reduced out-of-focus contamination and generated sharper contrast in acquired 2-D plane images when compared with the stand-alone inverted microscope. As a result, the dynamic fluid domain of the beating zebrafish heart was clearly segmented and the functional monitoring of the heart was achieved. Furthermore, the enhanced axial resolution established by thin plane illumination of PIP enabled the 3-D reconstruction of the branched cellular structures, which leads to the improvement on the functionality of the wide field microscopy. PMID:26819828

  17. Functional Magnetic Resonance Imaging for Imaging Neural Activity in the Human Brain: The Annual Progress

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available Functional magnetic resonance imaging (fMRI is recently developed and applied to measure the hemodynamic response related to neural activity. The fMRI can not only noninvasively record brain signals without risks of ionising radiation inherent in other scanning methods, such as CT or PET scans, but also record signal from all regions of the brain, unlike EEG/MEG which are biased towards the cortical surface. This paper introduces the fundamental principles and summarizes the research progress of the last year for imaging neural activity in the human brain. Aims of functional analysis of neural activity from fMRI include biological findings, functional connectivity, vision and hearing research, emotional research, neurosurgical planning, pain management, and many others. Besides formulations and basic processing methods, models and strategies of processing technology are introduced, including general linear model, nonlinear model, generative model, spatial pattern analysis, statistical analysis, correlation analysis, and multimodal combination. This paper provides readers the most recent representative contributions in the area.

  18. Real-time progressive hyperspectral image processing endmember finding and anomaly detection

    CERN Document Server

    Chang, Chein-I

    2016-01-01

    The book covers the most crucial parts of real-time hyperspectral image processing: causality and real-time capability. Recently, two new concepts of real time hyperspectral image processing, Progressive Hyperspectral Imaging (PHSI) and Recursive Hyperspectral Imaging (RHSI). Both of these can be used to design algorithms and also form an integral part of real time hyperpsectral image processing. This book focuses on progressive nature in algorithms on their real-time and causal processing implementation in two major applications, endmember finding and anomaly detection, both of which are fundamental tasks in hyperspectral imaging but generally not encountered in multispectral imaging. This book is written to particularly address PHSI in real time processing, while a book, Recursive Hyperspectral Sample and Band Processing: Algorithm Architecture and Implementation (Springer 2016) can be considered as its companion book. Includes preliminary background which is essential to those who work in hyperspectral ima...

  19. Following Scoliosis Progression in the Spine using Ultrasound Imaging

    NARCIS (Netherlands)

    Purnama, Ketut; Wilkinson, M.H.F.; Veldhuizen, A.G.; Ooijen, P.M.A. van; Sardjono, T.A.; Lubbers, Jacob; Verkerke, G.J.; Dossel, O; Schlegel, WC

    2009-01-01

    Scoliosis is a three-dimensional deformation of the spine which is characterized by a lateral deviation of the spine and axial rotation of the vertebrae. It must be monitored frequently to be in time to start the treatment in case of progression. Nowadays, X-ray is used, but has a detrimental effect

  20. Imaging of disease progression in a case of idiopathic moyamoya ...

    African Journals Online (AJOL)

    years, using serial magnetic resonance imaging with MR angiography. Comparison is also .... Selected indications for and applications of magnetic resonance ... Note the characteristic 'puff/spiral of smoke' appearance of the collateral vessels.

  1. Multifunctional Inorganic Nanoparticles: Recent Progress in Thermal Therapy and Imaging

    Directory of Open Access Journals (Sweden)

    Kondareddy Cherukula

    2016-04-01

    Full Text Available Nanotechnology has enabled the development of many alternative anti-cancer approaches, such as thermal therapies, which cause minimal damage to healthy cells. Current challenges in cancer treatment are the identification of the diseased area and its efficient treatment without generating many side effects. Image-guided therapies can be a useful tool to diagnose and treat the diseased tissue and they offer therapy and imaging using a single nanostructure. The present review mainly focuses on recent advances in the field of thermal therapy and imaging integrated with multifunctional inorganic nanoparticles. The main heating sources for heat-induced therapies are the surface plasmon resonance (SPR in the near infrared region and alternating magnetic fields (AMFs. The different families of inorganic nanoparticles employed for SPR- and AMF-based thermal therapies and imaging are described. Furthermore, inorganic nanomaterials developed for multimodal therapies with different and multi-imaging modalities are presented in detail. Finally, relevant clinical perspectives and the future scope of inorganic nanoparticles in image-guided therapies are discussed.

  2. Microwave Microscope

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Makes ultra-high-resolution field measurements. The Microwave Microscope (MWM) has been used in support of several NRL experimental programs involving sea...

  3. Rapid specimen preparation to improve the throughput of electron microscopic volume imaging for three-dimensional analyses of subcellular ultrastructures with serial block-face scanning electron microscopy.

    Science.gov (United States)

    Thai, Truc Quynh; Nguyen, Huy Bang; Saitoh, Sei; Wu, Bao; Saitoh, Yurika; Shimo, Satoshi; Elewa, Yaser Hosny Ali; Ichii, Osamu; Kon, Yasuhiro; Takaki, Takashi; Joh, Kensuke; Ohno, Nobuhiko

    2016-09-01

    Serial block-face imaging using scanning electron microscopy enables rapid observations of three-dimensional ultrastructures in a large volume of biological specimens. However, such imaging usually requires days for sample preparation to reduce charging and increase image contrast. In this study, we report a rapid procedure to acquire serial electron microscopic images within 1 day for three-dimensional analyses of subcellular ultrastructures. This procedure is based on serial block-face with two major modifications, including a new sample treatment device and direct polymerization on the rivets, to reduce the time and workload needed. The modified procedure without uranyl acetate can produce tens of embedded samples observable under serial block-face scanning electron microscopy within 1 day. The serial images obtained are similar to the block-face images acquired by common procedures, and are applicable to three-dimensional reconstructions at a subcellular resolution. Using this approach, regional immune deposits and the double contour or heterogeneous thinning of basement membranes were observed in the glomerular capillary loops of an autoimmune nephropathy model. These modifications provide options to improve the throughput of three-dimensional electron microscopic examinations, and will ultimately be beneficial for the wider application of volume imaging in life science and clinical medicine.

  4. A Novel Imaging Biomarker Extracted from Fluorescence Microscopic Imaging of TRA-8/DR5 Oligomers Predicts TRA-8 Therapeutic Efficacy in Breast and Pancreatic Cancer Mouse Models.

    Science.gov (United States)

    Kim, Harrison; Buchsbaum, Donald J; Zinn, Kurt R

    2016-06-01

    The aim of the study was to develop a reliable quantitative imaging biomarker from fluorescence microscopic imaging of TRA-8/death receptor 5 (DR5) oligomer to predict TRA-8 therapeutic efficacy in human breast and pancreatic cancer mouse models. Two breast (2LMP, SUM159) and two pancreatic (MIA PaCa-2, PANC1) cancer cell lines were used. 10(5) cells per cell line were placed in a culture dish and treated with Cy5.5-labeled TRA-8 overnight in vitro. Three fluorescence microphotographs (×20) were acquired from randomly selected areas, and about 300 cells were analyzed per cell line. Two-dimensional (2D) fluorescence signal distribution of Cy5.5-TRA-8 on each cell was measured. Gaussian curve fitting to the distribution was determined by the least square regression method, and the coefficient of determination (R (2)) of the fitting was found. In addition, two features of the best fitting Gaussian curve such as peak amplitude and the volume under the curve (VUC) were retrieved. A novel image biomarker was extracted by correlating the combination of R (2) value, peak amplitude, and the VUC with the logarithmic values of the half maximal inhibitory concentrations (IC50) of TRA-8 for the four cell lines or the percentage of tumor growth inhibition (%TGI) at a week of TRA-8 treatment in animal models. Cy5.5-TRA-8 binding to DR5 receptors resulted in an oligomer on each cell membrane, and its fluorescence signal distribution followed Gaussian curve. Peak amplitude of fluorescence signal in the oligomeric region, R (2) value of the Gaussian fitting, and the VUC in TRA-8-sensitive cells were significantly higher than those in resistant cells (p TRA-8 may serve as a predictive biomarker of TRA-8 therapy for cancer patients.

  5. Virtual pinhole confocal microscope

    Energy Technology Data Exchange (ETDEWEB)

    George, J.S.; Rector, D.M.; Ranken, D.M. [Los Alamos National Lab., NM (United States). Biophysics Group; Peterson, B. [SciLearn Inc. (United States); Kesteron, J. [VayTech Inc. (United States)

    1999-06-01

    Scanned confocal microscopes enhance imaging capabilities, providing improved contrast and image resolution in 3-D, but existing systems have significant technical shortcomings and are expensive. Researchers at Los Alamos National Laboratory have developed a novel approach--virtual pinhole confocal microscopy--that uses state of the art illumination, detection, and data processing technologies to produce an imager with a number of advantages: reduced cost, faster imaging, improved efficiency and sensitivity, improved reliability and much greater flexibility. Work at Los Alamos demonstrated proof of principle; prototype hardware and software have been used to demonstrate technical feasibility of several implementation strategies. The system uses high performance illumination, patterned in time and space. The authors have built functional confocal imagers using video display technologies (LCD or DLP) and novel scanner based on a micro-lens array. They have developed a prototype system for high performance data acquisition and processing, designed to support realtime confocal imaging. They have developed algorithms to reconstruct confocal images from a time series of spatially sub-sampled images; software development remains an area of active development. These advances allow the collection of high quality confocal images (in fluorescence, reflectance and transmission modes) with equipment that can inexpensively retrofit to existing microscopes. Planned future extensions to these technologies will significantly enhance capabilities for microscopic imaging in a variety of applications, including confocal endoscopy, and confocal spectral imaging.

  6. Luminescence imaging of polymer solar cells: visualization of progressing degradation

    Energy Technology Data Exchange (ETDEWEB)

    Seeland, Marco; Roesch, Roland; Hoppe, Harald [Institute of Physics, Ilmenau University of Technology, Ilmenau (Germany)

    2011-07-01

    We apply luminescence imaging as tool for the non-destructive visualization of degradation processes within bulk heterojunction polymer solar cells. The imaging technique is based on luminescence detection with a highly sensitive silicon-ccd camera and is able to visualize the with time advancing degradation patterns of polymer solar cells. The devices investigated have been aged under defined conditions and were characterized periodically with current-voltage-sweeps. This allows determining the time evolution of the photovoltaic parameters and - in combination with the luminescence images - understanding differences in the observed degradation behaviour. The versatile usability of the method is demonstrated in a correlation between local reduction of lateral luminescence and a fast decrease of the short-circuit-current due to the loss of active area. Differences in the degradation of photovoltaic parameters under varied aging conditions are discussed.

  7. Hyperspectral confocal microscope.

    Science.gov (United States)

    Sinclair, Michael B; Haaland, David M; Timlin, Jerilyn A; Jones, Howland D T

    2006-08-20

    We have developed a new, high performance, hyperspectral microscope for biological and other applications. For each voxel within a three-dimensional specimen, the microscope simultaneously records the emission spectrum from 500 nm to 800 nm, with better than 3 nm spectral resolution. The microscope features a fully confocal design to ensure high spatial resolution and high quality optical sectioning. Optical throughput and detection efficiency are maximized through the use of a custom prism spectrometer and a backside thinned electron multiplying charge coupled device (EMCCD) array. A custom readout mode and synchronization scheme enable 512-point spectra to be recorded at a rate of 8300 spectra per second. In addition, the EMCCD readout mode eliminates curvature and keystone artifacts that often plague spectral imaging systems. The architecture of the new microscope is described in detail, and hyperspectral images from several specimens are presented.

  8. Guideline report. Medical ultrasound imaging: progress and opportunities.

    Science.gov (United States)

    Burns, M

    1989-01-01

    Utilization of medical ultrasound has expanded rapidly during the past several years. In 1988, sales of ultrasound equipment will approach $600 million, which is higher than any other individual imaging modality, including the most capital intensive, such as magnetic resonance imaging (MRI), computed tomography (CT), and cath lab angiography. This growth would have been difficult to predict previously, since ultrasound appeared to be a relatively mature imaging modality not too long ago. There are several reasons for this growth. Technological developments have been quite rapid; ultrasound has become easier to use, image quality has improved dramatically, and diagnostic accuracy has been enhanced. There has been a proliferation of new equipment at all ends of the price spectrum, allowing the user a wide choice in instrument performance, multi-function capabilities, and automated features to increase patient throughput. The DRG environment and the prospect for more pre-admission tests have also been a stimulus. Hospital buying activity has expanded, and many more ultrasound exams are now being conducted on an outpatient basis. Sales to freestanding imaging centers and individual physicians have similarly increased. The hospital user is willing to pay a large premium for advanced technical performance and is prepared to retire or replace older technology in less than three years. This replacement cycle is much shorter than the four to five year period which existed prior to 1985. By comparison, some of the more traditional imaging areas, such as radiology, have replacement rates of eight to ten years. The reason for early replacement is obvious. Ultrasound exams in hospitals generate revenues at a rate that justifies the purchase of the most advanced equipment. It also improves the referral rate and positions the hospital as a high quality provider. Even with low utilization rates, an ultrasound instrument can normally pay for itself in less than one year of regular

  9. Development Progress of the Neutron Imaging Station in CPHS

    Science.gov (United States)

    Xiao, Yongshun; Chen, Zhiqiang; Yang, Yigang; Wang, Xuewu

    The neutron imaging station based on the proton-linac-driven neutron source at CPHS, is presently under construction at Tsinghua University. Itis driven by a high-intensity proton linac (ECR proton source, LEBT, RFQ, DTL and HEBT) with a 13-MeV proton beam and a beryllium target station for neutron production. The facility has achieved its mid-term objective to deliver a 3 MeV proton beam directly from the RFQ output to the neutron target station by the HEBT, with a peak current of 22 mA and a pulse length of 100 μs.In addition the neutron imaging station of the first stage to provide neutron radiography is installed. In this paper, the instrument design and engineering construction status of the neutron imaging station of CPHS is presented, including the preliminary neutron imaging experiments and the results. The beam energy of the CPHS will be enhanced to 13 MeV after the DTL is ready in 2015.

  10. 3D micro-particle image modeling and its application in measurement resolution investigation for visual sensing based axial localization in an optical microscope

    Science.gov (United States)

    Wang, Yuliang; Li, Xiaolai; Bi, Shusheng; Zhu, Xiaofeng; Liu, Jinhua

    2017-01-01

    Visual sensing based three dimensional (3D) particle localization in an optical microscope is important for both fundamental studies and practical applications. Compared with the lateral (X and Y) localization, it is more challenging to achieve a high resolution measurement of axial particle location. In this study, we aim to investigate the effect of different factors on axial measurement resolution through an analytical approach. Analytical models were developed to simulate 3D particle imaging in an optical microscope. A radius vector projection method was applied to convert the simulated particle images into radius vectors. With the obtained radius vectors, a term of axial changing rate was proposed to evaluate the measurement resolution of axial particle localization. Experiments were also conducted for comparison with that obtained through simulation. Moreover, with the proposed method, the effects of particle size on measurement resolution were discussed. The results show that the method provides an efficient approach to investigate the resolution of axial particle localization.

  11. Bioluminescence imaging of estrogen receptor activity during breast cancer progression.

    Science.gov (United States)

    Vantaggiato, Cristina; Dell'Omo, Giulia; Ramachandran, Balaji; Manni, Isabella; Radaelli, Enrico; Scanziani, Eugenio; Piaggio, Giulia; Maggi, Adriana; Ciana, Paolo

    2016-01-01

    Estrogen receptors (ER) are known to play an important regulatory role in mammary gland development as well as in its neoplastic transformation. Although several studies highlighted the contribution of ER signaling in the breast transformation, little is known about the dynamics of ER state of activity during carcinogenesis due to the lack of appropriate models for measuring the extent of receptor signaling in time, in the same animal. To this aim, we have developed a reporter mouse model for the non-invasive in vivo imaging of ER activity: the ERE-Luc reporter mouse. ERE-Luc is a transgenic mouse generated with a firefly luciferase (Luc) reporter gene driven by a minimal promoter containing an estrogen responsive element (ERE). This model allows to measure receptor signaling in longitudinal studies by bioluminescence imaging (BLI). Here, we have induced sporadic mammary cancers by treating systemically ERE-Luc reporter mice with DMBA (9,10-dimethyl 1,2-benzanthracene) and measured receptor signaling by in vivo imaging in individual animals from early stage until a clinically palpable tumor appeared in the mouse breast. We showed that DMBA administration induces an increase of bioluminescence in the whole abdominal area 6 h after treatment, the signal rapidly disappears. Several weeks later, strong bioluminescence is observed in the area corresponding to the mammary glands. In vivo and ex vivo imaging analysis demonstrated that this bioluminescent signal is localized in the breast area undergoing neoplastic transformation. We conclude that this non-invasive assay is a novel relevant tool to identify the activation of the ER signaling prior the morphological detection of the neoplastic transformation.

  12. Spatial calibration of digital scintigraphic images: work in progress

    Energy Technology Data Exchange (ETDEWEB)

    Esser, P.D.; Seldin, D.W.; Nichols, A.B.; Alderson, P.O.

    1982-09-01

    Accurate scintigraphic determination of organ dimensions is often difficult because of the wide variety of camera-collimator combinations and display formats used for imaging. An algorithm (SPACE-CAL) was developed for digital spatial calibration of up to six large- or small-field gamma cameras using various collimators and magnification factors. The algorithm employs a master calibration file that can be used at multiple terminals. An interactive subroutine permits the operator to measure distances and areas directly from the images. Evaluation of three operators' measurements of a pine-tree phantom acquired at various magnifications showed that distances could be measured with a high degree of accuracy. Calculation of ejection fraction from end-diastolic and end-systolic areas determined by SPACE-CAL showed a high correlation with automatic count determinations (r . 0.96) and angiographic calculations (r . 0.93) of ejection fraction in 12 patients. SPACE-CAL provides an easily implemented, reproducible, and rapid method for accurate analysis of organ dimensions in digital images.

  13. The World Under a Microscope

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Olympus sponsors the first national confocal microscopic-image competition The Olympus Cup National Confocal Microscopic-image Competition, the first of its kind in China,lifted its curtain in Beijing on November 1. Olympus (China) Co. Ltd. is the competition’s sole spon-

  14. Two-photon spectral fluorescence lifetime and second-harmonic generation imaging of the porcine cornea with a 12-femtosecond laser microscope

    Science.gov (United States)

    Batista, Ana; Breunig, Hans Georg; Uchugonova, Aisada; Morgado, António Miguel; König, Karsten

    2016-03-01

    Five dimensional microscopy with a 12-fs laser scanning microscope based on spectrally resolved two-photon autofluorescence lifetime and second-harmonic generation (SHG) imaging was used to characterize all layers of the porcine cornea. This setup allowed the simultaneous excitation of both metabolic cofactors, NAD(P)H and flavins, and their discrimination based on their spectral emission properties and fluorescence decay characteristics. Furthermore, the architecture of the stromal collagen fibrils was assessed by SHG imaging in both forward and backward directions. Information on the metabolic state and the tissue architecture of the porcine cornea were obtained with subcellular resolution, and high temporal and spectral resolutions.

  15. Progress Toward A Very High Angular Resolution Imaging Spectrometer (VERIS)

    Science.gov (United States)

    Korendyke, Clarence M.; Vourlidas, A.; Landi, E.; Seely, J.; Klimchuck, J.

    2007-07-01

    Recent imaging at arcsecond (TRACE) and sub-arcsecond (VAULT) spatial resolution clearly show that structures with fine spatial scales play a key role in the physics of the upper solar atmosphere. Both theoretical and observational considerations point to the importance of small spatial scales, impulsive energy release, strong dynamics, and extreme plasma nonuniformity. Fundamental questions regarding the nature, structure, properties and dynamics of loops and filamentary structures in the upper atmosphere have been raised. To address these questions, we are developing a next generation, VEry high angular Resolution Imaging Spectrometer (VERIS) as a sounding rocket instrument. VERIS will obtain the necessary high spatial resolution, high fidelity measurements of plasma temperatures, densities and velocities. With broad simultaneous temperature coverage, the VERIS observations will directly address unresolved issues relating to interconnections of various temperature solar plasmas. VERIS will provide the first ever subarcsecond spectra of transition region and coronal structures. It will do so with a sufficient spectral resolution of to allow centroided Doppler velocity determinations to better than 3 km/s. VERIS uses a novel two element, normal incidence optical design with highly reflective EUV coatings to access a spectral range with broad temperature coverage (0.03-15 MK) and density-sensitive line ratios. Finally, in addition to the spectra, VERIS will simultaneously obtain spectrally pure slot images (10x150 arcsec) in the +/-1 grating orders, which can be combined to make instantaneous line-of-sight velocity maps with 8km/s accuracy over an unprecedented field of view. The VERIS program is beginning the second year of its three year development cycle. All design activities and reviews are complete. Fabrication of all major components has begun. Brassboard electronics cards have been fabricated, assembled and tested. The paper presents the essential scientific

  16. Distinction between amorphous and healed planar deformation features in shocked quartz using composite color scanning electron microscope cathodoluminescence (SEM-CL) imaging

    Science.gov (United States)

    Hamers, Maartje F.; Pennock, Gill M.; Herwegh, Marco; Drury, Martyn R.

    2016-10-01

    Planar deformation features (PDFs) in quartz are one of the most reliable and most widely used forms of evidence for hypervelocity impact. PDFs can be identified in scanning electron microscope cathodoluminescence (SEM-CL) images, but not all PDFs show the same CL behavior: there are nonluminescent and red luminescent PDFs. This study aims to explain the origin of the different CL emissions in PDFs. Focused ion beam (FIB) thin foils were prepared of specific sample locations selected in composite color SEM-CL images and were analyzed in a transmission electron microscope (TEM). The FIB preparation technique allowed a direct, often one-to-one correlation between the CL images and the defect structure observed in TEM. This correlation shows that composite color SEM-CL imaging allows distinction between amorphous PDFs on one hand and healed PDFs and basal Brazil twins on the other: nonluminescent PDFs are amorphous, while healed PDFs and basal Brazil twins are red luminescent, with a dominant emission peak at 650 nm. We suggest that the red luminescence is the result of preferential beam damage along dislocations, fluid inclusions, and twin boundaries. Furthermore, a high-pressure phase (possibly stishovite) in PDFs can be detected in color SEM-CL images by its blue luminescence.

  17. Morphologic MRI features, diffusion tensor imaging and radiation dosimetric analysis to differentiate pseudo-progression from early tumor progression.

    Science.gov (United States)

    Agarwal, Ajay; Kumar, Sanath; Narang, Jayant; Schultz, Lonni; Mikkelsen, Tom; Wang, Sumei; Siddiqui, Sarmad; Poptani, Harish; Jain, Rajan

    2013-05-01

    Pseudo-progression (PsP) refers to the paradoxical increase of contrast enhancement within 12 weeks of chemo-radiation therapy in gliomas attributable to treatment effects rather than early tumor progression (ETP). This study was performed to evaluate the utility of morphologic imaging features, diffusion tensor imaging (DTI) and radiation dosimetric analysis of magnetic resonance imaging (MRI) changes in differentiating PsP from ETP. Serial MRI examinations of 163 patients treated for high-grade glioma were reviewed. 46 patients showed a recurrent or progressive enhancing lesion within 12 weeks of radiotherapy. We used an in-house modified scoring system based on 20 different morphologic features (modified VASARI features) to assess the MRI studies. DTI analyses were performed in 24 patients. MRI changes were defined as recurrent volume (Vrec) and registered with pretreatment computed tomography dataset, and the actual dose received by the Vrec during treatment was calculated using dose-volume histograms. Bidimensional product of T2-FLAIR signal abnormality and enhancing component was larger in the ETP group. DTI metrics revealed no significant difference between the two groups. There was no statistically significant difference in the location of Vrec between PsP and ETP groups. Morphologic MRI features and DTI have a limited role in differentiating between PsP and ETP. The larger sizes of the T2-FLAIR signal abnormality and the enhancing component of the lesion favor ETP. There was no correlation between the pattern of MRI changes and radiation dose distribution between PsP and ETP groups.

  18. Progress on characterization of a dualband IR imaging spectrometer

    Science.gov (United States)

    Beecken, Brian P.; LeVan, Paul D.; Lindh, Cory; Johnson, Randall S.

    2008-04-01

    A dualband infrared focal plane array is the central component of a compact, low mass, multispectral imaging spectrometer with perfect spectral registration. The prototype spectrometer design uses a grating blaze chosen to be efficient over both 3.75-6.05 and 7.5-12.1 μm, although the mercury cadmium telluride focal plane array limits the bandwidths with cutoff wavelengths near 5.2 and 10.5 μm. The spectrometer has been spectrally calibrated with flooded blackbody illumination and offset and gain corrections have been performed. The wavelength resolution is +/-0.024 μm in the MWIR and +/-0.083 μm in the LWIR, however this limitation is caused by the calibration method and not by the design. The potential for determining the temperature of a blackbody or greybody from the ratio of two narrow wavebands has been demonstrated.

  19. Progress in 193-nm top-surface imaging process development

    Science.gov (United States)

    Hutchinson, John M.; Rao, Veena; Zhang, Guojing; Pawloski, Adam R.; Fonseca, Carlos A.; Chambers, Janet; Holl, Susan M.; Das, Siddhartha; Henderson, Craig C.; Wheeler, David R.

    1998-06-01

    The maturity and acceptance of top surface imaging (TSI) technology has been hampered by several factors including inadequate resist sensitivity and silylation contrast, defects and line edge roughness and equipment performance/reliability issues. We found that the use of a chemically amplified resist can improve the sensitivity by a factor of 1.5 - 2X, without compromising line edge roughness. While the post-silylation contrast of this chemically amplified material is poor ((gamma) > 10) and the use of advanced silylation chemistries (disilanes) can further reduce the dose-to-size and increase the contrast. We have also demonstrated that using sulfur dioxide in the plasma etch process can improve the sidewall passivation of the resist lines, thus reducing the overall line edge roughness. Finally, we have been able to successfully use the TSI process to pattern deep sub-micron polysilicon and metal patterns.

  20. Proper alignment of the microscope.

    Science.gov (United States)

    Rottenfusser, Rudi

    2013-01-01

    The light microscope is merely the first element of an imaging system in a research facility. Such a system may include high-speed and/or high-resolution image acquisition capabilities, confocal technologies, and super-resolution methods of various types. Yet more than ever, the proverb "garbage in-garbage out" remains a fact. Image manipulations may be used to conceal a suboptimal microscope setup, but an artifact-free image can only be obtained when the microscope is optimally aligned, both mechanically and optically. Something else is often overlooked in the quest to get the best image out of the microscope: Proper sample preparation! The microscope optics can only do its job when its design criteria are matched to the specimen or vice versa. The specimen itself, the mounting medium, the cover slip, and the type of immersion medium (if applicable) are all part of the total optical makeup. To get the best results out of a microscope, understanding the functions of all of its variable components is important. Only then one knows how to optimize these components for the intended application. Different approaches might be chosen to discuss all of the microscope's components. We decided to follow the light path which starts with the light source and ends at the camera or the eyepieces. To add more transparency to this sequence, the section up to the microscope stage was called the "Illuminating Section", to be followed by the "Imaging Section" which starts with the microscope objective. After understanding the various components, we can start "working with the microscope." To get the best resolution and contrast from the microscope, the practice of "Koehler Illumination" should be understood and followed by every serious microscopist. Step-by-step instructions as well as illustrations of the beam path in an upright and inverted microscope are included in this chapter. A few practical considerations are listed in Section 3. Copyright © 2013 Elsevier Inc. All rights