WorldWideScience

Sample records for hyperspectral microarray scanner

  1. Design, construction, characterization, and application of a hyperspectral microarray scanner.

    Science.gov (United States)

    Sinclair, Michael B; Timlin, Jerilyn A; Haaland, David M; Werner-Washburne, Margaret

    2004-04-01

    We describe the design, construction, and operation of a hyperspectral microarray scanner for functional genomic research. The hyperspectral instrument operates with spatial resolutions ranging from 3 to 30 microm and records the emission spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray. This spectral information, when coupled with multivariate data analysis techniques, allows for identification and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray results presented in this study clearly demonstrate the separation of fluorescent label emission from the spectrally overlapping emission due to the underlying glass substrate. We also demonstrate separation of the emission due to green fluorescent protein expressed by yeast cells from the spectrally overlapping autofluorescence of the yeast cells and the growth media.

  2. Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.

    Energy Technology Data Exchange (ETDEWEB)

    Rohde, Rachel M.; Timlin, Jerilyn Ann

    2005-11-01

    This report summarizes research performed at Sandia National Laboratories (SNL) in collaboration with the Environmental Protection Agency (EPA) to assess microarray quality on arrays from two platforms of interest to the EPA. Custom microarrays from two novel, commercially produced array platforms were imaged with SNL's unique hyperspectral imaging technology and multivariate data analysis was performed to investigate sources of emission on the arrays. No extraneous sources of emission were evident in any of the array areas scanned. This led to the conclusions that either of these array platforms could produce high quality, reliable microarray data for the EPA toxicology programs. Hyperspectral imaging results are presented and recommendations for microarray analyses using these platforms are detailed within the report.

  3. Microarray Scanner for Fluorescence Detection

    Institute of Scientific and Technical Information of China (English)

    Wang Liqiang; Lu zukang; Li Yingsheng; Zheng Xufeng

    2003-01-01

    A novel pseudo confocal microarray scanner is introduced, in which one dimension scanning is performed by a galvanometer optical scanner and a telecentric objective, another dimension scanning is performed by a stepping motor.

  4. Adaptation of Industrial Hyperspectral Line Scanner for Archaeological Applications

    Science.gov (United States)

    Miljković, V.; Gajski, D.

    2016-06-01

    The spectral characteristic of the visible light reflected from any of archaeological artefact is the result of the interaction of its surface illuminated by incident light. Every particular surface depends on what material it is made of and/or which layers put on it has its spectral signature. Recent archaeometry recognises this information as very valuable data to extend present documentation of artefacts and as a new source for scientific exploration. However, the problem is having an appropriate hyperspectral imaging system available and adopted for applications in archaeology. In this paper, we present the new construction of the hyperspectral imaging system, made of industrial hyperspectral line scanner ImSpector V9 and CCD-sensor PixelView. The hyperspectral line scanner is calibrated geometrically, and hyperspectral data are geocoded and converted to the hyperspectral cube. The system abilities are evaluated for various archaeological artefacts made of different materials. Our experience in applications, visualisations, and interpretations of collected hyperspectral data are explored and presented.

  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. Hyper-spectral scanner design and analysis

    Energy Technology Data Exchange (ETDEWEB)

    Canavan, G.; Moses, J.; Smith, R.

    1996-06-01

    This is the final report of a two-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). An earlier project produced rough designs for key components of a compact hyper-spectral sensor for environmental and ecological measurements. Such sensors could be deployed on unmanned vehicles, aircraft, or satellites for measurements important to agriculture, the environment, and ecologies. This represents an important advance in remote sensing. Motorola invited us to propose an add-on, proof-of-principle sensor for their Comet satellite, whose primary mission is to demonstrate a channel of the IRIDIUM satellite communications system. Our project converted the preliminary designs from the previous effort into final designs for the telescope, camera, computer and interfaces that constitute the hyper-spectral scanning sensor. The work concentrated on design, fabrication, preliminary integration, and testing of the electronic circuit boards for the computer, data compression board, and interface board for the camera-computer and computer-modulator (transmitter) interfaces.

  7. Airborne Radiative Transfer Spectral Scanner: A new airborne hyperspectral imager for hyperspectral volcano observations

    Science.gov (United States)

    Jitsufuchi, T.

    2007-12-01

    In 2006, a new airborne hyperspectral imager, the Airborne Radiative Transfer Spectral Scanner (ARTS), was developed for hyperspectral volcano observations. ARTS provides hyperspectral images to support developing algorithms for the remote sensing of the geothermal distribution, the ash fall areas, and the volcanic gasses columnar content from the air. ARTS will be used mainly to assess volcanic activity and to mitigate volcanic disasters. ARTS is a pushbroom imaging spectrometer covering wavelengths from 380 to 2450nm and 8000 to 11500nm with 421 bands. The ARTS imaging spectrometer consists of three sensor head units (SHUs). These SHUs are the visible - near infrared (VNIR) SHU, the shortwave infrared (SWIR) SHU, and the long-wave infrared (LWIR) SHU. These sensor head units operate as a line scanner in the pushbroom mode from an aircraft. The VNIR SHU covers wavelengths from 380 to 1050nm with 288 spectrum bands. The field of view (FOV) is 40 degrees, and the image of this SHU is 1500 pixels wide cross-track, making the instantaneous field of view (IFOV) 0.49mrad. The SWIR SHU covers wavelengths from 900 to 2450nm with 101 spectrum bands. The LWIR SHU covers wavelengths from 8000 to 11500nm with 32 spectrum bands. SWIR SHU and LWIR SHU have FOVs of 40 degrees and 600-pixel-wide images cross-track, giving them an IFOV of 1.2mrad. ARTS has precise position and attitude measurement systems (GPS/IMU). Direct, accurate geo-corrections of each SHU image can be made using the GPS/IMU systems. ARTS will be used for the operational volcano observation beginning in 2008. We are now validating the in-flight performance of this sensor. In this study, we describe the ARTS optical, electrical, and mechanical systems; its data acquisition and system design; and present some preliminary in- flight performance test results obtained from measurements acquired aboard the Beechcraft King Air B200 aircraft. The validation results indicate that the geo-correction accuracy is

  8. Preliminary hyperspectral volcano observations using Airborne Radiative Spectral Scanner (ARTS)

    Science.gov (United States)

    Jitsufuchi, T.

    2008-12-01

    Airborne-imaging spectral systems can often efficiently identify volcanic phenomena that are difficult to detect by satellite imagery. Since 1990, the National Research Institute for Earth Science and Disaster Prevention (NIED) has been developing our original airborne-imaging spectral systems for volcano observations. In 2006, we developed a new airborne hyperspectral sensor, the Airborne Radiative Transfer Spectral Scanner (ARTS), for hyperspectral volcano observations. ARTS is a push-broom imaging spectrometer covering wavelengths from 380 to 1100nm (VNIR; 288 bands), 950 to 2450nm (SWIR; 101 bands), and 8000 to 11500nm (LWIR; 32 bands) and has precise position and attitude measurement systems (GPS/IMU) to achieve direct geo-correction of the acquired image. The ARTS specifications were planned to provide hyperspectral images to support developing algorithms for remotely sensing the geothermal distribution, ash- fall areas, and content of volcanic gas columns. ARTS will also be useful for operational volcanic observations to assess volcanic activity and to mitigate volcanic disasters.Before beginning the operational use of ARTS, it is important to validate its in-flight performance. Therefore, we have been conducting validation on the B200 platform. In this study, we present the results of two experiment observations, the overflight of ARTS instrument at the NIED building site on April 5, 2007, and the volcano observations flight over active volcano (Sakurajima volcano) just after its eruption on April 8, 2008. At the NIED building site, we validated the radiometric fidelity of all bands and the accuracy of geo-corrections. At the Sakurajima volcano, we tried to demonstrate the functions of ARTS, especially those for volcano observation. At the NIED building site, the validation results indicate that the geo-correction accuracy is typically less than a two-pixel difference (RMS), and that there was good agreement between the predicted radiance at the sensor and

  9. Restoration of Hyperspectral Push-Broom Scanner Data

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Nielsen, Allan Aasbjerg; Conradsen, Knut

    1997-01-01

    Several effects combine to distort the multispectral data that are obtained from push-broom scanners. We develop an algorithm for restoration of such data, illustrated on images from the ROSIS scanner. In push-broom scanners variation between elements in the detector array results in a strong...... striping along flight lines. A non-systematic striping is also present along flight lines. Furthermore, line drop-outs occur, and finally, various types of electronic noise of salt-and-pepper type are also present. We describe techniques for the correction for all these types of effects. Line drop...... back into the original spectral space results in noise corrected variables. The noise components will now have been removed from the entire original data set by working on a smaller set of noise contaminated transformed variables only. The application of the above techniques results in a dramatic...

  10. First Use of an Airborne Thermal Infrared Hyperspectral Scanner for Compositional Mapping

    Science.gov (United States)

    Kirkland, Laurel; Herr, Kenneth; Keim, Eric; Adams, Paul; Salisbury, John; Hackwell, John; Treiman, Allan

    2002-01-01

    In May 1999, the airborne thermal infrared hyperspectral imaging system, Spatially Enhanced Broadband Array Spectrograph System (SEBASS), was flown over Mon-non Mesa, NV, to provide the first test of such a system for geological mapping. Several types of carbonate deposits were identified using the 11.25 microns band. However, massive calcrete outcrops exhibited weak spectral contrast, which was confirmed by field and laboratory measurements. Because the weathered calcrete surface appeared relatively smooth in hand specimen, this weak spectral contrast was unexpected. Here we show that microscopic roughness not readily apparent to the eye has introduced both a cavity effect and volume scattering to reduce spectral contrast. The macroroughness of crevices and cobbles may also have a significant cavity effect. The diminished spectral contrast is important because it places higher signal-to-noise ratio (SNR) requirements for spectroscopic detection and identification. This effect should be factored into instrumentation planning and interpretations, especially interpretations without benefit of ground truth. SEBASS had the required high SNR and spectral resolution to allow us to demonstrate for the first time the ability of an airborne hyperspectral thermal infrared scanner to detect and identify spectrally subtle materials.

  11. High-content single-cell analysis on-chip using a laser microarray scanner.

    Science.gov (United States)

    Zhou, Jing; Wu, Yu; Lee, Sang-Kwon; Fan, Rong

    2012-12-07

    High-content cellomic analysis is a powerful tool for rapid screening of cellular responses to extracellular cues and examination of intracellular signal transduction pathways at the single-cell level. In conjunction with microfluidics technology that provides unique advantages in sample processing and precise control of fluid delivery, it holds great potential to transform lab-on-a-chip systems for high-throughput cellular analysis. However, high-content imaging instruments are expensive, sophisticated, and not readily accessible. Herein, we report on a laser scanning cytometry approach that exploits a bench-top microarray scanner as an end-point reader to perform rapid and automated fluorescence imaging of cells cultured on a chip. Using high-content imaging analysis algorithms, we demonstrated multiplexed measurements of morphometric and proteomic parameters from all single cells. Our approach shows the improvement of both sensitivity and dynamic range by two orders of magnitude as compared to conventional epifluorescence microscopy. We applied this technology to high-throughput analysis of mesenchymal stem cells on an extracellular matrix protein array and characterization of heterotypic cell populations. This work demonstrates the feasibility of a laser microarray scanner for high-content cellomic analysis and opens up new opportunities to conduct informative cellular analysis and cell-based screening in the lab-on-a-chip systems.

  12. Hyperspectral microscopic analysis of normal, benign and carcinoma microarray tissue sections

    Science.gov (United States)

    Maggioni, Mauro; Davis, Gustave L.; Warner, Frederick J.; Geshwind, Frank B.; Coppi, Andreas C.; DeVerse, Richard A.; Coifman, Ronald R.

    2006-02-01

    We apply a unique micro-optoelectromechanical tuned light source and new algorithms to the hyper-spectral microscopic analysis of human colon biopsies. The tuned light prototype (Plain Sight Systems Inc.) transmits any combination of light frequencies, range 440nm 700nm, trans-illuminating H and E stained tissue sections of normal (N), benign adenoma (B) and malignant carcinoma (M) colon biopsies, through a Nikon Biophot microscope. Hyper-spectral photomicrographs, randomly collected 400X magnication, are obtained with a CCD camera (Sensovation) from 59 different patient biopsies (20 N, 19 B, 20 M) mounted as a microarray on a single glass slide. The spectra of each pixel are normalized and analyzed to discriminate among tissue features: gland nuclei, gland cytoplasm and lamina propria/lumens. Spectral features permit the automatic extraction of 3298 nuclei with classification as N, B or M. When nuclei are extracted from each of the 59 biopsies the average classification among N, B and M nuclei is 97.1%; classification of the biopsies, based on the average nuclei classification, is 100%. However, when the nuclei are extracted from a subset of biopsies, and the prediction is made on nuclei in the remaining biopsies, there is a marked decrement in performance to 60% across the 3 classes. Similarly the biopsy classification drops to 54%. In spite of these classification differences, which we believe are due to instrument and biopsy normalization issues, hyper-spectral analysis has the potential to achieve diagnostic efficiency needed for objective microscopic diagnosis.

  13. Thermal remote sensing from Airborne Hyperspectral Scanner data in the framework of the SPARC and SEN2FLEX projects: an overview

    NARCIS (Netherlands)

    Sobrino, J.A.; Jimenez-Munoz, J.C.; Zarco-Tejada, P.J.; Sepulcre-Canto, G.; Miguel, de E.; Soria, G.; Romaguera, M.; Julien, Y.; Cuenca, J.; Hidalgo, V.; Franch, B.; Mattar, C.; Morales, L.; Gillespie, A.; Sabol, D.; Balick, L.; Su, Z.; Jia, L.; Gieske, A.; Timmermans, W.; Olioso, A.; Nerry, F.; Guanter, L.; Moreno, J.; Shen, Q.

    2009-01-01

    The AHS (Airborne Hyperspectral Scanner) instrument has 80 spectral bands covering the visible and near infrared (VNIR), short wave infrared (SWIR), mid infrared (MIR) and thermal infrared (TIR) spectral range. The instrument is operated by Instituto Nacional de T,cnica Aerospacial (INTA), and it ha

  14. Detection of analyte binding to microarrays using gold nanoparticle labels and a desktop scanner

    DEFF Research Database (Denmark)

    Han, Anpan; Dufva, Martin; Belleville, Erik

    2003-01-01

    Microarray hybridization or antibody binding can be detected by many techniques, however, only a few are suitable for widespread use since many of these detection techniques rely on bulky and expensive instruments. Here, we describe the usefulness of a simple and inexpensive detection method base...

  15. Thin-bedded reservoir analogs in an ancient delta using terrestrial laser scanner and high-resolution ground-based hyperspectral cameras

    Science.gov (United States)

    Snyder, Casey J.; Khan, Shuhab D.; Bhattacharya, Janok P.; Glennie, Craig; Seepersad, Darsel

    2016-08-01

    Ground-based terrestrial laser scanning and hyperspectral sensors were used to image fine-scale heterogeneity in outcrops of prodeltaic heterolithic facies of Parasequence 6 of the Cretaceous Ferron Notom delta in Southern Utah. Previous work shows that Parasequence 6 is an upward coarsening fluvial-dominated, wave-influenced deltaic deposit containing heterolithic thin-bedded facies representing distal delta front and proximal prodelta environments. Primarily, the thin beds have been interpreted as turbidites, storm beds (tempestites), and hyperpycnites. These deposits represent analogs for thin-bedded unconventional pay zones that lie at the margins of conventional deltaic sandstone reservoirs. The terrestrial laser scanner was used to create a centimeter- to decimeter-scale, digital representation of the outcrops in three dimensions. Hyperspectral sensors record electromagnetic radiation reflected off the outcrops in 840 contiguous bands, which were then used to generate a spectral signature for each pixel sampled. The spectral signatures are a function of mineralogy, chemistry, surface alteration, grain-size, and cements, and were used to distinguish thin mudstones from sandstones within an interbedded succession at the base of a deltaic parasequence. Comparison between the spectral signatures recorded from the outcrop and those of reference materials, and with previous facies architecture studies, enables lithofacies to be identified and subsequently accurately mapped. Hyperspectral data are then draped over the terrestrial laser scanner model to generate a spatially-accurate detailed three-dimensional (3D) geologic map of the heterogeneity. Approximately 100 m of outcrop was imaged laterally with the hyperspectral camera and terrestrial laser scanner on the previously mapped distal delta front and prodeltaic facies of Parasequence 6. Bed thickness data, based on measurements made along depositional dip versus strike, show that bed geometries are anisotropic

  16. Thermal remote sensing from Airborne Hyperspectral Scanner data in the framework of the SPARC and SEN2FLEX projects: an overview

    Directory of Open Access Journals (Sweden)

    J. A. Sobrino

    2009-06-01

    Full Text Available The AHS (Airborne Hyperspectral Scanner instrument has 80 spectral bands covering the visible and near infrared (VNIR, short wave infrared (SWIR, mid infrared (MIR and thermal infrared (TIR spectral range. The instrument is operated by Instituto Nacional de Técnica Aerospacial (INTA, and it has been involved in several field campaigns since 2004.

    This paper presents an overview of the work performed with the AHS thermal imagery provided in the framework of the SPARC and SEN2FLEX campaigns, carried out respectively in 2004 and 2005 over an agricultural area in Spain. The data collected in both campaigns allowed for the first time the development and testing of algorithms for land surface temperature and emissivity retrieval as well as the estimation of evapotranspiration from AHS data. Errors were found to be around 1.5 K for land surface temperature and 1 mm/day for evapotranspiration.

  17. Thermal remote sensing from Airborne Hyperspectral Scanner data in the framework of the SPARC and SEN2FLEX projects: an overview

    Directory of Open Access Journals (Sweden)

    Q. Shen

    2009-11-01

    Full Text Available The AHS (Airborne Hyperspectral Scanner instrument has 80 spectral bands covering the visible and near infrared (VNIR, short wave infrared (SWIR, mid infrared (MIR and thermal infrared (TIR spectral range. The instrument is operated by Instituto Nacional de Técnica Aerospacial (INTA, and it has been involved in several field campaigns since 2004.

    This paper presents an overview of the work performed with the AHS thermal imagery provided in the framework of the SPARC and SEN2FLEX campaigns, carried out respectively in 2004 and 2005 over an agricultural area in Spain. The data collected in both campaigns allowed for the first time the development and testing of algorithms for land surface temperature and emissivity retrieval as well as the estimation of evapotranspiration from AHS data. Errors were found to be around 1.5 K for land surface temperature and 1 mm/day for evapotranspiration.

  18. Scanner calibration revisited.

    Science.gov (United States)

    Pozhitkov, Alexander E

    2010-07-01

    Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (BMC Bioinformatics, 2005, 6, Art. No. S11 Suppl. 2.) reported usage of a Full Moon BioSystems slide for calibration. Inspired by the Shi et al. work, we have calibrated microarray scanners in our previous research. We were puzzled however, that most of the signal intensities from a biological sample fell below the sensitivity threshold level determined by the calibration slide. This conundrum led us to re-investigate the quality of calibration provided by the Full Moon BioSystems slide as well as the accuracy of the analysis performed by Shi et al. Signal intensities were recorded on three different microarray scanners at various photomultiplier gain levels using the same calibration slide from Full Moon BioSystems. Data analysis was conducted on raw signal intensities without normalization or transformation of any kind. Weighted least-squares method was used to fit the data. We found that initial analysis performed by Shi et al. did not take into account autofluorescence of the Full Moon BioSystems slide, which led to a grossly distorted microarray scanner response. Our analysis revealed that a power-law function, which is explicitly accounting for the slide autofluorescence, perfectly described a relationship between signal intensities and fluorophore quantities. Microarray scanners respond in a much less distorted fashion than was reported by Shi et al. Full Moon BioSystems calibration slides are inadequate for performing calibration. We recommend against using these slides.

  19. Scanner calibration revisited

    Directory of Open Access Journals (Sweden)

    Pozhitkov Alexander E

    2010-07-01

    Full Text Available Abstract Background Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (BMC Bioinformatics, 2005, 6, Art. No. S11 Suppl. 2. reported usage of a Full Moon BioSystems slide for calibration. Inspired by the Shi et al. work, we have calibrated microarray scanners in our previous research. We were puzzled however, that most of the signal intensities from a biological sample fell below the sensitivity threshold level determined by the calibration slide. This conundrum led us to re-investigate the quality of calibration provided by the Full Moon BioSystems slide as well as the accuracy of the analysis performed by Shi et al. Methods Signal intensities were recorded on three different microarray scanners at various photomultiplier gain levels using the same calibration slide from Full Moon BioSystems. Data analysis was conducted on raw signal intensities without normalization or transformation of any kind. Weighted least-squares method was used to fit the data. Results We found that initial analysis performed by Shi et al. did not take into account autofluorescence of the Full Moon BioSystems slide, which led to a grossly distorted microarray scanner response. Our analysis revealed that a power-law function, which is explicitly accounting for the slide autofluorescence, perfectly described a relationship between signal intensities and fluorophore quantities. Conclusions Microarray scanners respond in a much less distorted fashion than was reported by Shi et al. Full Moon BioSystems calibration slides are inadequate for performing calibration. We recommend against using these slides.

  20. Hyperspectral Systems Increase Imaging Capabilities

    Science.gov (United States)

    2010-01-01

    In 1983, NASA started developing hyperspectral systems to image in the ultraviolet and infrared wavelengths. In 2001, the first on-orbit hyperspectral imager, Hyperion, was launched aboard the Earth Observing-1 spacecraft. Based on the hyperspectral imaging sensors used in Earth observation satellites, Stennis Space Center engineers and Institute for Technology Development researchers collaborated on a new design that was smaller and used an improved scanner. Featured in Spinoff 2007, the technology is now exclusively licensed by Themis Vision Systems LLC, of Richmond, Virginia, and is widely used in medical and life sciences, defense and security, forensics, and microscopy.

  1. Using Visible Spectral Information to Predict Long-Wave Infrared Spectral Emissivity: A Case Study over the Sokolov Area of the Czech Republic with an Airborne Hyperspectral Scanner Sensor

    Directory of Open Access Journals (Sweden)

    Gila Notesco

    2013-11-01

    Full Text Available Remote-sensing platforms are often comprised of a cluster of different spectral range detectors or sensors to benefit from the spectral identification capabilities of each range. Missing data from these platforms, caused by problematic weather conditions, such as clouds, sensor failure, low temporal coverage or a narrow field of view (FOV, is one of the problems preventing proper monitoring of the Earth. One of the possible solutions is predicting a detector or sensor’s missing data using another detector/sensor. In this paper, we propose a new method of predicting spectral emissivity in the long-wave infrared (LWIR spectral region using the visible (VIS spectral region. The proposed method is suitable for two main scenarios of missing data: sensor malfunctions and narrow FOV. We demonstrate the usefulness and limitations of this prediction scheme using the airborne hyperspectral scanner (AHS sensor, which consists of both VIS and LWIR spectral regions, in a case study over the Sokolov area, Czech Republic.

  2. Kinetic identification of protein ligands in a 51,200 small-molecule library using microarrays and a label-free ellipsometric scanner

    Science.gov (United States)

    Landry, James P.; Proudian, Andrew P.; Malovichko, Galina; Zhu, Xiangdong

    2013-02-01

    Drug discovery begins by identifying protein-small molecule binding pairs. Afterwards, binding kinetics and biofunctional assays are performed, to reduce candidates for further development. High-throughput screening, typically employing fluorescence, is widely used to find protein ligands in small-molecule libraries, but is rarely used for binding kinetics measurement because: (1) attaching fluorophores to proteins can alter kinetics and (2) most label-free technologies for kinetics measurement are inherently low-throughput and consume expensive sensing surfaces. We addressed this need with polarization-modulated ellipsometric scanning microscopes, called oblique-incidence reflectivity difference (OI-RD). Label-free ligand screening and kinetics measurement are performed simultaneously on small-molecule microarrays printed on relatively inexpensive isocyanate-functionalized glass slides. As a microarray is reacted, an OI-RD microscope tracks the change in surface-bound macromolecule density in real-time at every spot. We report progress applying OI-RD to screen purified proteins and virus particles against a 51,200-compound library from the National Cancer Institute. Four microarrays, each containing 12,800 library compounds, are installed in four flow cells in an automated OI-RD microscope. The slides are reacted serially, each giving 12,800 binding curves with ~30 sec time resolution. The entire library is kinetically screened against a single probe in ~14 hours and multiple probes can be reacted sequentially under automation. Real-time binding detection identifies both high-affinity and low-affinity (transient binding) interactions; fluorescence endpoint images miss the latter. OI-RD and microarrays together is a powerful high-throughput tool for early stage drug discovery and development. The platform also has great potential for downstream steps such as in vitro inhibition assays.

  3. Scanner Art

    Science.gov (United States)

    Jaworski, Joy; Murphy, Kris

    2009-01-01

    In this article, the authors describe how they incorporated environmental awareness into their art curriculum. Here, they describe a digital photography project in which their students used flatbed scanners as cameras. Their students composed their objects directly on the scanner. The lesson enabled students to realize that artists have voices…

  4. Multipurpose Hyperspectral Imaging System

    Science.gov (United States)

    Mao, Chengye; Smith, David; Lanoue, Mark A.; Poole, Gavin H.; Heitschmidt, Jerry; Martinez, Luis; Windham, William A.; Lawrence, Kurt C.; Park, Bosoon

    2005-01-01

    A hyperspectral imaging system of high spectral and spatial resolution that incorporates several innovative features has been developed to incorporate a focal plane scanner (U.S. Patent 6,166,373). This feature enables the system to be used for both airborne/spaceborne and laboratory hyperspectral imaging with or without relative movement of the imaging system, and it can be used to scan a target of any size as long as the target can be imaged at the focal plane; for example, automated inspection of food items and identification of single-celled organisms. The spectral resolution of this system is greater than that of prior terrestrial multispectral imaging systems. Moreover, unlike prior high-spectral resolution airborne and spaceborne hyperspectral imaging systems, this system does not rely on relative movement of the target and the imaging system to sweep an imaging line across a scene. This compact system (see figure) consists of a front objective mounted at a translation stage with a motorized actuator, and a line-slit imaging spectrograph mounted within a rotary assembly with a rear adaptor to a charged-coupled-device (CCD) camera. Push-broom scanning is carried out by the motorized actuator which can be controlled either manually by an operator or automatically by a computer to drive the line-slit across an image at a focal plane of the front objective. To reduce the cost, the system has been designed to integrate as many as possible off-the-shelf components including the CCD camera and spectrograph. The system has achieved high spectral and spatial resolutions by using a high-quality CCD camera, spectrograph, and front objective lens. Fixtures for attachment of the system to a microscope (U.S. Patent 6,495,818 B1) make it possible to acquire multispectral images of single cells and other microscopic objects.

  5. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola;

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technol...

  6. Was the Scanner Calibration Slide used for its intended purpose?

    Science.gov (United States)

    2011-01-01

    In the article, Scanner calibration revisited, BMC Bioinformatics 2010, 11:361, Dr. Pozhitkov used the Scanner Calibration Slide, a key product of Full Moon BioSystems to generate data in his study of microarray scanner PMT response and proposed a mathematic model for PMT response [1]. In the end, the author concluded that "Full Moon BioSystems calibration slides are inadequate for performing calibration," and recommended "against using these slides." We found these conclusions are seriously flawed and misleading, and his recommendation against using the Scanner Calibration Slide was not properly supported. PMID:21510874

  7. Was the Scanner Calibration Slide used for its intended purpose?

    Directory of Open Access Journals (Sweden)

    Zong Yaping

    2011-04-01

    Full Text Available Abstract In the article, Scanner calibration revisited, BMC Bioinformatics 2010, 11:361, Dr. Pozhitkov used the Scanner Calibration Slide, a key product of Full Moon BioSystems to generate data in his study of microarray scanner PMT response and proposed a mathematic model for PMT response 1. In the end, the author concluded that "Full Moon BioSystems calibration slides are inadequate for performing calibration," and recommended "against using these slides." We found these conclusions are seriously flawed and misleading, and his recommendation against using the Scanner Calibration Slide was not properly supported.

  8. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

    2012-01-01

    -based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research.......In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...

  9. Hyperspectral remote sensing

    CERN Document Server

    Eismann, Michael

    2012-01-01

    Hyperspectral remote sensing is an emerging, multidisciplinary field with diverse applications that builds on the principles of material spectroscopy, radiative transfer, imaging spectrometry, and hyperspectral data processing. This book provides a holistic treatment that captures its multidisciplinary nature, emphasizing the physical principles of hyperspectral remote sensing.

  10. Hyperspectral image processing methods

    Science.gov (United States)

    Hyperspectral image processing refers to the use of computer algorithms to extract, store and manipulate both spatial and spectral information contained in hyperspectral images across the visible and near-infrared portion of the electromagnetic spectrum. A typical hyperspectral image processing work...

  11. Network Security Scanner

    OpenAIRE

    2011-01-01

    Network Security Scanner (NSS) is a tool that allows auditing and monitoring remote network computers for possible vulnerabilities, checks your network for all potential methods that a hacker might use to attack it. Network Security Scanner is a complete networking utilities package that includes a wide range of tools for network security auditing, vulnerability Auditing, scanning, monitoring and more. Network Security Scanner (NSS) is an easy to use, intuitive network security scanner that c...

  12. The Impact of Photobleaching on Microarray Analysis

    Directory of Open Access Journals (Sweden)

    Marcel von der Haar

    2015-09-01

    Full Text Available DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner’s laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube’s voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results.

  13. Denoising Of Hyperspectral Image

    Directory of Open Access Journals (Sweden)

    Ashumati Dhuppe

    2014-05-01

    Full Text Available The amount of noise included in a Hyperspectral images limits its application and has a negative impact on Hyperspectral image classification, unmixing, target detection, so on. Hyperspectral imaging (HSI systems can acquire both spectral and spatial information of ground surface simultaneously and have been used in a variety of applications such as object detection, material identification, land cover classification etc. In Hyperspectral images, because the noise intensity in different bands is different, to better suppress the noise in the high noise intensity bands & preserve the detailed information in the low noise intensity bands, the denoising strength should be adaptively adjusted with noise intensity in different bands. We propose a Hyperspectral image denoising algorithms employing a spectral spatial adaptive total variation (TV model, in which the spectral noise difference & spatial information differences are both considered in the process of noise reduction.

  14. Colorimetric Scanner Characterisation

    Directory of Open Access Journals (Sweden)

    Jon Y. Hardeberg

    2003-12-01

    Full Text Available In this paper, methods for the colorimetric characterisation of colour scanners are proposed and evaluated. These methods apply equally to other colour image input devices such as digital cameras. The goal of our characterisation is to establish the relationship between the device-dependent colour space of the scanner and the device-independent CIELAB colour space. The scanner characterisation is based on polynomial regression techniques. Several regression schemes have been tested. The retained method consists in applying a non-linear correction to the scanner RGB values followed by a 3rd order 3D polynomial regression function directly to CIELAB space. This method gives very good results in terms of residual colour differences. This is partly due to the fact that the RMS error that is minimised in the regression corresponds to ΔE*ab which is well correlated to visual colour differences.

  15. Twisting wire scanner

    CERN Document Server

    Gharibyan, V; Krouptchenkov, I; Nölle, D; Tiessen, H; Werner, M; Wittenburg, K

    2012-01-01

    A new type of 'two-in-one' wire scanner is proposed. Recent advances in linear motors' technology make it possible to combine translational and rotational movements. This will allow to scan the beam in two perpendicular directions using a single driving motor and a special fork attached to it. Vertical or horizontal mounting will help to escape problems associated with the 45 deg scanners. Test results of the translational part with linear motors is presented.

  16. Hyperspectral pansharpening: a review

    CERN Document Server

    Loncan, Laetitia; Bioucas-Dias, José M; Briottet, Xavier; Chanussot, Jocelyn; Dobigeon, Nicolas; Fabre, Sophie; Liao, Wenzhi; Licciardi, Giorgio A; Simões, Miguel; Tourneret, Jean-Yves; Veganzones, Miguel A; Vivone, Gemine; Wei, Qi; Yokoya, Naoto

    2015-01-01

    Pansharpening aims at fusing a panchromatic image with a multispectral one, to generate an image with the high spatial resolution of the former and the high spectral resolution of the latter. In the last decade, many algorithms have been presented in the literature for pansharpening using multispectral data. With the increasing availability of hyperspectral systems, these methods are now being adapted to hyperspectral images. In this work, we compare new pansharpening techniques designed for hyperspectral data with some of the state of the art methods for multispectral pansharpening, which have been adapted for hyperspectral data. Eleven methods from different classes (component substitution, multiresolution analysis, hybrid, Bayesian and matrix factorization) are analyzed. These methods are applied to three datasets and their effectiveness and robustness are evaluated with widely used performance indicators. In addition, all the pansharpening techniques considered in this paper have been implemented in a MAT...

  17. Cobalt-60 Container Scanner

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    This paper presents a special container scanner in which the radiation source is a conventional radiography 60Co projector of (100-300)×3 .7×1010Bq. With a specia l sensitive array detector, invented by Institute of Nuclear Energy Technology ( INET) of Tsinghua University and other technical innovations, t he characteristics of the 60Co scanner qualify it for use in c ontainer insp ection. Its contrast indicator (CI) and image quality indicator (IQI) for 10 0 mm steel are equal to 0.7% and 2.5%, respectively, and the steel penetration ( SP) is about 240 mm. The 60Co container scanner is much more ec onomical and more reliable than those scanners using an accelerator source. Also, its penetr ation ability is much better than that of an X-ray machine scanner. This paper p resents the system design, the main difficulties and their technical solutions, the inspection characteristics and the special features of the 60Co sc anner.

  18. Portable biochip scanner device

    Energy Technology Data Exchange (ETDEWEB)

    Perov, Alexander (Troitsk, RU); Sharonov, Alexei (Moscow, RU); Mirzabekov, Andrei D. (Darien, IL)

    2002-01-01

    A portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips) is provided. The portable biochip scanner device employs a laser for emitting an excitation beam. An optical fiber delivers the laser beam to a portable biochip scanner. A lens collimates the laser beam, the collimated laser beam is deflected by a dichroic mirror and focused by an objective lens onto a biochip. The fluorescence light from the biochip is collected and collimated by the objective lens. The fluorescence light is delivered to a photomultiplier tube (PMT) via an emission filter and a focusing lens. The focusing lens focuses the fluorescence light into a pinhole. A signal output of the PMT is processed and displayed.

  19. Biochip scanner device

    Energy Technology Data Exchange (ETDEWEB)

    Perov, Alexander (Troitsk, RU); Belgovskiy, Alexander I. (Mayfield Heights, OH); Mirzabekov, Andrei D. (Darien, IL)

    2001-01-01

    A biochip scanner device used to detect and acquire fluorescence signal data from biological microchips or biochips and method of use are provided. The biochip scanner device includes a laser for emitting a laser beam. A modulator, such as an optical chopper modulates the laser beam. A scanning head receives the modulated laser beam and a scanning mechanics coupled to the scanning head moves the scanning head relative to the biochip. An optical fiber delivers the modulated laser beam to the scanning head. The scanning head collects the fluorescence light from the biochip, launches it into the same optical fiber, which delivers the fluorescence into a photodetector, such as a photodiode. The biochip scanner device is used in a row scanning method to scan selected rows of the biochip with the laser beam size matching the size of the immobilization site.

  20. Surface characterization of carbohydrate microarrays.

    Science.gov (United States)

    Scurr, David J; Horlacher, Tim; Oberli, Matthias A; Werz, Daniel B; Kroeck, Lenz; Bufali, Simone; Seeberger, Peter H; Shard, Alexander G; Alexander, Morgan R

    2010-11-16

    Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.

  1. Ionization beam scanner

    CERN Multimedia

    CERN PhotoLab

    1973-01-01

    Inner structure of an ionization beam scanner, a rather intricate piece of apparatus which permits one to measure the density distribution of the proton beam passing through it. On the outside of the tank wall there is the coil for the longitudinal magnetic field, on the inside, one can see the arrangement of electrodes creating a highly homogeneous transverse electric field.

  2. Rapid and quantitative quality control of microarrays using cationic nanoparticles.

    Science.gov (United States)

    Sun, Ye; Fan, Wenhua; McCann, Michael P; Golovlev, Val

    2009-02-15

    The fabrication quality of microarrays significantly influences the accuracy and reproducibility of microarray experiments. In this report, we present a simple and fast quality control (QC) method for spotted oligonucleotide and cDNA microarrays. It employs a nonspecific electrostatic interaction of colloidal gold nanoparticles with the chemical groups of DNA molecules and other biomolecules immobilized on the microarray surface that bear positive or negative charges. An inexpensive flatbed scanner is used to visualize and quantify the binding of cationic gold particles to the anionic DNA probes on the microarray surface. An image analysis software was designed to assess the various parameters of the array spots including spot intensity, shape and array homogeneity, calculate the overall array quality score, and save the detailed array quality report in an Excel file. The gold staining technique is fast and sensitive. It can be completed in 10 min and detect less than 1% of the probe amount commonly recommended for microarrays. Compared to the current microarray QC method that utilizes the hybridization of probes with short random sequence oligonucleotides labeled with fluorophore, our gold staining method requires less time for the analysis, reduces the reagent cost, and eliminates the need for the expensive laser scanner.

  3. Near-infrared hyperspectral reflective confocal microscopy

    Science.gov (United States)

    Huang, Wei; Zhang, Yunhai; Miao, Xin; Xue, Xiaojun; Xiao, Yun

    2016-10-01

    A Near-Infrared HyperSpectral Reflective Confocal Microscopy (NIHS-RCM) is proposed in order to get high resolution images of deep biological tissues such as skin. The microscopy system uses a super-continuum laser for illumination, an acousto-optic tunable filter (AOTF) for rapid selection of near-infrared spectrum, a resonant galvanometer scanner for high speed imaging (15f/s) and near-infrared avalanche diode as detector. Porcine skin and other experiments show that the microscopy system could get deep tissue images (180 μm), and show the different ingredients of tissue with different wavelength of illumination. The system has the ability of selectively imaging of multiple ingredients at deep tissue which can be used in skin diseases diagnosis and other fields.

  4. Hyperspectral remote sensing for light pollution monitoring

    Directory of Open Access Journals (Sweden)

    P. Marcoionni

    2006-06-01

    Full Text Available industries. In this paper we introduce the results from a remote sensing campaign performed in September 2001 at night time. For the first time nocturnal light pollution was measured at high spatial and spectral resolution using two airborne hyperspectral sensors, namely the Multispectral Infrared and Visible Imaging Spectrometer (MIVIS and the Visible InfraRed Scanner (VIRS-200. These imagers, generally employed for day-time Earth remote sensing, were flown over the Tuscany coast (Italy on board of a Casa 212/200 airplane from an altitude of 1.5-2.0 km. We describe the experimental activities which preceded the remote sensing campaign, the optimization of sensor configuration, and the images as far acquired. The obtained results point out the novelty of the performed measurements and highlight the need to employ advanced remote sensing techniques as a spectroscopic tool for light pollution monitoring.

  5. Hyperspectral imaging system for whole corn ear surface inspection

    Science.gov (United States)

    Yao, Haibo; Kincaid, Russell; Hruska, Zuzana; Brown, Robert L.; Bhatnagar, Deepak; Cleveland, Thomas E.

    2013-05-01

    Aflatoxin is a mycotoxin produced mainly by Aspergillus flavus (A.flavus) and Aspergillus parasitiucus fungi that grow naturally in corn. Very serious health problems such as liver damage and lung cancer can result from exposure to high toxin levels in grain. Consequently, many countries have established strict guidelines for permissible levels in consumables. Conventional chemical-based analytical methods used to screen for aflatoxin such as thin-layer chromatography (TLC) and high performance liquid chromatography (HPLC) are time consuming, expensive, and require the destruction of samples as well as proper training for data interpretation. Thus, it has been a continuing effort within the research community to find a way to rapidly and non-destructively detect and possibly quantify aflatoxin contamination in corn. One of the more recent developments in this area is the use of spectral technology. Specifically, fluorescence hyperspectral imaging offers a potential rapid, and non-invasive method for contamination detection in corn infected with toxigenic A.flavus spores. The current hyperspectral image system is designed for scanning flat surfaces, which is suitable for imaging single or a group of corn kernels. In the case of a whole corn cob, it is preferred to be able to scan the circumference of the corn ear, appropriate for whole ear inspection. This paper discusses the development of a hyperspectral imaging system for whole corn ear imaging. The new instrument is based on a hyperspectral line scanner using a rotational stage to turn the corn ear.

  6. Hyperspectral image processing

    CERN Document Server

    Wang, Liguo

    2016-01-01

    Based on the authors’ research, this book introduces the main processing techniques in hyperspectral imaging. In this context, SVM-based classification, distance comparison-based endmember extraction, SVM-based spectral unmixing, spatial attraction model-based sub-pixel mapping, and MAP/POCS-based super-resolution reconstruction are discussed in depth. Readers will gain a comprehensive understanding of these cutting-edge hyperspectral imaging techniques. Researchers and graduate students in fields such as remote sensing, surveying and mapping, geosciences and information systems will benefit from this valuable resource.

  7. Microarrays, Integrated Analytical Systems

    Science.gov (United States)

    Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

  8. Learnable hyperspectral measures

    Directory of Open Access Journals (Sweden)

    A. Galal

    2012-07-01

    Full Text Available Hyperspectral measures are used to capture the degree of similarity between two spectra. Spectral Angle Mapper (SAM is an example of such measures. SAM similarity values range from 0 to 1. These values do not indicate whether the two spectra are similar or not. A static similarity threshold is imposed to recognize similar and dissimilar spectra. Adjusting such threshold is a troublesome process. To overcome this problem, the proposed approach aims to develop learnable hyperspectral measures. This is done through using hyperspectral measures values as similarity patterns and employing a classifier. The classifier acts as an adaptive similarity threshold. The derived similarity patterns are flexible as they are able to capture the specific notion of similarity that is appropriate for each spectral region. Two similarity patterns are proposed. The first pattern is the cosine similarity vector for the second spectral derivative pair. The second pattern is a composite vector of different similarity measures values. The proposed approach is applied on full hyperspectral space and subspaces. Experiments were conducted on a challenging benchmark dataset. Experimental results showed that, classifications based on second patterns were far better than first patterns. This is because first patterns were concerned only with the geometrical features of the spectral signatures, while second patterns combined various discriminatory features such as: orthogonal projections information, correlation coefficients, and probability distributions produced by the spectral signatures. The proposed approach results are statistically significant. This implies that using simple learnable measures overcomes complex and manually tuned techniques used in classification tasks.

  9. HYBASE : HYperspectral BAnd SElection

    NARCIS (Netherlands)

    Schwering, P.B.W.; Bekman, H.H.P.T.; Seijen, H.H. van

    2009-01-01

    Band selection is essential in the design of multispectral sensor systems. This paper describes the TNO hyperspectral band selection tool HYBASE. It calculates the optimum band positions given the number of bands and the width of the spectral bands. HYBASE is used to assess the minimum number of spe

  10. Hyperspectral data compression

    CERN Document Server

    Motta, Giovanni; Storer, James A

    2006-01-01

    Provides a survey of results in the field of compression of remote sensed 3D data, with a particular interest in hyperspectral imagery. This work covers topics such as compression architecture, lossless compression, lossy techniques, and more. It also describes a lossless algorithm based on vector quantization.

  11. Hyperspectral holographic Fourier-microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kalenkov, G S [Moscow Institute of Physics and Technology (State University), Moscow (Russian Federation); Kalenkov, S G [Moscow State University of Mechanical Engineering, Moscow (Russian Federation); Shtan' ko, A E [Moscow State University of Technology ' Stankin' , Moscow (Russian Federation)

    2015-04-30

    A detailed theory of the method of holographic recording of hyperspectral wave fields is developed. New experimentally obtained hyperspectral holographic images of microscopic objects are presented. The possibilities of the method are demonstrated experimentally using the examples of urgent microscopy problems: speckle noise suppression, obtaining hyperspectral image of a microscopic object, as well as synthesis of a colour image and obtaining an optical profile of a phase object. (holography)

  12. HYPERSPECTRAL ANALYSIS OF RICE PHENOLOGICAL STAGES IN NORTHEAST CHINA

    Directory of Open Access Journals (Sweden)

    M. L. Gnyp

    2012-07-01

    Full Text Available The objective of this contribution is to monitor rice (Oryza sativa L., irrigated lowland rice growth with multitemporal hyperspectral data during different phenological stages in Northeast China (Sanjiang Plain. Multitemporal hyperspectral data were measured with field spectroradiometers (ASD Inc.: QualitySpec and FieldSpec3 for two field experiments and nine farmers' fields. The field measurements were carried out together with corresponding measurements of agronomic data (aboveground biomass [AGB], Leaf Area Index [LAI], number of tillers. Eight selected standard hyperspectral vegetation indices (VIs, proved in several studies to be highly correlated with AGB or LAI, were calculated on the measured experimental field data. Additionally, the best two-band combinations for the Normalized Ratio Index (NRI were determined. The results indicate that the NRI performed better than the selected standard VIs at the stages of stem elongation, booting and heading and also across all stages. Especially during the stem elongation stage (R2 = 0.76 and across all stages (R2 = 0.70, the NRI performed best. When applying the NRI on the farmers' field data, the performance was lower (R2 < 0.60. Overall, the sensitive individual wavelengths (±10 nm for the best two-band combinations were detected at 711 and 799 nm (for tillering stage, 1575 and 1678 nm (for stem elongation stage, 515 and 695 nm (for booting stage, and 533 and 713 nm (for all stages. The results suggest that hyperspectral-based methods can estimate paddy rice AGB with a satisfying accuracy. In the context of precision agriculture, the findings are useful for future development of new hyperspectral devices such as scanners or cameras which could be fixed on tractors or unmanned aerial vehicles (UAVs.

  13. Improved hyperspectral imaging technologies Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Improved hyperspectral imaging technologies could enable lower-cost analysis for planetary science including atmospheric studies, mineralogical investigations, and...

  14. Signal stability of Cy3 and Cy5 on antibody microarrays

    Directory of Open Access Journals (Sweden)

    Kim Caroline

    2006-10-01

    Full Text Available Abstract Background The antibody microarray technique is a newly emerging proteomics tool for differential protein expression analyses that uses fluorescent dyes Cy 3 and Cy 5. Environmental factors, such as light exposure, can affect the signal intensity of fluorescent dyes on microarray slides thus, it is logical to scan microarray slides immediately after the final wash and drying processes. However, no research data are available concerning time-dependent changes of fluorescent signals on antibody microarray slides to this date. In the present study, microarray slides were preserved at -20°C after regular microarray experiments and were rescanned at day 10, 20 and 30 to evaluate change in signal intensity. Results Fluorescent intensities of microarray spots were detected using a confocal laser scanner after the experiment at day 0, and re-examined at day 10, 20 and 30, respectively. Fluorescent intensities of rescanned microarray spots did not show significant changes when compared with those scanned immediately after standard microarray experiments. Conclusion Microarray slides can be preserved and rescanned multiple times using a confocal laser scanner over a period of days or weeks.

  15. Plasmonically amplified fluorescence bioassay with microarray format

    Science.gov (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  16. 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.

  17. Laser Scanner Demonstration

    Energy Technology Data Exchange (ETDEWEB)

    Fuss, B.

    2005-09-06

    In the Summer of 2004 a request for proposals went out to potential vendors to offer a three-dimensional laser scanner for a number of unique metrology tasks at the Stanford Linear Accelerator Center (SLAC). Specifications were established including range, accuracy, scan density, resolution and field of view in consideration of anticipated department requirements. Four vendors visited the site to present their system and they were asked to perform three unique tests with their system on a two day visit to SLAC. Two of the three tests were created to emulate real-world applications at SLAC while the third was an accuracy and resolution series of experiments. The scope of these tests is presented and some of the vendor's results are included.

  18. Introduction to microarray technology.

    Science.gov (United States)

    Dufva, Martin

    2009-01-01

    DNA microarrays can be used for large number of application where high-throughput is needed. The ability to probe a sample for hundred to million different molecules at once has made DNA microarray one of the fastest growing techniques since its introduction about 15 years ago. Microarray technology can be used for large scale genotyping, gene expression profiling, comparative genomic hybridization and resequencing among other applications. Microarray technology is a complex mixture of numerous technology and research fields such as mechanics, microfabrication, chemistry, DNA behaviour, microfluidics, enzymology, optics and bioinformatics. This chapter will give an introduction to each five basic steps in microarray technology that includes fabrication, target preparation, hybridization, detection and data analysis. Basic concepts and nomenclature used in the field of microarray technology and their relationships will also be explained.

  19. BEPC II wire scanner system

    Institute of Scientific and Technical Information of China (English)

    SUI Yan-Feng; WANG Lin; ZHAO Ying; YUE Jun-Hui; LI Xiao-Ping; CAO Jian-She; MA Li

    2010-01-01

    To monitor the beam profile at the end of the linac non-destructively,a wire scanner as a new diagnostic instrument was designed,manufactured and installed in 2007.Since then,several measurements have been carried out using this device.This paper describes the whole system of the wire scanner and the testing results.

  20. Pure Nano-Rotation Scanner

    Directory of Open Access Journals (Sweden)

    Moo-Yeon Lee

    2012-01-01

    Full Text Available We developed and tested a novel rotation scanner for nano resolution and accurate rotary motion about the rotation center. The scanner consists of circular hinges and leaf springs so that the parasitic error at the center of the scanner in the X and Y directions is minimized, and rotation performance is optimized. Each sector of the scanner's system was devised to have nano resolution by minimizing the parasitic errors of the rotation center that arise due to displacements other than rotation. The analytic optimal design results of the proposed scanner were verified using finite element analyses. The piezoelectric actuators were used to attain nano-resolution performances, and a capacitive sensor was used to measure displacement. A feedback controller was used to minimize the rotation errors in the rotation scanner system under practical conditions. Finally, the performance evaluation test results showed that the resonance frequency was 542 Hz, the resolution was 0.09 μrad, and the rotation displacement was 497.2 μrad. Our test results revealed that the rotation scanner exhibited accurate rotation about the center of the scanner and had good nano precision.

  1. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP

    2012-11-01

    Full Text Available DNA Microarray is the emerging technique in Biotechnology. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. It also includes screening and diagnostic applications. The DNA microarray hybridization applications include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs, and short tandem repeats (STRs. In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.

  2. Intraoral 3D scanner

    Science.gov (United States)

    Kühmstedt, Peter; Bräuer-Burchardt, Christian; Munkelt, Christoph; Heinze, Matthias; Palme, Martin; Schmidt, Ingo; Hintersehr, Josef; Notni, Gunther

    2007-09-01

    Here a new set-up of a 3D-scanning system for CAD/CAM in dental industry is proposed. The system is designed for direct scanning of the dental preparations within the mouth. The measuring process is based on phase correlation technique in combination with fast fringe projection in a stereo arrangement. The novelty in the approach is characterized by the following features: A phase correlation between the phase values of the images of two cameras is used for the co-ordinate calculation. This works contrary to the usage of only phase values (phasogrammetry) or classical triangulation (phase values and camera image co-ordinate values) for the determination of the co-ordinates. The main advantage of the method is that the absolute value of the phase at each point does not directly determine the coordinate. Thus errors in the determination of the co-ordinates are prevented. Furthermore, using the epipolar geometry of the stereo-like arrangement the phase unwrapping problem of fringe analysis can be solved. The endoscope like measurement system contains one projection and two camera channels for illumination and observation of the object, respectively. The new system has a measurement field of nearly 25mm × 15mm. The user can measure two or three teeth at one time. So the system can by used for scanning of single tooth up to bridges preparations. In the paper the first realization of the intraoral scanner is described.

  3. Airborne Hyperspectral Imaging System

    Science.gov (United States)

    Behar, Alberto E.; Cooper, Moogega; Adler, John; Jacobson, Tobias

    2012-01-01

    A document discusses a hyperspectral imaging instrument package designed to be carried aboard a helicopter. It was developed to map the depths of Greenland's supraglacial lakes. The instrument is capable of telescoping to twice its original length, allowing it to be retracted with the door closed during takeoff and landing, and manually extended in mid-flight. While extended, the instrument platform provides the attached hyperspectral imager a nadir-centered and unobstructed view of the ground. Before flight, the instrument mount is retracted and securely strapped down to existing anchor points on the floor of the helicopter. When the helicopter reaches the destination lake, the door is opened and the instrument mount is manually extended. Power to the instrument package is turned on, and the data acquisition computer is commanded via a serial cable from an onboard user-operated laptop to begin data collection. After data collection is complete, the instrument package is powered down and the mount retracted, allowing the door to be closed in preparation for landing. The present design for the instrument mount consists of a three-segment telescoping cantilever to allow for a sufficient extended length to see around the landing struts and provide a nadir-centered and unobstructed field of view for the hyperspectral imager. This instrument works on the premise that water preferentially absorbs light with longer wavelengths on the red side of the visible spectrum. This property can be exploited in order to remotely determine the depths of bodies of pure freshwater. An imager flying over such a lake receives light scattered from the surface, the bulk of the water column, and from the lake bottom. The strength of absorption of longer-wavelength light depends on the depth of the water column. Through calibration with in situ measurements of the water depths, a depth-determining algorithm may be developed to determine lake depth from these spectral properties of the

  4. Quantitative Hyperspectral Reflectance Imaging

    Directory of Open Access Journals (Sweden)

    Ted A.G. Steemers

    2008-09-01

    Full Text Available Hyperspectral imaging is a non-destructive optical analysis technique that can for instance be used to obtain information from cultural heritage objects unavailable with conventional colour or multi-spectral photography. This technique can be used to distinguish and recognize materials, to enhance the visibility of faint or obscured features, to detect signs of degradation and study the effect of environmental conditions on the object. We describe the basic concept, working principles, construction and performance of a laboratory instrument specifically developed for the analysis of historical documents. The instrument measures calibrated spectral reflectance images at 70 wavelengths ranging from 365 to 1100 nm (near-ultraviolet, visible and near-infrared. By using a wavelength tunable narrow-bandwidth light-source, the light energy used to illuminate the measured object is minimal, so that any light-induced degradation can be excluded. Basic analysis of the hyperspectral data includes a qualitative comparison of the spectral images and the extraction of quantitative data such as mean spectral reflectance curves and statistical information from user-defined regions-of-interest. More sophisticated mathematical feature extraction and classification techniques can be used to map areas on the document, where different types of ink had been applied or where one ink shows various degrees of degradation. The developed quantitative hyperspectral imager is currently in use by the Nationaal Archief (National Archives of The Netherlands to study degradation effects of artificial samples and original documents, exposed in their permanent exhibition area or stored in their deposit rooms.

  5. Hyperspectral optical diffraction tomography

    CERN Document Server

    Jung, JaeHwang; Yoon, Jonghee; Park, YongKeun

    2015-01-01

    Here, we present a novel microscopic technique for measuring wavelength-dependent three-dimensional (3-D) distributions of the refractive indices (RIs) of microscopic samples in the visible wavelengths. Employing 3-D quantitative phase microscopy techniques with a wavelength-swept source, 3-D RI tomograms were obtained in the range of 450 - 700 nm with a spectral resolution of a few nanometers. The capability of the technique was demonstrated by measuring the hyperspectral 3-D RI tomograms of polystyrene beads, human red blood cells, and hepatocytes. The results demonstrate the potential for label-free molecular specific 3-D tomography of biological samples.

  6. Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays.

    Science.gov (United States)

    von der Haar, Marcel; Heuer, Christopher; Pähler, Martin; von der Haar, Kathrin; Lindner, Patrick; Scheper, Thomas; Stahl, Frank

    2016-11-30

    The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.

  7. Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Marcel von der Haar

    2016-11-01

    Full Text Available The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS. Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.

  8. Nogle muligheder i scanner data

    DEFF Research Database (Denmark)

    Juhl, Hans Jørn

    2000-01-01

    I artiklen gives en diskussion af en række af de muligheder for effektivisering af marketingaktiviteter, der er til stede for såvel mærkevareudbyder som detaillist, ved udnyttelse af information fra scanner data......I artiklen gives en diskussion af en række af de muligheder for effektivisering af marketingaktiviteter, der er til stede for såvel mærkevareudbyder som detaillist, ved udnyttelse af information fra scanner data...

  9. Microarray Analysis in Glioblastomas

    Science.gov (United States)

    Bhawe, Kaumudi M.; Aghi, Manish K.

    2016-01-01

    Microarray analysis in glioblastomas is done using either cell lines or patient samples as starting material. A survey of the current literature points to transcript-based microarrays and immunohistochemistry (IHC)-based tissue microarrays as being the preferred methods of choice in cancers of neurological origin. Microarray analysis may be carried out for various purposes including the following: To correlate gene expression signatures of glioblastoma cell lines or tumors with response to chemotherapy (DeLay et al., Clin Cancer Res 18(10):2930–2942, 2012)To correlate gene expression patterns with biological features like proliferation or invasiveness of the glioblastoma cells (Jiang et al., PLoS One 8(6):e66008, 2013)To discover new tumor classificatory systems based on gene expression signature, and to correlate therapeutic response and prognosis with these signatures (Huse et al., Annu Rev Med 64(1):59–70, 2013; Verhaak et al., Cancer Cell 17(1):98–110, 2010) While investigators can sometimes use archived tumor gene expression data available from repositories such as the NCBI Gene Expression Omnibus to answer their questions, new arrays must often be run to adequately answer specific questions. Here, we provide a detailed description of microarray methodologies, how to select the appropriate methodology for a given question, and analytical strategies that can be used. Experimental methodology for protein microarrays is outside the scope of this chapter, but basic sample preparation techniques for transcript-based microarrays are included here. PMID:26113463

  10. Hyperspectral image analysis. A tutorial

    DEFF Research Database (Denmark)

    Amigo Rubio, Jose Manuel; Babamoradi, Hamid; Elcoroaristizabal Martin, Saioa

    2015-01-01

    This tutorial aims at providing guidelines and practical tools to assist with the analysis of hyperspectral images. Topics like hyperspectral image acquisition, image pre-processing, multivariate exploratory analysis, hyperspectral image resolution, classification and final digital image processi...... to differentiate between several types of plastics by using Near infrared hyperspectral imaging and Partial Least Squares - Discriminant Analysis. Thus, the reader is guided through every single step and oriented in order to adapt those strategies to the user's case....... will be exposed, and some guidelines given and discussed. Due to the broad character of current applications and the vast number of multivariate methods available, this paper has focused on an industrial chemical framework to explain, in a step-wise manner, how to develop a classification methodology...

  11. Approximate Sparse Regularized Hyperspectral Unmixing

    Directory of Open Access Journals (Sweden)

    Chengzhi Deng

    2014-01-01

    Full Text Available Sparse regression based unmixing has been recently proposed to estimate the abundance of materials present in hyperspectral image pixel. In this paper, a novel sparse unmixing optimization model based on approximate sparsity, namely, approximate sparse unmixing (ASU, is firstly proposed to perform the unmixing task for hyperspectral remote sensing imagery. And then, a variable splitting and augmented Lagrangian algorithm is introduced to tackle the optimization problem. In ASU, approximate sparsity is used as a regularizer for sparse unmixing, which is sparser than l1 regularizer and much easier to be solved than l0 regularizer. Three simulated and one real hyperspectral images were used to evaluate the performance of the proposed algorithm in comparison to l1 regularizer. Experimental results demonstrate that the proposed algorithm is more effective and accurate for hyperspectral unmixing than state-of-the-art l1 regularizer.

  12. Sparse Representations of Hyperspectral Images

    KAUST Repository

    Swanson, Robin J.

    2015-11-23

    Hyperspectral image data has long been an important tool for many areas of sci- ence. The addition of spectral data yields significant improvements in areas such as object and image classification, chemical and mineral composition detection, and astronomy. Traditional capture methods for hyperspectral data often require each wavelength to be captured individually, or by sacrificing spatial resolution. Recently there have been significant improvements in snapshot hyperspectral captures using, in particular, compressed sensing methods. As we move to a compressed sensing image formation model the need for strong image priors to shape our reconstruction, as well as sparse basis become more important. Here we compare several several methods for representing hyperspectral images including learned three dimensional dictionaries, sparse convolutional coding, and decomposable nonlocal tensor dictionaries. Addi- tionally, we further explore their parameter space to identify which parameters provide the most faithful and sparse representations.

  13. Hyperspectral sensors and the conservation of monumental buildings

    Science.gov (United States)

    Camaiti, Mara; Benvenuti, Marco; Chiarantini, Leandro; Costagliola, Pilar; Moretti, Sandro; Paba, Francesca; Pecchioni, Elena; Vettori, Silvia

    2010-05-01

    -FieldSpec FP Pro spectroradiometer), which continuously acquires punctual reflectance spectra in the range 350-2500 nm, both in natural light conditions and by a contact probe (fixed geometry of shot). This instrument is used on field for the identification of different materials, as well as for the definition of maps (e.g geological maps) if coupled with other hyperspectral instruments. 2) Hyperspectral sensor SIM-GA (Selex Galileo Multisensor Hyperspectral System), a system with spatial acquisition of data which may be used on an earth as well as on an airborne platform. SIM-GA consists of two electro-optical heads, which operate in the VNIR and SWIR regions, respectively, between 400-1000 nm and 1000-2500 nm (3). Although the spectral signature in the VNIR of many minerals is known, the co-presence of more minerals on a surface can affect the quantitative analysis of gypsum. Different minerals, such as gypsum, calcite, weddellite, whewellite, and other components (i.e. carbon particles in black crusts) are, in fact, commonly found on historical surfaces. In order to illustrate the complexity, but also the potentiality of hyperspectral sensors (portable or remote sensing) for the characterization of stone surfaces, a case study, the Facade of Santa Maria Novella in Florence - Italy, will be presented. References 1) R.N. Clark and G.A. Swayze, 1995, "Mapping minerals, amorphous materials, environmental materials, vegetation, water, ice, and snow, and other materials: The USGS Tricorder Algorithm", in "Summaries of the Fifth Annual JPL Airborne Earth Science Workshop", JPL Publication 95-1,1,39-40 2) E. Ben-Dor, K. Patin, A. Banin and A. Karnieli, 2002, "Mapping of several soil properties using DATS-7915 hyperspectral scanner data. A case study over clayely soils in Israel", International Journal of Remote Sensing, 23(6), 1043-1062 3) S. Vettori, M. Benvenuti, M. Camaiti, L. Chiarantini, P. Costagliola, S. Moretti, E. Pecchioni, 2008, "Assessment of the deterioration status of

  14. Hyperspectral image analysis. A tutorial

    Energy Technology Data Exchange (ETDEWEB)

    Amigo, José Manuel, E-mail: jmar@food.ku.dk [Spectroscopy and Chemometrics Group, Department of Food Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 30, Frederiksberg C DK–1958 (Denmark); Babamoradi, Hamid [Spectroscopy and Chemometrics Group, Department of Food Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 30, Frederiksberg C DK–1958 (Denmark); Elcoroaristizabal, Saioa [Spectroscopy and Chemometrics Group, Department of Food Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 30, Frederiksberg C DK–1958 (Denmark); Chemical and Environmental Engineering Department, School of Engineering, University of the Basque Country, Alameda de Urquijo s/n, E-48013 Bilbao (Spain)

    2015-10-08

    This tutorial aims at providing guidelines and practical tools to assist with the analysis of hyperspectral images. Topics like hyperspectral image acquisition, image pre-processing, multivariate exploratory analysis, hyperspectral image resolution, classification and final digital image processing will be exposed, and some guidelines given and discussed. Due to the broad character of current applications and the vast number of multivariate methods available, this paper has focused on an industrial chemical framework to explain, in a step-wise manner, how to develop a classification methodology to differentiate between several types of plastics by using Near infrared hyperspectral imaging and Partial Least Squares – Discriminant Analysis. Thus, the reader is guided through every single step and oriented in order to adapt those strategies to the user's case. - Highlights: • Comprehensive tutorial of Hyperspectral Image analysis. • Hierarchical discrimination of six classes of plastics containing flame retardant. • Step by step guidelines to perform class-modeling on hyperspectral images. • Fusion of multivariate data analysis and digital image processing methods. • Promising methodology for real-time detection of plastics containing flame retardant.

  15. Hyperspectral Imager-Tracker

    Science.gov (United States)

    Agurok, Llya

    2013-01-01

    The Hyperspectral Imager-Tracker (HIT) is a technique for visualization and tracking of low-contrast, fast-moving objects. The HIT architecture is based on an innovative and only recently developed concept in imaging optics. This innovative architecture will give the Light Prescriptions Innovators (LPI) HIT the possibility of simultaneously collecting the spectral band images (hyperspectral cube), IR images, and to operate with high-light-gathering power and high magnification for multiple fast- moving objects. Adaptive Spectral Filtering algorithms will efficiently increase the contrast of low-contrast scenes. The most hazardous parts of a space mission are the first stage of a launch and the last 10 kilometers of the landing trajectory. In general, a close watch on spacecraft operation is required at distances up to 70 km. Tracking at such distances is usually associated with the use of radar, but its milliradian angular resolution translates to 100- m spatial resolution at 70-km distance. With sufficient power, radar can track a spacecraft as a whole object, but will not provide detail in the case of an accident, particularly for small debris in the onemeter range, which can only be achieved optically. It will be important to track the debris, which could disintegrate further into more debris, all the way to the ground. Such fragmentation could cause ballistic predictions, based on observations using high-resolution but narrow-field optics for only the first few seconds of the event, to be inaccurate. No optical imager architecture exists to satisfy NASA requirements. The HIT was developed for space vehicle tracking, in-flight inspection, and in the case of an accident, a detailed recording of the event. The system is a combination of five subsystems: (1) a roving fovea telescope with a wide 30 field of regard; (2) narrow, high-resolution fovea field optics; (3) a Coude optics system for telescope output beam stabilization; (4) a hyperspectral

  16. Wire Scanner Motion Control Card

    CERN Document Server

    Forde, S E

    2006-01-01

    Scientists require a certain beam quality produced by the accelerator rings at CERN. The discovery potential of LHC is given by the reachable luminosity at its interaction points. The luminosity is maximized by minimizing the beam size. Therefore an accurate beam size measurement is required for optimizing the luminosity. The wire scanner performs very accurate profile measurements, but as it can not be used at full intensity in the LHC ring, it is used for calibrating other profile monitors. As the current wire scanner system, which is used in the present CERN accelerators, has not been made for the required specification of the LHC, a new design of a wire scanner motion control card is part of the LHC wire scanner project. The main functions of this card are to control the wire scanner motion and to acquire the position of the wire. In case of further upgrades at a later stage, it is required to allow an easy update of the firmware, hence the programmable features of FPGAs will be used for this purpose. The...

  17. Hyperspectral Fluorescence and Reflectance Imaging Instrument

    Science.gov (United States)

    Ryan, Robert E.; O'Neal, S. Duane; Lanoue, Mark; Russell, Jeffrey

    2008-01-01

    The system is a single hyperspectral imaging instrument that has the unique capability to acquire both fluorescence and reflectance high-spatial-resolution data that is inherently spatially and spectrally registered. Potential uses of this instrument include plant stress monitoring, counterfeit document detection, biomedical imaging, forensic imaging, and general materials identification. Until now, reflectance and fluorescence spectral imaging have been performed by separate instruments. Neither a reflectance spectral image nor a fluorescence spectral image alone yields as much information about a target surface as does a combination of the two modalities. Before this system was developed, to benefit from this combination, analysts needed to perform time-consuming post-processing efforts to co-register the reflective and fluorescence information. With this instrument, the inherent spatial and spectral registration of the reflectance and fluorescence images minimizes the need for this post-processing step. The main challenge for this technology is to detect the fluorescence signal in the presence of a much stronger reflectance signal. To meet this challenge, the instrument modulates artificial light sources from ultraviolet through the visible to the near-infrared part of the spectrum; in this way, both the reflective and fluorescence signals can be measured through differencing processes to optimize fluorescence and reflectance spectra as needed. The main functional components of the instrument are a hyperspectral imager, an illumination system, and an image-plane scanner. The hyperspectral imager is a one-dimensional (line) imaging spectrometer that includes a spectrally dispersive element and a two-dimensional focal plane detector array. The spectral range of the current imaging spectrometer is between 400 to 1,000 nm, and the wavelength resolution is approximately 3 nm. The illumination system consists of narrowband blue, ultraviolet, and other discrete

  18. Aircraft Scanners = NASA Digital Aerial Scanners (TMS, TIMS, NS001): Pre 1996

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Aircraft Scanners data set contains digital imagery acquired from several multispectral scanners including NS-001 Mutispectral scanner, Daedalus thematic mapper...

  19. Detection of Honey Adulteration using Hyperspectral Imaging

    NARCIS (Netherlands)

    Shafiee, Sahameh; Polder, Gerrit; Minaei, Saeid; Moghadam-charkari, Nasrolah; Ruth, Van Saskia; Kuś, Piotr M.

    2016-01-01

    This study investigates the application of hyperspectral imaging system and data mining based classifiers for honey adulteration detection. Hyperspectral images from pure and adulterated samples were captured in using a VIS-NIR hyperspectral camera (400 – 1000 nm). After preprocessing the images, fi

  20. Contextual Detection of Anomalies within Hyperspectral Images

    Science.gov (United States)

    2011-03-01

    Hyperspectral Imagery (HSI), Unsupervised Target Detection, Target Identification, Contextual Anomaly Detection 16. SECURITY CLASSIFICATION OF: 17. LIMITATION...processing. Hyperspectral imaging has a wide range of applications within remote sensing, not limited to terrain classification , environmental monitoring...Johnson, R. J. (2008). Improved feature extraction, feature selection, and identification techniques that create a fast unsupervised hyperspectral

  1. Detection of Honey Adulteration using Hyperspectral Imaging

    NARCIS (Netherlands)

    Shafiee, Sahameh; Polder, Gerrit; Minaei, Saeid; Moghadam-charkari, Nasrolah; Ruth, Van Saskia; Kuś, Piotr M.

    2016-01-01

    This study investigates the application of hyperspectral imaging system and data mining based classifiers for honey adulteration detection. Hyperspectral images from pure and adulterated samples were captured in using a VIS-NIR hyperspectral camera (400 – 1000 nm). After preprocessing the images,

  2. Automated Ortho-Rectification of UAV-Based Hyperspectral Data over an Agricultural Field Using Frame RGB Imagery

    Directory of Open Access Journals (Sweden)

    Ayman Habib

    2016-09-01

    Full Text Available Low-cost Unmanned Airborne Vehicles (UAVs equipped with consumer-grade imaging systems have emerged as a potential remote sensing platform that could satisfy the needs of a wide range of civilian applications. Among these applications, UAV-based agricultural mapping and monitoring have attracted significant attention from both the research and professional communities. The interest in UAV-based remote sensing for agricultural management is motivated by the need to maximize crop yield. Remote sensing-based crop yield prediction and estimation are primarily based on imaging systems with different spectral coverage and resolution (e.g., RGB and hyperspectral imaging systems. Due to the data volume, RGB imaging is based on frame cameras, while hyperspectral sensors are primarily push-broom scanners. To cope with the limited endurance and payload constraints of low-cost UAVs, the agricultural research and professional communities have to rely on consumer-grade and light-weight sensors. However, the geometric fidelity of derived information from push-broom hyperspectral scanners is quite sensitive to the available position and orientation established through a direct geo-referencing unit onboard the imaging platform (i.e., an integrated Global Navigation Satellite System (GNSS and Inertial Navigation System (INS. This paper presents an automated framework for the integration of frame RGB images, push-broom hyperspectral scanner data and consumer-grade GNSS/INS navigation data for accurate geometric rectification of the hyperspectral scenes. The approach relies on utilizing the navigation data, together with a modified Speeded-Up Robust Feature (SURF detector and descriptor, for automating the identification of conjugate features in the RGB and hyperspectral imagery. The SURF modification takes into consideration the available direct geo-referencing information to improve the reliability of the matching procedure in the presence of repetitive texture

  3. Scanometric analysis of DNA microarrays using DNA intercalator-conjugated gold nanoparticles.

    Science.gov (United States)

    Cho, Hyunmin; Jung, Juyeon; Chung, Bong Hyun

    2012-08-07

    We introduce a scanometric detection method for the analysis of DNA microarrays using DNA intercalator-conjugated gold nanoparticles that can be analyzed with the naked eye or with an optical scanner after the enhancement of the AuNPs. Moreover, we successfully detected a hemagglutinin-subtyping DNA array using this method.

  4. Automatic Fusion of Hyperspectral Images and Laser Scans Using Feature Points

    Directory of Open Access Journals (Sweden)

    Xiao Zhang

    2015-01-01

    Full Text Available Automatic fusion of different kinds of image datasets is so intractable with diverse imaging principle. This paper presents a novel method for automatic fusion of two different images: 2D hyperspectral images acquired with a hyperspectral camera and 3D laser scans obtained with a laser scanner, without any other sensor. Only a few corresponding feature points are used, which are automatically extracted from a scene viewed by the two sensors. Extraction method of feature points relies on SURF algorithm and camera model, which can convert a 3D laser scan into a 2D laser image with the intensity of the pixels defined by the attributes in the laser scan. Moreover, Collinearity Equation and Direct Linear Transformation are used to create the initial corresponding relationship of the two images. Adjustment is also used to create corrected values to eliminate errors. The experimental result shows that this method is successfully validated with images collected by a hyperspectral camera and a laser scanner.

  5. Accounting for Variance in Hyperspectral Data Coming from Limitations of the Imaging System

    Science.gov (United States)

    Shurygin, B.; Shestakova, M.; Nikolenko, A.; Badasen, E.; Strakhov, P.

    2016-06-01

    to different preprocession parameters and, ultimatively, classification results. A multilevel system for denoting hyperspectral pushbroom scanners calibration quality was proposed.

  6. A case study in scanner optimisation.

    Science.gov (United States)

    Dudley, N J; Gibson, N M

    2014-02-01

    Ultrasound scanner preset programmes are factory set or tailored to user requirements. Scanners may, therefore, have different settings for the same application, even on similar equipment in a single department. The aims of this study were: (1) to attempt to match the performance of two scanners, where one was preferred and (2) to assess differences between six scanners used for breast ultrasound within our organisation. The Nottingham Ultrasound Quality Assurance software was used to compare imaging performance. Images of a Gammex RMI 404GS test object were collected from six scanners, using default presets, factory presets and settings matched to a preferred scanner. Resolution, low contrast performance and high contrast performance were measured. The performance of two scanners was successfully matched, where one had been preferred. Default presets varied across the six scanners, three different presets being used. The most used preset differed in settings across the scanners, most notably in the use of different frequency modes. The factory preset was more consistent across the scanners, the main variation being in dynamic range (55-70 dB). Image comparisons showed significant differences, which were reduced or eliminated by adjustment of settings to match a reference scanner. It is possible to match scanner performance using the Nottingham Ultrasound Quality Assurance software as a verification tool. Ultrasound users should be aware that scanners may not behave in a similar fashion, even with apparently equivalent presets. It should be possible to harmonise presets by consensus amongst users.

  7. Maize microarray annotation database

    Directory of Open Access Journals (Sweden)

    Berger Dave K

    2011-10-01

    Full Text Available Abstract Background Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a reporter - gene model match, (b number of reporters per gene model, (c potential for cross hybridization, (d sense/antisense orientation of reporters, (e position of reporter on B73 genome sequence (for eQTL studies, and (f functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database. Description Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i "annotation by sense gene model" (23,668 reporters, (ii "annotation by antisense gene model" (4,330; (iii "annotation by gDNA" without a WGS transcript hit (1,549; (iv "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390; (v "ambiguous annotation" (2,608; and (vi "inconclusive annotation" (6,489. Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank. The annotations are available in the Maize Microarray Annotation Database http://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to

  8. Hyperspectral image classification using functional data analysis.

    Science.gov (United States)

    Li, Hong; Xiao, Guangrun; Xia, Tian; Tang, Y Y; Li, Luoqing

    2014-09-01

    The large number of spectral bands acquired by hyperspectral imaging sensors allows us to better distinguish many subtle objects and materials. Unlike other classical hyperspectral image classification methods in the multivariate analysis framework, in this paper, a novel method using functional data analysis (FDA) for accurate classification of hyperspectral images has been proposed. The central idea of FDA is to treat multivariate data as continuous functions. From this perspective, the spectral curve of each pixel in the hyperspectral images is naturally viewed as a function. This can be beneficial for making full use of the abundant spectral information. The relevance between adjacent pixel elements in the hyperspectral images can also be utilized reasonably. Functional principal component analysis is applied to solve the classification problem of these functions. Experimental results on three hyperspectral images show that the proposed method can achieve higher classification accuracies in comparison to some state-of-the-art hyperspectral image classification methods.

  9. Compensation strategies for PET scanners with unconventional scanner geometry

    CERN Document Server

    Gundlich, B; Oehler, M

    2006-01-01

    The small animal PET scanner ClearPET®Neuro, developed at the Forschungszentrum Julich GmbH in cooperation with the Crystal Clear Collaboration (CERN), represents scanners with an unconventional geometry: due to axial and transaxial detector gaps ClearPet®Neuro delivers inhomogeneous sinograms with missing data. When filtered backprojection (FBP) or Fourier rebinning (FORE) are applied, strong geometrical artifacts appear in the images. In this contribution we present a method that takes the geometrical sensitivity into account and converts the measured sinograms into homogeneous and complete data. By this means artifactfree images are achieved using FBP or FORE. Besides an advantageous measurement setup that reduces inhomogeneities and data gaps in the sinograms, a modification of the measured sinograms is necessary. This modification includes two steps: a geometrical normalization and corrections for missing data. To normalize the measured sinograms, computed sinograms are used that describe the geometric...

  10. Medical hyperspectral imaging: a review

    Science.gov (United States)

    Lu, Guolan; Fei, Baowei

    2014-01-01

    Abstract. Hyperspectral imaging (HSI) is an emerging imaging modality for medical applications, especially in disease diagnosis and image-guided surgery. HSI acquires a three-dimensional dataset called hypercube, with two spatial dimensions and one spectral dimension. Spatially resolved spectral imaging obtained by HSI provides diagnostic information about the tissue physiology, morphology, and composition. This review paper presents an overview of the literature on medical hyperspectral imaging technology and its applications. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application. PMID:24441941

  11. Medical hyperspectral imaging: a review.

    Science.gov (United States)

    Lu, Guolan; Fei, Baowei

    2014-01-01

    Hyperspectral imaging (HSI) is an emerging imaging modality for medical applications, especially in disease diagnosis and image-guided surgery. HSI acquires a three-dimensional dataset called hypercube, with two spatial dimensions and one spectral dimension. Spatially resolved spectral imaging obtained by HSI provides diagnostic information about the tissue physiology, morphology, and composition. This review paper presents an overview of the literature on medical hyperspectral imaging technology and its applications. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application.

  12. New generation handheld hyperspectral imager

    Science.gov (United States)

    Wu, Huawen (Owen); Li, Hui; Tang, Shengjun

    2016-10-01

    A miniaturized hyper-spectral imager is enabled with image sensor integrated with dispersing elements in a very compact form factor, removing the need for expensive, moving, bulky and complex optics that have been used in conventional hyper-spectral imagers for decades. The result is a handheld spectral imager that can be installed on miniature UAV drones or conveyor belts in production lines. Eventually, small handhelds can be adapted for use in outpatient medical clinics for point-of-care diagnostics and other in-field applications.

  13. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao

    2011-01-01

    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  14. Microarray Applications in Cancer Research

    Science.gov (United States)

    Kim, Il-Jin; Kang, Hio Chung

    2004-01-01

    DNA microarray technology permits simultaneous analysis of thousands of DNA sequences for genomic research and diagnostics applications. Microarray technology represents the most recent and exciting advance in the application of hybridization-based technology for biological sciences analysis. This review focuses on the classification (oligonucleotide vs. cDNA) and application (mutation-genotyping vs. gene expression) of microarrays. Oligonucleotide microarrays can be used both in mutation-genotyping and gene expression analysis, while cDNA microarrays can only be used in gene expression analysis. We review microarray mutation analysis, including examining the use of three oligonucleotide microarrays developed in our laboratory to determine mutations in RET, β-catenin and K-ras genes. We also discuss the use of the Affymetrix GeneChip in mutation analysis. We review microarray gene expression analysis, including the classifying of such studies into four categories: class comparison, class prediction, class discovery and identification of biomarkers. PMID:20368836

  15. D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis

    Directory of Open Access Journals (Sweden)

    Marcelo F. Carazzolle

    2009-01-01

    Full Text Available The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix. Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner. In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core.

  16. A New Proton CT Scanner

    CERN Document Server

    Coutrakon, G; Boi, S; Dyshkant, A; Erdelyi, B; Hedin, D; Johnson, E; Krider, J; Rykalin, V; Uzunyan, S A; Zutshi, V; Fordt, R; Sellberg, G; Rauch, J E; Roman, M; Rubinov, P; Wilson, P; Naimuddin, M

    2014-01-01

    The design, construction, and preliminary testing of a second generation proton CT scanner is presented. All current treatment planning systems at proton therapy centers use X-ray CT as the primary imaging modality for treatment planning to calculate doses to tumor and healthy tissues. One of the limitations of X-ray CT is in the conversion of X-ray attenuation coefficients to relative (proton) stopping powers, or RSP. This results in more proton range uncertainty, larger target volumes and therefore, more dose to healthy tissues. To help improve this, we present a novel scanner capable of high dose rates, up to 2~MHz, and large area coverage, 20~x~24~cm$^2$, for imaging an adult head phantom and reconstructing more accurate RSP values.

  17. Normalization for triple-target microarray experiments

    Directory of Open Access Journals (Sweden)

    Magniette Frederic

    2008-04-01

    Full Text Available Abstract Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

  18. Microfabrication of fiber optic scanners

    Science.gov (United States)

    Fauver, Mark; Crossman-Bosworth, Janet L.; Seibel, Eric J.

    2002-06-01

    A cantilevered optical fiber is micromachined to function as a miniature resonant opto-mechanical scanner. By driving the base of the cantilevered fiber at a resonance frequency using a piezoelectric actuator, the free end of the cantilever beam becomes a scanned light source. The fiber scanners are designed to achieve wide field-of-view (FOV) and high scan frequency. We employ a non-linearly tapered profile fiber to achieve scan amplitudes of 1 mm at scan frequencies above 20 KHz. Scan angles of over 120 degree(s) (full angle) have been achieved. Higher order modes are also employed for scanning applications that require compactness while maintaining large angular FOV. Etching techniques are used to create the non-linearly tapered sections in single mode optical fiber. Additionally, micro-lenses are fabricated on the tips of the etched fibers, with lens diameters as small as 15 microns. Such lenses are capable of reducing the divergence angle of the emitted light to 5 degree(s) (full angle), with greater reduction expected by employing novel lens shaping techniques. Microfabricated optical fiber scanners have display applications ranging from micro-optical displays to larger panoramic displays. Applications for micro-image acquisition include small barcode readers to medical endoscopes.

  19. HYBASE - HYperspectral BAnd SElection tool

    NARCIS (Netherlands)

    Schwering, P.B.W.; Bekman, H.H.P.T.; Seijen, H.H. van

    2008-01-01

    Band selection is essential in the design of multispectral sensor systems. This paper describes the TNO hyperspectral band selection tool HYBASE. It calculates the optimum band positions given the number of bands and the width of the spectral bands. HYBASE is used to calculate the minimum number of

  20. Biolog phenotype microarrays.

    Science.gov (United States)

    Shea, April; Wolcott, Mark; Daefler, Simon; Rozak, David A

    2012-01-01

    Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism's physiological response to different metabolites and environments. Biolog phenotype assays achieve this by coupling tetrazolium dyes with minimally defined nutrients to measure the impact of hundreds of carbon, nitrogen, phosphorous, and sulfur sources on redox reactions that result from compound-induced effects on the electron transport chain. Over the years, we have used Biolog's reproducible and highly sensitive assays to distinguish closely related bacterial isolates, to understand their metabolic differences, and to model their metabolic behavior using flux balance analysis. This chapter describes Biolog phenotype microarray system components, reagents, and methods, particularly as they apply to bacterial identification, characterization, and metabolic analysis.

  1. Analyzing Microarray Data.

    Science.gov (United States)

    Hung, Jui-Hung; Weng, Zhiping

    2017-03-01

    Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice. Finally, hierarchical clustering is performed on the differentially expressed genes using the Cluster program, and the results are visualized using TreeView.

  2. Segmentation in dermatological hyperspectral images: dedicated methods

    OpenAIRE

    Koprowski, Robert; Olczyk, Paweł

    2016-01-01

    Background Segmentation of hyperspectral medical images is one of many image segmentation methods which require profiling. This profiling involves either the adjustment of existing, known image segmentation methods or a proposal of new dedicated methods of hyperspectral image segmentation. Taking into consideration the size of analysed data, the time of analysis is of major importance. Therefore, the authors proposed three new dedicated methods of hyperspectral image segmentation with special...

  3. Multiband and Lossless Compression of Hyperspectral Images

    Directory of Open Access Journals (Sweden)

    Raffaele Pizzolante

    2016-02-01

    Full Text Available Hyperspectral images are widely used in several real-life applications. In this paper, we investigate on the compression of hyperspectral images by considering different aspects, including the optimization of the computational complexity in order to allow implementations on limited hardware (i.e., hyperspectral sensors, etc.. We present an approach that relies on a three-dimensional predictive structure. Our predictive structure, 3D-MBLP, uses one or more previous bands as references to exploit the redundancies among the third dimension. The achieved results are comparable, and often better, with respect to the other state-of-art lossless compression techniques for hyperspectral images.

  4. Optimization of PET scanner geometry

    Energy Technology Data Exchange (ETDEWEB)

    Adam, Lars-Eric; Karp, J.S. [Univ. of Pennsylvania, Department of Radiology, Philadelphia, PA (United States)

    2000-12-01

    Modern positron emission tomographs (PET), when used for 3D imaging, have a wide open gantry without intra plane septa and only little shielding. In order to reduce the scatter contamination from activity inside and outside the field-of-view (FOV), and to block radiation originating from activity outside-the-FOV, we have investigated the implementation of septa and additional patient shielding on our existing whole body PET scanner. A series of Monte Carlo simulations, based on EGS4, were performed to predict the potential benefits. Our simulations include point and line sources at various radial and axial positions in the FOV of the scanner, and different sized uniform cylinders (up to 100 cm long and 50 cm in diameter). The scanner itself is based on 6 continuous NaI(Tl) crystals, an axial FOV of 25.6 cm, a ring diameter of 90 cm, and a transaxial FOV of 56 cm. The results show that septa can reduce the relative scatter fraction and effectively block radiation from outside-the-FOV, but they also reduce the sensitivity for true events, leading to a decrease of the trues-to-singles ratio that is not desirable. The use of septa is only advantageous for large objects, if the loss of true events is compensated for by increasing the injected activity. Patient shields that are mounted outside-the-FOV reduce the contamination from scattered and single events without interfering with true events. They are more effective for objects with a small diameter and less effective for objects with a large diameter. (author)

  5. Quantitative analysis of tumor mitochondrial RNA using microarray

    Institute of Scientific and Technical Information of China (English)

    Cheng-Bo Han; Xiao-Yun Mao; Yan Xin; Shao-Cheng Wang; Jia-Ming Ma; Yu-Jie Zhao

    2005-01-01

    AIM: To design a novel method to rapidly detect the quantitative alteration of mtRNA in patients with tumors.METHODS: Oligo 6.22 and Primer Premier 5.0 bio-soft were used to design 15 pairs of primers of mtRNA cDNA probes in light of the functional and structural property of mtDNA, and then RT-PCR amplification was used to produce 15 probes of mtRNA from one normal gastric mucosal tissue. Total RNA extracted from 9 gastric cancers and corresponding normal gastric mucosal tissues was reverse transcribed into cDNA labeled with fluorescein. The spotted mtDNA microarrays were made and hybridized. Finally,the microarrays were scanned with a GeneTACTM laser scanner to get the hybridized results. Northern blot was used to confirm the microarray results.RESULTS: The hybridized spots were distinct with clear and consistent backgrounds. After data was standardized according to the housekeeping genes, the results showed that the expression levels of some mitochondrial genes in gastric carcinoma were different from those in the corresponding non-cancerous regions.CONCLUSION: The mtDNA expression microarray can rapidly, massively and exactly detect the quantity of mtRNA in tissues and cells. In addition, the whole expressive information of mtRNA from a tumor patient on just one slide can be obtained using this method, providing an effective method to investigate the relationship between mtDNA expression and tumorigenesis.

  6. Open magnetic resonance imaging (MRI) scanners.

    Science.gov (United States)

    Hailey, D

    2006-11-01

    (1) In most MRI scanners, the patient examination table fits inside a long cylindrical tube. Large patients cannot be accommodated, and some persons experience claustrophobic reactions. Open MRI systems, in which the patient is placed between two plates, overcome these disadvantages. (2) Open MRI scanners are widely used in health care. High-field closed MRI systems are preferred for many examinations. (3) Early versions of open MRI scanners had low magnetic field strength, gave poorer image quality than most closed systems, and required longer examination times. Newer open scanners include machines with higher magnetic field strengths and improved image quality. (4) Closed high magnetic field scanners with short magnets and wide bore tubes offer improved comfort to patients, and may be an alternative to open scanners. (5) There is interest in using open systems for intra-operative and image-guided interventions.

  7. Hyperspectral remote sensing of vegetation

    Science.gov (United States)

    Thenkabail, Prasad S.; Lyon, John G.; Huete, Alfredo

    2011-01-01

    Hyperspectral narrow-band (or imaging spectroscopy) spectral data are fast emerging as practical solutions in modeling and mapping vegetation. Recent research has demonstrated the advances in and merit of hyperspectral data in a range of applications including quantifying agricultural crops, modeling forest canopy biochemical properties, detecting crop stress and disease, mapping leaf chlorophyll content as it influences crop production, identifying plants affected by contaminants such as arsenic, demonstrating sensitivity to plant nitrogen content, classifying vegetation species and type, characterizing wetlands, and mapping invasive species. The need for significant improvements in quantifying, modeling, and mapping plant chemical, physical, and water properties is more critical than ever before to reduce uncertainties in our understanding of the Earth and to better sustain it. There is also a need for a synthesis of the vast knowledge spread throughout the literature from more than 40 years of research.

  8. Modeling of a piezoelectric micro-scanner

    CERN Document Server

    Chaehoi, A; Cornez, D; Kirk, K

    2008-01-01

    Micro-scanners have been widely used in many optical applications. The micro-scanner presented in this paper uses multimorph-type bending actuators to tilt a square plate mirror. This paper presents a complete analytical model of the piezoelectric micro-scanner. This theoretical model based on strength of material equations calculates the force generated by the multimorphs on the mirror, the profile of the structure and the angular deflection of the mirror. The proposed model, used to optimize the design of the piezoelectric silicon micro-scanner, is intended for further HDL integration, allowing in this way system level simulation and optimization.

  9. Wide area Hyperspectral Motion Imaging

    Science.gov (United States)

    2017-02-03

    gigapixel resolution from an airborne platform . This huge amount of visual data requires algorithms for automated detection and tracking of targets of...constraints, it is not surprising that no military or commercial WAMI platform has a hyperspectral sensing capability. Therefore, today’s systems must...digital pulse stream , and a counter counts the number of pulses within a given integration period [2]. The magnitude of the count is proportional to

  10. Fractal Characterization of Hyperspectral Imagery

    Science.gov (United States)

    Qiu, Hon-Iie; Lam, Nina Siu-Ngan; Quattrochi, Dale A.; Gamon, John A.

    1999-01-01

    Two Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) hyperspectral images selected from the Los Angeles area, one representing urban and the other, rural, were used to examine their spatial complexity across their entire spectrum of the remote sensing data. Using the ICAMS (Image Characterization And Modeling System) software, we computed the fractal dimension values via the isarithm and triangular prism methods for all 224 bands in the two AVIRIS scenes. The resultant fractal dimensions reflect changes in image complexity across the spectral range of the hyperspectral images. Both the isarithm and triangular prism methods detect unusually high D values on the spectral bands that fall within the atmospheric absorption and scattering zones where signature to noise ratios are low. Fractal dimensions for the urban area resulted in higher values than for the rural landscape, and the differences between the resulting D values are more distinct in the visible bands. The triangular prism method is sensitive to a few random speckles in the images, leading to a lower dimensionality. On the contrary, the isarithm method will ignore the speckles and focus on the major variation dominating the surface, thus resulting in a higher dimension. It is seen where the fractal curves plotted for the entire bandwidth range of the hyperspectral images could be used to distinguish landscape types as well as for screening noisy bands.

  11. Compressive Sensing DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Richard G. Baraniuk

    2009-01-01

    Full Text Available Compressive sensing microarrays (CSMs are DNA-based sensors that operate using group testing and compressive sensing (CS principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.

  12. Portable optical fiber probe-based spectroscopic scanner for rapid cancer diagnosis: a new tool for intraoperative margin assessment.

    Science.gov (United States)

    Lue, Niyom; Kang, Jeon Woong; Yu, Chung-Chieh; Barman, Ishan; Dingari, Narahara Chari; Feld, Michael S; Dasari, Ramachandra R; Fitzmaurice, Maryann

    2012-01-01

    There continues to be a significant clinical need for rapid and reliable intraoperative margin assessment during cancer surgery. Here we describe a portable, quantitative, optical fiber probe-based, spectroscopic tissue scanner designed for intraoperative diagnostic imaging of surgical margins, which we tested in a proof of concept study in human tissue for breast cancer diagnosis. The tissue scanner combines both diffuse reflectance spectroscopy (DRS) and intrinsic fluorescence spectroscopy (IFS), and has hyperspectral imaging capability, acquiring full DRS and IFS spectra for each scanned image pixel. Modeling of the DRS and IFS spectra yields quantitative parameters that reflect the metabolic, biochemical and morphological state of tissue, which are translated into disease diagnosis. The tissue scanner has high spatial resolution (0.25 mm) over a wide field of view (10 cm × 10 cm), and both high spectral resolution (2 nm) and high spectral contrast, readily distinguishing tissues with widely varying optical properties (bone, skeletal muscle, fat and connective tissue). Tissue-simulating phantom experiments confirm that the tissue scanner can quantitatively measure spectral parameters, such as hemoglobin concentration, in a physiologically relevant range with a high degree of accuracy (tissues showed that the tissue scanner can detect small foci of breast cancer in a background of normal breast tissue. This tissue scanner is simpler in design, images a larger field of view at higher resolution and provides a more physically meaningful tissue diagnosis than other spectroscopic imaging systems currently reported in literatures. We believe this spectroscopic tissue scanner can provide real-time, comprehensive diagnostic imaging of surgical margins in excised tissues, overcoming the sampling limitation in current histopathology margin assessment. As such it is a significant step in the development of a platform technology for intraoperative management of cancer, a

  13. Portable optical fiber probe-based spectroscopic scanner for rapid cancer diagnosis: a new tool for intraoperative margin assessment.

    Directory of Open Access Journals (Sweden)

    Niyom Lue

    Full Text Available There continues to be a significant clinical need for rapid and reliable intraoperative margin assessment during cancer surgery. Here we describe a portable, quantitative, optical fiber probe-based, spectroscopic tissue scanner designed for intraoperative diagnostic imaging of surgical margins, which we tested in a proof of concept study in human tissue for breast cancer diagnosis. The tissue scanner combines both diffuse reflectance spectroscopy (DRS and intrinsic fluorescence spectroscopy (IFS, and has hyperspectral imaging capability, acquiring full DRS and IFS spectra for each scanned image pixel. Modeling of the DRS and IFS spectra yields quantitative parameters that reflect the metabolic, biochemical and morphological state of tissue, which are translated into disease diagnosis. The tissue scanner has high spatial resolution (0.25 mm over a wide field of view (10 cm × 10 cm, and both high spectral resolution (2 nm and high spectral contrast, readily distinguishing tissues with widely varying optical properties (bone, skeletal muscle, fat and connective tissue. Tissue-simulating phantom experiments confirm that the tissue scanner can quantitatively measure spectral parameters, such as hemoglobin concentration, in a physiologically relevant range with a high degree of accuracy (<5% error. Finally, studies using human breast tissues showed that the tissue scanner can detect small foci of breast cancer in a background of normal breast tissue. This tissue scanner is simpler in design, images a larger field of view at higher resolution and provides a more physically meaningful tissue diagnosis than other spectroscopic imaging systems currently reported in literatures. We believe this spectroscopic tissue scanner can provide real-time, comprehensive diagnostic imaging of surgical margins in excised tissues, overcoming the sampling limitation in current histopathology margin assessment. As such it is a significant step in the development of a

  14. Sampling scheme optimization from hyperspectral data

    NARCIS (Netherlands)

    Debba, P.

    2006-01-01

    This thesis presents statistical sampling scheme optimization for geo-environ-menta] purposes on the basis of hyperspectral data. It integrates derived products of the hyperspectral remote sensing data into individual sampling schemes. Five different issues are being dealt with.First, the optimized

  15. Sampling scheme optimization from hyperspectral data

    NARCIS (Netherlands)

    Debba, P.

    2006-01-01

    This thesis presents statistical sampling scheme optimization for geo-environ-menta] purposes on the basis of hyperspectral data. It integrates derived products of the hyperspectral remote sensing data into individual sampling schemes. Five different issues are being dealt with.First, the optimized

  16. Magnetic Scanometric DNA Microarray Detection of Methyl Tertiary Butyl Ether Degrading Bacteria for Environmental Monitoring

    Science.gov (United States)

    Chan, Mei-Lin; Jaramillo, Gerardo; Hristova, Krassimira R.; Horsley, David A.

    2010-01-01

    A magnetoresistive biosensing platform based on a single magnetic tunnel junction (MTJ) scanning probe and DNA microarrays labeled with magnetic particles has been developed to provide an inexpensive, sensitive and reliable detection of DNA. The biosensing platform was demonstrated on a DNA microarray assay for quantifying bacteria capable of degrading methyl tertiary-butyl ether (MTBE), where concentrations as low as 10 pM were detectable. Synthetic probe bacterial DNA was immobilized on a microarray glass slide surface, hybridized with the 48 base pair long biotinylated target DNA and subsequently incubated with streptavidin-coated 2.8 μm diameter magnetic particles. The biosensing platform then makes use of a micron-sized MTJ sensor that was raster scanned across a 3 mm by 5 mm glass slide area to capture the stray magnetic field from the tagged DNA and extract two dimensional magnetic field images of the microarray. The magnetic field output is then averaged over each 100 μm diameter DNA array spot to extract the magnetic spot intensity, analogous to the fluorescence spot intensity used in conventional optical scanners. The magnetic scanning result is compared with results from a commercial laser scanner and particle coverage optical counting to demonstrate the dynamic range and linear sensitivity of the biosensing platform as a potentially inexpensive, sensitive and portable alternative for DNA microarray detection for field applications. PMID:20889328

  17. Laser Scanner For Automatic Storage

    Science.gov (United States)

    Carvalho, Fernando D.; Correia, Bento A.; Rebordao, Jose M.; Rodrigues, F. Carvalho

    1989-01-01

    The automated magazines are beeing used at industry more and more. One of the problems related with the automation of a Store House is the identification of the products envolved. Already used for stock management, the Bar Codes allows an easy way to identify one product. Applied to automated magazines, the bar codes allows a great variety of items in a small code. In order to be used by the national producers of automated magazines, a devoted laser scanner has been develloped. The Prototype uses an He-Ne laser whose beam scans a field angle of 75 degrees at 16 Hz. The scene reflectivity is transduced by a photodiode into an electrical signal, which is then binarized. This digital signal is the input of the decodifying program. The machine is able to see barcodes and to decode the information. A parallel interface allows the comunication with the central unit, which is responsible for the management of automated magazine.

  18. Non-Destructive Testing Scanner

    Science.gov (United States)

    1990-01-01

    Bio-Imaging Research's technology that originated in an aerospace program has come full circle with a new aerospace adaptation called the Advanced Computed Tomography Inspection System, or ACTIS. The medical version of CT scans the human body for tumors or other abnormalities, the ACTIS system finds imperfections in aerospace structures and components, such as castings, assemblies, rocket motors and nozzles. ACTIS is described by its developer as the most versatile CT scanner available for non-destructive testing applications. ACTIS is a variable geometry system. ACTIS source and detectors can be moved closer together or farther apart to optimize the geometry for different sizes of test objects. The combination of variable geometry, three sources, and focusing detectors makes ACTIS cost effective for a broad range of applications. System can scan anything from very small turbine blades to large rocket assemblies.

  19. Combined PET/MRI scanner

    Science.gov (United States)

    Schlyer, David; Woody, Craig L.; Rooney, William; Vaska, Paul; Stoll, Sean; Pratte, Jean-Francois; O'Connor, Paul

    2007-10-23

    A combined PET/MRI scanner generally includes a magnet for producing a magnetic field suitable for magnetic resonance imaging, a radiofrequency (RF) coil disposed within the magnetic field produced by the magnet and a ring tomograph disposed within the magnetic field produced by the magnet. The ring tomograph includes a scintillator layer for outputting at least one photon in response to an annihilation event, a detection array coupled to the scintillator layer for detecting the at least one photon outputted by the scintillator layer and for outputting a detection signal in response to the detected photon and a front-end electronic array coupled to the detection array for receiving the detection signal, wherein the front-end array has a preamplifier and a shaper network for conditioning the detection signal.

  20. Reusable conductimetric array of interdigitated microelectrodes for the readout of low-density microarrays.

    Science.gov (United States)

    Mallén, Maria; Díaz-González, María; Bonilla, Diana; Salvador, Juan P; Marco, María P; Baldi, Antoni; Fernández-Sánchez, César

    2014-06-17

    Low-density protein microarrays are emerging tools in diagnostics whose deployment could be primarily limited by the cost of fluorescence detection schemes. This paper describes an electrical readout system of microarrays comprising an array of gold interdigitated microelectrodes and an array of polydimethylsiloxane microwells, which enabled multiplexed detection of up to thirty six biological events on the same substrate. Similarly to fluorescent readout counterparts, the microarray can be developed on disposable glass slide substrates. However, unlike them, the presented approach is compact and requires a simple and inexpensive instrumentation. The system makes use of urease labeled affinity reagents for developing the microarrays and is based on detection of conductivity changes taking place when ionic species are generated in solution due to the catalytic hydrolysis of urea. The use of a polydimethylsiloxane microwell array facilitates the positioning of the measurement solution on every spot of the microarray. Also, it ensures the liquid tightness and isolation from the surrounding ones during the microarray readout process, thereby avoiding evaporation and chemical cross-talk effects that were shown to affect the sensitivity and reliability of the system. The performance of the system is demonstrated by carrying out the readout of a microarray for boldenone anabolic androgenic steroid hormone. Analytical results are comparable to those obtained by fluorescent scanner detection approaches. The estimated detection limit is 4.0 ng mL(-1), this being below the threshold value set by the World Anti-Doping Agency and the European Community.

  1. 3D whole body scanners revisited

    NARCIS (Netherlands)

    Daanen, H.A.M.; Haar, F.B. ter

    2013-01-01

    An overview of whole body scanners in 1998 (H.A.M. Daanen, G.J. Van De Water. Whole body scanners, Displays 19 (1998) 111-120) shortly after they emerged to the market revealed that the systems were bulky, slow, expensive and low in resolution. This update shows that new developments in sensing and

  2. Long-Range WindScanner System

    DEFF Research Database (Denmark)

    Vasiljevic, Nikola; Lea, Guillaume; Courtney, Michael

    2016-01-01

    The technical aspects of a multi-Doppler LiDAR instrument, the long-range WindScanner system, are presented accompanied by an overview of the results from several field campaigns. The long-range WindScanner system consists of three spatially-separated, scanning coherent Doppler LiDARs and a remot...

  3. DNA Microarray-Based Diagnostics.

    Science.gov (United States)

    Marzancola, Mahsa Gharibi; Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

    The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.

  4. Evaluating Commercial Scanners for Astronomical Image Digitization

    Science.gov (United States)

    Simcoe, R. J.

    2009-08-01

    Many organizations have been interested in understanding if commercially available scanners are adequate for scientifically useful digitization. These scanners range in price from a few hundred to a few tens of thousands of dollars (USD), often with little apparent difference in performance specifications. This paper describes why the underlying technology used in flatbed scanners tends to effectively limit resolutions to the 600-1200 dots per inch (dpi) range and how the overall system Modulation Transfer Function (MTF) can be used to evaluate the quality of the digitized data for the small feature sizes found in astronomical images. Two scanners, the Epson V750 flatbed scanner and the Nikon Cool Scan 9000ED film strip scanner, are evaluated through their Modulation Transfer Functions (MTF). The MTF of the Harvard DASCH scanner is also shown for comparison. The particular goal of this evaluation was to understand if the scanners could be used for digitizing spectral plates at the University of Toronto. The plates of primary interest were about 15 mm (5/8 inch) wide by 180 mm (7~inches) long and ˜50 mm x 80 mm (2 x 3 inches). The results of the MTF work show that the Epson scanner, despite claims of high resolution, is of limited value for scientific imaging of feature sizes below about 50 μm and therefore not a good candidate for digitizing the spectral plates and problematic for scanning direct plates. The Nikon scanner is better and, except for some frustrating limitations in its software, its performance seems to hold promise as a digitizer for spectral plates in the University of Toronto collection.

  5. Oil spill detection using hyperspectral infrared camera

    Science.gov (United States)

    Yu, Hui; Wang, Qun; Zhang, Zhen; Zhang, Zhi-jie; Tang, Wei; Tang, Xin; Yue, Song; Wang, Chen-sheng

    2016-11-01

    Oil spill pollution is a severe environmental problem that persists in the marine environment and in inland water systems around the world. Remote sensing is an important part of oil spill response. The hyperspectral images can not only provide the space information but also the spectral information. Pixels of interests generally incorporate information from disparate component that requires quantitative decomposition of these pixels to extract desired information. Oil spill detection can be implemented by applying hyperspectral camera which can collect the hyperspectral data of the oil. By extracting desired spectral signature from hundreds of band information, one can detect and identify oil spill area in vast geographical regions. There are now numerous hyperspectral image processing algorithms developed for target detection. In this paper, we investigate several most widely used target detection algorithm for the identification of surface oil spills in ocean environment. In the experiments, we applied a hyperspectral camera to collect the real life oil spill. The experimental results shows the feasibility of oil spill detection using hyperspectral imaging and the performance of hyperspectral image processing algorithms were also validated.

  6. An Engineering Trade Space Analysis for a Space-Based Hyperspectral Chromotomographic Scanner

    Science.gov (United States)

    2009-03-26

    65 3.8 CCD/CMOS quantum efficiency . . . . . . . . . . . . . . . . . . . 66 3.9 Monolithic and...Hybrid CMOS . . . . . . . . . . . . . . . . . . . . 67 3.10 CCD vs CMOS at pixel level . . . . . . . . . . . . . . . . . . . . . 68 3.11 Monolithic ...simply an adaptation of the familiar Michelson interferometer. There are several different types of spectral filters. The key idea is that EM

  7. The use of microarray technology for cytogenetics.

    Science.gov (United States)

    Bejjani, Bassem A; Shaffer, Lisa G; Ballif, Blake C

    2010-01-01

    The use of microarray technology is revolutionizing the field of clinical cytogenetics. This new technology has transformed the cytogenetics laboratory by adapting techniques that have heretofore been the province of molecular geneticists. Intimate knowledge and comfortable familiarity with these techniques are now a must for the modern cytogeneticist, rather than a stimulating but discretionary intellectual exercise or an elective luxury. The cytogenetic laboratory of the future will likely have more scanners than microscopes, more software packages than darkrooms, and more technologists, supervisors, and directors with molecular training than ever before. This technical convergence between molecular diagnostics and clinical cytogenetics is exciting and has already resulted in many stimulating discoveries. However, the traditional skills of the cytogeneticist are needed now more than ever before. As our ability to inspect the genome increases, so does the variety of abnormalities that we uncover. Understanding the mechanisms of these aberrations to guide additional testing of the parents and genetic counseling of the patients and their families requires the expertise of individuals who are well-versed in meiotic mechanisms and chromosomal structures that may lead to these abnormalities. Cytogeneticists are uniquely positioned to understand these mechanisms and assist genetic counselors and clinicians in their daily interactions with patients and families.

  8. False alarm recognition in hyperspectral gas plume identification

    Science.gov (United States)

    Conger, James L [San Ramon, CA; Lawson, Janice K [Tracy, CA; Aimonetti, William D [Livermore, CA

    2011-03-29

    According to one embodiment, a method for analyzing hyperspectral data includes collecting first hyperspectral data of a scene using a hyperspectral imager during a no-gas period and analyzing the first hyperspectral data using one or more gas plume detection logics. The gas plume detection logic is executed using a low detection threshold, and detects each occurrence of an observed hyperspectral signature. The method also includes generating a histogram for all occurrences of each observed hyperspectral signature which is detected using the gas plume detection logic, and determining a probability of false alarm (PFA) for all occurrences of each observed hyperspectral signature based on the histogram. Possibly at some other time, the method includes collecting second hyperspectral data, and analyzing the second hyperspectral data using the one or more gas plume detection logics and the PFA to determine if any gas is present. Other systems and methods are also included.

  9. False alarm recognition in hyperspectral gas plume identification

    Energy Technology Data Exchange (ETDEWEB)

    Conger, James L. (San Ramon, CA); Lawson, Janice K. (Tracy, CA); Aimonetti, William D. (Livermore, CA)

    2011-03-29

    According to one embodiment, a method for analyzing hyperspectral data includes collecting first hyperspectral data of a scene using a hyperspectral imager during a no-gas period and analyzing the first hyperspectral data using one or more gas plume detection logics. The gas plume detection logic is executed using a low detection threshold, and detects each occurrence of an observed hyperspectral signature. The method also includes generating a histogram for all occurrences of each observed hyperspectral signature which is detected using the gas plume detection logic, and determining a probability of false alarm (PFA) for all occurrences of each observed hyperspectral signature based on the histogram. Possibly at some other time, the method includes collecting second hyperspectral data, and analyzing the second hyperspectral data using the one or more gas plume detection logics and the PFA to determine if any gas is present. Other systems and methods are also included.

  10. Hyperspectral Transformation from EO-1 ALI Imagery Using Pseudo-Hyperspectral Image Synthesis Algorithm

    Science.gov (United States)

    Tien Hoang, Nguyen; Koike, Katsuaki

    2016-06-01

    Hyperspectral remote sensing is more effective than multispectral remote sensing in many application fields because of having hundreds of observation bands with high spectral resolution. However, hyperspectral remote sensing resources are limited both in temporal and spatial coverage. Therefore, simulation of hyperspectral imagery from multispectral imagery with a small number of bands must be one of innovative topics. Based on this background, we have recently developed a method, Pseudo-Hyperspectral Image Synthesis Algorithm (PHISA), to transform Landsat imagery into hyperspectral imagery using the correlation of reflectance at the corresponding bands between Landsat and EO-1 Hyperion data. This study extends PHISA to simulate pseudo-hyperspectral imagery from EO-1 ALI imagery. The pseudo-hyperspectral imagery has the same number of bands as that of high-quality Hyperion bands and the same swath width as ALI scene. The hyperspectral reflectance data simulated from the ALI data show stronger correlation with the original Hyperion data than the one simulated from Landsat data. This high correlation originates from the concurrent observation by the ALI and Hyperion sensors that are on-board the same satellite. The accuracy of simulation results are verified by a statistical analysis and a surface mineral mapping. With a combination of the advantages of both ALI and Hyperion image types, the pseudo-hyperspectral imagery is proved to be useful for detailed identification of minerals for the areas outside the Hyperion coverage.

  11. Hyperspectral remote sensing for terrestrial applications

    Science.gov (United States)

    Thenkabail, Prasad S.; Teluguntla, Pardhasaradhi G.; Murali Krishna Gumma,; Venkateswarlu Dheeravath,

    2015-01-01

    Remote sensing data are considered hyperspectral when the data are gathered from numerous wavebands, contiguously over an entire range of the spectrum (e.g., 400–2500 nm). Goetz (1992) defines hyperspectral remote sensing as “The acquisition of images in hundreds of registered, contiguous spectral bands such that for each picture element of an image it is possible to derive a complete reflectance spectrum.” However, Jensen (2004) defines hyperspectral remote sensing as “The simultaneous acquisition of images in many relatively narrow, contiguous and/or non contiguous spectral bands throughout the ultraviolet, visible, and infrared portions of the electromagnetic spectrum.

  12. Determining Spectral Reflectance Coefficients from Hyperspectral Images Obtained from Low Altitudes

    Science.gov (United States)

    Walczykowski, P.; Jenerowicz, A.; Orych, A.; Siok, K.

    2016-06-01

    Remote Sensing plays very important role in many different study fields, like hydrology, crop management, environmental and ecosystem studies. For all mentioned areas of interest different remote sensing and image processing techniques, such as: image classification (object and pixel- based), object identification, change detection, etc. can be applied. Most of this techniques use spectral reflectance coefficients as the basis for the identification and distinction of different objects and materials, e.g. monitoring of vegetation stress, identification of water pollutants, yield identification, etc. Spectral characteristics are usually acquired using discrete methods such as spectrometric measurements in both laboratory and field conditions. Such measurements however can be very time consuming, which has led many international researchers to investigate the reliability and accuracy of using image-based methods. According to published and ongoing studies, in order to acquire these spectral characteristics from images, it is necessary to have hyperspectral data. The presented article describes a series of experiments conducted using the push-broom Headwall MicroHyperspec A-series VNIR. This hyperspectral scanner allows for registration of images with more than 300 spectral channels with a 1.9 nm spectral bandwidth in the 380- 1000 nm range. The aim of these experiments was to establish a methodology for acquiring spectral reflectance characteristics of different forms of land cover using such sensor. All research work was conducted in controlled conditions from low altitudes. Hyperspectral images obtained with this specific type of sensor requires a unique approach in terms of post-processing, especially radiometric correction. Large amounts of acquired imagery data allowed the authors to establish a new post- processing approach. The developed methodology allowed the authors to obtain spectral reflectance coefficients from a hyperspectral sensor mounted on an

  13. DETERMINING SPECTRAL REFLECTANCE COEFFICIENTS FROM HYPERSPECTRAL IMAGES OBTAINED FROM LOW ALTITUDES

    Directory of Open Access Journals (Sweden)

    P. Walczykowski

    2016-06-01

    Full Text Available Remote Sensing plays very important role in many different study fields, like hydrology, crop management, environmental and ecosystem studies. For all mentioned areas of interest different remote sensing and image processing techniques, such as: image classification (object and pixel- based, object identification, change detection, etc. can be applied. Most of this techniques use spectral reflectance coefficients as the basis for the identification and distinction of different objects and materials, e.g. monitoring of vegetation stress, identification of water pollutants, yield identification, etc. Spectral characteristics are usually acquired using discrete methods such as spectrometric measurements in both laboratory and field conditions. Such measurements however can be very time consuming, which has led many international researchers to investigate the reliability and accuracy of using image-based methods. According to published and ongoing studies, in order to acquire these spectral characteristics from images, it is necessary to have hyperspectral data. The presented article describes a series of experiments conducted using the push-broom Headwall MicroHyperspec A-series VNIR. This hyperspectral scanner allows for registration of images with more than 300 spectral channels with a 1.9 nm spectral bandwidth in the 380- 1000 nm range. The aim of these experiments was to establish a methodology for acquiring spectral reflectance characteristics of different forms of land cover using such sensor. All research work was conducted in controlled conditions from low altitudes. Hyperspectral images obtained with this specific type of sensor requires a unique approach in terms of post-processing, especially radiometric correction. Large amounts of acquired imagery data allowed the authors to establish a new post- processing approach. The developed methodology allowed the authors to obtain spectral reflectance coefficients from a hyperspectral sensor

  14. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.

    2012-01-01

    industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high......-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  15. Transfection microarray and the applications.

    Science.gov (United States)

    Miyake, Masato; Yoshikawa, Tomohiro; Fujita, Satoshi; Miyake, Jun

    2009-05-01

    Microarray transfection has been extensively studied for high-throughput functional analysis of mammalian cells. However, control of efficiency and reproducibility are the critical issues for practical use. By using solid-phase transfection accelerators and nano-scaffold, we provide a highly efficient and reproducible microarray-transfection device, "transfection microarray". The device would be applied to the limited number of available primary cells and stem cells not only for large-scale functional analysis but also reporter-based time-lapse cellular event analysis.

  16. Common hyperspectral image database design

    Science.gov (United States)

    Tian, Lixun; Liao, Ningfang; Chai, Ali

    2009-11-01

    This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

  17. A Cross-Platform Smartphone Brain Scanner

    DEFF Research Database (Denmark)

    Larsen, Jakob Eg; Stopczynski, Arkadiusz; Stahlhut, Carsten

    We describe a smartphone brain scanner with a low-costwireless 14-channel Emotiv EEG neuroheadset interfacingwith multiple mobile devices. This personal informaticssystem enables minimally invasive and continuouscapturing of brain imaging data in natural settings. Thesystem applies an inverse...

  18. Onboard Image Processing System for Hyperspectral Sensor

    National Research Council Canada - National Science Library

    Hihara, Hiroki; Moritani, Kotaro; Inoue, Masao; Hoshi, Yoshihiro; Iwasaki, Akira; Takada, Jun; Inada, Hitomi; Suzuki, Makoto; Seki, Taeko; Ichikawa, Satoshi; Tanii, Jun

    2015-01-01

    .... Since more than 100 channels are required for hyperspectral sensors on Earth observation satellites, fast and small-footprint lossless image compression capability is essential for reducing the size...

  19. Automated Feature Extraction from Hyperspectral Imagery Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed activities will result in the development of a novel hyperspectral feature-extraction toolkit that will provide a simple, automated, and accurate...

  20. Spherical stochastic neighbor embedding of hyperspectral data

    CSIR Research Space (South Africa)

    Lunga, D

    2012-07-01

    Full Text Available In hyperspectral imagery, low-dimensional representations are sought in order to explain well the nonlinear characteristics that are hidden in high-dimensional spectral channels. While many algorithms have been proposed for dimension reduction...

  1. Automated Feature Extraction from Hyperspectral Imagery Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In response to NASA Topic S7.01, Visual Learning Systems, Inc. (VLS) will develop a novel hyperspectral plug-in toolkit for its award winning Feature AnalystREG...

  2. Endmember extraction algorithms from hyperspectral images

    Directory of Open Access Journals (Sweden)

    M. C. Cantero

    2006-06-01

    Full Text Available During the last years, several high-resolution sensors have been developed for hyperspectral remote sensing applications. Some of these sensors are already available on space-borne devices. Space-borne sensors are currently acquiring a continual stream of hyperspectral data, and new efficient unsupervised algorithms are required to analyze the great amount of data produced by these instruments. The identification of image endmembers is a crucial task in hyperspectral data exploitation. Once the individual endmembers have been identified, several methods can be used to map their spatial distribution, associations and abundances. This paper reviews the Pixel Purity Index (PPI, N-FINDR and Automatic Morphological Endmember Extraction (AMEE algorithms developed to accomplish the task of finding appropriate image endmembers by applying them to real hyperspectral data. In order to compare the performance of these methods a metric based on the Root Mean Square Error (RMSE between the estimated and reference abundance maps is used.

  3. Endmember initialization method for hyperspectral data unmixing

    Science.gov (United States)

    Wang, Rui; Li, Hengchao; Liao, Wenzhi; Huang, Xin

    2016-10-01

    Spectral unmixing aims at finding the spectrally pure constituent materials (also called endmembers) and their respective fractional abundances in each pixel of the hyperspectral image scene. One important issue in hyperspectral data unmixing is the initialization of endmembers. Most unmixing methods initialize their endmembers by randomly selecting a specified number of pixels from the data or by vertex component analysis, which limits their performance in practice. We propose an endmember initialization method for hyperspectral data unmixing. Our initial endmembers include some of the true endmembers, which improves the accuracy of hyperpspectral unmixing effectively. The experimental results on both synthetic and real hyperspectral data illustrate the superiority of the proposed method compared with other state-of-the-art approaches.

  4. How flatbed scanners upset accurate film dosimetry.

    Science.gov (United States)

    van Battum, L J; Huizenga, H; Verdaasdonk, R M; Heukelom, S

    2016-01-21

    Film is an excellent dosimeter for verification of dose distributions due to its high spatial resolution. Irradiated film can be digitized with low-cost, transmission, flatbed scanners. However, a disadvantage is their lateral scan effect (LSE): a scanner readout change over its lateral scan axis. Although anisotropic light scattering was presented as the origin of the LSE, this paper presents an alternative cause. Hereto, LSE for two flatbed scanners (Epson 1680 Expression Pro and Epson 10000XL), and Gafchromic film (EBT, EBT2, EBT3) was investigated, focused on three effects: cross talk, optical path length and polarization. Cross talk was examined using triangular sheets of various optical densities. The optical path length effect was studied using absorptive and reflective neutral density filters with well-defined optical characteristics (OD range 0.2-2.0). Linear polarizer sheets were used to investigate light polarization on the CCD signal in absence and presence of (un)irradiated Gafchromic film. Film dose values ranged between 0.2 to 9 Gy, i.e. an optical density range between 0.25 to 1.1. Measurements were performed in the scanner's transmission mode, with red-green-blue channels. LSE was found to depend on scanner construction and film type. Its magnitude depends on dose: for 9 Gy increasing up to 14% at maximum lateral position. Cross talk was only significant in high contrast regions, up to 2% for very small fields. The optical path length effect introduced by film on the scanner causes 3% for pixels in the extreme lateral position. Light polarization due to film and the scanner's optical mirror system is the main contributor, different in magnitude for the red, green and blue channel. We concluded that any Gafchromic EBT type film scanned with a flatbed scanner will face these optical effects. Accurate dosimetry requires correction of LSE, therefore, determination of the LSE per color channel and dose delivered to the film.

  5. Effects of Lossy Compression of Hyperspectral Imagery

    Science.gov (United States)

    2007-11-02

    and Ma and Redmond [18] suggest using gia = 1/L. Ma and Redmond argue that, when Cref is generated by unsupervised classification methods, there is...Institute of Technology Lincoln Laboratory Effects of Lossy Compression of Hyperspectral Imagery J.K. Sit Group 103 (Jbrrnerly Group 97) M.K. Griffin S.M...Massachusetts EXECUTIVE SUMMARY Hyperspectral imaging (HSI) sensors provide imagery with hundreds of spectral bands, typ- ically covering VNIR and/or SWIR

  6. Discriminative Sparse Representations in Hyperspectral Imagery

    Science.gov (United States)

    2010-03-01

    classification , and unsupervised labeling (clustering) [2, 3, 4, 5, 6, 7, 8]. Recently, a non-parametric (Bayesian) approach to sparse modeling and com...DISCRIMINATIVE SPARSE REPRESENTATIONS IN HYPERSPECTRAL IMAGERY By Alexey Castrodad, Zhengming Xing John Greer, Edward Bosch Lawrence Carin and...00-00-2010 to 00-00-2010 4. TITLE AND SUBTITLE Discriminative Sparse Representations in Hyperspectral Imagery 5a. CONTRACT NUMBER 5b. GRANT

  7. Kernel based subspace projection of hyperspectral images

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Nielsen, Allan Aasbjerg; Arngren, Morten

    In hyperspectral image analysis an exploratory approach to analyse the image data is to conduct subspace projections. As linear projections often fail to capture the underlying structure of the data, we present kernel based subspace projections of PCA and Maximum Autocorrelation Factors (MAF). Th......). The MAF projection exploits the fact that interesting phenomena in images typically exhibit spatial autocorrelation. The analysis is based on nearinfrared hyperspectral images of maize grains demonstrating the superiority of the kernelbased MAF method....

  8. Uncertainty Propagation for Terrestrial Mobile Laser Scanner

    Science.gov (United States)

    Mezian, c.; Vallet, Bruno; Soheilian, Bahman; Paparoditis, Nicolas

    2016-06-01

    Laser scanners are used more and more in mobile mapping systems. They provide 3D point clouds that are used for object reconstruction and registration of the system. For both of those applications, uncertainty analysis of 3D points is of great interest but rarely investigated in the literature. In this paper we present a complete pipeline that takes into account all the sources of uncertainties and allows to compute a covariance matrix per 3D point. The sources of uncertainties are laser scanner, calibration of the scanner in relation to the vehicle and direct georeferencing system. We suppose that all the uncertainties follow the Gaussian law. The variances of the laser scanner measurements (two angles and one distance) are usually evaluated by the constructors. This is also the case for integrated direct georeferencing devices. Residuals of the calibration process were used to estimate the covariance matrix of the 6D transformation between scanner laser and the vehicle system. Knowing the variances of all sources of uncertainties, we applied uncertainty propagation technique to compute the variance-covariance matrix of every obtained 3D point. Such an uncertainty analysis enables to estimate the impact of different laser scanners and georeferencing devices on the quality of obtained 3D points. The obtained uncertainty values were illustrated using error ellipsoids on different datasets.

  9. Hybrid Prediction and Fractal Hyperspectral Image Compression

    Directory of Open Access Journals (Sweden)

    Shiping Zhu

    2015-01-01

    Full Text Available The data size of hyperspectral image is too large for storage and transmission, and it has become a bottleneck restricting its applications. So it is necessary to study a high efficiency compression method for hyperspectral image. Prediction encoding is easy to realize and has been studied widely in the hyperspectral image compression field. Fractal coding has the advantages of high compression ratio, resolution independence, and a fast decoding speed, but its application in the hyperspectral image compression field is not popular. In this paper, we propose a novel algorithm for hyperspectral image compression based on hybrid prediction and fractal. Intraband prediction is implemented to the first band and all the remaining bands are encoded by modified fractal coding algorithm. The proposed algorithm can effectively exploit the spectral correlation in hyperspectral image, since each range block is approximated by the domain block in the adjacent band, which is of the same size as the range block. Experimental results indicate that the proposed algorithm provides very promising performance at low bitrate. Compared to other algorithms, the encoding complexity is lower, the decoding quality has a great enhancement, and the PSNR can be increased by about 5 dB to 10 dB.

  10. Distributed Parallel Endmember Extraction of Hyperspectral Data Based on Spark

    Directory of Open Access Journals (Sweden)

    Zebin Wu

    2016-01-01

    Full Text Available Due to the increasing dimensionality and volume of remotely sensed hyperspectral data, the development of acceleration techniques for massive hyperspectral image analysis approaches is a very important challenge. Cloud computing offers many possibilities of distributed processing of hyperspectral datasets. This paper proposes a novel distributed parallel endmember extraction method based on iterative error analysis that utilizes cloud computing principles to efficiently process massive hyperspectral data. The proposed method takes advantage of technologies including MapReduce programming model, Hadoop Distributed File System (HDFS, and Apache Spark to realize distributed parallel implementation for hyperspectral endmember extraction, which significantly accelerates the computation of hyperspectral processing and provides high throughput access to large hyperspectral data. The experimental results, which are obtained by extracting endmembers of hyperspectral datasets on a cloud computing platform built on a cluster, demonstrate the effectiveness and computational efficiency of the proposed method.

  11. Segmentation and intensity estimation for microarray images with saturated pixels

    Directory of Open Access Journals (Sweden)

    Yang Yan

    2011-11-01

    Full Text Available Abstract Background Microarray image analysis processes scanned digital images of hybridized arrays to produce the input spot-level data for downstream analysis, so it can have a potentially large impact on those and subsequent analysis. Signal saturation is an optical effect that occurs when some pixel values for highly expressed genes or peptides exceed the upper detection threshold of the scanner software (216 - 1 = 65, 535 for 16-bit images. In practice, spots with a sizable number of saturated pixels are often flagged and discarded. Alternatively, the saturated values are used without adjustments for estimating spot intensities. The resulting expression data tend to be biased downwards and can distort high-level analysis that relies on these data. Hence, it is crucial to effectively correct for signal saturation. Results We developed a flexible mixture model-based segmentation and spot intensity estimation procedure that accounts for saturated pixels by incorporating a censored component in the mixture model. As demonstrated with biological data and simulation, our method extends the dynamic range of expression data beyond the saturation threshold and is effective in correcting saturation-induced bias when the lost information is not tremendous. We further illustrate the impact of image processing on downstream classification, showing that the proposed method can increase diagnostic accuracy using data from a lymphoma cancer diagnosis study. Conclusions The presented method adjusts for signal saturation at the segmentation stage that identifies a pixel as part of the foreground, background or other. The cluster membership of a pixel can be altered versus treating saturated values as truly observed. Thus, the resulting spot intensity estimates may be more accurate than those obtained from existing methods that correct for saturation based on already segmented data. As a model-based segmentation method, our procedure is able to identify inner

  12. Multi- and hyperspectral scene modeling

    Science.gov (United States)

    Borel, Christoph C.; Tuttle, Ronald F.

    2011-06-01

    This paper shows how to use a public domain raytracer POV-Ray (Persistence Of Vision Raytracer) to render multiand hyper-spectral scenes. The scripting environment allows automatic changing of the reflectance and transmittance parameters. The radiosity rendering mode allows accurate simulation of multiple-reflections between surfaces and also allows semi-transparent surfaces such as plant leaves. We show that POV-Ray computes occlusion accurately using a test scene with two blocks under a uniform sky. A complex scene representing a plant canopy is generated using a few lines of script. With appropriate rendering settings, shadows cast by leaves are rendered in many bands. Comparing single and multiple reflection renderings, the effect of multiple reflections is clearly visible and accounts for 25% of the overall apparent canopy reflectance in the near infrared.

  13. MEMS temperature scanner: principles, advances, and applications

    Science.gov (United States)

    Otto, Thomas; Saupe, Ray; Stock, Volker; Gessner, Thomas

    2010-02-01

    Contactless measurement of temperatures has gained enormous significance in many application fields, ranging from climate protection over quality control to object recognition in public places or military objects. Thereby measurement of linear or spatially temperature distribution is often necessary. For this purposes mostly thermographic cameras or motor driven temperature scanners are used today. Both are relatively expensive and the motor drive devices are limited regarding to the scanning rate additionally. An economic alternative are temperature scanner devices based on micro mirrors. The micro mirror, attached in a simple optical setup, reflects the emitted radiation from the observed heat onto an adapted detector. A line scan of the target object is obtained by periodic deflection of the micro scanner. Planar temperature distribution will be achieved by perpendicularly moving the target object or the scanner device. Using Planck radiation law the temperature of the object is calculated. The device can be adapted to different temperature ranges and resolution by using different detectors - cooled or uncooled - and parameterized scanner parameters. With the basic configuration 40 spatially distributed measuring points can be determined with temperatures in a range from 350°C - 1000°C. The achieved miniaturization of such scanners permits the employment in complex plants with high building density or in direct proximity to the measuring point. The price advantage enables a lot of applications, especially new application in the low-price market segment This paper shows principle, setup and application of a temperature measurement system based on micro scanners working in the near infrared range. Packaging issues and measurement results will be discussed as well.

  14. Microarray Technologies in Fungal Diagnostics.

    Science.gov (United States)

    Rupp, Steffen

    2017-01-01

    Microarray technologies have been a major research tool in the last decades. In addition they have been introduced into several fields of diagnostics including diagnostics of infectious diseases. Microarrays are highly parallelized assay systems that initially were developed for multiparametric nucleic acid detection. From there on they rapidly developed towards a tool for the detection of all kind of biological compounds (DNA, RNA, proteins, cells, nucleic acids, carbohydrates, etc.) or their modifications (methylation, phosphorylation, etc.). The combination of closed-tube systems and lab on chip devices with microarrays further enabled a higher automation degree with a reduced contamination risk. Microarray-based diagnostic applications currently complement and may in the future replace classical methods in clinical microbiology like blood cultures, resistance determination, microscopic and metabolic analyses as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel nucleic acid based biomarkers. Here I focus an microarray technologies in diagnostics and as research tools, based on nucleic acid-based arrays.

  15. Investigation of Tree Spectral Reflectance Characteristics Using a Mobile Terrestrial Line Spectrometer and Laser Scanner

    Directory of Open Access Journals (Sweden)

    Eetu Puttonen

    2013-07-01

    Full Text Available In mobile terrestrial hyperspectral imaging, individual trees often present large variations in spectral reflectance that may impact the relevant applications, but the related studies have been seldom reported. To fill this gap, this study was dedicated to investigating the spectral reflectance characteristics of individual trees with a Sensei mobile mapping system, which comprises a Specim line spectrometer and an Ibeo Lux laser scanner. The addition of the latter unit facilitates recording the structural characteristics of the target trees synchronously, and this is beneficial for revealing the characteristics of the spatial distributions of tree spectral reflectance with variations at different levels. Then, the parts of trees with relatively low-level variations can be extracted. At the same time, since it is difficult to manipulate the whole spectrum, the traditional concept of vegetation indices (VI based on some particular spectral bands was taken into account here. Whether the assumed VIs capable of behaving consistently for the whole crown of each tree was also checked. The specific analyses were deployed based on four deciduous tree species and six kinds of VIs. The test showed that with the help of the laser scanner data, the parts of individual trees with relatively low-level variations can be located. Based on these parts, the relatively stable spectral reflectance characteristics for different tree species can be learnt.

  16. Carbohydrate microarrays in plant science.

    Science.gov (United States)

    Fangel, Jonatan U; Pedersen, Henriette L; Vidal-Melgosa, Silvia; Ahl, Louise I; Salmean, Armando Asuncion; Egelund, Jack; Rydahl, Maja Gro; Clausen, Mads H; Willats, William G T

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities.

  17. Glass slides to DNA microarrays

    Directory of Open Access Journals (Sweden)

    Samuel D Conzone

    2004-03-01

    Full Text Available A tremendous interest in deoxyribonucleic acid (DNA characterization tools was spurred by the mapping and sequencing of the human genome. New tools were needed, beginning in the early 1990s, to cope with the unprecedented amount of genomic information that was being discovered. Such needs led to the development of DNA microarrays; tiny gene-based sensors traditionally prepared on coated glass microscope slides. The following review is intended to provide historical insight into the advent of the DNA microarray, followed by a description of the technology from both the application and fabrication points of view. Finally, the unmet challenges and needs associated with DNA microarrays will be described to define areas of potential future developments for the materials researcher.

  18. Phenotypic MicroRNA Microarrays

    OpenAIRE

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the bio...

  19. Manually operated small envelope scanner system

    Energy Technology Data Exchange (ETDEWEB)

    Sword, Charles Keith

    2017-04-18

    A scanner system and method for acquisition of position-based ultrasonic inspection data are described. The scanner system includes an inspection probe and a first non-contact linear encoder having a first sensor and a first scale to track inspection probe position. The first sensor is positioned to maintain a continuous non-contact interface between the first sensor and the first scale and to maintain a continuous alignment of the first sensor with the inspection probe. The scanner system may be used to acquire two-dimensional inspection probe position data by including a second non-contact linear encoder having a second sensor and a second scale, the second sensor positioned to maintain a continuous non-contact interface between the second sensor and the second scale and to maintain a continuous alignment of the second sensor with the first sensor.

  20. A flexible and wearable terahertz scanner

    Science.gov (United States)

    Suzuki, D.; Oda, S.; Kawano, Y.

    2016-12-01

    Imaging technologies based on terahertz (THz) waves have great potential for use in powerful non-invasive inspection methods. However, most real objects have various three-dimensional curvatures and existing THz technologies often encounter difficulties in imaging such configurations, which limits the useful range of THz imaging applications. Here, we report the development of a flexible and wearable THz scanner based on carbon nanotubes. We achieved room-temperature THz detection over a broad frequency band ranging from 0.14 to 39 THz and developed a portable THz scanner. Using this scanner, we performed THz imaging of samples concealed behind opaque objects, breakages and metal impurities of a bent film and multi-view scans of a syringe. We demonstrated a passive biometric THz scan of a human hand. Our results are expected to have considerable implications for non-destructive and non-contact inspections, such as medical examinations for the continuous monitoring of health conditions.

  1. Characterization of the Ferrara animal PET scanner

    CERN Document Server

    Di Domenico, G; Damiani, C; Del Guerra, A; Gilardi, M C; Motta, A; Zavattini, G

    2002-01-01

    A dedicated small animal PET scanner, YAPPET, was designed and built at Ferrara University. Each detector consists of a 20x20 matrix of 2x2x30 mm sup 3 YAP:Ce finger-like crystals glued together and directly coupled to a Hamamatsu position sensitive photomultiplier. The scanner is made from four detectors positioned on a rotating gantry at a distance of 7.5 cm from the center and the field of view (FOV) is 4 cm both in the transaxial direction and in the axial direction. The system operates in 3D acquisition mode. The performance parameters of YAPPET scanner such as spatial, energy and time resolution, as well as its sensitivity and counting rate have been determined. The average spatial resolution over the whole FOV is 1.8 mm at FWHM and 4.2 mm at FWTM. The sensitivity at the center is 640 cps/mu Ci.

  2. MEMS FPI-based smartphone hyperspectral imager

    Science.gov (United States)

    Rissanen, Anna; Saari, Heikki; Rainio, Kari; Stuns, Ingmar; Viherkanto, Kai; Holmlund, Christer; Näkki, Ismo; Ojanen, Harri

    2016-05-01

    This paper demonstrates a mobile phone- compatible hyperspectral imager based on a tunable MEMS Fabry-Perot interferometer. The realized iPhone 5s hyperspectral imager (HSI) demonstrator utilizes MEMS FPI tunable filter for visible-range, which consist of atomic layer deposited (ALD) Al2O3/TiO2-thin film Bragg reflectors. Characterization results for the mobile phone hyperspectral imager utilizing MEMS FPI chip optimized for 500 nm is presented; the operation range is λ = 450 - 550 nm with FWHM between 8 - 15 nm. Also a configuration of two cascaded FPIs (λ = 500 nm and λ = 650 nm) combined with an RGB colour camera is presented. With this tandem configuration, the overall wavelength tuning range of MEMS hyperspectral imagers can be extended to cover a larger range than with a single FPI chip. The potential applications of mobile hyperspectral imagers in the vis-NIR range include authentication, counterfeit detection and potential health/wellness and food sensing applications.

  3. Parallel hyperspectral image reconstruction using random projections

    Science.gov (United States)

    Sevilla, Jorge; Martín, Gabriel; Nascimento, José M. P.

    2016-10-01

    Spaceborne sensors systems are characterized by scarce onboard computing and storage resources and by communication links with reduced bandwidth. Random projections techniques have been demonstrated as an effective and very light way to reduce the number of measurements in hyperspectral data, thus, the data to be transmitted to the Earth station is reduced. However, the reconstruction of the original data from the random projections may be computationally expensive. SpeCA is a blind hyperspectral reconstruction technique that exploits the fact that hyperspectral vectors often belong to a low dimensional subspace. SpeCA has shown promising results in the task of recovering hyperspectral data from a reduced number of random measurements. In this manuscript we focus on the implementation of the SpeCA algorithm for graphics processing units (GPU) using the compute unified device architecture (CUDA). Experimental results conducted using synthetic and real hyperspectral datasets on the GPU architecture by NVIDIA: GeForce GTX 980, reveal that the use of GPUs can provide real-time reconstruction. The achieved speedup is up to 22 times when compared with the processing time of SpeCA running on one core of the Intel i7-4790K CPU (3.4GHz), with 32 Gbyte memory.

  4. Novel hyperspectral imager for lightweight UAVs

    Science.gov (United States)

    Saari, Heikki; Aallos, Ville-Veikko; Holmlund, Christer; Mäkynen, Jussi; Delauré, Bavo; Nackaerts, Kris; Michiels, Bart

    2010-04-01

    VTT Technical Research Centre of Finland has developed a new miniaturized staring hyperspectral imager with a weight of 350 g making the system compatible with lightweight UAS platforms. The instrument is able to record 2D spatial images at the selected wavelength bands simultaneously. The concept of the hyperspectral imager has been published in the SPIE Proc. 74741. The operational wavelength range of the imager can be tuned in the range 400 - 1100 nm and spectral resolution is in the range 5 - 10 nm @ FWHM. Presently the spatial resolution is 480 × 750 pixels but it can be increased simply by changing the image sensor. The field of view of the system is 20 × 30 degrees and ground pixel size at 100 m flying altitude is around 7.5 cm. The system contains batteries, image acquisition control system and memory for the image data. It can operate autonomously recording hyperspectral data cubes continuously or controlled by the autopilot system of the UAS. The new hyperspectral imager prototype was first tried in co-operation with the Flemish Institute for Technological Research (VITO) on their UAS helicopter. The instrument was configured for the spectral range 500 - 900 nm selected for the vegetation and natural water monitoring applications. The design of the UAS hyperspectral imager and its characterization results together with the analysis of the spectral data from first test flights will be presented.

  5. Metal Optics For Laser Profile Scanners

    Science.gov (United States)

    Klauke, T.; Hock, F.

    1987-01-01

    Laser scanners are a valuable tool for qualitiy control in hostile hot and vibrating environments. Their high measuring speed allows time minimisation of disturbing influences. The loss of accuracy of systems due to thermal distortion could be minimised by designing mechanical-optical systems with low temperature gradients and small differences between thermal expansions of the components. For application in the forging production a laser scanner measuring in situ a series of profile lines describing the hot forging tools has been designed using aluminium for all distortion sensitive mechanical and optical components.

  6. Hyperspectral imaging and its applications

    Science.gov (United States)

    Serranti, S.; Bonifazi, G.

    2016-04-01

    Hyperspectral imaging (HSI) is an emerging technique that combines the imaging properties of a digital camera with the spectroscopic properties of a spectrometer able to detect the spectral attributes of each pixel in an image. For these characteristics, HSI allows to qualitatively and quantitatively evaluate the effects of the interactions of light with organic and/or inorganic materials. The results of this interaction are usually displayed as a spectral signature characterized by a sequence of energy values, in a pre-defined wavelength interval, for each of the investigated/collected wavelength. Following this approach, it is thus possible to collect, in a fast and reliable way, spectral information that are strictly linked to chemical-physical characteristics of the investigated materials and/or products. Considering that in an hyperspectral image the spectrum of each pixel can be analyzed, HSI can be considered as one of the best nondestructive technology allowing to perform the most accurate and detailed information extraction. HSI can be applied in different wavelength fields, the most common are the visible (VIS: 400-700 nm), the near infrared (NIR: 1000-1700 nm) and the short wave infrared (SWIR: 1000-2500 nm). It can be applied for inspections from micro- to macro-scale, up to remote sensing. HSI produces a large amount of information due to the great number of continuous collected spectral bands. Such an approach, when successful, is quite challenging being usually reliable, robust and characterized by lower costs, if compared with those usually associated to commonly applied analytical off-line and/or on-line analytical approaches. More and more applications have been thus developed and tested, in these last years, especially in food inspection, with a large range of investigated products, such as fruits and vegetables, meat, fish, eggs and cereals, but also in medicine and pharmaceutical sector, in cultural heritage, in material characterization and in

  7. Combining microarrays and genetic analysis

    NARCIS (Netherlands)

    Alberts, Rudi; Fu, Jingyuan; Swertz, Morris A.; Lubbers, L. Alrik; Albers, Casper J.; Jansen, Ritsert C.

    2005-01-01

    Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a

  8. Combining microarrays and genetic analysis

    NARCIS (Netherlands)

    Alberts, Rudi; Fu, Jingyuan; Swertz, Morris A.; Lubbers, L. Alrik; Albers, Casper J.; Jansen, Ritsert C.

    2005-01-01

    Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a st

  9. Identification of invasive and expansive plant species based on airborne hyperspectral and ALS data

    Science.gov (United States)

    Szporak-Wasilewska, Sylwia; Kuc, Gabriela; Jóźwiak, Jacek; Demarchi, Luca; Chormański, Jarosław; Marcinkowska-Ochtyra, Adriana; Ochtyra, Adrian; Jarocińska, Anna; Sabat, Anita; Zagajewski, Bogdan; Tokarska-Guzik, Barbara; Bzdęga, Katarzyna; Pasierbiński, Andrzej; Fojcik, Barbara; Jędrzejczyk-Korycińska, Monika; Kopeć, Dominik; Wylazłowska, Justyna; Woziwoda, Beata; Michalska-Hejduk, Dorota; Halladin-Dąbrowska, Anna

    2017-04-01

    The aim of Natura 2000 network is to ensure the long term survival of most valuable and threatened species and habitats in Europe. The encroachment of invasive alien and expansive native plant species is among the most essential threat that can cause significant damage to protected habitats and their biodiversity. The phenomenon requires comprehensive and efficient repeatable solutions that can be applied to various areas in order to assess the impact on habitats. The aim of this study is to investigate of the issue of invasive and expansive plant species as they affect protected areas at a larger scale of Natura 2000 network in Poland. In order to determine the scale of the problem we have been developing methods of identification of invasive and expansive species and then detecting their occurrence and mapping their distribution in selected protected areas within Natura 2000 network using airborne hyperspectral and airborne laser scanning data. The aerial platform used consists of hyperspectral HySpex scanner (451 bands in VNIR and SWIR), Airborne Laser Scanner (FWF) Riegl Lite Mapper and RGB camera. It allowed to obtain simultaneous 1 meter resolution hyperspectral image, 0.1 m resolution orthophotomaps and point cloud data acquired with 7 points/m2. Airborne images were acquired three times per year during growing season to account for plant seasonal change (in May/June, July/August and September/October 2016). The hyperspectral images were radiometrically, geometrically and atmospherically corrected. Atmospheric correction was performed and validated using ASD FieldSpec 4 measurements. ALS point cloud data were used to generate several different topographic, vegetation and intensity products with 1 m spatial resolution. Acquired data (both hyperspectral and ALS) were used to test different classification methods including Mixture Tuned Matched Filtering (MTMF), Spectral Angle Mapper (SAM), Random Forest (RF), Support Vector Machines (SVM), among others

  10. Picky: oligo microarray design for large genomes

    National Research Council Canada - National Science Library

    Chou, Hui-Hsien; Hsia, An-Ping; Mooney, Denise L; Schnable, Patrick S

    2004-01-01

    Many large genomes are getting sequenced nowadays. Biologists are eager to start microarray analysis taking advantage of all known genes of a species, but existing microarray design tools were very inefficient for large genomes...

  11. Advanced hyperspectral imaging system with edge enhancement

    Science.gov (United States)

    Yushkov, K. B.; Molchanov, V. Y.

    2017-03-01

    We developed an acousto-optic hyperspectral imaging system with edge enhancement capability. The system is an add-on to a standard light microscope. Edge enhancement operation mode is aimed for analysis of low-contrast microscopic samples, e.g. unstained cytological smears and histological samples, live cells. Edge-enhancement imaging mode is based on a feature of acousto-optic tunable filters to perform band-pass spatial filtering when unturned from noncritical phase matching geometry is diffraction. Switching between standard hyperspectral imaging and edge-enhancement modes is performed by means of a telecentric amplitude mask.

  12. Hyperspectral photometric stereo for a single capture.

    Science.gov (United States)

    Ozawa, Keisuke; Sato, Imari; Yamaguchi, Masahiro

    2017-03-01

    We present a single-capture photometric stereo method using a hyperspectral camera. A spectrally and spatially designed illumination enables a point-wise estimation of reflectance spectra and surface normals from a single hyperspectral image. The illumination works as a reflectance probe in wide spectral regions where reflectance spectra are measured, and the full spectra are estimated by interpolation. It also works as the resource for shadings in other spectral regions. The accuracy of estimation is evaluated in a simulation. Also, we prepare an experimental setup and demonstrate a surface reconstruction against a real scene.

  13. Radiation calibration for LWIR Hyperspectral Imager Spectrometer

    Science.gov (United States)

    Yang, Zhixiong; Yu, Chunchao; Zheng, Wei-jian; Lei, Zhenggang; Yan, Min; Yuan, Xiaochun; Zhang, Peizhong

    2014-11-01

    The radiometric calibration of LWIR Hyperspectral imager Spectrometer is presented. The lab has been developed to LWIR Interferometric Hyperspectral imager Spectrometer Prototype(CHIPED-I) to study Lab Radiation Calibration, Two-point linear calibration is carried out for the spectrometer by using blackbody respectively. Firstly, calibration measured relative intensity is converted to the absolute radiation lightness of the object. Then, radiation lightness of the object is is converted the brightness temperature spectrum by the method of brightness temperature. The result indicated †that this method of Radiation Calibration calibration was very good.

  14. Hyperspectral Thermal Emission Spectrometer: Engineering Flight Campaign

    Science.gov (United States)

    Johnson, William R.; Hook, Simon J.; Shoen, Steven S.; Eng, Bjorn T.

    2013-01-01

    The Hyperspectral Thermal Emission Spectrometer (HyTES) successfully completed its first set of engineering test flights. HyTES was developed in support of the Hyperspectral Infrared Imager (HyspIRI). HyspIRI is one of the Tier II Decadal Survey missions. HyTES currently provides both high spectral resolution (17 nm) and high spatial resolution (2-5m) data in the thermal infrared (7.5-12 micron) part of the electromagnetic spectrum. HyTES data will be used to help determine the optimum band positions for the HyspIRI Thermal Infrared (TIR) sensor and provide antecedent data for HyspIRI related studies.

  15. Dedicated PET scanners for breast imaging

    Energy Technology Data Exchange (ETDEWEB)

    Freifelder, Richard; Karp, Joel S. [University of Pennsylvania, Department of Radiology, 110 Donner, 3400 Spruce Street, Philadelphia, PA 19104 (United States)

    1997-12-01

    We have used computer simulations to compare two designs for a PET scanner dedicated to breast imaging with a whole-body PET scanner. The new designs combine high spatial resolution, high sensitivity, and good energy resolution to detect small, low-contrast masses. The detectors are position sensitive NaI(Tl) scintillators. The first design is a ring scanner surrounding the breast and the second consists of two planar detectors placed on opposite sides of the breast. We have employed standard performance measures to compare the different designs: contrast, percentage standard deviation of the background, and signal-to-noise ratios of reconstructed images. The results of the simulations show that both of the proposed designs have better lesion detectability than a whole-body scanner. The results also show that contrast is higher in the ring breast system but that the noise is lower in the planar breast system. Overall, the ring system yields images with the best signal-to-noise ratios, although the planar system offers practical advantages for imaging the breast and axilla. (author)

  16. Dedicated PET scanners for breast imaging.

    Science.gov (United States)

    Freifelder, R; Karp, J S

    1997-12-01

    We have used computer simulations to compare two designs for a PET scanner dedicated to breast imaging with a whole-body PET scanner. The new designs combine high spatial resolution, high sensitivity, and good energy resolution to detect small, low-contrast masses. The detectors are position sensitive NaI(Tl) scintillators. The first design is a ring scanner surrounding the breast and the second consists of two planar detectors placed on opposite sides of the breast. We have employed standard performance measures to compare the different designs: contrast, percentage standard deviation of the background, and signal-to-noise ratios of reconstructed images. The results of the simulations show that both of the proposed designs have better lesion detectability than a whole-body scanner. The results also show that contrast is higher in the ring breast system but that the noise is lower in the planar breast system. Overall, the ring system yields images with the best signal-to-noise ratios, although the planar system offers practical advantages for imaging the breast and axilla.

  17. Dedicated PET scanners for breast imaging

    Science.gov (United States)

    Freifelder, Richard; Karp, Joel S.

    1997-12-01

    We have used computer simulations to compare two designs for a PET scanner dedicated to breast imaging with a whole-body PET scanner. The new designs combine high spatial resolution, high sensitivity, and good energy resolution to detect small, low-contrast masses. The detectors are position sensitive NaI(Tl) scintillators. The first design is a ring scanner surrounding the breast and the second consists of two planar detectors placed on opposite sides of the breast. We have employed standard performance measures to compare the different designs: contrast, percentage standard deviation of the background, and signal-to-noise ratios of reconstructed images. The results of the simulations show that both of the proposed designs have better lesion detectability than a whole-body scanner. The results also show that contrast is higher in the ring breast system but that the noise is lower in the planar breast system. Overall, the ring system yields images with the best signal-to-noise ratios, although the planar system offers practical advantages for imaging the breast and axilla.

  18. The PS Booster Fast Wire Scanner

    CERN Document Server

    Burger, S; Priestnall, K; Raich, U

    2003-01-01

    The very tight emittance budget for LHC type beams makes precise emittance measurements in the injector complex a necessity. The PS machine uses 2 fast wire scanners per transverse plane for emittance measurement of the circulating beams. In order to ease comparison the same type of wire scanners have been newly installed in the upstream machine, the PS Booster, where each of the 4 rings is equipped with 2 wire scanners measuring the horizontal and vertical profiles. Those wire scanners use new and more modern control and readout electronics featuring dedicated intelligent motor movement controllers, which relieves the very stringent real time constraints due to the very high speed of 20m/s. In order to be able to measure primary beams at the very low injection energy of the Booster (50MeV) secondary emission currents from the wire can be measured as well as secondary particle flows at higher primary particle energies during and after acceleration. The solution adopted for the control of the devices is descri...

  19. submitter Dynamical Models of a Wire Scanner

    CERN Document Server

    Barjau, Ana; Dehning, Bernd

    2016-01-01

    The accuracy of the beam profile measurements achievable by the current wire scanners at CERN is limited by the vibrations of their mechanical parts. In particular, the vibrations of the carbon wire represent the major source of wire position uncertainty which limits the beam profile measurement accuracy. In the coming years, due to the Large Hadron Collider (LHC) luminosity upgrade, a wire traveling speed up to 20 $m s^{−1}$ and a position measurement accuracy of the order of 1 μm will be required. A new wire scanner design based on the understanding of the wire vibration origin is therefore needed. We present the models developed to understand the main causes of the wire vibrations observed in an existing wire scanner. The development and tuning of those models are based on measurements and tests performed on that CERN proton synchrotron (PS) scanner. The final model for the (wire + fork) system has six degrees-of-freedom (DOF). The wire equations contain three different excitation terms: inertia...

  20. Learning and Teaching with a Computer Scanner

    Science.gov (United States)

    Planinsic, G.; Gregorcic, B.; Etkina, E.

    2014-01-01

    This paper introduces the readers to simple inquiry-based activities (experiments with supporting questions) that one can do with a computer scanner to help students learn and apply the concepts of relative motion in 1 and 2D, vibrational motion and the Doppler effect. We also show how to use these activities to help students think like…

  1. Inter laboratory comparison of industrial CT scanners

    DEFF Research Database (Denmark)

    Angel, Jais Andreas Breusch; Cantatore, Angela; De Chiffre, Leonardo

    2012-01-01

    In this report results from an intercomparison of industrial CT scanners are presented. Three audit items, similar to common industrial parts, were selected for circulation: a single polymer part with complex geometry (Item 1), a simple geometry part made of two polymers (Item 2) and a miniature...

  2. Rail profile control using laser triangulation scanners

    Science.gov (United States)

    Boronahin, Ð. ńlexandr M.; Larionov, Daniil Yu.; Podgornaya, Liudmila N.; Shalymov, Roman V.; Filatov, Yuri V.; Bokhman, Evgueny D.

    2016-11-01

    Rail track geometric parameters measurement requires knowledge of left and right rail head location in each section. First of all displacement in transverse plane of rail head point located at a distance of 14 mm below the running surface, must be controlled [1]. It is carried out by detecting of each rail profile using triangulation laser scanners. Optical image recognition is carried out successfully in the laboratory, approaches used for this purpose are widely known. However, laser scanners operation has several features on railways leading to necessity of traditional approaches adaptation for solving these particular problems. The most significant problem is images noisiness due to the solar flashes and the effect of "Moon path" on the smooth rail surface. Using of optical filters gives inadequate result, because scanner laser diodes radiation frequency varies with temperature changes that forbid the use of narrow-band filters. Consideration of these features requires additional constructive and algorithmic solutions, including involvement of information from other sensors of the system. The specific usage of optical scanners for rail profiles control is the subject of the paper.

  3. A PET scanner developed by CERN

    CERN Multimedia

    Laurent Guiraud

    1998-01-01

    This image shows a Position Emission Tomography (PET) scanner at the Hopital Cantonal Universitaire de Genève. Development of the multiwire proportional chamber at CERN in the mid-1970s was soon seen as a potential device for medical imaging. It is much more sensitive than previous devices and greatly reduced the dose of radiation received by the patient.

  4. Design and characterization of specMACS, a multipurpose hyperspectral cloud and sky imager

    Science.gov (United States)

    Ewald, Florian; Kölling, Tobias; Baumgartner, Andreas; Zinner, Tobias; Mayer, Bernhard

    2016-05-01

    The new spectrometer of the Munich Aerosol Cloud Scanner (specMACS) is a multipurpose hyperspectral cloud and sky imager designated, but is not limited to investigations of cloud-aerosol interactions in Earth's atmosphere. With its high spectral and spatial resolution, the instrument is designed to measure solar radiation in the visible and shortwave infrared region that is reflected from, or transmitted through clouds and aerosol layers. It is based on two hyperspectral cameras that measure in the solar spectral range between 400 and 2500 nm with a spectral bandwidth between 2.5 and 12.0 nm. The instrument was operated in ground-based campaigns as well as aboard the German High Altitude LOng Range (HALO) research aircraft, e.g., during the ACRIDICON-CHUVA campaign in Brazil during summer 2014. This paper describes the specMACS instrument hardware and software design and characterizes the instrument performance. During the laboratory characterization of the instrument, the radiometric response as well as the spatial and spectral resolution was assessed. Since the instrument is primarily intended for retrievals of atmospheric quantities by inversion of radiative models using measured radiances, a focus is placed on the determination of its radiometric response. Radiometric characterization was possible for both spectrometers, with an absolute accuracy of 3 % at their respective central wavelength regions. First measurements are presented which demonstrate the wide applicability of the instrument. They show that key demands are met regarding the radiometric and spectral accuracy which is required for the intended remote sensing techniques.

  5. HIGH RESOLUTION AIRBORNE LASER SCANNING AND HYPERSPECTRAL IMAGING WITH A SMALL UAV PLATFORM

    Directory of Open Access Journals (Sweden)

    M. Gallay

    2016-06-01

    Full Text Available The capabilities of unmanned airborne systems (UAS have become diverse with the recent development of lightweight remote sensing instruments. In this paper, we demonstrate our custom integration of the state-of-the-art technologies within an unmanned aerial platform capable of high-resolution and high-accuracy laser scanning, hyperspectral imaging, and photographic imaging. The technological solution comprises the latest development of a completely autonomous, unmanned helicopter by Aeroscout, the Scout B1-100 UAV helicopter. The helicopter is powered by a gasoline two-stroke engine and it allows for integrating 18 kg of a customized payload unit. The whole system is modular providing flexibility of payload options, which comprises the main advantage of the UAS. The UAS integrates two kinds of payloads which can be altered. Both payloads integrate a GPS/IMU with a dual GPS antenna configuration provided by OXTS for accurate navigation and position measurements during the data acquisition. The first payload comprises a VUX-1 laser scanner by RIEGL and a Sony A6000 E-Mount photo camera. The second payload for hyperspectral scanning integrates a push-broom imager AISA KESTREL 10 by SPECIM. The UAS was designed for research of various aspects of landscape dynamics (landslides, erosion, flooding, or phenology in high spectral and spatial resolution.

  6. High Resolution Airborne Laser Scanning and Hyperspectral Imaging with a Small Uav Platform

    Science.gov (United States)

    Gallay, Michal; Eck, Christoph; Zgraggen, Carlo; Kaňuk, Ján; Dvorný, Eduard

    2016-06-01

    The capabilities of unmanned airborne systems (UAS) have become diverse with the recent development of lightweight remote sensing instruments. In this paper, we demonstrate our custom integration of the state-of-the-art technologies within an unmanned aerial platform capable of high-resolution and high-accuracy laser scanning, hyperspectral imaging, and photographic imaging. The technological solution comprises the latest development of a completely autonomous, unmanned helicopter by Aeroscout, the Scout B1-100 UAV helicopter. The helicopter is powered by a gasoline two-stroke engine and it allows for integrating 18 kg of a customized payload unit. The whole system is modular providing flexibility of payload options, which comprises the main advantage of the UAS. The UAS integrates two kinds of payloads which can be altered. Both payloads integrate a GPS/IMU with a dual GPS antenna configuration provided by OXTS for accurate navigation and position measurements during the data acquisition. The first payload comprises a VUX-1 laser scanner by RIEGL and a Sony A6000 E-Mount photo camera. The second payload for hyperspectral scanning integrates a push-broom imager AISA KESTREL 10 by SPECIM. The UAS was designed for research of various aspects of landscape dynamics (landslides, erosion, flooding, or phenology) in high spectral and spatial resolution.

  7. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  8. Occurrence and characteristics of mutual interference between LIDAR scanners

    Science.gov (United States)

    Kim, Gunzung; Eom, Jeongsook; Park, Seonghyeon; Park, Yongwan

    2015-05-01

    The LIDAR scanner is at the heart of object detection of the self-driving car. Mutual interference between LIDAR scanners has not been regarded as a problem because the percentage of vehicles equipped with LIDAR scanners was very rare. With the growing number of autonomous vehicle equipped with LIDAR scanner operated close to each other at the same time, the LIDAR scanner may receive laser pulses from other LIDAR scanners. In this paper, three types of experiments and their results are shown, according to the arrangement of two LIDAR scanners. We will show the probability that any LIDAR scanner will interfere mutually by considering spatial and temporal overlaps. It will present some typical mutual interference scenario and report an analysis of the interference mechanism.

  9. Calibration and equivalency analysis of image plate scanners

    Energy Technology Data Exchange (ETDEWEB)

    Williams, G. Jackson, E-mail: williams270@llnl.gov; Maddox, Brian R.; Chen, Hui [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550 (United States); Kojima, Sadaoki [Institute of Laser Engineering, Osaka University, Yamada-oka, 2-6, Suita, Osaka 565-0871 (Japan); Millecchia, Matthew [Laboratory for Laser Energetics, University of Rochester, 250 East River Road, Rochester, New York 14623 (United States)

    2014-11-15

    A universal procedure was developed to calibrate image plate scanners using radioisotope sources. Techniques to calibrate scanners and sources, as well as cross-calibrate scanner models, are described to convert image plate dosage into physical units. This allows for the direct comparison of quantitative data between any facility and scanner. An empirical relation was also derived to establish sensitivity response settings for arbitrary gain settings. In practice, these methods may be extended to any image plate scanning system.

  10. Biclustering of time series microarray data.

    Science.gov (United States)

    Meng, Jia; Huang, Yufei

    2012-01-01

    Clustering is a popular data exploration technique widely used in microarray data analysis. In this chapter, we review ideas and algorithms of bicluster and its applications in time series microarray analysis. We introduce first the concept and importance of biclustering and its different variations. We then focus our discussion on the popular iterative signature algorithm (ISA) for searching biclusters in microarray dataset. Next, we discuss in detail the enrichment constraint time-dependent ISA (ECTDISA) for identifying biologically meaningful temporal transcription modules from time series microarray dataset. In the end, we provide an example of ECTDISA application to time series microarray data of Kaposi's Sarcoma-associated Herpesvirus (KSHV) infection.

  11. 21 CFR 892.1330 - Nuclear whole body scanner.

    Science.gov (United States)

    2010-04-01

    ...) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1330 Nuclear whole body scanner. (a) Identification. A nuclear whole body scanner is a device intended to measure and image the distribution of... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Nuclear whole body scanner. 892.1330 Section...

  12. The use of mobile 3D scanners in maxillofacial surgery.

    Science.gov (United States)

    Peters, Florian; Möhlhenrich, Stephan Christian; Ayoub, Nassim; Goloborodko, Evgeny; Ghassemi, Alireza; Lethaus, Bernd; Hölzle, Frank; Modabber, Ali

    There are many possibilities for the use of three-dimensional (3D) scanners in maxillofacial surgery. This study aimed to investigate whether the bundling and syncing of two 3D scanners has advantages over single-scanner acquisition in terms of scan quality and the time required to scan an object. Therefore, the speed and precision of 3D data acquisition with one scanner versus two synced scanners was measured in 30 subjects. This was done by analyzing the results obtained by scanning test objects attached to the forehead and cheeks of the subjects. Statistical methods included the Student t test for paired samples. Single-scanner recording resulted in significantly lower mean error of measurement than synced recording with two scanners for length (P scanner method resulted in a significantly lowermean error of measurement than the two-scanner method for frontal/lower plane angles (P scanners resulted in a significant reduction of scanning time (P 3D scanner, the bundling of two 3D scanners resulted in faster scanning times but lower scan quality.

  13. The Current Status of DNA Microarrays

    Science.gov (United States)

    Shi, Leming; Perkins, Roger G.; Tong, Weida

    DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manufacturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip® arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthesized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microarrays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.

  14. Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

    Directory of Open Access Journals (Sweden)

    Auvinen Petri

    2008-01-01

    Full Text Available We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan.

  15. Hyperspectral Image Recovery via Hybrid Regularization

    Science.gov (United States)

    Arablouei, Reza; de Hoog, Frank

    2016-12-01

    Natural images tend to mostly consist of smooth regions with individual pixels having highly correlated spectra. This information can be exploited to recover hyperspectral images of natural scenes from their incomplete and noisy measurements. To perform the recovery while taking full advantage of the prior knowledge, we formulate a composite cost function containing a square-error data-fitting term and two distinct regularization terms pertaining to spatial and spectral domains. The regularization for the spatial domain is the sum of total-variation of the image frames corresponding to all spectral bands. The regularization for the spectral domain is the l1-norm of the coefficient matrix obtained by applying a suitable sparsifying transform to the spectra of the pixels. We use an accelerated proximal-subgradient method to minimize the formulated cost function. We analyze the performance of the proposed algorithm and prove its convergence. Numerical simulations using real hyperspectral images exhibit that the proposed algorithm offers an excellent recovery performance with a number of measurements that is only a small fraction of the hyperspectral image data size. Simulation results also show that the proposed algorithm significantly outperforms an accelerated proximal-gradient algorithm that solves the classical basis-pursuit denoising problem to recover the hyperspectral image.

  16. Kernel based subspace projection of hyperspectral images

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Nielsen, Allan Aasbjerg; Arngren, Morten

    In hyperspectral image analysis an exploratory approach to analyse the image data is to conduct subspace projections. As linear projections often fail to capture the underlying structure of the data, we present kernel based subspace projections of PCA and Maximum Autocorrelation Factors (MAF...

  17. Super-resolution reconstruction of hyperspectral images

    Science.gov (United States)

    Elbakary, Mohamed; Alam, Mohammad S.

    2007-04-01

    Hyperspectral imagery is used for a wide variety of applications, including target detection, tacking, agricultural monitoring and natural resources exploration. The main reason for using hyperspectral imagery is that these images reveal spectral information about the scene that are not available in a single band. Unfortunately, many factors such as sensor noise and atmospheric scattering degrade the spatial quality of these images. Recently, many algorithms are introduced in the literature to improve the resolution of hyperspectral images [7]. In this paper, we propose a new method to produce high resolution bands from low resolution bands that are strongly correlated to the corresponding high resolution panchromatic image. The proposed method is based on using the local correlation instead of using the global correlation to improve the estimated interpolation in order to construct the high resolution image. The utilization of local correlation significantly improved the resolution of high resolution images when compared to the corresponding results obtained using the traditional algorithms. The local correlation is implemented by using predefined small windows across the low resolution image. In addition, numerous experiments are conducted to investigate the effect of the chosen window size in the image quality. Experiments results obtained using real life hyperspectral imagery is presented to verify the effectiveness of the proposed algorithm.

  18. Hyperspectral data exploitation theory and applications

    CERN Document Server

    Chang, Chein-I

    2007-01-01

    Authored by a panel of experts in the field, this book focuses on hyperspectral image analysis, systems, and applications. With discussion of application-based projects and case studies, this professional reference will bring you up-to-date on this pervasive technology, wether you are working in the military and defense fields, or in remote sensing technology, geoscience, or agriculture.

  19. High spatial resolution LWIR hyperspectral sensor

    Science.gov (United States)

    Roberts, Carson B.; Bodkin, Andrew; Daly, James T.; Meola, Joseph

    2015-06-01

    Presented is a new hyperspectral imager design based on multiple slit scanning. This represents an innovation in the classic trade-off between speed and resolution. This LWIR design has been able to produce data-cubes at 3 times the rate of conventional single slit scan devices. The instrument has a built-in radiometric and spectral calibrator.

  20. GPU Lossless Hyperspectral Data Compression System

    Science.gov (United States)

    Aranki, Nazeeh I.; Keymeulen, Didier; Kiely, Aaron B.; Klimesh, Matthew A.

    2014-01-01

    Hyperspectral imaging systems onboard aircraft or spacecraft can acquire large amounts of data, putting a strain on limited downlink and storage resources. Onboard data compression can mitigate this problem but may require a system capable of a high throughput. In order to achieve a high throughput with a software compressor, a graphics processing unit (GPU) implementation of a compressor was developed targeting the current state-of-the-art GPUs from NVIDIA(R). The implementation is based on the fast lossless (FL) compression algorithm reported in "Fast Lossless Compression of Multispectral-Image Data" (NPO- 42517), NASA Tech Briefs, Vol. 30, No. 8 (August 2006), page 26, which operates on hyperspectral data and achieves excellent compression performance while having low complexity. The FL compressor uses an adaptive filtering method and achieves state-of-the-art performance in both compression effectiveness and low complexity. The new Consultative Committee for Space Data Systems (CCSDS) Standard for Lossless Multispectral & Hyperspectral image compression (CCSDS 123) is based on the FL compressor. The software makes use of the highly-parallel processing capability of GPUs to achieve a throughput at least six times higher than that of a software implementation running on a single-core CPU. This implementation provides a practical real-time solution for compression of data from airborne hyperspectral instruments.

  1. Sparse-Based Modeling of Hyperspectral Data

    DEFF Research Database (Denmark)

    Calvini, Rosalba; Ulrici, Alessandro; Amigo Rubio, Jose Manuel

    2016-01-01

    One of the main issues of hyperspectral imaging data is to unravel the relevant, yet overlapped, huge amount of information contained in the spatial and spectral dimensions. When dealing with the application of multivariate models in such high-dimensional data, sparsity can improve...

  2. Parallel hyperspectral compressive sensing method on GPU

    Science.gov (United States)

    Bernabé, Sergio; Martín, Gabriel; Nascimento, José M. P.

    2015-10-01

    Remote hyperspectral sensors collect large amounts of data per flight usually with low spatial resolution. It is known that the bandwidth connection between the satellite/airborne platform and the ground station is reduced, thus a compression onboard method is desirable to reduce the amount of data to be transmitted. This paper presents a parallel implementation of an compressive sensing method, called parallel hyperspectral coded aperture (P-HYCA), for graphics processing units (GPU) using the compute unified device architecture (CUDA). This method takes into account two main properties of hyperspectral dataset, namely the high correlation existing among the spectral bands and the generally low number of endmembers needed to explain the data, which largely reduces the number of measurements necessary to correctly reconstruct the original data. Experimental results conducted using synthetic and real hyperspectral datasets on two different GPU architectures by NVIDIA: GeForce GTX 590 and GeForce GTX TITAN, reveal that the use of GPUs can provide real-time compressive sensing performance. The achieved speedup is up to 20 times when compared with the processing time of HYCA running on one core of the Intel i7-2600 CPU (3.4GHz), with 16 Gbyte memory.

  3. Mapping Waterhyacinth Infestations Using Airborne Hyperspectral Imagery

    Science.gov (United States)

    Waterhyacinth [Eichhornia crassipes (Mart.) Solms] is an exotic aquatic weed that often invades and clogs waterways in many tropical and subtropical regions of the world. The objective of this study was to evaluate airborne hyperspectral imagery and different image classification techniques for mapp...

  4. Mapping Soil Organic Matter with Hyperspectral Imaging

    Science.gov (United States)

    Moni, Christophe; Burud, Ingunn; Flø, Andreas; Rasse, Daniel

    2014-05-01

    Soil organic matter (SOM) plays a central role for both food security and the global environment. Soil organic matter is the 'glue' that binds soil particles together, leading to positive effects on soil water and nutrient availability for plant growth and helping to counteract the effects of erosion, runoff, compaction and crusting. Hyperspectral measurements of samples of soil profiles have been conducted with the aim of mapping soil organic matter on a macroscopic scale (millimeters and centimeters). Two soil profiles have been selected from the same experimental site, one from a plot amended with biochar and another one from a control plot, with the specific objective to quantify and map the distribution of biochar in the amended profile. The soil profiles were of size (30 x 10 x 10) cm3 and were scanned with two pushbroomtype hyperspectral cameras, one which is sensitive in the visible wavelength region (400 - 1000 nm) and one in the near infrared region (1000 - 2500 nm). The images from the two detectors were merged together into one full dataset covering the whole wavelength region. Layers of 15 mm were removed from the 10 cm high sample such that a total of 7 hyperspectral images were obtained from the samples. Each layer was analyzed with multivariate statistical techniques in order to map the different components in the soil profile. Moreover, a 3-dimensional visalization of the components through the depth of the sample was also obtained by combining the hyperspectral images from all the layers. Mid-infrared spectroscopy of selected samples of the measured soil profiles was conducted in order to correlate the chemical constituents with the hyperspectral results. The results show that hyperspectral imaging is a fast, non-destructive technique, well suited to characterize soil profiles on a macroscopic scale and hence to map elements and different organic matter quality present in a complete pedon. As such, we were able to map and quantify biochar in our

  5. Hyperspectral Remote Sensing for Tropical Rain Forest

    Directory of Open Access Journals (Sweden)

    Kamaruzaman Jusoff

    2009-01-01

    Full Text Available Problem statement: Sensing, mapping and monitoring the rain forest in forested regions of the world, particularly the tropics, has attracted a great deal of attention in recent years as deforestation and forest degradation account for up to 30% of anthropogenic carbon emissions and are now included in climate change negotiations. Approach: We reviewed the potential for air and spaceborne hyperspectral sensing to identify and map individual tree species measure carbon stocks, specifically Aboveground Biomass (AGB and provide an overview of a range of approaches that have been developed and used to map tropical rain forest across a diverse set of conditions and geographic areas. We provided a summary of air and spaceborne hyperspectral remote sensing measurements relevant to mapping the tropical forest and assess the relative merits and limitations of each. We then provided an overview of modern techniques of mapping the tropical forest based on species discrimination, leaf chlorophyll content, estimating aboveground forest productivity and monitoring forest health. Results: The challenges in hyperspectral Imaging of tropical forests is thrown out to researchers in such field as to come with the latest techniques of image processing and improved mapping resolution leading towards higher precision mapping accuracy. Some research results from an airborne hyperspectral imaging over Bukit Nanas forest reserve was shared implicating high potential of such very high resolution imaging techniques for tropical mixed dipterocarp forest inventory and mapping for species discrimination, aboveground forest productivity, leaf chlorophyll content and carbon mapping. Conclusion/Recommendations: We concluded that while spaceborne hyperspectral remote sensing has often been discounted as inadequate for the task, attempts to map with airborne sensors are still insufficient in tropical developing countries like Malaysia. However, we demonstrated this with a case

  6. Spectral Reconstruction for Obtaining Virtual Hyperspectral Images

    Science.gov (United States)

    Perez, G. J. P.; Castro, E. C.

    2016-12-01

    Hyperspectral sensors demonstrated its capabalities in identifying materials and detecting processes in a satellite scene. However, availability of hyperspectral images are limited due to the high development cost of these sensors. Currently, most of the readily available data are from multi-spectral instruments. Spectral reconstruction is an alternative method to address the need for hyperspectral information. The spectral reconstruction technique has been shown to provide a quick and accurate detection of defects in an integrated circuit, recovers damaged parts of frescoes, and it also aids in converting a microscope into an imaging spectrometer. By using several spectral bands together with a spectral library, a spectrum acquired by a sensor can be expressed as a linear superposition of elementary signals. In this study, spectral reconstruction is used to estimate the spectra of different surfaces imaged by Landsat 8. Four atmospherically corrected surface reflectance from three visible bands (499 nm, 585 nm, 670 nm) and one near-infrared band (872 nm) of Landsat 8, and a spectral library of ground elements acquired from the United States Geological Survey (USGS) are used. The spectral library is limited to 420-1020 nm spectral range, and is interpolated at one nanometer resolution. Singular Value Decomposition (SVD) is used to calculate the basis spectra, which are then applied to reconstruct the spectrum. The spectral reconstruction is applied for test cases within the library consisting of vegetation communities. This technique was successful in reconstructing a hyperspectral signal with error of less than 12% for most of the test cases. Hence, this study demonstrated the potential of simulating information at any desired wavelength, creating a virtual hyperspectral sensor without the need for additional satellite bands.

  7. Illumination compensation in ground based hyperspectral imaging

    Science.gov (United States)

    Wendel, Alexander; Underwood, James

    2017-07-01

    Hyperspectral imaging has emerged as an important tool for analysing vegetation data in agricultural applications. Recently, low altitude and ground based hyperspectral imaging solutions have come to the fore, providing very high resolution data for mapping and studying large areas of crops in detail. However, these platforms introduce a unique set of challenges that need to be overcome to ensure consistent, accurate and timely acquisition of data. One particular problem is dealing with changes in environmental illumination while operating with natural light under cloud cover, which can have considerable effects on spectral shape. In the past this has been commonly achieved by imaging known reference targets at the time of data acquisition, direct measurement of irradiance, or atmospheric modelling. While capturing a reference panel continuously or very frequently allows accurate compensation for illumination changes, this is often not practical with ground based platforms, and impossible in aerial applications. This paper examines the use of an autonomous unmanned ground vehicle (UGV) to gather high resolution hyperspectral imaging data of crops under natural illumination. A process of illumination compensation is performed to extract the inherent reflectance properties of the crops, despite variable illumination. This work adapts a previously developed subspace model approach to reflectance and illumination recovery. Though tested on a ground vehicle in this paper, it is applicable to low altitude unmanned aerial hyperspectral imagery also. The method uses occasional observations of reference panel training data from within the same or other datasets, which enables a practical field protocol that minimises in-field manual labour. This paper tests the new approach, comparing it against traditional methods. Several illumination compensation protocols for high volume ground based data collection are presented based on the results. The findings in this paper are

  8. Ghost signals in Allison emittance scanners

    Energy Technology Data Exchange (ETDEWEB)

    Stockli, Martin P.; /SNS Project, Oak Ridge /Tennessee U.; Leitner, M.; /LBL, Berkeley; Moehs, D.P.; /Fermilab; Keller, R.; /LBL, Berkeley; Welton, R.F.; /SNS Project, Oak

    2004-12-01

    For over 20 years, Allison scanners have been used to measure emittances of low-energy ion beams. We show that scanning large trajectory angles produces ghost signals caused by the sampled beamlet impacting on an electric deflection plate. The ghost signal strength is proportional to the amount of beam entering the scanner. Depending on the ions, and their velocity, the ghost signals can have the opposite or the same polarity as the main beam signals. The ghost signals cause significant errors in the emittance estimates because they appear at large trajectory angles. These ghost signals often go undetected because they partly overlap with the real signals, are mostly below the 1% level, and often hide in the noise. A simple deflection plate modification is shown to reduce the ghost signal strength by over 99%.

  9. Laser scanner 3D terrestri e mobile

    Directory of Open Access Journals (Sweden)

    Mario Ciamba

    2013-08-01

    Full Text Available Recentemente si è svolto a Roma un evento dimostrativo per informare, professionisti e ricercatori del settore inerente il rilievo strumentale, sulle recenti innovazioni che riguardano i laser scanner 3d. Il mercato della strumentazione dedicata al rilevamento architettonico e dell'ambiente, offre molte possibilità di scelta. Oggi i principali marchi producono strumenti sempre più efficienti ed ideati per ambiti di applicazione specifici, permettendo ai professionisti, la giusta scelta in termini di prestazioni ed economia.A demonstration event was recently held in Rome with the aim to inform professionals and researchers on recent innovations on instrumental survey related to the 3d laser scanner. The market of instrumentation for architectural survey offers many possibilitiesof choice. Today the major brands produce instruments that are more efficient and designed for specific areas of application, allowing the right choice in terms of performance and economy.

  10. Compact beamforming in medical ultrasound scanners

    DEFF Research Database (Denmark)

    Tomov, Borislav Gueorguiev

    2003-01-01

    This Ph.D. project was carried out at the Center for Fast Ultrasound Imaging, Technical University of Denmark, under the supervision of Prof. Jørgen Arendt Jensen, Assoc. Prof. Jens Sparsø and Prof. Erik Bruun. The goal was to investigate methods for efficient beamforming, which make it possible...... compact implementation of the beamformer compared to the case where conventional A/D conversion is used. The compact and economic beamforming is a key aspect in the progress of medical ultrasound imaging. Currently, 64 or 128 channels are widely used in scanners, top-of-the-range scanners have 256...... with an introduction into medical ultrasound, its basic principles, system evolution and its place among medical imaging techniques. Then, ultrasound acoustics is introduced, as a necessary base for understanding the concepts of acoustic focusing and beamforming, which follow. The necessary focusing information...

  11. Online unmixing of multitemporal hyperspectral images accounting for spectral variability

    CERN Document Server

    Thouvenin, Pierre-Antoine; Tourneret, Jean-Yves

    2015-01-01

    Hyperspectral unmixing is aimed at identifying the reference spectral signatures composing an hyperspectral image -- referred to as endmembers -- and their relative abundance fractions in each pixel. In practice, the identified signatures may vary spectrally from an image to another due to varying acquisition conditions inducing possibly significant estimation errors. Against this background, hyperspectral unmixing of several images acquired over the same area is of considerable interest. Indeed, such an analysis enables the endmembers of the scene to be tracked and the corresponding endmember variability to be characterized. Sequential endmember estimation from a set of hyperspectral images is expected to provide improved performance when compared to methods analyzing the images independently. However, the significant size of hyperspectral data precludes the use of batch procedures to jointly estimate the mixture parameters of a sequence of hyperspectral images. Provided that each elementary component is pre...

  12. Get Mobile – The Smartphone Brain Scanner

    DEFF Research Database (Denmark)

    Stahlhut, Carsten; Stopczynski, Arkadiusz; Petersen, Michael Kai

    This demonstration will provide live-interaction with a smartphone brain scanner consisting of a low-cost wireless 14-channel EEG headset (Emotiv Epoc) and a mobile device. With our system it is possible to perform real-time functional brain imaging on a smartphone device, including stimulus deli......) that are based on Linux operating systems. Thus our system runs on multiple platforms, including Maemo/MeeGo based smartphones, Android-based smartphones and tablet devices....

  13. Airborne hyperspectral and LiDAR data integration for weed detection

    Science.gov (United States)

    Tamás, János; Lehoczky, Éva; Fehér, János; Fórián, Tünde; Nagy, Attila; Bozsik, Éva; Gálya, Bernadett; Riczu, Péter

    2014-05-01

    Agriculture uses 70% of global available fresh water. However, ca. 50-70% of water used by cultivated plants, the rest of water transpirated by the weeds. Thus, to define the distribution of weeds is very important in precision agriculture and horticulture as well. To survey weeds on larger fields by traditional methods is often time consuming. Remote sensing instruments are useful to detect weeds in larger area. In our investigation a 3D airborne laser scanner (RIEGL LMS-Q680i) was used in agricultural field near Sopron to scouting weeds. Beside the airborne LiDAR, hyperspectral imaging system (AISA DUAL) and air photos helped to investigate weed coverage. The LiDAR survey was carried out at early April, 2012, before sprouting of cultivated plants. Thus, there could be detected emerging of weeds and direction of cultivation. However airborne LiDAR system was ideal to detect weeds, identification of weeds at species level was infeasible. Higher point density LiDAR - Terrestrial laser scanning - systems are appropriate to distinguish weed species. Based on the results, laser scanner is an effective tool to scouting of weeds. Appropriate weed detection and mapping systems could contribute to elaborate water and herbicide saving management technique. This publication was supported by the OTKA project K 105789.

  14. Microarray Inspector: tissue cross contamination detection tool for microarray data.

    Science.gov (United States)

    Stępniak, Piotr; Maycock, Matthew; Wojdan, Konrad; Markowska, Monika; Perun, Serhiy; Srivastava, Aashish; Wyrwicz, Lucjan S; Świrski, Konrad

    2013-01-01

    Microarray technology changed the landscape of contemporary life sciences by providing vast amounts of expression data. Researchers are building up repositories of experiment results with various conditions and samples which serve the scientific community as a precious resource. Ensuring that the sample is of high quality is of utmost importance to this effort. The task is complicated by the fact that in many cases datasets lack information concerning pre-experimental quality assessment. Transcription profiling of tissue samples may be invalidated by an error caused by heterogeneity of the material. The risk of tissue cross contamination is especially high in oncological studies, where it is often difficult to extract the sample. Therefore, there is a need of developing a method detecting tissue contamination in a post-experimental phase. We propose Microarray Inspector: customizable, user-friendly software that enables easy detection of samples containing mixed tissue types. The advantage of the tool is that it uses raw expression data files and analyses each array independently. In addition, the system allows the user to adjust the criteria of the analysis to conform to individual needs and research requirements. The final output of the program contains comfortable to read reports about tissue contamination assessment with detailed information about the test parameters and results. Microarray Inspector provides a list of contaminant biomarkers needed in the analysis of adipose tissue contamination. Using real data (datasets from public repositories) and our tool, we confirmed high specificity of the software in detecting contamination. The results indicated the presence of adipose tissue admixture in a range from approximately 4% to 13% in several tested surgical samples.

  15. A near-infrared confocal scanner

    Science.gov (United States)

    Lee, Seungwoo; Yoo, Hongki

    2014-06-01

    In the semiconductor industry, manufacturing of three-dimensional (3D) packages or 3D integrated circuits is a high-performance technique that requires combining several functions in a small volume. Through-silicon vias, which are vertical electrical connections extending through a wafer, can be used to direct signals between stacked chips, thus increasing areal density by stacking and connecting multiple patterned chips. While defect detection is essential in the semiconductor manufacturing process, it is difficult to identify defects within a wafer or to monitor the bonding results between bonded surfaces because silicon and many other semiconductor materials are opaque to visible wavelengths. In this context, near-infrared (NIR) imaging is a promising non-destructive method to detect defects within silicon chips, to inspect bonding between chips and to monitor the chip alignment since NIR transmits through silicon. In addition, a confocal scanner provides high-contrast, optically-sectioned images of the specimen due to its ability to reject out-of-focus noise. In this study, we report an NIR confocal scanner that rapidly acquires high-resolution images with a large field of view through silicon. Two orthogonal line-scanning images can be acquired without rotating the system or the specimen by utilizing two orthogonally configured resonant scanning mirrors. This NIR confocal scanner can be efficiently used as an in-line inspection system when manufacturing semiconductor devices by rapidly detecting defects on and beneath the surface.

  16. Optimizing Hyperspectral Imagery Anomaly Detection through Robust Parameter Design

    Science.gov (United States)

    2011-10-01

    Geoscience and Remote Sensing, IEEE Transactions on, 44 (8):2282 –2291 (2006). [8] Benediktsson, J.A., et al. “ Classification of hyperspectral data...1873 vol.4. 2001. [18] Chiang, S.S et al. “ Unsupervised Hyperspectral Image Analysis Using Indepen- dent Component Analysis.”. [19] Copeland, K.A.F. and...3):337 – 352 (2004). [34] Harsanyi, J.C. and C.I. Chang. “ Hyperspectral image classification and dimen- sionality reduction: an orthogonal subspace

  17. Diffusion Geometry Based Nonlinear Methods for Hyperspectral Change Detection

    Science.gov (United States)

    2010-05-12

    Schaum and A. Stocker, “Hyperspectral change detection and supervised matched filtering based on covariance equalization,” Proceedings of the SPIE, vol...5425, pp. 77- 90 (2004). 10. A. Schaum and A. Stocker, “Linear chromodynamics models for hyperspectral target detection,” Proceedings of the IEEE...Aerospace Conference (February 2003). 11. A. Schaum and A. Stocker, “Linear chromodynamics models for hyperspectral target detection

  18. A Gimbal-Stabilized Compact Hyperspectral Imaging System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Gimbal-stabilized Compact Hyperspectral Imaging System (GCHIS) fully integrates multi-sensor spectral imaging, stereovision, GPS and inertial measurement,...

  19. A Gimbal-Stabilized Compact Hyperspectral Imaging System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Gimbal-stabilized Compact Hyperspectral Imaging System (GCHIS) fully integrates multi-sensor spectral imaging, stereovision, GPS and inertial measurement,...

  20. Study on data mining technology in hyperspectral remote sensing

    Science.gov (United States)

    Su, Hongjun; Sheng, Yehua; Wen, Yongning; Tao, Hong

    2007-06-01

    In this paper, the problems rise in hyperspectral data mining and some key issues should pay attention to were proposed based on the analysis on the state-of-art of hyperspectral data mining. The problems are as follows: data mining precision, mining algorithm efficiency, new hyperspectral data mining algorithms, the uncertainty in hyperspectral data mining, visualization in hyperspectral data mining process, and knowledge presentation, interpretation, estimation and management etc.. Some key issues should emphasize in the future are: systematic hyperspectral data mining theory, dimensionality reduction, mining spatial and temporal knowledge from images, and mining distributed data and mining multi-agent data. Also the framework and architecture of hyperspectral data mining were put forward in this paper. Hyperspectral data mining framework includes some subparts as follows: data selection, data preprocessing, data transfer, data mining and pattern estimation. And the architecture is composed of database, data warehouse, database management system, repository, mining process, user interface etc.. At last, an algorithm which named Relational perspective map (RPM) was introduced into the field of hyperspectral data mining. By the experiment on the spectra data from USGS spectral library, it proves that this algorithm is suitable to discover those spectral features and to identify and discriminate object classes based on their spectra.

  1. Data Reduction and Rapid Analysis of Hyperspectral Data Sets Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Hyperspectral sensors offer great opportunities for increasingly sensitive automated target recognition (ATR) systems though a common problem is the lack of...

  2. Accurate detection of carcinoma cells by use of a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shohei Yamamura

    Full Text Available BACKGROUND: Accurate detection and analysis of circulating tumor cells plays an important role in the diagnosis and treatment of metastatic cancer treatment. METHODS AND FINDINGS: A cell microarray chip was used to detect spiked carcinoma cells among leukocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene; and the formation of monolayers of leukocytes in the microchambers was observed. Cultured human T lymphoblastoid leukemia (CCRF-CEM cells were used to examine the potential of the cell microarray chip for the detection of spiked carcinoma cells. A T lymphoblastoid leukemia suspension was dispersed on the chip surface, followed by 15 min standing to allow the leukocytes to settle down into the microchambers. Approximately 29 leukocytes were found in each microchamber when about 600,000 leukocytes in total were dispersed onto a cell microarray chip. Similarly, when leukocytes isolated from human whole blood were used, approximately 89 leukocytes entered each microchamber when about 1,800,000 leukocytes in total were placed onto the cell microarray chip. After washing the chip surface, PE-labeled anti-cytokeratin monoclonal antibody and APC-labeled anti-CD326 (EpCAM monoclonal antibody solution were dispersed onto the chip surface and allowed to react for 15 min; and then a microarray scanner was employed to detect any fluorescence-positive cells within 20 min. In the experiments using spiked carcinoma cells (NCI-H1650, 0.01 to 0.0001%, accurate detection of carcinoma cells was achieved with PE-labeled anti-cytokeratin monoclonal antibody. Furthermore, verification of carcinoma cells in the microchambers was performed by double staining with the above monoclonal antibodies. CONCLUSION: The potential application of the cell microarray chip for the detection of CTCs was shown, thus demonstrating accurate detection by double staining for cytokeratin and EpCAM at the single carcinoma cell level.

  3. Rapid and highly sensitive detection of malaria-infected erythrocytes using a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shouki Yatsushiro

    Full Text Available BACKGROUND: Malaria is one of the major human infectious diseases in many endemic countries. For prevention of the spread of malaria, it is necessary to develop an early, sensitive, accurate and conventional diagnosis system. METHODS AND FINDINGS: A cell microarray chip was used to detect for malaria-infected erythrocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene, and the formation of monolayers of erythrocytes in the microchambers was observed. Cultured Plasmodium falciparum strain 3D7 was used to examine the potential of the cell microarray chip for malaria diagnosis. An erythrocyte suspension in a nuclear staining dye, SYTO 59, was dispersed on the chip surface, followed by 10 min standing to allow the erythrocytes to settle down into the microchambers. About 130 erythrocytes were accommodated in each microchamber, there being over 2,700,000 erythrocytes in total on a chip. A microarray scanner was employed to detect any fluorescence-positive erythrocytes within 5 min, and 0.0001% parasitemia could be detected. To examine the contamination by leukocytes of purified erythrocytes from human blood, 20 µl of whole blood was mixed with 10 ml of RPMI 1640, and the mixture was passed through a leukocyte isolation filter. The eluted portion was centrifuged at 1,000×g for 2 min, and the pellet was dispersed in 1.0 ml of medium. SYTO 59 was added to the erythrocyte suspension, followed by analysis on a cell microarray chip. Similar accommodation of cells in the microchambers was observed. The number of contaminating leukocytes was less than 1 on a cell microarray chip. CONCLUSION: The potential of the cell microarray chip for the detection of malaria-infected erythrocytes was shown, it offering 10-100 times higher sensitivity than that of conventional light microscopy and easy operation in 15 min with purified erythrocytes.

  4. Point-of-care vertical flow allergen microarray assay: proof of concept.

    Science.gov (United States)

    Chinnasamy, Thiruppathiraja; Segerink, Loes I; Nystrand, Mats; Gantelius, Jesper; Andersson Svahn, Helene

    2014-09-01

    Sophisticated equipment, lengthy protocols, and skilled operators are required to perform protein microarray-based affinity assays. Consequently, novel tools are needed to bring biomarkers and biomarker panels into clinical use in different settings. Here, we describe a novel paper-based vertical flow microarray (VFM) system with a multiplexing capacity of at least 1480 microspot binding sites, colorimetric readout, high sensitivity, and assay time of Affinity binders were deposited on nitrocellulose membranes by conventional microarray printing. Buffers and reagents were applied vertically by use of a flow controlled syringe pump. As a clinical model system, we analyzed 31 precharacterized human serum samples using the array system with 10 allergen components to detect specific IgE reactivities. We detected bound analytes using gold nanoparticle conjugates with assay time of ≤10 min. Microarray images were captured by a consumer-grade flatbed scanner. A sensitivity of 1 ng/mL was demonstrated with the VFM assay with colorimetric readout. The reproducibility (CV) of the system was affinity point-of-care testing. © 2014 American Association for Clinical Chemistry.

  5. Study on Wusan Granule Anti-tumor Related Target Gene Screened by Cdna Microarray

    Institute of Scientific and Technical Information of China (English)

    YOU Zi-li; SHI Jin-ping; CHEN Hai-hong

    2006-01-01

    To screen Wusan Granule anti-tumor related target gene using cDNA microarray technique, both mRNA from Lewis lung carcinoma tissues treated by Wusan Granule and untreated control are reversibly transcribed to prepare cDNA probes which are labeled by Cy5 and Cy3. Then, the probes are hybridized to the mice cDNA microarray type MGEC-20S. After hybridization, the cDNA microarray is scanned by ScanArray 3 000 scanner and the data is analyzed by ImaGene 3 software to screen the differentially expressed genes. There are 45 differentially expressed genes including 18 known genes and 27 unknown genes between the two groups, and among them, 20 elevated genes and 25 reduced genes are identified. Additionally, the genes related to invasion and metastasis of malignant carcinomas are down-regulated and the genes related to apoptosis are up-regulated. The cDNA microarray technique is a high-throughput approach to screen the Wusan Granule anti-tumor related target genes, which allow us to explore the molecular biological mechanism on a genomic scale.

  6. Nanoliter homogenous ultra-high throughput screening microarray for lead discoveries and IC50 profiling.

    Science.gov (United States)

    Ma, Haiching; Horiuchi, Kurumi Y; Wang, Yuan; Kucharewicz, Stefan A; Diamond, Scott L

    2005-04-01

    Microfluidic technologies offer the potential for highly productive and low-cost ultra-high throughput screening and high throughput selectivity profiling. Such technologies need to provide the flexibility of plate-based assays as well as be less expensive to operate. Presented here is a unique microarray system (the Reaction Biology [Malvern, PA] DiscoveryDot), which runs over 6,000 homogeneous reactions per 1" x 3" microarray using chemical libraries or compound dilutions printed in 1-nl volumes. A simple and rapid piezo-activation method delivers from 30 to 300 pl of biochemical targets and detector chemistries to each reaction. The fluorescent signals are detected and analyzed with conventional microarray scanners and software. The DiscoveryDot platform is highly customizable, and reduces consumption of targets and reaction chemistries by >40-fold and the consumption of compounds by >10,000-fold, compared to 384-well plate assay. We demonstrate here that the DiscoveryDot platform is compatible with conventional large-volume well-based reactions, with a Z' factor of >0.6 for many enzymes, such as the caspase family enzymes, matrix metalloproteinase, serine proteases, kinases, and histone deacetylases. The platform is well equipped for 50% inhibitory concentration (IC50) profiling studies of enzyme inhibitors, with up to 10 dilution conditions of each test compound printed in duplicate, and each microarray chip can generate over 300 IC50 measurements against a given target.

  7. Integrated Amplification Microarrays for Infectious Disease Diagnostics

    Directory of Open Access Journals (Sweden)

    Darrell P. Chandler

    2012-11-01

    Full Text Available This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.

  8. Spotting effect in microarray experiments

    Directory of Open Access Journals (Sweden)

    Mary-Huard Tristan

    2004-05-01

    Full Text Available Abstract Background Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio and intensity across the array. Results Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure. Conclusions The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis.

  9. Recent micro-CT scanner developments at UGCT

    Science.gov (United States)

    Dierick, Manuel; Van Loo, Denis; Masschaele, Bert; Van den Bulcke, Jan; Van Acker, Joris; Cnudde, Veerle; Van Hoorebeke, Luc

    2014-04-01

    This paper describes two X-ray micro-CT scanners which were recently developed to extend the experimental possibilities of microtomography research at the Centre for X-ray Tomography (www.ugct.ugent.be) of the Ghent University (Belgium). The first scanner, called Nanowood, is a wide-range CT scanner with two X-ray sources (160 kVmax) and two detectors, resolving features down to 0.4 μm in small samples, but allowing samples up to 35 cm to be scanned. This is a sample size range of 3 orders of magnitude, making this scanner well suited for imaging multi-scale materials such as wood, stone, etc. Besides the traditional cone-beam acquisition, Nanowood supports helical acquisition, and it can generate images with significant phase-contrast contributions. The second scanner, known as the Environmental micro-CT scanner (EMCT), is a gantry based micro-CT scanner with variable magnification for scanning objects which are not easy to rotate in a standard micro-CT scanner, for example because they are physically connected to external experimental hardware such as sensor wiring, tubing or others. This scanner resolves 5 μm features, covers a field-of-view of about 12 cm wide with an 80 cm vertical travel range. Both scanners will be extensively described and characterized, and their potential will be demonstrated with some key application results.

  10. Recent micro-CT scanner developments at UGCT

    Energy Technology Data Exchange (ETDEWEB)

    Dierick, Manuel, E-mail: Manuel.Dierick@UGent.be [UGCT-Department of Physics and Astronomy, Faculty of Sciences, Ghent University, Proeftuinstraat 86, 9000 Ghent (Belgium); XRE, X-Ray Engineering bvba, De Pintelaan 111, 9000 Ghent (Belgium); Van Loo, Denis, E-mail: info@XRE.be [XRE, X-Ray Engineering bvba, De Pintelaan 111, 9000 Ghent (Belgium); Masschaele, Bert [UGCT-Department of Physics and Astronomy, Faculty of Sciences, Ghent University, Proeftuinstraat 86, 9000 Ghent (Belgium); XRE, X-Ray Engineering bvba, De Pintelaan 111, 9000 Ghent (Belgium); Van den Bulcke, Jan [UGCT-Woodlab-UGent, Department of Forest and Water Management, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent (Belgium); Van Acker, Joris, E-mail: Joris.VanAcker@UGent.be [UGCT-Woodlab-UGent, Department of Forest and Water Management, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent (Belgium); Cnudde, Veerle, E-mail: Veerle.Cnudde@UGent.be [UGCT-SGIG, Department of Geology and Soil Science, Faculty of Sciences, Ghent University, Krijgslaan 281, S8, 9000 Ghent (Belgium); Van Hoorebeke, Luc, E-mail: Luc.VanHoorebeke@UGent.be [UGCT-Department of Physics and Astronomy, Faculty of Sciences, Ghent University, Proeftuinstraat 86, 9000 Ghent (Belgium)

    2014-04-01

    This paper describes two X-ray micro-CT scanners which were recently developed to extend the experimental possibilities of microtomography research at the Centre for X-ray Tomography ( (www.ugct.ugent.be)) of the Ghent University (Belgium). The first scanner, called Nanowood, is a wide-range CT scanner with two X-ray sources (160 kV{sub max}) and two detectors, resolving features down to 0.4 μm in small samples, but allowing samples up to 35 cm to be scanned. This is a sample size range of 3 orders of magnitude, making this scanner well suited for imaging multi-scale materials such as wood, stone, etc. Besides the traditional cone-beam acquisition, Nanowood supports helical acquisition, and it can generate images with significant phase-contrast contributions. The second scanner, known as the Environmental micro-CT scanner (EMCT), is a gantry based micro-CT scanner with variable magnification for scanning objects which are not easy to rotate in a standard micro-CT scanner, for example because they are physically connected to external experimental hardware such as sensor wiring, tubing or others. This scanner resolves 5 μm features, covers a field-of-view of about 12 cm wide with an 80 cm vertical travel range. Both scanners will be extensively described and characterized, and their potential will be demonstrated with some key application results.

  11. Living Cell Microarrays: An Overview of Concepts

    Directory of Open Access Journals (Sweden)

    Rebecca Jonczyk

    2016-05-01

    Full Text Available Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.

  12. Hyperspectral image data compression based on DSP

    Science.gov (United States)

    Fan, Jiming; Zhou, Jiankang; Chen, Xinhua; Shen, Weimin

    2010-11-01

    The huge data volume of hyperspectral image challenges its transportation and store. It is necessary to find an effective method to compress the hyperspectral image. Through analysis and comparison of current various algorithms, a mixed compression algorithm based on prediction, integer wavelet transform and embedded zero-tree wavelet (EZW) is proposed in this paper. We adopt a high-powered Digital Signal Processor (DSP) of TMS320DM642 to realize the proposed algorithm. Through modifying the mixed algorithm and optimizing its algorithmic language, the processing efficiency of the program was significantly improved, compared the non-optimized one. Our experiment show that the mixed algorithm based on DSP runs much faster than the algorithm on personal computer. The proposed method can achieve the nearly real-time compression with excellent image quality and compression performance.

  13. Hyperspectral Image Analysis of Food Quality

    DEFF Research Database (Denmark)

    Arngren, Morten

    Assessing the quality of food is a vital step in any food processing line to ensurethe best food quality and maximum profit for the farmer and food manufacturer.Traditional quality evaluation methods are often destructive and labourintensive procedures relying on wet chemistry or subjective human...... inspection.Near-infrared spectroscopy can address these issues by offering a fast and objectiveanalysis of the food quality. A natural extension to these single spectrumNIR systems is to include image information such that each pixel holds a NIRspectrum. This augmented image information offers several...... extensions to the analysis offood quality. This dissertation is concerned with hyperspectral image analysisused to assess the quality of single grain kernels. The focus is to highlight thebenefits and challenges of using hyperspectral imaging for food quality presentedin two research directions. Initially...

  14. The hyperspectral imaging trade-off

    DEFF Research Database (Denmark)

    Carstensen, Jens Michael

    Although it has no clear-cut definition, hyperspectral imaging in the UV-Visible-NIR wavelength region seems to mean spectral image sampling in bands from 10 nm width or narrower that enables spectral reconstruction over some wavelength interval. For non-imaging spectral applications, this will b......Although it has no clear-cut definition, hyperspectral imaging in the UV-Visible-NIR wavelength region seems to mean spectral image sampling in bands from 10 nm width or narrower that enables spectral reconstruction over some wavelength interval. For non-imaging spectral applications...... acquisition 8. System price Spectral resolution has an obvious interest, but it is the experience of the author, that the vast majority of real spectral imaging applications only need to unmix 2-5 different components. This should be possible with a sensible choice of 10-20 wavelengths. This presentation...

  15. Hyperspectral all-sky imaging of auroras.

    Science.gov (United States)

    Sigernes, Fred; Ivanov, Yuriy; Chernouss, Sergey; Trondsen, Trond; Roldugin, Alexey; Fedorenko, Yury; Kozelov, Boris; Kirillov, Andrey; Kornilov, Ilia; Safargaleev, Vladimir; Holmen, Silje; Dyrland, Margit; Lorentzen, Dag; Baddeley, Lisa

    2012-12-03

    A prototype auroral hyperspectral all-sky camera has been constructed and tested. It uses electro-optical tunable filters to image the night sky as a function of wavelength throughout the visible spectrum with no moving mechanical parts. The core optical system includes a new high power all-sky lens with F-number equal to f/1.1. The camera has been tested at the Kjell Henriksen Observatory (KHO) during the auroral season of 2011/2012. It detects all sub classes of aurora above ~½ of the sub visual 1kR green intensity threshold at an exposure time of only one second. Supervised classification of the hyperspectral data shows promise as a new method to process and identify auroral forms.

  16. Field deployable pushbroom hyperspectral imagining polarimeter

    Science.gov (United States)

    Lowenstern, Mariano; Kudenov, Michael W.

    2016-05-01

    Hyperspectral polarimetry is demonstrated to measure the spectrum and polarization state of a scene. This information is important to identify material properties for applications such as remote sensing and agricultural monitoring, among others. We report the design and performance of a ruggedized, field deployable Hyperspectral Polarimeter Imaging (HPI) system over the VIS to NIR range (450-800 nm). An entrance slit was used to sample a scene in a pushbroom scanning mode, sampling over a 30 degree vertical by 110 degree horizontal field of view. Furthermore, athermalized achromatic retarders were implemented in a channel spectrum generator to measure the linear Stoke vectors. This paper reports the mechanical and optical layout of the system and its peripherals. We present preliminary spectral and polarimetry calibration techniques as well as testing results in field environments.

  17. Piecewise flat embeddings for hyperspectral image analysis

    Science.gov (United States)

    Hayes, Tyler L.; Meinhold, Renee T.; Hamilton, John F.; Cahill, Nathan D.

    2017-05-01

    Graph-based dimensionality reduction techniques such as Laplacian Eigenmaps (LE), Local Linear Embedding (LLE), Isometric Feature Mapping (ISOMAP), and Kernel Principal Components Analysis (KPCA) have been used in a variety of hyperspectral image analysis applications for generating smooth data embeddings. Recently, Piecewise Flat Embeddings (PFE) were introduced in the computer vision community as a technique for generating piecewise constant embeddings that make data clustering / image segmentation a straightforward process. In this paper, we show how PFE arises by modifying LE, yielding a constrained ℓ1-minimization problem that can be solved iteratively. Using publicly available data, we carry out experiments to illustrate the implications of applying PFE to pixel-based hyperspectral image clustering and classification.

  18. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M

    2005-03-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

  19. LIFTERS-hyperspectral imaging at LLNL

    Energy Technology Data Exchange (ETDEWEB)

    Fields, D. [Lawrence Livermore National Lab., CA (United States); Bennett, C.; Carter, M.

    1994-11-15

    LIFTIRS, the Livermore Imaging Fourier Transform InfraRed Spectrometer, recently developed at LLNL, is an instrument which enables extremely efficient collection and analysis of hyperspectral imaging data. LIFTIRS produces a spatial format of 128x128 pixels, with spectral resolution arbitrarily variable up to a maximum of 0.25 inverse centimeters. Time resolution and spectral resolution can be traded off for each other with great flexibility. We will discuss recent measurements made with this instrument, and present typical images and spectra.

  20. Synergetics Framework for Hyperspectral Image Classification

    Science.gov (United States)

    Müller, R.; Cerra, D.; Reinartz, P.

    2013-05-01

    In this paper a new classification technique for hyperspectral data based on synergetics theory is presented. Synergetics - originally introduced by the physicist H. Haken - is an interdisciplinary theory to find general rules for pattern formation through selforganization and has been successfully applied in fields ranging from biology to ecology, chemistry, cosmology, and thermodynamics up to sociology. Although this theory describes general rules for pattern formation it was linked also to pattern recognition. Pattern recognition algorithms based on synergetics theory have been applied to images in the spatial domain with limited success in the past, given their dependence on the rotation, shifting, and scaling of the images. These drawbacks can be discarded if such methods are applied to data acquired by a hyperspectral sensor in the spectral domain, as each single spectrum, related to an image element in the hyperspectral scene, can be analysed independently. The classification scheme based on synergetics introduces also methods for spatial regularization to get rid of "salt and pepper" classification results and for iterative parameter tuning to optimize class weights. The paper reports an experiment on a benchmark data set frequently used for method comparisons. This data set consists of a hyperspectral scene acquired by the Airborne Visible Infrared Imaging Spectrometer AVIRIS sensor of the Jet Propulsion Laboratory acquired over the Salinas Valley in CA, USA, with 15 vegetation classes. The results are compared to state-of-the-art methodologies like Support Vector Machines (SVM), Spectral Information Divergence (SID), Neural Networks, Logistic Regression, Factor Graphs or Spectral Angle Mapper (SAM). The outcomes are promising and often outperform state-of-the-art classification methodologies.

  1. The hyperspectral imaging trade-off

    DEFF Research Database (Denmark)

    Carstensen, Jens Michael

    structures in these projects. However, hyperspectral imaging is a sampling choice within spectral imaging that typically will impose some trade-offs, and these trade-offs will not be optimal for many applications. The purpose of this presentation is to point out and increase the awareness of these trade...... will show how spectral resolution in these situations can be traded off with improvements in the parameters above....

  2. Neural Network-Based Hyperspectral Algorithms

    Science.gov (United States)

    2016-06-07

    Neural Network-Based Hyperspectral Algorithms Walter F. Smith, Jr. and Juanita Sandidge Naval Research Laboratory Code 7340, Bldg 1105 Stennis Space...our effort is development of robust numerical inversion algorithms , which will retrieve inherent optical properties of the water column as well as...validate the resulting inversion algorithms with in-situ data and provide estimates of the error bounds associated with the inversion algorithm . APPROACH

  3. New hyperspectral discrimination measure for spectral similarity

    Science.gov (United States)

    Du, Yingzi; Chang, Chein-I.; Ren, Hsuan; D'Amico, Francis M.; Jensen, James O.

    2003-09-01

    Spectral angle mapper (SAM) has been widely used as a spectral similarity measure for multispectral and hyperspectral image analysis. It has been shown to be equivalent to Euclidean distance when the spectral angle is relatively small. Most recently, a stochastic measure, called spectral information divergence (SID) has been introduced to model the spectrum of a hyperspectral image pixel as a probability distribution so that spectral variations can be captured more effectively in a stochastic manner. This paper develops a new hyperspectral spectral discriminant measure, which is a mixture of SID and SAM. More specifically, let xi and xj denote two hyperspectral image pixel vectors with their corresponding spectra specified by si and sj. SAM is the spectral angle of xi and xj and is defined by [SAM(si,sj)]. Similarly, SID measures the information divergence between xi and xj and is defined by [SID(si,sj)]. The new measure, referred to as (SID,SAM)-mixed measure has two variations defined by SID(si,sj)xtan(SAM(si,sj)] and SID(si,sj)xsin[SAM(si,sj)] where tan [SAM(si,sj)] and sin[SAM(si,sj)] are the tangent and the sine of the angle between vectors x and y. The advantage of the developed (SID,SAM)-mixed measure combines both strengths of SID and SAM in spectral discriminability. In order to demonstrate its utility, a comparative study is conducted among the new measure, SID and SAM where the discriminatory power of the (SID,SAM)-mixed measure is significantly improved over SID and SAM.

  4. Radiometric consistency assessment of hyperspectral infrared sounders

    OpenAIRE

    Wang, L.; Y. Han; Jin, X.; Y. Chen; D. A. Tremblay

    2015-01-01

    The radiometric and spectral consistency among the Atmospheric Infrared Sounder (AIRS), the Infrared Atmospheric Sounding Interferometer (IASI), and the Cross-track Infrared Sounder (CrIS) is fundamental for the creation of long-term infrared (IR) hyperspectral radiance benchmark datasets for both inter-calibration and climate-related studies. In this study, the CrIS radiance measurements on Suomi National Polar-orbiting Partnership (SNPP) satellite are directly com...

  5. Compressive Hyperspectral Imaging and Anomaly Detection

    Science.gov (United States)

    2010-02-01

    Examples include the discrete cosine basis and various wavelets based bases. They have been thoroughly studied and widely considered in applications...the desired jointly sparse a"s, one shall adjust a and b. 4.4 Hyperspectral Image Reconstruction and Denoising We apply the model x* = Da’ + e! to...iteration for compressive sensing and sparse denoising ,’" Communications in Mathematical Sciences , 2008. W. Yin, "Analysis and generalizations of

  6. Positron Scanner for Locating Brain Tumors

    Science.gov (United States)

    Rankowitz, S.; Robertson, J. S.; Higinbotham, W. A.; Rosenblum, M. J.

    1962-03-01

    A system is described that makes use of positron emitting isotopes for locating brain tumors. This system inherently provides more information about the distribution of radioactivity in the head in less time than existing scanners which use one or two detectors. A stationary circular array of 32 scintillation detectors scans a horizontal layer of the head from many directions simultaneously. The data, consisting of the number of counts in all possible coincidence pairs, are coded and stored in the memory of a Two-Dimensional Pulse-Height Analyzer. A unique method of displaying and interpreting the data is described that enables rapid approximate analysis of complex source distribution patterns. (auth)

  7. A volume scanner for diffuse imaging

    Science.gov (United States)

    Vafa, Elham; Roberts, Nicolas; Sharafutdinova, Galiya; Holdsworth, John

    2016-11-01

    Non-invasive optical screening mammography has a significant barrier in the extreme scatter of human tissue at optical wavelengths. A volume scanner suited for high numerical aperture capture of scattered light from diffuse media has been designed, modelled using Trace Pro software and experimentally constructed. Modelling results indicate the presence of an embedded volume with different scatter properties from the bulk yields a measurable difference in the overall scatter pattern and intensity recorded. Work towards a full tomographic reconstruction from scattered light recorded on the two dimensional array detector is currently underway.

  8. A Cartographic Electron Beam Scanner Design Study.

    Science.gov (United States)

    1981-04-01

    0132 UNCLASSIFIED 6005 ETL-0257 NLEhmnnnnnununu lllhllIIhhlh EIIIIIIIIuuh hhhhhhhw-: o~"c ETL OVDFR U-C0EESE25SR7TINULIiE U..ARMYCOPSOFENINER ENINE ...17 2.3.4.4 Data Retrieval Process . . . . 2-21 2.3.5 Software .. ........... ... 2-25 2.4 Details of Scanner Experiments. 2-26 2.4.1 General...point processor and suitable interfaces were installed in the experimental Cartographic EBR System to provide complete compatibility with the software

  9. The Lick Observatory image-dissector scanner.

    Science.gov (United States)

    Robinson, L. B.; Wampler, E. J.

    1972-01-01

    A scanner that uses an image dissector to scan the output screen of an image tube has proven to be a sensitive and linear detector for faint astronomical spectra. The image-tube phosphor screen acts as a short-term storage element and allows the system to approach the performance of an ideal multichannel photon counter. Pulses resulting from individual photons, emitted from the output phosphor and detected by the image dissector, trigger an amplifier-discriminator and are counted in a 24-bit, 4096-word circulating memory. Aspects of system performance are discussed, giving attention to linearity, dynamic range, sensitivity, stability, and scattered light properties.

  10. Hyperspectral surveying for mineral resources in Alaska

    Science.gov (United States)

    Kokaly, Raymond F.; Graham, Garth E.; Hoefen, Todd M.; Kelley, Karen D.; Johnson, Michaela R.; Hubbard, Bernard E.

    2016-07-07

    Alaska is a major producer of base and precious metals and has a high potential for additional undiscovered mineral resources. However, discovery is hindered by Alaska’s vast size, remoteness, and rugged terrain. New methods are needed to overcome these obstacles in order to fully evaluate Alaska’s geology and mineral resource potential. Hyperspectral surveying is one method that can be used to rapidly acquire data about the distributions of surficial materials, including different types of bedrock and ground cover. In 2014, the U.S. Geological Survey began the Alaska Hyperspectral Project to assess the applicability of this method in Alaska. The primary study area is a remote part of the eastern Alaska Range where porphyry deposits are exposed. In collaboration with the Alaska Division of Geological and Geophysical Surveys, the University of Alaska Fairbanks, and the National Park Service, the U.S. Geological Survey is collecting and analyzing hyperspectral data with the goals of enhancing geologic mapping and developing methods to identify and characterize mineral deposits elsewhere in Alaska.

  11. PET and PVC Separation with Hyperspectral Imagery

    Directory of Open Access Journals (Sweden)

    Monica Moroni

    2015-01-01

    Full Text Available Traditional plants for plastic separation in homogeneous products employ material physical properties (for instance density. Due to the small intervals of variability of different polymer properties, the output quality may not be adequate. Sensing technologies based on hyperspectral imaging have been introduced in order to classify materials and to increase the quality of recycled products, which have to comply with specific standards determined by industrial applications. This paper presents the results of the characterization of two different plastic polymers—polyethylene terephthalate (PET and polyvinyl chloride (PVC—in different phases of their life cycle (primary raw materials, urban and urban-assimilated waste and secondary raw materials to show the contribution of hyperspectral sensors in the field of material recycling. This is accomplished via near-infrared (900–1700 nm reflectance spectra extracted from hyperspectral images acquired with a two-linear-spectrometer apparatus. Results have shown that a rapid and reliable identification of PET and PVC can be achieved by using a simple two near-infrared wavelength operator coupled to an analysis of reflectance spectra. This resulted in 100% classification accuracy. A sensor based on this identification method appears suitable and inexpensive to build and provides the necessary speed and performance required by the recycling industry.

  12. PET and PVC Separation with Hyperspectral Imagery

    Science.gov (United States)

    Moroni, Monica; Mei, Alessandro; Leonardi, Alessandra; Lupo, Emanuela; La Marca, Floriana

    2015-01-01

    Traditional plants for plastic separation in homogeneous products employ material physical properties (for instance density). Due to the small intervals of variability of different polymer properties, the output quality may not be adequate. Sensing technologies based on hyperspectral imaging have been introduced in order to classify materials and to increase the quality of recycled products, which have to comply with specific standards determined by industrial applications. This paper presents the results of the characterization of two different plastic polymers—polyethylene terephthalate (PET) and polyvinyl chloride (PVC)—in different phases of their life cycle (primary raw materials, urban and urban-assimilated waste and secondary raw materials) to show the contribution of hyperspectral sensors in the field of material recycling. This is accomplished via near-infrared (900–1700 nm) reflectance spectra extracted from hyperspectral images acquired with a two-linear-spectrometer apparatus. Results have shown that a rapid and reliable identification of PET and PVC can be achieved by using a simple two near-infrared wavelength operator coupled to an analysis of reflectance spectra. This resulted in 100% classification accuracy. A sensor based on this identification method appears suitable and inexpensive to build and provides the necessary speed and performance required by the recycling industry. PMID:25609050

  13. Hyperspectral imaging of skin and lung cancers

    Science.gov (United States)

    Zherdeva, Larisa A.; Bratchenko, Ivan A.; Alonova, Marina V.; Myakinin, Oleg O.; Artemyev, Dmitry N.; Moryatov, Alexander A.; Kozlov, Sergey V.; Zakharov, Valery P.

    2016-04-01

    The problem of cancer control requires design of new approaches for instrumental diagnostics, as the accuracy of cancer detection on the first step of diagnostics in clinics is slightly more than 50%. In this study, we present a method of visualization and diagnostics of skin and lung tumours based on registration and processing of tissues hyperspectral images. In a series of experiments registration of hyperspectral images of skin and lung tissue samples is carried out. Melanoma, basal cell carcinoma, nevi and benign tumours are studied in skin ex vivo and in vivo experiments; adenocarcinomas and squamous cell carcinomas are studied in ex vivo lung experiments. In a series of experiments the typical features of diffuse reflection spectra for pathological and normal tissues were found. Changes in tissues morphology during the tumour growth lead to the changes of blood and pigments concentration, such as melanin in skin. That is why tumours and normal tissues maybe differentiated with information about spectral response in 500-600 nm and 600 - 670 nm areas. Thus, hyperspectral imaging in the visible region may be a useful tool for cancer detection as it helps to estimate spectral properties of tissues and determine malignant regions for precise resection of tumours.

  14. Benthic habitat mapping using hyperspectral remote sensing

    Science.gov (United States)

    Vélez-Reyes, Miguel; Goodman, James A.; Castrodad-Carrau, Alexey; Jiménez-Rodriguez, Luis O.; Hunt, Shawn D.; Armstrong, Roy

    2006-09-01

    Benthic habitats are the different bottom environments as defined by distinct physical, geochemical, and biological characteristics. Remote sensing is increasingly being used to map and monitor the complex dynamics associated with estuarine and nearshore benthic habitats. Advantages of remote sensing technology include both the qualitative benefits derived from a visual overview, and more importantly, the quantitative abilities for systematic assessment and monitoring. Advancements in instrument capabilities and analysis methods are continuing to expand the accuracy and level of effectiveness of the resulting data products. Hyperspectral sensors in particular are rapidly emerging as a more complete solution, especially for the analysis of subsurface shallow aquatic systems. The spectral detail offered by hyperspectral instruments facilitates significant improvements in the capacity to differentiate and classify benthic habitats. This paper reviews two techniques for mapping shallow coastal ecosystems that both combine the retrieval of water optical properties with a linear unmixing model to obtain classifications of the seafloor. Example output using AVIRIS hyperspectral imagery of Kaneohe Bay, Hawaii is employed to demonstrate the application potential of the two approaches and compare their respective results.

  15. PET and PVC separation with hyperspectral imagery.

    Science.gov (United States)

    Moroni, Monica; Mei, Alessandro; Leonardi, Alessandra; Lupo, Emanuela; Marca, Floriana La

    2015-01-20

    Traditional plants for plastic separation in homogeneous products employ material physical properties (for instance density). Due to the small intervals of variability of different polymer properties, the output quality may not be adequate. Sensing technologies based on hyperspectral imaging have been introduced in order to classify materials and to increase the quality of recycled products, which have to comply with specific standards determined by industrial applications. This paper presents the results of the characterization of two different plastic polymers--polyethylene terephthalate (PET) and polyvinyl chloride (PVC)--in different phases of their life cycle (primary raw materials, urban and urban-assimilated waste and secondary raw materials) to show the contribution of hyperspectral sensors in the field of material recycling. This is accomplished via near-infrared (900-1700 nm) reflectance spectra extracted from hyperspectral images acquired with a two-linear-spectrometer apparatus. Results have shown that a rapid and reliable identification of PET and PVC can be achieved by using a simple two near-infrared wavelength operator coupled to an analysis of reflectance spectra. This resulted in 100% classification accuracy. A sensor based on this identification method appears suitable and inexpensive to build and provides the necessary speed and performance required by the recycling industry.

  16. Subpixel Target Enhancement in Hyperspectral Images

    Directory of Open Access Journals (Sweden)

    Manoj K. Arora

    2013-01-01

    Full Text Available Hyperspectral images due to their higher spectral resolution are increasingly being used for various remote sensing applications including information extraction at subpixel level. Typically whenever an object gets spectrally resolved but not spatially, mixed pixels in the images result. Numerous man made and/or natural disparate targets may thus occur inside such mixed pixels giving rise to subpixel target detection problem. Various spectral unmixing models such as linear mixture modeling (LMM are in vogue to recover components of a mixed pixel. Spectral unmixing outputs both the endmember spectrum and their corresponding abundance fractions inside the pixel. It, however, does not provide spatial distribution of these abundance fractions within a pixel. This limits the applicability of hyperspectral data for subpixel target detection. In this paper, a new inverse Euclidean distance based super-resolution mapping method has been presented. In this method, the subpixel target detection is performed by adjusting spatial distribution of abundance fraction within a pixel of an hyperspectral image. Results obtained at different resolutions indicate that super-resolution mapping may effectively be utilized in enhancing the target detection at sub-pixel level.

  17. Subpixel Target Enhancement in Hyperspectral Images

    Directory of Open Access Journals (Sweden)

    Manoj K. Arora

    2013-01-01

    Full Text Available Hyperspectral images due to their higher spectral resolution are increasingly being used for various remote sensing applications including information extraction at subpixel level. Typically whenever an object gets spectrally resolved but not spatially, mixed pixels in the images result. Numerous man made and/or natural disparatetar gets may thus occur inside such mixed pixels giving rise to subpixel target detection problem. Various spectral unmixing models such as linear mixture modeling (LMM are in vogue to recover components of a mixed pixel. Spectral unmixing outputs both the endmember spectrum and their corresponding a bundance fractions inside the pixel. It, however, does not provide spatial distribution of these abundance fractions within a pixel. This limits the applicability of hyperspectral data for subpixel target detection. In this paper, a new inverse Euclidean distance based super-resolution mapping method has been presented. In this method, the subpixel target detection is performed by adjusting spatial distribution of abundance fraction within a pixel of an hyperspectral image. Results obtainedat different resolutions indicate that super-resolution mapping may effectively be utilized in enhancing the target detection at sub-pixel level.Defence Science Journal, 2013, 63(1, pp.63-68, DOI:http://dx.doi.org/10.14429/dsj.63.3765

  18. Broadband QWIP FPAs for hyperspectral applications

    Science.gov (United States)

    Reisinger, Axel; Dennis, Richard; Patnaude, Kelly; Burrows, Douglas; Bundas, Jason; Beech, Kim; Faska, Ross; Sundaram, Mani

    2013-07-01

    Is a quantum well infrared photodetector (QWIP) suitable for hyperspectral applications? Yes, provided its spectral response is broad enough, the signal-to-noise ratio in narrow spectral slices across the entire response band is high enough, and the operating temperature is reasonable. We present the performance of a 640 × 512 QWIP focal plane array (FPA) with nearly uniform spectral response from 8 to 12 μm that achieves temporal noise equivalent temperature difference (NETD) lower than 200 mK in 20 nm wide spectral slices across the entire 8-12 μm band with the FPA operating at a temperature of 50 K or colder. A hyperspectral camera would feature a grating or prism to disperse 8-12 μm light across such a FPA or a hyperspectral filter on top of the FPA. Operating in pushbroom mode on an earth-observing satellite, the camera can be used for spectral mapping of vegetation, crops and forests, for pollution monitoring, and for studies in atmospheric chemistry.

  19. Establishment of Diagnostic Assay for Hantavirus with Microarray Techniques%基因芯片技术检测肾综合征出血热病毒核酸的研究

    Institute of Scientific and Technical Information of China (English)

    朱进; 陶开华; 操敏; 张云; 李越希; 张锦海; 唐家琪

    2004-01-01

    To establish a rapid, sensitive and specific diagnostic assay for Hantavirus with microarray techniques, specific primers and probes were designed according to the conservative and specific DNA sequence of 76-118 strain and R22 strain. The probes were spotted on glass slides to form microarrays.The Cy3-1abled single stranded DNA fragments prepared by dissymmetical PCR were hybridized with the probes on the glass slides. The microarrays were scanned and analyzed with a scanner. The results showed that the DNA microarray could detect the different typed DNA of HTN and SEO with adequate specificity and sensitivity. The developed DNA microarray and techniques might be a very useful method for diagnosis and prevention, and could be widely applied in specific pathogens detection ofinfectious diseases such as hemorrhagic fever with renal syndrome.

  20. Hyperspectral Imaging for Defect Detection of Pickling Cucumber

    Science.gov (United States)

    This book chapter reviews the recent progress on hyperspectral imaging technology for defect inspection of pickling cucumbers. The chapter first describes near-infrared hyperspectral reflectance imaging technique for the detection of bruises on pickling cucumbers. The technique showed good detection...

  1. Online Unmixing of Multitemporal Hyperspectral Images Accounting for Spectral Variability.

    Science.gov (United States)

    Thouvenin, Pierre-Antoine; Dobigeon, Nicolas; Tourneret, Jean-Yves

    2016-09-01

    Hyperspectral unmixing is aimed at identifying the reference spectral signatures composing a hyperspectral image and their relative abundance fractions in each pixel. In practice, the identified signatures may vary spectrally from an image to another due to varying acquisition conditions, thus inducing possibly significant estimation errors. Against this background, the hyperspectral unmixing of several images acquired over the same area is of considerable interest. Indeed, such an analysis enables the endmembers of the scene to be tracked and the corresponding endmember variability to be characterized. Sequential endmember estimation from a set of hyperspectral images is expected to provide improved performance when compared with methods analyzing the images independently. However, the significant size of the hyperspectral data precludes the use of batch procedures to jointly estimate the mixture parameters of a sequence of hyperspectral images. Provided that each elementary component is present in at least one image of the sequence, we propose to perform an online hyperspectral unmixing accounting for temporal endmember variability. The online hyperspectral unmixing is formulated as a two-stage stochastic program, which can be solved using a stochastic approximation. The performance of the proposed method is evaluated on synthetic and real data. Finally, a comparison with independent unmixing algorithms illustrates the interest of the proposed strategy.

  2. Hyperspectral Imagery Throughput and Fusion Evaluation over Compression and Interpolation

    Science.gov (United States)

    2008-07-01

    extending between two consecutive data points, and matches the first and second derivatives of adjacent polynomials at the seams . Thus, the CS provides...J. E. Fowler and J. T. Pucker “Three-Dimensional Wavelet- based Compression of Hyperspectral Imagery”, Ch. 14 in Hyperspectral Data Exploitation

  3. Multiview hyperspectral topography of tissue structural and functional characteristics

    Science.gov (United States)

    Liu, Peng; Huang, Jiwei; Zhang, Shiwu; Xu, Ronald X.

    2016-01-01

    Accurate and in vivo characterization of structural, functional, and molecular characteristics of biological tissue will facilitate quantitative diagnosis, therapeutic guidance, and outcome assessment in many clinical applications, such as wound healing, cancer surgery, and organ transplantation. We introduced and tested a multiview hyperspectral imaging technique for noninvasive topographic imaging of cutaneous wound oxygenation. The technique integrated a multiview module and a hyperspectral module in a single portable unit. Four plane mirrors were cohered to form a multiview reflective mirror set with a rectangular cross section. The mirror set was placed between a hyperspectral camera and the target biological tissue. For a single image acquisition task, a hyperspectral data cube with five views was obtained. The five-view hyperspectral image consisted of a main objective image and four reflective images. Three-dimensional (3-D) topography of the scene was achieved by correlating the matching pixels between the objective image and the reflective images. 3-D mapping of tissue oxygenation was achieved using a hyperspectral oxygenation algorithm. The multiview hyperspectral imaging technique was validated in a wound model, a tissue-simulating blood phantom, and in vivo biological tissue. The experimental results demonstrated the technical feasibility of using multiview hyperspectral imaging for 3-D topography of tissue functional properties.

  4. Hyperspectral microscopy to identify foodborne bacteria with optimum lighting source

    Science.gov (United States)

    Hyperspectral microscopy is an emerging technology for rapid detection of foodborne pathogenic bacteria. Since scattering spectral signatures from hyperspectral microscopic images (HMI) vary with lighting sources, it is important to select optimal lights. The objective of this study is to compare t...

  5. The application of hyperspectral remote sensing to coast environment investigation

    Institute of Scientific and Technical Information of China (English)

    ZHANG Liang; ZHANG bing; CHEN Zhengchao; ZHENG Lanfen; TONG Qingxi

    2009-01-01

    Requirements for monitoring the coastal zone environment are first summarized. Then the application of hyperspectral remote sensing to coast environment investigation is introduced, such as the classification of coast beaches and bottom matter, target recognition, mine detection, oil spill identification and ocean color remote sensing. Finally, what is needed to follow on in application of hyperspectral remote sensing to coast environment is recommended.

  6. Morphology-based fusion method of hyperspectral image

    Science.gov (United States)

    Yue, Song; Zhang, Zhijie; Ren, Tingting; Wang, Chensheng; Yu, Hui

    2014-11-01

    Hyperspectral image analysis method is widely used in all kinds of application including agriculture identification and forest investigation and atmospheric pollution monitoring. In order to accurately and steadily analyze hyperspectral image, considering the spectrum and spatial information which is provided by hyperspectral data together is necessary. The hyperspectral image has the characteristics of large amount of wave bands and information. Corresponding to the characteristics of hyperspectral image, a fast image fusion method that can fuse the hyperspectral image with high fidelity is studied and proposed in this paper. First of all, hyperspectral image is preprocessed before the morphological close operation. The close operation is used to extract wave band characteristic to reduce dimensionality of hyperspectral image. The spectral data is smoothed at the same time to avoid the discontinuity of the data by combination of spatial information and spectral information. On this basis, Mean-shift method is adopted to register key frames. Finally, the selected key frames by fused into one fusing image by the pyramid fusion method. The experiment results show that this method can fuse hyper spectral image in high quality. The fused image's attributes is better than the original spectral images comparing to the spectral images and reach the objective of fusion.

  7. Circumference estimation using 3D-whole body scanners and shadow scanner

    NARCIS (Netherlands)

    Daanen, H.A.M.

    1998-01-01

    Clothing designers and manufacturers use traditional body dimensions as their basis. When 3D-whole body scanners are introduced to determine the body dimensions, a conversion has to be made, since scan determined circumference measures are slightly larger than the traditional values. This pilot stud

  8. Microarray analysis of Escherichia coli0157:H7

    Institute of Scientific and Technical Information of China (English)

    Hui-Ying Jin; Kai-Hua Tao; Yue-Xi Li; Fa-Qing Li; Su-Qin Li

    2005-01-01

    AIM: To establish the rapid, specific, and sensitive method for detecting O157:H7 with DNA microchips.METHODS: Specific oligonucleotide probes (26-28 nt) of bacterial antigenic and virulent genes of E. coli O157:H7 and other related pathogen genes were pre-synthesized and immobilized on a solid support to make microchips. The four genes encoding O157 somatic antigen (rfbE), H7 fiagellar antigen (fliC) and toxins (SLT1, SLT2) were monitored by multiplex PCR with four pairs of specific primers. Fluorescence-Cy3 labeled samples for hybridization were generated by PCR with Cy3-labeled single prime. Hybridization was performed for 60 min at 45 ℃. Microchip images were taken using a confocal fluorescent scanner.RESULTS: Twelve different bacterial strains were detected with various combinations of four virulent genes. All the O157:H7 strains yielded positive results by multiplex PCR.The size of the PCR products generated with these primers varied from 210 to 678 bp. All the rfbE/fliC/SLT1/SLT2 probes specifically recognized Cy3-labeled fluorescent samples from O157:H7 strains, or strains containing O157 and H7 genes. No cross hybridization of O157:H7 fluorescent samples occurred in other probes. Non-O157:H7 pathogens failed to yield any signal under comparable conditions. If the Cy3-labeled fluorescent product of O157 single PCR was diluted 50-fold, no signal was found in agarose gel electrophoresis, but a positive signal was found in microarray hybridization.CONCLUSION: Microarray analysis of O157:H7 is a rapid,specific, and efficient method for identification and detection of bacterial pathogens.

  9. Spectral-Spatial Hyperspectral Image Classification Based on KNN

    Science.gov (United States)

    Huang, Kunshan; Li, Shutao; Kang, Xudong; Fang, Leyuan

    2016-12-01

    Fusion of spectral and spatial information is an effective way in improving the accuracy of hyperspectral image classification. In this paper, a novel spectral-spatial hyperspectral image classification method based on K nearest neighbor (KNN) is proposed, which consists of the following steps. First, the support vector machine is adopted to obtain the initial classification probability maps which reflect the probability that each hyperspectral pixel belongs to different classes. Then, the obtained pixel-wise probability maps are refined with the proposed KNN filtering algorithm that is based on matching and averaging nonlocal neighborhoods. The proposed method does not need sophisticated segmentation and optimization strategies while still being able to make full use of the nonlocal principle of real images by using KNN, and thus, providing competitive classification with fast computation. Experiments performed on two real hyperspectral data sets show that the classification results obtained by the proposed method are comparable to several recently proposed hyperspectral image classification methods.

  10. Kernel-based fisher discriminant analysis for hyperspectral target detection

    Institute of Scientific and Technical Information of China (English)

    GU Yan-feng; ZHANG Ye; YOU Di

    2007-01-01

    A new method based on kernel Fisher discriminant analysis (KFDA) is proposed for target detection of hyperspectral images. The KFDA combines kernel mapping derived from support vector machine and the classical linear Fisher discriminant analysis (LFDA), and it possesses good ability to process nonlinear data such as hyperspectral images. According to the Fisher rule that the ratio of the between-class and within-class scatters is maximized, the KFDA is used to obtain a set of optimal discriminant basis vectors in high dimensional feature space. All pixels in the hyperspectral images are projected onto the discriminant basis vectors and the target detection is performed according to the projection result. The numerical experiments are performed on hyperspectral data with 126 bands collected by Airborne Visible/Infrared Imaging Spectrometer (AVIRIS). The experimental results show the effectiveness of the proposed detection method and prove that this method has good ability to overcome small sample size and spectral variability in the hyperspectral target detection.

  11. Massively parallel processing of remotely sensed hyperspectral images

    Science.gov (United States)

    Plaza, Javier; Plaza, Antonio; Valencia, David; Paz, Abel

    2009-08-01

    In this paper, we develop several parallel techniques for hyperspectral image processing that have been specifically designed to be run on massively parallel systems. The techniques developed cover the three relevant areas of hyperspectral image processing: 1) spectral mixture analysis, a popular approach to characterize mixed pixels in hyperspectral data addressed in this work via efficient implementation of a morphological algorithm for automatic identification of pure spectral signatures or endmembers from the input data; 2) supervised classification of hyperspectral data using multi-layer perceptron neural networks with back-propagation learning; and 3) automatic target detection in the hyperspectral data using orthogonal subspace projection concepts. The scalability of the proposed parallel techniques is investigated using Barcelona Supercomputing Center's MareNostrum facility, one of the most powerful supercomputers in Europe.

  12. Pineal function: impact of microarray analysis

    DEFF Research Database (Denmark)

    Klein, David C; Bailey, Michael J; Carter, David A

    2009-01-01

    Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity...... foundation that microarray analysis has provided will broadly support future research on pineal function....

  13. The EADGENE Microarray Data Analysis Workshop

    NARCIS (Netherlands)

    Koning, de D.J.; Jaffrezic, F.; Lund, M.S.; Watson, M.; Channing, C.; Hulsegge, B.; Pool, M.H.; Buitenhuis, B.; Hedegaard, J.; Hornshoj, H.; Sorensen, P.; Marot, G.; Delmas, C.; Lê Cao, K.A.; San Cristobal, M.; Baron, M.D.; Malinverni, R.; Stella, A.; Brunner, R.M.; Seyfert, H.M.; Jensen, K.; Mouzaki, D.; Waddington, D.; Jiménez-Marín, A.; Perez-Alegre, M.; Perez-Reinado, E.; Closset, R.; Detilleux, J.C.; Dovc, P.; Lavric, M.; Nie, H.; Janss, L.

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10

  14. Antenna Near-Field Probe Station Scanner

    Science.gov (United States)

    Zaman, Afroz J. (Inventor); Lee, Richard Q. (Inventor); Darby, William G. (Inventor); Barr, Philip J. (Inventor); Lambert, Kevin M (Inventor); Miranda, Felix A. (Inventor)

    2011-01-01

    A miniaturized antenna system is characterized non-destructively through the use of a scanner that measures its near-field radiated power performance. When taking measurements, the scanner can be moved linearly along the x, y and z axis, as well as rotationally relative to the antenna. The data obtained from the characterization are processed to determine the far-field properties of the system and to optimize the system. Each antenna is excited using a probe station system while a scanning probe scans the space above the antenna to measure the near field signals. Upon completion of the scan, the near-field patterns are transformed into far-field patterns. Along with taking data, this system also allows for extensive graphing and analysis of both the near-field and far-field data. The details of the probe station as well as the procedures for setting up a test, conducting a test, and analyzing the resulting data are also described.

  15. Interferometric Laser Scanner for Direction Determination.

    Science.gov (United States)

    Kaloshin, Gennady; Lukin, Igor

    2016-01-21

    In this paper, we explore the potential capabilities of new laser scanning-based method for direction determination. The method for fully coherent beams is extended to the case when interference pattern is produced in the turbulent atmosphere by two partially coherent sources. The performed theoretical analysis identified the conditions under which stable pattern may form on extended paths of 0.5-10 km in length. We describe a method for selecting laser scanner parameters, ensuring the necessary operability range in the atmosphere for any possible turbulence characteristics. The method is based on analysis of the mean intensity of interference pattern, formed by two partially coherent sources of optical radiation. Visibility of interference pattern is estimated as a function of propagation pathlength, structure parameter of atmospheric turbulence, and spacing of radiation sources, producing the interference pattern. It is shown that, when atmospheric turbulences are moderately strong, the contrast of interference pattern of laser scanner may ensure its applicability at ranges up to 10 km.

  16. Interferometric Laser Scanner for Direction Determination

    Directory of Open Access Journals (Sweden)

    Gennady Kaloshin

    2016-01-01

    Full Text Available In this paper, we explore the potential capabilities of new laser scanning-based method for direction determination. The method for fully coherent beams is extended to the case when interference pattern is produced in the turbulent atmosphere by two partially coherent sources. The performed theoretical analysis identified the conditions under which stable pattern may form on extended paths of 0.5–10 km in length. We describe a method for selecting laser scanner parameters, ensuring the necessary operability range in the atmosphere for any possible turbulence characteristics. The method is based on analysis of the mean intensity of interference pattern, formed by two partially coherent sources of optical radiation. Visibility of interference pattern is estimated as a function of propagation pathlength, structure parameter of atmospheric turbulence, and spacing of radiation sources, producing the interference pattern. It is shown that, when atmospheric turbulences are moderately strong, the contrast of interference pattern of laser scanner may ensure its applicability at ranges up to 10 km.

  17. Integration of thermal and hyperspectral VNIR imagery for architectural and artistic heritage analysis and monitoring

    Science.gov (United States)

    Cavalli, Rosa Maria; Masini, Nicola; Pascucci, Simone; Palombo, Angelo; Pignatti, Stefano

    2010-05-01

    The application of integrated hyperspectral VNIR and thermal data for analyzing and monitoring the architectural and artistic heritage status is becoming a remarkable tool to be combined with other non-destructive techniques (e.g. GPR), and prior to destructive checking, in order to extract appropriate information and make useful decisions [1]. As the analysis of some kind of damages (e.g. water infiltrations) or alterations is not always fulfilled with visible and thermographic imagery, the proposed study aims at integrating hyperspectral reflectances and temperature and apparent thermal inertia behaviours. Hyperspectral data is able to discriminate materials on the basis of their different patterns of wavelength-specific absorption; in fact, they are successfully used for identifying minerals and rocks, as well as detecting soil properties including moisture, organic content and salinity [2]. Moreover, the potential to find out alterations or damages and monitoring them through non-destructive sensors is particularly appreciated in structural analysis for restoration works such as water infiltrations in outdoor cultural assets and moisture penetration in a wall that is a major source of paint alteration [3, 4]. The jointly use of the reflective and infrared (emitted, absorbed, reflected and transmitted) radiation for this research study is encouraged by the technical and operative characteristics of the observation systems at disposal that can provide high spectral resolution and high-frequency images with low Ne?R e Ne?T values and able to observe the variables and physical and optical parameters in quasi real-time and connected to the cultural heritage status. The following portable field instruments are used for this study: (a) HYSPEX hyperspectral scanner working in the VNIR (0.4-1.0μm) spectral region, which is an imaging spectrometer with a very high spectral and spatial resolution, (b) 2 FLIR SC7000 Thermal cams working in the MWIR (3-5 micron) and LWIR

  18. Recent micro-CT scanner developments at UGCT

    OpenAIRE

    Dierick, Manuel; Van Loo, Denis; Masschaele, Bert; Boone, Matthieu; Van Hoorebeke, Luc; Cnudde, Veerle

    2013-01-01

    UGCT is a user facility for multidisciplinary micro-CT research. The scanners at UGCT are custom designed and built by the Radiation Physics research group (UGent). This paper describes the two latest scanners that were developed in collaboration with XRE: HECTOR, a high energy micro-CT scanner, and EMCT, a gantry based micro-CT scanner with variable magnification. HECTOR is a 240 kV 280 W system with a nominal resolution of 4 micrometer. A 40x40 cm² flat panel detector which can be tiled res...

  19. In control: systematic assessment of microarray performance.

    Science.gov (United States)

    van Bakel, Harm; Holstege, Frank C P

    2004-10-01

    Expression profiling using DNA microarrays is a powerful technique that is widely used in the life sciences. How reliable are microarray-derived measurements? The assessment of performance is challenging because of the complicated nature of microarray experiments and the many different technology platforms. There is a mounting call for standards to be introduced, and this review addresses some of the issues that are involved. Two important characteristics of performance are accuracy and precision. The assessment of these factors can be either for the purpose of technology optimization or for the evaluation of individual microarray hybridizations. Microarray performance has been evaluated by at least four approaches in the past. Here, we argue that external RNA controls offer the most versatile system for determining performance and describe how such standards could be implemented. Other uses of external controls are discussed, along with the importance of probe sequence availability and the quantification of labelled material.

  20. The EADGENE Microarray Data Analysis Workshop

    DEFF Research Database (Denmark)

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

  1. Chaotic mixer improves microarray hybridization.

    Science.gov (United States)

    McQuain, Mark K; Seale, Kevin; Peek, Joel; Fisher, Timothy S; Levy, Shawn; Stremler, Mark A; Haselton, Frederick R

    2004-02-15

    Hybridization is an important aspect of microarray experimental design which influences array signal levels and the repeatability of data within an array and across different arrays. Current methods typically require 24h and use target inefficiently. In these studies, we compare hybridization signals obtained in conventional static hybridization, which depends on diffusional target delivery, with signals obtained in a dynamic hybridization chamber, which employs a fluid mixer based on chaotic advection theory to deliver targets across a conventional glass slide array. Microarrays were printed with a pattern of 102 identical probe spots containing a 65-mer oligonucleotide capture probe. Hybridization of a 725-bp fluorescently labeled target was used to measure average target hybridization levels, local signal-to-noise ratios, and array hybridization uniformity. Dynamic hybridization for 1h with 1 or 10ng of target DNA increased hybridization signal intensities approximately threefold over a 24-h static hybridization. Similarly, a 10- or 60-min dynamic hybridization of 10ng of target DNA increased hybridization signal intensities fourfold over a 24h static hybridization. In time course studies, static hybridization reached a maximum within 8 to 12h using either 1 or 10ng of target. In time course studies using the dynamic hybridization chamber, hybridization using 1ng of target increased to a maximum at 4h and that using 10ng of target did not vary over the time points tested. In comparison to static hybridization, dynamic hybridization reduced the signal-to-noise ratios threefold and reduced spot-to-spot variation twofold. Therefore, we conclude that dynamic hybridization based on a chaotic mixer design improves both the speed of hybridization and the maximum level of hybridization while increasing signal-to-noise ratios and reducing spot-to-spot variation.

  2. Hyperspectral Imaging for Cancer Surgical Margin Delineation: Registration of Hyperspectral and Histological Images.

    Science.gov (United States)

    Lu, Guolan; Halig, Luma; Wang, Dongsheng; Chen, Zhuo Georgia; Fei, Baowei

    2014-03-12

    The determination of tumor margins during surgical resection remains a challenging task. A complete removal of malignant tissue and conservation of healthy tissue is important for the preservation of organ function, patient satisfaction, and quality of life. Visual inspection and palpation is not sufficient for discriminating between malignant and normal tissue types. Hyperspectral imaging (HSI) technology has the potential to noninvasively delineate surgical tumor margin and can be used as an intra-operative visual aid tool. Since histological images provide the ground truth of cancer margins, it is necessary to warp the cancer regions in ex vivo histological images back to in vivo hyperspectral images in order to validate the tumor margins detected by HSI and to optimize the imaging parameters. In this paper, principal component analysis (PCA) is utilized to extract the principle component bands of the HSI images, which is then used to register HSI images with the corresponding histological image. Affine registration is chosen to model the global transformation. A B-spline free form deformation (FFD) method is used to model the local non-rigid deformation. Registration experiment was performed on animal hyperspectral and histological images. Experimental results from animals demonstrated the feasibility of the hyperspectral imaging method for cancer margin detection.

  3. Investigating coral hyperspectral properties across coral species and coral state using hyperspectral imaging

    Science.gov (United States)

    Mehrubeoglu, Mehrube; Smith, Dustin K.; Smith, Shane W.; Strychar, Kevin B.; McLauchlan, Lifford

    2013-09-01

    Coral reefs are one of the most diverse and threatened ecosystems in the world. Corals worldwide are at risk, and in many instances, dying due to factors that affect their environment resulting in deteriorating environmental conditions. Because corals respond quickly to the quality of the environment that surrounds them, corals have been identified as bioindicators of water quality and marine environmental health. The hyperspectral imaging system is proposed as a noninvasive tool to monitor different species of corals as well as coral state over time. This in turn can be used as a quick and non-invasive method to monitor environmental health that can later be extended to climate conditions. In this project, a laboratory-based hyperspectral imaging system is used to collect spectral and spatial information of corals. In the work presented here, MATLAB and ENVI software tools are used to view and process spatial information and coral spectral signatures to identify differences among the coral data. The results support the hypothesis that hyperspectral properties of corals vary among different coral species, and coral state over time, and hyperspectral imaging can be a used as a tool to document changes in coral species and state.

  4. Identification of scanner models by comparison of scanned hologram images.

    Science.gov (United States)

    Sugawara, Shigeru

    2014-08-01

    A method to identify scanner models that had been used to forge low-level counterfeit currencies was proposed in this study. The method identified a scanner model by characterizing differences between hologram images that exist in low-level counterfeit currencies. Twenty scanners of 18 different models were used to make samples of hologram images used in this study. The method was divided into two steps: identification of capturing conditions and identification of the scanner model. The first proposed protocol used correlations of spatial distribution of brightness to identify capturing conditions. A second proposed protocol used correlations of color distributions to identify a scanner model. The effectiveness of the protocols was demonstrated with numerical methods and sample images. The preliminary study revealed that it is necessary to consider the orientation of the holograms when the scanner models were identified, but 180° rotations can be ignored. Moreover, it is necessary to consider position in the main scanning direction of the bed for charged-coupled-device scanners. The demonstration showed that the first protocol could correctly identify the capturing conditions of almost all hologram images. However, one image could not be identified correctly; the protocol could distinguish images captured by charged-coupled-device scanners and those captured by contact image sensor scanners if the hologram was placed on the right or left edge of the scanner bed, but could not distinguish them if the hologram was placed on the inside. The demonstration also showed that the second protocol could correctly identify scanner models of all hologram images.

  5. Development of scintillation materials for PET scanners

    CERN Document Server

    Korzhik, Mikhail; Annenkov, Alexander N; Borissevitch, Andrei; Dossovitski, Alexei; Missevitch, Oleg; Lecoq, Paul

    2007-01-01

    The growing demand on PET methodology for a variety of applications ranging from clinical use to fundamental studies triggers research and development of PET scanners providing better spatial resolution and sensitivity. These efforts are primarily focused on the development of advanced PET detector solutions and on the developments of new scintillation materials as well. However Lu containing scintillation materials introduced in the last century such as LSO, LYSO, LuAP, LuYAP crystals still remain the best PET species in spite of the recent developments of bright, fast but relatively low density lanthanum bromide scintillators. At the same time Lu based materials have several drawbacks which are high temperature of crystallization and relatively high cost compared to alkali-halide scintillation materials. Here we describe recent results in the development of new scintillation materials for PET application.

  6. Gigapixel microscopy using a flatbed scanner

    CERN Document Server

    Zheng, Guoan; Yang, Changhuei

    2012-01-01

    Microscopy imaging systems with a very wide field-of-view (FOV) are highly sought in biomedical applications. In this paper, we report a wide FOV microscopy imaging system that uses a low-cost scanner and a closed-circuit-television (CCTV) lens. We show that such an imaging system is capable to capture a 10 mm * 7.5 mm FOV image with 0.77 micron resolution, resulting in 0.54 gigapixels (109 pixels) across the entire image (26400 pixels * 20400 pixels). The resolution and field curve of the proposed system were characterized by imaging a USAF resolution target and a hole-array target. A 1.6 gigapixel microscopy image (0.54 gigapixel with 3 colors) of a pathology slide was acquired by using such a system for application demonstration.

  7. MARS: Microarray analysis, retrieval, and storage system

    Directory of Open Access Journals (Sweden)

    Scheideler Marcel

    2005-04-01

    Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

  8. Vision Assisted Laser Scanner Navigation for Autonomous Robots

    DEFF Research Database (Denmark)

    Andersen, Jens Christian; Andersen, Nils Axel; Ravn, Ole

    2008-01-01

    This paper describes a navigation method based on road detection using both a laser scanner and a vision sensor. The method is to classify the surface in front of the robot into traversable segments (road) and obstacles using the laser scanner, this classifies the area just in front of the robot ...

  9. Convenient integrating sphere scanner for accurate luminous flux measurements

    Science.gov (United States)

    Winter, S.; Lindemann, M.; Jordan, W.; Binder, U.; Anokhin, M.

    2009-08-01

    Measurement results and applications of a recently developed device for the measurement of the spatial uniformity of integrating spheres are presented. Due to the complexity of their implementation, sphere scanners are mainly used by national metrology institutes to increase the accuracy of relative and absolute luminous flux measurements (Ohno et al 1997 J. IES 26 107-14, Ohno and Daubach 2001 J. IES 30 105-15, Ohno 1998 Metrologia 35 473-8, Hovila et al 2004 Metrologia 41 407-13). The major drawback of traditional scanners for integrating spheres is the necessity of a complex and time-consuming sphere modification, as the lamp holder has to be replaced by a new scanner holder with additional cables for power supply and for communication with the stepping motor control unit (Ohno et al 1997 J. IES 26 107-14). Therefore, with traditional scanners the relative spatial sphere responsivity already changes due to the installation of a special scanner holder. The new scanner simply substitutes the lamp under test: it can be screwed into an E27 lamp socket, as it needs only two electrical contacts. Two wires are simultaneously used for the power supply of the stepping motor control unit, the scanner light source (LED) and for the signal transmission of commands and results. The benefits of scanner-assisted measurements are shown for spotlight lamp calibrations.

  10. Verification of a CT scanner using a miniature step gauge

    DEFF Research Database (Denmark)

    Cantatore, Angela; Andreasen, J.L.; Carmignato, S.;

    2011-01-01

    The work deals with performance verification of a CT scanner using a 42mm miniature replica step gauge developed for optical scanner verification. Errors quantification and optimization of CT system set-up in terms of resolution and measurement accuracy are fundamental for use of CT scanning...

  11. Quantitative Assay for Starch by Colorimetry Using a Desktop Scanner

    Science.gov (United States)

    Matthews, Kurt R.; Landmark, James D.; Stickle, Douglas F.

    2004-01-01

    The procedure to produce standard curve for starch concentration measurement by image analysis using a color scanner and computer for data acquisition and color analysis is described. Color analysis is performed by a Visual Basic program that measures red, green, and blue (RGB) color intensities for pixels within the scanner image.

  12. Thermionic scanner pinpoints work function of emitter surfaces

    Science.gov (United States)

    Rasor, N. S.

    1966-01-01

    In the electron tube testing, a thermionic scanner makes accurate spatial resolution measurements of the metallic surface work functions of emitters. The scanner determines the emitter function and its local departures from the mean value on a point-by-point basis for display on an oscilloscope.

  13. Flux profile scanners for scattered high-energy electrons

    Science.gov (United States)

    Hicks, R. S.; Decowski, P.; Arroyo, C.; Breuer, M.; Celli, J.; Chudakov, E.; Kumar, K. S.; Olson, M.; Peterson, G. A.; Pope, K.; Ricci, J.; Savage, J.; Souder, P. A.

    2005-11-01

    The paper describes the design and performance of flux integrating Cherenkov scanners with air-core reflecting light guides used in a high-energy, high-flux electron scattering experiment at the Stanford Linear Accelerator Center. The scanners were highly radiation resistant and provided a good signal to background ratio leading to very good spatial resolution of the scattered electron flux profile scans.

  14. A ’Millipede’ scanner model - Energy consumption and performance

    NARCIS (Netherlands)

    Engelen, Johan B.C.; Khatib, Mohammed G.

    2008-01-01

    This short report (1) describes an energy model for the seek and read/write operations in a mass-balanced Y-scanner for parallel-probe storage by IBM [1] and (2) updates the settings of the MEMS model in DiskSim with recent published figures from this XY-scanner. To speedup system simulations, a str

  15. Study of PET scanner designs using clinical metrics to optimize the scanner axial FOV and crystal thickness

    Science.gov (United States)

    Surti, S.; Werner, M. E.; Karp, J. S.

    2013-06-01

    The aim of this study is to understand the trade-off between crystal thickness and scanner axial field-of-view FOV (AFOV) for clinical PET imaging. Clinical scanner design has evolved towards 20-25 mm thick crystals and 16-22 cm long scanner AFOV, as well as time-of-flight (TOF) imaging. While Monte Carlo studies demonstrate that longer AFOV and thicker crystals will lead to higher scanner sensitivity, cost has prohibited the building of commercial scanners with >22 cm AFOV. In this study, we performed a series of system simulations to optimize the use of a given amount of crystal material by evaluating the impact on system sensitivity and noise equivalent counts (NEC), as well as image quality in terms of lesion detectability. We evaluated two crystal types (LSO and LaBr3) and fixed the total crystal volume used for each type (8.2 L of LSO and 17.1 L of LaBr3) while varying the crystal thickness and scanner AFOV. In addition, all imaging times were normalized so that the total scan time needed to scan a 100 cm long object with multiple bed positions was kept constant. Our results show that the highest NEC cm-1 in a 35 cm diameter ×70 cm long line source cylinder is achieved for an LSO scanner with 10 mm long crystals and AFOV of 36 cm, while for LaBr3 scanners, the highest NEC cm-1 is obtained with 20 mm long crystals and an AFOV of 38 cm. Lesion phantom simulations show that the best lesion detection performance is achieved in scanners with long AFOV (≥36 cm) and using thin crystals (≤10 mm of LSO and ≤20 mm of LaBr3). This is due to a combination of improved NEC, as well as improved lesion contrast estimation due to better spatial resolution in thinner crystals. Alternatively, for lesion detection performance similar to that achieved in standard clinical scanner designs, the long AFOV scanners can be used to reduce the total scan time without increasing the amount of crystal used in the scanner. In addition, for LaBr3 based scanners, the reduced lesion

  16. Review: DNA microarray technology and drug development

    Directory of Open Access Journals (Sweden)

    Sana Khan

    2010-01-01

    Full Text Available On the contrary to slow and non specific traditional drug discovery methods, DNA microarray technology could accelerate the identification of potential drugs for treating diseases like cancer, AIDS and provide fruitful results in the drug discovery. The technique provides efficient automation and maximum flexibility to the researchers and can test thousand compounds at a time. Scientists find DNA microarray useful in disease diagnosis, monitoring desired and adverse outcomes of therapeutic interventions, as well as, in the selection, assessment and quality con-trol of the potential drugs. In the current scenario, where new pathogens are expected every year, DNA microarray promises as an efficient technology to detect new organisms in a short time. Classification of carcinomas at the molecular level and prediction of how various types of tumor respond to different therapeutic agents can be made possible with the use of microarray analysis. Also, microarray technique can prove instrumental in personalized medicines development by providing microarray data of a patient which could be used for identifying diseases, treatment specific to individual and trailing disease prognosis. Microarray analysis could be beneficial in the area of molecular medicines for analysis of genetic variations and functions of genes in normal individuals and diseased conditions. The technique can give satisfactory results in single nucleotide polymorphism (SNP analysis and pharmacogenomics studies. The challenges that arise with the technology are high degree of variability with data obtained, frequent up gradation of methods and machines and lack of trained manpower. Despite this, DNA micro-array promises to be the next generation sequencer which could explain how organisms evolve and adapt looking at the whole genome. In a nutshell, Microarray technology makes it possible for molecular biologists to analyze simultaneously thousands of DNA samples and monitor their

  17. An Approach for Characterizing and Comparing Hyperspectral Microscopy Systems

    Directory of Open Access Journals (Sweden)

    Silas J. Leavesley

    2013-07-01

    Full Text Available Hyperspectral imaging and analysis approaches offer accurate detection and quantification of fluorescently-labeled proteins and cells in highly autofluorescent tissues. However, selecting optimum acquisition settings for hyperspectral imaging is often a daunting task. In this study, we compared two hyperspectral systems—a widefield system with acoustic optical tunable filter (AOTF and charge coupled device (CCD camera, and a confocal system with diffraction gratings and photomultiplier tube (PMT array. We measured the effects of system parameters on hyperspectral image quality and linear unmixing results. Parameters that were assessed for the confocal system included pinhole diameter, laser power, PMT gain and for the widefield system included arc lamp intensity, and camera gain. The signal-to-noise ratio (SNR and the root-mean-square error (RMS error were measured to assess system performance. Photobleaching dynamics were studied. Finally, theoretical sensitivity studies were performed to estimate the incremental response (sensitivity and false-positive detection rates (specificity. Results indicate that hyperspectral imaging assays are highly dependent on system parameters and experimental conditions. For detection of green fluorescent protein (GFP-expressing cells in fixed lung tissues, a confocal pinhole of five airy disk units, high excitation intensity and low detector gain were optimal. The theoretical sensitivity studies revealed that widefield hyperspectral microscopy was able to detect GFP with fewer false positive occurrences than confocal microscopy, even though confocal microscopy offered improved signal and noise characteristics. These studies provide a framework for optimization that can be applied to a variety of hyperspectral imaging systems.

  18. Comparing methods for analysis of biomedical hyperspectral image data

    Science.gov (United States)

    Leavesley, Silas J.; Sweat, Brenner; Abbott, Caitlyn; Favreau, Peter F.; Annamdevula, Naga S.; Rich, Thomas C.

    2017-02-01

    Over the past 2 decades, hyperspectral imaging technologies have been adapted to address the need for molecule-specific identification in the biomedical imaging field. Applications have ranged from single-cell microscopy to whole-animal in vivo imaging and from basic research to clinical systems. Enabling this growth has been the availability of faster, more effective hyperspectral filtering technologies and more sensitive detectors. Hence, the potential for growth of biomedical hyperspectral imaging is high, and many hyperspectral imaging options are already commercially available. However, despite the growth in hyperspectral technologies for biomedical imaging, little work has been done to aid users of hyperspectral imaging instruments in selecting appropriate analysis algorithms. Here, we present an approach for comparing the effectiveness of spectral analysis algorithms by combining experimental image data with a theoretical "what if" scenario. This approach allows us to quantify several key outcomes that characterize a hyperspectral imaging study: linearity of sensitivity, positive detection cut-off slope, dynamic range, and false positive events. We present results of using this approach for comparing the effectiveness of several common spectral analysis algorithms for detecting weak fluorescent protein emission in the midst of strong tissue autofluorescence. Results indicate that this approach should be applicable to a very wide range of applications, allowing a quantitative assessment of the effectiveness of the combined biology, hardware, and computational analysis for detecting a specific molecular signature.

  19. Using hyperspectral imaging technology to identify diseased tomato leaves

    Science.gov (United States)

    Li, Cuiling; Wang, Xiu; Zhao, Xueguan; Meng, Zhijun; Zou, Wei

    2016-11-01

    In the process of tomato plants growth, due to the effect of plants genetic factors, poor environment factors, or disoperation of parasites, there will generate a series of unusual symptoms on tomato plants from physiology, organization structure and external form, as a result, they cannot grow normally, and further to influence the tomato yield and economic benefits. Hyperspectral image usually has high spectral resolution, not only contains spectral information, but also contains the image information, so this study adopted hyperspectral imaging technology to identify diseased tomato leaves, and developed a simple hyperspectral imaging system, including a halogen lamp light source unit, a hyperspectral image acquisition unit and a data processing unit. Spectrometer detection wavelength ranged from 400nm to 1000nm. After hyperspectral images of tomato leaves being captured, it was needed to calibrate hyperspectral images. This research used spectrum angle matching method and spectral red edge parameters discriminant method respectively to identify diseased tomato leaves. Using spectral red edge parameters discriminant method produced higher recognition accuracy, the accuracy was higher than 90%. Research results have shown that using hyperspectral imaging technology to identify diseased tomato leaves is feasible, and provides the discriminant basis for subsequent disease control of tomato plants.

  20. Research on hyperspectral dynamic scene and image sequence simulation

    Science.gov (United States)

    Sun, Dandan; Liu, Fang; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei

    2016-10-01

    This paper presents a simulation method of hyperspectral dynamic scene and image sequence for hyperspectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyperspectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyperspectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyperspectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyperspectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyperspectral images are consistent with the theoretical analysis results.

  1. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria...... and toxins, identification of allergen reactivity and autoantibodies. They have also demonstrated the ability to measure the absolute concentration of small molecules. Besides their capacity for parallel diagnostics, microarrays can be more sensitive than traditional methods such as enzyme...... and be amenable to automation or integrated into easy-to-use systems, such as micrototal analysis systems or point-of-care devices....

  2. Microarrays--analysis of signaling pathways.

    Science.gov (United States)

    Ramachandran, Anassuya; Black, Michael A; Shelling, Andrew N; Love, Donald R

    2008-01-01

    Microarrays provide a powerful means of analyzing the expression level of multiple transcripts in two sample populations. In this study, we have used microarray technology to identify genes that are differentially regulated in response to activin-treated ovarian cancer cells. We find a number of biologically relevant genes that are involved in regulating activin signaling and genes potentially contributing to activin-mediated growth arrest appear to be differentially regulated. Thus, microarrays are an important tool for dissecting gene expression changes in normal physiological processes and disease.

  3. DNA Microarrays in Herbal Drug Research

    Directory of Open Access Journals (Sweden)

    Preeti Chavan

    2006-01-01

    Full Text Available Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts.

  4. On the spectral quality of scanner illumination with LEDs

    Science.gov (United States)

    Cui, Chengwu

    2013-01-01

    Document scanner illumination has evolved along with general illumination technologies. LEDs have become more and more popular as the illumination sources for document scanning. LED technologies provide a wide range of choices both in terms of structural design and spectral compositions. In this report, we examine some popular LED technologies used for document scanner. We evaluate the color rendering performance of scanner models with different illumination technologies by examining their rendering of the Macbeth ColorChecker™ in sRGB. We found that more phosphors in phosphor conversion types of white LEDs may not be necessarily advantageous in terms of scanner color rendering performance. Also CIS type of scanner may be sensitive to the peak wavelength shift and can be particularly problematic when the peaks are out of certain range.

  5. Ultra-Miniature Lidar Scanner for Launch Range Data Collection

    Science.gov (United States)

    Geng, Jason

    2012-01-01

    The most critical component in lidar is its laser scanner, which delivers pulsed or CW laser to target with desirable field of view (FOV). Most existing lidars use a rotating or oscillating mirror for scanning, resulting in several drawbacks. A lidar scanning technology was developed that could achieve very high scanning speed, with an ultra-miniature size and much lighter weight. This technology promises at least a 10x performance improvement in these areas over existing lidar scanners. Features of the proposed ultra-miniature lidar scanner include the ability to make the entire scanner <2 mm in diameter; very high scanning speed (e.g. 5 - 20 kHz, in contrast to several hundred Hz in existing scanners); structure design to meet stringent requirements on size, weight, power, and compactness for various applications; and the scanning speed and FOV can be altered for obtaining high image resolutions of targeted areas and for diversified uses.

  6. Bayesian classifier applications of airborne hyperspectral imagery processing for forested areas

    Science.gov (United States)

    Kozoderov, Vladimir; Kondranin, Timofei; Dmitriev, Egor; Kamentsev, Vladimir

    2015-06-01

    Pattern recognition problem is outlined in the context of textural and spectral analysis of remote sensing imagery processing. Main attention is paid to Bayesian classifier that can be used to realize the processing procedures based on parallel machine-learning algorithms and high-productive computers. We consider the maximum of the posterior probability principle and the formalism of Markov random fields for the neighborhood description of the pixels for the related classes of objects with the emphasis on forests of different species and ages. The energy category of the selected classes serves to account for the likelihood measure between the registered radiances and the theoretical distribution functions approximating remotely sensed data. Optimization procedures are undertaken to solve the pattern recognition problem of the texture description for the forest classes together with finding thin nuances of their spectral distribution in the feature space. As a result, possible redundancy of the channels for imaging spectrometer due to their correlations is removed. Difficulties are revealed due to different sampling data while separating pixels, which characterize the sunlit tops, shaded space and intermediate cases of the Sun illumination conditions on the hyperspectral images. Such separation of pixels for the forest classes is maintained to enhance the recognition accuracy, but learning ensembles of data need to be agreed for these categories of pixels. We present some results of the Bayesian classifier applicability for recognizing airborne hyperspectral images using the relevant improvements in separating such pixels for the forest classes on a test area of the 4 × 10 km size encompassed by 13 airborne tracks, each forming the images by 500 pixels across the track and from 10,000 to 14,000 pixels along the track. The spatial resolution of each image is near to 1 m from the altitude near to 2 km above the ground level. The results of the hyperspectral imagery

  7. Hyperspectral Image Turbulence Measurements of the Atmosphere

    Science.gov (United States)

    Lane, Sarah E.; West, Leanne L.; Gimmestad, Gary G.; Kireev, Stanislav; Smith, William L., Sr.; Burdette, Edward M.; Daniels, Taumi; Cornman, Larry

    2012-01-01

    A Forward Looking Interferometer (FLI) sensor has the potential to be used as a means of detecting aviation hazards in flight. One of these hazards is mountain wave turbulence. The results from a data acquisition activity at the University of Colorado s Mountain Research Station will be presented here. Hyperspectral datacubes from a Telops Hyper-Cam are being studied to determine if evidence of a turbulent event can be identified in the data. These data are then being compared with D&P TurboFT data, which are collected at a much higher time resolution and broader spectrum.

  8. Dictionary-Based, Clustered Sparse Representation for Hyperspectral Image Classification

    Directory of Open Access Journals (Sweden)

    Zhen-tao Qin

    2015-01-01

    Full Text Available This paper presents a new, dictionary-based method for hyperspectral image classification, which incorporates both spectral and contextual characteristics of a sample clustered to obtain a dictionary of each pixel. The resulting pixels display a common sparsity pattern in identical clustered groups. We calculated the image’s sparse coefficients using the dictionary approach, which generated the sparse representation features of the remote sensing images. The sparse coefficients are then used to classify the hyperspectral images via a linear SVM. Experiments show that our proposed method of dictionary-based, clustered sparse coefficients can create better representations of hyperspectral images, with a greater overall accuracy and a Kappa coefficient.

  9. 3D Biomaterial Microarrays for Regenerative Medicine

    DEFF Research Database (Denmark)

    Gaharwar, Akhilesh K.; Arpanaei, Ayyoob; Andresen, Thomas Lars;

    2015-01-01

    Three dimensional (3D) biomaterial microarrays hold enormous promise for regenerative medicine because of their ability to accelerate the design and fabrication of biomimetic materials. Such tissue-like biomaterials can provide an appropriate microenvironment for stimulating and controlling stem...

  10. Quality Visualization of Microarray Datasets Using Circos

    Directory of Open Access Journals (Sweden)

    Martin Koch

    2012-08-01

    Full Text Available Quality control and normalization is considered the most important step in the analysis of microarray data. At present there are various methods available for quality assessments of microarray datasets. However there seems to be no standard visualization routine, which also depicts individual microarray quality. Here we present a convenient method for visualizing the results of standard quality control tests using Circos plots. In these plots various quality measurements are drawn in a circular fashion, thus allowing for visualization of the quality and all outliers of each distinct array within a microarray dataset. The proposed method is intended for use with the Affymetrix Human Genome platform (i.e., GPL 96, GPL570 and GPL571. Circos quality measurement plots are a convenient way for the initial quality estimate of Affymetrix datasets that are stored in publicly available databases.

  11. Geometric correction of APEX hyperspectral data

    Directory of Open Access Journals (Sweden)

    Vreys Kristin

    2016-03-01

    Full Text Available Hyperspectral imagery originating from airborne sensors is nowadays widely used for the detailed characterization of land surface. The correct mapping of the pixel positions to ground locations largely contributes to the success of the applications. Accurate geometric correction, also referred to as “orthorectification”, is thus an important prerequisite which must be performed prior to using airborne imagery for evaluations like change detection, or mapping or overlaying the imagery with existing data sets or maps. A so-called “ortho-image” provides an accurate representation of the earth’s surface, having been adjusted for lens distortions, camera tilt and topographic relief. In this paper, we describe the different steps in the geometric correction process of APEX hyperspectral data, as applied in the Central Data Processing Center (CDPC at the Flemish Institute for Technological Research (VITO, Mol, Belgium. APEX ortho-images are generated through direct georeferencing of the raw images, thereby making use of sensor interior and exterior orientation data, boresight calibration data and elevation data. They can be referenced to any userspecified output projection system and can be resampled to any output pixel size.

  12. Anomaly Detection from Hyperspectral Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    Qiandong Guo

    2016-12-01

    Full Text Available Hyperspectral remote sensing imagery contains much more information in the spectral domain than does multispectral imagery. The consecutive and abundant spectral signals provide a great potential for classification and anomaly detection. In this study, two real hyperspectral data sets were used for anomaly detection. One data set was an Airborne Visible/Infrared Imaging Spectrometer (AVIRIS data covering the post-attack World Trade Center (WTC and anomalies are fire spots. The other data set called SpecTIR contained fabric panels as anomalies compared to their background. Existing anomaly detection algorithms including the Reed–Xiaoli detector (RXD, the blocked adaptive computation efficient outlier nominator (BACON, the random selection based anomaly detector (RSAD, the weighted-RXD (W-RXD, and the probabilistic anomaly detector (PAD are reviewed here. The RXD generally sets strict assumptions to the background, which cannot be met in many scenarios, while BACON, RSAD, and W-RXD employ strategies to optimize the estimation of background information. The PAD firstly estimates both background information and anomaly information and then uses the information to conduct anomaly detection. Here, the BACON, RSAD, W-RXD, and PAD outperformed the RXD in terms of detection accuracy, and W-RXD and PAD required less time than BACON and RSAD.

  13. Dried fruits quality assessment by hyperspectral imaging

    Science.gov (United States)

    Serranti, Silvia; Gargiulo, Aldo; Bonifazi, Giuseppe

    2012-05-01

    Dried fruits products present different market values according to their quality. Such a quality is usually quantified in terms of freshness of the products, as well as presence of contaminants (pieces of shell, husk, and small stones), defects, mould and decays. The combination of these parameters, in terms of relative presence, represent a fundamental set of attributes conditioning dried fruits humans-senses-detectable-attributes (visual appearance, organolectic properties, etc.) and their overall quality in terms of marketable products. Sorting-selection strategies exist but sometimes they fail when a higher degree of detection is required especially if addressed to discriminate between dried fruits of relatively small dimensions and when aiming to perform an "early detection" of pathogen agents responsible of future moulds and decays development. Surface characteristics of dried fruits can be investigated by hyperspectral imaging (HSI). In this paper, specific and "ad hoc" applications addressed to propose quality detection logics, adopting a hyperspectral imaging (HSI) based approach, are described, compared and critically evaluated. Reflectance spectra of selected dried fruits (hazelnuts) of different quality and characterized by the presence of different contaminants and defects have been acquired by a laboratory device equipped with two HSI systems working in two different spectral ranges: visible-near infrared field (400-1000 nm) and near infrared field (1000-1700 nm). The spectra have been processed and results evaluated adopting both a simple and fast wavelength band ratio approach and a more sophisticated classification logic based on principal component (PCA) analysis.

  14. Onboard Image Processing System for Hyperspectral Sensor

    Directory of Open Access Journals (Sweden)

    Hiroki Hihara

    2015-09-01

    Full Text Available Onboard image processing systems for a hyperspectral sensor have been developed in order to maximize image data transmission efficiency for large volume and high speed data downlink capacity. Since more than 100 channels are required for hyperspectral sensors on Earth observation satellites, fast and small-footprint lossless image compression capability is essential for reducing the size and weight of a sensor system. A fast lossless image compression algorithm has been developed, and is implemented in the onboard correction circuitry of sensitivity and linearity of Complementary Metal Oxide Semiconductor (CMOS sensors in order to maximize the compression ratio. The employed image compression method is based on Fast, Efficient, Lossless Image compression System (FELICS, which is a hierarchical predictive coding method with resolution scaling. To improve FELICS’s performance of image decorrelation and entropy coding, we apply a two-dimensional interpolation prediction and adaptive Golomb-Rice coding. It supports progressive decompression using resolution scaling while still maintaining superior performance measured as speed and complexity. Coding efficiency and compression speed enlarge the effective capacity of signal transmission channels, which lead to reducing onboard hardware by multiplexing sensor signals into a reduced number of compression circuits. The circuitry is embedded into the data formatter of the sensor system without adding size, weight, power consumption, and fabrication cost.

  15. APEX - the Hyperspectral ESA Airborne Prism Experiment

    Directory of Open Access Journals (Sweden)

    Koen Meuleman

    2008-10-01

    Full Text Available The airborne ESA-APEX (Airborne Prism Experiment hyperspectral mission simulator is described with its distinct specifications to provide high quality remote sensing data. The concept of an automatic calibration, performed in the Calibration Home Base (CHB by using the Control Test Master (CTM, the In-Flight Calibration facility (IFC, quality flagging (QF and specific processing in a dedicated Processing and Archiving Facility (PAF, and vicarious calibration experiments are presented. A preview on major applications and the corresponding development efforts to provide scientific data products up to level 2/3 to the user is presented for limnology, vegetation, aerosols, general classification routines and rapid mapping tasks. BRDF (Bidirectional Reflectance Distribution Function issues are discussed and the spectral database SPECCHIO (Spectral Input/Output introduced. The optical performance as well as the dedicated software utilities make APEX a state-of-the-art hyperspectral sensor, capable of (a satisfying the needs of several research communities and (b helping the understanding of the Earth’s complex mechanisms.

  16. Onboard Image Processing System for Hyperspectral Sensor.

    Science.gov (United States)

    Hihara, Hiroki; Moritani, Kotaro; Inoue, Masao; Hoshi, Yoshihiro; Iwasaki, Akira; Takada, Jun; Inada, Hitomi; Suzuki, Makoto; Seki, Taeko; Ichikawa, Satoshi; Tanii, Jun

    2015-09-25

    Onboard image processing systems for a hyperspectral sensor have been developed in order to maximize image data transmission efficiency for large volume and high speed data downlink capacity. Since more than 100 channels are required for hyperspectral sensors on Earth observation satellites, fast and small-footprint lossless image compression capability is essential for reducing the size and weight of a sensor system. A fast lossless image compression algorithm has been developed, and is implemented in the onboard correction circuitry of sensitivity and linearity of Complementary Metal Oxide Semiconductor (CMOS) sensors in order to maximize the compression ratio. The employed image compression method is based on Fast, Efficient, Lossless Image compression System (FELICS), which is a hierarchical predictive coding method with resolution scaling. To improve FELICS's performance of image decorrelation and entropy coding, we apply a two-dimensional interpolation prediction and adaptive Golomb-Rice coding. It supports progressive decompression using resolution scaling while still maintaining superior performance measured as speed and complexity. Coding efficiency and compression speed enlarge the effective capacity of signal transmission channels, which lead to reducing onboard hardware by multiplexing sensor signals into a reduced number of compression circuits. The circuitry is embedded into the data formatter of the sensor system without adding size, weight, power consumption, and fabrication cost.

  17. Improved atmospheric characterization for hyperspectral exploitation

    Science.gov (United States)

    Wurst, Nathan P.; Meola, Joseph; Fiorino, Steven T.

    2017-05-01

    Airborne hyperspectral imaging (HSI)has shown utility in material detection and identification. Recent interest in longwave infrared (LWIR) HSI systems operating in the 7-14 micron range has developed due to strong spectral features of minerals, chemicals, and gaseous effluents. LWIR HSI has the advantage over other spectral bands by operating in day or night scenarios because emitted/reflected thermal radiation rather than reflected sunlight is measured. This research seeks to determine the most effective methods to perform model-based atmospheric compensation (AC) of LWIR HSI data using two existing atmospheric radiative transfer (RT) models, MODTRAN and LEEDR. MODTRAN is the more established RT model, but it lacks LEEDRs robust capability to generate realistic atmospheric profiles from probabilistic climatology or observations and forecasts from numerical weather prediction (NWP) models. The advantage of LEEDR's ability to generate atmospheres is tested by using LEEDR atmospheres, a MODTRAN standard model, and radiosonde data to perform AC on an airborne hyperspectral datacube with nadir looking geometry. This work investigates the potential benefit of LEEDR's weather/climatology tools for improving and/or expediting the AC process for LWIR HSI.

  18. Adaptive feature selection for hyperspectral data analysis

    Science.gov (United States)

    Korycinski, Donna; Crawford, Melba M.; Barnes, J. Wesley

    2004-02-01

    Hyperspectral data can potentially provide greatly improved capability for discrimination between many land cover types, but new methods are required to process these data and extract the required information. Data sets are extremely large, and the data are not well distributed across these high dimensional spaces. The increased number and resolution of spectral bands, many of which are highly correlated, is problematic for supervised statistical classification techniques when the number of training samples is small relative to the dimension of the input vector. Selection of the most relevant subset of features is one means of mitigating these effects. A new algorithm based on the tabu search metaheuristic optimization technique was developed to perform subset feature selection and implemented within a binary hierarchical tree framework. Results obtained using the new approach were compared to those from a greedy common greedy selection technique and to a Fisher discriminant based feature extraction method, both of which were implemented in the same binary hierarchical tree classification scheme. The tabu search based method generally yielded higher classification accuracies with lower variability than these other methods in experiments using hyperspectral data acquired by the EO-1 Hyperion sensor over the Okavango Delta of Botswana.

  19. Hyperspectral imaging applied to forensic medicine

    Science.gov (United States)

    Malkoff, Donald B.; Oliver, William R.

    2000-03-01

    Remote sensing techniques now include the use of hyperspectral infrared imaging sensors covering the mid-and- long wave regions of the spectrum. They have found use in military surveillance applications due to their capability for detection and classification of a large variety of both naturally occurring and man-made substances. The images they produce reveal the spatial distributions of spectral patterns that reflect differences in material temperature, texture, and composition. A program is proposed for demonstrating proof-of-concept in using a portable sensor of this type for crime scene investigations. It is anticipated to be useful in discovering and documenting the affects of trauma and/or naturally occurring illnesses, as well as detecting blood spills, tire patterns, toxic chemicals, skin injection sites, blunt traumas to the body, fluid accumulations, congenital biochemical defects, and a host of other conditions and diseases. This approach can significantly enhance capabilities for determining the circumstances of death. Potential users include law enforcement organizations (police, FBI, CIA), medical examiners, hospitals/emergency rooms, and medical laboratories. Many of the image analysis algorithms already in place for hyperspectral remote sensing and crime scene investigations can be applied to the interpretation of data obtained in this program.

  20. PATMA: parser of archival tissue microarray

    Directory of Open Access Journals (Sweden)

    Lukasz Roszkowiak

    2016-12-01

    Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  1. PATMA: parser of archival tissue microarray.

    Science.gov (United States)

    Roszkowiak, Lukasz; Lopez, Carlos

    2016-01-01

    Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  2. Hyperspectral Technique for Detecting Soil Parameters

    Science.gov (United States)

    Garfagnoli, F.; Ciampalini, A.; Moretti, S.; Chiarantini, L.

    2011-12-01

    In satellite and airborne remote sensing, hyperspectral technique has become a very powerful tool, due to the possibility of rapidly realizing chemical/mineralogical maps of the studied areas. Many studies are trying to customize the algorithms to identify several geo-physical soil properties. The specific objective of this study is to investigate those soil characteristics, such as clay mineral content, influencing degradation processes (soil erosion and shallow landslides), by means of correlation analysis, in order to examine the possibility of predicting the selected property using high-resolution reflectance spectra and images. The study area is located in the Mugello basin, about 30 km north of Firenze (Tuscany, Italy). Agriculturally suitable terrains are assigned mainly to annual crops, marginally to olive groves, vineyards and orchards. Soils mostly belong to Regosols and Cambisols orders. An ASD FieldSpec spectroradiometer was used to obtain reflectance spectra from about 80 dried, crushed and sieved samples under controlled laboratory conditions. Samples were collected simultaneously with the flight of SIM.GA hyperspectral camera from Selex Galileo, over an area of about 5 km2 and their positions were recorded with a differential GPS. The quantitative determination of clay minerals content was performed by means of XRD and Rietveld refinement. Different chemometric techniques were preliminarily tested to correlate mineralogical records with reflectance data. A one component partial least squares regression model yielded a preliminary R2 value of 0.65. A slightly better result was achieved by plotting the absorption peak depth at 2210 versus total clay content (band-depth analysis). The complete SIM.GA hyperspectral geocoded row dataset, with an approximate pixel resolution of 0.6 m (VNIR) and 1.2 m (SWIR), was firstly transformed into at sensor radiance values, by applying calibration coefficients and parameters from laboratory measurements to non

  3. APLIKASI INFO HALAL MENGGUNAKAN BARCODE SCANNER UNTUK SMARTPHONE ANDROID

    Directory of Open Access Journals (Sweden)

    Beki Subeki

    2016-05-01

    Full Text Available Abstract – In the production and trade of food products in the era of globalization, people are consuming, especially Muslims need to be given the knowledge, information and access to adequate in order to obtain the correct information about the halal status of products bought. The use of barcode scanners halal product information using the mobile platform is effective and useful for the public to find out information on a product. Barcode scanners can be read by optical scanners called barcode readers or scanned from an image by special software. In Indonesia, most mobile phones have the scanning software for 2D codes, and similar devices available via smartphone.   Keywords : Barcode Scanner, Mobile Platform, Halal Products, Smartphone     Abstrak - Dalam kegiatan produksi dan perdagangan produk pangan di era globalisasi ini, masyarakat yang mengkonsumsi, khususnya umat islam perlu diberikan pengetahuan tentang kehalalan produk, informasi dan akses yang memadai agar memperoleh informasi yang benar tentang status kehalalan produk yang dibelinya. Penggunaan barcode scanner informasi produk halal dengan menggunakan mobile platform dinilai cukup efektif dan berguna bagi masyarakat luas untuk mengetahui informasi sebuah produk. Barcode scanner dapat dibaca oleh pemindai optik yang disebut pembaca kode batang atau dipindai dari sebuah gambar oleh perangkat lunak khusus. Di Indonesia, kebanyakan telepon genggam memiliki perangkat lunak pemindai untuk kode 2D, dan perangkat sejenis tersedia melalui smartphone.   Kata Kunci: Barcode Scanner, Mobile Platform, Produk Halal, Smartphone

  4. Spectral Curve Fitting for Automatic Hyperspectral Data Analysis

    CERN Document Server

    Brown, Adrian J

    2014-01-01

    Automatic discovery and curve fitting of absorption bands in hyperspectral data can enable the analyst to identify materials present in a scene by comparison with library spectra. This procedure is common in laboratory spectra, but is challenging for sparse hyperspectral data. A procedure for robust discovery of overlapping bands in hyperspectral data is described in this paper. The method is capable of automatically discovering and fitting symmetric absorption bands, can separate overlapping absorption bands in a stable manner, and has relatively low sensitivity to noise. A comparison with techniques already available in the literature is presented using simulated spectra. An application is demonstrated utilizing the shortwave infrared (2.0-2.5 micron or 5000-4000 cm-1) region. A small hyperspectral scene is processed to demonstrate the ability of the method to detect small shifts in absorption wavelength caused by varying white mica chemistry in a natural setting.

  5. Unsupervised hyperspectral image analysis using independent component analysis (ICA)

    Energy Technology Data Exchange (ETDEWEB)

    S. S. Chiang; I. W. Ginsberg

    2000-06-30

    In this paper, an ICA-based approach is proposed for hyperspectral image analysis. It can be viewed as a random version of the commonly used linear spectral mixture analysis, in which the abundance fractions in a linear mixture model are considered to be unknown independent signal sources. It does not require the full rank of the separating matrix or orthogonality as most ICA methods do. More importantly, the learning algorithm is designed based on the independency of the material abundance vector rather than the independency of the separating matrix generally used to constrain the standard ICA. As a result, the designed learning algorithm is able to converge to non-orthogonal independent components. This is particularly useful in hyperspectral image analysis since many materials extracted from a hyperspectral image may have similar spectral signatures and may not be orthogonal. The AVIRIS experiments have demonstrated that the proposed ICA provides an effective unsupervised technique for hyperspectral image classification.

  6. FAPEC-based lossless and lossy hyperspectral data compression

    Science.gov (United States)

    Portell, Jordi; Artigues, Gabriel; Iudica, Riccardo; García-Berro, Enrique

    2015-10-01

    Data compression is essential for remote sensing based on hyperspectral sensors owing to the increasing amount of data generated by modern instrumentation. CCSDS issued the 123.0 standard for lossless hyperspectral compression, and a new lossy hyperspectral compression recommendation is being prepared. We have developed multispectral and hyperspectral pre-processing stages for FAPEC, a data compression algorithm based on an entropy coder. We can select a prediction-based lossless stage that offers excellent results and speed. Alternatively, a DWT-based lossless and lossy stage can be selected, which offers excellent results yet obviously requiring more compression time. Finally, a lossless stage based on our HPA algorithm can also be selected, only lossless for now but with the lossy option in preparation. Here we present the overall design of these data compression systems and the results obtained on a variety of real data, including ratios, speed and quality.

  7. Black Beauty's Rainbow: Hyperspectral Imaging of Northwest Africa 7034

    Science.gov (United States)

    Cannon, K. M.; Mustard, J. F.; Agee, C. B.; Wilson, J. H.; Greenberger, R. N.

    2014-07-01

    Hyperspectral imaging is used to characterize the first basaltic breccia from Mars, Northwest Africa 7034. Initial results show the spectral character of NWA 7034 is unlike other SNC meteorites and may be more representative of average martian crust.

  8. Wide-Field, Deep UV Raman Hyperspectral Imager Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ChemImage Sensor Systems (CISS), teaming with the University of South Carolina, proposes a revolutionary wide-field Raman hyperspectral imaging system capable of...

  9. Hyperspectral stimulated emission depletion microscopy and methods of use thereof

    Science.gov (United States)

    Timlin, Jerilyn A; Aaron, Jesse S

    2014-04-01

    A hyperspectral stimulated emission depletion ("STED") microscope system for high-resolution imaging of samples labeled with multiple fluorophores (e.g., two to ten fluorophores). The hyperspectral STED microscope includes a light source, optical systems configured for generating an excitation light beam and a depletion light beam, optical systems configured for focusing the excitation and depletion light beams on a sample, and systems for collecting and processing data generated by interaction of the excitation and depletion light beams with the sample. Hyperspectral STED data may be analyzed using multivariate curve resolution analysis techniques to deconvolute emission from the multiple fluorophores. The hyperspectral STED microscope described herein can be used for multi-color, subdiffraction imaging of samples (e.g., materials and biological materials) and for analyzing a tissue by Forster Resonance Energy Transfer ("FRET").

  10. Dental caries imaging using hyperspectral stimulated Raman scattering microscopy

    Science.gov (United States)

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

    2016-03-01

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

  11. M-estimation for robust sparse unmixing of hyperspectral images

    Science.gov (United States)

    Toomik, Maria; Lu, Shijian; Nelson, James D. B.

    2016-10-01

    Hyperspectral unmixing methods often use a conventional least squares based lasso which assumes that the data follows the Gaussian distribution. The normality assumption is an approximation which is generally invalid for real imagery data. We consider a robust (non-Gaussian) approach to sparse spectral unmixing of remotely sensed imagery which reduces the sensitivity of the estimator to outliers and relaxes the linearity assumption. The method consists of several appropriate penalties. We propose to use an lp norm with 0 Gaussian likelihood with a fixed function ρ(e) that restrains outliers. The M-estimate function reduces the effect of errors with large amplitudes or even assigns the outliers zero weights. Our experimental results on real hyperspectral data show that noise with large amplitudes (outliers) often exists in the data. This ability to mitigate the influence of such outliers can therefore offer greater robustness. Qualitative hyperspectral unmixing results on real hyperspectral image data corroborate the efficacy of the proposed method.

  12. Physical Retrieval of Surface Emissivity Spectrum from Hyperspectral Infrared Radiances

    Science.gov (United States)

    Li, Jun; Weisz, Elisabeth; Zhou, Daniel K.

    2007-01-01

    Retrieval of temperature, moisture profiles and surface skin temperature from hyperspectral infrared (IR) radiances requires spectral information about the surface emissivity. Using constant or inaccurate surface emissivities typically results in large retrieval errors, particularly over semi-arid or arid areas where the variation in emissivity spectrum is large both spectrally and spatially. In this study, a physically based algorithm has been developed to retrieve a hyperspectral IR emissivity spectrum simultaneously with the temperature and moisture profiles, as well as the surface skin temperature. To make the solution stable and efficient, the hyperspectral emissivity spectrum is represented by eigenvectors, derived from the laboratory measured hyperspectral emissivity database, in the retrieval process. Experience with AIRS (Atmospheric InfraRed Sounder) radiances shows that a simultaneous retrieval of the emissivity spectrum and the sounding improves the surface skin temperature as well as temperature and moisture profiles, particularly in the near surface layer.

  13. A survey of landmine detection using hyperspectral imaging

    Science.gov (United States)

    Makki, Ihab; Younes, Rafic; Francis, Clovis; Bianchi, Tiziano; Zucchetti, Massimo

    2017-02-01

    Hyperspectral imaging is a trending technique in remote sensing that finds its application in many different areas, such as agriculture, mapping, target detection, food quality monitoring, etc. This technique gives the ability to remotely identify the composition of each pixel of the image. Therefore, it is a natural candidate for the purpose of landmine detection, thanks to its inherent safety and fast response time. In this paper, we will present the results of several studies that employed hyperspectral imaging for the purpose of landmine detection, discussing the different signal processing techniques used in this framework for hyperspectral image processing and target detection. Our purpose is to highlight the progresses attained in the detection of landmines using hyperspectral imaging and to identify possible perspectives for future work, in order to achieve a better detection in real-time operation mode.

  14. Spatial context driven manifold learning for hyperspectral image classification

    CSIR Research Space (South Africa)

    Zhang, Y

    2014-06-01

    Full Text Available Manifold learning techniques have demonstrated various levels of success in their ability to represent spectral signature characteristics in hyperspectral imagery. Such images consists of spectral features with very subtle differences and at times...

  15. Confocal Scanner for Vertical Particle Tracks in the Nuclear Photoemulsion

    CERN Document Server

    Soroko, L M

    2005-01-01

    A confocal scanner for selective observation of the vertical particle tracks in the nuclear photoemulsion is described. The particle track being searched for is imaging at an angle of 45$^\\circ$ with respect to the optical axis of the system. The confocal scanner is provided with a new optical element, an "image hogonalizator", by means of which the extended image of the inclined vertical particle track is rotated over an angle of 90$^\\circ$. The stereoscopic version of the confocal scanner is presented as well. The described systems will be used in the experiments for investigation of the neutrino oscillations in the accelerators experiments.

  16. A general solution for the registration of optical multispectral scanners

    Science.gov (United States)

    Rader, M. L.

    1974-01-01

    The paper documents a general theory for registration (mapping) of data sets gathered by optical scanners such as the ERTS satellite MSS and the Skylab S-192 MSS. This solution is generally applicable to scanners which have rotating optics. Navigation data and ground control points are used in a statistically weighted adjustment based on a mathematical model of the dynamics of the spacecraft and the scanner system. This adjustment is very similar to the well known photogrammetric adjustments used in aerial mapping. Actual tests have been completed on NASA aircraft 24 channel MSS data, and the results are very encouraging.

  17. [Innovation and Future Technologies for PET Scanners].

    Science.gov (United States)

    Yamaya, Taiga

    2015-01-01

    Positron emission tomography (PET) plays important roles in cancer diagnosis, neuroimaging and molecular imaging research; but potential points remain for which big improvements could be made, including spatial resolution, sensitivity and manufacturing costs. Higher spatial resolution is essential to enable earlier diagnosis, and improved sensitivity results in reduced radiation exposure and shortened measurement time. Therefore, research on next generation PET technologies remains a hot topic worldwide. In this paper, innovation and future technologies for the next generation PET scanners, such as time-of-flight measurement and simultaneous PET/MRI measurement, are described. Among them, depth-of-interaction (DOI) measurement in the radiation sensor will be a key technology to get any significant improvement in sensitivity while maintaining high spatial resolution. DOI measurement also has a potential to expand PET application fields because it allows for more flexible detector arrangement. As an example, the world's first, open-type PET geometry "OpenPET", which is expected to lead to PET imaging during treatment, is under development. The DOI detector itself continues to evolve with the help of recently developed semiconductor photodetectors, often referred to as silicon photomultipliers.

  18. Fast and High Accuracy Wire Scanner

    CERN Document Server

    Koujili, M; Koopman, J; Ramos, D; Sapinski, M; De Freitas, J; Ait Amira, Y; Djerdir, A

    2009-01-01

    Scanning of a high intensity particle beam imposes challenging requirements on a Wire Scanner system. It is expected to reach a scanning speed of 20 m.s-1 with a position accuracy of the order of 1 μm. In addition a timing accuracy better than 1 millisecond is needed. The adopted solution consists of a fork holding a wire rotating by a maximum of 200°. Fork, rotor and angular position sensor are mounted on the same axis and located in a chamber connected to the beam vacuum. The requirements imply the design of a system with extremely low vibration, vacuum compatibility, radiation and temperature tolerance. The adopted solution consists of a rotary brushless synchronous motor with the permanent magnet rotor installed inside of the vacuum chamber and the stator installed outside. The accurate position sensor will be mounted on the rotary shaft inside of the vacuum chamber, has to resist a bake-out temperature of 200°C and ionizing radiation up to a dozen of kGy/year. A digital feedback controller allows maxi...

  19. Whole-body 35-GHz security scanner

    Science.gov (United States)

    Appleby, Roger; Anderton, Rupert N.; Price, Sean; Sinclair, Gordon N.; Coward, Peter R.

    2004-08-01

    A 35GHz imager designed for Security Scanning has been previously demonstrated. That imager was based on a folded conical scan technology and was constructed from low cost materials such as expanded polystyrene and printed circuit board. In conjunction with an illumination chamber it was used to collect indoor imagery of people with weapons and contraband hidden under their clothing. That imager had a spot size of 20mm and covered a field of view of 20 x 10 degrees that partially covered the body of an adult from knees to shoulders. A new variant of this imager has been designed and constructed. It has a field of view of 36 x 18 degrees and is capable of covering the whole body of an adult. This was achieved by increasing the number of direct detection receivers from the 32 used in the previous design to 58, and by implementing an improved optical design. The optics consist of a front grid, a polarisation device which converts linear to circular polarisation and a rotating scanner. This new design uses high-density expanded polystyrene as a correcting element on the back of the front grid. This gives an added degree of freedom that allows the optical design to be diffraction limited over a very wide field of view. Obscuration by the receivers and associated components is minimised by integrating the post detection electronics at the receiver array.

  20. From Beamline to Scanner with 225Ac

    Science.gov (United States)

    Robertson, Andrew K. H.; Ramogida, Caterina F.; Kunz, Peter; Rodriguez-Rodriguez, Cristina; Schaffer, Paul; Sossi, Vesna

    2016-09-01

    Due to the high linear energy transfer and short range of alpha-radiation, targeted radiation therapy using alpha-emitting pharmaceuticals that successfully target small disease clusters will kill target cells with limited harm to healthy tissue, potentially treating the most aggressive forms of cancer. As the parent of a decay chain with four alpha- and two beta-decays, 225Ac is a promising candidate for such a treatment. However, this requires retention of the entire decay chain at the target site, preventing the creation of freely circulating alpha-emitters that reduce therapeutic effect and increase toxicity to non-target tissues. Two major challenges to 225Ac pharmaceutical development exist: insufficient global supply, and the difficulty of preventing toxicity by retaining the entire decay chain at the target site. While TRIUMF works towards large-scale (C i amounts) production of 225Ac, we already use our Isotope Separation On-Line facility to provide small (overview of this research program and the journey of 225Ac from the beamline to the scanner. This research is funded by the Natural Sciences and Engineering Research Council of Canada.

  1. Upconversion applied for mid-IR hyperspectral image acquisition

    DEFF Research Database (Denmark)

    Tidemand-Lichtenberg, Peter; Kehlet, Louis Martinus; Sanders, Nicolai Højer;

    2015-01-01

    Different schemes for upconversion mid-IR hyperspectral imaging is implemented and compared in terms of spectral coverage, spectral resolution, speed and noise. Phasematch scanning and scanning of the object within the field of view is considered.......Different schemes for upconversion mid-IR hyperspectral imaging is implemented and compared in terms of spectral coverage, spectral resolution, speed and noise. Phasematch scanning and scanning of the object within the field of view is considered....

  2. Hyperspectral Imagery for Large Area Survey of Organophosphate Pesticides

    Science.gov (United States)

    2015-03-26

    forensic analysis. Hyperspectral imaging can be used for various parts of the electromagnetic spectrum (e.g. ultraviolet, visible, and infrared) (Edelmen...Cullen, P. J., & Aalders, M. C. G. (2012). Hyperspectral imaging for non-contact analysis of forensic traces. Forensic Science International, 223(1–3...colorimetric detection of organophosphate pesticides using copper catalyzed click chemistry . Talanta, 103(0), 110-115. doi:http

  3. Target detection algorithm for airborne thermal hyperspectral data

    OpenAIRE

    Marwaha, R.; Kumar, A.; Raju, P.L.N.; Y. V. N. Krishna Murthy

    2014-01-01

    Airborne hyperspectral imaging is constantly being used for classification purpose. But airborne thermal hyperspectral image usually is a challenge for conventional classification approaches. The Telops Hyper-Cam sensor is an interferometer-based imaging system that helps in the spatial and spectral analysis of targets utilizing a single sensor. It is based on the technology of Fourier-transform which yields high spectral resolution and enables high accuracy radiometric calibration. ...

  4. ADVANCES IN HYPERSPECTRAL AND MULTISPECTRAL IMAGE FUSION AND SPECTRAL UNMIXING

    OpenAIRE

    C. Lanaras; E. Baltsavias; K. Schindler

    2015-01-01

    In this work, we jointly process high spectral and high geometric resolution images and exploit their synergies to (a) generate a fused image of high spectral and geometric resolution; and (b) improve (linear) spectral unmixing of hyperspectral endmembers at subpixel level w.r.t. the pixel size of the hyperspectral image. We assume that the two images are radiometrically corrected and geometrically co-registered. The scientific contributions of this work are (a) a simultaneous approa...

  5. Processing of hyperspectral medical images applications in dermatology using Matlab

    CERN Document Server

    Koprowski, Robert

    2017-01-01

    This book presents new methods of analyzing and processing hyperspectral medical images, which can be used in diagnostics, for example for dermatological images. The algorithms proposed are fully automatic and the results obtained are fully reproducible. Their operation was tested on a set of several thousands of hyperspectral images and they were implemented in Matlab. The presented source code can be used without licensing restrictions. This is a valuable resource for computer scientists, bioengineers, doctoral students, and dermatologists interested in contemporary analysis methods.

  6. A Method of Microarray Data Storage Using Array Data Type

    OpenAIRE

    Tsoi, Lam C.; Zheng, W Jim

    2007-01-01

    A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store ...

  7. HYPERSPECTRAL HYPERION IMAGERY ANALYSIS AND ITS APPLICATION USING SPECTRAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    W. Pervez

    2015-03-01

    Full Text Available Rapid advancement in remote sensing open new avenues to explore the hyperspectral Hyperion imagery pre-processing techniques, analysis and application for land use mapping. The hyperspectral data consists of 242 bands out of which 196 calibrated/useful bands are available for hyperspectral applications. Atmospheric correction applied to the hyperspectral calibrated bands make the data more useful for its further processing/ application. Principal component (PC analysis applied to the hyperspectral calibrated bands reduced the dimensionality of the data and it is found that 99% of the data is held in first 10 PCs. Feature extraction is one of the important application by using vegetation delineation and normalized difference vegetation index. The machine learning classifiers uses the technique to identify the pixels having significant difference in the spectral signature which is very useful for classification of an image. Supervised machine learning classifier technique has been used for classification of hyperspectral image which resulted in overall efficiency of 86.6703 and Kappa co-efficient of 0.7998.

  8. Development of practical thermal infrared hyperspectral imaging system

    Science.gov (United States)

    Wang, Jianyu; Li, Chunlai; Lv, Gang; Yuan, Liyin; Liu, Enguang; Jin, Jian; Ji, Hongzhen

    2014-11-01

    As an optical remote sensing equipment, the thermal infrared hyperspectral imager operates in the thermal infrared spectral band and acquires about 180 wavebands in range of 8.0~12.5μm. The field of view of this imager is 13° and the spatial resolution is better than 1mrad. Its noise equivalent temperature difference (NETD) is less than 0.2K@300K(average). 1 The influence of background radiation of the thermal infrared hyperspectral imager,and a simulation model of simplified background radiation is builded. 2 The design and implementationof the Cryogenic Optics. 3 Thermal infrared focal plane array (FPA) and special dewar component for the thermal infrared hyperspectral imager. 4 Parts of test results of the thermal infrared hyperspectral imager.The hyperspectral imaging system is China's first success in developing this type of instrument, whose flight validation experiments have already been embarked on. The thermal infrared hyperspectral data acquired will play an important role in fields such as geological exploration and air pollutant identification.

  9. Hyperspectral imaging fluorescence excitation scanning for colon cancer detection

    Science.gov (United States)

    Leavesley, Silas J.; Walters, Mikayla; Lopez, Carmen; Baker, Thomas; Favreau, Peter F.; Rich, Thomas C.; Rider, Paul F.; Boudreaux, Carole W.

    2016-10-01

    Optical spectroscopy and hyperspectral imaging have shown the potential to discriminate between cancerous and noncancerous tissue with high sensitivity and specificity. However, to date, these techniques have not been effectively translated to real-time endoscope platforms. Hyperspectral imaging of the fluorescence excitation spectrum represents new technology that may be well suited for endoscopic implementation. However, the feasibility of detecting differences between normal and cancerous mucosa using fluorescence excitation-scanning hyperspectral imaging has not been evaluated. The goal of this study was to evaluate the initial feasibility of using fluorescence excitation-scanning hyperspectral imaging for measuring changes in fluorescence excitation spectrum concurrent with colonic adenocarcinoma using a small pre-pilot-scale sample size. Ex vivo analysis was performed using resected pairs of colorectal adenocarcinoma and normal mucosa. Adenocarcinoma was confirmed by histologic evaluation of hematoxylin and eosin (H&E) permanent sections. Specimens were imaged using a custom hyperspectral imaging fluorescence excitation-scanning microscope system. Results demonstrated consistent spectral differences between normal and cancerous tissues over the fluorescence excitation range of 390 to 450 nm that could be the basis for wavelength-dependent detection of colorectal cancers. Hence, excitation-scanning hyperspectral imaging may offer an alternative approach for discriminating adenocarcinoma from surrounding normal colonic mucosa, but further studies will be required to evaluate the accuracy of this approach using a larger patient cohort.

  10. Chromosomal microarray versus karyotyping for prenatal diagnosis.

    Science.gov (United States)

    Wapner, Ronald J; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C; Eng, Christine M; Zachary, Julia M; Savage, Melissa; Platt, Lawrence D; Saltzman, Daniel; Grobman, William A; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N; Thom, Elizabeth A; Beaudet, Arthur L; Ledbetter, David H; Shaffer, Lisa G; Jackson, Laird

    2012-12-06

    Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down's syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.).

  11. A hyperspectral imaging prototype for online quality evaluation of pickling cucumbers

    Science.gov (United States)

    A hyperspectral imaging prototype was developed for online evaluation of external and internal quality of pickling cucumbers. The prototype had several new, unique features including simultaneous reflectance and transmittance imaging and inline, real time calibration of hyperspectral images of each ...

  12. Hyperspectral Remote Sensing of Urban Areas: An Overview of Techniques and Applications

    Directory of Open Access Journals (Sweden)

    Helmi Z.M. Shafri

    2012-06-01

    Full Text Available Over the past two decades, hyperspectral remote sensing from airborne and satellite systems has been used as a data source for numerous applications. Hyperspectral imaging is quickly moving into the mainstream of remote sensing and is being applied to remote sensing research studies. Hyperspectral remote sensing has great potential for analysing complex urban scenes. However, operational applications within urban environments are still limited, despite several studies that have explored the capabilities of hyperspectral data to map urban areas. In this paper, we review the methods for urban classification using hyperspectral remote sensing data and their applications. The general trends indicate that combined spatial-spectral and sensor fusion approaches are the most optimal for hyperspectral urban analysis. It is also clear that urban hyperspectral mapping is currently limited to airborne data, despite the availability of spaceborne hyperspectral systems. Possible future research directions are also discussed.

  13. A lightweight hyperspectral mapping system and photogrammetric processing chain for unmanned aerial vehicles

    NARCIS (Netherlands)

    Suomalainen, J.M.; Anders, N.S.; Iqbal, S.; Roerink, G.J.; Franke, G.J.; Wenting, P.F.M.; Hünniger, D.; Bartholomeus, H.; Becker, R.; Kooistra, L.

    2014-01-01

    During the last years commercial hyperspectral imaging sensors have been miniaturized and their performance has been demonstrated on Unmanned Aerial Vehicles (UAV). However currently the commercial hyperspectral systems still require minimum payload capacity of approximately 3 kg, forcing usage of

  14. Hyperspectral Longwave Infrared Focal Plane Array and Camera Based on Quantum Well Infrared Photodetectors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop a hyperspectral focal plane array and camera imaging in a large number of sharp hyperspectral bands in the thermal infrared. The camera is...

  15. Hyperspectral Longwave Infrared Focal Plane Array and Camera Based on Quantum Well Infrared Photodetectors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop a hyperspectral camera imaging in a large number of sharp hyperspectral bands in the thermal infrared. The camera is particularly suitable for...

  16. Chemical Imaging of Heterogeneous Muscle Foods Using Near-Infrared Hyperspectral Imaging in Transmission Mode.

    Science.gov (United States)

    Wold, Jens Petter; Kermit, Martin; Segtnan, Vegard Herman

    2016-06-01

    Foods and biomaterials are, in general, heterogeneous and it is often a challenge to obtain spectral data which are representative for the chemical composition and distribution. This paper presents a setup for near-infrared (NIR) transmission imaging where the samples are completely trans-illuminated, probing the entire sample. The system measures falling samples at high speed and consists of an NIR imaging scanner covering the spectral range 760-1040 nm and a powerful line light source. The investigated samples were rather big: whole pork bellies of thickness up to 5 cm, salmon fillets with skin, and 3 cm thick model samples of ground pork meat. Partial least square regression models for fat were developed for ground pork and salmon fillet with high correlations (R = 0.98 and R = 0.95, respectively). The regression models were applied at pixel level in the hyperspectral transmission images and resulted in images of fat distribution where also deeply embedded fat clearly contributed to the result. The results suggest that it is possible to use transmission imaging for rapid, nondestructive, and representative sampling of very heterogeneous foods. The proposed system is suitable for industrial use. © The Author(s) 2016.

  17. 21 CFR 892.1300 - Nuclear rectilinear scanner.

    Science.gov (United States)

    2010-04-01

    ...) Identification. A nuclear rectilinear scanner is a device intended to image the distribution of radionuclides in the body by means of a detector (or detectors) whose position moves in two directions with respect...

  18. Whole-body 3D scanner and scan data report

    Science.gov (United States)

    Addleman, Stephen R.

    1997-03-01

    With the first whole-body 3D scanner now available the next adventure confronting the user is what to do with all of the data. While the system was built for anthropologists, it has created interest among users from a wide variety of fields. Users with applications in the fields of anthropology, costume design, garment design, entertainment, VR and gaming have a need for the data in formats unique to their fields. Data from the scanner is being converted to solid models for art and design and NURBS for computer graphics applications. Motion capture has made scan data move and dance. The scanner has created a need for advanced application software just as other scanners have in the past.

  19. Landsat 1-5 Multispectral Scanner V1

    Data.gov (United States)

    National Aeronautics and Space Administration — Abstract: The Landsat Multispectral Scanner (MSS) was a sensor onboard Landsats 1 through 5 and acquired images of the Earth nearly continuously from July 1972 to...

  20. APLIKASI INFO HALAL MENGGUNAKAN BARCODE SCANNER UNTUK SMARTPHONE ANDROID

    National Research Council Canada - National Science Library

    Beki Subeki; M Rahmat Jauhari

    2016-01-01

    ... to obtain the correct information about the halal status of products bought. The use of barcode scanners halal product information using the mobile platform is effective and useful for the public to find out information on a product...

  1. Building a 3D Computed Tomography Scanner From Surplus Parts.

    Science.gov (United States)

    Haidekker, Mark A

    2014-01-01

    Computed tomography (CT) scanners are expensive imaging devices, often out of reach for small research groups. Designing and building a CT scanner from modular components is possible, and this article demonstrates that realization of a CT scanner from components is surprisingly easy. However, the high costs of a modular X-ray source and detector limit the overall cost savings. In this article, the possibility of building a CT scanner with available surplus X-ray parts is discussed, and a practical device is described that incurred costs of less than $16,000. The image quality of this device is comparable with commercial devices. The disadvantage is that design constraints imposed by the available components lead to slow scan speeds and a resolution of 0.5 mm. Despite these limitations, a device such as this is attractive for imaging studies in the biological and biomedical sciences, as well as for advancing CT technology itself.

  2. Review: DNA Microarray Technology and Drug Development

    Directory of Open Access Journals (Sweden)

    Sushma Drabu

    2010-01-01

    Full Text Available

    On the contrary to slow and non specific traditional drug discovery methods, DNA microarray technology could
    accelerate the identification of potential drugs for treating diseases like cancer, AIDS and provide fruitful results in
    the drug discovery. The technique provides efficient automation and maximum flexibility to the researchers and
    can test thousand compounds at a time. Scientists find DNA microarray useful in disease diagnosis, monitoring
    desired and adverse outcomes of therapeutic interventions, as well as, in the selection, assessment and quality control
    of the potential drugs. In the current scenario, where new pathogens are expected every year, DNA microarray
    promises as an efficient technology to detect new organisms in a short time. Classification of carcinomas at the
    molecular level and prediction of how various types of tumor respond to different therapeutic agents can be made
    possible with the use of microarray analysis. Also, microarray technique can prove instrumental in personalized
    medicines development by providing microarray data of a patient which could be used for identifying diseases,
    treatment specific to individual and trailing disease prognosis. Microarray analysis could be beneficial in the area
    of molecular medicines for analysis of genetic variations and functions of genes in normal individuals and diseased
    conditions. The technique can give satisfactory results in single nucleotide polymorphism (SNP analysis and
    pharmacogenomics studies. The challenges that arise with the technology are high degree of variability with data
    obtained, frequent up gradation of methods and machines and lack of trained manpower. Despite this, DNA microarray
    promises to be the next generation sequencer which could explain how organisms evolve and adapt looking
    at the whole

  3. Fret Replica Inspection Laser Scanner (FRILS)

    Energy Technology Data Exchange (ETDEWEB)

    Kretz, S.; Hanley, K., E-mail: steve.kretz@opg.com, E-mail: kelly.hanley@opg.com [Ontario Power Generation, Inspection Maintenance and Commercial Services, Pickering, Ontario (Canada)

    2008-07-01

    In the stress analysis of flaws and artifacts found in pressure tubes, it is crucial to have detailed knowledge of the flaw geometry. Fuel channel inspections by ultrasonic or eddy current inspection methods alone cannot provide the complete required geometry information. Replicas, which are a negative impression of surface pressure tube indications, are scanned with a laser system which will provide the additional detail required. FRILS was initially developed in 1993 to establish in-house capability of profiling indications on the inside diameter surface of pressure tubes. The need of this profiling was initially a response to the discovery of fuel bundle bearing pad fretting (FBBPF) caused by flow induced fuel bundle vibration. The benefits of the system were soon realized as a tool for profiling debris type indications. Although the primary use of FRILS is to profile FBBBF and Debris Fretting, since its inception the FRILS inspection system has become an instrumental tool in flaw assessment for: Fuel Bundle Bearing Pad Frets (FBBPF); Debris Frets; Scratches; Crevice Corrosion; Oxide Jacking; Areas of surface roughness; and, Weld Profiling. Replicas are collected via acquisition from tooling on both the Channel and Gauging Apparatus for Reactors (CIGAR) and the Advanced Non-Destructive Examination (ANDE) systems. The ANDE system is a high speed data acquisition system which includes both an ultrasonic inspection tool and a replication tool. Although both of these tools were designed to be delivered with the UDM, the platform for these tools was built with flexibility allowing for adoption to other delivery systems. These tools were based on the experience of the CIGAR inspection system. The CIGAR system has also undergone many system upgrades resulting in reduced inspection times. The FRILS system - Fret Replication Inspection Laser Scanner system was developed and has been upgraded to meet the demands of the improved inspection and replication systems. FRILS

  4. Computer vision and laser scanner road environment perception

    OpenAIRE

    García, Fernando; Ponz Vila, Aurelio; Martín Gómez, David; Escalera, Arturo de la; Armingol, José M.

    2014-01-01

    Data fusion procedure is presented to enhance classical Advanced Driver Assistance Systems (ADAS). The novel vehicle safety approach, combines two classical sensors: computer vision and laser scanner. Laser scanner algorithm performs detection of vehicles and pedestrians based on pattern matching algorithms. Computer vision approach is based on Haar-Like features for vehicles and Histogram of Oriented Gradients (HOG) features for pedestrians. The high level fusion procedure uses Kalman Filter...

  5. QUEST Hierarchy for Hyperspectral Face Recognition

    Directory of Open Access Journals (Sweden)

    David M. Ryer

    2012-01-01

    Full Text Available A qualia exploitation of sensor technology (QUEST motivated architecture using algorithm fusion and adaptive feedback loops for face recognition for hyperspectral imagery (HSI is presented. QUEST seeks to develop a general purpose computational intelligence system that captures the beneficial engineering aspects of qualia-based solutions. Qualia-based approaches are constructed from subjective representations and have the ability to detect, distinguish, and characterize entities in the environment Adaptive feedback loops are implemented that enhance performance by reducing candidate subjects in the gallery and by injecting additional probe images during the matching process. The architecture presented provides a framework for exploring more advanced integration strategies beyond those presented. Algorithmic results and performance improvements are presented as spatial, spectral, and temporal effects are utilized; additionally, a Matlab-based graphical user interface (GUI is developed to aid processing, track performance, and to display results.

  6. Recent applications of hyperspectral imaging in microbiology.

    Science.gov (United States)

    Gowen, Aoife A; Feng, Yaoze; Gaston, Edurne; Valdramidis, Vasilis

    2015-05-01

    Hyperspectral chemical imaging (HSI) is a broad term encompassing spatially resolved spectral data obtained through a variety of modalities (e.g. Raman scattering, Fourier transform infrared microscopy, fluorescence and near-infrared chemical imaging). It goes beyond the capabilities of conventional imaging and spectroscopy by obtaining spatially resolved spectra from objects at spatial resolutions varying from the level of single cells up to macroscopic objects (e.g. foods). In tandem with recent developments in instrumentation and sampling protocols, applications of HSI in microbiology have increased rapidly. This article gives a brief overview of the fundamentals of HSI and a comprehensive review of applications of HSI in microbiology over the past 10 years. Technical challenges and future perspectives for these techniques are also discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Classifications of objects on hyperspectral images

    DEFF Research Database (Denmark)

    Kucheryavskiy, Sergey

    tablets have the same or similar excipient and different active ingredients, some of the pixels chemically will be identical. But these similar pixels will be associated with different classes when a classification model is being calibrated. This can give unstable model and poor classification results...... information about spatial relations of the pixels. This works well in general, especially for exploratory analysis or multivariate curve resolution, but for some specific tasks it is not beneficial at all. One of such tasks is classification or clustering of objects on hyperspectral images. An object here....... In the present work a classification method that combines classic image classification approach and MIA is proposed. The basic idea is to group all pixels and calculate spectral properties of the pixel group to be used further as a vector of predictors for calibration and class prediction. The grouping can...

  8. Metric Learning for Hyperspectral Image Segmentation

    Science.gov (United States)

    Bue, Brian D.; Thompson, David R.; Gilmore, Martha S.; Castano, Rebecca

    2011-01-01

    We present a metric learning approach to improve the performance of unsupervised hyperspectral image segmentation. Unsupervised spatial segmentation can assist both user visualization and automatic recognition of surface features. Analysts can use spatially-continuous segments to decrease noise levels and/or localize feature boundaries. However, existing segmentation methods use tasks-agnostic measures of similarity. Here we learn task-specific similarity measures from training data, improving segment fidelity to classes of interest. Multiclass Linear Discriminate Analysis produces a linear transform that optimally separates a labeled set of training classes. The defines a distance metric that generalized to a new scenes, enabling graph-based segmentation that emphasizes key spectral features. We describe tests based on data from the Compact Reconnaissance Imaging Spectrometer (CRISM) in which learned metrics improve segment homogeneity with respect to mineralogical classes.

  9. Food quality assessment by NIR hyperspectral imaging

    Science.gov (United States)

    Whitworth, Martin B.; Millar, Samuel J.; Chau, Astor

    2010-04-01

    Near infrared reflectance (NIR) spectroscopy is well established in the food industry for rapid compositional analysis of bulk samples. NIR hyperspectral imaging provides new opportunities to measure the spatial distribution of components such as moisture and fat, and to identify and measure specific regions of composite samples. An NIR hyperspectral imaging system has been constructed for food research applications, incorporating a SWIR camera with a cooled 14 bit HgCdTe detector and N25E spectrograph (Specim Ltd, Finland). Samples are scanned in a pushbroom mode using a motorised stage. The system has a spectral resolution of 256 pixels covering a range of 970-2500 nm and a spatial resolution of 320 pixels covering a swathe adjustable from 8 to 300 mm. Images are acquired at a rate of up to 100 lines s-1, enabling samples to be scanned within a few seconds. Data are captured using SpectralCube software (Specim) and analysed using ENVI and IDL (ITT Visual Information Solutions). Several food applications are presented. The strength of individual absorbance bands enables the distribution of particular components to be assessed. Examples are shown for detection of added gluten in wheat flour and to study the effect of processing conditions on fat distribution in chips/French fries. More detailed quantitative calibrations have been developed to study evolution of the moisture distribution in baguettes during storage at different humidities, to assess freshness of fish using measurements of whole cod and fillets, and for prediction of beef quality by identification and separate measurement of lean and fat regions.

  10. Liquid-crystal-based hyperspectral image projector

    Science.gov (United States)

    Linnenberger, Anna; Masterson, Hugh; Rice, Joseph P.; Stockley, Jay

    2010-04-01

    A hyperspectral image projector (HIP) is introduced that is built with liquid crystal based spatial light modulators (SLM) as opposed to micromirror arrays. The use of an SLM as a broadband intensity modulator presents several benefits to this application. With slight modifications to the SLM design, SLMs can be built for a wide range of spectral regimes, ranging from the ultraviolet (UV) to the long-wavelength infrared (LWIR). SLMs can have a large pixel pitch, significantly reducing diffraction in the mid-wavelength infrared (MWIR) and LWIR. Liquid crystal based devices offer direct analog intensity modulation, thus eliminating flicker from time sequential drive schemes. SLMs allow for an on-axis configuration, enabling a simple and compact optical layout. The design of the HIP system is broken into two parts consisting of a spectral and spatial engine. In the spectral engine a diffraction grating is used to disperse a broadband source into spectral components, where an SLM modulates the relative intensity of the components to dynamically generate complex spectra. The recombined output is fed to the spatial engine which is used to construct two-dimensional scenes. The system is used to simulate a broad range of real world environments, and will be delivered to the National Institute of Standards and Technology as an enabling tool for the development of calibration standards and performance testing techniques for multispectral and hyperspectral imagers. The focus of this paper is on a visible-band HIP system; however, related work is presented with regard to SLM use in the MWIR and LWIR.

  11. Face Recognition via Ensemble SIFT Matching of Uncorrelated Hyperspectral Bands and Spectral PCTs

    Science.gov (United States)

    2011-06-01

    Unsupervised Hyperspectral Target Detection Algorithm. Wright-Patterson AFB: Air Force Institute of Technology. Kirby, M., & Sirovich, L. (1990...Xu, Y., Hu, K., Tian, Y., & Peng, F. (2008). Classification of Hyperspectral imagery using SIFT for spectral matching. Image and Signal Processing...single hyperspectral band which also performs very well under temporal variation. 15. SUBJECT TERMS Face Recognition, SIFT, Ensemble Classification

  12. Hyperspectral and Multispectral Imaging Technique for Food Quality and Safety Evaluation

    Science.gov (United States)

    In this chapter, recently developed ARS line-scan hyperspectral-based sensing technologies to address agro-food safety concerns are presented including a case study using the laboratory-based hyperspectral imaging platforms. An online line-scan imaging system capable of both hyperspectral and multi...

  13. Posttranslational Modification Assays on Functional Protein Microarrays.

    Science.gov (United States)

    Neiswinger, Johnathan; Uzoma, Ijeoma; Cox, Eric; Rho, HeeSool; Jeong, Jun Seop; Zhu, Heng

    2016-10-03

    Protein microarray technology provides a straightforward yet powerful strategy for identifying substrates of posttranslational modifications (PTMs) and studying the specificity of the enzymes that catalyze these reactions. Protein microarray assays can be designed for individual enzymes or a mixture to establish connections between enzymes and substrates. Assays for four well-known PTMs-phosphorylation, acetylation, ubiquitylation, and SUMOylation-have been developed and are described here for use on functional protein microarrays. Phosphorylation and acetylation require a single enzyme and are easily adapted for use on an array. The ubiquitylation and SUMOylation cascades are very similar, and the combination of the E1, E2, and E3 enzymes plus ubiquitin or SUMO protein and ATP is sufficient for in vitro modification of many substrates.

  14. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  15. Hybridization and Selective Release of DNA Microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

    2011-11-29

    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy

  16. Meat quality evaluation by hyperspectral imaging technique: an overview.

    Science.gov (United States)

    Elmasry, Gamal; Barbin, Douglas F; Sun, Da-Wen; Allen, Paul

    2012-01-01

    During the last two decades, a number of methods have been developed to objectively measure meat quality attributes. Hyperspectral imaging technique as one of these methods has been regarded as a smart and promising analytical tool for analyses conducted in research and industries. Recently there has been a renewed interest in using hyperspectral imaging in quality evaluation of different food products. The main inducement for developing the hyperspectral imaging system is to integrate both spectroscopy and imaging techniques in one system to make direct identification of different components and their spatial distribution in the tested product. By combining spatial and spectral details together, hyperspectral imaging has proved to be a promising technology for objective meat quality evaluation. The literature presented in this paper clearly reveals that hyperspectral imaging approaches have a huge potential for gaining rapid information about the chemical structure and related physical properties of all types of meat. In addition to its ability for effectively quantifying and characterizing quality attributes of some important visual features of meat such as color, quality grade, marbling, maturity, and texture, it is able to measure multiple chemical constituents simultaneously without monotonous sample preparation. Although this technology has not yet been sufficiently exploited in meat process and quality assessment, its potential is promising. Developing a quality evaluation system based on hyperspectral imaging technology to assess the meat quality parameters and to ensure its authentication would bring economical benefits to the meat industry by increasing consumer confidence in the quality of the meat products. This paper provides a detailed overview of the recently developed approaches and latest research efforts exerted in hyperspectral imaging technology developed for evaluating the quality of different meat products and the possibility of its widespread

  17. Target detection algorithm for airborne thermal hyperspectral data

    Science.gov (United States)

    Marwaha, R.; Kumar, A.; Raju, P. L. N.; Krishna Murthy, Y. V. N.

    2014-11-01

    Airborne hyperspectral imaging is constantly being used for classification purpose. But airborne thermal hyperspectral image usually is a challenge for conventional classification approaches. The Telops Hyper-Cam sensor is an interferometer-based imaging system that helps in the spatial and spectral analysis of targets utilizing a single sensor. It is based on the technology of Fourier-transform which yields high spectral resolution and enables high accuracy radiometric calibration. The Hypercam instrument has 84 spectral bands in the 868 cm-1 to 1280 cm-1 region (7.8 μm to 11.5 μm), at a spectral resolution of 6 cm-1 (full-width-half-maximum) for LWIR (long wave infrared) range. Due to the Hughes effect, only a few classifiers are able to handle high dimensional classification task. MNF (Minimum Noise Fraction) rotation is a data dimensionality reducing approach to segregate noise in the data. In this, the component selection of minimum noise fraction (MNF) rotation transformation was analyzed in terms of classification accuracy using constrained energy minimization (CEM) algorithm as a classifier for Airborne thermal hyperspectral image and for the combination of airborne LWIR hyperspectral image and color digital photograph. On comparing the accuracy of all the classified images for airborne LWIR hyperspectral image and combination of Airborne LWIR hyperspectral image with colored digital photograph, it was found that accuracy was highest for MNF component equal to twenty. The accuracy increased by using the combination of airborne LWIR hyperspectral image with colored digital photograph instead of using LWIR data alone.

  18. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  19. Prominent feature selection of microarray data

    Institute of Scientific and Technical Information of China (English)

    Yihui Liu

    2009-01-01

    For wavelet transform, a set of orthogonal wavelet basis aims to detect the localized changing features contained in microarray data. In this research, we investigate the performance of the selected wavelet features based on wavelet detail coefficients at the second level and the third level. The genetic algorithm is performed to optimize wavelet detail coefficients to select the best discriminant features. Exper-iments are carried out on four microarray datasets to evaluate the performance of classification. Experimental results prove that wavelet features optimized from detail coefficients efficiently characterize the differences between normal tissues and cancer tissues.

  20. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    -linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting...... years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria...

  1. Microarrays - A Key Technology for Glycobiology

    Science.gov (United States)

    Liu, Yan; Feizi, Ten

    Carbohydrate chains of glycoproteins , glycolipids , and proteoglycans can mediate processes of biological and medical importance through their interactions with complementary proteins. The unraveling of these interactions is a priority therefore in biomedical sciences. Carbohydrate microarray technology is a new development at the frontiers of glycomics that has revolutionized the study of carbohydrate-protein interactions and the elucidation of their specificities in endogenous biological processes, immune defense mechanisms, and microbe-host interactions. In this chapter we briefly touch upon the principles of numerous platforms since the introduction of carbohydrate microarrays in 2002, and we highlight platforms that are beyond proof-of-concept, and have provided new biological information.

  2. Development and application of a microarray meter tool to optimize microarray experiments

    Directory of Open Access Journals (Sweden)

    Rouse Richard JD

    2008-07-01

    Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

  3. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results

    Directory of Open Access Journals (Sweden)

    Dai Yilin

    2012-06-01

    Full Text Available Abstract Background Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. Findings We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Conclusion Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  4. Improved spatial resolution in PET scanners using sampling techniques

    Science.gov (United States)

    Surti, Suleman; Scheuermann, Ryan; Werner, Matthew E.; Karp, Joel S.

    2009-01-01

    Increased focus towards improved detector spatial resolution in PET has led to the use of smaller crystals in some form of light sharing detector design. In this work we evaluate two sampling techniques that can be applied during calibrations for pixelated detector designs in order to improve the reconstructed spatial resolution. The inter-crystal positioning technique utilizes sub-sampling in the crystal flood map to better sample the Compton scatter events in the detector. The Compton scatter rejection technique, on the other hand, rejects those events that are located further from individual crystal centers in the flood map. We performed Monte Carlo simulations followed by measurements on two whole-body scanners for point source data. The simulations and measurements were performed for scanners using scintillators with Zeff ranging from 46.9 to 63 for LaBr3 and LYSO, respectively. Our results show that near the center of the scanner, inter-crystal positioning technique leads to a gain of about 0.5-mm in reconstructed spatial resolution (FWHM) for both scanner designs. In a small animal LYSO scanner the resolution improves from 1.9-mm to 1.6-mm with the inter-crystal technique. The Compton scatter rejection technique shows higher gains in spatial resolution but at the cost of reduction in scanner sensitivity. The inter-crystal positioning technique represents a modest acquisition software modification for an improvement in spatial resolution, but at a cost of potentially longer data correction and reconstruction times. The Compton scatter rejection technique, while also requiring a modest acquisition software change with no increased data correction and reconstruction times, will be useful in applications where the scanner sensitivity is very high and larger improvements in spatial resolution are desirable. PMID:19779586

  5. In vivo and in vitro hyperspectral imaging of cervical neoplasia

    Science.gov (United States)

    Wang, Chaojian; Zheng, Wenli; Bu, Yanggao; Chang, Shufang; Tong, Qingping; Zhang, Shiwu; Xu, Ronald X.

    2014-02-01

    Cervical cancer is a prevalent disease in many developing countries. Colposcopy is the most common approach for screening cervical intraepithelial neoplasia (CIN). However, its clinical efficacy heavily relies on the examiner's experience. Spectroscopy is a potentially effective method for noninvasive diagnosis of cervical neoplasia. In this paper, we introduce a hyperspectral imaging technique for noninvasive detection and quantitative analysis of cervical neoplasia. A hyperspectral camera is used to collect the reflectance images of the entire cervix under xenon lamp illumination, followed by standard colposcopy examination and cervical tissue biopsy at both normal and abnormal sites in different quadrants. The collected reflectance data are calibrated and the hyperspectral signals are extracted. Further spectral analysis and image processing works are carried out to classify tissue into different types based on the spectral characteristics at different stages of cervical intraepithelial neoplasia. The hyperspectral camera is also coupled with a lab microscope to acquire the hyperspectral transmittance images of the pathological slides. The in vivo and the in vitro imaging results are compared with clinical findings to assess the accuracy and efficacy of the method.

  6. a Diversified Deep Belief Network for Hyperspectral Image Classification

    Science.gov (United States)

    Zhong, P.; Gong, Z. Q.; Schönlieb, C.

    2016-06-01

    In recent years, researches in remote sensing demonstrated that deep architectures with multiple layers can potentially extract abstract and invariant features for better hyperspectral image classification. Since the usual real-world hyperspectral image classification task cannot provide enough training samples for a supervised deep model, such as convolutional neural networks (CNNs), this work turns to investigate the deep belief networks (DBNs), which allow unsupervised training. The DBN trained over limited training samples usually has many "dead" (never responding) or "potential over-tolerant" (always responding) latent factors (neurons), which decrease the DBN's description ability and thus finally decrease the hyperspectral image classification performance. This work proposes a new diversified DBN through introducing a diversity promoting prior over the latent factors during the DBN pre-training and fine-tuning procedures. The diversity promoting prior in the training procedures will encourage the latent factors to be uncorrelated, such that each latent factor focuses on modelling unique information, and all factors will be summed up to capture a large proportion of information and thus increase description ability and classification performance of the diversified DBNs. The proposed method was evaluated over the well-known real-world hyperspectral image dataset. The experiments demonstrate that the diversified DBNs can obtain much better results than original DBNs and comparable or even better performances compared with other recent hyperspectral image classification methods.

  7. Geographical classification of apple based on hyperspectral imaging

    Science.gov (United States)

    Guo, Zhiming; Huang, Wenqian; Chen, Liping; Zhao, Chunjiang; Peng, Yankun

    2013-05-01

    Attribute of apple according to geographical origin is often recognized and appreciated by the consumers. It is usually an important factor to determine the price of a commercial product. Hyperspectral imaging technology and supervised pattern recognition was attempted to discriminate apple according to geographical origins in this work. Hyperspectral images of 207 Fuji apple samples were collected by hyperspectral camera (400-1000nm). Principal component analysis (PCA) was performed on hyperspectral imaging data to determine main efficient wavelength images, and then characteristic variables were extracted by texture analysis based on gray level co-occurrence matrix (GLCM) from dominant waveband image. All characteristic variables were obtained by fusing the data of images in efficient spectra. Support vector machine (SVM) was used to construct the classification model, and showed excellent performance in classification results. The total classification rate had the high classify accuracy of 92.75% in the training set and 89.86% in the prediction sets, respectively. The overall results demonstrated that the hyperspectral imaging technique coupled with SVM classifier can be efficiently utilized to discriminate Fuji apple according to geographical origins.

  8. Undersampled Hyperspectral Image Reconstruction Based on Surfacelet Transform

    Directory of Open Access Journals (Sweden)

    Lei Liu

    2015-01-01

    Full Text Available Hyperspectral imaging is a crucial technique for military and environmental monitoring. However, limited equipment hardware resources severely affect the transmission and storage of a huge amount of data for hyperspectral images. This limitation has the potentials to be solved by compressive sensing (CS, which allows reconstructing images from undersampled measurements with low error. Sparsity and incoherence are two essential requirements for CS. In this paper, we introduce surfacelet, a directional multiresolution transform for 3D data, to sparsify the hyperspectral images. Besides, a Gram-Schmidt orthogonalization is used in CS random encoding matrix, two-dimensional and three-dimensional orthogonal CS random encoding matrixes and a patch-based CS encoding scheme are designed. The proposed surfacelet-based hyperspectral images reconstruction problem is solved by a fast iterative shrinkage-thresholding algorithm. Experiments demonstrate that reconstruction of spectral lines and spatial images is significantly improved using the proposed method than using conventional three-dimensional wavelets, and growing randomness of encoding matrix can further improve the quality of hyperspectral data. Patch-based CS encoding strategy can be used to deal with large data because data in different patches can be independently sampled.

  9. Hybrid tenso-vectorial compressive sensing for hyperspectral imaging

    Science.gov (United States)

    Li, Qun; Bernal, Edgar A.

    2016-05-01

    Hyperspectral imaging has a wide range of applications relying on remote material identification, including astronomy, mineralogy, and agriculture; however, due to the large volume of data involved, the complexity and cost of hyperspectral imagers can be prohibitive. The exploitation of redundancies along the spatial and spectral dimensions of a hyperspectral image of a scene has created new paradigms that overcome the limitations of traditional imaging systems. While compressive sensing (CS) approaches have been proposed and simulated with success on already acquired hyperspectral imagery, most of the existing work relies on the capability to simultaneously measure the spatial and spectral dimensions of the hyperspectral cube. Most real-life devices, however, are limited to sampling one or two dimensions at a time, which renders a significant portion of the existing work unfeasible. We propose a new variant of the recently proposed serial hybrid vectorial and tensorial compressive sensing (HCS-S) algorithm that, like its predecessor, is compatible with real-life devices both in terms of the acquisition and reconstruction requirements. The newly introduced approach is parallelizable, and we abbreviate it as HCS-P. Together, HCS-S and HCS-P comprise a generalized framework for hybrid tenso-vectorial compressive sensing, or HCS for short. We perform a detailed analysis that demonstrates the uniqueness of the signal reconstructed by both the original HCS-S and the proposed HCS-P algorithms. Last, we analyze the behavior of the HCS reconstruction algorithms in the presence of measurement noise, both theoretically and experimentally.

  10. Single-species microarrays and comparative transcriptomics.

    Directory of Open Access Journals (Sweden)

    Frédéric J J Chain

    Full Text Available BACKGROUND: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.

  11. Microarray Assisted Gene Discovery in Ulcerative Colitis

    DEFF Research Database (Denmark)

    Brusgaard, Klaus

    ), and microarray based expression studies. In IBD the increased production of chemo attractants from the inflamed microenvironment results in recruitment of activated CD4+ T lymphocytes which results in tissue damage. Where Th1 cell-derived cytokines has been reported to be essential mediators in CD with high (IFN...

  12. Shrinkage covariance matrix approach for microarray data

    Science.gov (United States)

    Karjanto, Suryaefiza; Aripin, Rasimah

    2013-04-01

    Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.

  13. Pineal function : Impact of microarray analysis

    NARCIS (Netherlands)

    Klein, David C.; Bailey, Michael J.; Carter, David A.; Kim, Jong-so; Shi, Qiong; Ho, Anthony K.; Chik, Constance L.; Gaildrat, Pascaline; Morin, Fabrice; Ganguly, Surajit; Rath, Martin F.; Moller, Morten; Sugden, David; Rangel, Zoila G.; Munson, Peter J.; Weller, Joan L.; Coon, Steven L.

    2010-01-01

    Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity to the retin

  14. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    -mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin...

  15. A Method of Microarray Data Storage Using Array Data Type

    Science.gov (United States)

    Tsoi, Lam C.; Zheng, W. Jim

    2009-01-01

    A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store microarray data by using array data type in an object-relational database management system – PostgreSQL. The implemented database can store all the microarray data from the same chip in an array data structure. The variable length array data type in PostgreSQL can store microarray data from same chip. The implementation of our schema can help to increase the data retrieval and space efficiency. PMID:17392028

  16. Characterization of a Large, Low-Cost 3D Scanner

    Directory of Open Access Journals (Sweden)

    Jeremy Straub

    2015-01-01

    Full Text Available Imagery-based 3D scanning can be performed by scanners with multiple form factors, ranging from small and inexpensive scanners requiring manual movement around a stationary object to large freestanding (nearly instantaneous units. Small mobile units are problematic for use in scanning living creatures, which may be unwilling or unable to (or for the very young and animals, unaware of the need to hold a fixed position for an extended period of time. Alternately, very high cost scanners that can capture a complete scan within a few seconds are available, but they are cost prohibitive for some applications. This paper seeks to assess the performance of a large, low-cost 3D scanner, presented in prior work, which is able to concurrently capture imagery from all around an object. It provides the capabilities of the large, freestanding units at a price point akin to the smaller, mobile ones. This allows access to 3D scanning technology (particularly for applications requiring instantaneous imaging at a lower cost. Problematically, prior analysis of the scanner’s performance was extremely limited. This paper characterizes the efficacy of the scanner for scanning both inanimate objects and humans. Given the importance of lighting to visible light scanning systems, the scanner’s performance under multiple lighting configurations is evaluated, characterizing its sensitivity to lighting design.

  17. Effects of sitting versus standing and scanner type on cashiers.

    Science.gov (United States)

    Lehman, K R; Psihogios, J P; Meulenbroek, R G

    2001-06-10

    In the retail supermarket industry where cashiers perform repetitive, light manual material-handling tasks when scanning and handling products, reports of musculoskeletal disorders and discomfort are high. Ergonomics tradeoffs exist between sitting and standing postures, which are further confounded by the checkstand design and point-of-sale technology, such as the scanner. A laboratory experiment study was conducted to understand the effects of working position (sitting versus standing) and scanner type (bi-optic versus single window) on muscle activity, upper limb and spinal posture, and subjective preference of cashiers. Ten cashiers from a Dutch retailer participated in the study. Cashiers exhibited lower muscle activity in the neck and shoulders when standing and using a bi-optic scanner. Shoulder abduction was also less for standing conditions. In addition, all cashiers preferred using the bi-optic scanner with mixed preferences for sitting (n = 6) and standing (n = 4). Static loading of the muscles was relatively high compared with benchmarks, suggesting that during the task of scanning, cashiers may not have adequate recovery time to prevent fatigue. It is recommended that retailers integrate bi-optic scanners into standing checkstands to minimize postural stress, fatigue and discomfort in cashiers.

  18. EGRONOMIC FINGERPRINT SCANNER DESIGN FOR PEOPLE WITH MOTOR NEURON DISEASES

    Directory of Open Access Journals (Sweden)

    Abdulkareem Al-Alwani

    2013-01-01

    Full Text Available Fingerprint devices have evolved with time for authentication and identification purposes. It is used in generic security and social applications where identification and logging is required when entering that premises. In some circumstances the lag time increases due to increase in human entrees such as at immigration points, airports, random security checkups, attendance loggers. The increase in overall time due to individual human delay factors present a major hindrance in smooth security as well as organizational operations. The delay could occur due to non-technical factor such as not placing the fingers firmly in the surface of the device. This is a major cause of concern for senior citizens and people with motor neuron diseases such as Parkinson’s, Huntington’s and Alzheimer’s disease. Therefore, a design is proposed in this research which can help the scanner to acquire fast and precise fingerprint scan of senior citizens and people with motor neuron diseases. This design uses ergonomically designed cover head for the scanner whose working is based on the Poka Yoke principle which assists firm finger placement on the scanner. In this research, 250 fingerprint scans were taken for statistical analysis using a normal fingerprint scanner and our proposed model scanner. Statistical comparison between the two results shows that our proposed model performs much better in terms of time consumption and accuracy.

  19. Moths on the Flatbed Scanner: The Art of Joseph Scheer

    Directory of Open Access Journals (Sweden)

    Stephen L. Buchmann

    2011-12-01

    Full Text Available During the past decade a few artists and even fewer entomologists discovered flatbed scanning technology, using extreme resolution graphical arts scanners for acquiring high magnification digital images of plants, animals and inanimate objects. They are not just for trip receipts anymore. The special attributes of certain scanners, to image thick objects is discussed along with the technical features of the scanners including magnification, color depth and shadow detail. The work of pioneering scanner artist, Joseph Scheer from New York’s Alfred University is highlighted. Representative flatbed-scanned images of moths are illustrated along with techniques to produce them. Collecting and preparing moths, and other objects, for scanning are described. Highlights of the Fulbright sabbatical year of professor Scheer in Arizona and Sonora, Mexico are presented, along with comments on moths in science, folklore, art and pop culture. The use of flatbed scanners is offered as a relatively new method for visualizing small objects while acquiring large files for creating archival inkjet prints for display and sale.

  20. Moths on the Flatbed Scanner: The Art of Joseph Scheer.

    Science.gov (United States)

    Buchmann, Stephen L

    2011-12-14

    During the past decade a few artists and even fewer entomologists discovered flatbed scanning technology, using extreme resolution graphical arts scanners for acquiring high magnification digital images of plants, animals and inanimate objects. They are not just for trip receipts anymore. The special attributes of certain scanners, to image thick objects is discussed along with the technical features of the scanners including magnification, color depth and shadow detail. The work of pioneering scanner artist, Joseph Scheer from New York's Alfred University is highlighted. Representative flatbed-scanned images of moths are illustrated along with techniques to produce them. Collecting and preparing moths, and other objects, for scanning are described. Highlights of the Fulbright sabbatical year of professor Scheer in Arizona and Sonora, Mexico are presented, along with comments on moths in science, folklore, art and pop culture. The use of flatbed scanners is offered as a relatively new method for visualizing small objects while acquiring large files for creating archival inkjet prints for display and sale.

  1. Hyperspectral Image Super-Resolution via Non-Negative Structured Sparse Representation.

    Science.gov (United States)

    Dong, Weisheng; Fu, Fazuo; Shi, Guangming; Cao, Xun; Wu, Jinjian; Li, Guangyu; Li, Guangyu

    2016-05-01

    Hyperspectral imaging has many applications from agriculture and astronomy to surveillance and mineralogy. However, it is often challenging to obtain high-resolution (HR) hyperspectral images using existing hyperspectral imaging techniques due to various hardware limitations. In this paper, we propose a new hyperspectral image super-resolution method from a low-resolution (LR) image and a HR reference image of the same scene. The estimation of the HR hyperspectral image is formulated as a joint estimation of the hyperspectral dictionary and the sparse codes based on the prior knowledge of the spatial-spectral sparsity of the hyperspectral image. The hyperspectral dictionary representing prototype reflectance spectra vectors of the scene is first learned from the input LR image. Specifically, an efficient non-negative dictionary learning algorithm using the block-coordinate descent optimization technique is proposed. Then, the sparse codes of the desired HR hyperspectral image with respect to learned hyperspectral basis are estimated from the pair of LR and HR reference images. To improve the accuracy of non-negative sparse coding, a clustering-based structured sparse coding method is proposed to exploit the spatial correlation among the learned sparse codes. The experimental results on both public datasets and real LR hypspectral images suggest that the proposed method substantially outperforms several existing HR hyperspectral image recovery techniques in the literature in terms of both objective quality metrics and computational efficiency.

  2. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  3. Design of a covalently bonded glycosphingolipid microarray.

    Science.gov (United States)

    Arigi, Emma; Blixt, Ola; Buschard, Karsten; Clausen, Henrik; Levery, Steven B

    2012-01-01

    Glycosphingolipids (GSLs) are well known ubiquitous constituents of all eukaryotic cell membranes, yet their normal biological functions are not fully understood. As with other glycoconjugates and saccharides, solid phase display on microarrays potentially provides an effective platform for in vitro study of their functional interactions. However, with few exceptions, the most widely used microarray platforms display only the glycan moiety of GSLs, which not only ignores potential modulating effects of the lipid aglycone, but inherently limits the scope of application, excluding, for example, the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2-mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin, a monoclonal antibody to sulfatide, Sulph 1; and a polyclonal antiserum reactive to asialo-G(M2)). Preliminary evaluation of the method indicated successful immobilization of the GSLs, and selective binding of test probes. The potential utility of this methodology for designing covalent microarrays that incorporate GSLs for serodiagnosis is discussed.

  4. 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...

  5. MICROARRAY ANALYSIS OF DIFFERENT GENE EXPRESSION OF HUMAN CERVICAL CANCER SUBCLONE CELL LINES

    Institute of Scientific and Technical Information of China (English)

    Chen Wei; Li Xu; Wang Xiang

    2006-01-01

    Objective To examine the differentially expressed invasion-related genes in two anchorage-independent uterine cervical carcinoma cell lines derived from the same patient using a cDNA array. Methods Two human uterine cervical carcinoma subclonal cell lines CS03 and CS07 derived from a single donor line CS1213 were established by limited dilution procedure. The two cDNA samples retro-transcribed from total RNA derived from CS03 and CS07 cells were screened by a cDNA microarray carrying 234 human cell-cycle related genes and 1011 human signal transduction and membrane receptor -associated genes, scanned with a ScanArray 3000 laser scanner. Results The cDNA microarray analysis showed that 12 genes in CS03 were up-regulated compared to CS07, and 24 genes in CS07 were up-regulated. The function of a number of differentially expressed genes was consistently associated with cell-cycle, cell proliferation, migration, apoptosis, signal transduction and tumor metastasis, including p34cdc2, TSC22, plasminogen activator inhibitor I (PAI-1)and desmosome associated protein(Pinin). Conclusion Multiple genes are differentially expressed in uterine cervical carcinoma cell lines even came from the same patient. It is suggested that these genes are involved in the different phenotypic characteristics and development of cervical carcinoma.

  6. Antibody Microarray for E. coli O157:H7 and Shiga Toxin in Microtiter Plates

    Directory of Open Access Journals (Sweden)

    Andrew G. Gehring

    2015-12-01

    Full Text Available Antibody microarray is a powerful analytical technique because of its inherent ability to simultaneously discriminate and measure numerous analytes, therefore making the technique conducive to both the multiplexed detection and identification of bacterial analytes (i.e., whole cells, as well as associated metabolites and/or toxins. We developed a sandwich fluorescent immunoassay combined with a high-throughput, multiwell plate microarray detection format. Inexpensive polystyrene plates were employed containing passively adsorbed, array-printed capture antibodies. During sample reaction, centrifugation was the only strategy found to significantly improve capture, and hence detection, of bacteria (pathogenic Escherichia coli O157:H7 to planar capture surfaces containing printed antibodies. Whereas several other sample incubation techniques (e.g., static vs. agitation had minimal effect. Immobilized bacteria were labeled with a red-orange-fluorescent dye (Alexa Fluor 555 conjugated antibody to allow for quantitative detection of the captured bacteria with a laser scanner. Shiga toxin 1 (Stx1 could be simultaneously detected along with the cells, but none of the agitation techniques employed during incubation improved detection of the relatively small biomolecule. Under optimal conditions, the assay had demonstrated limits of detection of ~5.8 × 105 cells/mL and 110 ng/mL for E. coli O157:H7 and Stx1, respectively, in a ~75 min total assay time.

  7. A High-Throughput, Precipitating Colorimetric Sandwich ELISA Microarray for Shiga Toxins

    Directory of Open Access Journals (Sweden)

    Andrew Gehring

    2014-06-01

    Full Text Available Shiga toxins 1 and 2 (Stx1 and Stx2 from Shiga toxin-producing E. coli (STEC bacteria were simultaneously detected with a newly developed, high-throughput antibody microarray platform. The proteinaceous toxins were immobilized and sandwiched between biorecognition elements (monoclonal antibodies and pooled horseradish peroxidase (HRP-conjugated monoclonal antibodies. Following the reaction of HRP with the precipitating chromogenic substrate (metal enhanced 3,3-diaminobenzidine tetrahydrochloride or DAB, the formation of a colored product was quantitatively measured with an inexpensive flatbed page scanner. The colorimetric ELISA microarray was demonstrated to detect Stx1 and Stx2 at levels as low as ~4.5 ng/mL within ~2 h of total assay time with a narrow linear dynamic range of ~1–2 orders of magnitude and saturation levels well above background. Stx1 and/or Stx2 produced by various strains of STEC were also detected following the treatment of cultured cells with mitomycin C (a toxin-inducing antibiotic and/or B-PER (a cell-disrupting, protein extraction reagent. Semi-quantitative detection of Shiga toxins was demonstrated to be sporadic among various STEC strains following incubation with mitomycin C; however, further reaction with B-PER generally resulted in the detection of or increased detection of Stx1, relative to Stx2, produced by STECs inoculated into either axenic broth culture or culture broth containing ground beef.

  8. WORKFLOW FOR BUILDING A HYPERSPECTRAL UAV: CHALLENGES AND OPPORTUNITIES

    Directory of Open Access Journals (Sweden)

    C. Proctor

    2015-08-01

    Full Text Available Owing to the limited payload capacities of most UAV platforms within an academic research budget, many UAV systems utilize commercial RGB cameras or modified sensors with some capacity for sensing in the NIR. However, many applications require higher spectral fidelity that only hyperspectral sensors can offer. For instance, the Photochemical Reflectance Index relies upon the narrow band absorbance of xanthophyll pigments at 531 and 570nm to quantify photosynthetic light use efficiency which are important indicators of productivity and stress in agricultural and forest ecosystems. Thus, our research group has been working on building a research paradigm around a commercial off-the-shelf hyperspectral sensor and UAV. This paper discusses some of the key decisions made regarding selection of equipment and navigating the regulatory and logistical landmines. The imagery collected to date and the options available to process and utilize hyperspectral data are discussed at the end.

  9. Hyperspectral image classification based on volumetric texture and dimensionality reduction

    Science.gov (United States)

    Su, Hongjun; Sheng, Yehua; Du, Peijun; Chen, Chen; Liu, Kui

    2015-06-01

    A novel approach using volumetric texture and reduced-spectral features is presented for hyperspectral image classification. Using this approach, the volumetric textural features were extracted by volumetric gray-level co-occurrence matrices (VGLCM). The spectral features were extracted by minimum estimated abundance covariance (MEAC) and linear prediction (LP)-based band selection, and a semi-supervised k-means (SKM) clustering method with deleting the worst cluster (SKMd) bandclustering algorithms. Moreover, four feature combination schemes were designed for hyperspectral image classification by using spectral and textural features. It has been proven that the proposed method using VGLCM outperforms the gray-level co-occurrence matrices (GLCM) method, and the experimental results indicate that the combination of spectral information with volumetric textural features leads to an improved classification performance in hyperspectral imagery.

  10. Using independent component analysis for material estimation in hyperspectral images.

    Science.gov (United States)

    Kuan, Chia-Yun; Healey, Glenn

    2004-06-01

    We develop a method for automated material estimation in hyperspectral images. The method models a hyperspectral pixel as a linear mixture of unknown materials. The method is particularly useful for applications in which material regions in a scene are smaller than one pixel. In contrast to many material estimation methods, the new method uses the statistics of large numbers of pixels rather than attempting to identify a small number of the purest pixels. The method is based on maximizing the independence of material abundances at each pixel. We show how independent component analysis algorithms can be adapted for use with this problem. We demonstrate properties of the method by application to airborne hyperspectral data.

  11. Hyperspectral Imaging and Related Field Methods: Building the Science

    Science.gov (United States)

    Goetz, Alexander F. H.; Steffen, Konrad; Wessman, Carol

    1999-01-01

    The proposal requested funds for the computing power to bring hyperspectral image processing into undergraduate and graduate remote sensing courses. This upgrade made it possible to handle more students in these oversubscribed courses and to enhance CSES' summer short course entitled "Hyperspectral Imaging and Data Analysis" provided for government, industry, university and military. Funds were also requested to build field measurement capabilities through the purchase of spectroradiometers, canopy radiation sensors and a differential GPS system. These instruments provided systematic and complete sets of field data for the analysis of hyperspectral data with the appropriate radiometric and wavelength calibration as well as atmospheric data needed for application of radiative transfer models. The proposed field equipment made it possible to team-teach a new field methods course, unique in the country, that took advantage of the expertise of the investigators rostered in three different departments, Geology, Geography and Biology.

  12. Parallel computation for blood cell classification in medical hyperspectral imagery

    Science.gov (United States)

    Li, Wei; Wu, Lucheng; Qiu, Xianbo; Ran, Qiong; Xie, Xiaoming

    2016-09-01

    With the advantage of fine spectral resolution, hyperspectral imagery provides great potential for cell classification. This paper provides a promising classification system including the following three stages: (1) band selection for a subset of spectral bands with distinctive and informative features, (2) spectral-spatial feature extraction, such as local binary patterns (LBP), and (3) followed by an effective classifier. Moreover, these three steps are further implemented on graphics processing units (GPU) respectively, which makes the system real-time and more practical. The GPU parallel implementation is compared with the serial implementation on central processing units (CPU). Experimental results based on real medical hyperspectral data demonstrate that the proposed system is able to offer high accuracy and fast speed, which are appealing for cell classification in medical hyperspectral imagery.

  13. Super pixel-level dictionary learning for hyperspectral image classification

    Science.gov (United States)

    Zhao, Wei; Zhu, Wen; Liao, Bo; Fu, Xiangzheng

    2017-08-01

    This paper presents a superpixel-level dictionary learning model for hyperspectral data. The idea is to divide the hyperspectral image into a number of super-pixels by means of the super-pixel segmentation method. Each super-pixel is a spatial neighborhood called contextual group. That is, each pixel is represented using a linear combination of a few dictionary items learned from the train data, but since pixels inside a super-pixel are often consisting of the same materials, their linear combinations are constrained to use common items from the dictionary. To this end, the sparse coefficients of the context group have a common sparse pattern by using the joint sparse regularizer for dictionary learning. The sparse coefficients are then used for classification using linear support vector machines. The validity of the proposed method is experimentally verified on a real hyperspectral images.

  14. D Hyperspectral Frame Imager Camera Data in Photogrammetric Mosaicking

    Science.gov (United States)

    Mäkeläinen, A.; Saari, H.; Hippi, I.; Sarkeala, J.; Soukkamäki, J.

    2013-08-01

    A new 2D hyperspectral frame camera system has been developed by VTT (Technical Research Center of Finland) and Rikola Ltd. It contains frame based and very light camera with RGB-NIR sensor and it is suitable for light weight and cost effective UAV planes. MosaicMill Ltd. has converted the camera data into proper format for photogrammetric processing, and camera's geometrical accuracy and stability are evaluated to guarantee required accuracies for end user applications. MosaicMill Ltd. has also applied its' EnsoMOSAIC technology to process hyperspectral data into orthomosaics. This article describes the main steps and results on applying hyperspectral sensor in orthomosaicking. The most promising results as well as challenges in agriculture and forestry are also described.

  15. Passive IR polarimetric hyperspectral imaging contributions to multisensor humanitarian demining

    Science.gov (United States)

    Iannarilli, Frank J., Jr.; Scott, Herman E.; Jones, Stephen H.

    2001-10-01

    Supported by the Army Humanitarian Demining MURI, we most recently have focused on determining the unique strengths of passive IR sensing as a function of attribute diversity. Our initial findings identify polarimetric hyperspectral imaging.as a robust means to rapidly survey and detect partially exposed, non-metallic anti-personnel (AP) mines. We are investigating the discrimination gains expected from the combined polarimetric hyperspectral attributes under laboratory and field conditions. A principal components analysis of our earliest data indicates that this combination of attributes is about three times more effective in discriminating AP mines or mine-like materials than conventional hyperspectral sensing. In addition, we have uncovered a distinguishing spectral behavior of the Fresnel reflectance across resonance features that can be measured only by spectrally-resolved polarimetry.

  16. Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jianping Hua

    2004-01-01

    Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

  17. Post-normalization quality assessment visualization of microarray data

    NARCIS (Netherlands)

    McClure, John; Wit, Ernst

    2003-01-01

    Post-normalization checking of microarrays rarely occurs, despite the problems that using unreliable data for inference can cause. This paper considers a number of different ways to check microarrays after normalization for a variety of potential problems. Four types of problem with microarray data

  18. SIMAGE : simulation of DNA-microarray gene expression data

    NARCIS (Netherlands)

    Albers, Casper J.; Jansen, Ritsert C.; Kok, Jan; Kuipers, Oscar P.; Hijum, Sacha A.F.T. van

    2006-01-01

    Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing methods for best analysis of a given DNA microarray experiment, (iii) educating students, lab-workers and other

  19. Design and performance of HEAD PENN-PET scanner

    Energy Technology Data Exchange (ETDEWEB)

    Freifelder, R.; Karp, J.S. (Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Radiology); Geagan, M.; Muehllehner, G. (UGM Medical Systems Inc., Philadelphia, PA (United States))

    1994-08-01

    A new PET scanner for brain imaging (and animals) has been designed with very high sensitivity and spatial resolution. The design is an evolution of the PENN-PET scanner, which uses large position-sensitive NaI(Tl) detectors, with Anger-type positioning logic, and which allows 3-D volume imaging, without septa. The new design is built with a single annular crystal coupled to 180 photomultiplier tubes, and uses local triggering electronics to subdivide the detector into small zones and to determine coincident events within the detector. The axial acceptance angle of [+-] 27 deg, with a field-of-view of 25.6 cm, is larger than any currently operating PET scanner. Performance measurements are presented.

  20. Calibration procedure for a laser triangulation scanner with uncertainty evaluation

    Science.gov (United States)

    Genta, Gianfranco; Minetola, Paolo; Barbato, Giulio

    2016-11-01

    Most of low cost 3D scanning devices that are nowadays available on the market are sold without a user calibration procedure to correct measurement errors related to changes in environmental conditions. In addition, there is no specific international standard defining a procedure to check the performance of a 3D scanner along time. This paper aims at detailing a thorough methodology to calibrate a 3D scanner and assess its measurement uncertainty. The proposed procedure is based on the use of a reference ball plate and applied to a triangulation laser scanner. Experimental results show that the metrological performance of the instrument can be greatly improved by the application of the calibration procedure that corrects systematic errors and reduces the device's measurement uncertainty.

  1. Spectral reflectance estimation using a six-color scanner

    Science.gov (United States)

    Tominaga, Shoji; Kohno, Satoshi; Kakinuma, Hirokazu; Nohara, Fuminori; Horiuchi, Takahiko

    2009-01-01

    A method is proposed for estimating the spectral reflectance function of an object surface by using a six-color scanner. The scanner is regarded as a six-band spectral imaging system, since it captures six color channels in total from two separate scans using two difference lamps. First, we describe the basic characteristics of the imaging systems for a HP color scanner and a multiband camera used for comparison. Second, we describe a computational method for recovering surface-spectral reflectances from the noisy sensor outputs. A LMMSE estimator is presented as an optimal estimator. We discuss the reflectance estimation for non-flat surfaces with shading effect. A solution method is presented for the reliable reflectance estimation. Finally, the performance of the proposed method is examined in detail on experiments using the Macbeth Color Checker and non-flat objects.

  2. Dental impressions using 3D digital scanners: virtual becomes reality.

    Science.gov (United States)

    Birnbaum, Nathan S; Aaronson, Heidi B

    2008-10-01

    The technologies that have made the use of three-dimensional (3D) digital scanners an integral part of many industries for decades have been improved and refined for application to dentistry. Since the introduction of the first dental impressioning digital scanner in the 1980s, development engineers at a number of companies have enhanced the technologies and created in-office scanners that are increasingly user-friendly and able to produce precisely fitting dental restorations. These systems are capable of capturing 3D virtual images of tooth preparations, from which restorations may be fabricated directly (ie, CAD/CAM systems) or fabricated indirectly (ie, dedicated impression scanning systems for the creation of accurate master models). The use of these products is increasing rapidly around the world and presents a paradigm shift in the way in which dental impressions are made. Several of the leading 3D dental digital scanning systems are presented and discussed in this article.

  3. Hyperspectral Cubesat Constellation for Rapid Natural Hazard Response

    Science.gov (United States)

    Mandl, D.; Huemmrich, K. F.; Ly, V. T.; Handy, M.; Ong, L.; Crum, G.

    2015-12-01

    With the advent of high performance space networks that provide total coverage for Cubesats, the paradigm for low cost, high temporal coverage with hyperspectral instruments becomes more feasible. The combination of ground cloud computing resources, high performance with low power consumption onboard processing, total coverage for the cubesats and social media provide an opprotunity for an architecture that provides cost-effective hyperspectral data products for natural hazard response and decision support. This paper provides a series of pathfinder efforts to create a scalable Intelligent Payload Module(IPM) that has flown on a variety of airborne vehicles including Cessna airplanes, Citation jets and a helicopter and will fly on an Unmanned Aerial System (UAS) hexacopter to monitor natural phenomena. The IPM's developed thus far were developed on platforms that emulate a satellite environment which use real satellite flight software, real ground software. In addition, science processing software has been developed that perform hyperspectral processing onboard using various parallel processing techniques to enable creation of onboard hyperspectral data products while consuming low power. A cubesat design was developed that is low cost and that is scalable to larger consteallations and thus can provide daily hyperspectral observations for any spot on earth. The design was based on the existing IPM prototypes and metrics that were developed over the past few years and a shrunken IPM that can perform up to 800 Mbps throughput. Thus this constellation of hyperspectral cubesats could be constantly monitoring spectra with spectral angle mappers after Level 0, Level 1 Radiometric Correction, Atmospheric Correction processing. This provides the opportunity daily monitoring of any spot on earth on a daily basis at 30 meter resolution which is not available today.

  4. Microarray on digital versatile disc for identification and genotyping of Salmonella and Campylobacter in meat products.

    Science.gov (United States)

    Tortajada-Genaro, Luis Antonio; Rodrigo, Alejandro; Hevia, Elizabeth; Mena, Salvador; Niñoles, Regina; Maquieira, Ángel

    2015-09-01

    Highly portable, cost-effective, and rapid-response devices are required for the subtyping of the most frequent food-borne bacteria; thereby the sample rejection strategies and hygienization techniques along the food chain can be tailor-designed. Here, a novel biosensor is presented for the generic detection of Salmonella and Campylobacter and the discrimination between their most prevalent serovars (Salmonella Enteritidis, Salmonella Typhimurium) and species (Campylobacter jejuni, Campylobacter coli), respectively. The method is based on DNA microarray developed on a standard digital versatile disc (DVD) as support for a hybridization assay and a DVD driver as scanner. This approach was found to be highly sensitive (detection limit down to 0.2 pg of genomic DNA), reproducible (relative standard deviation 4-19 %), and high working capacity (20 samples per disc). The inclusivity and exclusivity assays indicated that designed oligonucleotides (primers and probes) were able to discriminate targeted pathogens from other Salmonella serovars, Campylobacter species, or common food-borne pathogens potentially present in the indigenous microflora. One hundred isolates from meat samples, collected in a poultry factory, were analyzed by the DVD microarraying and fluorescent real-time PCR. An excellent correlation was observed for both generic and specific detection (relative sensitivity 93-99 % and relative specificity 93-100 %). Therefore, the developed assay has been shown to be a reliable tool to be used in routine food safety analysis, especially in settings with limited infrastructure due to the excellent efficiency-cost ratio of compact disc technology. Graphical Abstract DNA microarray performed by DVD technology for pathogen genotyping.

  5. A sandwiched microarray platform for benchtop cell-based high throughput screening

    Science.gov (United States)

    Wu, Jinhui; Wheeldon, Ian; Guo, Yuqi; Lu, Tingli; Du, Yanan; Wang, Ben; He, Jiankang; Hu, Yiqiao; Khademhosseini, Ali

    2010-01-01

    The emergence of combinatorial chemistries and the increased discovery of natural compounds have led to the production of expansive libraries of drug candidates and vast numbers of compounds with potentially interesting biological activities. Despite broad interest in high throughput screening (HTS) across varied fields of biological research, there has not been an increase in accessible HTS technologies. Here, we present a simple microarray sandwich system suitable for screening chemical libraries in cell-based assays at the benchtop. The microarray platform delivers chemical compounds to isolated cell cultures by ‘sandwiching’ chemical-laden arrayed posts with cell-seeded microwells. In this way, an array of sealed cell-based assays was generated without cross-contamination between neighboring assays. After chemical exposure, cell viability was analyzed by fluorescence detection of cell viability indicator assays on a per microwell basis in a standard microarray scanner. We demonstrate the efficacy of the system by generating four hits from toxicology screens towards MCF-7 human breast cancer cells. Three of the hits were identified in a combinatorial screen of a library of natural compounds in combination with verapamil, a P-glycoprotein inhibitor. A fourth hit, 9-methoxy-camptothecin, was identified by screening the natural compound library in the absence of verapamil. The method developed here miniaturizes existing HTS systems and enables the screening of a wide array of individual or combinatorial libraries in a reproducible and scalable manner. We anticipate broad application of such a system as it is amenable to combinatorial drug screening in a simple, robust and portable platform. PMID:20965560

  6. Hyperspectral anomaly detection using enhanced global factors

    Science.gov (United States)

    Paciencia, Todd J.; Bauer, Kenneth W.

    2016-05-01

    Dimension reduction techniques have become one popular unsupervised approach used towards detecting anomalies in hyperspectral imagery. Although demonstrating promising results in the literature on specific images, these methods can become difficult to directly interpret and often require tuning of their parameters to achieve high performance on a specific set of images. This lack of generality is also compounded by the need to remove noise and atmospheric absorption spectral bands from the image prior to detection. Without a process for this band selection and to make the methods adaptable to different image compositions, performance becomes difficult to maintain across a wider variety of images. Here, we present a framework that uses factor analysis to provide a robust band selection and more meaningful dimension reduction with which to detect anomalies in the imagery. Measurable characteristics of the image are used to create an automated decision process that allows the algorithm to adjust to a particular image, while maintaining high detection performance. The framework and its algorithms are detailed, and results are shown for forest, desert, sea, rural, urban, anomaly-sparse, and anomaly-dense imagery types from different sensors. Additionally, the method is compared to current state-of-the-art methods and is shown to be computationally efficient.

  7. Hyperspectral range imaging for transportation systems evaluation

    Science.gov (United States)

    Bridgelall, Raj; Rafert, J. B.; Atwood, Don; Tolliver, Denver D.

    2016-04-01

    Transportation agencies expend significant resources to inspect critical infrastructure such as roadways, railways, and pipelines. Regular inspections identify important defects and generate data to forecast maintenance needs. However, cost and practical limitations prevent the scaling of current inspection methods beyond relatively small portions of the network. Consequently, existing approaches fail to discover many high-risk defect formations. Remote sensing techniques offer the potential for more rapid and extensive non-destructive evaluations of the multimodal transportation infrastructure. However, optical occlusions and limitations in the spatial resolution of typical airborne and space-borne platforms limit their applicability. This research proposes hyperspectral image classification to isolate transportation infrastructure targets for high-resolution photogrammetric analysis. A plenoptic swarm of unmanned aircraft systems will capture images with centimeter-scale spatial resolution, large swaths, and polarization diversity. The light field solution will incorporate structure-from-motion techniques to reconstruct three-dimensional details of the isolated targets from sequences of two-dimensional images. A comparative analysis of existing low-power wireless communications standards suggests an application dependent tradeoff in selecting the best-suited link to coordinate swarming operations. This study further produced a taxonomy of specific roadway and railway defects, distress symptoms, and other anomalies that the proposed plenoptic swarm sensing system would identify and characterize to estimate risk levels.

  8. Infrared hyperspectral standoff detection of explosives

    Science.gov (United States)

    Fuchs, F.; Hugger, S.; Jarvis, J.; Blattmann, V.; Kinzer, M.; Yang, Q. K.; Ostendorf, R.; Bronner, W.; Driad, R.; Aidam, R.; Wagner, J.

    2013-05-01

    In this work we demonstrate imaging standoff detection of solid traces of explosives using infrared laser backscattering spectroscopy. Our system relies on active laser illumination in the 7 μm-10 μm spectral range at fully eye-safe power levels. This spectral region comprises many characteristic absorption features of common explosives, and the atmospheric transmission is sufficiently high for stand-off detection. The key component of our system is an external cavity quantum cascade laser with a tuning range of 300 cm-1 that enables us to scan the illumination wavelength over several of the characteristic spectral features of a large number of different explosives using a single source. We employ advanced hyperspectral image analysis to obtain fully automated detection and identification of the target substances even on substrates that interfere with the fingerprint spectrum of the explosive to be detected due to their own wavelength-dependent scattering contributions to the measured backscattering spectrum. Only the pure target spectra of the explosives have to be provided to the detection routine that nevertheless accomplishes reliable background suppression without any a-priory-information about the substrate.

  9. Resolving Mixed Algal Species in Hyperspectral Images

    Directory of Open Access Journals (Sweden)

    Mehrube Mehrubeoglu

    2013-12-01

    Full Text Available We investigated a lab-based hyperspectral imaging system’s response from pure (single and mixed (two algal cultures containing known algae types and volumetric combinations to characterize the system’s performance. The spectral response to volumetric changes in single and combinations of algal mixtures with known ratios were tested. Constrained linear spectral unmixing was applied to extract the algal content of the mixtures based on abundances that produced the lowest root mean square error. Percent prediction error was computed as the difference between actual percent volumetric content and abundances at minimum RMS error. Best prediction errors were computed as 0.4%, 0.4% and 6.3% for the mixed spectra from three independent experiments. The worst prediction errors were found as 5.6%, 5.4% and 13.4% for the same order of experiments. Additionally, Beer-Lambert’s law was utilized to relate transmittance to different volumes of pure algal suspensions demonstrating linear logarithmic trends for optical property measurements.

  10. Enhanced sensitivity for hyperspectral infrared chemical detection

    Energy Technology Data Exchange (ETDEWEB)

    Jacobson, P. L. (Phillip L.); Petrin, R. R. (Roger R.); Koskelo, A. C. (Aaron C.); Quick, C. R. (Charles R.); Romero, J. J. (Jerry J.)

    2001-01-01

    The sensitivity of imaging, hyperspectral, passive remote sensors in the long-wavelength infrared (LWIR) spectral region is currently limited by the ability to achieve an accurate, time-invariant, pixel-to-pixel calibration of the elements composing the Focal Plane Array (FPA). Pursuing conventional techniques to improve the accuracy of the calibration will always be limited by the trade-off between the time required to collect calibration data of improved precision and the drift in the pixel response that occurs on a timescale comparable to the calibration time. This paper will present the results from a study of a method to circumvent these problems. Improvements in detection capability can be realized by applying a quick, repetitive dither of the field of view (FOV) of the imager (by a small angular amount), so that radiance/spectral differences between individual target areas can be measured by a single FPA pixel. By performing this difference measurement repetitively both residual differences in the pixel-to-pixel calibration and l/f detector drift noise can effectively be eliminated. In addition, variations in the atmosphere and target scene caused by the motion of the sensor platform will cause signal drifts that this technique would be able to remove. This method allows improvements in sensitivity that could potentially scale as the square root of the observation time.

  11. Data acquisition with the APEX hyperspectral sensor

    Directory of Open Access Journals (Sweden)

    Vreys Kristin

    2016-03-01

    Full Text Available APEX (Airborne Prism EXperiment is a high spectral and spatial resolution hyperspectral sensor developed by a Swiss-Belgian consortium on behalf of the European Space Agency. Since the acceptance of the instrument in 2010, it has been operated jointly by the Flemish Institute for Technological Research (VITO, Mol, Belgium and the Remote Sensing Laboratories (RSL, Zurich, Switzerland. During this period, several flight campaigns have been performed across Europe, gathering over 4 Terabytes of raw data. Following radiometric, geometric and atmospheric processing, this data has been provided to a multitude of Belgian and European researchers, institutes and agencies, including the European Space Agency (ESA, the European Facility for Airborne Research (EUFAR and the Belgian Science Policy Office (BelSPO. The applications of APEX data span a wide range of research topics, e.g. landcover mapping (mountainous, coastal, countryside and urban regions, the assessment of important structural and (biophysical characteristics of vegetative and non-vegetative species, the tracing of atmospheric gases, and water content analysis (chlorophyll, suspended matter. Recurrent instrument calibration, accurate flight planning and preparation, and experienced pilots and instrument operators are crucial to successful data acquisition campaigns. In this paper, we highlight in detail these practical aspects of a typical APEX data acquisition campaign.

  12. Hyperspectral aerosol optical depths from TCAP flights

    Energy Technology Data Exchange (ETDEWEB)

    Shinozuka, Yohei [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Bay Area Environmental REsearch Institute; Johnson, Roy R [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Flynn, Connor J [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Russell, Philip B [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Schmid, Beat [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-06-01

    4STAR (Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research), a hyperspectral airborne sunphotometer, acquired aerosol optical depths (AOD) at 1 Hz during all July 2012 flights of the Two Column Aerosol Project (TCAP). Root-mean-square differences from AERONET ground-based observations were 0.01 at wavelengths between 500-1020 nm, 0.02 at 380 and 1640 nm and 0.03 at 440 nm in four clear-sky fly-over events, and similar in ground side-by-side comparisons. Changes in the above-aircraft AOD across 3- km-deep spirals were typically consistent with integrals of coincident in situ (on DOE Gulfstream 1 with 4STAR) and lidar (on NASA B200) extinction measurements within 0.01, 0.03, 0.01, 0.02, 0.02, 0.02 at 355, 450, 532, 550, 700, 1064 nm, respectively, despite atmospheric variations and combined measurement uncertainties. Finer vertical differentials of the 4STAR measurements matched the in situ ambient extinction profile within 14% for one homogeneous column. For the AOD observed between 350-1660 nm, excluding strong

  13. Hyperspectral Cubesat Constellation for Natural Hazard Response

    Science.gov (United States)

    Mandl, Daniel; Crum, Gary; Ly, Vuong; Handy, Matthew; Huemmrich, Karl F.; Ong, Lawrence; Holt, Ben; Maharaja, Rishabh

    2016-01-01

    The authors on this paper are team members of the Earth Observing 1 (E0-1) mission which has flown an imaging spectrometer (hyperspectral) instrument called Hyperion for the past 15+ years. The satellite is able to image any spot on Earth in the nadir looking direction every 16 days and with slewing, of the satellite for up to a 23 degree view angle, any spot on the Earth can be imaged approximately every 2 to 3 days. EO-1 has been used to track many natural hazards such as wildfires, volcanoes and floods. An enhanced capability that has been sought is the ability to image natural hazards in a daily time series for space-based imaging spectrometers. The Hyperion cannot provide this capability on EO-1 with the present polar orbit. However, a constellation of cubesats, each with the same imaging spectrometer, positioned strategically can be used to provide daily coverage or even diurnal coverage, cost-effectively. This paper sought to design a cubesat constellation mission that would accomplish this goal and then to articulate the key tradeoffs.

  14. Food inspection using hyperspectral imaging and SVDD

    Science.gov (United States)

    Uslu, Faruk Sukru; Binol, Hamidullah; Bal, Abdullah

    2016-05-01

    Nowadays food inspection and evaluation is becoming significant public issue, therefore robust, fast, and environmentally safe methods are studied instead of human visual assessment. Optical sensing is one of the potential methods with the properties of being non-destructive and accurate. As a remote sensing technology, hyperspectral imaging (HSI) is being successfully applied by researchers because of having both spatial and detailed spectral information about studied material. HSI can be used to inspect food quality and safety estimation such as meat quality assessment, quality evaluation of fish, detection of skin tumors on chicken carcasses, and classification of wheat kernels in the food industry. In this paper, we have implied an experiment to detect fat ratio in ground meat via Support Vector Data Description which is an efficient and robust one-class classifier for HSI. The experiments have been implemented on two different ground meat HSI data sets with different fat percentage. Addition to these implementations, we have also applied bagging technique which is mostly used as an ensemble method to improve the prediction ratio. The results show that the proposed methods produce high detection performance for fat ratio in ground meat.

  15. Application of binary optical element to infrared hyperspectral detection

    Institute of Scientific and Technical Information of China (English)

    SUN; Qiang(孙强); YU; Bin(于斌); LIU; Yuling(刘玉玲); LU; Zhenwu(卢振武); CHEN; Bo(陈波); WANG; Zhaoqi(王肇圻); MU; Guoguang(母国光)

    2003-01-01

    Binary optical element (BOE) is applied to infrared hyperspectral detector. A new type of infrared hyperspectral detecting image system is designed based on the characteristics of abundant color-dispersion of BOE, and an example of combining refractive-diffractive zoom optical system with Cassegrain system is presented. The system not only has simple structure, long back-working distance and few requirements for material but also can increase the image resolution, abilities of accepting ray energy and registration. Consequently, by adding an appropriate stare array detector to the system, the detecting precision can be raised.

  16. Plugin procedure in segmentation and application to hyperspectral image segmentation

    CERN Document Server

    Girard, R

    2010-01-01

    In this article we give our contribution to the problem of segmentation with plug-in procedures. We give general sufficient conditions under which plug in procedure are efficient. We also give an algorithm that satisfy these conditions. We give an application of the used algorithm to hyperspectral images segmentation. Hyperspectral images are images that have both spatial and spectral coherence with thousands of spectral bands on each pixel. In the proposed procedure we combine a reduction dimension technique and a spatial regularisation technique. This regularisation is based on the mixlet modelisation of Kolaczyck and Al.

  17. Bread Water Content Measurement Based on Hyperspectral Imaging

    DEFF Research Database (Denmark)

    Liu, Zhi; Møller, Flemming

    2011-01-01

    for bread quality based on near-infrared hyperspectral imaging against the conventional manual loss-in-weight method. For this purpose, the hyperspectral components unmixing technology is used for measuring the water content quantitatively. And the definition on bread water content index is presented......Water content is one of the most important properties of the bread for tasting assesment or store monitoring. Traditional bread water content measurement methods mostly are processed manually, which is destructive and time consuming. This paper proposes an automated water content measurement...... for this measurement. The proposed measurement scheme is relatively inexpensive to implement, easy to set up. The experimental results demonstrate the effectiveness....

  18. Spatial-spectral method for classification of hyperspectral images.

    Science.gov (United States)

    Bian, Xiaoyong; Zhang, Tianxu; Yan, Luxin; Zhang, Xiaolong; Fang, Houzhang; Liu, Hai

    2013-03-15

    Spatial-spectral approach with spatially adaptive classification of hyperspectral images is proposed. The rotation-invariant spatial texture information for each object is exploited and incorporated into the classifier by using the modified local Gabor binary pattern to distinguish different types of classes of interest. The proposed method can effectively suppress anisotropic texture in spatially separate classes as well as improve the discrimination among classes. Moreover, it becomes more robust with the within-class variation. Experimental results on the classification of three real hyperspectral remote sensing images demonstrate the effectiveness of the proposed approach.

  19. Hyperspectral imaging using the single-pixel Fourier transform technique

    Science.gov (United States)

    Jin, Senlin; Hui, Wangwei; Wang, Yunlong; Huang, Kaicheng; Shi, Qiushuai; Ying, Cuifeng; Liu, Dongqi; Ye, Qing; Zhou, Wenyuan; Tian, Jianguo

    2017-03-01

    Hyperspectral imaging technology is playing an increasingly important role in the fields of food analysis, medicine and biotechnology. To improve the speed of operation and increase the light throughput in a compact equipment structure, a Fourier transform hyperspectral imaging system based on a single-pixel technique is proposed in this study. Compared with current imaging spectrometry approaches, the proposed system has a wider spectral range (400-1100 nm), a better spectral resolution (1 nm) and requires fewer measurement data (a sample rate of 6.25%). The performance of this system was verified by its application to the non-destructive testing of potatoes.

  20. On the unmixing of MEx/OMEGA hyperspectral data

    CERN Document Server

    Themelis, Konstantinos E; Sykioti, Olga; Rontogiannis, Athanasios A; Koutroumbas, Konstantinos D; Daglis, Ioannis A

    2011-01-01

    This article presents a comparative study of three different types of estimators used for supervised linear unmixing of two MEx/OMEGA hyperspectral cubes. The algorithms take into account the constraints of the abundance fractions, in order to get physically interpretable results. Abundance maps show that the Bayesian maximum a posteriori probability (MAP) estimator proposed in Themelis and Rontogiannis (2008) outperforms the other two schemes, offering a compromise between complexity and estimation performance. Thus, the MAP estimator is a candidate algorithm to perform ice and minerals detection on large hyperspectral datasets.

  1. Graph Regularized Nonnegative Matrix Factorization for Hyperspectral Data Unmixing

    CERN Document Server

    Rajabi, Roozbeh; Ghassemian, Hassan

    2011-01-01

    Spectral unmixing is an important tool in hyperspectral data analysis for estimating endmembers and abundance fractions in a mixed pixel. This paper examines the applicability of a recently developed algorithm called graph regularized nonnegative matrix factorization (GNMF) for this aim. The proposed approach exploits the intrinsic geometrical structure of the data besides considering positivity and full additivity constraints. Simulated data based on the measured spectral signatures, is used for evaluating the proposed algorithm. Results in terms of abundance angle distance (AAD) and spectral angle distance (SAD) show that this method can effectively unmix hyperspectral data.

  2. Standoff midwave infrared hyperspectral imaging of ship plumes

    Science.gov (United States)

    Gagnon, Marc-André; Gagnon, Jean-Philippe; Tremblay, Pierre; Savary, Simon; Farley, Vincent; Guyot, Éric; Lagueux, Philippe; Chamberland, Martin; Marcotte, Frédérick

    2016-05-01

    Characterization of ship plumes is very challenging due to the great variety of ships, fuel, and fuel grades, as well as the extent of a gas plume. In this work, imaging of ship plumes from an operating ferry boat was carried out using standoff midwave (3-5 μm) infrared hyperspectral imaging. Quantitative chemical imaging of combustion gases was achieved by fitting a radiative transfer model. Combustion efficiency maps and mass flow rates are presented for carbon monoxide (CO) and carbon dioxide (CO2). The results illustrate how valuable information about the combustion process of a ship engine can be successfully obtained using passive hyperspectral remote sensing imaging.

  3. Quantitative and comparative analysis of hyperspectral data fusion performance

    Institute of Scientific and Technical Information of China (English)

    王强; 张晔; 李硕; 沈毅

    2002-01-01

    Hyperspectral data fusion technique is the key to hyperspectral data processing in recent years. Manyfusion methods have been proposed, but little research has been done to evaluate the performances of differentdata fusion methods. In order to meet the urgent need, quantitative correlation analysis (QCA) is proposed toanalyse and compare the performances of different fusion methods directly from data before and after fusion. Ex-periment results show that the new method is effective and the results of comparison are in agreement with theresults of application.

  4. A collection of hyperspectral images for imaging systems research

    Science.gov (United States)

    Skauli, Torbjørn; Farrell, Joyce

    2013-01-01

    A set of hyperspectral image data are made available, intended for use in modeling of imaging systems. The set contains images of faces, landscapes and buildings. The data cover wavelengths from 0.4 to 2.5 micrometers, spanning the visible, NIR and SWIR electromagnetic spectral ranges. The images have been recorded with two HySpex line-scan imaging spectrometers covering the spectral ranges 0.4 to 1 micrometers and 1 to 2.5 micrometers. The hyperspectral data set includes measured illuminants and software for converting the radiance data to estimated reflectance. The images are being made available for download at http://scien.stanford.edu

  5. The potential of spectral and hyperspectral-imaging techniques for bacterial detection in food: A case study on lactic acid bacteria.

    Science.gov (United States)

    Foca, Giorgia; Ferrari, Carlotta; Ulrici, Alessandro; Sciutto, Giorgia; Prati, Silvia; Morandi, Stefano; Brasca, Milena; Lavermicocca, Paola; Lanteri, Silvia; Oliveri, Paolo

    2016-06-01

    Official methods for the detection of bacteria are based on culture techniques. These methods have limitations such as time consumption, cost, detection limits and the impossibility to analyse a large number of samples. For these reasons, the development of rapid, low-cost and non-destructive analytical methods is a task of growing interest. In the present study, the capability of spectral and hyperspectral techniques to detect bacterial surface contamination was investigated preliminarily on gel cultures, and subsequently on sliced cooked ham. In more detail, two species of lactic acid bacteria (LAB) were considered, namely Lactobacillus curvatus and Lactobacillus sakei, both of which are responsible for common alterations in sliced cooked ham. Three techniques were investigated, with different equipment, respectively: a macroscopic hyperspectral scanner operating in the NIR (10,470-5880cm(-1)) region, a FT-NIR spectrophotometer equipped with a transmission arm as the sampling tool, working in the 12,500-5800cm(-1) region, and a FT-MIR microscopy operating in the 4000-675cm(-1) region. Multivariate exploratory data analysis, in particular principal component analysis (PCA), was applied in order to extract useful information from original data and from hyperspectrograms. The results obtained demonstrate that the spectroscopic and imaging techniques investigated can represent an effective and sensitive tool to detect surface bacterial contamination in samples and, in particular, to recognise species to which bacteria belong.

  6. Calibration of Images with 3D range scanner data

    OpenAIRE

    Adalid López, Víctor Javier

    2009-01-01

    Projecte fet en col.laboració amb EPFL 3D laser range scanners are used in extraction of the 3D data in a scene. Main application areas are architecture, archeology and city planning. Thought the raw scanner data has a gray scale values, the 3D data can be merged with colour camera image values to get textured 3D model of the scene. Also these devices are able to take a reliable copy in 3D form objects, with a high level of accuracy. Therefore, they scanned scenes can be use...

  7. Performance Assessment of Wire-Scanners at CERN

    CERN Document Server

    Baud, G; Emery, J; Gras, JJ; Guerrero, A; Piselli, E

    2013-01-01

    This article describes the current fast wire-scanner devices installed in circular accelerators at CERN with an emphasis on the error studies carried out during the last two runs. At present the wire-scanners have similar acquisition systems but are varied in terms of mechanics. Several measurement campaigns were performed aimed at establishing optimal operational settings and to identify and assess systematic errors. In several cases the results led to direct performance improvements while in others this helped in defining the requirements for new detectors.

  8. Satellite orientation and position for geometric correction of scanner imagery.

    Science.gov (United States)

    Salamonowicz, P.H.

    1986-01-01

    The USGS Mini Image Processing System currently relies on a polynomial method for geometric correction of Landsat multispectral scanner (MSS) data. A large number of ground control points are required because polynomials do not model the sources of error. In order to reduce the number of necessary points, a set of mathematical equations modeling the Landsat satellite motions and MSS scanner has been derived and programmed. A best fit to the equations is obtained by using a least-squares technique that permits computation of the satellite orientation and position parameters based on only a few control points.-from Author

  9. Free-space wavelength-multiplexed optical scanner.

    Science.gov (United States)

    Yaqoob, Z; Rizvi, A A; Riza, N A

    2001-12-10

    A wavelength-multiplexed optical scanning scheme is proposed for deflecting a free-space optical beam by selection of the wavelength of the light incident on a wavelength-dispersive optical element. With fast tunable lasers or optical filters, this scanner features microsecond domain scan setting speeds and large- diameter apertures of several centimeters or more for subdegree angular scans. Analysis performed indicates an optimum scan range for a given diffraction order and grating period. Limitations include beam-spreading effects based on the varying scanner aperture sizes and the instantaneous information bandwidth of the data-carrying laser beam.

  10. Impact of lighting and attire on 3D scanner performance

    Science.gov (United States)

    Ajjimaporn, Pann; Feist, Dakota; Straub, Jeremy; Kerlin, Scott

    2015-05-01

    This paper considers the impact of lighting and attire on the performance of a previously created low-cost 3D scanning system. It considers the effect of adjusting the lighting configuration and of the subject's clothing on the quality of the scans and the number and types of objects that can be scanned. The experimentation performed tested different types (colors and textures) of clothing to assess which produced the best scans and multiple lighting configurations. This paper presents the results from this experimentation and, from this, make generalizations about optimizing visible light scanner performance before concluding with a discussion of scanner efficacy.

  11. Scanner baseliner monitoring and control in high volume manufacturing

    Science.gov (United States)

    Samudrala, Pavan; Chung, Woong Jae; Aung, Nyan; Subramany, Lokesh; Gao, Haiyong; Gomez, Juan-Manuel

    2016-03-01

    We analyze performance of different customized models on baseliner overlay data and demonstrate the reduction in overlay residuals by ~10%. Smart Sampling sets were assessed and compared with the full wafer measurements. We found that performance of the grid can still be maintained by going to one-third of total sampling points, while reducing metrology time by 60%. We also demonstrate the feasibility of achieving time to time matching using scanner fleet manager and thus identify the tool drifts even when the tool monitoring controls are within spec limits. We also explore the scanner feedback constant variation with illumination sources.

  12. Localization of a mobile laser scanner via dimensional reduction

    Science.gov (United States)

    Lehtola, Ville V.; Virtanen, Juho-Pekka; Vaaja, Matti T.; Hyyppä, Hannu; Nüchter, Andreas

    2016-11-01

    We extend the concept of intrinsic localization from a theoretical one-dimensional (1D) solution onto a 2D manifold that is embedded in a 3D space, and then recover the full six degrees of freedom for a mobile laser scanner with a simultaneous localization and mapping algorithm (SLAM). By intrinsic localization, we mean that no reference coordinate system, such as global navigation satellite system (GNSS), nor inertial measurement unit (IMU) are used. Experiments are conducted with a 2D laser scanner mounted on a rolling prototype platform, VILMA. The concept offers potential in being extendable to other wheeled platforms.

  13. A ’Millipede’ scanner model - Energy consumption and performance

    OpenAIRE

    Engelen, Johan B.C.; Khatib, Mohammed G.

    2008-01-01

    This short report (1) describes an energy model for the seek and read/write operations in a mass-balanced Y-scanner for parallel-probe storage by IBM [1] and (2) updates the settings of the MEMS model in DiskSim with recent published figures from this XY-scanner. To speedup system simulations, a straight forward second-order model is used without control loop. Read/write operation is modeled by quasi-static calculations. To approximate seek behavior, ’bang-bang’ control is assumed; the result...

  14. Estimating Single Tree Stem Volume of Pinus sylvestris Using Airborne Laser Scanner and Multispectral Line Scanner Data

    Directory of Open Access Journals (Sweden)

    Barbara Koch

    2011-05-01

    Full Text Available So far, only a few studies have been carried out in central European forests to estimate individual tree stem volume of pine trees from high resolution remote sensing data. In this article information derived from airborne laser scanner and multispectral line scanner data were tested to predict the stem volume of 178 pines (Pinus sylvestris in a study site in the south-west of Germany. First, tree crowns were automatically delineated using both multispectral and laser scanner data. Next, tree height, crown diameter and crown volume were derived for each crown segment. All combinations of the derived tree features were used as explanatory variables in allometric models to predict the stem volume. A model with tree height and crown diameter had the best performance with respect to the prediction accuracy determined by a leave-one-out cross-validation: Root Mean Square Error (RMSE = 24.02% and Bias = 1.36%.

  15. Viral diagnosis in Indian livestock using customized microarray chips.

    Science.gov (United States)

    Yadav, Brijesh S; Pokhriyal, Mayank; Ratta, Barkha; Kumar, Ajay; Saxena, Meeta; Sharma, Bhaskar

    2015-01-01

    Viral diagnosis in Indian livestock using customized microarray chips is gaining momentum in recent years. Hence, it is possible to design customized microarray chip for viruses infecting livestock in India. Customized microarray chips identified Bovine herpes virus-1 (BHV-1), Canine Adeno Virus-1 (CAV-1), and Canine Parvo Virus-2 (CPV-2) in clinical samples. Microarray identified specific probes were further confirmed using RT-PCR in all clinical and known samples. Therefore, the application of microarray chips during viral disease outbreaks in Indian livestock is possible where conventional methods are unsuitable. It should be noted that customized application requires a detailed cost efficiency calculation.

  16. Open issues in hyperspectral imaging for diagnostics on paintings: when high-spectral and spatial resolution turns into data redundancy

    Science.gov (United States)

    Cucci, Costanza; Casini, Andrea; Picollo, Marcello; Poggesi, Marco; Stefani, Lorenzo

    2011-06-01

    Hyper-Spectral Imaging (HSI) has emerged in the last decade as one of the most promising technologies for diagnostics and documentation of polychrome surfaces. Despite the fact that presently HSI is a well-established technique for non-invasive investigations on paintings, a number of technological issues remain open and are still topics for on-going studies. In particular, it is known that high spatial resolution is a crucial parameter for obtaining high quality images, whereas the possibility to identify pictorial materials strictly depends on the spectral resolution and on the extent of the spectral region investigated. At the same time, by increasing the sampling rates in both the spatial and spectral dimensions, the size of the data-set will be enlarged and the acquisition times will be lengthened. As a consequence, a good compromise between the acquisition of highquality data and their application should always be reached, taking into account the specific purposes of the HSI application. The above questions are discussed in the present work, which illustrates two applications of the latest version of a hyperspectral scanner designed at IFAC-CNR for the digitization of artworks. The prototype has recently been upgraded, with new visualization software as well as mechanical and optical improvements. This high performance system operates in the 400-1000nm spectral range, with a spectral resolution of about 2-3 nm and a spatial sampling of 0.1 mm over areas of about 1 m2. Three case-studies are presented, which highlight the importance of both high spatial and high spectral sampling rate in hyperspectral imaging. Two of the examples reported focus on the full exploitation of the spatial resolution: the first one is a study performed on a small painting, dated from the eighteenth century and belonging to the Uffizi Gallery in Florence; the second case-study refers to the valuable "Carrand diptych" (14th century) from the Bargello Museum in Florence. The last

  17. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  18. Protein microarrays: applications and future challenges.

    Science.gov (United States)

    Stoll, Dieter; Templin, Markus F; Bachmann, Jutta; Joos, Thomas O

    2005-03-01

    Within the last decade protein microarray technology has been successfully applied for the simultaneous identification, quantification and functional analysis of proteins in basic and applied proteome research. These miniaturized and parallelized assay systems have the potential to replace state-of-the-art singleplex analysis systems. However, prior to their general application in robust, reliable, routine and high-throughput applications it is mandatory that they demonstrate robustness, sensitivity, automation and appropriate pricing. In this review, the current state of protein microarray technology will be summarized. Recent applications for the simultaneous determination of a variety of parameters using only minute amounts of sample will be described and future challenges of this cutting-edge technology will be discussed.

  19. PMD: A Resource for Archiving and Analyzing Protein Microarray data.

    Science.gov (United States)

    Xu, Zhaowei; Huang, Likun; Zhang, Hainan; Li, Yang; Guo, Shujuan; Wang, Nan; Wang, Shi-Hua; Chen, Ziqing; Wang, Jingfang; Tao, Sheng-Ce

    2016-01-27

    Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

  20. Microarray for serotyping of Bartonella species

    OpenAIRE

    Raoult Didier; Nappez Claude; Bonhomme Cyrille J

    2007-01-01

    Abstract Background Bacteria of the genus Bartonella are responsible for a large variety of human and animal diseases. Serological typing of Bartonella is a method that can be used for differentiation and identification of Bartonella subspecies. Results We have developed a novel multiple antigenic microarray to serotype Bartonella strains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29 Bartonella strains. We then tested the microarra...

  1. Undetected sex chromosome aneuploidy by chromosomal microarray.

    Science.gov (United States)

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay

    2012-11-01

    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting.

  2. Hybridization thermodynamics of NimbleGen Microarrays

    Directory of Open Access Journals (Sweden)

    Posekany Alexandra

    2010-01-01

    Full Text Available Abstract Background While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets. Results We demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex. Conclusions This analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals.

  3. Weighted analysis of general microarray experiments

    Directory of Open Access Journals (Sweden)

    Kristiansson Erik

    2007-10-01

    Full Text Available Abstract Background In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be invalid and typically lead to too optimistic p-values. A method called WAME has been proposed where a variance is estimated for each sample and a covariance is estimated for each pair of samples. The current version of WAME is, however, limited to experiments with paired design, e.g. two-channel microarrays. Results The WAME procedure is extended to general microarray experiments, making it capable of handling both one- and two-channel datasets. Two public one-channel datasets are analysed and WAME detects both unequal variances and correlations. WAME is compared to other common methods: fold-change ranking, ordinary linear model with t-tests, LIMMA and weighted LIMMA. The p-value distributions are shown to differ greatly between the examined methods. In a resampling-based simulation study, the p-values generated by WAME are found to be substantially more correct than the alternatives when a relatively small proportion of the genes is regulated. WAME is also shown to have higher power than the other methods. WAME is available as an R-package. Conclusion The WAME procedure is generalized and the limitation to paired-design microarray datasets is removed. The examined other methods produce invalid p-values in many cases, while WAME is shown to produce essentially valid p-values when a relatively small proportion of genes is regulated. WAME is also shown to have higher power than the examined alternative methods.

  4. Linking microarray reporters with protein functions

    Directory of Open Access Journals (Sweden)

    Gaj Stan

    2007-09-01

    Full Text Available Abstract Background The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Conclusion Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.

  5. Hyperspectral image reconstruction using RGB color for foodborne pathogen detection on agar plates

    Science.gov (United States)

    Yoon, Seung-Chul; Shin, Tae-Sung; Park, Bosoon; Lawrence, Kurt C.; Heitschmidt, Gerald W.

    2014-03-01

    This paper reports the latest development of a color vision technique for detecting colonies of foodborne pathogens grown on agar plates with a hyperspectral image classification model that was developed using full hyperspectral data. The hyperspectral classification model depended on reflectance spectra measured in the visible and near-infrared spectral range from 400 and 1,000 nm (473 narrow spectral bands). Multivariate regression methods were used to estimate and predict hyperspectral data from RGB color values. The six representative non-O157 Shiga-toxin producing Eschetichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) were grown on Rainbow agar plates. A line-scan pushbroom hyperspectral image sensor was used to scan 36 agar plates grown with pure STEC colonies at each plate. The 36 hyperspectral images of the agar plates were divided in half to create training and test sets. The mean Rsquared value for hyperspectral image estimation was about 0.98 in the spectral range between 400 and 700 nm for linear, quadratic and cubic polynomial regression models and the detection accuracy of the hyperspectral image classification model with the principal component analysis and k-nearest neighbors for the test set was up to 92% (99% with the original hyperspectral images). Thus, the results of the study suggested that color-based detection may be viable as a multispectral imaging solution without much loss of prediction accuracy compared to hyperspectral imaging.

  6. Microarray for serotyping of Bartonella species

    Directory of Open Access Journals (Sweden)

    Raoult Didier

    2007-06-01

    Full Text Available Abstract Background Bacteria of the genus Bartonella are responsible for a large variety of human and animal diseases. Serological typing of Bartonella is a method that can be used for differentiation and identification of Bartonella subspecies. Results We have developed a novel multiple antigenic microarray to serotype Bartonella strains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29 Bartonella strains. We then tested the microarray for serotyping of Bartonella strains and defining the profile of monoclonal antibodies. Bartonella strains gave a strong positive signal and all were correctly identified. Screening of monoclonal antibodies towards the Gro EL protein of B. clarridgeiae identified 3 groups of antibodies, which were observed with variable affinities against Bartonella strains. Conclusion We demonstrated that microarray of spotted bacteria can be a practical tool for serotyping of unidentified strains or species (and also for affinity determination by polyclonal and monoclonal antibodies. This could be used in research and for identification of bacterial strains.

  7. Chicken sperm transcriptome profiling by microarray analysis.

    Science.gov (United States)

    Singh, R P; Shafeeque, C M; Sharma, S K; Singh, R; Mohan, J; Sastry, K V H; Saxena, V K; Azeez, P A

    2016-03-01

    It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development. Therefore, we attempted to characterize transcriptome of the sperm of fertile chickens using microarray analysis. Spermatozoal RNA was pooled from 10 fertile males and used for RNA preparation. Prior to performing the microarray, RNA quality was assessed using a bioanalyzer, and gDNA and somatic cell RNA contamination was assessed by CD4 and PTPRC gene amplification. The chicken sperm transcriptome was cross-examined by analysing sperm and testes RNA on a 4 × 44K chicken array, and results were verified by RT-PCR. Microarray analysis identified 21,639 predominantly nuclear-encoded transcripts in chicken sperm. The majority (66.55%) of the sperm transcripts were shared with the testes, while surprisingly, 33.45% transcripts were detected (raw signal intensity greater than 50) only in the sperm and not in the testes. The greatest proportion of up-regulated transcripts were responsible for signal transduction (63.20%) followed by embryonic development (56.76%) and cell structure (56.25%). Of the 20 most abundant transcripts, 18 remain uncharacterized, whereas the least abundant genes were mostly associated with the ribosome. These findings lay a foundation for more detailed investigations on sperm RNAs in chickens to identify sperm-based biomarkers for fertility.

  8. Microarrays for rapid identification of plant viruses.

    Science.gov (United States)

    Boonham, Neil; Tomlinson, Jenny; Mumford, Rick

    2007-01-01

    Many factors affect the development and application of diagnostic techniques. Plant viruses are an inherently diverse group that, unlike cellular pathogens, possess no nucleotide sequence type (e.g., ribosomal RNA sequences) in common. Detection of plant viruses is becoming more challenging as globalization of trade, particularly in ornamentals, and the potential effects of climate change enhance the movement of viruses and their vectors, transforming the diagnostic landscape. Techniques for assessing seed, other propagation materials and field samples for the presence of specific viruses include biological indexing, electron microscopy, antibody-based detection, including enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and microarray detection. Of these, microarray detection provides the greatest capability for parallel yet specific testing, and can be used to detect individual, or combinations of viruses and, using current approaches, to do so with a sensitivity comparable to ELISA. Methods based on PCR provide the greatest sensitivity among the listed techniques but are limited in parallel detection capability even in "multiplexed" applications. Various aspects of microarray technology, including probe development, array fabrication, assay target preparation, hybridization, washing, scanning, and interpretation are presented and discussed, for both current and developing technology.

  9. An imputation approach for oligonucleotide microarrays.

    Directory of Open Access Journals (Sweden)

    Ming Li

    Full Text Available Oligonucleotide microarrays are commonly adopted for detecting and qualifying the abundance of molecules in biological samples. Analysis of microarray data starts with recording and interpreting hybridization signals from CEL images. However, many CEL images may be blemished by noises from various sources, observed as "bright spots", "dark clouds", and "shadowy circles", etc. It is crucial that these image defects are correctly identified and properly processed. Existing approaches mainly focus on detecting defect areas and removing affected intensities. In this article, we propose to use a mixed effect model for imputing the affected intensities. The proposed imputation procedure is a single-array-based approach which does not require any biological replicate or between-array normalization. We further examine its performance by using Affymetrix high-density SNP arrays. The results show that this imputation procedure significantly reduces genotyping error rates. We also discuss the necessary adjustments for its potential extension to other oligonucleotide microarrays, such as gene expression profiling. The R source code for the implementation of approach is freely available upon request.

  10. A New Distribution Family for Microarray Data

    Directory of Open Access Journals (Sweden)

    Diana Mabel Kelmansky

    2017-02-01

    Full Text Available The traditional approach with microarray data has been to apply transformations that approximately normalize them, with the drawback of losing the original scale. The alternative stand point taken here is to search for models that fit the data, characterized by the presence of negative values, preserving their scale; one advantage of this strategy is that it facilitates a direct interpretation of the results. A new family of distributions named gpower-normal indexed by p∈R is introduced and it is proven that these variables become normal or truncated normal when a suitable gpower transformation is applied. Expressions are given for moments and quantiles, in terms of the truncated normal density. This new family can be used to model asymmetric data that include non-positive values, as required for microarray analysis. Moreover, it has been proven that the gpower-normal family is a special case of pseudo-dispersion models, inheriting all the good properties of these models, such as asymptotic normality for small variances. A combined maximum likelihood method is proposed to estimate the model parameters, and it is applied to microarray and contamination data. Rcodes are available from the authors upon request.

  11. Demonstration: A smartphone 3D functional brain scanner

    DEFF Research Database (Denmark)

    Stahlhut, Carsten; Stopczynski, Arkadiusz; Larsen, Jakob Eg

    We demonstrate a fully portable 3D real-time functional brain scanner consisting of a wireless 14-channel ‘Neuroheadset‘ (Emotiv EPOC) and a Nokia N900 smartphone. The novelty of our system is the ability to perform real-time functional brain imaging on a smartphone device, including stimulus del......, tablet computers, and netbooks) that are based on Linux operating systems....

  12. Feature-space transformation improves supervised segmentation across scanners

    DEFF Research Database (Denmark)

    van Opbroek, Annegreet; Achterberg, Hakim C.; de Bruijne, Marleen

    2015-01-01

    Image-segmentation techniques based on supervised classification generally perform well on the condition that training and test samples have the same feature distribution. However, if training and test images are acquired with different scanners or scanning parameters, their feature distributions...

  13. Free-space wavelength-multiplexed optical scanner demonstration.

    Science.gov (United States)

    Yaqoob, Zahid; Riza, Nabeel A

    2002-09-10

    Experimental demonstration of a no-moving-parts free-space wavelength-multiplexed optical scanner (W-MOS) is presented. With fast tunable lasers or optical filters and planar wavelength dispersive elements such as diffraction gratings, this microsecond-speed scanner enables large several-centimeter apertures for subdegree angular scans. The proposed W-MOS design incorporates a unique optical amplifier and variable optical attenuator combination that enables the calibration and modulation of the scanner response, leading to any desired scanned laser beam power shaping. The experimental setup uses a tunable laser centered at 1560 nm and a 600-grooves/mm blazed reflection grating to accomplish an angular scan of 12.92 degrees as the source is tuned over an 80-nm bandwidth. The values for calculated maximum optical beam divergance, required wavelength resolution, beam-pointing accuracy, and measured scanner insertion loss are 1.076 mrad, 0.172 nm, 0.06 mrad, and 4.88 dB, respectively.

  14. Measurement Report for the PS-boosterWire Scanner

    CERN Document Server

    Vollinger, Christine; Kramer, Patrick; CERN. Geneva. ATS Department

    2017-01-01

    This Note discusses the EM-measurements carried out on the prototype of the PS-Booster wire scanner. The aim of these measurements was to identify intrinsic resonances that are to be evaluated for their contribution to the longitudinal beam impedance of the machine.

  15. Sea surface temperature mapping using a thermal infrared scanner

    Digital Repository Service at National Institute of Oceanography (India)

    RameshKumar, M.R.; Pandya, R.M.; Mathur, K.M.; Charyulu, R.J.K.; Rao, L.V.G.

    1 metre water column below the sea surface. A thermal infrared scanner developed by the Space Applications Centre (ISRO), Ahmedabad was operated on board R.V. Gaveshani in April/May 1984 for mapping SST over the eastern Arabian Sea. SST values...

  16. Phosphor Scanner For Imaging X-Ray Diffraction

    Science.gov (United States)

    Carter, Daniel C.; Hecht, Diana L.; Witherow, William K.

    1992-01-01

    Improved optoelectronic scanning apparatus generates digitized image of x-ray image recorded in phosphor. Scanning fiber-optic probe supplies laser light stimulating luminescence in areas of phosphor exposed to x rays. Luminescence passes through probe and fiber to integrating sphere and photomultiplier. Sensitivity and resolution exceed previously available scanners. Intended for use in x-ray crystallography, medical radiography, and molecular biology.

  17. Scanners, optical character readers, Cyrillic alphabet and Russian translations

    Science.gov (United States)

    Johnson, Gordon G.

    1995-01-01

    The writing of code for capture, in a uniform format, of bit maps of words and characters from scanner PICT files is presented. The coding of Dynamic Pattern Matched for the identification of the characters, words and sentences in preparation for translation is discussed.

  18. Benchmarking Advanced Control Algorithms for a Laser Scanner System

    DEFF Research Database (Denmark)

    Stoustrup, Jakob; Ordys, A.W.; Smillie, I.

    1996-01-01

    The paper describes tests performed on the laser scanner system toassess feasibility of modern control techniques in achieving a requiredperformance in the trajectory following problem. The two methods tested areQTR H-infinity and Predictive Control. The results are ilustated ona simulation example....

  19. MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs

    Directory of Open Access Journals (Sweden)

    Ferhatosmanoglu Nilgun

    2009-09-01

    Full Text Available Abstract Background Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. Description An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided. Conclusion A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http://db.cse.ohio-state.edu/MicroarrayDesigner. Source code and binary distributions are available for academic use upon request.

  20. Principle of small target detection for hyperspectral imagery

    Institute of Scientific and Technical Information of China (English)

    GENG XiuRui; ZHAO Yongchao

    2007-01-01

    This paper generalizes the progress of algorithms in small target detection for hyperspectral imaging,and finds that whitening the image is the key point of many methods in small target detection. An algorithm is presented to detect desired targets by converting large targets into small ones based on the weighted sample autocorrelation matrix.

  1. Consideration of smoothing techniques for hyperspectral remote sensing

    NARCIS (Netherlands)

    Vaiphasa, C.

    2006-01-01

    Spectral smoothing filters are popularly used in a large number of modern hyperspectral remote sensing studies for removing noise from the data. However, most of these studies subjectively apply ad hoc measures to select filter types and their parameters. We argue that this subjectively minded appro

  2. An airborne pushbroom hyperspectral imager with wide field of view

    Institute of Scientific and Technical Information of China (English)

    Peixin Hu; Qirnin Lu; Rong Shu; Jianyu Wang

    2005-01-01

    @@ An airborne pushbroom hyperspectral imager (APHI) with wide field (42° field of view) is presented.It is composed of two 22°field of view (FOV) imagers and can provide 1304 pixels in spatial dimension,124 bands in spectral dimension in one frame. APHI has a bandwidth ranging from 400 to 900 nm.

  3. Classification of Salmonella serotypes with hyperspectral microscope imagery

    Science.gov (United States)

    Previous research has demonstrated an optical method with acousto-optic tunable filter (AOTF) based hyperspectral microscope imaging (HMI) had potential for classifying gram-negative from gram-positive foodborne pathogenic bacteria rapidly and nondestructively with a minimum sample preparation. In t...

  4. Superpixel sparse representation for target detection in hyperspectral imagery

    Science.gov (United States)

    Dong, Chunhua; Naghedolfeizi, Masoud; Aberra, Dawit; Qiu, Hao; Zeng, Xiangyan

    2017-05-01

    Sparse Representation (SR) is an effective classification method. Given a set of data vectors, SR aims at finding the sparsest representation of each data vector among the linear combinations of the bases in a given dictionary. In order to further improve the classification performance, the joint SR that incorporates interpixel correlation information of neighborhoods has been proposed for image pixel classification. However, SR and joint SR demand significant amount of computational time and memory, especially when classifying a large number of pixels. To address this issue, we propose a superpixel sparse representation (SSR) algorithm for target detection in hyperspectral imagery. We firstly cluster hyperspectral pixels into nearly uniform hyperspectral superpixels using our proposed patch-based SLIC approach based on their spectral and spatial information. The sparse representations of these superpixels are then obtained by simultaneously decomposing superpixels over a given dictionary consisting of both target and background pixels. The class of a hyperspectral pixel is determined by a competition between its projections on target and background subdictionaries. One key advantage of the proposed superpixel representation algorithm with respect to pixelwise and joint sparse representation algorithms is that it reduces computational cost while still maintaining competitive classification performance. We demonstrate the effectiveness of the proposed SSR algorithm through experiments on target detection in the in-door and out-door scene data under daylight illumination as well as the remote sensing data. Experimental results show that SSR generally outperforms state of the art algorithms both quantitatively and qualitatively.

  5. [Hyperspectral image compression technology research based on EZW].

    Science.gov (United States)

    Wei, Jun-Xia; Xiangli, Bin; Duan, Xiao-Feng; Xu, Zhao-Hui; Xue, Li-Jun

    2011-08-01

    Along with the development of hyperspectral remote sensing technology, hyperspectral imaging technology has been applied in the aspect of aviation and spaceflight, which is different from multispectral imaging, and with the band width of nanoscale spectral imaging the target continuously, the image resolution is very high. However, with the increasing number of band, spectral data quantity will be more and more, and these data storage and transmission is the problem that the authors must face. Along with the development of wavelet compression technology, in field of image compression, many people adopted and improved EZW, the present paper used the method in hyperspectral spatial dimension compression, but does not involved the spectrum dimension compression. From hyperspectral image compression reconstruction results, whether from the peak signal-to-noise ratio (PSNR) and spectral curve or from the subjective comparison of source and reconstruction image, the effect is well. If the first compression of image from spectrum dimension is made, then compression on space dimension, the authors believe the effect will be better.

  6. Advances in Spectral-Spatial Classification of Hyperspectral Images

    Science.gov (United States)

    Fauvel, Mathieu; Tarabalka, Yuliya; Benediktsson, Jon Atli; Chanussot, Jocelyn; Tilton, James C.

    2012-01-01

    Recent advances in spectral-spatial classification of hyperspectral images are presented in this paper. Several techniques are investigated for combining both spatial and spectral information. Spatial information is extracted at the object (set of pixels) level rather than at the conventional pixel level. Mathematical morphology is first used to derive the morphological profile of the image, which includes characteristics about the size, orientation and contrast of the spatial structures present in the image. Then the morphological neighborhood is defined and used to derive additional features for classification. Classification is performed with support vector machines using the available spectral information and the extracted spatial information. Spatial post-processing is next investigated to build more homogeneous and spatially consistent thematic maps. To that end, three presegmentation techniques are applied to define regions that are used to regularize the preliminary pixel-wise thematic map. Finally, a multiple classifier system is defined to produce relevant markers that are exploited to segment the hyperspectral image with the minimum spanning forest algorithm. Experimental results conducted on three real hyperspectral images with different spatial and spectral resolutions and corresponding to various contexts are presented. They highlight the importance of spectral-spatial strategies for the accurate classification of hyperspectral images and validate the proposed methods.

  7. Interpretation of Absorption Bands in Airborne Hyperspectral Radiance Data

    Directory of Open Access Journals (Sweden)

    W. David Miller

    2009-04-01

    Full Text Available It is demonstrated that hyperspectral imagery can be used, without atmospheric correction, to determine the presence of accessory phytoplankton pigments in coastal waters using derivative techniques. However, care must be taken not to confuse other absorptions for those caused by the presence of pigments. Atmospheric correction, usually the first step to making products from hyperspectral data, may not completely remove Fraunhofer lines and atmospheric absorption bands and these absorptions may interfere with identification of phytoplankton accessory pigments. Furthermore, the ability to resolve absorption bands depends on the spectral resolution of the spectrometer, which for a fixed spectral range also determines the number of observed bands. Based on this information, a study was undertaken to determine under what circumstances a hyperspectral sensor may determine the presence of pigments. As part of the study a hyperspectral imager was used to take high spectral resolution data over two different water masses. In order to avoid the problems associated with atmospheric correction this data was analyzed as radiance data without atmospheric correction. Here, the purpose was to identify spectral regions that might be diagnostic for photosynthetic pigments. Two well proven techniques were used to aid in absorption band recognition, the continuum removal of the spectra and the fourth derivative. The findings in this study suggest that interpretation of absorption bands in remote sensing data, whether atmospherically corrected or not, have to be carefully reviewed when they are interpreted in terms of photosynthetic pigments.

  8. Detecting red blotch disease in grape leaves using hyperspectral imaging

    Science.gov (United States)

    Mehrubeoglu, Mehrube; Orlebeck, Keith; Zemlan, Michael J.; Autran, Wesley

    2016-05-01

    Red blotch disease is a viral disease that affects grapevines. Symptoms appear as irregular blotches on grape leaves with pink and red veins on the underside of the leaves. Red blotch disease causes a reduction in the accumulation of sugar in grapevines affecting the quality of grapes and resulting in delayed harvest. Detecting and monitoring this disease early is important for grapevine management. This work focuses on the use of hyperspectral imaging for detection and mapping red blotch disease in grape leaves. Grape leaves with known red blotch disease have been imaged with a portable hyperspectral imaging system both on and off the vine to investigate the spectral signature of red blotch disease as well as to identify the diseased areas on the leaves. Modified reflectance calculated at spectral bands corresponding to 566 nm (green) and 628 nm (red), and modified reflectance ratios computed at two sets of bands (566 nm / 628 nm, 680 nm / 738 nm) were selected as effective features to differentiate red blotch from healthy-looking and dry leaf. These two modified reflectance and two ratios of modified reflectance values were then used to train the support vector machine classifier in a supervised learning scheme. Once the SVM classifier was defined, two-class classification was achieved for grape leaf hyperspectral images. Identification of the red blotch disease on grape leaves as well as mapping different stages of the disease using hyperspectral imaging are presented in this paper.

  9. Consideration of smoothing techniques for hyperspectral remote sensing

    NARCIS (Netherlands)

    Vaiphasa, C.

    2006-01-01

    Spectral smoothing filters are popularly used in a large number of modern hyperspectral remote sensing studies for removing noise from the data. However, most of these studies subjectively apply ad hoc measures to select filter types and their parameters. We argue that this subjectively minded

  10. Advances in Spectral-Spatial Classification of Hyperspectral Images

    Science.gov (United States)

    Fauvel, Mathieu; Tarabalka, Yuliya; Benediktsson, Jon Atli; Chanussot, Jocelyn; Tilton, James C.

    2012-01-01

    Recent advances in spectral-spatial classification of hyperspectral images are presented in this paper. Several techniques are investigated for combining both spatial and spectral information. Spatial information is extracted at the object (set of pixels) level rather than at the conventional pixel level. Mathematical morphology is first used to derive the morphological profile of the image, which includes characteristics about the size, orientation, and contrast of the spatial structures present in the image. Then, the morphological neighborhood is defined and used to derive additional features for classification. Classification is performed with support vector machines (SVMs) using the available spectral information and the extracted spatial information. Spatial postprocessing is next investigated to build more homogeneous and spatially consistent thematic maps. To that end, three presegmentation techniques are applied to define regions that are used to regularize the preliminary pixel-wise thematic map. Finally, a multiple-classifier (MC) system is defined to produce relevant markers that are exploited to segment the hyperspectral image with the minimum spanning forest algorithm. Experimental results conducted on three real hyperspectral images with different spatial and spectral resolutions and corresponding to various contexts are presented. They highlight the importance of spectral–spatial strategies for the accurate classification of hyperspectral images and validate the proposed methods.

  11. Fast algorithm for exploring and compressing of large hyperspectral images

    DEFF Research Database (Denmark)

    Kucheryavskiy, Sergey

    2011-01-01

    A new method for calculation of latent variable space for exploratory analysis and dimension reduction of large hyperspectral images is proposed. The method is based on significant downsampling of image pixels with preservation of pixels’ structure in feature (variable) space. To achieve this, in...

  12. Principle of small target detection for hyperspectral imagery

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper generalizes the progress of algorithms in small target detection for hyperspectral imaging, and finds that whitening the image is the key point of many methods in small target detection. An al-gorithm is presented to detect desired targets by converting large targets into small ones based on the weighted sample autocorrelation matrix.

  13. Shortwave infrared hyperspectral Imaging for cotton foreign matter classification

    Science.gov (United States)

    Various types of cotton foreign matter seriously reduce the commercial value of cotton lint and further degrade the quality of textile products for consumers. This research was aimed to investigate the potential of a non-contact technique, i.e., liquid crystal tunable filter (LCTF) hyperspectral ima...

  14. Hyperspectral Data, Change Detection and the MAD Transformation

    DEFF Research Database (Denmark)

    Nielsen, Allan Aasbjerg; Müller, Andreas; Dorigo, Wouter

    2004-01-01

    This paper deals with the application of the MAD transformation to change detection in bi-tempotal hyperspectral data. Several processing schemes are proposed in order to facilitate both the actual change detection, the many variables involved and the spatial nature of the data....

  15. Recent Advances in Techniques for Hyperspectral Image Processing

    Science.gov (United States)

    Plaza, Antonio; Benediktsson, Jon Atli; Boardman, Joseph W.; Brazile, Jason; Bruzzone, Lorenzo; Camps-Valls, Gustavo; Chanussot, Jocelyn; Fauvel, Mathieu; Gamba, Paolo; Gualtieri, Anthony; Marconcini, Mattia; Tilton, James C.; Trianni, Giovanna

    2009-01-01

    Imaging spectroscopy, also known as hyperspectral imaging, has been transformed in less than 30 years from being a sparse research tool into a commodity product available to a broad user community. Currently, there is a need for standardized data processing techniques able to take into account the special properties of hyperspectral data. In this paper, we provide a seminal view on recent advances in techniques for hyperspectral image processing. Our main focus is on the design of techniques able to deal with the highdimensional nature of the data, and to integrate the spatial and spectral information. Performance of the discussed techniques is evaluated in different analysis scenarios. To satisfy time-critical constraints in specific applications, we also develop efficient parallel implementations of some of the discussed algorithms. Combined, these parts provide an excellent snapshot of the state-of-the-art in those areas, and offer a thoughtful perspective on future potentials and emerging challenges in the design of robust hyperspectral imaging algorithms

  16. Identification of seedling cabbages and weeds using hyperspectral imaging

    Science.gov (United States)

    Target detectionis one of research focues for precision chemical application. This study developed a method to identify seedling cabbages and weeds using hyperspectral spectral imaging. In processing the image data, with ENVI software, after dimension reduction, noise reduction, de-correlation for h...

  17. Physics-based Detection of Subpixel Targets in Hyperspectral Imagery

    Science.gov (United States)

    2007-01-01

    IEEE Proceedings of the1999 Aerospace Conference, vol. 4, pp 177-181, March 1999. [4] E. A. Ashton and A. Schaum , “Algorithms for the detection...34Anomaly Detection from Hyperspectral Imagery," IEEE Signal Processing Magazine, vol. 19, no. 1, pp. 58-69, January 2002. [104] A.D. Stocker and P. Schaum

  18. Feature Selection on Hyperspectral Data for Dismount Skin Analysis

    Science.gov (United States)

    2014-03-27

    USA, 2010. ADA511354. [37] Nunez, A. and M. Mendenhall . “Detection of Human Skin in Near Infrared Hyperspectral Imagery”. Geoscience and Remote...Sensing Symposium, 2008. IGARSS 2008. IEEE International, volume 2, II–621 –II–624. july 2008. [38] Nunez, A., M. Mendenhall , and K. Gross. “Melanosome

  19. Hyperspectral Based Skin Detection for Person of Interest Identification

    Science.gov (United States)

    2015-03-01

    pp. 91–98. [8] A.S. Nunez and Michael J. Mendenhall , “Detection of human skin in near infrared hyperspectral imagery,” in Geoscience and Remote Sensing...Symposium, 2008. IGARSS 2008. IEEE International, July 2008, vol. 2, pp. II–621–II–624. [9] A.S. Nunez, Michael J. Mendenhall , and K. Gross

  20. Hyperspectral image visualization using t-distributed stochastic neighbor embedding

    Science.gov (United States)

    Zhang, Biyin; Yu, Xin

    2015-12-01

    Hyperspectral image visualization reduces high-dimensional spectral bands to three color channels, which are sought in order to explain well the nonlinear data characteristics that are hidden in the high-dimensional spectral bands. Despite the surge in the linear visualization techniques, the development of nonlinear visualization has been limited. The paper presents a new technique for visualization of hyperspectral image using t-distributed stochastic neighbor embedding, called VHI-tSNE, which learns a nonlinear mapping between the high-dimensional spectral space and the three-dimensional color space. VHI-tSNE transforms hyperspectral data into bilateral probability similarities, and employs a heavy-tailed distribution in three-dimensional color space to alleviate the crowding problem and optimization problem in SNE technique. We evaluate the performance of VHI-tSNE in experiments on several hyperspectral imageries, in which we compare it to the performance of other state-of-art techniques. The results of experiments demonstrated the strength of the proposed technique.