Accelerator-based Single-shot Ultrafast Transmission Electron Microscope with Picosecond Temporal Resolution and Nanometer Spatial Resolution

OpenAIRE

Xiang, D.; Fu, F.; Zhang, J.; Huang, X.; Wang, L.; Wang, X.; Wan, W.

2014-01-01

We present feasibility study of an accelerator-based ultrafast transmission electron microscope (u-TEM) capable of producing a full field image in a single-shot with simultaneous picosecond temporal resolution and nanometer spatial resolution. We study key physics related to performance of u-TEMs, and discuss major challenges as well as possible solutions for practical realization of u-TEMs. The feasibility of u-TEMs is confirmed through simulations using realistic electron beam parameters. W...

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

Directory of Open Access Journals (Sweden)

María Muñoz-Amatriaín

2011-11-01

Full Text Available Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a single nucleotide polymorphism (SNP-based genotyping platform was developed and used to genotype 373 individuals in four barley ( L. mapping populations. This led to a 2943 SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

High resolution optical DNA mapping

Science.gov (United States)

Baday, Murat

Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

High-resolution mapping of forest carbon stocks in the Colombian Amazon

Directory of Open Access Journals (Sweden)

G. P. Asner

2012-07-01

Full Text Available High-resolution mapping of tropical forest carbon stocks can assist forest management and improve implementation of large-scale carbon retention and enhancement programs. Previous high-resolution approaches have relied on field plot and/or light detection and ranging (LiDAR samples of aboveground carbon density, which are typically upscaled to larger geographic areas using stratification maps. Such efforts often rely on detailed vegetation maps to stratify the region for sampling, but existing tropical forest maps are often too coarse and field plots too sparse for high-resolution carbon assessments. We developed a top-down approach for high-resolution carbon mapping in a 16.5 million ha region (> 40% of the Colombian Amazon – a remote landscape seldom documented. We report on three advances for large-scale carbon mapping: (i employing a universal approach to airborne LiDAR-calibration with limited field data; (ii quantifying environmental controls over carbon densities; and (iii developing stratification- and regression-based approaches for scaling up to regions outside of LiDAR coverage. We found that carbon stocks are predicted by a combination of satellite-derived elevation, fractional canopy cover and terrain ruggedness, allowing upscaling of the LiDAR samples to the full 16.5 million ha region. LiDAR-derived carbon maps have 14% uncertainty at 1 ha resolution, and the regional map based on stratification has 28% uncertainty in any given hectare. High-resolution approaches with quantifiable pixel-scale uncertainties will provide the most confidence for monitoring changes in tropical forest carbon stocks. Improved confidence will allow resource managers and decision makers to more rapidly and effectively implement actions that better conserve and utilize forests in tropical regions.

Accelerator-based single-shot ultrafast transmission electron microscope with picosecond temporal resolution and nanometer spatial resolution

Science.gov (United States)

Xiang, D.; Fu, F.; Zhang, J.; Huang, X.; Wang, L.; Wang, X.; Wan, W.

2014-09-01

We present feasibility study of an accelerator-based ultrafast transmission electron microscope (u-TEM) capable of producing a full field image in a single-shot with simultaneous picosecond temporal resolution and nanometer spatial resolution. We study key physics related to performance of u-TEMs and discuss major challenges as well as possible solutions for practical realization of u-TEMs. The feasibility of u-TEMs is confirmed through simulations using realistic electron beam parameters. We anticipate that u-TEMs with a product of temporal and spatial resolution beyond 10-19 ms will open up new opportunities in probing matter at ultrafast temporal and ultrasmall spatial scales.

Stable long-term chronic brain mapping at the single-neuron level.

Science.gov (United States)

Fu, Tian-Ming; Hong, Guosong; Zhou, Tao; Schuhmann, Thomas G; Viveros, Robert D; Lieber, Charles M

2016-10-01

Stable in vivo mapping and modulation of the same neurons and brain circuits over extended periods is critical to both neuroscience and medicine. Current electrical implants offer single-neuron spatiotemporal resolution but are limited by such factors as relative shear motion and chronic immune responses during long-term recording. To overcome these limitations, we developed a chronic in vivo recording and stimulation platform based on flexible mesh electronics, and we demonstrated stable multiplexed local field potentials and single-unit recordings in mouse brains for at least 8 months without probe repositioning. Properties of acquired signals suggest robust tracking of the same neurons over this period. This recording and stimulation platform allowed us to evoke stable single-neuron responses to chronic electrical stimulation and to carry out longitudinal studies of brain aging in freely behaving mice. Such advantages could open up future studies in mapping and modulating changes associated with learning, aging and neurodegenerative diseases.

Single image super resolution algorithm based on edge interpolation in NSCT domain

Science.gov (United States)

Zhang, Mengqun; Zhang, Wei; He, Xinyu

2017-11-01

In order to preserve the texture and edge information and to improve the space resolution of single frame, a superresolution algorithm based on Contourlet (NSCT) is proposed. The original low resolution image is transformed by NSCT, and the directional sub-band coefficients of the transform domain are obtained. According to the scale factor, the high frequency sub-band coefficients are amplified by the interpolation method based on the edge direction to the desired resolution. For high frequency sub-band coefficients with noise and weak targets, Bayesian shrinkage is used to calculate the threshold value. The coefficients below the threshold are determined by the correlation among the sub-bands of the same scale to determine whether it is noise and de-noising. The anisotropic diffusion filter is used to effectively enhance the weak target in the low contrast region of the target and background. Finally, the high-frequency sub-band is amplified by the bilinear interpolation method to the desired resolution, and then combined with the high-frequency subband coefficients after de-noising and small target enhancement, the NSCT inverse transform is used to obtain the desired resolution image. In order to verify the effectiveness of the proposed algorithm, the proposed algorithm and several common image reconstruction methods are used to test the synthetic image, motion blurred image and hyperspectral image, the experimental results show that compared with the traditional single resolution algorithm, the proposed algorithm can obtain smooth edges and good texture features, and the reconstructed image structure is well preserved and the noise is suppressed to some extent.

High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

Science.gov (United States)

MacFaden, Sean W.; O'Neil-Dunne, Jarlath P. M.; Royar, Anna R.; Lu, Jacqueline W. T.; Rundle, Andrew G.

2012-01-01

Urban tree canopy is widely believed to have myriad environmental, social, and human-health benefits, but a lack of precise canopy estimates has hindered quantification of these benefits in many municipalities. This problem was addressed for New York City using object-based image analysis (OBIA) to develop a comprehensive land-cover map, including tree canopy to the scale of individual trees. Mapping was performed using a rule-based expert system that relied primarily on high-resolution LIDAR, specifically its capacity for evaluating the height and texture of aboveground features. Multispectral imagery was also used, but shadowing and varying temporal conditions limited its utility. Contextual analysis was a key part of classification, distinguishing trees according to their physical and spectral properties as well as their relationships to adjacent, nonvegetated features. The automated product was extensively reviewed and edited via manual interpretation, and overall per-pixel accuracy of the final map was 96%. Although manual editing had only a marginal effect on accuracy despite requiring a majority of project effort, it maximized aesthetic quality and ensured the capture of small, isolated trees. Converting high-resolution LIDAR and imagery into usable information is a nontrivial exercise, requiring significant processing time and labor, but an expert system-based combination of OBIA and manual review was an effective method for fine-scale canopy mapping in a complex urban environment.

Machine Learning Based Single-Frame Super-Resolution Processing for Lensless Blood Cell Counting

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Xiwei Huang

2016-11-01

Full Text Available A lensless blood cell counting system integrating microfluidic channel and a complementary metal oxide semiconductor (CMOS image sensor is a promising technique to miniaturize the conventional optical lens based imaging system for point-of-care testing (POCT. However, such a system has limited resolution, making it imperative to improve resolution from the system-level using super-resolution (SR processing. Yet, how to improve resolution towards better cell detection and recognition with low cost of processing resources and without degrading system throughput is still a challenge. In this article, two machine learning based single-frame SR processing types are proposed and compared for lensless blood cell counting, namely the Extreme Learning Machine based SR (ELMSR and Convolutional Neural Network based SR (CNNSR. Moreover, lensless blood cell counting prototypes using commercial CMOS image sensors and custom designed backside-illuminated CMOS image sensors are demonstrated with ELMSR and CNNSR. When one captured low-resolution lensless cell image is input, an improved high-resolution cell image will be output. The experimental results show that the cell resolution is improved by 4×, and CNNSR has 9.5% improvement over the ELMSR on resolution enhancing performance. The cell counting results also match well with a commercial flow cytometer. Such ELMSR and CNNSR therefore have the potential for efficient resolution improvement in lensless blood cell counting systems towards POCT applications.

Pulsed single-photon spectrometer by frequency-to-time mapping using chirped fiber Bragg gratings.

Science.gov (United States)

Davis, Alex O C; Saulnier, Paul M; Karpiński, Michał; Smith, Brian J

2017-05-29

A fiber-integrated spectrometer for single-photon pulses outside the telecommunications wavelength range based upon frequency-to-time mapping, implemented by chromatic group delay dispersion (GDD), and precise temporally-resolved single-photon counting, is presented. A chirped fiber Bragg grating provides low-loss GDD, mapping the frequency distribution of an input pulse onto the temporal envelope of the output pulse. Time-resolved detection with fast single-photon-counting modules enables monitoring of a wavelength range from 825 nm to 835 nm with nearly uniform efficiency at 55 pm resolution (24 GHz at 830 nm). To demonstrate the versatility of this technique, spectral interference of heralded single photons and the joint spectral intensity distribution of a photon-pair source are measured. This approach to single-photon-level spectral measurements provides a route to realize applications of time-frequency quantum optics at visible and near-infrared wavelengths, where multiple spectral channels must be simultaneously monitored.

Comparison Effectiveness of Pixel Based Classification and Object Based Classification Using High Resolution Image In Floristic Composition Mapping (Study Case: Gunung Tidar Magelang City)

Science.gov (United States)

Ardha Aryaguna, Prama; Danoedoro, Projo

2016-11-01

Developments of analysis remote sensing have same way with development of technology especially in sensor and plane. Now, a lot of image have high spatial and radiometric resolution, that's why a lot information. Vegetation object analysis such floristic composition got a lot advantage of that development. Floristic composition can be interpreted using a lot of method such pixel based classification and object based classification. The problems for pixel based method on high spatial resolution image are salt and paper who appear in result of classification. The purpose of this research are compare effectiveness between pixel based classification and object based classification for composition vegetation mapping on high resolution image Worldview-2. The results show that pixel based classification using majority 5×5 kernel windows give the highest accuracy between another classifications. The highest accuracy is 73.32% from image Worldview-2 are being radiometric corrected level surface reflectance, but for overall accuracy in every class, object based are the best between another methods. Reviewed from effectiveness aspect, pixel based are more effective then object based for vegetation composition mapping in Tidar forest.

Spatiotemporal High-Resolution Cloud Mapping with a Ground-Based IR Scanner

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Benjamin Brede

2017-01-01

Full Text Available The high spatiotemporal variability of clouds requires automated monitoring systems. This study presents a retrieval algorithm that evaluates observations of a hemispherically scanning thermal infrared radiometer, the NubiScope, to produce georeferenced, spatially explicit cloud maps. The algorithm uses atmospheric temperature and moisture profiles and an atmospheric radiative transfer code to differentiate between cloudy and cloudless measurements. In case of a cloud, it estimates its position by using the temperature profile and viewing geometry. The proposed algorithm was tested with 25 cloud maps generated by the Fmask algorithm from Landsat 7 images. The overall cloud detection rate was ranging from 0.607 for zenith angles of 0 to 10° to 0.298 for 50–60° on a pixel basis. The overall detection of cloudless pixels was 0.987 for zenith angles of 30–40° and much more stable over the whole range of zenith angles compared to cloud detection. This proves the algorithm’s capability in detecting clouds, but even better cloudless areas. Cloud-base height was best estimated up to a height of 4000 m compared to ceilometer base heights but showed large deviation above that level. This study shows the potential of the NubiScope system to produce high spatial and temporal resolution cloud maps. Future development is needed for a more accurate determination of cloud height with thermal infrared measurements.

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

Science.gov (United States)

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-07-07

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Multishot versus single-shot pulse sequences in very high field fMRI: a comparison using retinotopic mapping.

Directory of Open Access Journals (Sweden)

Jascha D Swisher

Full Text Available High-resolution functional MRI is a leading application for very high field (7 Tesla human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI.

Gaussian Multiple Instance Learning Approach for Mapping the Slums of the World Using Very High Resolution Imagery

Energy Technology Data Exchange (ETDEWEB)

Vatsavai, Raju [ORNL

2013-01-01

In this paper, we present a computationally efficient algo- rithm based on multiple instance learning for mapping infor- mal settlements (slums) using very high-resolution remote sensing imagery. From remote sensing perspective, infor- mal settlements share unique spatial characteristics that dis- tinguish them from other urban structures like industrial, commercial, and formal residential settlements. However, regular pattern recognition and machine learning methods, which are predominantly single-instance or per-pixel classi- fiers, often fail to accurately map the informal settlements as they do not capture the complex spatial patterns. To overcome these limitations we employed a multiple instance based machine learning approach, where groups of contigu- ous pixels (image patches) are modeled as generated by a Gaussian distribution. We have conducted several experi- ments on very high-resolution satellite imagery, represent- ing four unique geographic regions across the world. Our method showed consistent improvement in accurately iden- tifying informal settlements.

Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

Science.gov (United States)

Teo, Audrey S M; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel M

2015-01-01

Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35-300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.

In-situ investigations of structural changes during cyclic loading by high resolution reciprocal space mapping

DEFF Research Database (Denmark)

Diederichs, Annika M.; Thiel, Felix; Lienert, Ulrich

2017-01-01

dislocation structures can be identified using advanced electron microscopy and synchrotron techniques. A detailed characterization of the microstructure during cyclic loading by in-situ monitoring the internal structure within individual grains with high energy x-rays can help to understand and predict...... the materials behavior during cyclic deformation and to improve the material design. While monitoring macroscopic stress and strain during cyclic loading, reciprocal space maps of diffraction peaks from single grains are obtained with high resolution. High Resolution Reciprocal Space Mapping was applied...

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

International Nuclear Information System (INIS)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard

2013-01-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard, E-mail: rh15@mrc-lmb.cam.ac.uk

2013-12-15

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

High-resolution mapping of European fishing pressure on the benthic habitats

DEFF Research Database (Denmark)

Eigaard, Ole Ritzau; Bastardie, Francois; Hintzen, Niels T.

effort. Consequently, most logbook information is not well suited for quantitative estimation of seafloor impact (swept area and impact severity) of the different gears and trips. We present a method to overcome this information deficiency of official statistics and develop high-resolution large......) and gear width estimates were assigned to individual interpolated vessel tracks based on VMS data. The outcome was European wide highresolution fishing intensity maps (total yearly swept area within grid cells of 1*1 minutes longitude and latitude) for 2010, 2011 and 2012. Finally the high-resolution...... fishing pressure maps were overlaid with existing marine habitat maps to identify areas of potential ecosystem service conflicts...

Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

Science.gov (United States)

Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

2017-08-31

Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

Single-cell resolution mapping of neuronal damage in acute focal cerebral ischemia using thallium autometallography.

Science.gov (United States)

Stöber, Franziska; Baldauf, Kathrin; Ziabreva, Iryna; Harhausen, Denise; Zille, Marietta; Neubert, Jenni; Reymann, Klaus G; Scheich, Henning; Dirnagl, Ulrich; Schröder, Ulrich H; Wunder, Andreas; Goldschmidt, Jürgen

2014-01-01

Neuronal damage shortly after onset or after brief episodes of cerebral ischemia has remained difficult to assess with clinical and preclinical imaging techniques as well as with microscopical methods. We here show, in rodent models of middle cerebral artery occlusion (MCAO), that neuronal damage in acute focal cerebral ischemia can be mapped with single-cell resolution using thallium autometallography (TlAMG), a histochemical technique for the detection of the K(+)-probe thallium (Tl(+)) in the brain. We intravenously injected rats and mice with thallium diethyldithiocarbamate (TlDDC), a lipophilic chelate complex that releases Tl(+) after crossing the blood-brain barrier. We found, within the territories of the affected arteries, areas of markedly reduced neuronal Tl(+) uptake in all animals at all time points studied ranging from 15 minutes to 24 hours after MCAO. In large lesions at early time points, areas with neuronal and astrocytic Tl(+) uptake below thresholds of detection were surrounded by putative penumbral zones with preserved but diminished Tl(+) uptake. At 24 hours, the areas of reduced Tl(+)uptake matched with areas delineated by established markers of neuronal damage. The results suggest the use of (201)TlDDC for preclinical and clinical single-photon emission computed tomography (SPECT) imaging of hyperacute alterations in brain K(+) metabolism and prediction of tissue viability in cerebral ischemia.

USGS Imagery Only Base Map Service from The National Map

Data.gov (United States)

U.S. Geological Survey, Department of the Interior — USGS Imagery Only is a tile cache base map of orthoimagery in The National Map visible to the 1:18,000 scale. Orthoimagery data are typically high resolution images...

Nanoscale magnetic field mapping with a single spin scanning probe magnetometer

Energy Technology Data Exchange (ETDEWEB)

Rondin, L.; Tetienne, J.-P.; Spinicelli, P.; Roch, J.-F.; Jacques, V. [Laboratoire de Photonique Quantique et Moleculaire, Ecole Normale Superieure de Cachan and CNRS UMR 8537, 94235 Cachan Cedex (France); Dal Savio, C.; Karrai, K. [Attocube systems AG, Koeniginstrasse 11A RGB, Munich 80539 (Germany); Dantelle, G. [Laboratoire de Physique de la Matiere Condensee, Ecole Polytechnique and CNRS UMR 7643, 91128 Palaiseau (France); Thiaville, A.; Rohart, S. [Laboratoire de Physique des Solides, Universite Paris-Sud and CNRS UMR 8502, 91405 Orsay (France)

2012-04-09

We demonstrate quantitative magnetic field mapping with nanoscale resolution, by applying a lock-in technique on the electron spin resonance frequency of a single nitrogen-vacancy defect placed at the apex of an atomic force microscope tip. In addition, we report an all-optical magnetic imaging technique which is sensitive to large off-axis magnetic fields, thus extending the operation range of diamond-based magnetometry. Both techniques are illustrated by using a magnetic hard disk as a test sample. Owing to the non-perturbing and quantitative nature of the magnetic probe, this work should open up numerous perspectives in nanomagnetism and spintronics.

Mapping brain structure and function: cellular resolution, global perspective.

Science.gov (United States)

Zupanc, Günther K H

2017-04-01

A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity. Combination of the high-resolution anatomical and physiological maps, followed by theoretical systems analysis of the deduced network, will offer unprecedented opportunities for a better understanding of how the brain, as a whole, processes sensory information and generates behavior.

Lenses and effective spatial resolution in macroscopic optical mapping

International Nuclear Information System (INIS)

Bien, Harold; Parikh, Puja; Entcheva, Emilia

2007-01-01

Optical mapping of excitation dynamically tracks electrical waves travelling through cardiac or brain tissue by the use of fluorescent dyes. There are several characteristics that set optical mapping apart from other imaging modalities: dynamically changing signals requiring short exposure times, dim fluorescence demanding sensitive sensors and wide fields of view (low magnification) resulting in poor optical performance. These conditions necessitate the use of optics with good light gathering ability, i.e. lenses having high numerical aperture. Previous optical mapping studies often used sensor resolution to estimate the minimum spatial feature resolvable, assuming perfect optics and infinite contrast. We examine here the influence of finite contrast and real optics on the effective spatial resolution in optical mapping under broad-field illumination for both lateral (in-plane) resolution and axial (depth) resolution of collected fluorescence signals

High resolution mapping of urban areas using SPOT-5 images and ancillary data

Directory of Open Access Journals (Sweden)

Elif Sertel

2015-08-01

Full Text Available This research aims to propose new rule sets to be used for object based classification of SPOT-5 images to accurately create detailed urban land cover/use maps. In addition to SPOT-5 satellite images, Normalized Difference Vegetation Index (NDVI and Normalized Difference Water Index (NDWI maps, cadastral maps, Openstreet maps, road maps and Land Cover maps, were also integrated into classification to increase the accuracy of resulting maps. Gaziantep city, one of the highly populated cities of Turkey with different landscape patterns was selected as the study area. Different rule sets involving spectral, spatial and geometric characteristics were developed to be used for object based classification of 2.5 m resolution Spot-5 satellite images to automatically create urban map of the region. Twenty different land cover/use classes obtained from European Urban Atlas project were applied and an automatic classification approach was suggested for high resolution urban map creation and updating. Integration of different types of data into the classification decision tree increased the performance and accuracy of the suggested approach. The accuracy assessment results illustrated that with the usage of newly proposed rule set algorithms in object-based classification, urban areas represented with seventeen different sub-classes could be mapped with 94 % or higher overall accuracy.

Increased-resolution OCT thickness mapping of the human macula: a statistically based registration.

Science.gov (United States)

Bernardes, Rui; Santos, Torcato; Cunha-Vaz, José

2008-05-01

To describe the development of a technique that enhances spatial resolution of retinal thickness maps of the Stratus OCT (Carl Zeiss Meditec, Inc., Dublin, CA). A retinal thickness atlas (RT-atlas) template was calculated, and a macular coordinate system was established, to pursue this objective. The RT-atlas was developed from principal component analysis of retinal thickness analyzer (RTA) maps acquired from healthy volunteers. The Stratus OCT radial thickness measurements were registered on the RT-atlas, from which an improved macular thickness map was calculated. Thereafter, Stratus OCT circular scans were registered on the previously calculated map to enhance spatial resolution. The developed technique was applied to Stratus OCT thickness data from healthy volunteers and from patients with diabetic retinopathy (DR) or age-related macular degeneration (AMD). Results showed that for normal, or close to normal, macular thickness maps from healthy volunteers and patients with DR, this technique can be an important aid in determining retinal thickness. Efforts are under way to improve the registration of retinal thickness data in patients with AMD. The developed technique enhances the evaluation of data acquired by the Stratus OCT, helping the detection of early retinal thickness abnormalities. Moreover, a normative database of retinal thickness measurements gained from this technique, as referenced to the macular coordinate system, can be created without errors induced by missed fixation and eye tilt.

Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean.

Science.gov (United States)

Galeano, Carlos H; Cortés, Andrés J; Fernández, Andrea C; Soler, Álvaro; Franco-Herrera, Natalia; Makunde, Godwill; Vanderleyden, Jos; Blair, Matthew W

2012-06-26

In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. In short, this study illustrates the power of intron-based markers for linkage and association mapping in

Time-efficient, high-resolution, whole brain three-dimensional macromolecular proton fraction mapping.

Science.gov (United States)

Yarnykh, Vasily L

2016-05-01

Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole brain MPF mapping technique using a minimal number of source images for scan time reduction. The described technique was based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole brain three-dimensional MPF mapping with isotropic 1.25 × 1.25 × 1.25 mm(3) voxel size and a scan time of 20 min. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from eight healthy subjects. Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details, including gray matter structures with high iron content. The proposed synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. © 2015 Wiley Periodicals, Inc.

High-resolution mapping of motor vehicle carbon dioxide emissions

Science.gov (United States)

McDonald, Brian C.; McBride, Zoe C.; Martin, Elliot W.; Harley, Robert A.

2014-05-01

A fuel-based inventory for vehicle emissions is presented for carbon dioxide (CO2) and mapped at various spatial resolutions (10 km, 4 km, 1 km, and 500 m) using fuel sales and traffic count data. The mapping is done separately for gasoline-powered vehicles and heavy-duty diesel trucks. Emission estimates from this study are compared with the Emissions Database for Global Atmospheric Research (EDGAR) and VULCAN. All three inventories agree at the national level within 5%. EDGAR uses road density as a surrogate to apportion vehicle emissions, which leads to 20-80% overestimates of on-road CO2 emissions in the largest U.S. cities. High-resolution emission maps are presented for Los Angeles, New York City, San Francisco-San Jose, Houston, and Dallas-Fort Worth. Sharp emission gradients that exist near major highways are not apparent when emissions are mapped at 10 km resolution. High CO2 emission fluxes over highways become apparent at grid resolutions of 1 km and finer. Temporal variations in vehicle emissions are characterized using extensive day- and time-specific traffic count data and are described over diurnal, day of week, and seasonal time scales. Clear differences are observed when comparing light- and heavy-duty vehicle traffic patterns and comparing urban and rural areas. Decadal emission trends were analyzed from 2000 to 2007 when traffic volumes were increasing and a more recent period (2007-2010) when traffic volumes declined due to recession. We found large nonuniform changes in on-road CO2 emissions over a period of 5 years, highlighting the importance of timely updates to motor vehicle emission inventories.

Single-edition quadrangle maps

Science.gov (United States)

,

1998-01-01

In August 1993, the U.S. Geological Survey's (USGS) National Mapping Division and the U.S. Department of Agriculture's Forest Service signed an Interagency Agreement to begin a single-edition joint mapping program. This agreement established the coordination for producing and maintaining single-edition primary series topographic maps for quadrangles containing National Forest System lands. The joint mapping program saves money by eliminating duplication of effort by the agencies and results in a more frequent revision cycle for quadrangles containing national forests. Maps are revised on the basis of jointly developed standards and contain normal features mapped by the USGS, as well as additional features required for efficient management of National Forest System lands. Single-edition maps look slightly different but meet the content, accuracy, and quality criteria of other USGS products. The Forest Service is responsible for the land management of more than 191 million acres of land throughout the continental United States, Alaska, and Puerto Rico, including 155 national forests and 20 national grasslands. These areas make up the National Forest System lands and comprise more than 10,600 of the 56,000 primary series 7.5-minute quadrangle maps (15-minute in Alaska) covering the United States. The Forest Service has assumed responsibility for maintaining these maps, and the USGS remains responsible for printing and distributing them. Before the agreement, both agencies published similar maps of the same areas. The maps were used for different purposes, but had comparable types of features that were revised at different times. Now, the two products have been combined into one so that the revision cycle is stabilized and only one agency revises the maps, thus increasing the number of current maps available for National Forest System lands. This agreement has improved service to the public by requiring that the agencies share the same maps and that the maps meet a

MBARI Mapping AUV: A High-Resolution Deep Ocean Seafloor Mapping Capability

Science.gov (United States)

Caress, D. W.; Kirkwood, W. J.; Thomas, H.; McEwen, R.; Henthorn, R.; McGill, P.; Thompson, D.; Sibenac, M.; Jensen, S.; Shane, F.; Hamilton, A.

2005-05-01

The Monterey Bay Aquarium Research Institute (MBARI) is developing an autonomous seafloor mapping capability for deep ocean science applications. The MBARI Mapping AUV is a 0.53 m (21 in) diameter, 5.1 m (16.7 ft) long, Dorado-class vehicle designed to carry four mapping sonars. The primary sensor is a 200 kHz multibeam sonar producing swath bathymetry and sidescan. In addition, the vehicle carries 100 kHz and 410 kHz chirp sidescan sonars, and a 2-16 kHz sweep chirp subbottom profiler. Navigation and attitude data are obtained from an inertial navigation system (INS) incorporating a ring laser gyro and a 300 kHz Doppler velocity log (DVL). The vehicle also includes acoustic modem, ultra-short baseline navigation, and long-baseline navigation systems. The Mapping AUV is powered by 6 kWhr of Li-polymer batteries, providing expected mission duration of 12 hours at a typical speed of 1.5 m/s. All components of the vehicle are rated to 6000 m depth, allowing MBARI to conduct high-resolution mapping of the deep-ocean seafloor. The sonar package is also be mountable on ROV Ventana, allowing surveys at altitudes less than 20 m at topographically challenging sites. The vehicle was assembled and extensively tested during 2004; this year we are commencing operations for MBARI science projects while continuing the process of testing and integrating the complete suite of sensors and systems. MBARI is beginning to use this capability to observe the changing morphology of dynamic systems such as submarine canyons and active slumps, to map deep-water benthic habitats at resolutions comparable to ROV and submersible observations, to provide basemaps for ROV dives, and to provide high resolution bathymetry and subbottom profiles as part of a variety of projects requiring knowledge of the seafloor. We will present initial results from surveys in and around Monterey Canyon, including high resolution repeat surveys of four sites along the canyon axis.

A multi-resolution HEALPix data structure for spherically mapped point data

Directory of Open Access Journals (Sweden)

Robert W. Youngren

2017-06-01

Full Text Available Data describing entities with locations that are points on a sphere are described as spherically mapped. Several data structures designed for spherically mapped data have been developed. One of them, known as Hierarchical Equal Area iso-Latitude Pixelization (HEALPix, partitions the sphere into twelve diamond-shaped equal-area base cells and then recursively subdivides each cell into four diamond-shaped subcells, continuing to the desired level of resolution. Twelve quadtrees, one associated with each base cell, store the data records associated with that cell and its subcells.HEALPix has been used successfully for numerous applications, notably including cosmic microwave background data analysis. However, for applications involving sparse point data HEALPix has possible drawbacks, including inefficient memory utilization, overwriting of proximate points, and return of spurious points for certain queries.A multi-resolution variant of HEALPix specifically optimized for sparse point data was developed. The new data structure allows different areas of the sphere to be subdivided at different levels of resolution. It combines HEALPix positive features with the advantages of multi-resolution, including reduced memory requirements and improved query performance.An implementation of the new Multi-Resolution HEALPix (MRH data structure was tested using spherically mapped data from four different scientific applications (warhead fragmentation trajectories, weather station locations, galaxy locations, and synthetic locations. Four types of range queries were applied to each data structure for each dataset. Compared to HEALPix, MRH used two to four orders of magnitude less memory for the same data, and on average its queries executed 72% faster. Keywords: Computer science

A Method of Spatial Mapping and Reclassification for High-Spatial-Resolution Remote Sensing Image Classification

Directory of Open Access Journals (Sweden)

Guizhou Wang

2013-01-01

Full Text Available This paper presents a new classification method for high-spatial-resolution remote sensing images based on a strategic mechanism of spatial mapping and reclassification. The proposed method includes four steps. First, the multispectral image is classified by a traditional pixel-based classification method (support vector machine. Second, the panchromatic image is subdivided by watershed segmentation. Third, the pixel-based multispectral image classification result is mapped to the panchromatic segmentation result based on a spatial mapping mechanism and the area dominant principle. During the mapping process, an area proportion threshold is set, and the regional property is defined as unclassified if the maximum area proportion does not surpass the threshold. Finally, unclassified regions are reclassified based on spectral information using the minimum distance to mean algorithm. Experimental results show that the classification method for high-spatial-resolution remote sensing images based on the spatial mapping mechanism and reclassification strategy can make use of both panchromatic and multispectral information, integrate the pixel- and object-based classification methods, and improve classification accuracy.

High-resolution mapping based on an Unmanned Aerial Vehicle (UAV) to capture paleoseismic offsets along the Altyn-Tagh fault, China.

Science.gov (United States)

Gao, Mingxing; Xu, Xiwei; Klinger, Yann; van der Woerd, Jerome; Tapponnier, Paul

2017-08-15

The recent dramatic increase in millimeter- to centimeter- resolution topographic datasets obtained via multi-view photogrammetry raises the possibility of mapping detailed offset geomorphology and constraining the spatial characteristics of active faults. Here, for the first time, we applied this new method to acquire high-resolution imagery and generate topographic data along the Altyn Tagh fault, which is located in a remote high elevation area and shows preserved ancient earthquake surface ruptures. A digital elevation model (DEM) with a resolution of 0.065 m and an orthophoto with a resolution of 0.016 m were generated from these images. We identified piercing markers and reconstructed offsets based on both the orthoimage and the topography. The high-resolution UAV data were used to accurately measure the recent seismic offset. We obtained the recent offset of 7 ± 1 m. Combined with the high resolution satellite image, we measured cumulative offsets of 15 ± 2 m, 20 ± 2 m, 30 ± 2 m, which may be due to multiple paleo-earthquakes. Therefore, UAV mapping can provide fine-scale data for the assessment of the seismic hazards.

An atlas of high-resolution IRAS maps on nearby galaxies

Science.gov (United States)

Rice, Walter

1993-01-01

An atlas of far-infrared IRAS maps with near 1 arcmin angular resolution of 30 optically large galaxies is presented. The high-resolution IRAS maps were produced with the Maximum Correlation Method (MCM) image construction and enhancement technique developed at IPAC. The MCM technique, which recovers the spatial information contained in the overlapping detector data samples of the IRAS all-sky survey scans, is outlined and tests to verify the structural reliability and photometric integrity of the high-resolution maps are presented. The infrared structure revealed in individual galaxies is discussed. The atlas complements the IRAS Nearby Galaxy High-Resolution Image Atlas, the high-resolution galaxy images encoded in FITS format, which is provided to the astronomical community as an IPAC product.

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

Science.gov (United States)

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Column ratio mapping: A processing technique for atomic resolution high-angle annular dark-field (HAADF) images

International Nuclear Information System (INIS)

Robb, Paul D.; Craven, Alan J.

2008-01-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [1 1 0]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 A-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Contour Detection for UAV-Based Cadastral Mapping

Directory of Open Access Journals (Sweden)

Sophie Crommelinck

2017-02-01

Full Text Available Unmanned aerial vehicles (UAVs provide a flexible and low-cost solution for the acquisition of high-resolution data. The potential of high-resolution UAV imagery to create and update cadastral maps is being increasingly investigated. Existing procedures generally involve substantial fieldwork and many manual processes. Arguably, multiple parts of UAV-based cadastral mapping workflows could be automated. Specifically, as many cadastral boundaries coincide with visible boundaries, they could be extracted automatically using image analysis methods. This study investigates the transferability of gPb contour detection, a state-of-the-art computer vision method, to remotely sensed UAV images and UAV-based cadastral mapping. Results show that the approach is transferable to UAV data and automated cadastral mapping: object contours are comprehensively detected at completeness and correctness rates of up to 80%. The detection quality is optimal when the entire scene is covered with one orthoimage, due to the global optimization of gPb contour detection. However, a balance between high completeness and correctness is hard to achieve, so a combination with area-based segmentation and further object knowledge is proposed. The localization quality exhibits the usual dependency on ground resolution. The approach has the potential to accelerate the process of general boundary delineation during the creation and updating of cadastral maps.

Advanced Ecosystem Mapping Techniques for Large Arctic Study Domains Using Calibrated High-Resolution Imagery

Science.gov (United States)

Macander, M. J.; Frost, G. V., Jr.

2015-12-01

Regional-scale mapping of vegetation and other ecosystem properties has traditionally relied on medium-resolution remote sensing such as Landsat (30 m) and MODIS (250 m). Yet, the burgeoning availability of high-resolution (environments has not been previously evaluated. Image segmentation, or object-based image analysis, automatically partitions high-resolution imagery into homogeneous image regions that can then be analyzed based on spectral, textural, and contextual information. We applied eCognition software to delineate waterbodies and vegetation classes, in combination with other techniques. Texture metrics were evaluated to determine the feasibility of using high-resolution imagery to algorithmically characterize periglacial surface forms (e.g., ice-wedge polygons), which are an important physical characteristic of permafrost-dominated regions but which cannot be distinguished by medium-resolution remote sensing. These advanced mapping techniques provide products which can provide essential information supporting a broad range of ecosystem science and land-use planning applications in northern Alaska and elsewhere in the circumpolar Arctic.

High-Resolution Urban Greenery Mapping for Micro-Climate Modelling Based on 3d City Models

Science.gov (United States)

Hofierka, J.; Gallay, M.; Kaňuk, J.; Šupinský, J.; Šašak, J.

2017-10-01

Urban greenery has various positive micro-climate effects including mitigation of heat islands. The primary root of heat islands in cities is in absorption of solar radiation by the mass of building structures, roads and other solid materials. The absorbed heat is subsequently re-radiated into the surroundings and increases ambient temperatures. The vegetation can stop and absorb most of incoming solar radiation mostly via the photosynthesis and evapotranspiration process. However, vegetation in mild climate of Europe manifests considerable annual seasonality which can also contribute to the seasonal change in the cooling effect of the vegetation on the urban climate. Modern methods of high-resolution mapping and new generations of sensors have brought opportunity to record the dynamics of urban greenery in a high resolution in spatial, spectral, and temporal domains. In this paper, we use the case study of the city of Košice in Eastern Slovakia to demonstrate the methodology of 3D mapping and modelling the urban greenery during one vegetation season in 2016. The purpose of this monitoring is to capture 3D effects of urban greenery on spatial distribution of solar radiation in urban environment. Terrestrial laser scanning was conducted on four selected sites within Košice in ultra-high spatial resolution. The entire study area, which included these four smaller sites, comprised 4 km2 of the central part of the city was flown within a single airborne lidar and photogrammetric mission to capture the upper parts of buildings and vegetation. The acquired airborne data were used to generate a 3D city model and the time series of terrestrial lidar data were integrated with the 3D city model. The results show that the terrestrial and airborne laser scanning techniques can be effectively used to monitor seasonal changes in foliage of trees in order to assess the transmissivity of the canopy for microclimate modelling.

Mapping of odor-related neuronal activity in the olfactory bulb by high-resolution 2-deoxyglucose autoradiography

International Nuclear Information System (INIS)

Lancet, D.; Greer, C.A.; Kauer, J.S.; Shepherd, G.M.

1982-01-01

The spatial distribution of odor-induced neuronal activity in the olfactory bulb, the first relay station of the olfactory pathway, is believed to reflect important aspects of chemosensory coding. We report here the application of high-resolution 2-deoxyglucose autoradiography to the mapping of spatial patterns of metabolic activity at the level of single neurons in the olfactory bulb. It was found that glomeruli, which are synaptic complexes containing the first synaptic relay, tend to be uniformly active or inactive during odor exposure. Differential 2-deoxyglucose uptake was also observed in the somata of projection neurons (mitral cells) and interneurons (periglomerular and granule cells). This confirms and extends our previous studies in which odor-specific laminar and focal uptake patterns were revealed by the conventional x-ray film 2-deoxyglucose method due to Sokoloff and colleagues [Sokoloff, L., Reivich, M., Kennedy, C., DesRosiers, M. H., Patlak, C. S., Pettigrew, K. D., Sakurada, O. and Shinohara, M. (1977) J. Neurochem. 28, 897-916]. Based on results obtained by the two methods, it is suggested that the glomerulus as a whole serves as a functional unit of activity. The high-resolution results are interpreted in terms of the well-characterized synaptic organization of the olfactory bulb and also serve to illustrate the capability of the 2-deoxyglucose autoradiographic technique to map metabolic activity in single neurons of the vertebrate central nervous system

Automated high resolution mapping of coffee in Rwanda using an expert Bayesian network

Science.gov (United States)

Mukashema, A.; Veldkamp, A.; Vrieling, A.

2014-12-01

African highland agro-ecosystems are dominated by small-scale agricultural fields that often contain a mix of annual and perennial crops. This makes such systems difficult to map by remote sensing. We developed an expert Bayesian network model to extract the small-scale coffee fields of Rwanda from very high resolution data. The model was subsequently applied to aerial orthophotos covering more than 99% of Rwanda and on one QuickBird image for the remaining part. The method consists of a stepwise adjustment of pixel probabilities, which incorporates expert knowledge on size of coffee trees and fields, and on their location. The initial naive Bayesian network, which is a spectral-based classification, yielded a coffee map with an overall accuracy of around 50%. This confirms that standard spectral variables alone cannot accurately identify coffee fields from high resolution images. The combination of spectral and ancillary data (DEM and a forest map) allowed mapping of coffee fields and associated uncertainties with an overall accuracy of 87%. Aggregated to district units, the mapped coffee areas demonstrated a high correlation with the coffee areas reported in the detailed national coffee census of 2009 (R2 = 0.92). Unlike the census data our map provides high spatial resolution of coffee area patterns of Rwanda. The proposed method has potential for mapping other perennial small scale cropping systems in the East African Highlands and elsewhere.

Sparse PDF maps for non-linear multi-resolution image operations

KAUST Repository

Hadwiger, Markus

2012-11-01

We introduce a new type of multi-resolution image pyramid for high-resolution images called sparse pdf maps (sPDF-maps). Each pyramid level consists of a sparse encoding of continuous probability density functions (pdfs) of pixel neighborhoods in the original image. The encoded pdfs enable the accurate computation of non-linear image operations directly in any pyramid level with proper pre-filtering for anti-aliasing, without accessing higher or lower resolutions. The sparsity of sPDF-maps makes them feasible for gigapixel images, while enabling direct evaluation of a variety of non-linear operators from the same representation. We illustrate this versatility for antialiased color mapping, O(n) local Laplacian filters, smoothed local histogram filters (e.g., median or mode filters), and bilateral filters. © 2012 ACM.

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage

Science.gov (United States)

Pintilie, Grigore; Chen, Dong-Hua; Haase-Pettingell, Cameron A.; King, Jonathan A.; Chiu, Wah

2016-01-01

CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å), whereas other components are at slightly lower resolutions: portal (9.2 Å), hub (8.5 Å), tailspike (10.9 Å), and needle (10.5 Å). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density. PMID:26743049

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami

Science.gov (United States)

Chikkaraddy, Rohit; Turek, V. A.; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F.; Baumberg, Jeremy J.

2018-01-01

Fabricating nanocavities in which optically-active single quantum emitters are precisely positioned, is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore, and obtain enhancements of $\\geq4\\times10^3$ with high quantum yield ($\\geq50$%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of $\\pm1.5$ nm. Our approach introduces a straightforward non-invasive way to measure and quantify confined optical modes on the nanoscale.

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami.

Science.gov (United States)

Chikkaraddy, Rohit; Turek, V A; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F; Baumberg, Jeremy J

2018-01-10

Fabricating nanocavities in which optically active single quantum emitters are precisely positioned is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5 nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore and obtain enhancements of ≥4 × 10 3 with high quantum yield (≥50%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of ±1.5 nm. Our approach introduces a straightforward noninvasive way to measure and quantify confined optical modes on the nanoscale.

The simple map for a single-null divertor tokamak

International Nuclear Information System (INIS)

Punjabi, A.; Verma, A.; Boozer, A.

1996-01-01

We present the simple map for a single-null divertor tokamak. The simple map is an area-preserving map based on the idea that magnetic field lines are a single-degree-of-freedom time-dependent Hamiltonian system, and that the basic features of such systems near the X-point are generic. We obtain the properties of this map and the resulting footprints of field lines on the divertor plate. These include the width of the stochastic layer, the edge safety factor, the area of the footprint and the amount of magnetic flux diverted. We give the safety factor profile, the average and median values of strike angles, lengths and the Liapunov exponents. We describe how the effects of magnetic perturbations can be included in the simple map. We show how the map can be applied to the problem of the determination of heat flux on the divertor plate in tokamaks. (Author)

High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

Directory of Open Access Journals (Sweden)

Bonavita Gina

2002-08-01

Full Text Available Abstract Background The Blau syndrome (MIM 186580, an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order of microsatellite markers, hampered us from further refining the genetic locus for the Blau syndrome. To address this problem, we constructed our own high-resolution physical map for the Blau susceptibility region. Results We generated a high-resolution physical map that provides more than 90% coverage of a refined Blau susceptibility region. The map consists of four contigs of sequence tagged site-based bacterial artificial chromosomes with a total of 124 bacterial artificial chromosomes, and spans approximately 7.5 Mbp; however, three gaps still exist in this map with sizes of 425, 530 and 375 kbp, respectively, estimated from radiation hybrid mapping. Conclusions Our high-resolution map will assist genetic studies of loci in the interval from D16S3080, near D16S409, and D16S408 (16q12.1 to 16q13.

The iMars WebGIS - Spatio-Temporal Data Queries and Single Image Map Web Services

Science.gov (United States)

Walter, Sebastian; Steikert, Ralf; Schreiner, Bjoern; Muller, Jan-Peter; van Gasselt, Stephan; Sidiropoulos, Panagiotis; Lanz-Kroechert, Julia

2017-04-01

Server backend which in turn delivers the response back to the MapCache instance. Web frontend: We have implemented a web-GIS frontend based on various OpenLayers components. The basemap is a global color-hillshaded HRSC bundle-adjusted DTM mosaic with a resolution of 50 m per pixel. The new bundle-block-adjusted qudrangle mosaics of the MC-11 quadrangle, both image and DTM, are included with opacity slider options. The layer user interface has been adapted on the base of the ol3-layerswitcher and extended by foldable and switchable groups, layer sorting (by resolution, by time and alphabeticallly) and reordering (drag-and-drop). A collapsible time panel accomodates a time slider interface where the user can filter the visible data by a range of Mars or Earth dates and/or by solar longitudes. The visualisation of time-series of single images is controlled by a specific toolbar enabling the workflow of image selection (by point or bounding box), dynamic image loading and playback of single images in a video player-like environment. During a stress-test campaign we could demonstrate that the system is capable of serving up to 10 simultaneous users on its current lightweight development hardware. It is planned to relocate the software to more powerful hardware by the time of this conference. Conclusions/Outlook: The iMars webGIS is an expert tool for the detection and visualization of surface changes. We demonstrate a technique to dynamically retrieve and display single images based on the time-series structure of the data. Together with the multi-temporal database and its MapServer/MapCache backend it provides a stable and high performance environment for the dissemination of the various iMars products. Acknowledgements: This research has received funding from the EU's FP7 Programme under iMars 607379 and by the German Space Agency (DLR Bonn), grant 50 QM 1301 (HRSC on Mars Express).

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

Science.gov (United States)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R; Murshudov, Garib N; Short, Judith M; Scheres, Sjors H W; Henderson, Richard

2013-12-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

Evaluation of the influence of source and spatial resolution of DEMs on derivative products used in landslide mapping

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Rubini Mahalingam

2016-11-01

Full Text Available Landslides are a major geohazard, which result in significant human, infrastructure, and economic losses. Landslide susceptibility mapping can help communities plan and prepare for these damaging events. Digital elevation models (DEMs are one of the most important data-sets used in landslide hazard assessment. Despite their frequent use, limited research has been completed to date on how the DEM source and spatial resolution can influence the accuracy of the produced landslide susceptibility maps. The aim of this paper is to analyse the influence of spatial resolutions and source of DEMs on landslide susceptibility mapping. For this purpose, Advanced Spaceborne Thermal Emission and Reflection (ASTER, National Elevation Dataset (NED, and Light Detection and Ranging (LiDAR DEMs were obtained for two study sections of approximately 140 km2 in north-west Oregon. Each DEM was resampled to 10, 30, and 50 m and slope and aspect grids were derived for each resolution. A set of nine spatial databases was constructed using geoinformation science (GIS for each of the spatial resolution and source. Additional factors such as distance to river and fault maps were included. An analytical hierarchical process (AHP, fuzzy logic model, and likelihood ratio-AHP representing qualitative, quantitative, and hybrid landslide mapping techniques were used for generating landslide susceptibility maps. The results from each of the techniques were verified with the Cohen's kappa index, confusion matrix, and a validation index based on agreement with detailed landslide inventory maps. The spatial resolution of 10 m, derived from the LiDAR data-set showed higher predictive accuracy in all the three techniques used for producing landslide susceptibility maps. At a resolution of 10 m, the output maps based on NED and ASTER had higher misclassification compared to the LiDAR-based outputs. Further, the 30-m LiDAR output showed improved results over the 10-m NED and 10-m

Accuracy assessment of cadastral maps using high resolution aerial photos

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Alwan Imzahim

2018-01-01

Full Text Available A cadastral map is a map that shows the boundaries and ownership of land parcels. Some cadastral maps show additional details, such as survey district names, unique identifying numbers for parcels, certificate of title numbers, positions of existing structures, section or lot numbers and their respective areas, adjoining and adjacent street names, selected boundary dimensions and references to prior maps. In Iraq / Baghdad Governorate, the main problem is that the cadastral maps are georeferenced to a local geodetic datum known as Clark 1880 while the widely used reference system for navigation purpose (GPS and GNSS and uses Word Geodetic System 1984 (WGS84 as a base reference datum. The objective of this paper is to produce a cadastral map with scale 1:500 (metric scale by using aerial photographs 2009 with high ground spatial resolution 10 cm reference WGS84 system. The accuracy assessment for the cadastral maps updating approach to urban large scale cadastral maps (1:500-1:1000 was ± 0.115 meters; which complies with the American Social for Photogrammetry and Remote Sensing Standards (ASPRS.

An Efficient Method for Mapping High-Resolution Global River Discharge Based on the Algorithms of Drainage Network Extraction

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Jiaye Li

2018-04-01

Full Text Available River discharge, which represents the accumulation of surface water flowing into rivers and ultimately into the ocean or other water bodies, may have great impacts on water quality and the living organisms in rivers. However, the global knowledge of river discharge is still poor and worth exploring. This study proposes an efficient method for mapping high-resolution global river discharge based on the algorithms of drainage network extraction. Using the existing global runoff map and digital elevation model (DEM data as inputs, this method consists of three steps. First, the pixels of the runoff map and the DEM data are resampled into the same resolution (i.e., 0.01-degree. Second, the flow direction of each pixel of the DEM data (identified by the optimal flow path method used in drainage network extraction is determined and then applied to the corresponding pixel of the runoff map. Third, the river discharge of each pixel of the runoff map is calculated by summing the runoffs of all the pixels in the upstream of this pixel, similar to the upslope area accumulation step in drainage network extraction. Finally, a 0.01-degree global map of the mean annual river discharge is obtained. Moreover, a 0.5-degree global map of the mean annual river discharge is produced to display the results with a more intuitive perception. Compared against the existing global river discharge databases, the 0.01-degree map is of a generally high accuracy for the selected river basins, especially for the Amazon River basin with the lowest relative error (RE of 0.3% and the Yangtze River basin within the RE range of ±6.0%. However, it is noted that the results of the Congo and Zambezi River basins are not satisfactory, with RE values over 90%, and it is inferred that there may be some accuracy problems with the runoff map in these river basins.

The Mapping X-ray Fluorescence Spectrometer (MapX)

Science.gov (United States)

Sarrazin, P.; Blake, D. F.; Marchis, F.; Bristow, T.; Thompson, K.

2017-12-01

Many planetary surface processes leave traces of their actions as features in the size range 10s to 100s of microns. The Mapping X-ray Fluorescence Spectrometer (MapX) will provide elemental imaging at 100 micron spatial resolution, yielding elemental chemistry at a scale where many relict physical, chemical, or biological features can be imaged and interpreted in ancient rocks on planetary bodies and planetesimals. MapX is an arm-based instrument positioned on a rock or regolith with touch sensors. During an analysis, an X-ray source (tube or radioisotope) bombards the sample with X-rays or alpha-particles / gamma-rays, resulting in sample X-ray Fluorescence (XRF). X-rays emitted in the direction of an X-ray sensitive CCD imager pass through a 1:1 focusing lens (X-ray micro-pore Optic (MPO)) that projects a spatially resolved image of the X-rays onto the CCD. The CCD is operated in single photon counting mode so that the energies and positions of individual X-ray photons are recorded. In a single analysis, several thousand frames are both stored and processed in real-time. Higher level data products include single-element maps with a lateral spatial resolution of 100 microns and quantitative XRF spectra from ground- or instrument- selected Regions of Interest (ROI). XRF spectra from ROI are compared with known rock and mineral compositions to extrapolate the data to rock types and putative mineralogies. When applied to airless bodies and implemented with an appropriate radioisotope source for alpha-particle excitation, MapX will be able to analyze biogenic elements C, N, O, P, S, in addition to the cations of the rock-forming elements >Na, accessible with either X-ray or gamma-ray excitation. The MapX concept has been demonstrated with a series of lab-based prototypes and is currently under refinement and TRL maturation.

MAP-MRF-Based Super-Resolution Reconstruction Approach for Coded Aperture Compressive Temporal Imaging

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Tinghua Zhang

2018-02-01

Full Text Available Coded Aperture Compressive Temporal Imaging (CACTI can afford low-cost temporal super-resolution (SR, but limits are imposed by noise and compression ratio on reconstruction quality. To utilize inter-frame redundant information from multiple observations and sparsity in multi-transform domains, a robust reconstruction approach based on maximum a posteriori probability and Markov random field (MAP-MRF model for CACTI is proposed. The proposed approach adopts a weighted 3D neighbor system (WNS and the coordinate descent method to perform joint estimation of model parameters, to achieve the robust super-resolution reconstruction. The proposed multi-reconstruction algorithm considers both total variation (TV and ℓ 2 , 1 norm in wavelet domain to address the minimization problem for compressive sensing, and solves it using an accelerated generalized alternating projection algorithm. The weighting coefficient for different regularizations and frames is resolved by the motion characteristics of pixels. The proposed approach can provide high visual quality in the foreground and background of a scene simultaneously and enhance the fidelity of the reconstruction results. Simulation results have verified the efficacy of our new optimization framework and the proposed reconstruction approach.

High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.

Science.gov (United States)

Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

2015-06-01

Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome. © 2014 CIRAD. New Phytologist © 2014 New Phytologist Trust.

High resolution hybrid optical and acoustic sea floor maps (Invited)

Science.gov (United States)

Roman, C.; Inglis, G.

2013-12-01

This abstract presents a method for creating hybrid optical and acoustic sea floor reconstructions at centimeter scale grid resolutions with robotic vehicles. Multibeam sonar and stereo vision are two common sensing modalities with complementary strengths that are well suited for data fusion. We have recently developed an automated two stage pipeline to create such maps. The steps can be broken down as navigation refinement and map construction. During navigation refinement a graph-based optimization algorithm is used to align 3D point clouds created with both the multibeam sonar and stereo cameras. The process combats the typical growth in navigation error that has a detrimental affect on map fidelity and typically introduces artifacts at small grid sizes. During this process we are able to automatically register local point clouds created by each sensor to themselves and to each other where they overlap in a survey pattern. The process also estimates the sensor offsets, such as heading, pitch and roll, that describe how each sensor is mounted to the vehicle. The end results of the navigation step is a refined vehicle trajectory that ensures the points clouds from each sensor are consistently aligned, and the individual sensor offsets. In the mapping step, grid cells in the map are selectively populated by choosing data points from each sensor in an automated manner. The selection process is designed to pick points that preserve the best characteristics of each sensor and honor some specific map quality criteria to reduce outliers and ghosting. In general, the algorithm selects dense 3D stereo points in areas of high texture and point density. In areas where the stereo vision is poor, such as in a scene with low contrast or texture, multibeam sonar points are inserted in the map. This process is automated and results in a hybrid map populated with data from both sensors. Additional cross modality checks are made to reject outliers in a robust manner. The final

GRANULOMETRIC MAPS FROM HIGH RESOLUTION SATELLITE IMAGES

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Catherine Mering

2011-05-01

Full Text Available A new method of land cover mapping from satellite images using granulometric analysis is presented here. Discontinuous landscapes such as steppian bushes of semi arid regions and recently growing urban settlements are especially concerned by this study. Spatial organisations of the land cover are quantified by means of the size distribution analysis of the land cover units extracted from high resolution remotely sensed images. A granulometric map is built by automatic classification of every pixel of the image according to the granulometric density inside a sliding neighbourhood. Granulometric mapping brings some advantages over traditional thematic mapping by remote sensing by focusing on fine spatial events and small changes in one peculiar category of the landscape.

High temporal resolution mapping of seismic noise sources using heterogeneous supercomputers

Science.gov (United States)

Gokhberg, Alexey; Ermert, Laura; Paitz, Patrick; Fichtner, Andreas

2017-04-01

Time- and space-dependent distribution of seismic noise sources is becoming a key ingredient of modern real-time monitoring of various geo-systems. Significant interest in seismic noise source maps with high temporal resolution (days) is expected to come from a number of domains, including natural resources exploration, analysis of active earthquake fault zones and volcanoes, as well as geothermal and hydrocarbon reservoir monitoring. Currently, knowledge of noise sources is insufficient for high-resolution subsurface monitoring applications. Near-real-time seismic data, as well as advanced imaging methods to constrain seismic noise sources have recently become available. These methods are based on the massive cross-correlation of seismic noise records from all available seismic stations in the region of interest and are therefore very computationally intensive. Heterogeneous massively parallel supercomputing systems introduced in the recent years combine conventional multi-core CPU with GPU accelerators and provide an opportunity for manifold increase and computing performance. Therefore, these systems represent an efficient platform for implementation of a noise source mapping solution. We present the first results of an ongoing research project conducted in collaboration with the Swiss National Supercomputing Centre (CSCS). The project aims at building a service that provides seismic noise source maps for Central Europe with high temporal resolution (days to few weeks depending on frequency and data availability). The service is hosted on the CSCS computing infrastructure; all computationally intensive processing is performed on the massively parallel heterogeneous supercomputer "Piz Daint". The solution architecture is based on the Application-as-a-Service concept in order to provide the interested external researchers the regular access to the noise source maps. The solution architecture includes the following sub-systems: (1) data acquisition responsible for

High-Resolution Geologic Mapping of Martian Terraced Fan Deposits

Science.gov (United States)

Wolak, J. M.; Patterson, A. B.; Smith, S. D.; Robbins, N. N.

2018-06-01

This abstract documents our initial progress (year 1) mapping terraced fan features on Mars. Our objective is to investigate the role of fluids during fan formation and produce the first high-resolution geologic map (1:18k) of a terraced fan.

High-Resolution Reciprocal Space Mapping for Characterizing Deformation Structures

DEFF Research Database (Denmark)

Pantleon, Wolfgang; Wejdemann, Christian; Jakobsen, Bo

2014-01-01

With high-angular resolution three-dimensional X-ray diffraction (3DXRD), quantitative information is gained about dislocation structures in individual grains in the bulk of a macroscopic specimen by acquiring reciprocal space maps. In high-resolution 3D reciprocal space maps of tensile......-deformed copper, individual, almost dislocation-free subgrains are identified from high-intensity peaks and distinguished by their unique combination of orientation and elastic strain; dislocation walls manifest themselves as a smooth cloud of lower intensity. The elastic strain shows only minor variations within...... dynamics is followed in situ during varying loading conditions by reciprocal space mapping: during uninterrupted tensile deformation, formation of subgrains is observed concurrently with broadening of Bragg reflections shortly after the onset of plastic deformation. When the traction is terminated, stress...

Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

Science.gov (United States)

Payne, Adam

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

Mapping Rice Cropping Systems in Vietnam Using an NDVI-Based Time-Series Similarity Measurement Based on DTW Distance

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Xudong Guan

2016-01-01

Full Text Available Normalized Difference Vegetation Index (NDVI derived from Moderate Resolution Imaging Spectroradiometer (MODIS time-series data has been widely used in the fields of crop and rice classification. The cloudy and rainy weather characteristics of the monsoon season greatly reduce the likelihood of obtaining high-quality optical remote sensing images. In addition, the diverse crop-planting system in Vietnam also hinders the comparison of NDVI among different crop stages. To address these problems, we apply a Dynamic Time Warping (DTW distance-based similarity measure approach and use the entire yearly NDVI time series to reduce the inaccuracy of classification using a single image. We first de-noise the NDVI time series using S-G filtering based on the TIMESAT software. Then, a standard NDVI time-series base for rice growth is established based on field survey data and Google Earth sample data. NDVI time-series data for each pixel are constructed and the DTW distance with the standard rice growth NDVI time series is calculated. Then, we apply thresholds to extract rice growth areas. A qualitative assessment using statistical data and a spatial assessment using sampled data from the rice-cropping map reveal a high mapping accuracy at the national scale between the statistical data, with the corresponding R2 being as high as 0.809; however, the mapped rice accuracy decreased at the provincial scale due to the reduced number of rice planting areas per province. An analysis of the results indicates that the 500-m resolution MODIS data are limited in terms of mapping scattered rice parcels. The results demonstrate that the DTW-based similarity measure of the NDVI time series can be effectively used to map large-area rice cropping systems with diverse cultivation processes.

High resolution mapping of riffle-pool dynamics based on ADCP and close-range remote sensing data

Science.gov (United States)

Salmela, Jouni; Kasvi, Elina; Alho, Petteri

2017-04-01

Present development of mobile laser scanning (MLS) and close-range photogrammetry with unmanned aerial vehicle (UAV) enable us to create seamless digital elevation models (DEMs) of the riverine environment. Remote-controlled flow measurement platforms have also improved spatio-temporal resolution of the flow field data. In this study, acoustic Doppler current profiler (ADCP) attached to remote-controlled mini-boat, UAV-based bathymetry and MLS techniques were utilized to create the high-resolution DEMs of the river channel. These high-resolution measurements can be used in many fluvial applications such as computational fluid dynamics, channel change detection, habitat mapping or hydro-electric power plant planning. In this study we aim: 1) to analyze morphological changes of river channel especially riffle and pool formations based on fine-scale DEMs and ADCP measurements, 2) to analyze flow fields and their effect on morphological changes. The interest was mainly focused on reach-scale riffle-pool dynamics within two-year period of 2013 and 2014. The study was performed in sub-arctic meandering Pulmankijoki River located in Northern Finland. The river itself has shallow and clear water and sandy bed sediment. Discharge remains typically below 10 m3s-1 most of the year but during snow melt period in spring the discharge may exceed 70 m3s-1. We compared DEMs and ADCP measurements to understand both magnitude and spatio-temporal change of the river bed. Models were accurate enough to study bed form changes and locations and persistence of riffles and pools. We analyzed their locations with relation to flow during the peak and low discharge. Our demonstrated method has improved significantly spatio-temporal resolution of riverine DEMs compared to other cross-sectional and photogrammetry based models. Together with flow field measurements we gained better understanding of riverbed-water interaction

Comparison of Manual Mapping and Automated Object-Based Image Analysis of Non-Submerged Aquatic Vegetation from Very-High-Resolution UAS Images

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Eva Husson

2016-09-01

Full Text Available Aquatic vegetation has important ecological and regulatory functions and should be monitored in order to detect ecosystem changes. Field data collection is often costly and time-consuming; remote sensing with unmanned aircraft systems (UASs provides aerial images with sub-decimetre resolution and offers a potential data source for vegetation mapping. In a manual mapping approach, UAS true-colour images with 5-cm-resolution pixels allowed for the identification of non-submerged aquatic vegetation at the species level. However, manual mapping is labour-intensive, and while automated classification methods are available, they have rarely been evaluated for aquatic vegetation, particularly at the scale of individual vegetation stands. We evaluated classification accuracy and time-efficiency for mapping non-submerged aquatic vegetation at three levels of detail at five test sites (100 m × 100 m differing in vegetation complexity. We used object-based image analysis and tested two classification methods (threshold classification and Random Forest using eCognition®. The automated classification results were compared to results from manual mapping. Using threshold classification, overall accuracy at the five test sites ranged from 93% to 99% for the water-versus-vegetation level and from 62% to 90% for the growth-form level. Using Random Forest classification, overall accuracy ranged from 56% to 94% for the growth-form level and from 52% to 75% for the dominant-taxon level. Overall classification accuracy decreased with increasing vegetation complexity. In test sites with more complex vegetation, automated classification was more time-efficient than manual mapping. This study demonstrated that automated classification of non-submerged aquatic vegetation from true-colour UAS images was feasible, indicating good potential for operative mapping of aquatic vegetation. When choosing the preferred mapping method (manual versus automated the desired level of

Structure and Evolution of Hawaii's Loihi Seamount from High-resolution Mapping

Science.gov (United States)

Clague, D. A.; Paduan, J. B.; Moyer, C. L.; Glazer, B. T.; Caress, D. W.; Yoerger, D.; Kaiser, C. L.

2016-12-01

Loihi Seamount has been mapped repeatedly using shipboard multibeam sonars with improving resolution over time. Simrad EM302 data with 25m resolution at the 950m summit and 90m at the 5000m base of the volcano were collected from Schmidt Ocean Institute's R/V Falkor in 2014. A contracted multibeam survey in 1997 employing a deep-towed vehicle has 7m resolution for the summit and upper north and south rift zones, but suffered from poor navigation. Woods Hole Oceanographic Institution's AUV Sentry surveyed most of the summit and low-T hydrothermal vents on the base of the south rift in 2013 and 2014. The 2m resolution of most data is more precise than the navigation. The 6 summit surveys were reprocessed using MB-System to remove abundant bad bottom picks and adjust the navigation to produce a spatially accurate map. The 3 summit pits, including Pele's Pit that formed in 1996, are complex collapse structures and nested inside a larger caldera that was modified by large landslides on the east and west summit flanks. The pits cut low shields that once formed a complex of overlapping summit shields, similar to Kilauea before the current caldera formed 1500 to 1790 CE. An 11m section of ash deposits crops out on the east rim of the summit along a caldera-bounding fault and is analogous to Kilauea where the caldera-bounding faults expose ash erupted as the present caldera formed. Most of the Loihi ash section is 3300 to 5880 yr BP, indicating that the larger caldera structure at Loihi is younger than 3300 yr BP. The landslides on the east and west edges of the summit are therefore younger 3300 yr BP. The uppermost south rift has several small pit craters between cones and pillow ridges, also analogous to Kilauea. Two cones near the deep low-T vents are steep pillow mounds with slopes of talus. High-resolution mapping reveals, for the first time, the many similarities between the structure and evolution of submarine Loihi Seamount and subaerial Kilauea Volcano.

Single-resolution and multiresolution extended-Kalman-filter-based reconstruction approaches to optical refraction tomography.

Science.gov (United States)

Naik, Naren; Vasu, R M; Ananthasayanam, M R

2010-02-20

The problem of reconstruction of a refractive-index distribution (RID) in optical refraction tomography (ORT) with optical path-length difference (OPD) data is solved using two adaptive-estimation-based extended-Kalman-filter (EKF) approaches. First, a basic single-resolution EKF (SR-EKF) is applied to a state variable model describing the tomographic process, to estimate the RID of an optically transparent refracting object from noisy OPD data. The initialization of the biases and covariances corresponding to the state and measurement noise is discussed. The state and measurement noise biases and covariances are adaptively estimated. An EKF is then applied to the wavelet-transformed state variable model to yield a wavelet-based multiresolution EKF (MR-EKF) solution approach. To numerically validate the adaptive EKF approaches, we evaluate them with benchmark studies of standard stationary cases, where comparative results with commonly used efficient deterministic approaches can be obtained. Detailed reconstruction studies for the SR-EKF and two versions of the MR-EKF (with Haar and Daubechies-4 wavelets) compare well with those obtained from a typically used variant of the (deterministic) algebraic reconstruction technique, the average correction per projection method, thus establishing the capability of the EKF for ORT. To the best of our knowledge, the present work contains unique reconstruction studies encompassing the use of EKF for ORT in single-resolution and multiresolution formulations, and also in the use of adaptive estimation of the EKF's noise covariances.

Effective deep learning training for single-image super-resolution in endomicroscopy exploiting video-registration-based reconstruction.

Science.gov (United States)

Ravì, Daniele; Szczotka, Agnieszka Barbara; Shakir, Dzhoshkun Ismail; Pereira, Stephen P; Vercauteren, Tom

2018-06-01

Probe-based confocal laser endomicroscopy (pCLE) is a recent imaging modality that allows performing in vivo optical biopsies. The design of pCLE hardware, and its reliance on an optical fibre bundle, fundamentally limits the image quality with a few tens of thousands fibres, each acting as the equivalent of a single-pixel detector, assembled into a single fibre bundle. Video registration techniques can be used to estimate high-resolution (HR) images by exploiting the temporal information contained in a sequence of low-resolution (LR) images. However, the alignment of LR frames, required for the fusion, is computationally demanding and prone to artefacts. In this work, we propose a novel synthetic data generation approach to train exemplar-based Deep Neural Networks (DNNs). HR pCLE images with enhanced quality are recovered by the models trained on pairs of estimated HR images (generated by the video registration algorithm) and realistic synthetic LR images. Performance of three different state-of-the-art DNNs techniques were analysed on a Smart Atlas database of 8806 images from 238 pCLE video sequences. The results were validated through an extensive image quality assessment that takes into account different quality scores, including a Mean Opinion Score (MOS). Results indicate that the proposed solution produces an effective improvement in the quality of the obtained reconstructed image. The proposed training strategy and associated DNNs allows us to perform convincing super-resolution of pCLE images.

Simulated cosmic microwave background maps at 0.5 deg resolution: Basic results

Science.gov (United States)

Hinshaw, G.; Bennett, C. L.; Kogut, A.

1995-01-01

We have simulated full-sky maps of the cosmic microwave background (CMB) anisotropy expected from cold dark matter (CDM) models at 0.5 deg and 1.0 deg angular resolution. Statistical properties of the maps are presented as a function of sky coverage, angular resolution, and instrument noise, and the implications of these results for observability of the Doppler peak are discussed. The rms fluctuations in a map are not a particularly robust probe of the existence of a Doppler peak; however, a full correlation analysis can provide reasonable sensitivity. We find that sensitivity to the Doppler peak depends primarily on the fraction of sky covered, and only secondarily on the angular resolution and noise level. Color plates of the simulated maps are presented to illustrate the anisotropies.

An evaluation for spatial resolution, using a single target on a medical image

Energy Technology Data Exchange (ETDEWEB)

Lee, Kyung Sung [Dept. of Radiotechnology, Cheju Halla University, Cheju (Korea, Republic of)

2016-12-15

Hitherto, spatial resolution has commonly been evaluated by test patterns or phantoms built on some specific distances (from close to far) between two objects (or double targets). This evaluation method's shortcoming is that resolution is restricted to target distances of phantoms made for test. Therefore, in order to solve the problem, this study proposes and verifies a new method to efficiently test spatial resolution with a single target. For the research I used PSF and JND to propose an idea to measure spatial resolution. After that, I made experiments by commonly used phantoms to verify my new evaluation hypothesis inferred from the above method. To analyse the hypothesis, I used LabVIEW program and got a line pixel from digital image. The result was identical to my spatial-resolution hypothesis inferred from a single target. The findings of the experiment proves only a single target can be enough to relatively evaluate spatial resolution on a digital image. In other words, the limit of the traditional spatial-resolution evaluation method, based on double targets, can be overcome by my new evaluation one using a single target.

Advancing the quantification of humid tropical forest cover loss with multi-resolution optical remote sensing data: Sampling & wall-to-wall mapping

Science.gov (United States)

Broich, Mark

Humid tropical forest cover loss is threatening the sustainability of ecosystem goods and services as vast forest areas are rapidly cleared for industrial scale agriculture and tree plantations. Despite the importance of humid tropical forest in the provision of ecosystem services and economic development opportunities, the spatial and temporal distribution of forest cover loss across large areas is not well quantified. Here I improve the quantification of humid tropical forest cover loss using two remote sensing-based methods: sampling and wall-to-wall mapping. In all of the presented studies, the integration of coarse spatial, high temporal resolution data with moderate spatial, low temporal resolution data enable advances in quantifying forest cover loss in the humid tropics. Imagery from the Moderate Resolution Imaging Spectroradiometer (MODIS) are used as the source of coarse spatial resolution, high temporal resolution data and imagery from the Landsat Enhanced Thematic Mapper Plus (ETM+) sensor are used as the source of moderate spatial, low temporal resolution data. In a first study, I compare the precision of different sampling designs for the Brazilian Amazon using the annual deforestation maps derived by the Brazilian Space Agency for reference. I show that sampling designs can provide reliable deforestation estimates; furthermore, sampling designs guided by MODIS data can provide more efficient estimates than the systematic design used for the United Nations Food and Agricultural Organization Forest Resource Assessment 2010. Sampling approaches, such as the one demonstrated, are viable in regions where data limitations, such as cloud contamination, limit exhaustive mapping methods. Cloud-contaminated regions experiencing high rates of change include Insular Southeast Asia, specifically Indonesia and Malaysia. Due to persistent cloud cover, forest cover loss in Indonesia has only been mapped at a 5-10 year interval using photo interpretation of single

Study on the Spatial Resolution of Single and Multiple Coincidences Compton Camera

Science.gov (United States)

Andreyev, Andriy; Sitek, Arkadiusz; Celler, Anna

2012-10-01

In this paper we study the image resolution that can be obtained from the Multiple Coincidences Compton Camera (MCCC). The principle of MCCC is based on a simultaneous acquisition of several gamma-rays emitted in cascade from a single nucleus. Contrary to a standard Compton camera, MCCC can theoretically provide the exact location of a radioactive source (based only on the identification of the intersection point of three cones created by a single decay), without complicated tomographic reconstruction. However, practical implementation of the MCCC approach encounters several problems, such as low detection sensitivities result in very low probability of coincident triple gamma-ray detection, which is necessary for the source localization. It is also important to evaluate how the detection uncertainties (finite energy and spatial resolution) influence identification of the intersection of three cones, thus the resulting image quality. In this study we investigate how the spatial resolution of the reconstructed images using the triple-cone reconstruction (TCR) approach compares to images reconstructed from the same data using standard iterative method based on single-cone. Results show, that FWHM for the point source reconstructed with TCR was 20-30% higher than the one obtained from the standard iterative reconstruction based on expectation maximization (EM) algorithm and conventional single-cone Compton imaging. Finite energy and spatial resolutions of the MCCC detectors lead to errors in conical surfaces definitions (“thick” conical surfaces) which only amplify in image reconstruction when intersection of three cones is being sought. Our investigations show that, in spite of being conceptually appealing, the identification of triple cone intersection constitutes yet another restriction of the multiple coincidence approach which limits the image resolution that can be obtained with MCCC and TCR algorithm.

High-resolution and large dynamic range nanomechanical mapping in tapping-mode atomic force microscopy

International Nuclear Information System (INIS)

Sahin, Ozgur; Erina, Natalia

2008-01-01

High spatial resolution imaging of material properties is an important task for the continued development of nanomaterials and studies of biological systems. Time-varying interaction forces between the vibrating tip and the sample in a tapping-mode atomic force microscope contain detailed information about the elastic, adhesive, and dissipative response of the sample. We report real-time measurement and analysis of the time-varying tip-sample interaction forces with recently introduced torsional harmonic cantilevers. With these measurements, high-resolution maps of elastic modulus, adhesion force, energy dissipation, and topography are generated simultaneously in a single scan. With peak tapping forces as low as 0.6 nN, we demonstrate measurements on blended polymers and self-assembled molecular architectures with feature sizes at 1, 10, and 500 nm. We also observed an elastic modulus measurement range of four orders of magnitude (1 MPa to 10 GPa) for a single cantilever under identical feedback conditions, which can be particularly useful for analyzing heterogeneous samples with largely different material components.

Mapping Deforestation in North Korea Using Phenology-Based Multi-Index and Random Forest

Directory of Open Access Journals (Sweden)

Yihua Jin

2016-12-01

Full Text Available Phenology-based multi-index with the random forest (RF algorithm can be used to overcome the shortcomings of traditional deforestation mapping that involves pixel-based classification, such as ISODATA or decision trees, and single images. The purpose of this study was to investigate methods to identify specific types of deforestation in North Korea, and to increase the accuracy of classification, using phenological characteristics extracted with multi-index and random forest algorithms. The mapping of deforestation area based on RF was carried out by merging phenology-based multi-indices (i.e., normalized difference vegetation index (NDVI, normalized difference water index (NDWI, and normalized difference soil index (NDSI derived from MODIS (Moderate Resolution Imaging Spectroradiometer products and topographical variables. Our results showed overall classification accuracy of 89.38%, with corresponding kappa coefficients of 0.87. In particular, for forest and farm land categories with similar phenological characteristic (e.g., paddy, plateau vegetation, unstocked forest, hillside field, this approach improved the classification accuracy in comparison with pixel-based methods and other classes. The deforestation types were identified by incorporating point data from high-resolution imagery, outcomes of image classification, and slope data. Our study demonstrated that the proposed methodology could be used for deciding on the restoration priority and monitoring the expansion of deforestation areas.

Combining pixel and object based image analysis of ultra-high resolution multibeam bathymetry and backscatter for habitat mapping in shallow marine waters

Science.gov (United States)

Ierodiaconou, Daniel; Schimel, Alexandre C. G.; Kennedy, David; Monk, Jacquomo; Gaylard, Grace; Young, Mary; Diesing, Markus; Rattray, Alex

2018-06-01

Habitat mapping data are increasingly being recognised for their importance in underpinning marine spatial planning. The ability to collect ultra-high resolution (cm) multibeam echosounder (MBES) data in shallow waters has facilitated understanding of the fine-scale distribution of benthic habitats in these areas that are often prone to human disturbance. Developing quantitative and objective approaches to integrate MBES data with ground observations for predictive modelling is essential for ensuring repeatability and providing confidence measures for habitat mapping products. Whilst supervised classification approaches are becoming more common, users are often faced with a decision whether to implement a pixel based (PB) or an object based (OB) image analysis approach, with often limited understanding of the potential influence of that decision on final map products and relative importance of data inputs to patterns observed. In this study, we apply an ensemble learning approach capable of integrating PB and OB Image Analysis from ultra-high resolution MBES bathymetry and backscatter data for mapping benthic habitats in Refuge Cove, a temperate coastal embayment in south-east Australia. We demonstrate the relative importance of PB and OB seafloor derivatives for the five broad benthic habitats that dominate the site. We found that OB and PB approaches performed well with differences in classification accuracy but not discernible statistically. However, a model incorporating elements of both approaches proved to be significantly more accurate than OB or PB methods alone and demonstrate the benefits of using MBES bathymetry and backscatter combined for class discrimination.

Object-based Landslide Mapping: Examples, Challenges and Opportunities

Science.gov (United States)

Hölbling, Daniel; Eisank, Clemens; Friedl, Barbara; Chang, Kang-Tsung; Tsai, Tsai-Tsung; Birkefeldt Møller Pedersen, Gro; Betts, Harley; Cigna, Francesca; Chiang, Shou-Hao; Aubrey Robson, Benjamin; Bianchini, Silvia; Füreder, Petra; Albrecht, Florian; Spiekermann, Raphael; Weinke, Elisabeth; Blaschke, Thomas; Phillips, Chris

2016-04-01

Over the last decade, object-based image analysis (OBIA) has been increasingly used for mapping landslides that occur after triggering events such as heavy rainfall. The increasing availability and quality of Earth Observation (EO) data in terms of temporal, spatial and spectral resolution allows for comprehensive mapping of landslides at multiple scales. Most often very high resolution (VHR) or high resolution (HR) optical satellite images are used in combination with a digital elevation model (DEM) and its products such as slope and curvature. Semi-automated object-based mapping makes use of various characteristics of image objects that are derived through segmentation. OBIA enables numerous spectral, spatial, contextual and textural image object properties to be applied during an analysis. This is especially useful when mapping complex natural features such as landslides and constitutes an advantage over pixel-based image analysis. However, several drawbacks in the process of object-based landslide mapping have not been overcome yet. The developed classification routines are often rather complex and limited regarding their transferability across areas and sensors. There is still more research needed to further improve present approaches and to fully exploit the capabilities of OBIA for landslide mapping. In this study several examples of object-based landslide mapping from various geographical regions with different characteristics are presented. Examples from the Austrian and Italian Alps are shown, whereby one challenge lies in the detection of small-scale landslides on steep slopes while preventing the classification of false positives with similar spectral properties (construction areas, utilized land, etc.). Further examples feature landslides mapped in Iceland, where the differentiation of landslides from other landscape-altering processes in a highly dynamic volcanic landscape poses a very distinct challenge, and in Norway, which is exposed to multiple

Atomic resolution electrostatic potential mapping of graphene sheets by off-axis electron holography

Energy Technology Data Exchange (ETDEWEB)

Cooper, David, E-mail: david.cooper@cea.fr [University Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054, Grenoble (France); Pan, Cheng-Ta; Haigh, Sarah [School of Materials, The University of Manchester, Manchester M13 9PL (United Kingdom)

2014-06-21

Off-axis electron holography has been performed at atomic resolution with the microscope operated at 80 kV to provide electrostatic potential maps from single, double, and triple layer graphene. These electron holograms have been reconstructed in order to obtain information about atomically resolved and mean inner potentials. We propose that off-axis electron holography can now be used to measure the electrical properties in a range of two-dimensional semiconductor materials and three dimensional devices comprising stacked layers of films to provide important information about their electrical properties.

Atomic resolution electrostatic potential mapping of graphene sheets by off-axis electron holography

International Nuclear Information System (INIS)

Cooper, David; Pan, Cheng-Ta; Haigh, Sarah

2014-01-01

Off-axis electron holography has been performed at atomic resolution with the microscope operated at 80 kV to provide electrostatic potential maps from single, double, and triple layer graphene. These electron holograms have been reconstructed in order to obtain information about atomically resolved and mean inner potentials. We propose that off-axis electron holography can now be used to measure the electrical properties in a range of two-dimensional semiconductor materials and three dimensional devices comprising stacked layers of films to provide important information about their electrical properties.

Monitoring microstructural evolution in-situ during cyclic deformation by high resolution reciprocal space mapping

DEFF Research Database (Denmark)

Diederichs, Annika Martina; Thiel, Felix; Fischer, Torben

2017-01-01

The recently developed synchrotron technique High Resolution Reciprocal Space Mapping (HRRSM) is used to characterize the deformation structures evolving during cyclic deformation of commercially pure, polycrystalline aluminium AA1050. Insight into the structural reorganization within single grains...... is gained by in-situ monitoring of the microstructural evolution during cyclic deformation. By HRRSM, a large number of individual subgrains can be resolved within individual grains in the bulk of polycrystalline specimens and their fate, their individual orientation and elastic stresses, tracked during...

Single Image Super-Resolution Based on Multi-Scale Competitive Convolutional Neural Network.

Science.gov (United States)

Du, Xiaofeng; Qu, Xiaobo; He, Yifan; Guo, Di

2018-03-06

Deep convolutional neural networks (CNNs) are successful in single-image super-resolution. Traditional CNNs are limited to exploit multi-scale contextual information for image reconstruction due to the fixed convolutional kernel in their building modules. To restore various scales of image details, we enhance the multi-scale inference capability of CNNs by introducing competition among multi-scale convolutional filters, and build up a shallow network under limited computational resources. The proposed network has the following two advantages: (1) the multi-scale convolutional kernel provides the multi-context for image super-resolution, and (2) the maximum competitive strategy adaptively chooses the optimal scale of information for image reconstruction. Our experimental results on image super-resolution show that the performance of the proposed network outperforms the state-of-the-art methods.

Localization-based super-resolution imaging of cellular structures.

Science.gov (United States)

Kanchanawong, Pakorn; Waterman, Clare M

2013-01-01

Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures.

Single image super-resolution based on compressive sensing and improved TV minimization sparse recovery

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Vishnukumar, S.; Wilscy, M.

2017-12-01

In this paper, we propose a single image Super-Resolution (SR) method based on Compressive Sensing (CS) and Improved Total Variation (TV) Minimization Sparse Recovery. In the CS framework, low-resolution (LR) image is treated as the compressed version of high-resolution (HR) image. Dictionary Training and Sparse Recovery are the two phases of the method. K-Singular Value Decomposition (K-SVD) method is used for dictionary training and the dictionary represents HR image patches in a sparse manner. Here, only the interpolated version of the LR image is used for training purpose and thereby the structural self similarity inherent in the LR image is exploited. In the sparse recovery phase the sparse representation coefficients with respect to the trained dictionary for LR image patches are derived using Improved TV Minimization method. HR image can be reconstructed by the linear combination of the dictionary and the sparse coefficients. The experimental results show that the proposed method gives better results quantitatively as well as qualitatively on both natural and remote sensing images. The reconstructed images have better visual quality since edges and other sharp details are preserved.

aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

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Niedworok, Christian J.; Brown, Alexander P. Y.; Jorge Cardoso, M.; Osten, Pavel; Ourselin, Sebastien; Modat, Marc; Margrie, Troy W.

2016-01-01

The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain. PMID:27384127

Low-Cost Ultra-High Spatial and Temporal Resolution Mapping of Intertidal Rock Platforms

Science.gov (United States)

Bryson, M.; Johnson-Roberson, M.; Murphy, R.

2012-07-01

Intertidal ecosystems have primarily been studied using field-based sampling; remote sensing offers the ability to collect data over large areas in a snapshot of time which could compliment field-based sampling methods by extrapolating them into the wider spatial and temporal context. Conventional remote sensing tools (such as satellite and aircraft imaging) provide data at relatively course, sub-meter resolutions or with limited temporal resolutions and relatively high costs for small-scale environmental science and ecology studies. In this paper, we describe a low-cost, kite-based imaging system and photogrammetric pipeline that was developed for constructing highresolution, 3D, photo-realistic terrain models of intertidal rocky shores. The processing pipeline uses automatic image feature detection and matching, structure-from-motion and photo-textured terrain surface reconstruction algorithms that require minimal human input and only a small number of ground control points and allow the use of cheap, consumer-grade digital cameras. The resulting maps combine colour and topographic information at sub-centimeter resolutions over an area of approximately 100m, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Results of the system are presented for an intertidal rock platform at Cape Banks, Sydney, Australia. Potential uses of this technique include mapping of plant (micro- and macro-algae) and animal (e.g. gastropods) assemblages at multiple spatial and temporal scales.

Clinical high-resolution mapping of the proteoglycan-bound water fraction in articular cartilage of the human knee joint.

Science.gov (United States)

Bouhrara, Mustapha; Reiter, David A; Sexton, Kyle W; Bergeron, Christopher M; Zukley, Linda M; Spencer, Richard G

2017-11-01

We applied our recently introduced Bayesian analytic method to achieve clinically-feasible in-vivo mapping of the proteoglycan water fraction (PgWF) of human knee cartilage with improved spatial resolution and stability as compared to existing methods. Multicomponent driven equilibrium single-pulse observation of T 1 and T 2 (mcDESPOT) datasets were acquired from the knees of two healthy young subjects and one older subject with previous knee injury. Each dataset was processed using Bayesian Monte Carlo (BMC) analysis incorporating a two-component tissue model. We assessed the performance and reproducibility of BMC and of the conventional analysis of stochastic region contraction (SRC) in the estimation of PgWF. Stability of the BMC analysis of PgWF was tested by comparing independent high-resolution (HR) datasets from each of the two young subjects. Unlike SRC, the BMC-derived maps from the two HR datasets were essentially identical. Furthermore, SRC maps showed substantial random variation in estimated PgWF, and mean values that differed from those obtained using BMC. In addition, PgWF maps derived from conventional low-resolution (LR) datasets exhibited partial volume and magnetic susceptibility effects. These artifacts were absent in HR PgWF images. Finally, our analysis showed regional variation in PgWF estimates, and substantially higher values in the younger subjects as compared to the older subject. BMC-mcDESPOT permits HR in-vivo mapping of PgWF in human knee cartilage in a clinically-feasible acquisition time. HR mapping reduces the impact of partial volume and magnetic susceptibility artifacts compared to LR mapping. Finally, BMC-mcDESPOT demonstrated excellent reproducibility in the determination of PgWF. Published by Elsevier Inc.

Super-resolution from single photon emission: toward biological application

Science.gov (United States)

Moreva, E.; Traina, P.; Forneris, J.; Ditalia Tchernij, S.; Guarina, L.; Franchino, C.; Picollo, F.; Ruo Berchera, I.; Brida, G.; Degiovanni, I. P.; Carabelli, V.; Olivero, P.; Genovese, M.

2017-08-01

Properties of quantum light represent a tool for overcoming limits of classical optics. Several experiments have demonstrated this advantage ranging from quantum enhanced imaging to quantum illumination. In this work, experimental demonstration of quantum-enhanced resolution in confocal fluorescence microscopy will be presented. This is achieved by exploiting the non-classical photon statistics of fluorescence emission of single nitrogen-vacancy (NV) color centers in diamond. By developing a general model of super-resolution based on the direct sampling of the kth-order autocorrelation function of the photoluminescence signal, we show the possibility to resolve, in principle, arbitrarily close emitting centers. Finally, possible applications of NV-based fluorescent nanodiamonds in biosensing and future developments will be presented.

Snow Cover Maps from MODIS Images at 250 m Resolution, Part 2: Validation

Directory of Open Access Journals (Sweden)

Marc Zebisch

2013-03-01

Full Text Available The performance of a new algorithm for binary snow cover monitoring based on Moderate Resolution Imaging Spectroradiometer (MODIS satellite images at 250 m resolution is validated using snow cover maps (SCA based on Landsat 7 ETM+ images and in situ snow depth measurements from ground stations in selected test sites in Central Europe. The advantages of the proposed algorithm are the improved ground resolution of 250 m and the near real-time availability with respect to the 500 m standard National Aeronautics and Space Administration (NASA MODIS snow products (MOD10 and MYD10. It allows a more accurate snow cover monitoring at a local scale, especially in mountainous areas characterized by large landscape heterogeneity. The near real-time delivery makes the product valuable as input for hydrological models, e.g., for flood forecast. A comparison to sixteen snow cover maps derived from Landsat ETM/ETM+ showed an overall accuracy of 88.1%, which increases to 93.6% in areas outside of forests. A comparison of the SCA derived from the proposed algorithm with standard MODIS products, MYD10 and MOD10, indicates an agreement of around 85.4% with major discrepancies in forested areas. The validation of MODIS snow cover maps with 148 in situ snow depth measurements shows an accuracy ranging from 94% to around 82%, where the lowest accuracies is found in very rugged terrain restricted to in situ stations along north facing slopes, which lie in shadow in winter during the early morning acquisition.

Evaluation of ALOS PALSAR Data for High-Resolution Mapping of Vegetated Wetlands in Alaska

Directory of Open Access Journals (Sweden)

Daniel Clewley

2015-06-01

Full Text Available As the largest natural source of methane, wetlands play an important role in the carbon cycle. High-resolution maps of wetland type and extent are required to quantify wetland responses to climate change. Mapping northern wetlands is particularly important because of a disproportionate increase in temperatures at higher latitudes. Synthetic aperture radar data from a spaceborne platform can be used to map wetland types and dynamics over large areas. Following from earlier work by Whitcomb et al. (2009 using Japanese Earth Resources Satellite (JERS-1 data, we applied the “random forests” classification algorithm to variables from L-band ALOS PALSAR data for 2007, topographic data (e.g., slope, elevation and locational information (latitude, longitude to derive a map of vegetated wetlands in Alaska, with a spatial resolution of 50 m. We used the National Wetlands Inventory and National Land Cover Database (for upland areas to select training and validation data and further validated classification results with an independent dataset that we created. A number of improvements were made to the method of Whitcomb et al. (2009: (1 more consistent training data in upland areas; (2 better distribution of training data across all classes by taking a stratified random sample of all available training pixels; and (3 a more efficient implementation, which allowed classification of the entire state as a single entity (rather than in separate tiles, which eliminated discontinuities at tile boundaries. The overall accuracy for discriminating wetland from upland was 95%, and the accuracy at the level of wetland classes was 85%. The total area of wetlands mapped was 0.59 million km2, or 36% of the total land area of the state of Alaska. The map will be made available to download from NASA’s wetland monitoring website.

Spectrally Resolved and Functional Super-resolution Microscopy via Ultrahigh-Throughput Single-Molecule Spectroscopy.

Science.gov (United States)

Yan, Rui; Moon, Seonah; Kenny, Samuel J; Xu, Ke

2018-03-20

As an elegant integration of the spatial and temporal dimensions of single-molecule fluorescence, single-molecule localization microscopy (SMLM) overcomes the diffraction-limited resolution barrier of optical microscopy by localizing single molecules that stochastically switch between fluorescent and dark states over time. While this type of super-resolution microscopy (SRM) technique readily achieves remarkable spatial resolutions of ∼10 nm, it typically provides no spectral information. Meanwhile, current scanning-based single-location approaches for mapping the positions and spectra of single molecules are limited by low throughput and are difficult to apply to densely labeled (bio)samples. In this Account, we summarize the rationale, design, and results of our recent efforts toward the integration of the spectral dimension of single-molecule fluorescence with SMLM to achieve spectrally resolved SMLM (SR-SMLM) and functional SRM ( f-SRM). By developing a wide-field scheme for spectral measurement and implementing single-molecule fluorescence on-off switching typical of SMLM, we first showed that in densely labeled (bio)samples it is possible to record the fluorescence spectra and positions of millions of single molecules synchronously within minutes, giving rise to ultrahigh-throughput single-molecule spectroscopy and SR-SMLM. This allowed us to first show statistically that for many dyes, single molecules of the same species exhibit near identical emission in fixed cells. This narrow distribution of emission wavelengths, which contrasts markedly with previous results at solid surfaces, allowed us to unambiguously identify single molecules of spectrally similar dyes. Crosstalk-free, multiplexed SRM was thus achieved for four dyes that were merely 10 nm apart in emission spectrum, with the three-dimensional SRM images of all four dyes being automatically aligned within one image channel. The ability to incorporate single-molecule fluorescence measurement with

Land use/land cover mapping using multi-scale texture processing of high resolution data

Science.gov (United States)

Wong, S. N.; Sarker, M. L. R.

2014-02-01

Land use/land cover (LULC) maps are useful for many purposes, and for a long time remote sensing techniques have been used for LULC mapping using different types of data and image processing techniques. In this research, high resolution satellite data from IKONOS was used to perform land use/land cover mapping in Johor Bahru city and adjacent areas (Malaysia). Spatial image processing was carried out using the six texture algorithms (mean, variance, contrast, homogeneity, entropy, and GLDV angular second moment) with five difference window sizes (from 3×3 to 11×11). Three different classifiers i.e. Maximum Likelihood Classifier (MLC), Artificial Neural Network (ANN) and Supported Vector Machine (SVM) were used to classify the texture parameters of different spectral bands individually and all bands together using the same training and validation samples. Results indicated that texture parameters of all bands together generally showed a better performance (overall accuracy = 90.10%) for land LULC mapping, however, single spectral band could only achieve an overall accuracy of 72.67%. This research also found an improvement of the overall accuracy (OA) using single-texture multi-scales approach (OA = 89.10%) and single-scale multi-textures approach (OA = 90.10%) compared with all original bands (OA = 84.02%) because of the complementary information from different bands and different texture algorithms. On the other hand, all of the three different classifiers have showed high accuracy when using different texture approaches, but SVM generally showed higher accuracy (90.10%) compared to MLC (89.10%) and ANN (89.67%) especially for the complex classes such as urban and road.

Land use/land cover mapping using multi-scale texture processing of high resolution data

International Nuclear Information System (INIS)

Wong, S N; Sarker, M L R

2014-01-01

Land use/land cover (LULC) maps are useful for many purposes, and for a long time remote sensing techniques have been used for LULC mapping using different types of data and image processing techniques. In this research, high resolution satellite data from IKONOS was used to perform land use/land cover mapping in Johor Bahru city and adjacent areas (Malaysia). Spatial image processing was carried out using the six texture algorithms (mean, variance, contrast, homogeneity, entropy, and GLDV angular second moment) with five difference window sizes (from 3×3 to 11×11). Three different classifiers i.e. Maximum Likelihood Classifier (MLC), Artificial Neural Network (ANN) and Supported Vector Machine (SVM) were used to classify the texture parameters of different spectral bands individually and all bands together using the same training and validation samples. Results indicated that texture parameters of all bands together generally showed a better performance (overall accuracy = 90.10%) for land LULC mapping, however, single spectral band could only achieve an overall accuracy of 72.67%. This research also found an improvement of the overall accuracy (OA) using single-texture multi-scales approach (OA = 89.10%) and single-scale multi-textures approach (OA = 90.10%) compared with all original bands (OA = 84.02%) because of the complementary information from different bands and different texture algorithms. On the other hand, all of the three different classifiers have showed high accuracy when using different texture approaches, but SVM generally showed higher accuracy (90.10%) compared to MLC (89.10%) and ANN (89.67%) especially for the complex classes such as urban and road

Localization-based super-resolution imaging meets high-content screening.

Science.gov (United States)

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

Directory of Open Access Journals (Sweden)

Wang Zhiquan

2007-07-01

Full Text Available Abstract Background Radiation hybrid (RH maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL, haplotype map construction and refinement of candidate gene searches. Results A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1 as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement. Conclusion The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.

Force scanning: a rapid, high-resolution approach for spatial mechanical property mapping

International Nuclear Information System (INIS)

Darling, E M

2011-01-01

Atomic force microscopy (AFM) can be used to co-localize mechanical properties and topographical features through property mapping techniques. The most common approach for testing biological materials at the microscale and nanoscale is force mapping, which involves taking individual force curves at discrete sites across a region of interest. The limitations of force mapping include long testing times and low resolution. While newer AFM methodologies, like modulated scanning and torsional oscillation, circumvent this problem, their adoption for biological materials has been limited. This could be due to their need for specialized software algorithms and/or hardware. The objective of this study is to develop a novel force scanning technique using AFM to rapidly capture high-resolution topographical images of soft biological materials while simultaneously quantifying their mechanical properties. Force scanning is a straightforward methodology applicable to a wide range of materials and testing environments, requiring no special modification to standard AFMs. Essentially, if a contact-mode image can be acquired, then force scanning can be used to produce a spatial modulus map. The current study first validates this technique using agarose gels, comparing results to ones achieved by the standard force mapping approach. Biologically relevant demonstrations are then presented for high-resolution modulus mapping of individual cells, cell-cell interfaces, and articular cartilage tissue.

Mapping Urban Ecosystem Services Using High Resolution Aerial Photography

Science.gov (United States)

Pilant, A. N.; Neale, A.; Wilhelm, D.

2010-12-01

Ecosystem services (ES) are the many life-sustaining benefits we receive from nature: e.g., clean air and water, food and fiber, cultural-aesthetic-recreational benefits, pollination and flood control. The ES concept is emerging as a means of integrating complex environmental and economic information to support informed environmental decision making. The US EPA is developing a web-based National Atlas of Ecosystem Services, with a component for urban ecosystems. Currently, the only wall-to-wall, national scale land cover data suitable for this analysis is the National Land Cover Data (NLCD) at 30 m spatial resolution with 5 and 10 year updates. However, aerial photography is acquired at higher spatial resolution (0.5-3 m) and more frequently (1-5 years, typically) for most urban areas. Land cover was mapped in Raleigh, NC using freely available USDA National Agricultural Imagery Program (NAIP) with 1 m ground sample distance to test the suitability of aerial photography for urban ES analysis. Automated feature extraction techniques were used to extract five land cover classes, and an accuracy assessment was performed using standard techniques. Results will be presented that demonstrate applications to mapping ES in urban environments: greenways, corridors, fragmentation, habitat, impervious surfaces, dark and light pavement (urban heat island). Automated feature extraction results mapped over NAIP color aerial photograph. At this scale, we can look at land cover and related ecosystem services at the 2-10 m scale. Small features such as individual trees and sidewalks are visible and mappable. Classified aerial photo of Downtown Raleigh NC Red: impervious surface Dark Green: trees Light Green: grass Tan: soil

Estimated Depth Maps of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery (Draft)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Estimated shallow-water, depth maps were produced using rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations in the...

Mapping the layer count of few-layer hexagonal boron nitride at high lateral spatial resolutions

Science.gov (United States)

Mohsin, Ali; Cross, Nicholas G.; Liu, Lei; Watanabe, Kenji; Taniguchi, Takashi; Duscher, Gerd; Gu, Gong

2018-01-01

Layer count control and uniformity of two dimensional (2D) layered materials are critical to the investigation of their properties and to their electronic device applications, but methods to map 2D material layer count at nanometer-level lateral spatial resolutions have been lacking. Here, we demonstrate a method based on two complementary techniques widely available in transmission electron microscopes (TEMs) to map the layer count of multilayer hexagonal boron nitride (h-BN) films. The mass-thickness contrast in high-angle annular dark-field (HAADF) imaging in the scanning transmission electron microscope (STEM) mode allows for thickness determination in atomically clean regions with high spatial resolution (sub-nanometer), but is limited by surface contamination. To complement, another technique based on the boron K ionization edge in the electron energy loss spectroscopy spectrum (EELS) of h-BN is developed to quantify the layer count so that surface contamination does not cause an overestimate, albeit at a lower spatial resolution (nanometers). The two techniques agree remarkably well in atomically clean regions with discrepancies within  ±1 layer. For the first time, the layer count uniformity on the scale of nanometers is quantified for a 2D material. The methodology is applicable to layer count mapping of other 2D layered materials, paving the way toward the synthesis of multilayer 2D materials with homogeneous layer count.

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

DEFF Research Database (Denmark)

Cao, Hongzhi; Hastie, Alex R.; Cao, Dandan

2014-01-01

mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost......-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion. RESULTS: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger...... fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides...

Learning-based compressed sensing for infrared image super resolution

Science.gov (United States)

Zhao, Yao; Sui, Xiubao; Chen, Qian; Wu, Shaochi

2016-05-01

This paper presents an infrared image super-resolution method based on compressed sensing (CS). First, the reconstruction model under the CS framework is established and a Toeplitz matrix is selected as the sensing matrix. Compared with traditional learning-based methods, the proposed method uses a set of sub-dictionaries instead of two coupled dictionaries to recover high resolution (HR) images. And Toeplitz sensing matrix allows the proposed method time-efficient. Second, all training samples are divided into several feature spaces by using the proposed adaptive k-means classification method, which is more accurate than the standard k-means method. On the basis of this approach, a complex nonlinear mapping from the HR space to low resolution (LR) space can be converted into several compact linear mappings. Finally, the relationships between HR and LR image patches can be obtained by multi-sub-dictionaries and HR infrared images are reconstructed by the input LR images and multi-sub-dictionaries. The experimental results show that the proposed method is quantitatively and qualitatively more effective than other state-of-the-art methods.

High-resolution Mapping of Permafrost and Soil Freeze/thaw Dynamics in the Tibetan Plateau Based on Multi-sensor Satellite Observations

Science.gov (United States)

Zhang, W.; Yi, Y.; Yang, K.; Kimball, J. S.

2016-12-01

The Tibetan Plateau (TP) is underlain by the world's largest extent of alpine permafrost ( 2.5×106 km2), dominated by sporadic and discontinuous permafrost with strong sensitivity to climate warming. Detailed permafrost distributions and patterns in most of the TP region are still unknown due to extremely sparse in-situ observations in this region characterized by heterogeneous land cover and large temporal dynamics in surface soil moisture conditions. Therefore, satellite-based temperature and moisture observations are essential for high-resolution mapping of permafrost distribution and soil active layer changes in the TP region. In this study, we quantify the TP regional permafrost distribution at 1-km resolution using a detailed satellite data-driven soil thermal process model (GIPL2). The soil thermal model is calibrated and validated using in-situ soil temperature/moisture observations from the CAMP/Tibet field campaign (9 sites: 0-300 cm soil depth sampling from 1997-2007), a multi-scale soil moisture and temperature monitoring network in the central TP (CTP-SMTMN, 57 sites: 5-40 cm, 2010-2014) and across the whole plateau (China Meteorology Administration, 98 sites: 0-320 cm, 2000-2015). Our preliminary results using the CAMP/Tibet and CTP-SMTMN network observations indicate strong controls of surface thermal and soil moisture conditions on soil freeze/thaw dynamics, which vary greatly with underlying topography, soil texture and vegetation cover. For regional mapping of soil freeze/thaw and permafrost dynamics, we use the most recent soil moisture retrievals from the NASA SMAP (Soil Moisture Active Passive) sensor to account for the effects of temporal soil moisture dynamics on soil thermal heat transfer, with surface thermal conditions defined by MODIS (Moderate Resolution Imaging Spectroradiometer) land surface temperature records. Our study provides the first 1-km map of spatial patterns and recent changes of permafrost conditions in the TP.

Conflict resolution efforts through stakeholder mapping in Labanan Research Forest, Berau, East Kalimantan, Indonesia

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Wiati, C. B.; Indriyanti, S. Y.; Maharani, R.; Subarudi

2018-04-01

Conflict resolution in Labanan Research Forest (LRF) by the Dipterocarps Forest Ecosystem Research and Development Center (Balai Besar Penelitian dan Pengembangan Ekosistem Hutan Dipterokarpa – B2P2EHD) needs support from other parties that are also interested in such forest management. This paper aimed to presented conflict resolution in LRF through stakeholder mapping for its engagement. This research was conducted for seven months (June to December 2015) with interviews and literature study as its data collection. Collected data were analysed by a stakeholder analysis and matrix based on their interest and power levels. Two important findings were: (1) There are 19 parties having interests in the existence of LRF should be engaged; (2) Conflict resolution of LRF can be achieved: (a) ensuring key stakeholders which have high interest and high power level has same perception in existence and management of LRF, (b) establishing a partnership with primary stakeholders which have high interest and high power levels; (c) building partnerships between primary stakeholders which have high interest but low power levels, (d) building partnerships between key and secondary stakeholders which have low interest but high power levels and (e) gaining support from primary and secondary stakeholders which have low interest and low power levels. Stakeholder mapping is an important tool for tenure conflict resolution through mapping the power and interest of the conflicted parties and finding the proper parties to be approached.

High resolution population distribution maps for Southeast Asia in 2010 and 2015.

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Gaughan, Andrea E; Stevens, Forrest R; Linard, Catherine; Jia, Peng; Tatem, Andrew J

2013-01-01

Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

High resolution population distribution maps for Southeast Asia in 2010 and 2015.

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Andrea E Gaughan

Full Text Available Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

Wild boar mapping using population-density statistics: From polygons to high resolution raster maps.

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Pittiglio, Claudia; Khomenko, Sergei; Beltran-Alcrudo, Daniel

2018-01-01

The wild boar is an important crop raider as well as a reservoir and agent of spread of swine diseases. Due to increasing densities and expanding ranges worldwide, the related economic losses in livestock and agricultural sectors are significant and on the rise. Its management and control would strongly benefit from accurate and detailed spatial information on species distribution and abundance, which are often available only for small areas. Data are commonly available at aggregated administrative units with little or no information about the distribution of the species within the unit. In this paper, a four-step geostatistical downscaling approach is presented and used to disaggregate wild boar population density statistics from administrative units of different shape and size (polygons) to 5 km resolution raster maps by incorporating auxiliary fine scale environmental variables. 1) First a stratification method was used to define homogeneous bioclimatic regions for the analysis; 2) Under a geostatistical framework, the wild boar densities at administrative units, i.e. subnational areas, were decomposed into trend and residual components for each bioclimatic region. Quantitative relationships between wild boar data and environmental variables were estimated through multiple regression and used to derive trend components at 5 km spatial resolution. Next, the residual components (i.e., the differences between the trend components and the original wild boar data at administrative units) were downscaled at 5 km resolution using area-to-point kriging. The trend and residual components obtained at 5 km resolution were finally added to generate fine scale wild boar estimates for each bioclimatic region. 3) These maps were then mosaicked to produce a final output map of predicted wild boar densities across most of Eurasia. 4) Model accuracy was assessed at each different step using input as well as independent data. We discuss advantages and limits of the method and its

Towards high resolution mapping of 3-D mesoscale dynamics from observations

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B. Buongiorno Nardelli

2012-10-01

Full Text Available The MyOcean R&D project MESCLA (MEsoSCaLe dynamical Analysis through combined model, satellite and in situ data was devoted to the high resolution 3-D retrieval of tracer and velocity fields in the oceans, based on the combination of in situ and satellite observations and quasi-geostrophic dynamical models. The retrieval techniques were also tested and compared with the output of a primitive equation model, with particular attention to the accuracy of the vertical velocity field as estimated through the Q vector formulation of the omega equation. The project focused on a test case, covering the region where the Gulf Stream separates from the US East Coast. This work demonstrated that innovative methods for the high resolution mapping of 3-D mesoscale dynamics from observations can be used to build the next generations of operational observation-based products.

4 Vesta in Color: High Resolution Mapping from Dawn Framing Camera Images

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Reddy, V.; LeCorre, L.; Nathues, A.; Sierks, H.; Christensen, U.; Hoffmann, M.; Schroeder, S. E.; Vincent, J. B.; McSween, H. Y.; Denevi, B. W.;

A novel intra-operative, high-resolution atrial mapping approach.

Science.gov (United States)

Yaksh, Ameeta; van der Does, Lisette J M E; Kik, Charles; Knops, Paul; Oei, Frans B S; van de Woestijne, Pieter C; Bekkers, Jos A; Bogers, Ad J J C; Allessie, Maurits A; de Groot, Natasja M S

2015-12-01

A new technique is demonstrated for extensive high-resolution intra-operative atrial mapping that will facilitate the localization of atrial fibrillation (AF) sources and identification of the substrate perpetuating AF. Prior to the start of extra-corporal circulation, a 8 × 24-electrode array (2-mm inter-electrode distance) is placed subsequently on all the right and left epicardial atrial sites, including Bachmann's bundle, for recording of unipolar electrograms during sinus rhythm and (induced) AF. AF is induced by high-frequency pacing at the right atrial free wall. A pacemaker wire stitched to the right atrium serves as a reference signal. The indifferent pole is connected to a steal wire fixed to subcutaneous tissue. Electrograms are recorded by a computerized mapping system and, after amplification (gain 1000), filtering (bandwidth 0.5-400 Hz), sampling (1 kHz) and analogue to digital conversion (16 bits), automatically stored on hard disk. During the mapping procedure, real-time visualization secures electrogram quality. Analysis will be performed offline. This technique was performed in 168 patients of 18 years and older, with coronary and/or structural heart disease, with or without AF, electively scheduled for cardiac surgery and a ventricular ejection fraction above 40 %. The mean duration of the entire mapping procedure including preparation time was 9 ± 2 min. Complications related to the mapping procedure during or after cardiac surgery were not observed. We introduce the first epicardial atrial mapping approach with a high resolution of ≥1728 recording sites which can be performed in a procedure time of only 9±2 mins. This mapping technique can potentially identify areas responsible for initiation and persistence of AF and hopefully can individualize both diagnosis and therapy of AF.

Large-Area, High-Resolution Tree Cover Mapping with Multi-Temporal SPOT5 Imagery, New South Wales, Australia

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Adrian Fisher

2016-06-01

Full Text Available Tree cover maps are used for many purposes, such as vegetation mapping, habitat connectivity and fragmentation studies. Small remnant patches of native vegetation are recognised as ecologically important, yet they are underestimated in remote sensing products derived from Landsat. High spatial resolution sensors are capable of mapping small patches of trees, but their use in large-area mapping has been limited. In this study, multi-temporal Satellite pour l’Observation de la Terre 5 (SPOT5 High Resolution Geometrical data was pan-sharpened to 5 m resolution and used to map tree cover for the Australian state of New South Wales (NSW, an area of over 800,000 km2. Complete coverages of SPOT5 panchromatic and multispectral data over NSW were acquired during four consecutive summers (2008–2011 for a total of 1256 images. After pre-processing, the imagery was used to model foliage projective cover (FPC, a measure of tree canopy density commonly used in Australia. The multi-temporal imagery, FPC models and 26,579 training pixels were used in a binomial logistic regression model to estimate the probability of each pixel containing trees. The probability images were classified into a binary map of tree cover using local thresholds, and then visually edited to reduce errors. The final tree map was then attributed with the mean FPC value from the multi-temporal imagery. Validation of the binary map based on visually assessed high resolution reference imagery revealed an overall accuracy of 88% (±0.51% standard error, while comparison against airborne lidar derived data also resulted in an overall accuracy of 88%. A preliminary assessment of the FPC map by comparing against 76 field measurements showed a very good agreement (r2 = 0.90 with a root mean square error of 8.57%, although this may not be representative due to the opportunistic sampling design. The map represents a regionally consistent and locally relevant record of tree cover for NSW, and

Kite aerial photography for low-cost, ultra-high spatial resolution multi-spectral mapping of intertidal landscapes.

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Mitch Bryson

Full Text Available Intertidal ecosystems have primarily been studied using field-based sampling; remote sensing offers the ability to collect data over large areas in a snapshot of time that could complement field-based sampling methods by extrapolating them into the wider spatial and temporal context. Conventional remote sensing tools (such as satellite and aircraft imaging provide data at limited spatial and temporal resolutions and relatively high costs for small-scale environmental science and ecologically-focussed studies. In this paper, we describe a low-cost, kite-based imaging system and photogrammetric/mapping procedure that was developed for constructing high-resolution, three-dimensional, multi-spectral terrain models of intertidal rocky shores. The processing procedure uses automatic image feature detection and matching, structure-from-motion and photo-textured terrain surface reconstruction algorithms that require minimal human input and only a small number of ground control points and allow the use of cheap, consumer-grade digital cameras. The resulting maps combine imagery at visible and near-infrared wavelengths and topographic information at sub-centimeter resolutions over an intertidal shoreline 200 m long, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Results of the system are presented for an intertidal rocky shore at Jervis Bay, New South Wales, Australia. Potential uses of this technique include mapping of plant (micro- and macro-algae and animal (e.g. gastropods assemblages at multiple spatial and temporal scales.

Kite aerial photography for low-cost, ultra-high spatial resolution multi-spectral mapping of intertidal landscapes.

Science.gov (United States)

Bryson, Mitch; Johnson-Roberson, Matthew; Murphy, Richard J; Bongiorno, Daniel

2013-01-01

Intertidal ecosystems have primarily been studied using field-based sampling; remote sensing offers the ability to collect data over large areas in a snapshot of time that could complement field-based sampling methods by extrapolating them into the wider spatial and temporal context. Conventional remote sensing tools (such as satellite and aircraft imaging) provide data at limited spatial and temporal resolutions and relatively high costs for small-scale environmental science and ecologically-focussed studies. In this paper, we describe a low-cost, kite-based imaging system and photogrammetric/mapping procedure that was developed for constructing high-resolution, three-dimensional, multi-spectral terrain models of intertidal rocky shores. The processing procedure uses automatic image feature detection and matching, structure-from-motion and photo-textured terrain surface reconstruction algorithms that require minimal human input and only a small number of ground control points and allow the use of cheap, consumer-grade digital cameras. The resulting maps combine imagery at visible and near-infrared wavelengths and topographic information at sub-centimeter resolutions over an intertidal shoreline 200 m long, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Results of the system are presented for an intertidal rocky shore at Jervis Bay, New South Wales, Australia. Potential uses of this technique include mapping of plant (micro- and macro-algae) and animal (e.g. gastropods) assemblages at multiple spatial and temporal scales.

AUTOMATIC INTERPRETATION OF HIGH RESOLUTION SAR IMAGES: FIRST RESULTS OF SAR IMAGE SIMULATION FOR SINGLE BUILDINGS

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J. Tao

2012-09-01

Full Text Available Due to the all-weather data acquisition capabilities, high resolution space borne Synthetic Aperture Radar (SAR plays an important role in remote sensing applications like change detection. However, because of the complex geometric mapping of buildings in urban areas, SAR images are often hard to interpret. SAR simulation techniques ease the visual interpretation of SAR images, while fully automatic interpretation is still a challenge. This paper presents a method for supporting the interpretation of high resolution SAR images with simulated radar images using a LiDAR digital surface model (DSM. Line features are extracted from the simulated and real SAR images and used for matching. A single building model is generated from the DSM and used for building recognition in the SAR image. An application for the concept is presented for the city centre of Munich where the comparison of the simulation to the TerraSAR-X data shows a good similarity. Based on the result of simulation and matching, special features (e.g. like double bounce lines, shadow areas etc. can be automatically indicated in SAR image.

A high-resolution comparative RH map of porcine chromosome (SSC) 2.

NARCIS (Netherlands)

Rattink, A.P.; Faivre, M.; Jungerius, B.J.; Groenen, M.A.M.; Harlizius, B.

2001-01-01

A high-resolution comparative map was constructed for porcine Chromosome (SSC) 2, where a QTL for back fat thickness (BFT) is located. A radiation hybrid (RH) map containing 33 genes and 25 microsatellite markers was constructed for this chromosome with a 3000-rad porcine RH panel. In total, 16

Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

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Gómez Marcela

2009-12-01

Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).

Science.gov (United States)

Galeano, Carlos H; Fernández, Andrea C; Gómez, Marcela; Blair, Matthew W

2009-12-23

Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation

Clickstream data yields high-resolution maps of science

Energy Technology Data Exchange (ETDEWEB)

Bollen, Johan [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory; Hagberg, Aric [Los Alamos National Laboratory; Bettencourt, Luis [Los Alamos National Laboratory; Chute, Ryan [Los Alamos National Laboratory; Rodriguez, Marko A [Los Alamos National Laboratory; Balakireva, Lyudmila [Los Alamos National Laboratory

2009-01-01

Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantagees of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science.

Mapping Sub-Antarctic Cushion Plants Using Random Forests to Combine Very High Resolution Satellite Imagery and Terrain Modelling

Science.gov (United States)

Bricher, Phillippa K.; Lucieer, Arko; Shaw, Justine; Terauds, Aleks; Bergstrom, Dana M.

2013-01-01

Monitoring changes in the distribution and density of plant species often requires accurate and high-resolution baseline maps of those species. Detecting such change at the landscape scale is often problematic, particularly in remote areas. We examine a new technique to improve accuracy and objectivity in mapping vegetation, combining species distribution modelling and satellite image classification on a remote sub-Antarctic island. In this study, we combine spectral data from very high resolution WorldView-2 satellite imagery and terrain variables from a high resolution digital elevation model to improve mapping accuracy, in both pixel- and object-based classifications. Random forest classification was used to explore the effectiveness of these approaches on mapping the distribution of the critically endangered cushion plant Azorella macquariensis Orchard (Apiaceae) on sub-Antarctic Macquarie Island. Both pixel- and object-based classifications of the distribution of Azorella achieved very high overall validation accuracies (91.6–96.3%, κ = 0.849–0.924). Both two-class and three-class classifications were able to accurately and consistently identify the areas where Azorella was absent, indicating that these maps provide a suitable baseline for monitoring expected change in the distribution of the cushion plants. Detecting such change is critical given the threats this species is currently facing under altering environmental conditions. The method presented here has applications to monitoring a range of species, particularly in remote and isolated environments. PMID:23940805

Exploiting High Resolution Multi-Seasonal Textural Measures and Spectral Information for Reedbed Mapping

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Alex Okiemute Onojeghuo

2016-02-01

Full Text Available Reedbeds across the UK are amongst the most important habitats for rare and endangered birds, wildlife and organisms. However, over the past century, this valued wetland habitat has experienced a drastic reduction in quality and spatial coverage due to pressures from human related activities. To this end, conservation organisations across the UK have been charged with the task of conserving and expanding this threatened habitat. With this backdrop, the study aimed to develop a methodology for accurate reedbed mapping through the combined use of multi-seasonal texture measures and spectral information contained in high resolution QuickBird satellite imagery. The key objectives were to determine the most effective single-date (autumn or summer and multi-seasonal QuickBird imagery suitable for reedbed mapping over the study area; to evaluate the effectiveness of combining multi-seasonal texture measures and spectral information for reedbed mapping using a variety of combinations; and to evaluate the most suitable classification technique for reedbed mapping from three selected classification techniques, namely maximum likelihood classifier, spectral angular mapper and artificial neural network. Using two selected grey-level co-occurrence textural measures (entropy and angular second moment, a series of experiments were conducted using varied combinations of single-date and multi-seasonal QuickBird imagery. Overall, the results indicate the multi-seasonal pansharpened multispectral bands (eight layers combined with all eight grey level co-occurrence matrix texture measures (entropy and angular second moment computed using windows 3 × 3 and 7 × 7 produced the optimal reedbed (76.5% and overall classification (78.1% accuracies using the maximum likelihood classifier technique. Using the optimal 16 layer multi-seasonal pansharpened multispectral and texture combined image dataset, a total reedbed area of 9.8 hectares was successfully mapped over the

Ecosystem services - from assessements of estimations to quantitative, validated, high-resolution, continental-scale mapping via airborne LIDAR

Science.gov (United States)

Zlinszky, András; Pfeifer, Norbert

2016-04-01

"Ecosystem services" defined vaguely as "nature's benefits to people" are a trending concept in ecology and conservation. Quantifying and mapping these services is a longtime demand of both ecosystems science and environmental policy. The current state of the art is to use existing maps of land cover, and assign certain average ecosystem service values to their unit areas. This approach has some major weaknesses: the concept of "ecosystem services", the input land cover maps and the value indicators. Such assessments often aim at valueing services in terms of human currency as a basis for decision-making, although this approach remains contested. Land cover maps used for ecosystem service assessments (typically the CORINE land cover product) are generated from continental-scale satellite imagery, with resolution in the range of hundreds of meters. In some rare cases, airborne sensors are used, with higher resolution but less covered area. Typically, general land cover classes are used instead of categories defined specifically for the purpose of ecosystem service assessment. The value indicators are developed for and tested on small study sites, but widely applied and adapted to other sites far away (a process called benefit transfer) where local information may not be available. Upscaling is always problematic since such measurements investigate areas much smaller than the output map unit. Nevertheless, remote sensing is still expected to play a major role in conceptualization and assessment of ecosystem services. We propose that an improvement of several orders of magnitude in resolution and accuracy is possible through the application of airborne LIDAR, a measurement technique now routinely used for collection of countrywide three-dimensional datasets with typically sub-meter resolution. However, this requires a clear definition of the concept of ecosystem services and the variables in focus: remote sensing can measure variables closely related to "ecosystem

Genome-wide high-resolution mapping of UV-induced mitotic recombination events in Saccharomyces cerevisiae.

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Yi Yin

2013-10-01

Full Text Available In the yeast Saccharomyces cerevisiae and most other eukaryotes, mitotic recombination is important for the repair of double-stranded DNA breaks (DSBs. Mitotic recombination between homologous chromosomes can result in loss of heterozygosity (LOH. In this study, LOH events induced by ultraviolet (UV light are mapped throughout the genome to a resolution of about 1 kb using single-nucleotide polymorphism (SNP microarrays. UV doses that have little effect on the viability of diploid cells stimulate crossovers more than 1000-fold in wild-type cells. In addition, UV stimulates recombination in G1-synchronized cells about 10-fold more efficiently than in G2-synchronized cells. Importantly, at high doses of UV, most conversion events reflect the repair of two sister chromatids that are broken at approximately the same position whereas at low doses, most conversion events reflect the repair of a single broken chromatid. Genome-wide mapping of about 380 unselected crossovers, break-induced replication (BIR events, and gene conversions shows that UV-induced recombination events occur throughout the genome without pronounced hotspots, although the ribosomal RNA gene cluster has a significantly lower frequency of crossovers.

Vegetation mapping from high-resolution satellite images in the heterogeneous arid environments of Socotra Island (Yemen)

Science.gov (United States)

Malatesta, Luca; Attorre, Fabio; Altobelli, Alfredo; Adeeb, Ahmed; De Sanctis, Michele; Taleb, Nadim M.; Scholte, Paul T.; Vitale, Marcello

2013-01-01

Socotra Island (Yemen), a global biodiversity hotspot, is characterized by high geomorphological and biological diversity. In this study, we present a high-resolution vegetation map of the island based on combining vegetation analysis and classification with remote sensing. Two different image classification approaches were tested to assess the most accurate one in mapping the vegetation mosaic of Socotra. Spectral signatures of the vegetation classes were obtained through a Gaussian mixture distribution model, and a sequential maximum a posteriori (SMAP) classification was applied to account for the heterogeneity and the complex spatial pattern of the arid vegetation. This approach was compared to the traditional maximum likelihood (ML) classification. Satellite data were represented by a RapidEye image with 5 m pixel resolution and five spectral bands. Classified vegetation relevés were used to obtain the training and evaluation sets for the main plant communities. Postclassification sorting was performed to adjust the classification through various rule-based operations. Twenty-eight classes were mapped, and SMAP, with an accuracy of 87%, proved to be more effective than ML (accuracy: 66%). The resulting map will represent an important instrument for the elaboration of conservation strategies and the sustainable use of natural resources in the island.

Soil property maps of Africa at 250 m resolution

Science.gov (United States)

Kempen, Bas; Hengl, Tomislav; Heuvelink, Gerard B. M.; Leenaars, Johan G. B.; Walsh, Markus G.; MacMillan, Robert A.; Mendes de Jesus, Jorge S.; Shepherd, Keith; Sila, Andrew; Desta, Lulseged T.; Tondoh, Jérôme E.

2015-04-01

Vast areas of arable land in sub-Saharan Africa suffer from low soil fertility and physical soil constraints, and significant amounts of nutrients are lost yearly due to unsustainable soil management practices. At the same time it is expected that agriculture in Africa must intensify to meet the growing demand for food and fiber the next decades. Protection and sustainable management of Africa's soil resources is crucial to achieve this. In this context, comprehensive, accurate and up-to-date soil information is an essential input to any agricultural or environmental management or policy and decision-making model. In Africa, detailed soil information has been fragmented and limited to specific zones of interest for decades. To help bridge the soil information gap in Africa, the Africa Soil Information Service (AfSIS) project was established in 2008. AfSIS builds on recent advances in digital soil mapping, infrared spectroscopy, remote sensing, (geo)statistics, and integrated soil fertility management to improve the way soils are evaluated, mapped, and monitored. Over the period 2008-2014, the AfSIS project has compiled two soil profile data sets (about 28,000 unique locations): the Africa Soil Profiles (legacy) database and the AfSIS Sentinel Site (new soil samples) database -- the two data sets represent the most comprehensive soil sample database of the African continent to date. In addition a large set of high-resolution environmental data layers (covariates) was assembled. The point data were used in the AfSIS project to generate a set of maps of key soil properties for the African continent at 250 m spatial resolution: sand, silt and clay fractions, bulk density, organic carbon, total nitrogen, pH, cation-exchange capacity, exchangeable bases (Ca, K, Mg, Na), exchangeable acidity, and Al content. These properties were mapped for six depth intervals up to 2 m: 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, 60-100 cm, and 100-200 cm. Random forests modelling was used to

Detection and Characterization of Single-Trial fMRI BOLD Responses : Paradigm Free Mapping

NARCIS (Netherlands)

Gaudes, Cesar Caballero; Petridou, Natalia; Dryden, Ian L.; Bai, Li; Francis, Susan T.; Gowland, Penny A.

This work presents a novel method of mapping the brain's response to single stimuli in space and time without prior knowledge of the paradigm timing: paradigm free mapping (PFM). This method is based on deconvolution of the hemodynamic response from the voxel time series assuming a linear response

Mapping organism expression levels at cellular resolution in developing Drosophila

Science.gov (United States)

Knowles, David W.; Keranen, Soile; Biggin, Mark D.; Sudar, Damir

2002-05-01

The development of an animal embryo is orchestrated by a network of genetically determined, temporal and spatial gene expression patterns that determine the animals final form. To understand such networks, we are developing novel quantitative optical imaging techniques to map gene expression levels at cellular and sub-cellular resolution within pregastrula Drosophila. Embryos at different stages of development are labeled for total DNA and specific gene products using different fluorophors and imaged in 3D with confocal microscopy. Innovative steps have been made which allow the DNA-image to be automatically segmented to produce a morphological mask of the individual nuclear boundaries. For each stage of development an average morphology is chosen to which images from different embryo are compared. The morphological mask is then used to quantify gene-product on a per nuclei basis. What results is an atlas of the relative amount of the specific gene product expressed within the nucleus of every cell in the embryo at the various stages of development. We are creating a quantitative database of transcription factor and target gene expression patterns in wild-type and factor mutant embryos with single cell resolution. Our goal is to uncover the rules determining how patterns of gene expression are generated.

Strategies for haplotype-based association mapping in complex pedigreed populations

DEFF Research Database (Denmark)

Boleckova, J; Christensen, Ole Fredslund; Sørensen, Peter

2012-01-01

In association mapping, haplotype-based methods are generally regarded to provide higher power and increased precision than methods based on single markers. For haplotype-based association mapping most studies use a fixed haplotype effect in the model. However, an increase in haplotype length inc...

High resolution population maps for low income nations: combining land cover and census in East Africa.

Directory of Open Access Journals (Sweden)

Andrew J Tatem

2007-12-01

Full Text Available Between 2005 and 2050, the human population is forecast to grow by 2.7 billion, with the vast majority of this growth occurring in low income countries. This growth is likely to have significant social, economic and environmental impacts, and make the achievement of international development goals more difficult. The measurement, monitoring and potential mitigation of these impacts require high resolution, contemporary data on human population distributions. In low income countries, however, where the changes will be concentrated, the least information on the distribution of population exists. In this paper we investigate whether satellite imagery in combination with land cover information and census data can be used to create inexpensive, high resolution and easily-updatable settlement and population distribution maps over large areas.We examine various approaches for the production of maps of the East African region (Kenya, Uganda, Burundi, Rwanda and Tanzania and where fine resolution census data exists, test the accuracies of map production approaches and existing population distribution products. The results show that combining high resolution census, settlement and land cover information is important in producing accurate population distribution maps.We find that this semi-automated population distribution mapping at unprecedented spatial resolution produces more accurate results than existing products and can be undertaken for as little as $0.01 per km(2. The resulting population maps are a product of the Malaria Atlas Project (MAP: http://www.map.ox.ac.uk and are freely available.

High Resolution Population Maps for Low Income Nations: Combining Land Cover and Census in East Africa

Science.gov (United States)

Tatem, Andrew J.; Noor, Abdisalan M.; von Hagen, Craig; Di Gregorio, Antonio; Hay, Simon I.

2007-01-01

Background Between 2005 and 2050, the human population is forecast to grow by 2.7 billion, with the vast majority of this growth occurring in low income countries. This growth is likely to have significant social, economic and environmental impacts, and make the achievement of international development goals more difficult. The measurement, monitoring and potential mitigation of these impacts require high resolution, contemporary data on human population distributions. In low income countries, however, where the changes will be concentrated, the least information on the distribution of population exists. In this paper we investigate whether satellite imagery in combination with land cover information and census data can be used to create inexpensive, high resolution and easily-updatable settlement and population distribution maps over large areas. Methodology/Principal Findings We examine various approaches for the production of maps of the East African region (Kenya, Uganda, Burundi, Rwanda and Tanzania) and where fine resolution census data exists, test the accuracies of map production approaches and existing population distribution products. The results show that combining high resolution census, settlement and land cover information is important in producing accurate population distribution maps. Conclusions We find that this semi-automated population distribution mapping at unprecedented spatial resolution produces more accurate results than existing products and can be undertaken for as little as $0.01 per km2. The resulting population maps are a product of the Malaria Atlas Project (MAP: http://www.map.ox.ac.uk) and are freely available. PMID:18074022

Mapping mountain meadow with high resolution and polarimetric SAR data

International Nuclear Information System (INIS)

Tian, Bangsen; Li, Zhen; Xu, Juan; Fu, Sitao; Liu, Jiuli

2014-01-01

This paper presents a method to map the large grassland in the eastern margin of the Tibetan Plateau with the high resolution polarimetric SAR (PolSAR) imagery. When PolSAR imagery is used for land cover classification, the brightness of a SAR image is affected by topography due to varying projection between ground and image coordinates. The objective of this paper is twofold: (1) we first extend the theory of SAR terrain correction to the polarimetric case, to utilize the entire available polarimetric signature, where correction is performed explicitly based on a matrix format like covariance matrix. (2) Next, the orthoectified PolSAR is applied to classify mountain meadow and investigate the potential of PolSAR in mapping grassland. In this paper, the gamma naught radiometric correction estimates the local illuminated area at each grid point in the radar geometry. Then, each element of the coherency matrix is divided by the local area to produce a polarimetric product. Secondly, the impact of radiometric correction upon classification accuracy is investigated. A supervised classification is performed on the orthorectified Radarsat-2 PolSAR to map the spatial distribution of meadow and evaluate monitoring capabilities of mountain meadow

Measurable realistic image-based 3D mapping

Science.gov (United States)

Liu, W.; Wang, J.; Wang, J. J.; Ding, W.; Almagbile, A.

2011-12-01

Maps with 3D visual models are becoming a remarkable feature of 3D map services. High-resolution image data is obtained for the construction of 3D visualized models.The3D map not only provides the capabilities of 3D measurements and knowledge mining, but also provides the virtual experienceof places of interest, such as demonstrated in the Google Earth. Applications of 3D maps are expanding into the areas of architecture, property management, and urban environment monitoring. However, the reconstruction of high quality 3D models is time consuming, and requires robust hardware and powerful software to handle the enormous amount of data. This is especially for automatic implementation of 3D models and the representation of complicated surfacesthat still need improvements with in the visualisation techniques. The shortcoming of 3D model-based maps is the limitation of detailed coverage since a user can only view and measure objects that are already modelled in the virtual environment. This paper proposes and demonstrates a 3D map concept that is realistic and image-based, that enables geometric measurements and geo-location services. Additionally, image-based 3D maps provide more detailed information of the real world than 3D model-based maps. The image-based 3D maps use geo-referenced stereo images or panoramic images. The geometric relationships between objects in the images can be resolved from the geometric model of stereo images. The panoramic function makes 3D maps more interactive with users but also creates an interesting immersive circumstance. Actually, unmeasurable image-based 3D maps already exist, such as Google street view, but only provide virtual experiences in terms of photos. The topographic and terrain attributes, such as shapes and heights though are omitted. This paper also discusses the potential for using a low cost land Mobile Mapping System (MMS) to implement realistic image 3D mapping, and evaluates the positioning accuracy that a measureable

High and ultra-high resolution metabolite mapping of the human brain using 1H FID MRSI at 9.4T.

Science.gov (United States)

Nassirpour, Sahar; Chang, Paul; Henning, Anke

2018-03-01

Magnetic resonance spectroscopic imaging (MRSI) is a promising technique for mapping the spatial distribution of multiple metabolites in the human brain. These metabolite maps can be used as a diagnostic tool to gain insight into several biochemical processes and diseases in the brain. In comparison to lower field strengths, MRSI at ultra-high field strengths benefits from a higher signal to noise ratio (SNR) as well as higher chemical shift dispersion, and hence spectral resolution. This study combines the benefits of an ultra-high field magnet with the advantages of an ultra-short TE and TR single-slice FID-MRSI sequence (such as negligible J-evolution and loss of SNR due to T 2 relaxation effects) and presents the first metabolite maps acquired at 9.4T in the healthy human brain at both high (voxel size of 97.6µL) and ultra-high (voxel size of 24.4µL) spatial resolutions in a scan time of 11 and 46min respectively. In comparison to lower field strengths, more anatomically-detailed maps with higher SNR from a larger number of metabolites are shown. A total of 12 metabolites including glutamate (Glu), glutamine (Gln), N-acetyl-aspartyl-glutamate (NAAG), Gamma-aminobutyric acid (GABA) and glutathione (GSH) are reliably mapped. Comprehensive description of the methodology behind these maps is provided. Copyright © 2016 Elsevier Inc. All rights reserved.

Mapping yeast origins of replication via single-stranded DNA detection.

Science.gov (United States)

Feng, Wenyi; Raghuraman, M K; Brewer, Bonita J

2007-02-01

Studies in th Saccharomyces cerevisiae have provided a framework for understanding how eukaryotic cells replicate their chromosomal DNA to ensure faithful transmission of genetic information to their daughter cells. In particular, S. cerevisiae is the first eukaryote to have its origins of replication mapped on a genomic scale, by three independent groups using three different microarray-based approaches. Here we describe a new technique of origin mapping via detection of single-stranded DNA in yeast. This method not only identified the majority of previously discovered origins, but also detected new ones. We have also shown that this technique can identify origins in Schizosaccharomyces pombe, illustrating the utility of this method for origin mapping in other eukaryotes.

Application of mapped plots for single-owner forest surveys

Science.gov (United States)

Paul C. Van Deusen; Francis Roesch

2009-01-01

Mapped plots are used for the nation forest inventory conducted by the U.S. Forest Service. Mapped plots are also useful foro single ownership inventoires. Mapped plots can handle boundary overlap and can aprovide less variable estimates for specified forest conditions. Mapping is a good fit for fixed plot inventories where the fixed area plot is used for both mapping...

Modeling, Designing, and Implementing an Avatar-based Interactive Map

Directory of Open Access Journals (Sweden)

Stefan Andrei

2016-03-01

Full Text Available Designing interactive maps has always been a challenge due to the geographical complexity of the earth’s landscape and the difficulty of resolving details to a high resolution. In the past decade or so, one of the most impressive map-based software application, the Global Positioning System (GPS, has probably the highest level of interaction with the user. This article describes an innovative technique for designing an avatar-based virtual interactive map for the Lamar University Campus, which will entail the buildings’ exterior as well as their interiors. Many universities provide 2D or 3D maps and even interactive maps. However, these maps do not provide a complete interaction with the user. To the best of our knowledge, this project is the first avatar-based interaction game that allows 100% interaction with the user. This work provides tremendous help to the freshman students and visitors of Lamar University. As an important marketing tool, the main objective is to get better visibility of the campus worldwide and to increase the number of students attending Lamar University.

Analysis of single-photon time resolution of FBK silicon photomultipliers

International Nuclear Information System (INIS)

Acerbi, Fabio; Ferri, Alessandro; Gola, Alberto; Zorzi, Nicola; Piemonte, Claudio

2015-01-01

We characterized and analyzed an important feature of silicon photomultipliers: the single-photon time resolution (SPTR). We characterized the SPTR of new RGB (Red–Green–Blue) type Silicon Photomultipliers and SPADs produced at FBK (Trento, Italy), studying its main limiting factors. We compared time resolution of 1×1 mm 2 and 3×3 mm 2 SiPMs and a single SiPM cell (i.e. a SPAD with integrated passive-quenching), employing a mode-locked pulsed laser with 2-ps wide pulses. We estimated the contribution of front-end electronic-noise, of cell-to-cell uniformity, and intrinsic cell time-resolution. At a single-cell level, we compared the results obtained with different layouts. With a circular cell with a top metallization covering part of the edge and enhancing the signal extraction, we reached ~20 ps FWHM of time resolution

Scanning, Multibeam, Single Photon Lidars for Rapid, Large Scale, High Resolution, Topographic and Bathymetric Mapping

Directory of Open Access Journals (Sweden)

John J. Degnan

2016-11-01

Full Text Available Several scanning, single photon sensitive, 3D imaging lidars are herein described that operate at aircraft above ground levels (AGLs between 1 and 11 km, and speeds in excess of 200 knots. With 100 beamlets and laser fire rates up to 60 kHz, we, at the Sigma Space Corporation (Lanham, MD, USA, have interrogated up to 6 million ground pixels per second, all of which can record multiple returns from volumetric scatterers such as tree canopies. High range resolution has been achieved through the use of subnanosecond laser pulsewidths, detectors and timing receivers. The systems are presently being deployed on a variety of aircraft to demonstrate their utility in multiple applications including large scale surveying, bathymetry, forestry, etc. Efficient noise filters, suitable for near realtime imaging, have been shown to effectively eliminate the solar background during daytime operations. Geolocation elevation errors measured to date are at the subdecimeter level. Key differences between our Single Photon Lidars, and competing Geiger Mode lidars are also discussed.

A Silicon d-spacing Mapping Measurement System With Resolution of 10-9

International Nuclear Information System (INIS)

Zhang Xiaowei; Sugiyama, Hiroshi; Fugimoto, Hiroyuki; Waseda, Atsushi; Takatomi, Toshikazu

2010-01-01

For determination of the Avogadro's number, a self-referenced lattice comparator established at the Photon Factory to deal with a d-spacing mapping measurement over the cross section of a 4 ∼ 5 inches FZ silicon rod. For uncertainty of 1x10 -8 of the unit cell volume, it is necessary to measure lattice parameter of silicon with resolution of 3x10 -9 at least. In this paper, we report the principle of our lattice comparator, characterize our measurement system, and show some mapping measurement results of FZ silicon with resolution of 3x10 -9 .

Single image super-resolution based on approximated Heaviside functions and iterative refinement

Science.gov (United States)

Wang, Xin-Yu; Huang, Ting-Zhu; Deng, Liang-Jian

2018-01-01

One method of solving the single-image super-resolution problem is to use Heaviside functions. This has been done previously by making a binary classification of image components as “smooth” and “non-smooth”, describing these with approximated Heaviside functions (AHFs), and iteration including l1 regularization. We now introduce a new method in which the binary classification of image components is extended to different degrees of smoothness and non-smoothness, these components being represented by various classes of AHFs. Taking into account the sparsity of the non-smooth components, their coefficients are l1 regularized. In addition, to pick up more image details, the new method uses an iterative refinement for the residuals between the original low-resolution input and the downsampled resulting image. Experimental results showed that the new method is superior to the original AHF method and to four other published methods. PMID:29329298

Airborne 3D Imaging Lidar for Contiguous Decimeter Resolution Terrain Mapping and Shallow Water Bathymetry

Science.gov (United States)

Degnan, J. J.; Wells, D. N.; Huet, H.; Chauvet, N.; Lawrence, D. W.; Mitchell, S. E.; Eklund, W. D.

2005-12-01

A 3D imaging lidar system, developed for the University of Florida at Gainesville and operating at the water transmissive wavelength of 532 nm, is designed to contiguously map underlying terrain and/or perform shallow water bathymetry on a single overflight from an altitude of 600 m with a swath width of 225 m and a horizontal spatial resolution of 20 cm. Each 600 psec pulse from a frequency-doubled, low power (~3 microjoules @ 8 kHz = 24 mW), passively Q-switched Nd:YAG microchip laser is passed through a holographic element which projects a 10x10 array of spots onto a 2m x 2m target area. The individual ground spots are then imaged onto individual anodes within a 10x10 segmented anode photomultiplier. The latter is followed by a 100 channel multistop ranging receiver with a range resolution of about 4 cm. The multistop feature permits single photon detection in daylight with wide range gates as well as multiple single photon returns per pixel per laser fire from volumetric scatterers such as tree canopies or turbid water columns. The individual single pulse 3D images are contiguously mosaiced together through the combined action of the platform velocity and a counter-rotating dual wedge optical scanner whose rotations are synchronized to the laser pulse train. The paper provides an overview of the lidar opto-mechanical design, the synchronized dual wedge scanner and servo controller, and the experimental results obtained to date.

High resolution digital soil mapping as a future instrument for developing sustainable landuse strategies

Science.gov (United States)

Gries, Philipp; Funke, Lisa-Marie; Baumann, Frank; Schmidt, Karsten; Behrens, Thorsten; Scholten, Thomas

2016-04-01

Climate change, increase in population and intensification of land use pose a great challenge for sustainable handling of soils. Intelligent landuse systems are able to minimize and/or avoid soil erosion and loss of soil fertility. A successful application of such systems requires area-wide soil information with high resolution. Containing three consecutive steps, the project INE-2-H („innovative sustainable landuse") at the University of Tuebingen is about creating high-resolution soil information using Digital Soil Mapping (DSM) techniques to develop sustainable landuse strategies. Input data includes soil data from fieldwork (texture and carbon content), the official digital soil and geological map (1:50.000) as well as a wide selection of local, complex and combined terrain parameters. First, soil maps have been created using the DSM approach and Random Forest (RF). Due to high resolution (10x10 m pixels), those maps show a more detailed spatial variability of soil information compared to the official maps used. Root mean square errors (RMSE) of the modelled maps vary from 2.11 % to 6.87 % and the coefficients of determination (R²) go from 0.42 to 0.68. Second, soil erosion potentials have been estimated according to the Universal Soil Loss Equation (USLE). Long-term average annual soil loss ranges from 0.56 to 24.23 [t/ha/a]. Third, combining high-resolution erosion potentials with expert-knowledge of local farmers will result in a landuse system adapted to local conditions. This system will include sustainable strategies reducing soil erosion and conserving soil fertility.

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

Science.gov (United States)

Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

2018-06-01

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

Angstrom-Resolution Magnetic Resonance Imaging of Single Molecules via Wave-Function Fingerprints of Nuclear Spins

Science.gov (United States)

Ma, Wen-Long; Liu, Ren-Bao

2016-08-01

Single-molecule sensitivity of nuclear magnetic resonance (NMR) and angstrom resolution of magnetic resonance imaging (MRI) are the highest challenges in magnetic microscopy. Recent development in dynamical-decoupling- (DD) enhanced diamond quantum sensing has enabled single-nucleus NMR and nanoscale NMR. Similar to conventional NMR and MRI, current DD-based quantum sensing utilizes the "frequency fingerprints" of target nuclear spins. The frequency fingerprints by their nature cannot resolve different nuclear spins that have the same noise frequency or differentiate different types of correlations in nuclear-spin clusters, which limit the resolution of single-molecule MRI. Here we show that this limitation can be overcome by using "wave-function fingerprints" of target nuclear spins, which is much more sensitive than the frequency fingerprints to the weak hyperfine interaction between the targets and a sensor under resonant DD control. We demonstrate a scheme of angstrom-resolution MRI that is capable of counting and individually localizing single nuclear spins of the same frequency and characterizing the correlations in nuclear-spin clusters. A nitrogen-vacancy-center spin sensor near a diamond surface, provided that the coherence time is improved by surface engineering in the near future, may be employed to determine with angstrom resolution the positions and conformation of single molecules that are isotope labeled. The scheme in this work offers an approach to breaking the resolution limit set by the "frequency gradients" in conventional MRI and to reaching the angstrom-scale resolution.

Analysis of single-photon time resolution of FBK silicon photomultipliers

Energy Technology Data Exchange (ETDEWEB)

Acerbi, Fabio, E-mail: acerbi@fbk.eu; Ferri, Alessandro; Gola, Alberto; Zorzi, Nicola; Piemonte, Claudio

2015-07-01

We characterized and analyzed an important feature of silicon photomultipliers: the single-photon time resolution (SPTR). We characterized the SPTR of new RGB (Red–Green–Blue) type Silicon Photomultipliers and SPADs produced at FBK (Trento, Italy), studying its main limiting factors. We compared time resolution of 1×1 mm{sup 2} and 3×3 mm{sup 2} SiPMs and a single SiPM cell (i.e. a SPAD with integrated passive-quenching), employing a mode-locked pulsed laser with 2-ps wide pulses. We estimated the contribution of front-end electronic-noise, of cell-to-cell uniformity, and intrinsic cell time-resolution. At a single-cell level, we compared the results obtained with different layouts. With a circular cell with a top metallization covering part of the edge and enhancing the signal extraction, we reached ~20 ps FWHM of time resolution.

3D high- and super-resolution imaging using single-objective SPIM.

Science.gov (United States)

Galland, Remi; Grenci, Gianluca; Aravind, Ajay; Viasnoff, Virgile; Studer, Vincent; Sibarita, Jean-Baptiste

2015-07-01

Single-objective selective-plane illumination microscopy (soSPIM) is achieved with micromirrored cavities combined with a laser beam-steering unit installed on a standard inverted microscope. The illumination and detection are done through the same objective. soSPIM can be used with standard sample preparations and features high background rejection and efficient photon collection, allowing for 3D single-molecule-based super-resolution imaging of whole cells or cell aggregates. Using larger mirrors enabled us to broaden the capabilities of our system to image Drosophila embryos.

ActionMap: A web-based software that automates loci assignments to framework maps.

Science.gov (United States)

Albini, Guillaume; Falque, Matthieu; Joets, Johann

2003-07-01

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

Elemental mapping in achromatic atomic-resolution energy-filtered transmission electron microscopy

Energy Technology Data Exchange (ETDEWEB)

Forbes, B.D. [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia); Houben, L. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Mayer, J. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Central Facility for Electron Microscopy, RWTH Aachen University, D-52074 Aachen (Germany); Dunin-Borkowski, R.E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Gruenberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Allen, L.J., E-mail: lja@unimelb.edu.au [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia)

2014-12-15

We present atomic-resolution energy-filtered transmission electron microscopy (EFTEM) images obtained with the chromatic-aberration-corrected FEI Titan PICO at the Ernst-Ruska Centre, Jülich, Germany. We find qualitative agreement between experiment and simulation for the background-subtracted EFTEM images of the Ti–L{sub 2,3} and O–K edges for a specimen of SrTiO{sub 3} oriented down the [110] zone axis. The simulations utilize the transition potential formulation for inelastic scattering, which permits a detailed investigation of contributions to the EFTEM image. We find that energy-filtered images of the Ti–L{sub 2,3} and O–K edges are lattice images and that the background-subtracted core-loss maps may not be directly interpretable as elemental maps. Simulations show that this is a result of preservation of elastic contrast, whereby the qualitative details of the image are determined primarily by elastic, coherent scattering. We show that this effect places a constraint on the range of specimen thicknesses which could theoretically yield directly useful elemental maps. In general, interpretation of EFTEM images is ideally accompanied by detailed simulations. - Highlights: • Achromatic atomic-resolution EFTEM images were obtained for STO 〈110〉. • Simulations were in qualitative agreement with Ti–L{sub 2,3} and O–K edge maps. • The experimental EFTEM maps are not directly interpretable as elemental maps. • Image intensities are strongly determined by preservation of elastic contrast. • Interpretation of EFTEM images is ideally accompanied by detailed simulations.

High-resolution three-dimensional mapping of semiconductor dopant potentials

DEFF Research Database (Denmark)

Twitchett, AC; Yates, TJV; Newcomb, SB

2007-01-01

Semiconductor device structures are becoming increasingly three-dimensional at the nanometer scale. A key issue that must be addressed to enable future device development is the three-dimensional mapping of dopant distributions, ideally under "working conditions". Here we demonstrate how a combin......Semiconductor device structures are becoming increasingly three-dimensional at the nanometer scale. A key issue that must be addressed to enable future device development is the three-dimensional mapping of dopant distributions, ideally under "working conditions". Here we demonstrate how...... a combination of electron holography and electron tomography can be used to determine quantitatively the three-dimensional electrostatic potential in an electrically biased semiconductor device with nanometer spatial resolution....

Photoacoustic bio-quantification of graphene based nanomaterials at a single cell level (Conference Presentation)

Science.gov (United States)

Nedosekin, Dmitry A.; Nolan, Jacqueline; Biris, Alexandru S.; Zharov, Vladimir P.

2017-03-01

Arkansas Nanomedicine Center at the University of Arkansas for Medical Sciences in collaboration with other Arkansas Universities and the FDA-based National Center of Toxicological Research in Jefferson, AR is developing novel techniques for rapid quantification of graphene-based nanomaterials (GBNs) in various biological samples. All-carbon GBNs have wide range of potential applications in industry, agriculture, food processing and medicine; however, quantification of GBNs is difficult in carbon reach biological tissues. The accurate quantification of GBNs is essential for research on material toxicity and the development of GBNs-based drug delivery platforms. We have developed microscopy and cytometry platforms for detection and quantification of GBNs in single cells, tissue and blood samples using photoacoustic contrast of GBNs. We demonstrated PA quantification of individual graphene uptake by single cells. High-resolution PA microscopy provided mapping of GBN distribution within live cells to establish correlation with intracellular toxic phenomena using apoptotic and necrotic assays. This new methodology and corresponding technical platform provide the insight on possible toxicological risks of GBNs at singe cells levels. In addition, in vivo PA image flow cytometry demonstrated the capability to monitor of GBNs pharmacokinetics in mouse model and to map the resulting biodistribution of GBNs in mouse tissues. The integrated PA platform provided an unprecedented sensitivity toward GBNs and allowed to enhance conventional toxicology research by providing a direct correlation between uptake of GBNs at a single cell level and cell viability status.

The high resolution mapping of the Venice Lagoon tidal network

Science.gov (United States)

Madricardo, Fantina; Foglini, Federica; Kruss, Aleksandra; Bellafiore, Debora; Trincardi, Fabio

2017-04-01

One of the biggest challenges of the direct observation of the ocean is to achieve a high resolution mapping of its seafloor morphology and benthic habitats. So far, sonars have mapped just 0.05% of the ocean floor with less than ten-meter resolution. The recent efforts of the scientific community have been devoted towards the mapping of both Deep Ocean and very shallow coastal areas. Coastal and transitional environments in particular undergo strong morphological changes due to natural and anthropogenic pressure. Nowadays, only about 5% of the seafloor of these environments † have been mapped: the shallowness of these environments has prevented the use of underwater acoustics to reveal their morphological features. The recent technological development of multibeam echosounder systems, however, enables these instruments to achieve very high performances also in such shallow environments. In this work, we present results and case studies of an extensive multibeam survey carried out in the Lagoon of Venice in 2013. The Lagoon of Venice is the biggest lagoon in the Mediterranean Sea with a surface of about 550 km2 and with an average depth of about 1 m. In the last century, the morphological and ecological properties of the lagoon changed dramatically: the surface of the salt marshes was reduced by 60% and some parts of the lagoon are deepening with a net sediment flux exiting from the inlets. Moreover, major engineering interventions are currently ongoing at the inlets (MOSE project). These changes at the inlets could affect substantially the lagoon environment. To understand and monitor the future evolution of the Lagoon of Venice, ISMAR within the project RITMARE (a National Research Programme funded by the Italian Ministry of University and Research) carried out an extensive survey, involving a team of more than 25 scientists, to collect high resolution (0.5 m) bathymetry of key study areas such as the tidal inlets and channels. Following a broad

High resolution surface scanning of Thick-GEM for single photo-electron detection

International Nuclear Information System (INIS)

Hamar, G.; Varga, D.

2012-01-01

An optical system for high resolution scanning of TGEM UV photon detection systems is introduced. The structure exploits the combination of a single Au-coated TGEM under study, and an asymmetric MWPC (Close Cathode Chamber) as post-amplification stage. A pulsed UV LED source with emission down to 240 nm has been focused to a spot of 0.07 mm on the TGEM surface, and single photo-electron charge spectra has been recorded over selected two dimensional regions. This way, the TGEM gain (order of 10–100) and TGEM photo-electron detection efficiency is clearly separated, unlike in case of continuous illumination. The surface structure connected to the TGEM photon detection is well observable, including inefficiencies in the holes and at the symmetry points between holes. The detection efficiency as well as the gas gain are fluctuating from hole to hole. The gain is constant in the hexagon around any hole, pointing to the fact that the gain depends on hole geometry, and less on the position where the electron enters. The detection probability map strongly changes with the field strength above the TGEM surface, in relation to the change of the actual surface field configuration. The results can be confronted with position-dependent simulations of TGEM electron transfer and gas multiplication. -- Highlights: ► First demonstration of Thick GEM surface scanning with single photo-electrons. ► Resolution of 0.1 mm is sufficient to identify structures connected to TGEM surface field structure. ► Gain and detection efficiency and separately measurable. ► Detection efficiency is high in a ring around the holes, and gain is constant in the hexagonal collection regions.

HIGH RESOLUTION NEAR-INFRARED SURVEY OF THE PIPE NEBULA. I. A DEEP INFRARED EXTINCTION MAP OF BARNARD 59

International Nuclear Information System (INIS)

Roman-Zuniga, Carlos G.; Alves, Joao F.; Lada, Charles J.

2009-01-01

We present our analysis of a fully sampled, high resolution dust extinction map of the Barnard 59 complex in the Pipe Nebula. The map was constructed with the infrared color excess technique applied to a photometric catalog that combines data from both ground and space based observations. The map resolves for the first time the high density center of the main core in the complex, which is associated with the formation of a small cluster of stars. We found that the central core in Barnard 59 shows an unexpected lack of significant substructure consisting of only two significant fragments. Overall, the material appears to be consistent with being a single, large core with a density profile that can be well fit by a King model. A series of NH 3 pointed observations toward the high column density center of the core appear to show that the core is still thermally dominated, with subsonic non-thermal motions. The stars in the cluster could be providing feedback to support the core against collapse, but the relatively narrow radio lines suggest that an additional source of support, for example, a magnetic field, may be required to stabilize the core. Outside the central core our observations reveal the structure of peripheral cores and resolve an extended filament into a handful of significant substructures whose spacing and masses appear to be consistent with Jeans fragmentation.

High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

Science.gov (United States)

Reddy, Umesh K; Nimmakayala, Padma; Levi, Amnon; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Tomason, Yan R; Vajja, Gopinath; Reddy, Rishi; Abburi, Lavanya; Wehner, Todd C; Ronin, Yefim; Karol, Abraham

2014-09-15

We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication. Copyright © 2014 Reddy et al.

High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

Science.gov (United States)

Aksoy, B.; Rehman, A.; Bayraktar, H.; Alaca, B. E.

2017-04-01

Micropatterns are generated on a vast selection of polymeric substrates for various applications ranging from stretchable electronics to cellular mechanobiological systems. When these patterned substrates are exposed to external loading, strain field is primarily affected by the presence of microfabricated structures and similarly by fabrication-related defects. The capturing of such nonhomogeneous strain fields is of utmost importance in cases where study of the mechanical behavior with a high spatial resolution is necessary. Image-based non-contact strain measurement techniques are favorable and have recently been extended to scanning tunneling microscope and scanning electron microscope images for the characterization of mechanical properties of metallic materials, e.g. steel and aluminum, at the microscale. A similar real-time analysis of strain heterogeneity in elastomers is yet to be achieved during the entire loading sequence. The available measurement methods for polymeric materials mostly depend on cross-head displacement or precalibrated strain values. Thus, they suffer either from the lack of any real-time analysis, spatiotemporal distribution or high resolution in addition to a combination of these factors. In this work, these challenges are addressed by integrating a tensile stretcher with an inverted optical microscope and developing a subpixel particle tracking algorithm. As a proof of concept, the patterns with a critical dimension of 200 µm are generated on polydimethylsiloxane substrates and strain distribution in the vicinity of the patterns is captured with a high spatiotemporal resolution. In the field of strain measurement, there is always a tradeoff between minimum measurable strain value and spatial resolution. Current noncontact techniques on elastomers can deliver a strain resolution of 0.001% over a minimum length of 5 cm. More importantly, inhomogeneities within this quite large region cannot be captured. The proposed technique can

High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

International Nuclear Information System (INIS)

Aksoy, B; Alaca, B E; Rehman, A; Bayraktar, H

2017-01-01

Micropatterns are generated on a vast selection of polymeric substrates for various applications ranging from stretchable electronics to cellular mechanobiological systems. When these patterned substrates are exposed to external loading, strain field is primarily affected by the presence of microfabricated structures and similarly by fabrication-related defects. The capturing of such nonhomogeneous strain fields is of utmost importance in cases where study of the mechanical behavior with a high spatial resolution is necessary. Image-based non-contact strain measurement techniques are favorable and have recently been extended to scanning tunneling microscope and scanning electron microscope images for the characterization of mechanical properties of metallic materials, e.g. steel and aluminum, at the microscale. A similar real-time analysis of strain heterogeneity in elastomers is yet to be achieved during the entire loading sequence. The available measurement methods for polymeric materials mostly depend on cross-head displacement or precalibrated strain values. Thus, they suffer either from the lack of any real-time analysis, spatiotemporal distribution or high resolution in addition to a combination of these factors. In this work, these challenges are addressed by integrating a tensile stretcher with an inverted optical microscope and developing a subpixel particle tracking algorithm. As a proof of concept, the patterns with a critical dimension of 200 µ m are generated on polydimethylsiloxane substrates and strain distribution in the vicinity of the patterns is captured with a high spatiotemporal resolution. In the field of strain measurement, there is always a tradeoff between minimum measurable strain value and spatial resolution. Current noncontact techniques on elastomers can deliver a strain resolution of 0.001% over a minimum length of 5 cm. More importantly, inhomogeneities within this quite large region cannot be captured. The proposed technique can

Studies of x-ray localization and thickness dependence in atomic-scale elemental mapping by STEM energy-dispersive x-ray spectroscopy using single-frame scanning method.

Science.gov (United States)

Lu, Ping; Moya, Jaime M; Yuan, Renliang; Zuo, Jian Min

2018-03-01

The delocalization of x-ray signals limits the spatial resolution in atomic-scale elemental mapping by scanning transmission electron microscopy (STEM) using energy-dispersive x-ray spectroscopy (EDS). In this study, using a SrTiO 3 [001] single crystal, we show that the x-ray localization to atomic columns is strongly dependent on crystal thickness, and a thin crystal is critical for improving the spatial resolution in atomic-scale EDS mapping. A single-frame scanning technique is used in this study instead of the multiple-frame technique to avoid peak broadening due to tracking error. The strong thickness dependence is realized by measuring the full width at half maxima (FWHM) as well as the peak-to-valley (P/V) ratio of the EDS profiles for Ti K and Sr K + L, obtained at several crystal thicknesses. A FWHM of about 0.16 nm and a P/V ratio of greater than 7.0 are obtained for Ti K for a crystal thickness of less than 20 nm. With increasing crystal thickness, the FWHM and P/V ratio increases and decreases, respectively, indicating the advantage of using a thin crystal for high-resolution EDS mapping. Published by Elsevier B.V.

Soil process-oriented modelling of within-field variability based on high-resolution 3D soil type distribution maps.

Science.gov (United States)

Bönecke, Eric; Lück, Erika; Gründling, Ralf; Rühlmann, Jörg; Franko, Uwe

2016-04-01

Today, the knowledge of within-field variability is essential for numerous purposes, including practical issues, such as precision and sustainable soil management. Therefore, process-oriented soil models have been applied for a considerable time to answer question of spatial soil nutrient and water dynamics, although, they can only be as consistent as their variation and resolution of soil input data. Traditional approaches, describe distribution of soil types, soil texture or other soil properties for greater soil units through generalised point information, e.g. from classical soil survey maps. Those simplifications are known to be afflicted with large uncertainties. Varying soil, crop or yield conditions are detected even within such homogenised soil units. However, recent advances of non-invasive soil survey and on-the-go monitoring techniques, made it possible to obtain vertical and horizontal dense information (3D) about various soil properties, particularly soil texture distribution which serves as an essential soil key variable affecting various other soil properties. Thus, in this study we based our simulations on detailed 3D soil type distribution (STD) maps (4x4 m) to adjacently built-up sufficient informative soil profiles including various soil physical and chemical properties. Our estimates of spatial STD are based on high-resolution lateral and vertical changes of electrical resistivity (ER), detected by a relatively new multi-sensor on-the-go ER monitoring device. We performed an algorithm including fuzzy-c-mean (FCM) logic and traditional soil classification to estimate STD from those inverted and layer-wise available ER data. STD is then used as key input parameter for our carbon, nitrogen and water transport model. We identified Pedological horizon depths and inferred hydrological soil variables (field capacity, permanent wilting point) from pedotransferfunctions (PTF) for each horizon. Furthermore, the spatial distribution of soil organic carbon

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

Science.gov (United States)

Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

2012-01-01

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits. PMID:22247776

Benthic Habitat Mapping Using Multispectral High-Resolution Imagery: Evaluation of Shallow Water Atmospheric Correction Techniques

Directory of Open Access Journals (Sweden)

Francisco Eugenio

2017-11-01

Full Text Available Remote multispectral data can provide valuable information for monitoring coastal water ecosystems. Specifically, high-resolution satellite-based imaging systems, as WorldView-2 (WV-2, can generate information at spatial scales needed to implement conservation actions for protected littoral zones. However, coastal water-leaving radiance arriving at the space-based sensor is often small as compared to reflected radiance. In this work, complex approaches, which usually use an accurate radiative transfer code to correct the atmospheric effects, such as FLAASH, ATCOR and 6S, have been implemented for high-resolution imagery. They have been assessed in real scenarios using field spectroradiometer data. In this context, the three approaches have achieved excellent results and a slightly superior performance of 6S model-based algorithm has been observed. Finally, for the mapping of benthic habitats in shallow-waters marine protected environments, a relevant application of the proposed atmospheric correction combined with an automatic deglinting procedure is presented. This approach is based on the integration of a linear mixing model of benthic classes within the radiative transfer model of the water. The complete methodology has been applied to selected ecosystems in the Canary Islands (Spain but the obtained results allow the robust mapping of the spatial distribution and density of seagrass in coastal waters and the analysis of multitemporal variations related to the human activity and climate change in littoral zones.

High Temporal Resolution Mapping of Seismic Noise Sources Using Heterogeneous Supercomputers

Science.gov (United States)

Paitz, P.; Gokhberg, A.; Ermert, L. A.; Fichtner, A.

2017-12-01

The time- and space-dependent distribution of seismic noise sources is becoming a key ingredient of modern real-time monitoring of various geo-systems like earthquake fault zones, volcanoes, geothermal and hydrocarbon reservoirs. We present results of an ongoing research project conducted in collaboration with the Swiss National Supercomputing Centre (CSCS). The project aims at building a service providing seismic noise source maps for Central Europe with high temporal resolution. We use source imaging methods based on the cross-correlation of seismic noise records from all seismic stations available in the region of interest. The service is hosted on the CSCS computing infrastructure; all computationally intensive processing is performed on the massively parallel heterogeneous supercomputer "Piz Daint". The solution architecture is based on the Application-as-a-Service concept to provide the interested researchers worldwide with regular access to the noise source maps. The solution architecture includes the following sub-systems: (1) data acquisition responsible for collecting, on a periodic basis, raw seismic records from the European seismic networks, (2) high-performance noise source mapping application responsible for the generation of source maps using cross-correlation of seismic records, (3) back-end infrastructure for the coordination of various tasks and computations, (4) front-end Web interface providing the service to the end-users and (5) data repository. The noise source mapping itself rests on the measurement of logarithmic amplitude ratios in suitably pre-processed noise correlations, and the use of simplified sensitivity kernels. During the implementation we addressed various challenges, in particular, selection of data sources and transfer protocols, automation and monitoring of daily data downloads, ensuring the required data processing performance, design of a general service-oriented architecture for coordination of various sub-systems, and

Detailed Maps Depicting the Shallow-Water Benthic Habitats of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Detailed, shallow-water coral reef ecosystem maps were generated by rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations...

Improved coastal wetland mapping using very-high 2-meter spatial resolution imagery

Science.gov (United States)

McCarthy, Matthew J.; Merton, Elizabeth J.; Muller-Karger, Frank E.

2015-08-01

Accurate wetland maps are a fundamental requirement for land use management and for wetland restoration planning. Several wetland map products are available today; most of them based on remote sensing images, but their different data sources and mapping methods lead to substantially different estimations of wetland location and extent. We used two very high-resolution (2 m) WorldView-2 satellite images and one (30 m) Landsat 8 Operational Land Imager (OLI) image to assess wetland coverage in two coastal areas of Tampa Bay (Florida): Fort De Soto State Park and Weedon Island Preserve. An initial unsupervised classification derived from WorldView-2 was more accurate at identifying wetlands based on ground truth data collected in the field than the classification derived from Landsat 8 OLI (82% vs. 46% accuracy). The WorldView-2 data was then used to define the parameters of a simple and efficient decision tree with four nodes for a more exacting classification. The criteria for the decision tree were derived by extracting radiance spectra at 1500 separate pixels from the WorldView-2 data within field-validated regions. Results for both study areas showed high accuracy in both wetland (82% at Fort De Soto State Park, and 94% at Weedon Island Preserve) and non-wetland vegetation classes (90% and 83%, respectively). Historical, published land-use maps overestimate wetland surface cover by factors of 2-10 in the study areas. The proposed methods improve speed and efficiency of wetland map production, allow semi-annual monitoring through repeat satellite passes, and improve the accuracy and precision with which wetlands are identified.

Single photon imaging at ultra-high resolution

Energy Technology Data Exchange (ETDEWEB)

Bellazzini, R. [INFN sez. Pisa, Pisa (Italy); Spandre, G. [INFN sez. Pisa, Pisa (Italy)], E-mail: Gloria.Spandre@pi.infn.it; Minuti, M.; Brez, A.; Baldini, L.; Latronico, L.; Omodei, N.; Sgro, C.; Bregeon, J.; Razzano, M.; Pinchera, M. [INFN sez. Pisa, Pisa (Italy); Tremsin, A.; McPhate, J.; Vallerga, J.V.; Siegmund, O. [SSL, Berkeley (United States)

2008-06-11

We present a detection system capable of imaging both single photon/positive ion and multiple coincidence photons/positive ions with extremely high spatial resolution. In this detector the photoelectrons excited by the incoming photons are multiplied by microchannel plate(s) (MCP). The process of multiplication is spatially constrained within an MCP pore, which can be as small as 4 {mu}m for commercially available MCPs. An electron cloud originated by a single photoelectron is then encoded by a pixellated custom analog ASIC consisting of 105 K charge sensitive pixels of 50 {mu}m in size arranged on a hexagonal grid. Each pixel registers the charge with an accuracy of <100 electrons rms. Computation of the event centroid from the readout charges results in an accurate event position. A large number of simultaneous photons spatially separated by {approx}0.4 mm can be detected simultaneously allowing multiple coincidence operation for the experiments where a large number of incoming photons/positive ions have to be detected simultaneously. The experimental results prove that the spatial resolution of the readout system itself is {approx}3 {mu}m FWHM enabling detection resolution better than 6 {mu}m for the small pore MCPs. An attractive feature of the detection system is its capability to register the timing of each incoming photon/positive ion (in single photon detection mode) or of the first incoming particle (for the multiple coincidence detection) with an accuracy of {approx}130 ps FWHM. There is also virtually no dark count noise in the detection system making it suitable for low count rate applications.

Facile and high spatial resolution ratio-metric luminescence thermal mapping in microfluidics by near infrared excited upconversion nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Wang, Yu; Li, Shunbo; Wen, Weijia, E-mail: phwen@ust.hk [Department of Physics, KAUST-HKUST Joint Micro/Nanofluidic Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Cao, Wenbin [Nano Science and Technology Program, Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong)

2016-02-01

A local area temperature monitor is important for precise control of chemical and biological processes in microfluidics. In this work, we developed a facile method to realize micron spatial resolution of temperature mapping in a microfluidic channel quickly and cost effectively. Based on the temperature dependent fluorescence emission of NaYF{sub 4}:Yb{sup 3+}, Er{sup 3+} upconversion nanoparticles (UCNPs) under near-infrared irradiation, ratio-metric imaging of UCNPs doped polydimethylsiloxane can map detailed temperature distribution in the channel. Unlike some reported strategies that utilize temperature sensitive organic dye (such as Rhodamine) to achieve thermal sensing, our method is highly chemically inert and physically stable without any performance degradation in long term operation. Moreover, this method can be easily scaled up or down, since the spatial and temperature resolution is determined by an optical imaging system. Our method supplied a simple and efficient solution for temperature mapping on a heterogeneous surface where usage of an infrared thermal camera was limited.

Facile and high spatial resolution ratio-metric luminescence thermal mapping in microfluidics by near infrared excited upconversion nanoparticles

International Nuclear Information System (INIS)

Wang, Yu; Li, Shunbo; Wen, Weijia; Cao, Wenbin

2016-01-01

A local area temperature monitor is important for precise control of chemical and biological processes in microfluidics. In this work, we developed a facile method to realize micron spatial resolution of temperature mapping in a microfluidic channel quickly and cost effectively. Based on the temperature dependent fluorescence emission of NaYF 4 :Yb 3+ , Er 3+ upconversion nanoparticles (UCNPs) under near-infrared irradiation, ratio-metric imaging of UCNPs doped polydimethylsiloxane can map detailed temperature distribution in the channel. Unlike some reported strategies that utilize temperature sensitive organic dye (such as Rhodamine) to achieve thermal sensing, our method is highly chemically inert and physically stable without any performance degradation in long term operation. Moreover, this method can be easily scaled up or down, since the spatial and temperature resolution is determined by an optical imaging system. Our method supplied a simple and efficient solution for temperature mapping on a heterogeneous surface where usage of an infrared thermal camera was limited

FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

Science.gov (United States)

Saha, Mitul; Morais, Marc C

2012-12-15

Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

Downscaling GRACE Remote Sensing Datasets to High-Resolution Groundwater Storage Change Maps of California’s Central Valley

Directory of Open Access Journals (Sweden)

Michelle E. Miro

2018-01-01

Full Text Available NASA’s Gravity Recovery and Climate Experiment (GRACE has already proven to be a powerful data source for regional groundwater assessments in many areas around the world. However, the applicability of GRACE data products to more localized studies and their utility to water management authorities have been constrained by their limited spatial resolution (~200,000 km2. Researchers have begun to address these shortcomings with data assimilation approaches that integrate GRACE-derived total water storage estimates into complex regional models, producing higher-resolution estimates of hydrologic variables (~2500 km2. Here we take those approaches one step further by developing an empirically based model capable of downscaling GRACE data to a high-resolution (~16 km2 dataset of groundwater storage changes over a portion of California’s Central Valley. The model utilizes an artificial neural network to generate a series of high-resolution maps of groundwater storage change from 2002 to 2010 using GRACE estimates of variations in total water storage and a series of widely available hydrologic variables (PRISM precipitation and temperature data, digital elevation model (DEM-derived slope, and Natural Resources Conservation Service (NRCS soil type. The neural network downscaling model is able to accurately reproduce local groundwater behavior, with acceptable Nash-Sutcliffe efficiency (NSE values for calibration and validation (ranging from 0.2445 to 0.9577 and 0.0391 to 0.7511, respectively. Ultimately, the model generates maps of local groundwater storage change at a 100-fold higher resolution than GRACE gridded data products without the use of computationally intensive physical models. The model’s simulated maps have the potential for application to local groundwater management initiatives in the region.

Evaluating kriging as a tool to improve moderate resolution maps of forest biomass

Science.gov (United States)

Elizabeth A. Freeman; Gretchen G. Moisen

2007-01-01

The USDA Forest Service, Forest Inventory and Analysis program (FIA) recently produced a nationwide map of forest biomass by modeling biomass collected on forest inventory plots as nonparametric functions of moderate resolution satellite data and other environmental variables using Cubist software. Efforts are underway to develop methods to enhance this initial map. We...

Multistudy fine mapping of chromosome 2q identifies XRCC5 as a chronic obstructive pulmonary disease susceptibility gene

DEFF Research Database (Denmark)

Hersh, Craig P; Pillai, Sreekumar G; Zhu, Guohua

2010-01-01

RATIONALE: Several family-based studies have identified genetic linkage for lung function and airflow obstruction to chromosome 2q. OBJECTIVES: We hypothesized that merging results of high-resolution single nucleotide polymorphism (SNP) mapping in four separate populations would lead to the ident......RATIONALE: Several family-based studies have identified genetic linkage for lung function and airflow obstruction to chromosome 2q. OBJECTIVES: We hypothesized that merging results of high-resolution single nucleotide polymorphism (SNP) mapping in four separate populations would lead...... the National Emphysema Treatment Trial and 330 community control subjects. Significant associations from the combined results across the two case-control studies were followed up in 1,839 individuals from 603 families from the International COPD Genetics Network (ICGN) and in 949 individuals from 127 families...

Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines

Directory of Open Access Journals (Sweden)

Robert Silas Allen

2013-09-01

Full Text Available Forward genetic screens have identified numerous genes involved in development and metabolism, and remain a cornerstone of biological research. However to locate a causal mutation, the practice of crossing to a polymorphic background to generate a mapping population can be problematic if the mutant phenotype is difficult to recognise in the hybrid F2 progeny, or dependent on parental specific traits. Here in a screen for leaf hyponasty mutants, we have performed a single backcross of an Ethane Methyl Sulphonate (EMS generated hyponastic mutant to its parent. Whole genome deep sequencing of a bulked homozygous F2 population and analysis via the Next Generation EMS mutation mapping pipeline (NGM unambiguously determined the causal mutation to be a single nucleotide polymorphisim (SNP residing in HASTY, a previously characterised gene involved in microRNA biogenesis. We have evaluated the feasibility of this backcross approach using three additional SNP mapping pipelines; SHOREmap, the GATK pipeline, and the samtools pipeline. Although there was variance in the identification of EMS SNPs, all returned the same outcome in clearly identifying the causal mutation in HASTY. The simplicity of performing a single parental backcross and genome sequencing a small pool of segregating mutants has great promise for identifying mutations that may be difficult to map using conventional approaches.

Hyperspectral Data for Mangrove Species Mapping: A Comparison of Pixel-Based and Object-Based Approach

Directory of Open Access Journals (Sweden)

Muhammad Kamal

2011-10-01

Full Text Available Visual image interpretation and digital image classification have been used to map and monitor mangrove extent and composition for decades. The presence of a high-spatial resolution hyperspectral sensor can potentially improve our ability to differentiate mangrove species. However, little research has explored the use of pixel-based and object-based approaches on high-spatial hyperspectral datasets for this purpose. This study assessed the ability of CASI-2 data for mangrove species mapping using pixel-based and object-based approaches at the mouth of the Brisbane River area, southeast Queensland, Australia. Three mapping techniques used in this study: spectral angle mapper (SAM and linear spectral unmixing (LSU for the pixel-based approaches, and multi-scale segmentation for the object-based image analysis (OBIA. The endmembers for the pixel-based approach were collected based on existing vegetation community map. Nine targeted classes were mapped in the study area from each approach, including three mangrove species: Avicennia marina, Rhizophora stylosa, and Ceriops australis. The mapping results showed that SAM produced accurate class polygons with only few unclassified pixels (overall accuracy 69%, Kappa 0.57, the LSU resulted in a patchy polygon pattern with many unclassified pixels (overall accuracy 56%, Kappa 0.41, and the object-based mapping produced the most accurate results (overall accuracy 76%, Kappa 0.67. Our results demonstrated that the object-based approach, which combined a rule-based and nearest-neighbor classification method, was the best classifier to map mangrove species and its adjacent environments.

Object-Based Paddy Rice Mapping Using HJ-1A/B Data and Temporal Features Extracted from Time Series MODIS NDVI Data.

Science.gov (United States)

Singha, Mrinal; Wu, Bingfang; Zhang, Miao

2016-12-22

Accurate and timely mapping of paddy rice is vital for food security and environmental sustainability. This study evaluates the utility of temporal features extracted from coarse resolution data for object-based paddy rice classification of fine resolution data. The coarse resolution vegetation index data is first fused with the fine resolution data to generate the time series fine resolution data. Temporal features are extracted from the fused data and added with the multi-spectral data to improve the classification accuracy. Temporal features provided the crop growth information, while multi-spectral data provided the pattern variation of paddy rice. The achieved overall classification accuracy and kappa coefficient were 84.37% and 0.68, respectively. The results indicate that the use of temporal features improved the overall classification accuracy of a single-date multi-spectral image by 18.75% from 65.62% to 84.37%. The minimum sensitivity (MS) of the paddy rice classification has also been improved. The comparison showed that the mapped paddy area was analogous to the agricultural statistics at the district level. This work also highlighted the importance of feature selection to achieve higher classification accuracies. These results demonstrate the potential of the combined use of temporal and spectral features for accurate paddy rice classification.

Wide-area mapping of resting state hemodynamic correlations at microvascular resolution with multi-contrast optical imaging (Conference Presentation)

Science.gov (United States)

Senarathna, Janaka; Hadjiabadi, Darian; Gil, Stacy; Thakor, Nitish V.; Pathak, Arvind P.

2017-02-01

Different brain regions exhibit complex information processing even at rest. Therefore, assessing temporal correlations between regions permits task-free visualization of their `resting state connectivity'. Although functional MRI (fMRI) is widely used for mapping resting state connectivity in the human brain, it is not well suited for `microvascular scale' imaging in rodents because of its limited spatial resolution. Moreover, co-registered cerebral blood flow (CBF) and total hemoglobin (HbT) data are often unavailable in conventional fMRI experiments. Therefore, we built a customized system that combines laser speckle contrast imaging (LSCI), intrinsic optical signal (IOS) imaging and fluorescence imaging (FI) to generate multi-contrast functional connectivity maps at a spatial resolution of 10 μm. This system comprised of three illumination sources: a 632 nm HeNe laser (for LSCI), a 570 nm ± 5 nm filtered white light source (for IOS), and a 473 nm blue laser (for FI), as well as a sensitive CCD camera operating at 10 frames per second for image acquisition. The acquired data enabled visualization of changes in resting state neurophysiology at microvascular spatial scales. Moreover, concurrent mapping of CBF and HbT-based temporal correlations enabled in vivo mapping of how resting brain regions were linked in terms of their hemodynamics. Additionally, we complemented this approach by exploiting the transit times of a fluorescent tracer (Dextran-FITC) to distinguish arterial from venous perfusion. Overall, we demonstrated the feasibility of wide area mapping of resting state connectivity at microvascular resolution and created a new toolbox for interrogating neurovascular function.

A LiDAR based analysis of hydraulic hazard mapping

Science.gov (United States)

Cazorzi, F.; De Luca, A.; Checchinato, A.; Segna, F.; Dalla Fontana, G.

2012-04-01

Mapping hydraulic hazard is a ticklish procedure as it involves technical and socio-economic aspects. On the one hand no dangerous areas should be excluded, on the other hand it is important not to exceed, beyond the necessary, with the surface assigned to some use limitations. The availability of a high resolution topographic survey allows nowadays to face this task with innovative procedures, both in the planning (mapping) and in the map validation phases. The latter is the object of the present work. It should be stressed that the described procedure is proposed purely as a preliminary analysis based on topography only, and therefore does not intend in any way to replace more sophisticated analysis methods requiring based on hydraulic modelling. The reference elevation model is a combination of the digital terrain model and the digital building model (DTM+DBM). The option of using the standard surface model (DSM) is not viable, as the DSM represents the vegetation canopy as a solid volume. This has the consequence of unrealistically considering the vegetation as a geometric obstacle to water flow. In some cases the topographic model construction requires the identification and digitization of the principal breaklines, such as river banks, ditches and similar natural or artificial structures. The geometrical and topological procedure for the validation of the hydraulic hazard maps is made of two steps. In the first step the whole area is subdivided into fluvial segments, with length chosen as a reasonable trade-off between the need to keep the hydrographical unit as complete as possible, and the need to separate sections of the river bed with significantly different morphology. Each of these segments is made of a single elongated polygon, whose shape can be quite complex, especially for meandering river sections, where the flow direction (i.e. the potential energy gradient associated to the talweg) is often inverted. In the second step the segments are analysed

Deciphering Stress State of Seismogenic Faults in Oklahoma and Kansas Based on High-resolution Stress Maps

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Qin, Y.; Chen, X.; Haffener, J.; Trugman, D. T.; Carpenter, B.; Reches, Z.

2017-12-01

Induced seismicity in Oklahoma and Kansas delineates clear fault trends. It is assumed that fluid injection reactivates faults which are optimally oriented relative to the regional tectonic stress field. We utilized recently improved earthquake locations and more complete focal mechanism catalogs to quantitatively analyze the stress state of seismogenic faults with high-resolution stress maps. The steps of analysis are: (1) Mapping the faults by clustering seismicity using a nearest-neighbor approach, manually picking the fault in each cluster and calculating the fault geometry using principal component analysis. (2) Running a stress inversion with 0.2° grid spacing to produce an in-situ stress map. (3) The fault stress state is determined from fault geometry and a 3D Mohr circle. The parameter `understress' is calculated to quantify the criticalness of these faults. If it approaches 0, the fault is critically stressed; while understress=1 means there is no shear stress on the fault. Our results indicate that most of the active faults have a planar shape (planarity>0.8), and dip steeply (dip>70°). The fault trends are distributed mainly in conjugate set ranges of [50°,70°] and [100°,120°]. More importantly, these conjugate trends are consistent with mapped basement fractures in southern Oklahoma, suggesting similar basement features from regional tectonics. The fault length data shows a loglinear relationship with the maximum earthquake magnitude with an expected maximum magnitude range from 3.2 to 4.4 for most seismogenic faults. Based on 3D local Mohr circle, we find that 61% of the faults have low understress (0.5) are located within highest-rate injection zones and therefore are likely to be influenced by high pore pressure. The faults that hosted the largest earthquakes, M5.7 Prague and M5.8 Pawnee are critically stressed (understress 0.2). These differences may help in understanding earthquake sequences, for example, the predominantly aftershock

A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits

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Laurent Pascal

2006-03-01

annotation of the currently existing bovine genome sequence draft to establish the final architecture of BTA6. Hence, a sequence-based map will provide a key resource to facilitate prospective continued efforts for the selection and validation of relevant positional and functional candidates underlying QTL for milk production and growth-related traits mapped on BTA6 and on similar chromosomal regions from evolutionary closely related species like sheep and goat. Furthermore, the high-resolution sequence-referenced BTA6 map will enable precise identification of multi-species conserved chromosome segments and evolutionary breakpoints in mammalian phylogenetic studies.

Reporting of quantitative oxygen mapping in EPR imaging

Science.gov (United States)

Subramanian, Sankaran; Devasahayam, Nallathamby; McMillan, Alan; Matsumoto, Shingo; Munasinghe, Jeeva P.; Saito, Keita; Mitchell, James B.; Chandramouli, Gadisetti V. R.; Krishna, Murali C.

2012-01-01

Oxygen maps derived from electron paramagnetic resonance spectral-spatial imaging (EPRI) are based upon the relaxivity of molecular oxygen with paramagnetic spin probes. This technique can be combined with MRI to facilitate mapping of pO 2 values in specific anatomic locations with high precision. The co-registration procedure, which matches the physical and digital dimensions of EPR and MR images, may present the pO 2 map at the higher MRI resolution, exaggerating the spatial resolution of oxygen, making it difficult to precisely distinguish hypoxic regions from normoxic regions. The latter distinction is critical in monitoring the treatment of cancer by radiation and chemotherapy, since it is well-established that hypoxic regions are three or four times more resistant to treatment compared to normoxic regions. The aim of this article is to describe pO 2 maps based on the intrinsic resolution of EPRI. A spectral parameter that affects the intrinsic spatial resolution of EPRI is the full width at half maximum (FWHM) height of the gradient-free EPR absorption line in frequency-encoded imaging. In single point imaging too, the transverse relaxation times (T2∗) limit the resolution since the signal decays by exp(-tp/T2∗) where the delay time after excitation pulse, t p, is related to the resolution. Although the spin densities of two point objects may be resolved at this separation, it is inadequate to evaluate quantitative changes of pO 2 levels since the linewidths are proportionately affected by pO 2. A spatial separation of at least twice this resolution is necessary to correctly identify a change in pO 2 level. In addition, the pO 2 values are blurred by uncertainties arising from spectral dimensions. Blurring due to noise and low resolution modulates the pO 2 levels at the boundaries of hypoxic and normoxic regions resulting in higher apparent pO 2 levels in hypoxic regions. Therefore, specification of intrinsic resolution and pO 2 uncertainties are

Surface Water Mapping from Suomi NPP-VIIRS Imagery at 30 m Resolution via Blending with Landsat Data

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Chang Huang

2016-07-01

Full Text Available Monitoring the dynamics of surface water using remotely sensed data generally requires both high spatial and high temporal resolutions. One effective and popular approach for achieving this is image fusion. This study adopts a widely accepted fusion model, the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM, for blending the newly available coarse-resolution Suomi NPP-VIIRS data with Landsat data in order to derive water maps at 30 m resolution. The Pan-sharpening technique was applied to preprocessing NPP-VIIRS data to achieve a higher-resolution before blending. The modified Normalized Difference Water Index (mNDWI was employed for mapping surface water area. Two fusion alternatives, blend-then-index (BI or index-then-blend (IB, were comparatively analyzed against a Landsat derived water map. A case study of mapping Poyang Lake in China, where water distribution pattern is complex and the water body changes frequently and drastically, was conducted. It has been revealed that the IB method derives more accurate results with less computation time than the BI method. The BI method generally underestimates water distribution, especially when the water area expands radically. The study has demonstrated the feasibility of blending NPP-VIIRS with Landsat for achieving surface water mapping at both high spatial and high temporal resolutions. It suggests that IB is superior to BI for water mapping in terms of efficiency and accuracy. The finding of this study also has important reference values for other blending works, such as image blending for vegetation cover monitoring.

Mapping Entomological Dengue Risk Levels in Martinique Using High-Resolution Remote-Sensing Environmental Data

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Vanessa Machault

2014-12-01

Full Text Available Controlling dengue virus transmission mainly involves integrated vector management. Risk maps at appropriate scales can provide valuable information for assessing entomological risk levels. Here, results from a spatio-temporal model of dwellings potentially harboring Aedes aegypti larvae from 2009 to 2011 in Tartane (Martinique, French Antilles using high spatial resolution remote-sensing environmental data and field entomological and meteorological information are presented. This tele-epidemiology methodology allows monitoring the dynamics of diseases closely related to weather/climate and environment variability. A Geoeye-1 image was processed to extract landscape elements that could surrogate societal or biological information related to the life cycle of Aedes vectors. These elements were subsequently included into statistical models with random effect. Various environmental and meteorological conditions have indeed been identified as risk/protective factors for the presence of Aedes aegypti immature stages in dwellings at a given date. These conditions were used to produce dynamic high spatio-temporal resolution maps from the presence of most containers harboring larvae. The produced risk maps are examples of modeled entomological maps at the housing level with daily temporal resolution. This finding is an important contribution to the development of targeted operational control systems for dengue and other vector-borne diseases, such as chikungunya, which is also present in Martinique.

High resolution surface scanning of Thick-GEM for single photo-electron detection

Energy Technology Data Exchange (ETDEWEB)

Hamar, G., E-mail: hamar.gergo@wigner.mta.hu [Wigner Research Centre for Physics, Budapest (Hungary); Varga, D., E-mail: vdezso@mail.cern.ch [Eoetvoes Lorand University, Budapest (Hungary)

2012-12-01

An optical system for high resolution scanning of TGEM UV photon detection systems is introduced. The structure exploits the combination of a single Au-coated TGEM under study, and an asymmetric MWPC (Close Cathode Chamber) as post-amplification stage. A pulsed UV LED source with emission down to 240 nm has been focused to a spot of 0.07 mm on the TGEM surface, and single photo-electron charge spectra has been recorded over selected two dimensional regions. This way, the TGEM gain (order of 10-100) and TGEM photo-electron detection efficiency is clearly separated, unlike in case of continuous illumination. The surface structure connected to the TGEM photon detection is well observable, including inefficiencies in the holes and at the symmetry points between holes. The detection efficiency as well as the gas gain are fluctuating from hole to hole. The gain is constant in the hexagon around any hole, pointing to the fact that the gain depends on hole geometry, and less on the position where the electron enters. The detection probability map strongly changes with the field strength above the TGEM surface, in relation to the change of the actual surface field configuration. The results can be confronted with position-dependent simulations of TGEM electron transfer and gas multiplication. -- Highlights: Black-Right-Pointing-Pointer First demonstration of Thick GEM surface scanning with single photo-electrons. Black-Right-Pointing-Pointer Resolution of 0.1 mm is sufficient to identify structures connected to TGEM surface field structure. Black-Right-Pointing-Pointer Gain and detection efficiency and separately measurable. Black-Right-Pointing-Pointer Detection efficiency is high in a ring around the holes, and gain is constant in the hexagonal collection regions.

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

Science.gov (United States)

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

2012-01-01

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

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

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Pramod K Avti

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

Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

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Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

2015-01-01

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

Adaptive Markov Random Fields for Example-Based Super-resolution of Faces

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Stephenson Todd A

2006-01-01

Full Text Available Image enhancement of low-resolution images can be done through methods such as interpolation, super-resolution using multiple video frames, and example-based super-resolution. Example-based super-resolution, in particular, is suited to images that have a strong prior (for those frameworks that work on only a single image, it is more like image restoration than traditional, multiframe super-resolution. For example, hallucination and Markov random field (MRF methods use examples drawn from the same domain as the image being enhanced to determine what the missing high-frequency information is likely to be. We propose to use even stronger prior information by extending MRF-based super-resolution to use adaptive observation and transition functions, that is, to make these functions region-dependent. We show with face images how we can adapt the modeling for each image patch so as to improve the resolution.

Adaptive Markov Random Fields for Example-Based Super-resolution of Faces

Science.gov (United States)

Stephenson, Todd A.; Chen, Tsuhan

2006-12-01

Image enhancement of low-resolution images can be done through methods such as interpolation, super-resolution using multiple video frames, and example-based super-resolution. Example-based super-resolution, in particular, is suited to images that have a strong prior (for those frameworks that work on only a single image, it is more like image restoration than traditional, multiframe super-resolution). For example, hallucination and Markov random field (MRF) methods use examples drawn from the same domain as the image being enhanced to determine what the missing high-frequency information is likely to be. We propose to use even stronger prior information by extending MRF-based super-resolution to use adaptive observation and transition functions, that is, to make these functions region-dependent. We show with face images how we can adapt the modeling for each image patch so as to improve the resolution.

Detailed Maps Depicting the Shallow-Water Benthic Habitats of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery (Draft)

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National Oceanic and Atmospheric Administration, Department of Commerce — Detailed, shallow-water coral reef ecosystem maps were generated by rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations...

New Geospatial Approaches for Efficiently Mapping Forest Biomass Logistics at High Resolution over Large Areas

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John Hogland

2018-04-01

Full Text Available Adequate biomass feedstock supply is an important factor in evaluating the financial feasibility of alternative site locations for bioenergy facilities and for maintaining profitability once a facility is built. We used newly developed spatial analysis and logistics software to model the variables influencing feedstock supply and to estimate and map two components of the supply chain for a bioenergy facility: (1 the total biomass stocks available within an economically efficient transportation distance; (2 the cost of logistics to move the required stocks from the forest to the facility. Both biomass stocks and flows have important spatiotemporal dynamics that affect procurement costs and project viability. Though seemingly straightforward, these two components can be difficult to quantify and map accurately in a useful and spatially explicit manner. For an 8 million hectare study area, we used raster-based methods and tools to quantify and visualize these supply metrics at 10 m2 spatial resolution. The methodology and software leverage a novel raster-based least-cost path modeling algorithm that quantifies off-road and on-road transportation and other logistics costs. The results of the case study highlight the efficiency, flexibility, fine resolution, and spatial complexity of model outputs developed for facility siting and procurement planning.

Mapping Urban Tree Canopy Coverage and Structure using Data Fusion of High Resolution Satellite Imagery and Aerial Lidar

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Elmes, A.; Rogan, J.; Williams, C. A.; Martin, D. G.; Ratick, S.; Nowak, D.

2015-12-01

Urban tree canopy (UTC) coverage is a critical component of sustainable urban areas. Trees provide a number of important ecosystem services, including air pollution mitigation, water runoff control, and aesthetic and cultural values. Critically, urban trees also act to mitigate the urban heat island (UHI) effect by shading impervious surfaces and via evaporative cooling. The cooling effect of urban trees can be seen locally, with individual trees reducing home HVAC costs, and at a citywide scale, reducing the extent and magnitude of an urban areas UHI. In order to accurately model the ecosystem services of a given urban forest, it is essential to map in detail the condition and composition of these trees at a fine scale, capturing individual tree crowns and their vertical structure. This paper presents methods for delineating UTC and measuring canopy structure at fine spatial resolution (body of methods, relying on a data fusion method to combine the information contained in high resolution WorldView-3 satellite imagery and aerial lidar data using an object-based image classification approach. The study area, Worcester, MA, has recently undergone a large-scale tree removal and reforestation program, following a pest eradication effort. Therefore, the urban canopy in this location provides a wide mix of tree age class and functional type, ideal for illustrating the effectiveness of the proposed methods. Early results show that the object-based classifier is indeed capable of identifying individual tree crowns, while continued research will focus on extracting crown structural characteristics using lidar-derived metrics. Ultimately, the resulting fine resolution UTC map will be compared with previously created UTC maps of the same area but for earlier dates, producing a canopy change map corresponding to the Worcester area tree removal and replanting effort.

Name-Based Address Mapping for Virtual Private Networks

Science.gov (United States)

Surányi, Péter; Shinjo, Yasushi; Kato, Kazuhiko

IPv4 private addresses are commonly used in local area networks (LANs). With the increasing popularity of virtual private networks (VPNs), it has become common that a user connects to multiple LANs at the same time. However, private address ranges for LANs frequently overlap. In such cases, existing systems do not allow the user to access the resources on all LANs at the same time. In this paper, we propose name-based address mapping for VPNs, a novel method that allows connecting to hosts through multiple VPNs at the same time, even when the address ranges of the VPNs overlap. In name-based address mapping, rather than using the IP addresses used on the LANs (the real addresses), we assign a unique virtual address to each remote host based on its domain name. The local host uses the virtual addresses to communicate with remote hosts. We have implemented name-based address mapping for layer 3 OpenVPN connections on Linux and measured its performance. The communication overhead of our system is less than 1.5% for throughput and less than 0.2ms for each name resolution.

Enhanced Resolution Maps of Energetic Neutral Atoms from IBEX

Science.gov (United States)

Teodoro, L. A.; Elphic, R. C.; Janzen, P.; Reisenfeld, D.; Wilson, J. T.

2017-12-01

The discovery by the Interstellar Boundary Explorer (IBEX) of a "Ribbon" in the measurements of Energetic Neutral Particles (ENA) was a major surprise that lead to the re-thinking of the Physics underpinning the heliosphere-intergalactic medium boundary dynamics. Several physical models have been proposed and tested in their ability to mimic the IBEX observations. Some of the ENA IBEX's include the following features: 1) The presence of fine structure within the ribbon suggests that the physical properties of it exhibit small-scale spacial structure and possibly rapid small-scale variations. 2) The ribbon is a fairly narrow feature at low energies and broadens with increasing energy;The IBEX detectors were designed to maximize count rate by incorporating wide angular and broad energy acceptance. Thus far, the existing mapping software used by the IBEX Science Operation Center has not been design with the "Ribbon" ( 20o wide) in mind: the current generation of maps are binned in 6o longitude pixels by 6o latitude pixels (so the pixels are all of the same size in angle and are quite "blocky"). Furthermore, the instrumental point spread function has not been deconvolved, making any potential narrow features broader than they are. An improvement in the spatial resolution of the IBEX maps would foster a better understanding of the Ribbon and its substructure, and thus reply to some of the basic and profound questions related to its origin, the nature of the outer boundaries of the our solar system and the surrounding interstellar Galactic medium.Here we report on the application of the Bayesian image reconstruction algorithm "Speedy Pixons" to the ENA data with the aim to sharpen the ENA IBEX maps. A preliminary application allow us to conclude that: The peaks in the count rate do appear to be more enhanced in the reconstruction; The reconstruction is clearly denoised; The "Ribbon" is better defined in the reconstruction. We are currently studying the implications of

Comparative high-resolution mapping of the wax inhibitors Iw1 and Iw2 in hexaploid wheat.

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Haibin Wu

Full Text Available The wax (glaucousness on wheat leaves and stems is mainly controlled by two sets of genes: glaucousness loci (W1 and W2 and non-glaucousness loci (Iw1 and Iw2. The non-glaucousness (Iw loci act as inhibitors of the glaucousness loci (W. High-resolution comparative genetic linkage maps of the wax inhibitors Iw1 originating from Triticum dicoccoides, and Iw2 from Aegilops tauschii were developed by comparative genomics analyses of Brachypodium, sorghum and rice genomic sequences corresponding to the syntenic regions of the Iw loci in wheat. Eleven Iw1 and eight Iw2 linked EST markers were developed and mapped to linkage maps on the distal regions of chromosomes 2BS and 2DS, respectively. The Iw1 locus mapped within a 0.96 cM interval flanked by the BE498358 and CA499581 EST markers that are collinear with 122 kb, 202 kb, and 466 kb genomic regions in the Brachypodium 5S chromosome, the sorghum 6S chromosome and the rice 4S chromosome, respectively. The Iw2 locus was located in a 4.1 to 5.4-cM interval in chromosome 2DS that is flanked by the CJ886319 and CJ519831 EST markers, and this region is collinear with a 2.3 cM region spanning the Iw1 locus on chromosome 2BS. Both Iw1 and Iw2 co-segregated with the BF474014 and CJ876545 EST markers, indicating they are most likely orthologs on 2BS and 2DS. These high-resolution maps can serve as a framework for chromosome landing, physical mapping and map-based cloning of the wax inhibitors in wheat.

Fusion of Pixel-based and Object-based Features for Road Centerline Extraction from High-resolution Satellite Imagery

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CAO Yungang

2016-10-01

Full Text Available A novel approach for road centerline extraction from high spatial resolution satellite imagery is proposed by fusing both pixel-based and object-based features. Firstly, texture and shape features are extracted at the pixel level, and spectral features are extracted at the object level based on multi-scale image segmentation maps. Then, extracted multiple features are utilized in the fusion framework of Dempster-Shafer evidence theory to roughly identify the road network regions. Finally, an automatic noise removing algorithm combined with the tensor voting strategy is presented to accurately extract the road centerline. Experimental results using high-resolution satellite imageries with different scenes and spatial resolutions showed that the proposed approach compared favorably with the traditional methods, particularly in the aspect of eliminating the salt noise and conglutination phenomenon.

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Science.gov (United States)

2012-01-01

Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia

Effects of the intensity levels and beam map resolutions on static IMRT plans

International Nuclear Information System (INIS)

Sun Xuepeng; Xia Ping; Yu Naichang

2004-01-01

In this study we focus on how the intensity level and multileaf collimator (MLC) resolution affect the quality of IMRT plans using the static MLC delivery technique. The planning process is based on a least-square dose-based quadratic function and uses a simulated annealing algorithm to sample the discrete variables. Three clinical cases are studied empirically: a medulloblastoma, a prostate, and an oropharyngeal carcinoma. The intensity levels used are 3, 5, 10, 20, and continuous; the map resolution varies from 0.15-1.5 cm, with the leaf width equal to the step size. The influence of these two parameters are studied by comparing the cost value and the cost of delivery time from a trade-off point of view. An 'efficient frontier' is drawn by connecting the plans with the lowest cost value at any given resolutions. For each case, a practical delivery region is defined by doubling the delivery time needed at a normal setting (five levels, 1.0 cm). Within this region, the 'efficient frontier' demonstrates that the plans with five intensity levels are the most efficient comparing with plans with higher levels. This is a confirmation of the conclusion from Keller-Reichenbecher et al. [Int. J. Radiat. Oncol., Biol., Phys. 45, 1315-1324 (1999)]. It indicates that to further improve the plan quality with the minimal cost of extra delivery time, the most economical way is to improve the resolution rather than using higher intensity levels

High-resolution YAC-cosmid-STS map of human chromosome 13.

Science.gov (United States)

Cayanis, E; Russo, J J; Kalachikov, S; Ye, X; Park, S H; Sunjevaric, I; Bonaldo, M F; Lawton, L; Venkatraj, V S; Schon, E; Soares, M B; Rothstein, R; Warburton, D; Edelman, I S; Zhang, P; Efstratiadis, A; Fischer, S G

1998-01-01

We have assembled a high-resolution physical map of human chromosome 13 DNA (approximately 114 Mb) from hybridization, PCR, and FISH mapping data using a specifically designed set of computer programs. Although the mapping of 13p is limited, 13q (approximately 98 Mb) is covered by an almost continuous contig of 736 YACs aligned to 597 contigs of cosmids. Of a total of 10,789 cosmids initially selected from a chromosome 13-specific cosmid library (16,896 colonies) using inter-Alu PCR probes from the YACs and probes for markers mapped to chromosome 13, 511 were assembled in contigs that were established from cross-hybridization relationships between the cosmids. The 13q YAC-cosmid map was annotated with 655 sequence tagged sites (STSs) with an average spacing of 1 STS per 150 kb. This set of STSs, each identified by a D number and cytogenetic location, includes database markers (198), expressed sequence tags (93), and STSs generated by sequencing of the ends of cosmid inserts (364). Additional annotation has been provided by positioning 197 cosmids mapped by FISH on 13q. The final (comprehensive) map, a list of STS primers, and raw data used in map assembly are available at our Web site (genome1.ccc.columbia.edu/ approximately genome/) and can serve as a resource to facilitate accurate localization of additional markers, provide substrates for sequencing, and assist in the discovery of chromosome 13 genes associated with hereditary diseases.

Comparing orbiter and rover image-based mapping of an ancient sedimentary environment, Aeolis Palus, Gale crater, Mars

Science.gov (United States)

Stack, Kathryn M.; Edwards, Christopher; Grotzinger, J. P.; Gupta, S.; Sumner, D.; Edgar, Lauren; Fraeman, A.; Jacob, S.; LeDeit, L.; Lewis, K.W.; Rice, M.S.; Rubin, D.; Calef, F.; Edgett, K.; Williams, R.M.E.; Williford, K.H.

2016-01-01

This study provides the first systematic comparison of orbital facies maps with detailed ground-based geology observations from the Mars Science Laboratory (MSL) Curiosity rover to examine the validity of geologic interpretations derived from orbital image data. Orbital facies maps were constructed for the Darwin, Cooperstown, and Kimberley waypoints visited by the Curiosity rover using High Resolution Imaging Science Experiment (HiRISE) images. These maps, which represent the most detailed orbital analysis of these areas to date, were compared with rover image-based geologic maps and stratigraphic columns derived from Curiosity’s Mast Camera (Mastcam) and Mars Hand Lens Imager (MAHLI). Results show that bedrock outcrops can generally be distinguished from unconsolidated surficial deposits in high-resolution orbital images and that orbital facies mapping can be used to recognize geologic contacts between well-exposed bedrock units. However, process-based interpretations derived from orbital image mapping are difficult to infer without known regional context or observable paleogeomorphic indicators, and layer-cake models of stratigraphy derived from orbital maps oversimplify depositional relationships as revealed from a rover perspective. This study also shows that fine-scale orbital image-based mapping of current and future Mars landing sites is essential for optimizing the efficiency and science return of rover surface operations.

Blanding’s Turtle (Emydoidea blandingii Potential Habitat Mapping Using Aerial Orthophotographic Imagery and Object Based Classification

Directory of Open Access Journals (Sweden)

Douglas J. King

2012-01-01

Full Text Available Blanding’s turtle (Emydoidea blandingii is a threatened species under Canada’s Species at Risk Act. In southern Québec, field based inventories are ongoing to determine its abundance and potential habitat. The goal of this research was to develop means for mapping of potential habitat based on primary habitat attributes that can be detected with high-resolution remotely sensed imagery. Using existing spring leaf-off 20 cm resolution aerial orthophotos of a portion of Gatineau Park where some Blanding’s turtle observations had been made, habitat attributes were mapped at two scales: (1 whole wetlands; (2 within wetland habitat features of open water, vegetation (used for camouflage and thermoregulation, and logs (used for spring sun-basking. The processing steps involved initial pixel-based classification to eliminate most areas of non-wetland, followed by object-based segmentations and classifications using a customized rule sequence to refine the wetland map and to map the within wetland habitat features. Variables used as inputs to the classifications were derived from the orthophotos and included image brightness, texture, and segmented object shape and area. Independent validation using field data and visual interpretation showed classification accuracy for all habitat attributes to be generally over 90% with a minimum of 81.5% for the producer’s accuracy of logs. The maps for each attribute were combined to produce a habitat suitability map for Blanding’s turtle. Of the 115 existing turtle observations, 92.3% were closest to a wetland of the two highest suitability classes. High-resolution imagery combined with object-based classification and habitat suitability mapping methods such as those presented provide a much more spatially explicit representation of detailed habitat attributes than can be obtained through field work alone. They can complement field efforts to document and track turtle activities and can contribute to

EMODnet High Resolution Seabed Mapping - further developing a high resolution digital bathymetry for European seas

Science.gov (United States)

Schaap, D.; Schmitt, T.

2017-12-01

Access to marine data is a key issue for the EU Marine Strategy Framework Directive and the EU Marine Knowledge 2020 agenda and includes the European Marine Observation and Data Network (EMODnet) initiative. EMODnet aims at assembling European marine data, data products and metadata from diverse sources in a uniform way. The EMODnet Bathymetry project has developed Digital Terrain Models (DTM) for the European seas. These have been produced from survey and aggregated data sets that are indexed with metadata by adopting the SeaDataNet Catalogue services. SeaDataNet is a network of major oceanographic data centres around the European seas that manage, operate and further develop a pan-European infrastructure for marine and ocean data management. The latest EMODnet Bathymetry DTM release has a grid resolution of 1/8 arcminute and covers all European sea regions. Use has been made of circa 7800 gathered survey datasets and composite DTMs. Catalogues and the EMODnet DTM are published at the dedicated EMODnet Bathymetry portal including a versatile DTM viewing and downloading service. End December 2016 the Bathymetry project has been succeeded by EMODnet High Resolution Seabed Mapping (HRSM). This continues gathering of bathymetric in-situ data sets with extra efforts for near coastal waters and coastal zones. In addition Satellite Derived Bathymetry data are included to fill gaps in coverage of the coastal zones. The extra data and composite DTMs will increase the coverage of the European seas and its coastlines, and provide input for producing an EMODnet DTM with a common resolution of 1/16 arc minutes. The Bathymetry Viewing and Download service will be upgraded to provide a multi-resolution map and including 3D viewing. The higher resolution DTMs will also be used to determine best-estimates of the European coastline for a range of tidal levels (HAT, MHW, MSL, Chart Datum, LAT), thereby making use of a tidal model for Europe. Extra challenges will be `moving to the

Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex.

Science.gov (United States)

Ma, Jiong; Kelich, Joseph M; Junod, Samuel L; Yang, Weidong

2017-04-01

The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside of the sub-micrometer supramolecular complex. Here, we combined super-resolution single-point edge-excitation subdiffraction (SPEED) microscopy and nanobody-specific labeling to reveal the spatial distribution of scaffold Nups within three separate layers in the native NPC with a precision of ∼3 nm. Our data reveal both the radial and axial spatial distributions for Pom121, Nup37 and Nup35 and provide evidence for their copy numbers of 8, 32 and 16, respectively, per NPC. This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes. © 2017. Published by The Company of Biologists Ltd.

High Resolution Urban Land Cover Mapping Using NAIP Aerial Photography and Image Processing for the USEPA National Atlas of Sustainability and Ecosystem Services

Science.gov (United States)

Pilant, A. N.; Baynes, J.; Dannenberg, M.

2012-12-01

The US EPA National Atlas for Sustainability is a web-based, easy-to-use, mapping application that allows users to view and analyze multiple ecosystem services in a specific region. The Atlas provides users with a visual method for interpreting ecosystem services and understanding how they can be conserved and enhanced for a sustainable future. The Urban Atlas component of the National Atlas will provide fine-scale information linking human health and well-being to environmental conditions such as urban heat islands, near-road pollution, resource use, access to recreation, drinking water quality and other quality of life indicators. The National Land Cover Data (NLCD) derived from 30 m scale 2006 Landsat imagery provides the land cover base for the Atlas. However, urban features and phenomena occur at finer spatial scales, so higher spatial resolution and more current LC maps are required. We used 4 band USDA NAIP imagery (1 m pixel size) and various classification approaches to produce urban land cover maps with these classes: impervious surface, grass and herbaceous, trees and forest, soil and barren, and water. Here we present the remote sensing methods used and results from four pilot cities in this effort, highlighting the pros and cons of the approach, and the benefits to sustainability and ecosystem services analysis. Example of high resolution land cover map derived from USDA NAIP aerial photo. Compare 30 m and 1 m resolution land cover maps of downtown Durham, NC.

Mapping plastic greenhouse with medium spatial resolution satellite data: Development of a new spectral index

Science.gov (United States)

Yang, Dedi; Chen, Jin; Zhou, Yuan; Chen, Xiang; Chen, Xuehong; Cao, Xin

2017-06-01

Plastic greenhouses (PGs) are an important agriculture development technique to protect and control the growing environment for food crops. The extensive use of PGs can change the agriculture landscape and affects the local environment. Accurately mapping and estimating the coverage of PGs is a necessity to the strategic planning of modern agriculture. Unfortunately, PG mapping over large areas is methodologically challenging, as the medium spatial resolution satellite imagery (such as Landsat data) used for analysis lacks spatial details and spectral variations. To fill the gap, the paper proposes a new plastic greenhouse index (PGI) based on the spectral, sensitivity, and separability analysis of PGs using medium spatial resolution images. In the context of the Landsat Enhanced Thematic Mapper Plus (ETM+) imagery, the paper examines the effectiveness and capability of the proposed PGI. The results indicate that PGs in Landsat ETM+ image can be successfully detected by the PGI if the PG fraction is greater than 12% in a mixed pixel. A kappa coefficient of 0.83 and overall accuracy of 91.2% were achieved when applying the proposed PGI in the case of Weifang District, Shandong, China. These results show that the proposed index can be applied to identifying transparent PGs in atmospheric corrected Landsat image and has the potential for the digital mapping of plastic greenhouse coverage over a large area.

Building Daily 30-meter Spatial Resolution Maps of Surface Water Bodies from MODIS Data Using a Novel Technique for Transferring Information Across Space and Time

Science.gov (United States)

Khandelwal, A.; Karpatne, A.; Kumar, V.

2017-12-01

In this paper, we present novel methods for producing surface water maps at 30 meter spatial resolution at a daily temporal resolution. These new methods will make use of the MODIS spectral data from Terra (available daily since 2000) to produce daily maps at 250 meter and 500 meter resolution, and then refine them using the relative elevation ordering of pixels at 30 meter resolution. The key component of these methods is the use of elevation structure (relative elevation ordering) of a water body. Elevation structure is not explicitly available at desired resolution for most water bodies in the world and hence it will be estimated using our previous work that uses the history of imperfect labels. In this paper, we will present a new technique that uses elevation structure (unlike existing pixel based methods) to enforce temporal consistency in surface water extents (lake area on nearby dates is likely to be very similar). This will greatly improve the quality of the MODIS scale land/water labels since daily MODIS data can have a large amount of missing (or poor quality) data due to clouds and other factors. The quality of these maps will be further improved using elevation based resolution refinement approach that will make use of elevation structure estimated at Landsat scale. With the assumption that elevation structure does not change over time, it provides a very effective way to transfer information between datasets even when they are not observed concurrently. In this work, we will derive elevation structure at Landsat scale from monthly water extent maps spanning 1984-2015, publicly available through a joint effort of Google Earth Engine and the European Commission's Joint Research Centre (JRC). This elevation structure will then be used to refine spatial resolution of Modis scale maps from 2000 onwards. We will present the analysis of these methods on a large and diverse set of water bodies across the world.

Radio frequency phototube and optical clock: High resolution, high rate and highly stable single photon timing technique

Energy Technology Data Exchange (ETDEWEB)

Margaryan, Amur

2011-10-01

A new timing technique for single photons based on the radio frequency phototube and optical clock or femtosecond optical frequency comb generator is proposed. The technique has a 20 ps resolution for single photons, is capable of operating with MHz frequencies and achieving 10 fs instability level.

Resting state rCBF mapping with single-photon emission tomography and positron emission tomography: magnitude and origin of differences

International Nuclear Information System (INIS)

Jonsson, C.; Kimiaei, S.; Larsson, S.A.; Pagani, M.; Ingvar, M.; Thurfjell, L.; Jacobsson, H.

1998-01-01

Single-photon emission tomography (SPET), using technetium-99m hexamethylpropylene amine oxime, and positron emission tomography (PET), using oxygen-15 butanol were compared in six healthy male volunteers with regard to the mapping of resting state regional cerebral blood flow (rCBF). A computerized brain atlas was utilized for 3D regional analyses and comparison of 64 selected and normalized volumes of interest (VOIs). The normalized mean rCBF values in SPET, as compared to PET, were higher in most of the Brodmann areas in the frontal and parietal lobes (4.8% and 8.7% respectively). The average differences were small in the temporal (2.3%) and occipital (1.1%) lobes. PET values were clearly higher in small VOIs like the thalamus (12.3%), hippocampus (12.3%) and basal ganglia (9.9%). A resolution phantom study showed that the in-plane SPET/PET system resolution was 11.0/7.5 mm. In conclusion, SPET and PET data demonstrated a fairly good agreement despite the superior spatial resolution of PET. The differences between SPET and PET rCBF are mainly due to physiological and physical factors, the data processing, normalization and co-registration methods. In order to further improve mapping of rCBF with SPET it is imperative not only to improve the spatial resolution but also to apply accurate correction techniques for scatter, attenuation and non-linear extraction. (orig.)

Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

Science.gov (United States)

Yi, Liuxi; Gao, Fengyun; Siqin, Bateer; Zhou, Yu; Li, Qiang; Zhao, Xiaoqing; Jia, Xiaoyun; Zhang, Hui

2017-01-01

Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

Quantitive DNA Fiber Mapping

Energy Technology Data Exchange (ETDEWEB)

Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

2008-01-28

Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

A Lithology Based Map Unit Schema For Onegeology Regional Geologic Map Integration

Science.gov (United States)

Moosdorf, N.; Richard, S. M.

2012-12-01

A system of lithogenetic categories for a global lithological map (GLiM, http://www.ifbm.zmaw.de/index.php?id=6460&L=3) has been compiled based on analysis of lithology/genesis categories for regional geologic maps for the entire globe. The scheme is presented for discussion and comment. Analysis of units on a variety of regional geologic maps indicates that units are defined based on assemblages of rock types, as well as their genetic type. In this compilation of continental geology, outcropping surface materials are dominantly sediment/sedimentary rock; major subdivisions of the sedimentary category include clastic sediment, carbonate sedimentary rocks, clastic sedimentary rocks, mixed carbonate and clastic sedimentary rock, colluvium and residuum. Significant areas of mixed igneous and metamorphic rock are also present. A system of global categories to characterize the lithology of regional geologic units is important for Earth System models of matter fluxes to soils, ecosystems, rivers and oceans, and for regional analysis of Earth surface processes at global scale. Because different applications of the classification scheme will focus on different lithologic constituents in mixed units, an ontology-type representation of the scheme that assigns properties to the units in an analyzable manner will be pursued. The OneGeology project is promoting deployment of geologic map services at million scale for all nations. Although initial efforts are commonly simple scanned map WMS services, the intention is to move towards data-based map services that categorize map units with standard vocabularies to allow use of a common map legend for better visual integration of the maps (e.g. see OneGeology Europe, http://onegeology-europe.brgm.fr/ geoportal/ viewer.jsp). Current categorization of regional units with a single lithology from the CGI SimpleLithology (http://resource.geosciml.org/201202/ Vocab2012html/ SimpleLithology201012.html) vocabulary poorly captures the

Methodology of high-resolution photography for mural condition database

Science.gov (United States)

Higuchi, R.; Suzuki, T.; Shibata, M.; Taniguchi, Y.

2015-08-01

Digital documentation is one of the most useful techniques to record the condition of cultural heritage. Recently, high-resolution images become increasingly useful because it is possible to show general views of mural paintings and also detailed mural conditions in a single image. As mural paintings are damaged by environmental stresses, it is necessary to record the details of painting condition on high-resolution base maps. Unfortunately, the cost of high-resolution photography and the difficulty of operating its instruments and software have commonly been an impediment for researchers and conservators. However, the recent development of graphic software makes its operation simpler and less expensive. In this paper, we suggest a new approach to make digital heritage inventories without special instruments, based on our recent our research project in Üzümlü church in Cappadocia, Turkey. This method enables us to achieve a high-resolution image database with low costs, short time, and limited human resources.

High resolution orientation mapping of secondary phases in ATI 718Plus® alloy

Directory of Open Access Journals (Sweden)

Krakow Robert

2014-01-01

Full Text Available The polycrystalline superalloy ATI 718Plus ® (hereafter 718Plus has been developed to replace the established alloy Inconel 718 by offering higher temperature capability for applications in gas turbines. The alloy exhibits two secondary phases in the austenitic matrix; it is strengthened by the γ′-phase with η-phase discontinuously precipitated at the grain boundaries. It can be utilized to control grain growth during forging. Generally, hexagonal η phase has been reported to possess a defined crystallographic orientation with the matrix. However, the material studied here exhibits blocky η-phase that has been precipitated and grown during thermo-mechanical processing. Therefore a measurable change in orientation relationship is expected. The standard technique for orientation mapping is electron back-scattered diffraction with spatial resolution of 100 nm. That is insufficient for studying η-phase in 718Plus. By applying high resolution orientation mapping in the transmission electron microscope (Philips CM 300 FEGTEM equipped with a Nanomegas ASTARTM system a resolution of 3 nm was achieved. The indexed diffraction data was analysed using the Matlab Toolbox Mtex. The analysis included grain reconstruction and exclusion of low confidence measurements. The data set allows generating phase boundary maps indicating interfaces characteristics. Quantitative assessment shows that only 19% of the γ-η-interfaces fulfil the orientation relationship.

High-resolution Ceres Low Altitude Mapping Orbit Atlas derived from Dawn Framing Camera images

Science.gov (United States)

Roatsch, Th.; Kersten, E.; Matz, K.-D.; Preusker, F.; Scholten, F.; Jaumann, R.; Raymond, C. A.; Russell, C. T.

2017-06-01

The Dawn spacecraft Framing Camera (FC) acquired over 31,300 clear filter images of Ceres with a resolution of about 35 m/pxl during the eleven cycles in the Low Altitude Mapping Orbit (LAMO) phase between December 16 2015 and August 8 2016. We ortho-rectified the images from the first four cycles and produced a global, high-resolution, uncontrolled photomosaic of Ceres. This global mosaic is the basis for a high-resolution Ceres atlas that consists of 62 tiles mapped at a scale of 1:250,000. The nomenclature used in this atlas was proposed by the Dawn team and was approved by the International Astronomical Union (IAU). The full atlas is available to the public through the Dawn Geographical Information System (GIS) web page [http://dawngis.dlr.de/atlas] and will become available through the NASA Planetary Data System (PDS) (http://pdssbn.astro.umd.edu/).

A multi-temporal analysis approach for land cover mapping in support of nuclear incident response

Science.gov (United States)

Sah, Shagan; van Aardt, Jan A. N.; McKeown, Donald M.; Messinger, David W.

2012-06-01

Remote sensing can be used to rapidly generate land use maps for assisting emergency response personnel with resource deployment decisions and impact assessments. In this study we focus on constructing accurate land cover maps to map the impacted area in the case of a nuclear material release. The proposed methodology involves integration of results from two different approaches to increase classification accuracy. The data used included RapidEye scenes over Nine Mile Point Nuclear Power Station (Oswego, NY). The first step was building a coarse-scale land cover map from freely available, high temporal resolution, MODIS data using a time-series approach. In the case of a nuclear accident, high spatial resolution commercial satellites such as RapidEye or IKONOS can acquire images of the affected area. Land use maps from the two image sources were integrated using a probability-based approach. Classification results were obtained for four land classes - forest, urban, water and vegetation - using Euclidean and Mahalanobis distances as metrics. Despite the coarse resolution of MODIS pixels, acceptable accuracies were obtained using time series features. The overall accuracies using the fusion based approach were in the neighborhood of 80%, when compared with GIS data sets from New York State. The classifications were augmented using this fused approach, with few supplementary advantages such as correction for cloud cover and independence from time of year. We concluded that this method would generate highly accurate land maps, using coarse spatial resolution time series satellite imagery and a single date, high spatial resolution, multi-spectral image.

Single image super-resolution via regularized extreme learning regression for imagery from microgrid polarimeters

Science.gov (United States)

Sargent, Garrett C.; Ratliff, Bradley M.; Asari, Vijayan K.

2017-08-01

The advantage of division of focal plane imaging polarimeters is their ability to obtain temporally synchronized intensity measurements across a scene; however, they sacrifice spatial resolution in doing so due to their spatially modulated arrangement of the pixel-to-pixel polarizers and often result in aliased imagery. Here, we propose a super-resolution method based upon two previously trained extreme learning machines (ELM) that attempt to recover missing high frequency and low frequency content beyond the spatial resolution of the sensor. This method yields a computationally fast and simple way of recovering lost high and low frequency content from demosaicing raw microgrid polarimetric imagery. The proposed method outperforms other state-of-the-art single-image super-resolution algorithms in terms of structural similarity and peak signal-to-noise ratio.

Water Bodies’ Mapping from Sentinel-2 Imagery with Modified Normalized Difference Water Index at 10-m Spatial Resolution Produced by Sharpening the SWIR Band

Directory of Open Access Journals (Sweden)

Yun Du

2016-04-01

Full Text Available Monitoring open water bodies accurately is an important and basic application in remote sensing. Various water body mapping approaches have been developed to extract water bodies from multispectral images. The method based on the spectral water index, especially the Modified Normalized Difference Water Index (MDNWI calculated from the green and Shortwave-Infrared (SWIR bands, is one of the most popular methods. The recently launched Sentinel-2 satellite can provide fine spatial resolution multispectral images. This new dataset is potentially of important significance for regional water bodies’ mapping, due to its free access and frequent revisit capabilities. It is noted that the green and SWIR bands of Sentinel-2 have different spatial resolutions of 10 m and 20 m, respectively. Straightforwardly, MNDWI can be produced from Sentinel-2 at the spatial resolution of 20 m, by upscaling the 10-m green band to 20 m correspondingly. This scheme, however, wastes the detailed information available at the 10-m resolution. In this paper, to take full advantage of the 10-m information provided by Sentinel-2 images, a novel 10-m spatial resolution MNDWI is produced from Sentinel-2 images by downscaling the 20-m resolution SWIR band to 10 m based on pan-sharpening. Four popular pan-sharpening algorithms, including Principle Component Analysis (PCA, Intensity Hue Saturation (IHS, High Pass Filter (HPF and À Trous Wavelet Transform (ATWT, were applied in this study. The performance of the proposed method was assessed experimentally using a Sentinel-2 image located at the Venice coastland. In the experiment, six water indexes, including 10-m NDWI, 20-m MNDWI and 10-m MNDWI, produced by four pan-sharpening algorithms, were compared. Three levels of results, including the sharpened images, the produced MNDWI images and the finally mapped water bodies, were analysed quantitatively. The results showed that MNDWI can enhance water bodies and suppressbuilt

Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

Directory of Open Access Journals (Sweden)

Huihui Yu

Full Text Available Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs and simple sequence repeats (SSRs, thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs from low-coverage sequences of a recombinant inbred line (RIL population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.

Surface Temperature Mapping of the University of Northern Iowa Campus Using High Resolution Thermal Infrared Aerial Imageries

Directory of Open Access Journals (Sweden)

Ramanathan Sugumaran

2008-08-01

Full Text Available The goal of this project was to map the surface temperature of the University of Northern Iowa campus using high-resolution thermal infrared aerial imageries. A thermal camera with a spectral bandwidth of 3.0-5.0 μm was flown at the average altitude of 600 m, achieving ground resolution of 29 cm. Ground control data was used to construct the pixelto-temperature conversion model, which was later used to produce temperature maps of the entire campus and also for validation of the model. The temperature map then was used to assess the building rooftop conditions and steam line faults in the study area. Assessment of the temperature map revealed a number of building structures that may be subject to insulation improvement due to their high surface temperatures leaks. Several hot spots were also identified on the campus for steam pipelines faults. High-resolution thermal infrared imagery proved highly effective tool for precise heat anomaly detection on the campus, and it can be used by university facility services for effective future maintenance of buildings and grounds.

Surface Temperature Mapping of the University of Northern Iowa Campus Using High Resolution Thermal Infrared Aerial Imageries

Science.gov (United States)

Savelyev, Alexander; Sugumaran, Ramanathan

2008-01-01

The goal of this project was to map the surface temperature of the University of Northern Iowa campus using high-resolution thermal infrared aerial imageries. A thermal camera with a spectral bandwidth of 3.0-5.0 μm was flown at the average altitude of 600 m, achieving ground resolution of 29 cm. Ground control data was used to construct the pixel- to-temperature conversion model, which was later used to produce temperature maps of the entire campus and also for validation of the model. The temperature map then was used to assess the building rooftop conditions and steam line faults in the study area. Assessment of the temperature map revealed a number of building structures that may be subject to insulation improvement due to their high surface temperatures leaks. Several hot spots were also identified on the campus for steam pipelines faults. High-resolution thermal infrared imagery proved highly effective tool for precise heat anomaly detection on the campus, and it can be used by university facility services for effective future maintenance of buildings and grounds. PMID:27873800

Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy.

Science.gov (United States)

Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L; de Pablo, Pedro J; Raman, Arvind

2013-06-07

Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.

Mapping whole-brain activity with cellular resolution by light-sheet microscopy and high-throughput image analysis (Conference Presentation)

Science.gov (United States)

Silvestri, Ludovico; Rudinskiy, Nikita; Paciscopi, Marco; Müllenbroich, Marie Caroline; Costantini, Irene; Sacconi, Leonardo; Frasconi, Paolo; Hyman, Bradley T.; Pavone, Francesco S.

2016-03-01

Mapping neuronal activity patterns across the whole brain with cellular resolution is a challenging task for state-of-the-art imaging methods. Indeed, despite a number of technological efforts, quantitative cellular-resolution activation maps of the whole brain have not yet been obtained. Many techniques are limited by coarse resolution or by a narrow field of view. High-throughput imaging methods, such as light sheet microscopy, can be used to image large specimens with high resolution and in reasonable times. However, the bottleneck is then moved from image acquisition to image analysis, since many TeraBytes of data have to be processed to extract meaningful information. Here, we present a full experimental pipeline to quantify neuronal activity in the entire mouse brain with cellular resolution, based on a combination of genetics, optics and computer science. We used a transgenic mouse strain (Arc-dVenus mouse) in which neurons which have been active in the last hours before brain fixation are fluorescently labelled. Samples were cleared with CLARITY and imaged with a custom-made confocal light sheet microscope. To perform an automatic localization of fluorescent cells on the large images produced, we used a novel computational approach called semantic deconvolution. The combined approach presented here allows quantifying the amount of Arc-expressing neurons throughout the whole mouse brain. When applied to cohorts of mice subject to different stimuli and/or environmental conditions, this method helps finding correlations in activity between different neuronal populations, opening the possibility to infer a sort of brain-wide 'functional connectivity' with cellular resolution.

High resolution transmission electron microscopy studies of {sigma} phase in Ni-based single crystal superalloys

Energy Technology Data Exchange (ETDEWEB)

Sun Fei [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Zhang Jianxin, E-mail: jianxin@sdu.edu.cn [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Liu Pan [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Feng Qiang [National Center for Materials Service Safety, University of Science and Technology Beijing, Beijing 100083 (China); State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Han Xiaodong; Mao Shengcheng [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China)

2012-09-25

Graphical abstract: (a) TEM micrograph of {sigma} phase; (b) HRTEM image of {sigma}/{gamma} interface corresponding to the area of the white frame in (a); (c) an enlarged image of area from the white frame in (b). The combination of {sigma}/{gamma} interface appears very well, and a two-atomic-layer step is shown on the {sigma}/{gamma} interface. In addition, {sigma} phase has the orientation relationship of [0 0 1]{sub {gamma}}//[1 1 2{sup Macron }]{sub {sigma}}, (2{sup Macron} 2 0){sub {gamma}}//(1{sup Macron} 1 0){sub {sigma}}, (2{sup Macron }2{sup Macron} 0){sub {gamma}}//(1 1 1){sub {sigma}}; [0 1 1]{sub {gamma}}//[1 1 0]{sub {sigma}}, (1 1{sup Macron} 1){sub {gamma}}//(0 0 1{sup Macron }){sub {sigma}} with the {gamma} phase. Highlights: Black-Right-Pointing-Pointer Elemental characteristic of {sigma} phase is studied by HAADF techniques and EDS analysis. Black-Right-Pointing-Pointer Interfacial characteristics of {sigma}/{gamma} interface are revealed by HRTEM. Black-Right-Pointing-Pointer An atomic structural {sigma}/{gamma} interface with a two-atomic-layer step has been proposed. - Abstract: By means of high resolution transmission electron microscopy (HRTEM) and high-angle annular dark-field image technique (HAADF), morphological of plate-shaped {sigma} phase and interfacial characteristics between plate-shaped {sigma} phase and {gamma} phase in Ni-based single crystal superalloys have been studied. On the basis of HRTEM observations, an atomic structural interface between {sigma} phase and {gamma} phase with a step has been proposed. {sigma} Phase has the relationship of [0 0 1]{sub {gamma}}//[1 1 2{sup Macron }]{sub {sigma}}, (2{sup Macron} 2 0){sub {gamma}}//(1{sup Macron} 1 0){sub {sigma},} (2{sup Macron }2{sup Macron} 0){sub {gamma}}//(1 1 1){sub {sigma}}; [0 1 1]{sub {gamma}}//[1 1 0]{sub {sigma}}, (1 1{sup Macron} 1){sub {gamma}}//(0 0 1{sup Macron }){sub {sigma}} with the {gamma} phase. The compositional characteristics of the {sigma} phase which

Template based rodent brain extraction and atlas mapping.

Science.gov (United States)

Weimin Huang; Jiaqi Zhang; Zhiping Lin; Su Huang; Yuping Duan; Zhongkang Lu

2016-08-01

Accurate rodent brain extraction is the basic step for many translational studies using MR imaging. This paper presents a template based approach with multi-expert refinement to automatic rodent brain extraction. We first build the brain appearance model based on the learning exemplars. Together with the template matching, we encode the rodent brain position into the search space to reliably locate the rodent brain and estimate the rough segmentation. With the initial mask, a level-set segmentation and a mask-based template learning are implemented further to the brain region. The multi-expert fusion is used to generate a new mask. We finally combine the region growing based on the histogram distribution learning to delineate the final brain mask. A high-resolution rodent atlas is used to illustrate that the segmented low resolution anatomic image can be well mapped to the atlas. Tested on a public data set, all brains are located reliably and we achieve the mean Jaccard similarity score at 94.99% for brain segmentation, which is a statistically significant improvement compared to two other rodent brain extraction methods.

Resting state rCBF mapping with single-photon emission tomography and positron emission tomography: magnitude and origin of differences

Energy Technology Data Exchange (ETDEWEB)

Jonsson, C.; Kimiaei, S.; Larsson, S.A. [Section of Nuclear Medicine, Department of Hospital Physics, Karolinska Hospital and Department of Medical Radiation Physics, Stockholm University, Stockholm (Sweden); Pagani, M. [Institute of Experimental Medicine, CNR, Rome (Italy); Ingvar, M. [Section of Cognitive Neurophysiology, Karolinska Hospital, Stockholm (Sweden); Thurfjell, L. [Center of Image Analysis, Uppsala University, Uppsala (Sweden); Jacobsson, H. [Department of Diagnostic Radiology, Karolinska Hospital, Stockholm (Sweden)

1998-02-01

Single-photon emission tomography (SPET), using technetium-99m hexamethylpropylene amine oxime, and positron emission tomography (PET), using oxygen-15 butanol were compared in six healthy male volunteers with regard to the mapping of resting state regional cerebral blood flow (rCBF). A computerized brain atlas was utilized for 3D regional analyses and comparison of 64 selected and normalized volumes of interest (VOIs). The normalized mean rCBF values in SPET, as compared to PET, were higher in most of the Brodmann areas in the frontal and parietal lobes (4.8% and 8.7% respectively). The average differences were small in the temporal (2.3%) and occipital (1.1%) lobes. PET values were clearly higher in small VOIs like the thalamus (12.3%), hippocampus (12.3%) and basal ganglia (9.9%). A resolution phantom study showed that the in-plane SPET/PET system resolution was 11.0/7.5 mm. In conclusion, SPET and PET data demonstrated a fairly good agreement despite the superior spatial resolution of PET. The differences between SPET and PET rCBF are mainly due to physiological and physical factors, the data processing, normalization and co-registration methods. In order to further improve mapping of rCBF with SPET it is imperative not only to improve the spatial resolution but also to apply accurate correction techniques for scatter, attenuation and non-linear extraction. (orig.) With 6 figs., 3 tabs., 23 refs.

High-resolution AUV mapping of the 2015 flows at Axial Seamount, Juan de Fuca Ridge

Science.gov (United States)

Paduan, J. B.; Chadwick, W. W., Jr.; Clague, D. A.; Le Saout, M.; Caress, D. W.; Thomas, H. J.; Yoerger, D.

2016-12-01

Lava flows erupted in April 2015 at Axial Seamount were mapped at 1-m resolution with the AUV Sentry in August 2015 and the MBARI Mapping AUVs in July 2016 and observed and sampled with ROVs on those same expeditions. Thirty percent of terrain covered by new flows had been mapped by the MBARI AUVs prior to the eruption. Differencing of before and after maps (using ship-collected bathymetry where the AUV had not mapped before) allows calculation of extents and volumes of flows and shows new fissures. The maps reveal unexpected fissure patterns and shifts in the style of flow emplacement through a single eruption. There were 11 separate flows totaling 1.48 x 108 m3 of lava erupted from numerous en echelon fissures over 19 km on the NE caldera floor, on the NE flank, and down the N rift zone. Flows in and around the caldera have maximum thicknesses of 5-19 m. Most erupted as sheet flows and spread along intricate channels that terminated in thin margins. Some utilized pre-existing fissures. Some flows erupted from short fissures, while at least two longer new fissures produced little or no lava. A flow on the upper N rift has a spectacular lava channel flanked by narrow lava pillars supporting a thin roof left after the flow drained. A shatter ring still emanating warm fluid is visible in the map as a 15-m wide low cone. Hundreds of exploded pillows were observed but are not discernable in the bathymetry. The northern-most three flows deep on the N rift are similar in area to the others but comprise the bulk of the eruption volume. Differencing of ship-based bathymetry shows only these flows. Near the eruptive fissures they are sheet flows, but as they flowed downslope they built complexes of coalesced pillow mounds up to 67-128 m thick. Changes in flow morphology occurred through the course of the eruption. Large pillow mounds had molten cores that deformed as the eruption progressed. One flow began as a thin, effusive sheet flow but as the eruption rate decreased, a

A Three-Dimensional Target Depth-Resolution Method with a Single-Vector Sensor.

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Zhao, Anbang; Bi, Xuejie; Hui, Juan; Zeng, Caigao; Ma, Lin

2018-04-12

This paper mainly studies and verifies the target number category-resolution method in multi-target cases and the target depth-resolution method of aerial targets. Firstly, target depth resolution is performed by using the sign distribution of the reactive component of the vertical complex acoustic intensity; the target category and the number resolution in multi-target cases is realized with a combination of the bearing-time recording information; and the corresponding simulation verification is carried out. The algorithm proposed in this paper can distinguish between the single-target multi-line spectrum case and the multi-target multi-line spectrum case. This paper presents an improved azimuth-estimation method for multi-target cases, which makes the estimation results more accurate. Using the Monte Carlo simulation, the feasibility of the proposed target number and category-resolution algorithm in multi-target cases is verified. In addition, by studying the field characteristics of the aerial and surface targets, the simulation results verify that there is only amplitude difference between the aerial target field and the surface target field under the same environmental parameters, and an aerial target can be treated as a special case of a surface target; the aerial target category resolution can then be realized based on the sign distribution of the reactive component of the vertical acoustic intensity so as to realize three-dimensional target depth resolution. By processing data from a sea experiment, the feasibility of the proposed aerial target three-dimensional depth-resolution algorithm is verified.

Fast, High Resolution, and Wide Modulus Range Nanomechanical Mapping with Bimodal Tapping Mode.

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Kocun, Marta; Labuda, Aleksander; Meinhold, Waiman; Revenko, Irène; Proksch, Roger

2017-10-24

Tapping mode atomic force microscopy (AFM), also known as amplitude modulated (AM) or AC mode, is a proven, reliable, and gentle imaging mode with widespread applications. Over the several decades that tapping mode has been in use, quantification of tip-sample mechanical properties such as stiffness has remained elusive. Bimodal tapping mode keeps the advantages of single-frequency tapping mode while extending the technique by driving and measuring an additional resonant mode of the cantilever. The simultaneously measured observables of this additional resonance provide the additional information necessary to extract quantitative nanomechanical information about the tip-sample mechanics. Specifically, driving the higher cantilever resonance in a frequency modulated (FM) mode allows direct measurement of the tip-sample interaction stiffness and, with appropriate modeling, the set point-independent local elastic modulus. Here we discuss the advantages of bimodal tapping, coined AM-FM imaging, for modulus mapping. Results are presented for samples over a wide modulus range, from a compliant gel (∼100 MPa) to stiff materials (∼100 GPa), with the same type of cantilever. We also show high-resolution (subnanometer) stiffness mapping of individual molecules in semicrystalline polymers and of DNA in fluid. Combined with the ability to remain quantitative even at line scan rates of nearly 40 Hz, the results demonstrate the versatility of AM-FM imaging for nanomechanical characterization in a wide range of applications.

Modeling Photo-Bleaching Kinetics to Create High Resolution Maps of Rod Rhodopsin in the Human Retina.

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Martin Ehler

Full Text Available We introduce and describe a novel non-invasive in-vivo method for mapping local rod rhodopsin distribution in the human retina over a 30-degree field. Our approach is based on analyzing the brightening of detected lipofuscin autofluorescence within small pixel clusters in registered imaging sequences taken with a commercial 488nm confocal scanning laser ophthalmoscope (cSLO over a 1 minute period. We modeled the kinetics of rhodopsin bleaching by applying variational optimization techniques from applied mathematics. The physical model and the numerical analysis with its implementation are outlined in detail. This new technique enables the creation of spatial maps of the retinal rhodopsin and retinal pigment epithelium (RPE bisretinoid distribution with an ≈ 50μm resolution.

Modeling Photo-Bleaching Kinetics to Create High Resolution Maps of Rod Rhodopsin in the Human Retina

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Ehler, Martin; Dobrosotskaya, Julia; Cunningham, Denise; Wong, Wai T.; Chew, Emily Y.; Czaja, Wojtek; Bonner, Robert F.

2015-01-01

We introduce and describe a novel non-invasive in-vivo method for mapping local rod rhodopsin distribution in the human retina over a 30-degree field. Our approach is based on analyzing the brightening of detected lipofuscin autofluorescence within small pixel clusters in registered imaging sequences taken with a commercial 488nm confocal scanning laser ophthalmoscope (cSLO) over a 1 minute period. We modeled the kinetics of rhodopsin bleaching by applying variational optimization techniques from applied mathematics. The physical model and the numerical analysis with its implementation are outlined in detail. This new technique enables the creation of spatial maps of the retinal rhodopsin and retinal pigment epithelium (RPE) bisretinoid distribution with an ≈ 50μm resolution. PMID:26196397

Bayesian reconstruction of photon interaction sequences for high-resolution PET detectors

Energy Technology Data Exchange (ETDEWEB)

Pratx, Guillem; Levin, Craig S [Molecular Imaging Program at Stanford, Department of Radiology, Stanford, CA (United States)], E-mail: cslevin@stanford.edu

2009-09-07

Realizing the full potential of high-resolution positron emission tomography (PET) systems involves accurately positioning events in which the annihilation photon deposits all its energy across multiple detector elements. Reconstructing the complete sequence of interactions of each photon provides a reliable way to select the earliest interaction because it ensures that all the interactions are consistent with one another. Bayesian estimation forms a natural framework to maximize the consistency of the sequence with the measurements while taking into account the physics of {gamma}-ray transport. An inherently statistical method, it accounts for the uncertainty in the measured energy and position of each interaction. An algorithm based on maximum a posteriori (MAP) was evaluated for computer simulations. For a high-resolution PET system based on cadmium zinc telluride detectors, 93.8% of the recorded coincidences involved at least one photon multiple-interactions event (PMIE). The MAP estimate of the first interaction was accurate for 85.2% of the single photons. This represents a two-fold reduction in the number of mispositioned events compared to minimum pair distance, a simpler yet efficient positioning method. The point-spread function of the system presented lower tails and higher peak value when MAP was used. This translated into improved image quality, which we quantified by studying contrast and spatial resolution gains.

Radiation hybrid mapping as one of the main methods of the creation of high resolution maps of human and animal genomes

International Nuclear Information System (INIS)

Sulimova, G.E.; Kompanijtsev, A.A.; Mojsyak, E.V.; Rakhmanaliev, Eh.R.; Klimov, E.A.; Udina, I.G.; Zakharov, I.A.

2000-01-01

Radiation hybrid mapping (RH mapping) is considered as one of the main method of constructing physical maps of mammalian genomes. In introduction, theoretical prerequisites of developing of the RH mapping and statistical methods of data analysis are discussed. Comparative characteristics of universal commercial panels of the radiation hybrid somatic cells (RH panels) are shown. In experimental part of the work, RH mapping is used to localize nucleotide sequences adjacent to Not I sites of human chromosome 3 with the aim to integrate contig map of Nor I clones to comprehensive maps of human genome. Five nucleotide sequences adjacent to the sites of integration of papilloma virus in human genome and expressed in the cells of cervical cancer involved localized. It is demonstrated that the region 13q14.3-q21.1 was enriched with nucleotide sequences involved in the processes of carcinogenesis. RH mapping can be considered as one of the most perspective applications of modern radiation biology in the field of molecular genetics, that is, in constructing physical maps of mammalian genomes with high resolution level [ru

3D single-molecule super-resolution microscopy with a tilted light sheet.

Science.gov (United States)

Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E

2018-01-09

Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The result is simple and flexible 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validate TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed tetrapod PSFs for fiducial bead tracking and live axial drift correction.

Land cover mapping and change detection in urban watersheds using QuickBird high spatial resolution satellite imagery

Science.gov (United States)

Hester, David Barry

The objective of this research was to develop methods for urban land cover analysis using QuickBird high spatial resolution satellite imagery. Such imagery has emerged as a rich commercially available remote sensing data source and has enjoyed high-profile broadcast news media and Internet applications, but methods of quantitative analysis have not been thoroughly explored. The research described here consists of three studies focused on the use of pan-sharpened 61-cm spatial resolution QuickBird imagery, the spatial resolution of which is the highest of any commercial satellite. In the first study, a per-pixel land cover classification method is developed for use with this imagery. This method utilizes a per-pixel classification approach to generate an accurate six-category high spatial resolution land cover map of a developing suburban area. The primary objective of the second study was to develop an accurate land cover change detection method for use with QuickBird land cover products. This work presents an efficient fuzzy framework for transforming map uncertainty into accurate and meaningful high spatial resolution land cover change analysis. The third study described here is an urban planning application of the high spatial resolution QuickBird-based land cover product developed in the first study. This work both meaningfully connects this exciting new data source to urban watershed management and makes an important empirical contribution to the study of suburban watersheds. Its analysis of residential roads and driveways as well as retail parking lots sheds valuable light on the impact of transportation-related land use on the suburban landscape. Broadly, these studies provide new methods for using state-of-the-art remote sensing data to inform land cover analysis and urban planning. These methods are widely adaptable and produce land cover products that are both meaningful and accurate. As additional high spatial resolution satellites are launched and the

Mapping Sub-Saharan African Agriculture in High-Resolution Satellite Imagery with Computer Vision & Machine Learning

Science.gov (United States)

Debats, Stephanie Renee

Smallholder farms dominate in many parts of the world, including Sub-Saharan Africa. These systems are characterized by small, heterogeneous, and often indistinct field patterns, requiring a specialized methodology to map agricultural landcover. In this thesis, we developed a benchmark labeled data set of high-resolution satellite imagery of agricultural fields in South Africa. We presented a new approach to mapping agricultural fields, based on efficient extraction of a vast set of simple, highly correlated, and interdependent features, followed by a random forest classifier. The algorithm achieved similar high performance across agricultural types, including spectrally indistinct smallholder fields, and demonstrated the ability to generalize across large geographic areas. In sensitivity analyses, we determined multi-temporal images provided greater performance gains than the addition of multi-spectral bands. We also demonstrated how active learning can be incorporated in the algorithm to create smaller, more efficient training data sets, which reduced computational resources, minimized the need for humans to hand-label data, and boosted performance. We designed a patch-based uncertainty metric to drive the active learning framework, based on the regular grid of a crowdsourcing platform, and demonstrated how subject matter experts can be replaced with fleets of crowdsourcing workers. Our active learning algorithm achieved similar performance as an algorithm trained with randomly selected data, but with 62% less data samples. This thesis furthers the goal of providing accurate agricultural landcover maps, at a scale that is relevant for the dominant smallholder class. Accurate maps are crucial for monitoring and promoting agricultural production. Furthermore, improved agricultural landcover maps will aid a host of other applications, including landcover change assessments, cadastral surveys to strengthen smallholder land rights, and constraints for crop modeling

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

Science.gov (United States)

Ganguly, Sangram; Kalia, Subodh; Li, Shuang; Michaelis, Andrew; Nemani, Ramakrishna R.; Saatchi, Sassan A

2017-01-01

Uncertainties in input land cover estimates contribute to a significant bias in modeled above ground biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

Science.gov (United States)

Ganguly, S.; Kalia, S.; Li, S.; Michaelis, A.; Nemani, R. R.; Saatchi, S.

2017-12-01

Uncertainties in input land cover estimates contribute to a significant bias in modeled above gound biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition/ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree/non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial/satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

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Koon-Kiu Yan

2017-07-01

Full Text Available Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains (TADs. From a visual examination of the chromosomal contact map, however, it is clear that the organization of the domains is not simple or obvious. Instead, TADs exhibit various length scales and, in many cases, a nested arrangement. Here, by exploiting the resemblance between TADs in a chromosomal contact map and densely connected modules in a network, we formulate TAD identification as a network optimization problem and propose an algorithm, MrTADFinder, to identify TADs from intra-chromosomal contact maps. MrTADFinder is based on the network-science concept of modularity. A key component of it is deriving an appropriate background model for contacts in a random chain, by numerically solving a set of matrix equations. The background model preserves the observed coverage of each genomic bin as well as the distance dependence of the contact frequency for any pair of bins exhibited by the empirical map. Also, by introducing a tunable resolution parameter, MrTADFinder provides a self-consistent approach for identifying TADs at different length scales, hence the acronym "Mr" standing for Multiple Resolutions. We then apply MrTADFinder to various Hi-C datasets. The identified domain boundaries are marked by characteristic signatures in chromatin marks and transcription factors (TF that are consistent with earlier work. Moreover, by calling TADs at different length scales, we observe that boundary signatures change with resolution, with different chromatin features having different characteristic length scales. Furthermore, we report an enrichment of HOT (high-occupancy target regions near TAD boundaries and investigate the role of different TFs in determining boundaries at various resolutions. To further explore the interplay between TADs and epigenetic marks, as tumor mutational

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis.

Science.gov (United States)

Bakker, Erin; Achenbach, Ute; Bakker, Jeroen; van Vliet, Joke; Peleman, Johan; Segers, Bart; van der Heijden, Stefan; van der Linde, Piet; Graveland, Robert; Hutten, Ronald; van Eck, Herman; Coppoolse, Eric; van der Vossen, Edwin; Bakker, Jaap; Goverse, Aska

2004-06-01

The resistance gene H1 confers resistance to the potato cyst nematode Globodera rostochiensis and is located at the distal end of the long arm of chromosome V of potato. For marker enrichment of the H1 locus, a bulked segregant analysis (BSA) was carried out using 704 AFLP primer combinations. A second source of markers tightly linked to H1 is the ultra-high-density (UHD) genetic map of the potato cross SH x RH. This map has been produced with 387 AFLP primer combinations and consists of 10,365 AFLP markers in 1,118 bins (http://www.dpw.wageningen-ur.nl/uhd/). Comparing these two methods revealed that BSA resulted in one marker/cM and the UHD map in four markers/cM in the H1 interval. Subsequently, a high-resolution genetic map of the H1 locus has been developed using a segregating F(1) SH x RH population consisting of 1,209 genotypes. Two PCR-based markers were designed at either side of the H1 gene to screen the 1,209 genotypes for recombination events. In the high-resolution genetic map, two of the four co-segregating AFLP markers could be separated from the H1 gene. Marker EM1 is located at a distance of 0.2 cM, and marker EM14 is located at a distance of 0.8 cM. The other two co-segregating markers CM1 (in coupling) and EM15 (in repulsion) could not be separated from the H1 gene.

New learning based super-resolution: use of DWT and IGMRF prior.

Science.gov (United States)

Gajjar, Prakash P; Joshi, Manjunath V

2010-05-01

In this paper, we propose a new learning-based approach for super-resolving an image captured at low spatial resolution. Given the low spatial resolution test image and a database consisting of low and high spatial resolution images, we obtain super-resolution for the test image. We first obtain an initial high-resolution (HR) estimate by learning the high-frequency details from the available database. A new discrete wavelet transform (DWT) based approach is proposed for learning that uses a set of low-resolution (LR) images and their corresponding HR versions. Since the super-resolution is an ill-posed problem, we obtain the final solution using a regularization framework. The LR image is modeled as the aliased and noisy version of the corresponding HR image, and the aliasing matrix entries are estimated using the test image and the initial HR estimate. The prior model for the super-resolved image is chosen as an Inhomogeneous Gaussian Markov random field (IGMRF) and the model parameters are estimated using the same initial HR estimate. A maximum a posteriori (MAP) estimation is used to arrive at the cost function which is minimized using a simple gradient descent approach. We demonstrate the effectiveness of the proposed approach by conducting the experiments on gray scale as well as on color images. The method is compared with the standard interpolation technique and also with existing learning-based approaches. The proposed approach can be used in applications such as wildlife sensor networks, remote surveillance where the memory, the transmission bandwidth, and the camera cost are the main constraints.

High resolution, monochromatic x-ray topography capability at CHESS

Energy Technology Data Exchange (ETDEWEB)

Finkelstein, K. D., E-mail: kdf1@cornell.edu; Pauling, A.; Brown, Z. [CHESS, Cornell University, Ithaca, NY (United States); Jones, R. [Department of Physics, University of Connecticut, Storrs, CT (United States); Tarun, A.; Misra, D. S. [IIa Technologies (Singapore); Jupitz, S. [St. Mary’s College of Maryland, St. Mary’s City, MD (United States); Sagan, D. C. [CLASSE, Cornell University, Ithaca, NY (United States)

2016-07-27

CHESS has a monochromatic x-ray topography capability serving continually expanding user interest. The setup consists of a beam expanding monochromator, 6-circle diffactometer, and CHESS designed CMOS camera with real time sample-alignment capability. This provides rocking curve mapping with angle resolution as small as 2 µradians, spatial resolution to 3 microns, and field of view up to 7mm. Thus far the capability has been applied for: improving CVD-diamond growth, evaluating perfection of ultra-thin diamond membranes, correlating performance of diamond-based electronics with crystal defect structure, and defect analysis of single crystal silicon carbide. This paper describes our topography system, explains its capabilities, and presents experimental results from several applications.

High resolution, monochromatic x-ray topography capability at CHESS

International Nuclear Information System (INIS)

Finkelstein, K. D.; Pauling, A.; Brown, Z.; Jones, R.; Tarun, A.; Misra, D. S.; Jupitz, S.; Sagan, D. C.

2016-01-01

CHESS has a monochromatic x-ray topography capability serving continually expanding user interest. The setup consists of a beam expanding monochromator, 6-circle diffactometer, and CHESS designed CMOS camera with real time sample-alignment capability. This provides rocking curve mapping with angle resolution as small as 2 µradians, spatial resolution to 3 microns, and field of view up to 7mm. Thus far the capability has been applied for: improving CVD-diamond growth, evaluating perfection of ultra-thin diamond membranes, correlating performance of diamond-based electronics with crystal defect structure, and defect analysis of single crystal silicon carbide. This paper describes our topography system, explains its capabilities, and presents experimental results from several applications.

High resolution critical habitat mapping and classification of tidal freshwater wetlands in the ACE Basin

Science.gov (United States)

Strickland, Melissa Anne

In collaboration with the South Carolina Department of Natural Resources ACE Basin National Estuarine Research Reserve (ACE Basin NERR), the tidal freshwater ecosystems along the South Edisto River in the ACE Basin are being accurately mapped and classified using a LIDAR-Remote Sensing Fusion technique that integrates LAS LIDAR data into texture images and then merges the elevation textures and multispectral imagery for very high resolution mapping. This project discusses the development and refinement of an ArcGIS Toolbox capable of automating protocols and procedures for marsh delineation and microhabitat identification. The result is a high resolution habitat and land use map used for the identification of threatened habitat. Tidal freshwater wetlands are also a critical habitat for colonial wading birds and an accurate assessment of community diversity and acreage of this habitat type in the ACE Basin will support SCDNR's conservation and protection efforts. The maps developed by this study will be used to better monitor the freshwater/saltwater interface and establish a baseline for an ACE NERR monitoring program to track the rates and extent of alterations due to projected environmental stressors. Preliminary ground-truthing in the field will provide information about the accuracy of the mapping tool.

High-resolution mapping and ablation of recurrent left lateral accessory pathway conduction

Directory of Open Access Journals (Sweden)

Francesco Solimene, MD

2017-08-01

Full Text Available Proper localization of the anatomical target during ablation of the accessory pathways (AP and the ability to detect clear AP potentials on the ablation catheter are crucial for successful AP ablation. We report a case of recurring AP conduction that was finally eliminated using a novel ablation catheter equipped with high-resolution mini-electrodes. Smaller and closer electrodes result in high mapping resolution with less signal averaging and cancellation effects. Owing to improved sensitivity, the new catheter seems effective in detecting fragmented and high frequency signals, thus allowing more effective radiofrequency application and improving ablation success.

High resolution ultrasound and photoacoustic imaging of single cells

Directory of Open Access Journals (Sweden)

Eric M. Strohm

2016-03-01

Full Text Available High resolution ultrasound and photoacoustic images of stained neutrophils, lymphocytes and monocytes from a blood smear were acquired using a combined acoustic/photoacoustic microscope. Photoacoustic images were created using a pulsed 532 nm laser that was coupled to a single mode fiber to produce output wavelengths from 532 nm to 620 nm via stimulated Raman scattering. The excitation wavelength was selected using optical filters and focused onto the sample using a 20× objective. A 1000 MHz transducer was co-aligned with the laser spot and used for ultrasound and photoacoustic images, enabling micrometer resolution with both modalities. The different cell types could be easily identified due to variations in contrast within the acoustic and photoacoustic images. This technique provides a new way of probing leukocyte structure with potential applications towards detecting cellular abnormalities and diseased cells at the single cell level.

The Role of Resolution in the Estimation of Fractal Dimension Maps From SAR Data

Directory of Open Access Journals (Sweden)

Gerardo Di Martino

2017-12-01

Full Text Available This work is aimed at investigating the role of resolution in fractal dimension map estimation, analyzing the role of the different surface spatial scales involved in the considered estimation process. The study is performed using a data set of actual Cosmo/SkyMed Synthetic Aperture Radar (SAR images relevant to two different areas, the region of Bidi in Burkina Faso and the city of Naples in Italy, acquired in stripmap and enhanced spotlight modes. The behavior of fractal dimension maps in the presence of areas with distinctive characteristics from the viewpoint of land-cover and surface features is discussed. Significant differences among the estimated maps are obtained in the presence of fine textural details, which significantly affect the fractal dimension estimation for the higher resolution spotlight images. The obtained results show that if we are interested in obtaining a reliable estimate of the fractal dimension of the observed natural scene, stripmap images should be chosen in view of both economic and computational considerations. In turn, the combination of fractal dimension maps obtained from stripmap and spotlight images can be used to identify areas on the scene presenting non-fractal behavior (e.g., urban areas. Along this guideline, a simple example of stripmap-spotlight data fusion is also presented.

NIR-Red Spectra-Based Disaggregation of SMAP Soil Moisture to 250 m Resolution Based on SMAPEx-4/5 in Southeastern Australia

Directory of Open Access Journals (Sweden)

Nengcheng Chen

2017-01-01

Full Text Available To meet the demand of regional hydrological and agricultural applications, a new method named near infrared-red (NIR-red spectra-based disaggregation (NRSD was proposed to perform a disaggregation of Soil Moisture Active Passive (SMAP products from 36 km to 250 m resolution. The NRSD combined proposed normalized soil moisture index (NSMI with SMAP data to obtain 250 m resolution soil moisture mapping. The experiment was conducted in southeastern Australia during SMAP Experiments (SMAPEx 4/5 and validated with the in situ SMAPEx network. Results showed that NRSD performed a decent downscaling (root-mean-square error (RMSE = 0.04 m3/m3 and 0.12 m3/m3 during SMAPEx-4 and SMAPEx-5, respectively. Based on the validation, it was found that the proposed NSMI was a new alternative indicator for denoting the heterogeneity of soil moisture at sub-kilometer scales. Attributed to the excellent performance of the NSMI, NRSD has a higher overall accuracy, finer spatial representation within SMAP pixels and wider applicable scope on usability tests for land cover, vegetation density and drought condition than the disaggregation based on physical and theoretical scale change (DISPATCH has at 250 m resolution. This revealed that the NRSD method is expected to provide soil moisture mapping at 250-resolution for large-scale hydrological and agricultural studies.

Mapping Impervious Surface Expansion using Medium-resolution Satellite Image Time Series: A Case Study in the Yangtze River Delta, China

Science.gov (United States)

Gao, Feng; DeColstoun, Eric Brown; Ma, Ronghua; Weng, Qihao; Masek, Jeffrey G.; Chen, Jin; Pan, Yaozhong; Song, Conghe

2012-01-01

Cities have been expanding rapidly worldwide, especially over the past few decades. Mapping the dynamic expansion of impervious surface in both space and time is essential for an improved understanding of the urbanization process, land-cover and land-use change, and their impacts on the environment. Landsat and other medium-resolution satellites provide the necessary spatial details and temporal frequency for mapping impervious surface expansion over the past four decades. Since the US Geological Survey opened the historical record of the Landsat image archive for free access in 2008, the decades-old bottleneck of data limitation has gone. Remote-sensing scientists are now rich with data, and the challenge is how to make best use of this precious resource. In this article, we develop an efficient algorithm to map the continuous expansion of impervious surface using a time series of four decades of medium-resolution satellite images. The algorithm is based on a supervised classification of the time-series image stack using a decision tree. Each imerpervious class represents urbanization starting in a different image. The algorithm also allows us to remove inconsistent training samples because impervious expansion is not reversible during the study period. The objective is to extract a time series of complete and consistent impervious surface maps from a corresponding times series of images collected from multiple sensors, and with a minimal amount of image preprocessing effort. The approach was tested in the lower Yangtze River Delta region, one of the fastest urban growth areas in China. Results from nearly four decades of medium-resolution satellite data from the Landsat Multispectral Scanner (MSS), Thematic Mapper (TM), Enhanced Thematic Mapper plus (ETM+) and China-Brazil Earth Resources Satellite (CBERS) show a consistent urbanization process that is consistent with economic development plans and policies. The time-series impervious spatial extent maps derived

Using object-based image analysis to conduct high-resolution conifer extraction at regional spatial scales

Science.gov (United States)

Coates, Peter S.; Gustafson, K. Benjamin; Roth, Cali L.; Chenaille, Michael P.; Ricca, Mark A.; Mauch, Kimberly; Sanchez-Chopitea, Erika; Kroger, Travis J.; Perry, William M.; Casazza, Michael L.

2017-08-10

The distribution and abundance of pinyon (Pinus monophylla) and juniper (Juniperus osteosperma, J. occidentalis) trees (hereinafter, "pinyon-juniper") in sagebrush (Artemisia spp.) ecosystems of the Great Basin in the Western United States has increased substantially since the late 1800s. Distributional expansion and infill of pinyon-juniper into sagebrush ecosystems threatens the ecological function and economic viability of these ecosystems within the Great Basin, and is now a major contemporary challenge facing land and wildlife managers. Particularly, pinyon-juniper encroachment into intact sagebrush ecosystems has been identified as a primary threat facing populations of greater sage-grouse (Centrocercus urophasianus; hereinafter, "sage-grouse"), which is a sagebrush obligate species. Even seemingly innocuous scatterings of isolated pinyon-juniper in an otherwise intact sagebrush landscape can negatively affect survival and reproduction of sage-grouse. Therefore, accurate and high-resolution maps of pinyon-juniper distribution and abundance (indexed by canopy cover) across broad geographic extents would help guide land management decisions that better target areas for pinyon-juniper removal projects (for example, fuel reduction, habitat improvement for sage-grouse, and other sagebrush species) and facilitate science that further quantifies ecological effects of pinyon-juniper encroachment on sage-grouse populations and sagebrush ecosystem processes. Hence, we mapped pinyon-juniper (referred to as conifers for actual mapping) at a 1 × 1-meter (m) high resolution across the entire range of previously mapped sage-grouse habitat in Nevada and northeastern California.We used digital orthophoto quad tiles from National Agriculture Imagery Program (2010, 2013) as base imagery, and then classified conifers using automated feature extraction methodology with the program Feature Analyst™. This method relies on machine learning algorithms that extract features from

National-scale crop type mapping and area estimation using multi-resolution remote sensing and field survey

Science.gov (United States)

Song, X. P.; Potapov, P.; Adusei, B.; King, L.; Khan, A.; Krylov, A.; Di Bella, C. M.; Pickens, A. H.; Stehman, S. V.; Hansen, M.

2016-12-01

Reliable and timely information on agricultural production is essential for ensuring world food security. Freely available medium-resolution satellite data (e.g. Landsat, Sentinel) offer the possibility of improved global agriculture monitoring. Here we develop and test a method for estimating in-season crop acreage using a probability sample of field visits and producing wall-to-wall crop type maps at national scales. The method is first illustrated for soybean cultivated area in the US for 2015. A stratified, two-stage cluster sampling design was used to collect field data to estimate national soybean area. The field-based estimate employed historical soybean extent maps from the U.S. Department of Agriculture (USDA) Cropland Data Layer to delineate and stratify U.S. soybean growing regions. The estimated 2015 U.S. soybean cultivated area based on the field sample was 341,000 km2 with a standard error of 23,000 km2. This result is 1.0% lower than USDA's 2015 June survey estimate and 1.9% higher than USDA's 2016 January estimate. Our area estimate was derived in early September, about 2 months ahead of harvest. To map soybean cover, the Landsat image archive for the year 2015 growing season was processed using an active learning approach. Overall accuracy of the soybean map was 84%. The field-based sample estimated area was then used to calibrate the map such that the soybean acreage of the map derived through pixel counting matched the sample-based area estimate. The strength of the sample-based area estimation lies in the stratified design that takes advantage of the spatially explicit cropland layers to construct the strata. The success of the mapping was built upon an automated system which transforms Landsat images into standardized time-series metrics. The developed method produces reliable and timely information on soybean area in a cost-effective way and could be implemented in an operational mode. The approach has also been applied for other crops in

Three very high resolution optical images for land use mapping of a suburban catchment: input to distributed hydrological models

Science.gov (United States)

Jacqueminet, Christine; Kermadi, Saïda; Michel, Kristell; Jankowfsky, Sonja; Braud, Isabelle; Branger, Flora; Beal, David; Gagnage, Matthieu

2010-05-01

Keywords : land cover mapping, very high resolution, remote sensing processing techniques, object oriented approach, distributed hydrological model, peri-urban area Urbanization and other modifications of land use affect the hydrological cycle of suburban catchments. In order to quantify these impacts, the AVuPUR project (Assessing the Vulnerability of Peri-Urban Rivers) is currently developing a distributed hydrological model that includes anthropogenic features. The case study is the Yzeron catchment (150 km²), located close to Lyon city, France. This catchment experiences a growing of urbanization and a modification of traditional land use since the middle of the 20th century, resulting in an increase of flooding, water pollution and river banks erosion. This contribution discusses the potentials of automated data processing techniques on three different VHR images, in order to produce appropriate and detailed land cover data for the models. Of particular interest is the identification of impermeable surfaces (buildings, roads, and parking places) and permeable surfaces (forest areas, agricultural fields, gardens, trees…) within the catchment, because their infiltration capacity and their impact on runoff generation are different. Three aerial and spatial images were acquired: (1) BD Ortho IGN aerial images, 0.50 m resolution, visible bands, may 5th 2008; (2) QuickBird satellite image, 2.44 m resolution, visible and near-infrared bands, august 29th 2008; (3) Spot satellite image, 2.50 m resolution, visible and near-infrared bands, September 22nd 2008. From these images, we developed three image processing methods: (1) a pixel-based method associated to a segmentation using Matlab®, (2) a pixel-based method using ENVI®, (3) an object-based classification using Definiens®. We extracted six land cover types from the BD Ortho IGN (visible bands) and height classes from the satellite images (visible and near infrared bands). The three classified images are

TRANSFER OF TECHNOLOGY FOR CADASTRAL MAPPING IN TAJIKISTAN USING HIGH RESOLUTION SATELLITE DATA

Directory of Open Access Journals (Sweden)

R. Kaczynski

2012-07-01

Full Text Available European Commission funded project entitled: "Support to the mapping and certification capacity of the Agency of Land Management, Geodesy and Cartography" in Tajikistan was run by FINNMAP FM-International and Human Dynamics from Nov. 2006 to June 2011. The Agency of Land Management, Geodesy and Cartography is the state agency responsible for development, implementation, monitoring and evaluation of state policies on land tenure and land management, including the on-going land reform and registration of land use rights. The specific objective was to support and strengthen the professional capacity of the "Fazo" Institute in the field of satellite geodesy, digital photogrammetry, advanced digital satellite image processing of high resolution satellite data and digital cartography. Lectures and on-the-job trainings for the personnel of "Fazo" and Agency in satellite geodesy, digital photogrammetry, cartography and the use of high resolution satellite data for cadastral mapping have been organized. Standards and Quality control system for all data and products have been elaborated and implemented in the production line. Technical expertise and trainings in geodesy, photogrammetry and satellite image processing to the World Bank project "Land Registration and Cadastre System for Sustainable Agriculture" has also been completed in Tajikistan. The new map projection was chosen and the new unclassified geodetic network has been established for all of the country in which all agricultural parcel boundaries are being mapped. IKONOS, QuickBird and WorldView1 panchromatic data have been used for orthophoto generation. Average accuracy of space triangulation of non-standard (long up to 90km satellite images of QuickBird Pan and IKONOS Pan on ICPs: RMSEx = 0.5m and RMSEy = 0.5m have been achieved. Accuracy of digital orthophoto map is RMSExy = 1.0m. More then two and half thousands of digital orthophoto map sheets in the scale of 1:5000 with pixel size 0.5m

Observing the Sun with the Atacama Large Millimeter/submillimeter Array (ALMA): Fast-Scan Single-Dish Mapping

Science.gov (United States)

White, S. M.; Iwai, K.; Phillips, N. M.; Hills, R. E.; Hirota, A.; Yagoubov, P.; Siringo, G.; Shimojo, M.; Bastian, T. S.; Hales, A. S.; Sawada, T.; Asayama, S.; Sugimoto, M.; Marson, R. G.; Kawasaki, W.; Muller, E.; Nakazato, T.; Sugimoto, K.; Brajša, R.; Skokić, I.; Bárta, M.; Kim, S.; Remijan, A. J.; de Gregorio, I.; Corder, S. A.; Hudson, H. S.; Loukitcheva, M.; Chen, B.; De Pontieu, B.; Fleishmann, G. D.; Gary, D. E.; Kobelski, A.; Wedemeyer, S.; Yan, Y.

2017-07-01

The Atacama Large Millimeter/submillimeter Array (ALMA) radio telescope has commenced science observations of the Sun starting in late 2016. Since the Sun is much larger than the field of view of individual ALMA dishes, the ALMA interferometer is unable to measure the background level of solar emission when observing the solar disk. The absolute temperature scale is a critical measurement for much of ALMA solar science, including the understanding of energy transfer through the solar atmosphere, the properties of prominences, and the study of shock heating in the chromosphere. In order to provide an absolute temperature scale, ALMA solar observing will take advantage of the remarkable fast-scanning capabilities of the ALMA 12 m dishes to make single-dish maps of the full Sun. This article reports on the results of an extensive commissioning effort to optimize the mapping procedure, and it describes the nature of the resulting data. Amplitude calibration is discussed in detail: a path that uses the two loads in the ALMA calibration system as well as sky measurements is described and applied to commissioning data. Inspection of a large number of single-dish datasets shows significant variation in the resulting temperatures, and based on the temperature distributions, we derive quiet-Sun values at disk center of 7300 K at λ = 3 mm and 5900 K at λ = 1.3 mm. These values have statistical uncertainties of about 100 K, but systematic uncertainties in the temperature scale that may be significantly larger. Example images are presented from two periods with very different levels of solar activity. At a resolution of about 25'', the 1.3 mm wavelength images show temperatures on the disk that vary over about a 2000 K range. Active regions and plages are among the hotter features, while a large sunspot umbra shows up as a depression, and filament channels are relatively cool. Prominences above the solar limb are a common feature of the single-dish images.

Real-time high-resolution PC-based system for measurement of errors on compact disks

Science.gov (United States)

Tehranchi, Babak; Howe, Dennis G.

1994-10-01

Hardware and software utilities are developed to directly monitor the Eight-to-Fourteen (EFM) demodulated data bytes at the input of a CD player's Cross-Interleaved Reed-Solomon Code (CIRC) block decoder. The hardware is capable of identifying erroneous data with single-byte resolution in the serial data stream read from a Compact Disc by a CDD 461 Philips CD-ROM drive. In addition, the system produces graphical maps that show the physical location of the measured errors on the entire disc, or via a zooming and planning feature, on user selectable local disc regions.

Application of Low-Cost UASs and Digital Photogrammetry for High-Resolution Snow Depth Mapping in the Arctic

Directory of Open Access Journals (Sweden)

Emiliano Cimoli

2017-11-01

Full Text Available The repeat acquisition of high-resolution snow depth measurements has important research and civil applications in the Arctic. Currently the surveying methods for capturing the high spatial and temporal variability of the snowpack are expensive, in particular for small areal extents. An alternative methodology based on Unmanned Aerial Systems (UASs and digital photogrammetry was tested over varying surveying conditions in the Arctic employing two diverse and low-cost UAS-camera combinations (500 and 1700 USD, respectively. Six areas, two in Svalbard and four in Greenland, were mapped covering from 1386 to 38,410 m2. The sites presented diverse snow surface types, underlying topography and light conditions in order to test the method under potentially limiting conditions. The resulting snow depth maps achieved spatial resolutions between 0.06 and 0.09 m. The average difference between UAS-estimated and measured snow depth, checked with conventional snow probing, ranged from 0.015 to 0.16 m. The impact of image pre-processing was explored, improving point cloud density and accuracy for different image qualities and snow/light conditions. Our UAS photogrammetry results are expected to be scalable to larger areal extents. While further validation is needed, with the inclusion of extra validation points, the study showcases the potential of this cost-effective methodology for high-resolution monitoring of snow dynamics in the Arctic and beyond.

Perfusion maps of the whole liver based on high temporal and spatial resolution contrast-enhanced MRI (4D THRIVE): Feasibility and initial results in focal liver lesions

International Nuclear Information System (INIS)

Coenegrachts, Kenneth; Ghekiere, Johan; Denolin, Vincent; Gabriele, Beck; Herigault, Gwen; Haspeslagh, Marc; Daled, Peter; Bipat, Shandra; Stoker, Jaap; Rigauts, Hans

2010-01-01

Purpose: To prospectively evaluate a new imaging sequence (4D THRIVE) for whole liver perfusion in high temporal and spatial resolution. Feasibility of parametric mapping and its potential for characterizing focal liver lesions (FLLs) are investigated. Materials and methods: Fifteen patients suspected for colorectal liver metastases (LMs) were included. Parametric maps were evaluated qualitatively (ring-enhancement and lesion heterogeneity) and compared to three-phased contrast-enhanced MRI. Quantitative analysis was based on average perfusion values of entire FLLs. Reference standard comprised surgery with histopathology or follow-up imaging. Fisher's exact test was used for qualitative and Kruskal-Wallis test for quantitative analysis. Results: In total 29 LMs, 17 hemangiomas and 4 focal nodular hyperplasias were evaluated. FLLs could be differentiated by qualitative assessment of parametric maps respectively three-phased contrast-enhanced MRI (Fisher's p < 0.001 for comparisons between LMs and hemangiomas and LMs and FNHs for both ring-enhancement and lesion heterogeneity) rather than by quantitative analysis of parametric maps (Chi-square for Kep = 0.33 (p = 0.847) and Chi-square for Kel = 1.35 (p = 0.509)). Conclusion: This preliminary study shows potential of 4D THRIVE for whole liver imaging enabling calculation of parametric maps. Qualitative rather than quantitative analysis was accurate for differentiating malignant and benign FLLs.

Dynamic inundation mapping of Hurricane Harvey flooding in the Houston metro area using hyper-resolution modeling and quantitative image reanalysis

Science.gov (United States)

Noh, S. J.; Lee, J. H.; Lee, S.; Zhang, Y.; Seo, D. J.

2017-12-01

Hurricane Harvey was one of the most extreme weather events in Texas history and left significant damages in the Houston and adjoining coastal areas. To understand better the relative impact to urban flooding of extreme amount and spatial extent of rainfall, unique geography, land use and storm surge, high-resolution water modeling is necessary such that natural and man-made components are fully resolved. In this presentation, we reconstruct spatiotemporal evolution of inundation during Hurricane Harvey using hyper-resolution modeling and quantitative image reanalysis. The two-dimensional urban flood model used is based on dynamic wave approximation and 10 m-resolution terrain data, and is forced by the radar-based multisensor quantitative precipitation estimates. The model domain includes Buffalo, Brays, Greens and White Oak Bayous in Houston. The model is simulated using hybrid parallel computing. To evaluate dynamic inundation mapping, we combine various qualitative crowdsourced images and video footages with LiDAR-based terrain data.

Creating Geologically Based Radon Potential Maps for Kentucky

Science.gov (United States)

Overfield, B.; Hahn, E.; Wiggins, A.; Andrews, W. M., Jr.

2017-12-01

Radon potential in the United States, Kentucky in particular, has historically been communicated using a single hazard level for each county; however, physical phenomena are not controlled by administrative boundaries, so single-value county maps do not reflect the significant variations in radon potential in each county. A more accurate approach uses bedrock geology as a predictive tool. A team of nurses, health educators, statisticians, and geologists partnered to create 120 county maps showing spatial variations in radon potential by intersecting residential radon test kit results (N = 60,000) with a statewide 1:24,000-scale bedrock geology coverage to determine statistically valid radon-potential estimates for each geologic unit. Maps using geology as a predictive tool for radon potential are inherently more detailed than single-value county maps. This mapping project revealed that areas in central and south-central Kentucky with the highest radon potential are underlain by shales and karstic limestones.

Rapid simultaneous high-resolution mapping of myelin water fraction and relaxation times in human brain using BMC-mcDESPOT.

Science.gov (United States)

Bouhrara, Mustapha; Spencer, Richard G

2017-02-15

A number of central nervous system (CNS) diseases exhibit changes in myelin content and magnetic resonance longitudinal, T 1 , and transverse, T 2 , relaxation times, which therefore represent important biomarkers of CNS pathology. Among the methods applied for measurement of myelin water fraction (MWF) and relaxation times, the multicomponent driven equilibrium single pulse observation of T 1 and T 2 (mcDESPOT) approach is of particular interest. mcDESPOT permits whole brain mapping of multicomponent T 1 and T 2 , with data acquisition accomplished within a clinically realistic acquisition time. Unfortunately, previous studies have indicated the limited performance of mcDESPOT in the setting of the modest signal-to-noise range of high-resolution mapping, required for the depiction of small structures and to reduce partial volume effects. Recently, we showed that a new Bayesian Monte Carlo (BMC) analysis substantially improved determination of MWF from mcDESPOT imaging data. However, our previous study was limited in that it did not discuss determination of relaxation times. Here, we extend the BMC analysis to the simultaneous determination of whole-brain MWF and relaxation times using the two-component mcDESPOT signal model. Simulation analyses and in-vivo human brain studies indicate the overall greater performance of this approach compared to the stochastic region contraction (SRC) algorithm, conventionally used to derive parameter estimates from mcDESPOT data. SRC estimates of the transverse relaxation time of the long T 2 fraction, T 2,l , and the longitudinal relaxation time of the short T 1 fraction, T 1,s , clustered towards the lower and upper parameter search space limits, respectively, indicating failure of the fitting procedure. We demonstrate that this effect is absent in the BMC analysis. Our results also showed improved parameter estimation for BMC as compared to SRC for high-resolution mapping. Overall we find that the combination of BMC analysis

Modelling and mapping the suitability of European forest formations at 1-km resolution

DEFF Research Database (Denmark)

Casalegno, Stefano; Amatulli, Giuseppe; Bastrup-Birk, Annemarie

2011-01-01

factors. Here, we used the bootstrap-aggregating machine-learning ensemble classifier Random Forest (RF) to derive a 1-km resolution European forest formation suitability map. The statistical model use as inputs more than 6,000 field data forest inventory plots and a large set of environmental variables...

Temporal resolution and motion artifacts in single-source and dual-source cardiac CT.

Science.gov (United States)

Schöndube, Harald; Allmendinger, Thomas; Stierstorfer, Karl; Bruder, Herbert; Flohr, Thomas

2013-03-01

The temporal resolution of a given image in cardiac computed tomography (CT) has so far mostly been determined from the amount of CT data employed for the reconstruction of that image. The purpose of this paper is to examine the applicability of such measures to the newly introduced modality of dual-source CT as well as to methods aiming to provide improved temporal resolution by means of an advanced image reconstruction algorithm. To provide a solid base for the examinations described in this paper, an extensive review of temporal resolution in conventional single-source CT is given first. Two different measures for assessing temporal resolution with respect to the amount of data involved are introduced, namely, either taking the full width at half maximum of the respective data weighting function (FWHM-TR) or the total width of the weighting function (total TR) as a base of the assessment. Image reconstruction using both a direct fan-beam filtered backprojection with Parker weighting as well as using a parallel-beam rebinning step are considered. The theory of assessing temporal resolution by means of the data involved is then extended to dual-source CT. Finally, three different advanced iterative reconstruction methods that all use the same input data are compared with respect to the resulting motion artifact level. For brevity and simplicity, the examinations are limited to two-dimensional data acquisition and reconstruction. However, all results and conclusions presented in this paper are also directly applicable to both circular and helical cone-beam CT. While the concept of total TR can directly be applied to dual-source CT, the definition of the FWHM of a weighting function needs to be slightly extended to be applicable to this modality. The three different advanced iterative reconstruction methods examined in this paper result in significantly different images with respect to their motion artifact level, despite exactly the same amount of data being used

Temporal resolution and motion artifacts in single-source and dual-source cardiac CT

International Nuclear Information System (INIS)

Schöndube, Harald; Allmendinger, Thomas; Stierstorfer, Karl; Bruder, Herbert; Flohr, Thomas

2013-01-01

Purpose: The temporal resolution of a given image in cardiac computed tomography (CT) has so far mostly been determined from the amount of CT data employed for the reconstruction of that image. The purpose of this paper is to examine the applicability of such measures to the newly introduced modality of dual-source CT as well as to methods aiming to provide improved temporal resolution by means of an advanced image reconstruction algorithm. Methods: To provide a solid base for the examinations described in this paper, an extensive review of temporal resolution in conventional single-source CT is given first. Two different measures for assessing temporal resolution with respect to the amount of data involved are introduced, namely, either taking the full width at half maximum of the respective data weighting function (FWHM-TR) or the total width of the weighting function (total TR) as a base of the assessment. Image reconstruction using both a direct fan-beam filtered backprojection with Parker weighting as well as using a parallel-beam rebinning step are considered. The theory of assessing temporal resolution by means of the data involved is then extended to dual-source CT. Finally, three different advanced iterative reconstruction methods that all use the same input data are compared with respect to the resulting motion artifact level. For brevity and simplicity, the examinations are limited to two-dimensional data acquisition and reconstruction. However, all results and conclusions presented in this paper are also directly applicable to both circular and helical cone-beam CT. Results: While the concept of total TR can directly be applied to dual-source CT, the definition of the FWHM of a weighting function needs to be slightly extended to be applicable to this modality. The three different advanced iterative reconstruction methods examined in this paper result in significantly different images with respect to their motion artifact level, despite exactly the same

High-spatial resolution resistivity mapping of large-area YBCO films by a near-field millimeter-wave microscope

International Nuclear Information System (INIS)

Golosovsky, M.; Galkin, A.; Davidov, D.

1996-01-01

The authors demonstrate a new millimeter-wave technique for the resistivity mapping of large-area conducting films, namely, a near-field resistivity microscope. The microscope is based on the idea that electromagnetic waves are transmitted through a narrow resonant slit with high efficiency. By scanning this slit at fixed height above an inhomogeneous conducting surface and measuring the intensity and phase of the reflected wave, the resistivity of this surface may be determined with a 10--100 microm spatial resolution using 80-GHz radiation. Using this technique, they map normal-sate resistivity of 1 in x 1 in YBCO films at ambient temperature. In some films they find inhomogeneities of the normal-state sheet resistance of the order of 10%--20%

Towards a Global High Resolution Peatland Map in 2020

Science.gov (United States)

Barthelmes, Alexandra; Barthelmes, Karen-Doreen; Joosten, Hans; Dommain, Rene; Margalef, Olga

2015-04-01

Some 3% of land area on planet Earth (approx. 4 million km2) is covered by peatlands. About 10% (~ 0.3 % of the land area) are drained and responsible for a disproportional 5 % of the global anthropogenic CO2 emissions (Victoria et al., 2012). Additionally, peatland drainage and degradation lead to land subsidence, soil degradation, water pollution, and enhanced susceptibility to fire (Holden et al., 2004; Joosten et al., 2012). The global importance of peatlands for carbon storage and climate change mitigation has currently been recognized in international policy - since 2008 organic soils are subject of discussion in the UN Framework Convention on Climate Change (UNFCCC) (Joosten, 2011). In May 2013 the European Parliament decided that the global post 2020 climate agreement should include the obligation to report emissions and removals from peatland drainage and rewetting. Implementation of such program, however, necessitates the rapid availability of reliable, comprehensive, high resolution, spatially explicit data on the extent and status of peatlands. For many reporting countries this requires an innovation in peatland mapping, i.e. the better and integrative use of novel, but already available methods and technologies. We developed an approach that links various science networks, methodologies and data bases, including those of peatland/landscape ecology for understanding where and how peatlands may occur, those of remote sensing for identifying possible locations, and those of pedology (legacy soil maps) and (palaeo-)ecology for ground truthing. Such integration of old field data, specialized knowledge, and modern RS and GIS technologies enables acquiring a rapid, comprehensive, detailed and rather reliable overview, even on a continental scale. We illustrate this approach with a high resolution overview of peatland distribution, area, status and greenhouse gas fluxes e.g. for the East African countries Rwanda, Burundi, Uganda and Zambia. Furthermore, we

USGS Topo Base Map from The National Map

Data.gov (United States)

U.S. Geological Survey, Department of the Interior — The USGS Topographic Base Map from The National Map. This tile cached web map service combines the most current data services (Boundaries, Names, Transportation,...

Subpixel Mapping of Hyperspectral Image Based on Linear Subpixel Feature Detection and Object Optimization

Science.gov (United States)

Liu, Zhaoxin; Zhao, Liaoying; Li, Xiaorun; Chen, Shuhan

2018-04-01

Owing to the limitation of spatial resolution of the imaging sensor and the variability of ground surfaces, mixed pixels are widesperead in hyperspectral imagery. The traditional subpixel mapping algorithms treat all mixed pixels as boundary-mixed pixels while ignoring the existence of linear subpixels. To solve this question, this paper proposed a new subpixel mapping method based on linear subpixel feature detection and object optimization. Firstly, the fraction value of each class is obtained by spectral unmixing. Secondly, the linear subpixel features are pre-determined based on the hyperspectral characteristics and the linear subpixel feature; the remaining mixed pixels are detected based on maximum linearization index analysis. The classes of linear subpixels are determined by using template matching method. Finally, the whole subpixel mapping results are iteratively optimized by binary particle swarm optimization algorithm. The performance of the proposed subpixel mapping method is evaluated via experiments based on simulated and real hyperspectral data sets. The experimental results demonstrate that the proposed method can improve the accuracy of subpixel mapping.

Large scale mapping: an empirical comparison of pixel-based and ...

African Journals Online (AJOL)

In the past, large scale mapping was carried using precise ground survey methods. Later, paradigm shift in data collection using medium to low resolution and, recently, high resolution images brought to bear the problem of accurate data analysis and fitness-for-purpose challenges. Using high resolution satellite images ...

Tip-enhanced Raman mapping with top-illumination AFM.

Science.gov (United States)

Chan, K L Andrew; Kazarian, Sergei G

2011-04-29

Tip-enhanced Raman mapping is a powerful, emerging technique that offers rich chemical information and high spatial resolution. Currently, most of the successes in tip-enhanced Raman scattering (TERS) measurements are based on the inverted configuration where tips and laser are approaching the sample from opposite sides. This results in the limitation of measurement for transparent samples only. Several approaches have been developed to obtain tip-enhanced Raman mapping in reflection mode, many of which involve certain customisations of the system. We have demonstrated in this work that it is also possible to obtain TERS nano-images using an upright microscope (top-illumination) with a gold-coated Si atomic force microscope (AFM) cantilever without significant modification to the existing integrated AFM/Raman system. A TERS image of a single-walled carbon nanotube has been achieved with a spatial resolution of ∼ 20-50 nm, demonstrating the potential of this technique for studying non-transparent nanoscale materials.

Tip-enhanced Raman mapping with top-illumination AFM

Energy Technology Data Exchange (ETDEWEB)

Chan, K L Andrew; Kazarian, Sergei G, E-mail: s.kazarian@imperial.ac.uk [Department of Chemical Engineering, Imperial College London, SW7 2AZ (United Kingdom)

2011-04-29

Tip-enhanced Raman mapping is a powerful, emerging technique that offers rich chemical information and high spatial resolution. Currently, most of the successes in tip-enhanced Raman scattering (TERS) measurements are based on the inverted configuration where tips and laser are approaching the sample from opposite sides. This results in the limitation of measurement for transparent samples only. Several approaches have been developed to obtain tip-enhanced Raman mapping in reflection mode, many of which involve certain customisations of the system. We have demonstrated in this work that it is also possible to obtain TERS nano-images using an upright microscope (top-illumination) with a gold-coated Si atomic force microscope (AFM) cantilever without significant modification to the existing integrated AFM/Raman system. A TERS image of a single-walled carbon nanotube has been achieved with a spatial resolution of {approx} 20-50 nm, demonstrating the potential of this technique for studying non-transparent nanoscale materials.

Tip-enhanced Raman mapping with top-illumination AFM

International Nuclear Information System (INIS)

Chan, K L Andrew; Kazarian, Sergei G

2011-01-01

Tip-enhanced Raman mapping is a powerful, emerging technique that offers rich chemical information and high spatial resolution. Currently, most of the successes in tip-enhanced Raman scattering (TERS) measurements are based on the inverted configuration where tips and laser are approaching the sample from opposite sides. This results in the limitation of measurement for transparent samples only. Several approaches have been developed to obtain tip-enhanced Raman mapping in reflection mode, many of which involve certain customisations of the system. We have demonstrated in this work that it is also possible to obtain TERS nano-images using an upright microscope (top-illumination) with a gold-coated Si atomic force microscope (AFM) cantilever without significant modification to the existing integrated AFM/Raman system. A TERS image of a single-walled carbon nanotube has been achieved with a spatial resolution of ∼ 20-50 nm, demonstrating the potential of this technique for studying non-transparent nanoscale materials.

Diffusion Based Photon Mapping

DEFF Research Database (Denmark)

Schjøth, Lars; Fogh Olsen, Ole; Sporring, Jon

2007-01-01

. To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....

Diffusion Based Photon Mapping

DEFF Research Database (Denmark)

Schjøth, Lars; Olsen, Ole Fogh; Sporring, Jon

2006-01-01

. To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....

Clickstream data yields high-resolution maps of science.

Science.gov (United States)

Bollen, Johan; Van de Sompel, Herbert; Hagberg, Aric; Bettencourt, Luis; Chute, Ryan; Rodriguez, Marko A; Balakireva, Lyudmila

2009-01-01

Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantages of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science. Over the course of 2007 and 2008, we collected nearly 1 billion user interactions recorded by the scholarly web portals of some of the most significant publishers, aggregators and institutional consortia. The resulting reference data set covers a significant part of world-wide use of scholarly web portals in 2006, and provides a balanced coverage of the humanities, social sciences, and natural sciences. A journal clickstream model, i.e. a first-order Markov chain, was extracted from the sequences of user interactions in the logs. The clickstream model was validated by comparing it to the Getty Research Institute's Architecture and Art Thesaurus. The resulting model was visualized as a journal network that outlines the relationships between various scientific domains and clarifies the connection of the social sciences and humanities to the natural sciences. Maps of science resulting from large-scale clickstream data provide a detailed, contemporary view of scientific activity and correct the underrepresentation of the social sciences and humanities that is commonly found in citation data.

Mapping cortical mesoscopic networks of single spiking cortical or sub-cortical neurons.

Science.gov (United States)

Xiao, Dongsheng; Vanni, Matthieu P; Mitelut, Catalin C; Chan, Allen W; LeDue, Jeffrey M; Xie, Yicheng; Chen, Andrew Cn; Swindale, Nicholas V; Murphy, Timothy H

2017-02-04

Understanding the basis of brain function requires knowledge of cortical operations over wide-spatial scales, but also within the context of single neurons. In vivo, wide-field GCaMP imaging and sub-cortical/cortical cellular electrophysiology were used in mice to investigate relationships between spontaneous single neuron spiking and mesoscopic cortical activity. We make use of a rich set of cortical activity motifs that are present in spontaneous activity in anesthetized and awake animals. A mesoscale spike-triggered averaging procedure allowed the identification of motifs that are preferentially linked to individual spiking neurons by employing genetically targeted indicators of neuronal activity. Thalamic neurons predicted and reported specific cycles of wide-scale cortical inhibition/excitation. In contrast, spike-triggered maps derived from single cortical neurons yielded spatio-temporal maps expected for regional cortical consensus function. This approach can define network relationships between any point source of neuronal spiking and mesoscale cortical maps.

High resolution mapping of soil organic carbon stocks using remote sensing variables in the semi-arid rangelands of eastern Australia.

Science.gov (United States)

Wang, Bin; Waters, Cathy; Orgill, Susan; Gray, Jonathan; Cowie, Annette; Clark, Anthony; Liu, De Li

2018-07-15

Efficient and effective modelling methods to assess soil organic carbon (SOC) stock are central in understanding the global carbon cycle and informing related land management decisions. However, mapping SOC stocks in semi-arid rangelands is challenging due to the lack of data and poor spatial coverage. The use of remote sensing data to provide an indirect measurement of SOC to inform digital soil mapping has the potential to provide more reliable and cost-effective estimates of SOC compared with field-based, direct measurement. Despite this potential, the role of remote sensing data in improving the knowledge of soil information in semi-arid rangelands has not been fully explored. This study firstly investigated the use of high spatial resolution satellite data (seasonal fractional cover data; SFC) together with elevation, lithology, climatic data and observed soil data to map the spatial distribution of SOC at two soil depths (0-5cm and 0-30cm) in semi-arid rangelands of eastern Australia. Overall, model performance statistics showed that random forest (RF) and boosted regression trees (BRT) models performed better than support vector machine (SVM). The models obtained moderate results with R 2 of 0.32 for SOC stock at 0-5cm and 0.44 at 0-30cm, RMSE of 3.51MgCha -1 at 0-5cm and 9.16MgCha -1 at 0-30cm without considering SFC covariates. In contrast, by including SFC, the model accuracy for predicting SOC stock improved by 7.4-12.7% at 0-5cm, and by 2.8-5.9% at 0-30cm, highlighting the importance of including SFC to enhance the performance of the three modelling techniques. Furthermore, our models produced a more accurate and higher resolution digital SOC stock map compared with other available mapping products for the region. The data and high-resolution maps from this study can be used for future soil carbon assessment and monitoring. Copyright © 2018 Elsevier B.V. All rights reserved.

Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping

Directory of Open Access Journals (Sweden)

Trognitz Friederike

2007-02-01

Full Text Available Abstract Background The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the use of conventional chromosome-specific SSR, RFLP, AFLP, as well as gene- or locus-specific markers. The ease of detection of DNA polymorphisms depends on both frequency and form of sequence variation. The narrow genetic background of close relatives and inbreds complicates the detection of persisting, reduced polymorphism and is a challenge to the development of reliable molecular markers. Nonetheless, monomorphic DNA fragments representing not directly usable conventional markers can contain considerable variation at the level of single nucleotide polymorphisms (SNPs. This can be used for the design of allele-specific molecular markers. The reproducible detection of allele-specific markers based on SNPs has been a technical challenge. Results We present a fast and cost-effective protocol for the detection of allele-specific SNPs by applying Sequence Polymorphism-Derived (SPD markers. These markers proved highly efficient for fingerprinting of individuals possessing a homogeneous genetic background. SPD markers are obtained from within non-informative, conventional molecular marker fragments that are screened for SNPs to design allele-specific PCR primers. The method makes use of primers containing a single, 3'-terminal Locked Nucleic Acid (LNA base. We demonstrate the applicability of the technique by successful genetic mapping of allele-specific SNP markers derived from monomorphic Conserved Ortholog Set II (COSII markers mapped to Solanum chromosomes, in S. caripense. By using SPD markers it was possible for the first time to map the S. caripense alleles

Remote sensing-based fire frequency mapping in a savannah ...

African Journals Online (AJOL)

Moderate Resolution Imaging Spectroradiometer (MODIS) images from 2000 to 2006 were obtained and classified for burnt area mapping. Linear pixel unmixing was used for image classification and subsequent mapping of burnt areas. The results showed that it was feasible to have discrimination of burnt areas and ...

High-resolution linkage map of mouse chromosome 13 in the vicinity of the host resistance locus Lgn1

Energy Technology Data Exchange (ETDEWEB)

Beckers, M.C.; Ernst, E.; Diez, E. [McGill Univ., Quebec (Canada)] [and others

1997-02-01

Natural resistance of inbred mouse strains to infection with Legionella pneumophila is controlled by the expression of a single dominant gene on chromosome 13, designated Lgn1. The genetic difference at Lgn1 is phenotypically expressed as the presence or absence of intracellular replication of L. pneumophila in host macrophages. In our effort to identify the Lgn1 gene by positional cloning, we have generated a high-resolution linkage map of the Lgn1 chromosomal region. For this, we have carried out extensive segregation analysis in a total of 1270 (A/J x C57BL/6J) X A/J informative backcross mice segregating the resistance allele of C57BL/6J and the susceptibility allele of A/J. Additional segregation analyses were carried out in three preexisting panels of C57BL/6J X Mus spretus interspecific backcross mice. A total of 39 DNA markers were mapped within an interval of approximately 30 cM overlapping the Lgn1 region. Combined pedigree analyses for the 5.4-cM segment overlapping Lgn1 indicated the locus order and the interlocus distances (in cM): D13Mit128-(1.4)-D13Mit194-(0.1)-D13Mit147-(0.9)-Dl3Mit36-(0.9)-D13Mit146-(0.2)-Lgn1/D 13Mit37-(1.0)-D13Mit70. Additional genetic linkage studies of markers not informative in the A/J X C57BL/6J cross positioned D13Mit30, -72, -195, and -203, D13Gor4, D13Hun35, and Mtap5 in the immediate vicinity of the Lgn1 locus. The marker density and resolution of this genetic linkage map should allow the construction of a physical map of the region and the isolation of YAC clones overlapping the gene. 60 refs., 2 figs., 2 tabs.

Quantitative high-resolution genomic analysis of single cancer cells.

Science.gov (United States)

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Influence of the interaction volume on the kinetic energy resolution of a velocity map imaging spectrometer

International Nuclear Information System (INIS)

Zhang Peng; Feng Zheng-Peng; Luo Si-Qiang; Wang Zhe

2016-01-01

We investigate the influence of the interaction volume on the energy resolution of a velocity map imaging spectrometer. The simulation results show that the axial interaction size has a significant influence on the resolution. This influence is increased for a higher kinetic energy. We further show that the radial interaction size has a minor influence on the energy resolution for the electron or ion with medium energy, but it is crucial for the resolution of the electron or ion with low kinetic energy. By tracing the flight trajectories we show how the electron or ion energy resolution is influenced by the interaction size. (paper)

Functional magnetic resonance microscopy at single-cell resolution in Aplysia californica

Science.gov (United States)

Radecki, Guillaume; Nargeot, Romuald; Jelescu, Ileana Ozana; Le Bihan, Denis; Ciobanu, Luisa

2014-01-01

In this work, we show the feasibility of performing functional MRI studies with single-cell resolution. At ultrahigh magnetic field, manganese-enhanced magnetic resonance microscopy allows the identification of most motor neurons in the buccal network of Aplysia at low, nontoxic Mn2+ concentrations. We establish that Mn2+ accumulates intracellularly on injection into the living Aplysia and that its concentration increases when the animals are presented with a sensory stimulus. We also show that we can distinguish between neuronal activities elicited by different types of stimuli. This method opens up a new avenue into probing the functional organization and plasticity of neuronal networks involved in goal-directed behaviors with single-cell resolution. PMID:24872449

Creating soil moisture maps based on radar satellite imagery

Science.gov (United States)

Hnatushenko, Volodymyr; Garkusha, Igor; Vasyliev, Volodymyr

2017-10-01

The presented work is related to a study of mapping soil moisture basing on radar data from Sentinel-1 and a test of adequacy of the models constructed on the basis of data obtained from alternative sources. Radar signals are reflected from the ground differently, depending on its properties. In radar images obtained, for example, in the C band of the electromagnetic spectrum, soils saturated with moisture usually appear in dark tones. Although, at first glance, the problem of constructing moisture maps basing on radar data seems intuitively clear, its implementation on the basis of the Sentinel-1 data on an industrial scale and in the public domain is not yet available. In the process of mapping, for verification of the results, measurements of soil moisture obtained from logs of the network of climate stations NOAA US Climate Reference Network (USCRN) were used. This network covers almost the entire territory of the United States. The passive microwave radiometers of Aqua and SMAP satellites data are used for comparing processing. In addition, other supplementary cartographic materials were used, such as maps of soil types and ready moisture maps. The paper presents a comparison of the effect of the use of certain methods of roughening the quality of radar data on the result of mapping moisture. Regression models were constructed showing dependence of backscatter coefficient values Sigma0 for calibrated radar data of different spatial resolution obtained at different times on soil moisture values. The obtained soil moisture maps of the territories of research, as well as the conceptual solutions about automation of operations of constructing such digital maps, are presented. The comparative assessment of the time required for processing a given set of radar scenes with the developed tools and with the ESA SNAP product was carried out.

Mapping Mangroves Extents on the Red Sea Coastline in Egypt using Polarimetric SAR and High Resolution Optical Remote Sensing Data

Directory of Open Access Journals (Sweden)

Ayman Abdel-Hamid

2018-02-01

Full Text Available Mangroves ecosystems dominate the coastal wetlands of tropical and subtropical regions throughout the world. They are among the most productive forest ecosystems. They provide various ecological and economic ecosystem services. Despite of their economic and ecological importance, mangroves experience high yearly loss rates. There is a growing demand for mapping and assessing changes in mangroves extents especially in the context of climate change, land use change, and related threats to coastal ecosystems. The main objective of this study is to develop an approach for mapping of mangroves extents on the Red Sea coastline in Egypt, through the integration of both L-band SAR data of ALOS/PALSAR, and high resolution optical data of RapidEye. This was achieved via using object-based image analysis method, through applying different machine learning algorithms, and evaluating various features such as spectral properties, texture features, and SAR derived parameters for discrimination of mangroves ecosystem classes. Three non-parametric machine learning algorithms were tested for mangroves mapping; random forest (RF, support vector machine (SVM, and classification and regression trees (CART. As an input for the classifiers, we tested various features including vegetation indices (VIs and texture analysis using the gray-level co-occurrence matrix (GLCM. The object-based analysis method allowed clearly discriminating the different land cover classes within mangroves ecosystem. The highest overall accuracy (92.15% was achieved by the integrated SAR and optical data. Among all classifiers tested, RF performed better than other classifiers. Using L-band SAR data integrated with high resolution optical data was beneficial for mapping and characterization of mangroves growing in small patches. The maps produced represents an important updated reference suitable for developing a regional action plan for conservation and management of mangroves resources along

Low-Power Photothermal Probing of Single Plasmonic Nanostructures with Nanomechanical String Resonators

DEFF Research Database (Denmark)

Schmid, Silvan; Wu, Kaiyu; Larsen, Peter Emil

2014-01-01

We demonstrate the direct photothermal probing and mapping of single plasmonic nanostructures via the temperature-induced detuning of nanomechanical string resonators. Single Au nanoslits and nanorods are illuminated with a partially polarized focused laser beam (λ = 633 nm) with irradiances...... in the range of 0.26–38 μW/μm2. Photothermal heating maps with a resolution of ∼375 nm are obtained by scanning the laser over the nanostructures. Based on the string sensitivities, absorption efficiencies of 2.3 ± 0.3 and 1.1 ± 0.7 are extracted for a single nanoslit (53 nm × 1 μm) and nanorod (75 nm × 185 nm......). Our results show that nanomechanical resonators are a unique and robust analysis tool for the low-power investigation of thermoplasmonic effects in plasmonic hot spots....

Multiple and single snapshot compressive beamforming

DEFF Research Database (Denmark)

Gerstoft, Peter; Xenaki, Angeliki; Mecklenbrauker, Christoph F.

2015-01-01

and multiple snapshots. CS does not require inversion of the data covariance matrix and thus works well even for a single snapshot where it gives higher resolution than conventional beamforming. For multiple snapshots, CS outperforms conventional high-resolution methods even with coherent arrivals and at low......-lagged superposition of source amplitudes at all hypothetical DOAs. Regularizing with an ‘1-norm constraint renders the problem solvable with convex optimization, and promoting sparsity gives highresolution DOA maps. Here the sparse source distribution is derived using maximum a posteriori estimates for both single...

A high-resolution land-use map; Nogales, Sonora, Mexico

Science.gov (United States)

Norman, Laura M.; Villarreal, Miguel L.; Wallace, Cynthia S.A.; Gil Anaya, Claudia Z.; Diaz Arcos, Israel; Gray, Floyd

2010-01-01

The cities of Nogales, Sonora, and Nogales, Arizona, are located in the Ambos Nogales Watershed, a topographically irregular bowl-shaped area with a northward gradient. Throughout history, residents in both cities have been affected by flooding. Currently, the primary method for regulating this runoff is to build a series of detention basins in Nogales, Sonora. Additionally, the municipality also is considering land-use planning to help mitigate flooding. This paper describes the production of a 10-meter resolution land-use map, derived from 2008 aerial photos of the Nogales, Sonora Watershed for modeling impacts of the detention basin construction and in support of an ?Early Warning Hazard System? for the region.

High spatial resolution mapping of folds and fractures using Unmanned Aerial Vehicle (UAV) photogrammetry

Science.gov (United States)

Cruden, A. R.; Vollgger, S.

2016-12-01

The emerging capability of UAV photogrammetry combines a simple and cost-effective method to acquire digital aerial images with advanced computer vision algorithms that compute spatial datasets from a sequence of overlapping digital photographs from various viewpoints. Depending on flight altitude and camera setup, sub-centimeter spatial resolution orthophotographs and textured dense point clouds can be achieved. Orientation data can be collected for detailed structural analysis by digitally mapping such high-resolution spatial datasets in a fraction of time and with higher fidelity compared to traditional mapping techniques. Here we describe a photogrammetric workflow applied to a structural study of folds and fractures within alternating layers of sandstone and mudstone at a coastal outcrop in SE Australia. We surveyed this location using a downward looking digital camera mounted on commercially available multi-rotor UAV that autonomously followed waypoints at a set altitude and speed to ensure sufficient image overlap, minimum motion blur and an appropriate resolution. The use of surveyed ground control points allowed us to produce a geo-referenced 3D point cloud and an orthophotograph from hundreds of digital images at a spatial resolution automatically extracted from these high-resolution datasets using open-source software. This resulted in an extensive and statistically relevant orientation dataset that was used to 1) interpret the progressive development of folds and faults in the region, and 2) to generate a 3D structural model that underlines the complex internal structure of the outcrop and quantifies spatial variations in fold geometries. Overall, our work highlights how UAV photogrammetry can contribute to new insights in structural analysis.

Advances in the Validation of Satellite-Based Maps of Volcanic Sulfur Dioxide Plumes

Science.gov (United States)

Realmuto, V. J.; Berk, A.; Acharya, P. K.; Kennett, R.

2013-12-01

The monitoring of volcanic gas emissions with gas cameras, spectrometer arrays, tethersondes, and UAVs presents new opportunities for the validation of satellite-based retrievals of gas concentrations. Gas cameras and spectrometer arrays provide instantaneous observations of the gas burden, or concentration along an optical path, over broad sections of a plume, similar to the observations acquired by nadir-viewing satellites. Tethersondes and UAVs provide us with direct measurements of the vertical profiles of gas concentrations within plumes. This presentation will focus on our current efforts to validate ASTER-based maps of sulfur dioxide plumes at Turrialba and Kilauea Volcanoes (located in Costa Rica and Hawaii, respectively). These volcanoes, which are the subjects of comprehensive monitoring programs, are challenging targets for thermal infrared (TIR) remote sensing due the warm and humid atmospheric conditions. The high spatial resolution of ASTER in the TIR (90 meters) allows us to map the plumes back to their source vents, but also requires us to pay close attention to the temperature and emissivity of the surfaces beneath the plumes. Our knowledge of the surface and atmospheric conditions is never perfect, and we employ interactive mapping techniques that allow us to evaluate the impact of these uncertainties on our estimates of plume composition. To accomplish this interactive mapping we have developed the Plume Tracker tool kit, which integrates retrieval procedures, visualization tools, and a customized version of the MODTRAN radiative transfer (RT) model under a single graphics user interface (GUI). We are in the process of porting the RT calculations to graphics processing units (GPUs) with the goal of achieving a 100-fold increase in the speed of computation relative to conventional CPU-based processing. We will report on our progress with this evolution of Plume Tracker. Portions of this research were conducted at the Jet Propulsion Laboratory

Spectrally based mapping of riverbed composition

Science.gov (United States)

Legleiter, Carl; Stegman, Tobin K.; Overstreet, Brandon T.

2016-01-01

Remote sensing methods provide an efficient means of characterizing fluvial systems. This study evaluated the potential to map riverbed composition based on in situ and/or remote measurements of reflectance. Field spectra and substrate photos from the Snake River, Wyoming, USA, were used to identify different sediment facies and degrees of algal development and to quantify their optical characteristics. We hypothesized that accounting for the effects of depth and water column attenuation to isolate the reflectance of the streambed would enhance distinctions among bottom types and facilitate substrate classification. A bottom reflectance retrieval algorithm adapted from coastal research yielded realistic spectra for the 450 to 700 nm range; but bottom reflectance-based substrate classifications, generated using a random forest technique, were no more accurate than classifications derived from above-water field spectra. Additional hypothesis testing indicated that a combination of reflectance magnitude (brightness) and indices of spectral shape provided the most accurate riverbed classifications. Convolving field spectra to the response functions of a multispectral satellite and a hyperspectral imaging system did not reduce classification accuracies, implying that high spectral resolution was not essential. Supervised classifications of algal density produced from hyperspectral data and an inferred bottom reflectance image were not highly accurate, but unsupervised classification of the bottom reflectance image revealed distinct spectrally based clusters, suggesting that such an image could provide additional river information. We attribute the failure of bottom reflectance retrieval to yield more reliable substrate maps to a latent correlation between depth and bottom type. Accounting for the effects of depth might have eliminated a key distinction among substrates and thus reduced discriminatory power. Although further, more systematic study across a broader

Ionospheric correction for spaceborne single-frequency GPS based ...

Indian Academy of Sciences (India)

A modified ionospheric correction method and the corresponding approximate algorithm for spaceborne single-frequency Global Positioning System (GPS) users are proposed in this study. Single Layer Model (SLM) mapping function for spaceborne GPS was analyzed. SLM mapping functions at different altitudes were ...

Object-based Morphological Building Index for Building Extraction from High Resolution Remote Sensing Imagery

Directory of Open Access Journals (Sweden)

LIN Xiangguo

2017-06-01

Full Text Available Building extraction from high resolution remote sensing images is a hot research topic in the field of photogrammetry and remote sensing. In this article, an object-based morphological building index (OBMBI is constructed based on both image segmentation and graph-based top-hat reconstruction, and OBMBI is used for building extraction from high resolution remote sensing images. First, bidirectional mapping relationship between pixels, objects and graph-nodes are constructed. Second, the OBMBI image is built based on both graph-based top-hat reconstruction and the above mapping relationship. Third, a binary thresholding is performed on the OBMBI image, and the binary image is converted into vector format to derive the building polygons. Finally, the post-processing is made to optimize the extracted building polygons. Two images, including an aerial image and a panchromatic satellite image, are used to test both the proposed method and classic PanTex method. The experimental results suggest that our proposed method has a higher accuracy in building extraction than the classic PanTex method. On average, the correctness, the completeness and the quality of our method are respectively 9.49%, 11.26% and 14.11% better than those of the PanTex.

Spatio Temporal Detection and Virtual Mapping of Landslide Using High-Resolution Airborne Laser Altimetry (lidar) in Densely Vegetated Areas of Tropics

Science.gov (United States)

Bibi, T.; Azahari Razak, K.; Rahman, A. Abdul; Latif, A.

2017-10-01

Landslides are an inescapable natural disaster, resulting in massive social, environmental and economic impacts all over the world. The tropical, mountainous landscape in generally all over Malaysia especially in eastern peninsula (Borneo) is highly susceptible to landslides because of heavy rainfall and tectonic disturbances. The purpose of the Landslide hazard mapping is to identify the hazardous regions for the execution of mitigation plans which can reduce the loss of life and property from future landslide incidences. Currently, the Malaysian research bodies e.g. academic institutions and government agencies are trying to develop a landslide hazard and risk database for susceptible areas to backing the prevention, mitigation, and evacuation plan. However, there is a lack of devotion towards landslide inventory mapping as an elementary input of landslide susceptibility, hazard and risk mapping. The developing techniques based on remote sensing technologies (satellite, terrestrial and airborne) are promising techniques to accelerate the production of landslide maps, shrinking the time and resources essential for their compilation and orderly updates. The aim of the study is to provide a better perception regarding the use of virtual mapping of landslides with the help of LiDAR technology. The focus of the study is spatio temporal detection and virtual mapping of landslide inventory via visualization and interpretation of very high-resolution data (VHR) in forested terrain of Mesilau river, Kundasang. However, to cope with the challenges of virtual inventory mapping on in forested terrain high resolution LiDAR derivatives are used. This study specifies that the airborne LiDAR technology can be an effective tool for mapping landslide inventories in a complex climatic and geological conditions, and a quick way of mapping regional hazards in the tropics.

Assessment of an Operational System for Crop Type Map Production Using High Temporal and Spatial Resolution Satellite Optical Imagery

Directory of Open Access Journals (Sweden)

Jordi Inglada

2015-09-01

Full Text Available Crop area extent estimates and crop type maps provide crucial information for agricultural monitoring and management. Remote sensing imagery in general and, more specifically, high temporal and high spatial resolution data as the ones which will be available with upcoming systems, such as Sentinel-2, constitute a major asset for this kind of application. The goal of this paper is to assess to what extent state-of-the-art supervised classification methods can be applied to high resolution multi-temporal optical imagery to produce accurate crop type maps at the global scale. Five concurrent strategies for automatic crop type map production have been selected and benchmarked using SPOT4 (Take5 and Landsat 8 data over 12 test sites spread all over the globe (four in Europe, four in Africa, two in America and two in Asia. This variety of tests sites allows one to draw conclusions applicable to a wide variety of landscapes and crop systems. The results show that a random forest classifier operating on linearly temporally gap-filled images can achieve overall accuracies above 80% for most sites. Only two sites showed low performances: Madagascar due to the presence of fields smaller than the pixel size and Burkina Faso due to a mix of trees and crops in the fields. The approach is based on supervised machine learning techniques, which need in situ data collection for the training step, but the map production is fully automatic.

Mapping Monthly Water Scarcity in Global Transboundary Basins at Country-Basin Mesh Based Spatial Resolution.

Science.gov (United States)

Degefu, Dagmawi Mulugeta; Weijun, He; Zaiyi, Liao; Liang, Yuan; Zhengwei, Huang; Min, An

2018-02-01

Currently fresh water scarcity is an issue with huge socio-economic and environmental impacts. Transboundary river and lake basins are among the sources of fresh water facing this challenge. Previous studies measured blue water scarcity at different spatial and temporal resolutions. But there is no global water availability and footprint assessment done at country-basin mesh based spatial and monthly temporal resolutions. In this study we assessed water scarcity at these spatial and temporal resolutions. Our results showed that around 1.6 billion people living within the 328 country-basin units out of the 560 we assessed in this study endures severe water scarcity at least for a month within the year. In addition, 175 country-basin units goes through severe water scarcity for 3-12 months in the year. These sub-basins include nearly a billion people. Generally, the results of this study provide insights regarding the number of people and country-basin units experiencing low, moderate, significant and severe water scarcity at a monthly temporal resolution. These insights might help these basins' sharing countries to design and implement sustainable water management and sharing schemes.

Integrating pipeline data management application and Google maps dataset on web based GIS application unsing open source technology Sharp Map and Open Layers

Energy Technology Data Exchange (ETDEWEB)

Wisianto, Arie; Sania, Hidayatus [PT PERTAMINA GAS, Bontang (Indonesia); Gumilar, Oki [PT PERTAMINA GAS, Jakarta (Indonesia)

2010-07-01

PT Pertamina Gas operates 3 pipe segments carrying natural gas from producers to PT Pupuk Kaltim in the Kalimantan area. The company wants to build a pipeline data management system consisting of pipeline facilities, inspections and risk assessments which would run on Geographic Information Systems (GIS) platforms. The aim of this paper is to present the integration of the pipeline data management system with GIS. A web based GIS application is developed using the combination of Google maps datasets with local spatial datasets. In addition, Open Layers is used to integrate pipeline data model and Google Map dataset into a single map display on Sharp Map. The GIS based pipeline data management system developed herein constitutes a low cost, powerful and efficient web based GIS solution.

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

Science.gov (United States)

Zhou, Shiguo; Goldstein, Steve; Place, Michael; Bechner, Michael; Patino, Diego; Potamousis, Konstantinos; Ravindran, Prabu; Pape, Louise; Rincon, Gonzalo; Hernandez-Ortiz, Juan; Medrano, Juan F; Schwartz, David C

2015-08-28

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation. The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts

Quantitative high-resolution genomic analysis of single cancer cells.

Directory of Open Access Journals (Sweden)

Juliane Hannemann

Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Clickstream Data Yields High-Resolution Maps of Science

Science.gov (United States)

Bollen, Johan; Van de Sompel, Herbert; Rodriguez, Marko A.; Balakireva, Lyudmila

2009-01-01

Background Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantages of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science. Methodology Over the course of 2007 and 2008, we collected nearly 1 billion user interactions recorded by the scholarly web portals of some of the most significant publishers, aggregators and institutional consortia. The resulting reference data set covers a significant part of world-wide use of scholarly web portals in 2006, and provides a balanced coverage of the humanities, social sciences, and natural sciences. A journal clickstream model, i.e. a first-order Markov chain, was extracted from the sequences of user interactions in the logs. The clickstream model was validated by comparing it to the Getty Research Institute's Architecture and Art Thesaurus. The resulting model was visualized as a journal network that outlines the relationships between various scientific domains and clarifies the connection of the social sciences and humanities to the natural sciences. Conclusions Maps of science resulting from large-scale clickstream data provide a detailed, contemporary view of scientific activity and correct the underrepresentation of the social sciences and humanities that is commonly found in citation data. PMID:19277205

Clickstream data yields high-resolution maps of science.

Directory of Open Access Journals (Sweden)

Johan Bollen

Full Text Available BACKGROUND: Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams that are issued by a variety of users across many different domains. Given these advantages of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science. METHODOLOGY: Over the course of 2007 and 2008, we collected nearly 1 billion user interactions recorded by the scholarly web portals of some of the most significant publishers, aggregators and institutional consortia. The resulting reference data set covers a significant part of world-wide use of scholarly web portals in 2006, and provides a balanced coverage of the humanities, social sciences, and natural sciences. A journal clickstream model, i.e. a first-order Markov chain, was extracted from the sequences of user interactions in the logs. The clickstream model was validated by comparing it to the Getty Research Institute's Architecture and Art Thesaurus. The resulting model was visualized as a journal network that outlines the relationships between various scientific domains and clarifies the connection of the social sciences and humanities to the natural sciences. CONCLUSIONS: Maps of science resulting from large-scale clickstream data provide a detailed, contemporary view of scientific activity and correct the underrepresentation of the social sciences and humanities that is commonly found in citation data.

Mapping turbidity in the Charles River, Boston using a high-resolution satellite.

Science.gov (United States)

Hellweger, Ferdi L; Miller, Will; Oshodi, Kehinde Sarat

2007-09-01

The usability of high-resolution satellite imagery for estimating spatial water quality patterns in urban water bodies is evaluated using turbidity in the lower Charles River, Boston as a case study. Water turbidity was surveyed using a boat-mounted optical sensor (YSI) at 5 m spatial resolution, resulting in about 4,000 data points. The ground data were collected coincidently with a satellite imagery acquisition (IKONOS), which consists of multispectral (R, G, B) reflectance at 1 m resolution. The original correlation between the raw ground and satellite data was poor (R2 = 0.05). Ground data were processed by removing points affected by contamination (e.g., sensor encounters a particle floc), which were identified visually. Also, the ground data were corrected for the memory effect introduced by the sensor's protective casing using an analytical model. Satellite data were processed to remove pixels affected by permanent non-water features (e.g., shoreline). In addition, water pixels within a certain buffer distance from permanent non-water features were removed due to contamination by the adjacency effect. To determine the appropriate buffer distance, a procedure that explicitly considers the distance of pixels to the permanent non-water features was applied. Two automatic methods for removing the effect of temporary non-water features (e.g., boats) were investigated, including (1) creating a water-only mask based on an unsupervised classification and (2) removing (filling) all local maxima in reflectance. After the various processing steps, the correlation between the ground and satellite data was significantly better (R2 = 0.70). The correlation was applied to the satellite image to develop a map of turbidity in the lower Charles River, which reveals large-scale patterns in water clarity. However, the adjacency effect prevented the application of this method to near-shore areas, where high-resolution patterns were expected (e.g., outfall plumes).

A 30 ps Timing Resolution for Single Photons with Multi-pixel Burle MCP-PMT

Energy Technology Data Exchange (ETDEWEB)

Va' vra, J.; Benitez, J.; Coleman, J.; Leith, D.W.G.S.; Mazaheri, G.; Ratcliff, B.; Schwiening, J.; /SLAC

2006-07-05

We have achieved {approx}30 psec single-photoelectron and {approx}12ps for multi-photoelectron timing resolution with a new 64 pixel Burle MCP-PMT with 10 micron microchannel holes. We have also demonstrated that this detector works in a magnetic field of 15kG, and achieved a single-photoelectron timing resolution of better than 60 psec. The study is relevant for a new focusing DIRC RICH detector for particle identification at future Colliders such as the super B-factory or ILC, and for future TOF techniques. This study shows that a highly pixilated MCP-PMT can deliver excellent timing resolution.

Towards a better understanding of the overall health impact of the game of squash: automatic and high-resolution motion analysis from a single camera view

Directory of Open Access Journals (Sweden)

Brumann Christopher

2017-09-01

Full Text Available In this paper, we present a method for locating and tracking players in the game of squash using Gaussian mixture model background subtraction and agglomerative contour clustering from a calibrated single camera view. Furthermore, we describe a method for player re-identification after near total occlusion, based on stored color- and region-descriptors. For camera calibration, no additional pattern is needed, as the squash court itself can serve as a 3D calibration object. In order to exclude non-rally situations from motion analysis, we further classify each video frame into game phases using a multilayer perceptron. By considering a player’s position as well as the current game phase we are able to visualize player-individual motion patterns expressed as court coverage using pseudo colored heat-maps. In total, we analyzed two matches (six games, 1:28h of high quality commercial videos used in sports broadcasting and compute high resolution (1cm per pixel heat-maps. 130184 manually labeled frames (game phases and player identification show an identification correctness of 79.28±8.99% (mean±std. Game phase classification is correct in 60.87±7.62% and the heat-map visualization correctness is 72.47±7.27%.

Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution

NARCIS (Netherlands)

van Ommering, K.; Somers, P.A.; Koets, M.; Schleipen, J.J.H.B.; IJzendoorn, van L.J.; Prins, M.W.J.

2010-01-01

Particle labels are used in biosensors to detect the presence and concentration of analyte molecules. In this paper we demonstrate an optical technique to measure the mobility and height of bound particle labels on a biosensor surface with single-label resolution. The technique is based on the

Electric field imaging of single atoms

Science.gov (United States)

Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel; Findlay, Scott D.; Kohno, Yuji; Matsumoto, Takao; Ishikawa, Ryo; Ikuhara, Yuichi

2017-01-01

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

Quantitative atomic resolution elemental mapping via absolute-scale energy dispersive X-ray spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen, Z. [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia); Weyland, M. [Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800 (Australia); Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800 (Australia); Sang, X.; Xu, W.; Dycus, J.H.; LeBeau, J.M. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695 (United States); D' Alfonso, A.J.; Allen, L.J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Findlay, S.D., E-mail: scott.findlay@monash.edu [School of Physics and Astronomy, Monash University, Clayton, Victoria 3800 (Australia)

2016-09-15

Quantitative agreement on an absolute scale is demonstrated between experiment and simulation for two-dimensional, atomic-resolution elemental mapping via energy dispersive X-ray spectroscopy. This requires all experimental parameters to be carefully characterized. The agreement is good, but some discrepancies remain. The most likely contributing factors are identified and discussed. Previous predictions that increasing the probe forming aperture helps to suppress the channelling enhancement in the average signal are confirmed experimentally. It is emphasized that simple column-by-column analysis requires a choice of sample thickness that compromises between being thick enough to yield a good signal-to-noise ratio while being thin enough that the overwhelming majority of the EDX signal derives from the column on which the probe is placed, despite strong electron scattering effects. - Highlights: • Absolute scale quantification of 2D atomic-resolution EDX maps is demonstrated. • Factors contributing to remaining small quantitative discrepancies are identified. • Experiment confirms large probe-forming apertures suppress channelling enhancement. • The thickness range suitable for reliable column-by-column analysis is discussed.

USGS "Did You Feel It?" internet-based macroseismic intensity maps

Science.gov (United States)

Wald, D.J.; Quitoriano, V.; Worden, B.; Hopper, M.; Dewey, J.W.

2011-01-01

The U.S. Geological Survey (USGS) "Did You Feel It?" (DYFI) system is an automated approach for rapidly collecting macroseismic intensity data from Internet users' shaking and damage reports and generating intensity maps immediately following earthquakes; it has been operating for over a decade (1999-2011). DYFI-based intensity maps made rapidly available through the DYFI system fundamentally depart from more traditional maps made available in the past. The maps are made more quickly, provide more complete coverage and higher resolution, provide for citizen input and interaction, and allow data collection at rates and quantities never before considered. These aspects of Internet data collection, in turn, allow for data analyses, graphics, and ways to communicate with the public, opportunities not possible with traditional data-collection approaches. Yet web-based contributions also pose considerable challenges, as discussed herein. After a decade of operational experience with the DYFI system and users, we document refinements to the processing and algorithmic procedures since DYFI was first conceived. We also describe a number of automatic post-processing tools, operations, applications, and research directions, all of which utilize the extensive DYFI intensity datasets now gathered in near-real time. DYFI can be found online at the website http://earthquake.usgs.gov/dyfi/. ?? 2011 by the Istituto Nazionale di Geofisica e Vulcanologia.

High-Resolution Remote Sensing Image Building Extraction Based on Markov Model

Science.gov (United States)

Zhao, W.; Yan, L.; Chang, Y.; Gong, L.

2018-04-01

With the increase of resolution, remote sensing images have the characteristics of increased information load, increased noise, more complex feature geometry and texture information, which makes the extraction of building information more difficult. To solve this problem, this paper designs a high resolution remote sensing image building extraction method based on Markov model. This method introduces Contourlet domain map clustering and Markov model, captures and enhances the contour and texture information of high-resolution remote sensing image features in multiple directions, and further designs the spectral feature index that can characterize "pseudo-buildings" in the building area. Through the multi-scale segmentation and extraction of image features, the fine extraction from the building area to the building is realized. Experiments show that this method can restrain the noise of high-resolution remote sensing images, reduce the interference of non-target ground texture information, and remove the shadow, vegetation and other pseudo-building information, compared with the traditional pixel-level image information extraction, better performance in building extraction precision, accuracy and completeness.

High-resolution charge carrier mobility mapping of heterogeneous organic semiconductors

Science.gov (United States)

Button, Steven W.; Mativetsky, Jeffrey M.

2017-08-01

Organic electronic device performance is contingent on charge transport across a heterogeneous landscape of structural features. Methods are therefore needed to unravel the effects of local structure on overall electrical performance. Using conductive atomic force microscopy, we construct high-resolution out-of-plane hole mobility maps from arrays of 5000 to 16 000 current-voltage curves. To demonstrate the efficacy of this non-invasive approach for quantifying and mapping local differences in electrical performance due to structural heterogeneities, we investigate two thin film test systems, one bearing a heterogeneous crystal structure [solvent vapor annealed 5,11-Bis(triethylsilylethynyl)anthradithiophene (TES-ADT)—a small molecule organic semiconductor] and one bearing a heterogeneous chemical composition [p-DTS(FBTTh2)2:PC71BM—a high-performance organic photovoltaic active layer]. TES-ADT shows nearly an order of magnitude difference in hole mobility between semicrystalline and crystalline areas, along with a distinct boundary between the two regions, while p-DTS(FBTTh2)2:PC71BM exhibits subtle local variations in hole mobility and a nanoscale domain structure with features below 10 nm in size. We also demonstrate mapping of the built-in potential, which plays a significant role in organic light emitting diode and organic solar cell operation.

Feasibility of in vivo three-dimensional T 2* mapping using dicarboxy-PROXYL and CW-EPR-based single-point imaging.

Science.gov (United States)

Kubota, Harue; Komarov, Denis A; Yasui, Hironobu; Matsumoto, Shingo; Inanami, Osamu; Kirilyuk, Igor A; Khramtsov, Valery V; Hirata, Hiroshi

2017-06-01

The aim of this study was to demonstrate the feasibility of in vivo three-dimensional (3D) relaxation time T 2 * mapping of a dicarboxy-PROXYL radical using continuous-wave electron paramagnetic resonance (CW-EPR) imaging. Isotopically substituted dicarboxy-PROXYL radicals, 3,4-dicarboxy-2,2,5,5-tetra( 2 H 3 )methylpyrrolidin-(3,4- 2 H 2 )-(1- 15 N)-1-oxyl ( 2 H, 15 N-DCP) and 3,4-dicarboxy-2,2,5,5-tetra( 2 H 3 )methylpyrrolidin-(3,4- 2 H 2 )-1-oxyl ( 2 H-DCP), were used in the study. A clonogenic cell survival assay was performed with the 2 H-DCP radical using squamous cell carcinoma (SCC VII) cells. The time course of EPR signal intensities of intravenously injected 2 H, 15 N-DCP and 2 H-DCP radicals were determined in tumor-bearing hind legs of mice (C3H/HeJ, male, n = 5). CW-EPR-based single-point imaging (SPI) was performed for 3D T 2 * mapping. 2 H-DCP radical did not exhibit cytotoxicity at concentrations below 10 mM. The in vivo half-life of 2 H, 15 N-DCP in tumor tissues was 24.7 ± 2.9 min (mean ± standard deviation [SD], n = 5). The in vivo time course of the EPR signal intensity of the 2 H, 15 N-DCP radical showed a plateau of 10.2 ± 1.2 min (mean ± SD) where the EPR signal intensity remained at more than 90% of the maximum intensity. During the plateau, in vivo 3D T 2 * maps with 2 H, 15 N-DCP were obtained from tumor-bearing hind legs, with a total acquisition time of 7.5 min. EPR signals of 2 H, 15 N-DCP persisted long enough after bolus intravenous injection to conduct in vivo 3D T 2 * mapping with CW-EPR-based SPI.

Dipole-magnet field models based on a conformal map

Directory of Open Access Journals (Sweden)

P. L. Walstrom

2012-10-01

Full Text Available In general, generation of charged-particle transfer maps for conventional iron-pole-piece dipole magnets to third and higher order requires a model for the midplane field profile and its transverse derivatives (soft-edge model to high order and numerical integration of map coefficients. An exact treatment of the problem for a particular magnet requires use of measured magnetic data. However, in initial design of beam transport systems, users of charged-particle optics codes generally rely on magnet models built into the codes. Indeed, if maps to third order are adequate for the problem, an approximate analytic field model together with numerical map coefficient integration can capture the important features of the transfer map. The model described in this paper is based on the fact that, except at very large distances from the magnet, the magnetic field for parallel pole-face magnets with constant pole gap height and wide pole faces is basically two dimensional (2D. The field for all space outside of the pole pieces is given by a single (complex analytic expression and includes a parameter that controls the rate of falloff of the fringe field. Since the field function is analytic in the complex plane outside of the pole pieces, it satisfies two basic requirements of a field model for higher-order map codes: it is infinitely differentiable at the midplane and also a solution of the Laplace equation. It is apparently the only simple model available that combines an exponential approach to the central field with an inverse cubic falloff of field at large distances from the magnet in a single expression. The model is not intended for detailed fitting of magnetic field data, but for use in numerical map-generating codes for studying the effect of extended fringe fields on higher-order transfer maps. It is based on conformally mapping the area between the pole pieces to the upper half plane, and placing current filaments on the pole faces. An

Weed map generation from UAV image mosaics based on crop row detection

DEFF Research Database (Denmark)

Midtiby, Henrik Skov

To control weed in a field effectively with a minimum of herbicides, knowledge about the weed patches is required. Based on images acquired by Unmanned Aerial Vehicles (UAVs), a vegetation map of the entire field can be generated. Manual analysis, which is often required, to detect weed patches...... is used as input for the method. Issues related to perspective distortion are reduced by using an orthomosaic, which is a high resolution image of the entire field, built from hundreds of images taken by a UAV. A vegetation map is generated from the orthomosaic by calculating the excess green color index...

Temporal resolution requirements of satellite constellations for 30 m global burned area mapping

Science.gov (United States)

Melchiorre, A.; Boschetti, L.

2017-12-01

Global burned area maps have been generated systematically with daily, coarse resolution satellite data (Giglio et al. 2013). The production of moderate resolution (10 - 30 m) global burned area products would meet the needs of several user communities: improved carbon emission estimations due to heterogeneous landscapes and for local scale air quality and fire management applications (Mouillot et al. 2014; van der Werf et al. 2010). While the increased spatial resolution reduces the influence of mixed burnt/unburnt pixels and it would increase the spectral separation of burned areas, moderate resolution satellites have reduced temporal resolution (10 - 16 days). Fire causes a land-cover change spectrally visible for a period ranging from a few weeks in savannas to over a year in forested ecosystems (Roy et al. 2010); because clouds, smoke, and other optically thick aerosols limit the number of available observations (Roy et al. 2008; Smith and Wooster 2005), burned areas might disappear before they are observed by moderate resolution sensors. Data fusion from a constellation of different sensors has been proposed to overcome these limits (Boschetti et al. 2015; Roy 2015). In this study, we estimated the probability of moderate resolution satellites and virtual constellations (including Landsat-8/9, Sentinel-2A/B) to provide sufficient observations for burned area mapping globally, and by ecosystem. First, we estimated the duration of the persistence of the signal associated with burned areas by combining the MODIS Global Burned Area and the Nadir BRDF-Adjusted Reflectance Product by characterizing the post-fire trends in reflectance to determine the length of the period in which the burn class is spectrally distinct from the unburned and, therefore, detectable. The MODIS-Terra daily cloud data were then used to estimate the probability of cloud cover. The cloud probability was used at each location to estimate the minimum revisit time needed to obtain at least one

Low-cost, portable, robust and high-resolution single-camera stereo-DIC system and its application in high-temperature deformation measurements

Science.gov (United States)

Chi, Yuxi; Yu, Liping; Pan, Bing

2018-05-01

A low-cost, portable, robust and high-resolution single-camera stereo-digital image correlation (stereo-DIC) system for accurate surface three-dimensional (3D) shape and deformation measurements is described. This system adopts a single consumer-grade high-resolution digital Single Lens Reflex (SLR) camera and a four-mirror adaptor, rather than two synchronized industrial digital cameras, for stereo image acquisition. In addition, monochromatic blue light illumination and coupled bandpass filter imaging are integrated to ensure the robustness of the system against ambient light variations. In contrast to conventional binocular stereo-DIC systems, the developed pseudo-stereo-DIC system offers the advantages of low cost, portability, robustness against ambient light variations, and high resolution. The accuracy and precision of the developed single SLR camera-based stereo-DIC system were validated by measuring the 3D shape of a stationary sphere along with in-plane and out-of-plane displacements of a translated planar plate. Application of the established system to thermal deformation measurement of an alumina ceramic plate and a stainless-steel plate subjected to radiation heating was also demonstrated.

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

NARCIS (Netherlands)

Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it

Sparsity-Based Pixel Super Resolution for Lens-Free Digital In-line Holography.

Science.gov (United States)

Song, Jun; Leon Swisher, Christine; Im, Hyungsoon; Jeong, Sangmoo; Pathania, Divya; Iwamoto, Yoshiko; Pivovarov, Misha; Weissleder, Ralph; Lee, Hakho

2016-04-21

Lens-free digital in-line holography (LDIH) is a promising technology for portable, wide field-of-view imaging. Its resolution, however, is limited by the inherent pixel size of an imaging device. Here we present a new computational approach to achieve sub-pixel resolution for LDIH. The developed method is a sparsity-based reconstruction with the capability to handle the non-linear nature of LDIH. We systematically characterized the algorithm through simulation and LDIH imaging studies. The method achieved the spatial resolution down to one-third of the pixel size, while requiring only single-frame imaging without any hardware modifications. This new approach can be used as a general framework to enhance the resolution in nonlinear holographic systems.

Regional-Scale High Spatial Resolution Mapping of Aboveground Net Primary Productivity (ANPP from Field Survey and Landsat Data: A Case Study for the Country of Wales

Directory of Open Access Journals (Sweden)

Emma J. Tebbs

2017-08-01

Full Text Available This paper presents an alternative approach for high spatial resolution vegetation productivity mapping at a regional scale, using a combination of Normalised Difference Vegetation Index (NDVI imagery and widely distributed ground-based Above-ground Net Primary Production (ANPP estimates. Our method searches through all available single-date NDVI imagery to identify the images which give the best NDVI–ANPP relationship. The derived relationships are then used to predict ANPP values outside of field survey plots. This approach enables the use of the high spatial resolution (30 m Landsat 8 sensor, despite its low revisit frequency that is further reduced by cloud cover. This is one of few studies to investigate the NDVI–ANPP relationship across a wide range of temperate habitats and strong relationships were observed (R2 = 0.706, which increased when only grasslands were considered (R2 = 0.833. The strongest NDVI–ANPP relationships occurred during the spring “green-up” period. A reserved subset of 20% of ground-based ANPP estimates was used for validation and results showed that our method was able to estimate ANPP with a RMSE of 15–21%. This work is important because we demonstrate a general methodological framework for mapping of ANPP from local to regional scales, with the potential to be applied to any temperate ecosystems with a pronounced green up period. Our approach allows spatial extrapolation outside of field survey plots to produce a continuous surface product, useful for capturing spatial patterns and representing small-scale heterogeneity, and well-suited for modelling applications. The data requirements for implementing this approach are also discussed.

High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms.

Directory of Open Access Journals (Sweden)

Steven Y C Tong

Full Text Available We have developed a single nucleotide polymorphism (SNP nucleated high-resolution melting (HRM technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE and an allele specific real-time PCR (AS kinetic PCR SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs and provides a Simpson's Index of Diversity (D of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.

Earth mapping - aerial or satellite imagery comparative analysis

Science.gov (United States)

Fotev, Svetlin; Jordanov, Dimitar; Lukarski, Hristo

Nowadays, solving the tasks for revision of existing map products and creation of new maps requires making a choice of the land cover image source. The issue of the effectiveness and cost of the usage of aerial mapping systems versus the efficiency and cost of very-high resolution satellite imagery is topical [1, 2, 3, 4]. The price of any remotely sensed image depends on the product (panchromatic or multispectral), resolution, processing level, scale, urgency of task and on whether the needed image is available in the archive or has to be requested. The purpose of the present work is: to make a comparative analysis between the two approaches for mapping the Earth having in mind two parameters: quality and cost. To suggest an approach for selection of the map information sources - airplane-based or spacecraft-based imaging systems with very-high spatial resolution. Two cases are considered: area that equals approximately one satellite scene and area that equals approximately the territory of Bulgaria.

Smartphones Based Mobile Mapping Systems

Science.gov (United States)

Al-Hamad, A.; El-Sheimy, N.

2014-06-01

The past 20 years have witnessed an explosive growth in the demand for geo-spatial data. This demand has numerous sources and takes many forms; however, the net effect is an ever-increasing thirst for data that is more accurate, has higher density, is produced more rapidly, and is acquired less expensively. For mapping and Geographic Information Systems (GIS) projects, this has been achieved through the major development of Mobile Mapping Systems (MMS). MMS integrate various navigation and remote sensing technologies which allow mapping from moving platforms (e.g. cars, airplanes, boats, etc.) to obtain the 3D coordinates of the points of interest. Such systems obtain accuracies that are suitable for all but the most demanding mapping and engineering applications. However, this accuracy doesn't come cheaply. As a consequence of the platform and navigation and mapping technologies used, even an "inexpensive" system costs well over 200 000 USD. Today's mobile phones are getting ever more sophisticated. Phone makers are determined to reduce the gap between computers and mobile phones. Smartphones, in addition to becoming status symbols, are increasingly being equipped with extended Global Positioning System (GPS) capabilities, Micro Electro Mechanical System (MEMS) inertial sensors, extremely powerful computing power and very high resolution cameras. Using all of these components, smartphones have the potential to replace the traditional land MMS and portable GPS/GIS equipment. This paper introduces an innovative application of smartphones as a very low cost portable MMS for mapping and GIS applications.

Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

Directory of Open Access Journals (Sweden)

Meuwissen Theo HE

2007-04-01

Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

Under the Microscope: Single-Domain Antibodies for Live-Cell Imaging and Super-Resolution Microscopy

Directory of Open Access Journals (Sweden)

Bjoern Traenkle

2017-08-01

Full Text Available Single-domain antibodies (sdAbs have substantially expanded the possibilities of advanced cellular imaging such as live-cell or super-resolution microscopy to visualize cellular antigens and their dynamics. In addition to their unique properties including small size, high stability, and solubility in many environments, sdAbs can be efficiently functionalized according to the needs of the respective imaging approach. Genetically encoded intrabodies fused to fluorescent proteins (chromobodies have become versatile tools to study dynamics of endogenous proteins in living cells. Additionally, sdAbs conjugated to organic dyes were shown to label cellular structures with high density and minimal fluorophore displacement making them highly attractive probes for super-resolution microscopy. Here, we review recent advances of the chromobody technology to visualize localization and dynamics of cellular targets and the application of chromobody-based cell models for compound screening. Acknowledging the emerging importance of super-resolution microscopy in cell biology, we further discuss advantages and challenges of sdAbs for this technology.

Under the Microscope: Single-Domain Antibodies for Live-Cell Imaging and Super-Resolution Microscopy.

Science.gov (United States)

Traenkle, Bjoern; Rothbauer, Ulrich

2017-01-01

Single-domain antibodies (sdAbs) have substantially expanded the possibilities of advanced cellular imaging such as live-cell or super-resolution microscopy to visualize cellular antigens and their dynamics. In addition to their unique properties including small size, high stability, and solubility in many environments, sdAbs can be efficiently functionalized according to the needs of the respective imaging approach. Genetically encoded intrabodies fused to fluorescent proteins (chromobodies) have become versatile tools to study dynamics of endogenous proteins in living cells. Additionally, sdAbs conjugated to organic dyes were shown to label cellular structures with high density and minimal fluorophore displacement making them highly attractive probes for super-resolution microscopy. Here, we review recent advances of the chromobody technology to visualize localization and dynamics of cellular targets and the application of chromobody-based cell models for compound screening. Acknowledging the emerging importance of super-resolution microscopy in cell biology, we further discuss advantages and challenges of sdAbs for this technology.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

Science.gov (United States)

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-04-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

High spatial resolution mapping of land cover types in a priority area for conservation in the Brazilian savanna

Science.gov (United States)

Ribeiro, F.; Roberts, D. A.; Hess, L. L.; Davis, F. W.; Caylor, K. K.; Nackoney, J.; Antunes Daldegan, G.

2017-12-01

Savannas are heterogeneous landscapes consisting of highly mixed land cover types that lack clear distinct boundaries. The Brazilian Cerrado is a Neotropical savanna considered a biodiversity hotspot for conservation due to its biodiversity richness and rapid transformation of its landscape by crop and pasture activities. The Cerrado is one of the most threatened Brazilian biomes and only 2.2% of its original extent is strictly protected. Accurate mapping and monitoring of its ecosystems and adjacent land use are important to select areas for conservation and to improve our understanding of the dynamics in this biome. Land cover mapping of savannas is difficult due to spectral similarity between land cover types resulting from similar vegetation structure, floristically similar components, generalization of land cover classes, and heterogeneity usually expressed as small patch sizes within the natural landscape. These factors are the major contributor to misclassification and low map accuracies among remote sensing studies in savannas. Specific challenges to map the Cerrado's land cover types are related to the spectral similarity between classes of land use and natural vegetation, such as natural grassland vs. cultivated pasture, and forest ecosystem vs. crops. This study seeks to classify and evaluate the land cover patterns across an area ranked as having extremely high priority for future conservation in the Cerrado. The main objective of this study is to identify the representativeness of each vegetation type across the landscape using high to moderate spatial resolution imagery using an automated scheme. A combination of pixel-based and object-based approaches were tested using RapidEye 3A imagery (5m spatial resolution) to classify the Cerrado's major land cover types. The random forest classifier was used to map the major ecosystems present across the area, and demonstrated to have an effective result with 68% of overall accuracy. Post

High-resolution hyperspectral ground mapping for robotic vision

Science.gov (United States)

Neuhaus, Frank; Fuchs, Christian; Paulus, Dietrich

2018-04-01

Recently released hyperspectral cameras use large, mosaiced filter patterns to capture different ranges of the light's spectrum in each of the camera's pixels. Spectral information is sparse, as it is not fully available in each location. We propose an online method that avoids explicit demosaicing of camera images by fusing raw, unprocessed, hyperspectral camera frames inside an ego-centric ground surface map. It is represented as a multilayer heightmap data structure, whose geometry is estimated by combining a visual odometry system with either dense 3D reconstruction or 3D laser data. We use a publicly available dataset to show that our approach is capable of constructing an accurate hyperspectral representation of the surface surrounding the vehicle. We show that in many cases our approach increases spatial resolution over a demosaicing approach, while providing the same amount of spectral information.

A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.

Science.gov (United States)

Yin, Hang; Sweeney, Sarah; Raha, Debasish; Snyder, Michael; Lin, Haifan

2011-12-01

Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP-Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications.

Real-time frequency-to-time mapping based on spectrally-discrete chromatic dispersion.

Science.gov (United States)

Dai, Yitang; Li, Jilong; Zhang, Ziping; Yin, Feifei; Li, Wangzhe; Xu, Kun

2017-07-10

Traditional photonics-assisted real-time Fourier transform (RTFT) usually suffers from limited chromatic dispersion, huge volume, or large time delay and attendant loss. In this paper we propose frequency-to-time mapping (FTM) by spectrally-discrete dispersion to increase frequency sensitivity greatly. The novel media has periodic ON/OFF intensity frequency response while quadratic phase distribution along disconnected channels, which de-chirps matched optical input to repeated Fourier-transform-limited output. Real-time FTM is then obtained within each period. Since only discrete phase retardation rather than continuously-changed true time delay is required, huge equivalent dispersion is then available by compact device. Such FTM is theoretically analyzed, and implementation by cascaded optical ring resonators is proposed. After a numerical example, our theory is demonstrated by a proof-of-concept experiment, where a single loop containing 0.5-meters-long fiber is used. FTM under 400-MHz unambiguous bandwidth and 25-MHz resolution is reported. Highly-sensitive and linear mapping is achieved with 6.25 ps/MHz, equivalent to ~4.6 × 10 4 -km standard single mode fiber. Extended instantaneous bandwidth is expected by ring cascading. Our proposal may provide a promising method for real-time, low-latency Fourier transform.

Monturaqui meteorite impact crater, Chile: A field test of the utility of satellite-based mapping of ejecta at small craters

Science.gov (United States)

Rathbun, K.; Ukstins, I.; Drop, S.

2017-12-01

Monturaqui Crater is a small ( 350 m diameter), simple meteorite impact crater located in the Atacama Desert of northern Chile that was emplaced in Ordovician granite overlain by discontinuous Pliocene ignimbrite. Ejecta deposits are granite and ignimbrite, with lesser amounts of dark impact melt and rare tektites and iron shale. The impact restructured existing drainage systems in the area that have subsequently eroded through the ejecta. Satellite-based mapping and modeling, including a synthesis of photographic satellite imagery and ASTER thermal infrared imagery in ArcGIS, were used to construct a basic geological interpretation of the site with special emphasis on understanding ejecta distribution patterns. This was combined with field-based mapping to construct a high-resolution geologic map of the crater and its ejecta blanket and field check the satellite-based geologic interpretation. The satellite- and modeling-based interpretation suggests a well-preserved crater with an intact, heterogeneous ejecta blanket that has been subjected to moderate erosion. In contrast, field mapping shows that the crater has a heavily-eroded rim and ejecta blanket, and the ejecta is more heterogeneous than previously thought. In addition, the erosion rate at Monturaqui is much higher than erosion rates reported elsewhere in the Atacama Desert. The bulk compositions of the target rocks at Monturaqui are similar and the ejecta deposits are highly heterogeneous, so distinguishing between them with remote sensing is less effective than with direct field observations. In particular, the resolution of available imagery for the site is too low to resolve critical details that are readily apparent in the field on the scale of 10s of cm, and which significantly alter the geologic interpretation. The limiting factors for effective remote interpretation at Monturaqui are its target composition and crater size relative to the resolution of the remote sensing methods employed. This

Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?

Science.gov (United States)

Calabrese, Evan; Badea, Alexandra; Coe, Christopher L; Lubach, Gabriele R; Styner, Martin A; Johnson, G Allan

2014-11-01

Interest in mapping white matter pathways in the brain has peaked with the recognition that altered brain connectivity may contribute to a variety of neurologic and psychiatric diseases. Diffusion tractography has emerged as a popular method for postmortem brain mapping initiatives, including the ex-vivo component of the human connectome project, yet it remains unclear to what extent computer-generated tracks fully reflect the actual underlying anatomy. Of particular concern is the fact that diffusion tractography results vary widely depending on the choice of acquisition protocol. The two major acquisition variables that consume scan time, spatial resolution, and diffusion sampling, can each have profound effects on the resulting tractography. In this analysis, we determined the effects of the temporal tradeoff between spatial resolution and diffusion sampling on tractography in the ex-vivo rhesus macaque brain, a close primate model for the human brain. We used the wealth of autoradiography-based connectivity data available for the rhesus macaque brain to assess the anatomic accuracy of six time-matched diffusion acquisition protocols with varying balance between spatial and diffusion sampling. We show that tractography results vary greatly, even when the subject and the total acquisition time are held constant. Further, we found that focusing on either spatial resolution or diffusion sampling at the expense of the other is counterproductive. A balanced consideration of both sampling domains produces the most anatomically accurate and consistent results. Copyright © 2014 Wiley Periodicals, Inc.

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

DEFF Research Database (Denmark)

Vranken, Charlotte; Deen, Jochem; Dirix, Lieve

2014-01-01

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore...... to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay...... the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes...

A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

Directory of Open Access Journals (Sweden)

Daniel Fulop

2016-10-01

Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

Nominal 30-m Cropland Extent Map of Continental Africa by Integrating Pixel-Based and Object-Based Algorithms Using Sentinel-2 and Landsat-8 Data on Google Earth Engine

Directory of Open Access Journals (Sweden)

Jun Xiong

2017-10-01

Full Text Available A satellite-derived cropland extent map at high spatial resolution (30-m or better is a must for food and water security analysis. Precise and accurate global cropland extent maps, indicating cropland and non-cropland areas, are starting points to develop higher-level products such as crop watering methods (irrigated or rainfed, cropping intensities (e.g., single, double, or continuous cropping, crop types, cropland fallows, as well as for assessment of cropland productivity (productivity per unit of land, and crop water productivity (productivity per unit of water. Uncertainties associated with the cropland extent map have cascading effects on all higher-level cropland products. However, precise and accurate cropland extent maps at high spatial resolution over large areas (e.g., continents or the globe are challenging to produce due to the small-holder dominant agricultural systems like those found in most of Africa and Asia. Cloud-based geospatial computing platforms and multi-date, multi-sensor satellite image inventories on Google Earth Engine offer opportunities for mapping croplands with precision and accuracy over large areas that satisfy the requirements of broad range of applications. Such maps are expected to provide highly significant improvements compared to existing products, which tend to be coarser in resolution, and often fail to capture fragmented small-holder farms especially in regions with high dynamic change within and across years. To overcome these limitations, in this research we present an approach for cropland extent mapping at high spatial resolution (30-m or better using the 10-day, 10 to 20-m, Sentinel-2 data in combination with 16-day, 30-m, Landsat-8 data on Google Earth Engine (GEE. First, nominal 30-m resolution satellite imagery composites were created from 36,924 scenes of Sentinel-2 and Landsat-8 images for the entire African continent in 2015–2016. These composites were generated using a median-mosaic of

Example-Based Super-Resolution Fluorescence Microscopy.

Science.gov (United States)

Jia, Shu; Han, Boran; Kutz, J Nathan

2018-04-23

Capturing biological dynamics with high spatiotemporal resolution demands the advancement in imaging technologies. Super-resolution fluorescence microscopy offers spatial resolution surpassing the diffraction limit to resolve near-molecular-level details. While various strategies have been reported to improve the temporal resolution of super-resolution imaging, all super-resolution techniques are still fundamentally limited by the trade-off associated with the longer image acquisition time that is needed to achieve higher spatial information. Here, we demonstrated an example-based, computational method that aims to obtain super-resolution images using conventional imaging without increasing the imaging time. With a low-resolution image input, the method provides an estimate of its super-resolution image based on an example database that contains super- and low-resolution image pairs of biological structures of interest. The computational imaging of cellular microtubules agrees approximately with the experimental super-resolution STORM results. This new approach may offer potential improvements in temporal resolution for experimental super-resolution fluorescence microscopy and provide a new path for large-data aided biomedical imaging.

Annealing as grown large volume CZT single crystals for increased spectral resolution

International Nuclear Information System (INIS)

Li, Longxia

2008-01-01

The spectroscopic performance of current large-volume Cadmium 10% Zinc Telluride, Cd 0.9 Zn 0.1 Te, (CZT) detectors is impaired by cumulative effect of tellurium precipitates (secondary phases) presented in CZT single-crystal grown by low-pressure Bridgman techniques(1). This statistical effect may limit the energy resolution of large-volume CZT detectors (typically 2-5% at 662 keV for 12-mm thick devices). The stochastic nature of the interaction prevents the use of any electronic or digital charge correction techniques without a significant reduction in the detector efficiency. This volume constraint hampers the utility of CZT since the detectors are inefficient at detecting photons >1MeV and/or in low fluency situations. During the project, seven runs CZT ingots have been grown, in these ingots the indium dopant concentrations have been changed in the range between 0.5ppm to 6ppm. The I-R mapping imaging method has been employed to study the Te-precipitates. The Teprecipitates in as-grown CZT wafers, and after annealing wafers have been systematically studied by using I-R mapping system (home installed, resolution of 1.5 (micro)m). We employed our I-R standard annealing CZT (Zn=4%) procedure or two-steps annealing into radiation CZT (Zn=10%), we achieved the 'non'-Te precipitates (size 10 9-10 (Omega)-cm. We believe that the Te-precipitates are the p-type defects, its reducing number causes the CZT became n+-type, therefore we varied or reduced the indium dapant concentration during the growth and changed the Te-precipitates size and density by using different Cd-temperature and different annealing procedures. We have made the comparisons among Te-precipitates size, density and Indium dopant concentrations, and we found that the CZT with smaller size of Te-precipitates is suitable for radiation uses but non-Te precipitates is impossible to be used in the radiation detectors, because the CZT would became un-dopant or 'intrinsic' with non radiation affection (we

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus).

Science.gov (United States)

Feng, Xiu; Yu, Xiaomu; Fu, Beide; Wang, Xinhua; Liu, Haiyang; Pang, Meixia; Tong, Jingou

2018-04-02

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several

On the downscaling of actual evapotranspiration maps based on combination of MODIS and landsat-based actual evapotranspiration estimates

Science.gov (United States)

Singh, Ramesh K.; Senay, Gabriel B.; Velpuri, Naga Manohar; Bohms, Stefanie; Verdin, James P.

2014-01-01

 Downscaling is one of the important ways of utilizing the combined benefits of the high temporal resolution of Moderate Resolution Imaging Spectroradiometer (MODIS) images and fine spatial resolution of Landsat images. We have evaluated the output regression with intercept method and developed the Linear with Zero Intercept (LinZI) method for downscaling MODIS-based monthly actual evapotranspiration (AET) maps to the Landsat-scale monthly AET maps for the Colorado River Basin for 2010. We used the 8-day MODIS land surface temperature product (MOD11A2) and 328 cloud-free Landsat images for computing AET maps and downscaling. The regression with intercept method does have limitations in downscaling if the slope and intercept are computed over a large area. A good agreement was obtained between downscaled monthly AET using the LinZI method and the eddy covariance measurements from seven flux sites within the Colorado River Basin. The mean bias ranged from −16 mm (underestimation) to 22 mm (overestimation) per month, and the coefficient of determination varied from 0.52 to 0.88. Some discrepancies between measured and downscaled monthly AET at two flux sites were found to be due to the prevailing flux footprint. A reasonable comparison was also obtained between downscaled monthly AET using LinZI method and the gridded FLUXNET dataset. The downscaled monthly AET nicely captured the temporal variation in sampled land cover classes. The proposed LinZI method can be used at finer temporal resolution (such as 8 days) with further evaluation. The proposed downscaling method will be very useful in advancing the application of remotely sensed images in water resources planning and management.

Feasibility of high-resolution one-dimensional relaxation imaging at low magnetic field using a single-sided NMR scanner applied to articular cartilage

Science.gov (United States)

Rössler, Erik; Mattea, Carlos; Stapf, Siegfried

2015-02-01

Low field Nuclear Magnetic Resonance increases the contrast of the longitudinal relaxation rate in many biological tissues; one prominent example is hyaline articular cartilage. In order to take advantage of this increased contrast and to profile the depth-dependent variations, high resolution parameter measurements are carried out which can be of critical importance in an early diagnosis of cartilage diseases such as osteoarthritis. However, the maximum achievable spatial resolution of parameter profiles is limited by factors such as sensor geometry, sample curvature, and diffusion limitation. In this work, we report on high-resolution single-sided NMR scanner measurements with a commercial device, and quantify these limitations. The highest achievable spatial resolution on the used profiler, and the lateral dimension of the sensitive volume were determined. Since articular cartilage samples are usually bent, we also focus on averaging effects inside the horizontally aligned sensitive volume and their impact on the relaxation profiles. Taking these critical parameters into consideration, depth-dependent relaxation time profiles with the maximum achievable vertical resolution of 20 μm are discussed, and are correlated with diffusion coefficient profiles in hyaline articular cartilage in order to reconstruct T2 maps from the diffusion-weighted CPMG decays of apparent relaxation rates.

Fine-scale mapping of vector habitats using very high resolution satellite imagery: a liver fluke case-study.

Science.gov (United States)

De Roeck, Els; Van Coillie, Frieke; De Wulf, Robert; Soenen, Karen; Charlier, Johannes; Vercruysse, Jozef; Hantson, Wouter; Ducheyne, Els; Hendrickx, Guy

2014-12-01

The visualization of vector occurrence in space and time is an important aspect of studying vector-borne diseases. Detailed maps of possible vector habitats provide valuable information for the prediction of infection risk zones but are currently lacking for most parts of the world. Nonetheless, monitoring vector habitats from the finest scales up to farm level is of key importance to refine currently existing broad-scale infection risk models. Using Fasciola hepatica, a parasite liver fluke, as a case in point, this study illustrates the potential of very high resolution (VHR) optical satellite imagery to efficiently and semi-automatically detect detailed vector habitats. A WorldView2 satellite image capable of transmitted by freshwater snails. The vector thrives in small water bodies (SWBs), such as ponds, ditches and other humid areas consisting of open water, aquatic vegetation and/or inundated grass. These water bodies can be as small as a few m2 and are most often not present on existing land cover maps because of their small size. We present a classification procedure based on object-based image analysis (OBIA) that proved valuable to detect SWBs at a fine scale in an operational and semi-automated way. The classification results were compared to field and other reference data such as existing broad-scale maps and expert knowledge. Overall, the SWB detection accuracy reached up to 87%. The resulting fine-scale SWB map can be used as input for spatial distribution modelling of the liver fluke snail vector to enable development of improved infection risk mapping and management advice adapted to specific, local farm situations.

Virginia Base Mapping Program (VBMP) 2002; Multiple Resolutions (1"=100',1"= 200',1"=400' scale) Digital Orthophotography for the South Zone of the Virginia State Plane Grid

Data.gov (United States)

Federal Emergency Management Agency, Department of Homeland Security — These files contain 2-foot GSD high-resolution orthorectified aerial image map products in GeoTIFF version 6.0 file format. GeoTIFF files are uncompressed raster...

Common fixed points of single-valued and multivalued maps

Directory of Open Access Journals (Sweden)

Yicheng Liu

2005-01-01

Full Text Available We define a new property which contains the property (EA for a hybrid pair of single- and multivalued maps and give some new common fixed point theorems under hybrid contractive conditions. Our results extend previous ones. As an application, we give a partial answer to the problem raised by Singh and Mishra.

Detailed Mapping of Historical and Preinstrumental Earthquake Ruptures in Central Asia Using Multi-Scale, Multi-Platform Photogrammetry

Science.gov (United States)

Elliott, A. J.; Walker, R. T.; Parsons, B.; Ren, Z.; Ainscoe, E. A.; Abdrakhmatov, K.; Mackenzie, D.; Arrowsmith, R.; Gruetzner, C.

2016-12-01

In regions of the planet with long historical records, known past seismic events can be attributed to specific fault sources through the identification and measurement of single-event scarps in high-resolution imagery and topography. The level of detail captured by modern remote sensing is now sufficient to map and measure complete earthquake ruptures that were originally only sparsely mapped or overlooked entirely. We can thus extend the record of mapped earthquake surface ruptures into the preinstrumental period and capture the wealth of information preserved in the numerous historical earthquake ruptures throughout regions like Central Asia. We investigate two major late 19th and early 20th century earthquakes that are well located macroseismically but whose fault sources had proved enigmatic in the absence of detailed imagery and topography. We use high-resolution topographic models derived from photogrammetry of satellite, low-altitude, and ground-based optical imagery to map and measure the coseismic scarps of the 1889 M8.3 Chilik, Kazakhstan and 1932 M7.6 Changma, China earthquakes. Measurement of the scarps on the combined imagery and topography reveals the extent and slip distribution of coseismic rupture in each of these events, showing both earthquakes involved multiple faults with variable kinematics. We use a 1-m elevation model of the Changma fault derived from Pleiades satellite imagery to map the changing kinematics of the 1932 rupture along strike. For the 1889 Chilik earthquake we use 1.5-m SPOT-6 satellite imagery to produce a regional elevation model of the fault ruptures, from which we identify three distinct, intersecting fault systems that each have >20 km of fresh, single-event scarps. Along sections of each of these faults we construct high resolution (330 points per sq m) elevation models using quadcopter- and helikite-mounted cameras. From the detailed topography we measure single-event oblique offsets of 6-10 m, consistent with the large

DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.

Directory of Open Access Journals (Sweden)

Ram Vinay Pandey

Full Text Available With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/

Lightweight Hyperspectral Mapping System and a Novel Photogrammetric Processing Chain for UAV-based Sensing

Science.gov (United States)

Suomalainen, Juha; Franke, Jappe; Anders, Niels; Iqbal, Shahzad; Wenting, Philip; Becker, Rolf; Kooistra, Lammert

2014-05-01

We have developed a lightweight Hyperspectral Mapping System (HYMSY) and a novel processing chain for UAV based mapping. The HYMSY consists of a custom pushbroom spectrometer (range 450-950nm, FWHM 9nm, ~20 lines/s, 328 pixels/line), a consumer camera (collecting 16MPix raw image every 2 seconds), a GPS-Inertia Navigation System (GPS-INS), and synchronization and data storage units. The weight of the system at take-off is 2.0kg allowing us to mount it on a relatively small octocopter. The novel processing chain exploits photogrammetry in the georectification process of the hyperspectral data. At first stage the photos are processed in a photogrammetric software producing a high-resolution RGB orthomosaic, a Digital Surface Model (DSM), and photogrammetric UAV/camera position and attitude at the moment of each photo. These photogrammetric camera positions are then used to enhance the internal accuracy of GPS-INS data. These enhanced GPS-INS data are then used to project the hyperspectral data over the photogrammetric DSM, producing a georectified end product. The presented photogrammetric processing chain allows fully automated georectification of hyperspectral data using a compact GPS-INS unit while still producingin UAV use higher georeferencing accuracy than would be possible using the traditional processing method. During 2013, we have operated HYMSY on 150+ octocopter flights at 60+ sites or days. On typical flight we have produced for a 2-10ha area: a RGB orthoimagemosaic at 1-5cm resolution, a DSM in 5-10cm resolution, and hyperspectral datacube at 10-50cm resolution. The targets have mostly consisted of vegetated targets including potatoes, wheat, sugar beets, onions, tulips, coral reefs, and heathlands,. In this poster we present the Hyperspectral Mapping System and the photogrammetric processing chain with some of our first mapping results.

GERLUMPH DATA RELEASE 1: HIGH-RESOLUTION COSMOLOGICAL MICROLENSING MAGNIFICATION MAPS AND eResearch TOOLS

International Nuclear Information System (INIS)

Vernardos, G.; Fluke, C. J.; Croton, D.; Bate, N. F.

2014-01-01

As synoptic all-sky surveys begin to discover new multiply lensed quasars, the flow of data will enable statistical cosmological microlensing studies of sufficient size to constrain quasar accretion disk and supermassive black hole properties. In preparation for this new era, we are undertaking the GPU-Enabled, High Resolution cosmological MicroLensing parameter survey (GERLUMPH). We present here the GERLUMPH Data Release 1, which consists of 12,342 high resolution cosmological microlensing magnification maps and provides the first uniform coverage of the convergence, shear, and smooth matter fraction parameter space. We use these maps to perform a comprehensive numerical investigation of the mass-sheet degeneracy, finding excellent agreement with its predictions. We study the effect of smooth matter on microlensing induced magnification fluctuations. In particular, in the minima and saddle-point regions, fluctuations are enhanced only along the critical line, while in the maxima region they are always enhanced for high smooth matter fractions (≈0.9). We describe our approach to data management, including the use of an SQL database with a Web interface for data access and online analysis, obviating the need for individuals to download large volumes of data. In combination with existing observational databases and online applications, the GERLUMPH archive represents a fundamental component of a new microlensing eResearch cloud. Our maps and tools are publicly available at http://gerlumph.swin.edu.au/

GERLUMPH DATA RELEASE 1: HIGH-RESOLUTION COSMOLOGICAL MICROLENSING MAGNIFICATION MAPS AND eResearch TOOLS

Energy Technology Data Exchange (ETDEWEB)

Vernardos, G.; Fluke, C. J.; Croton, D. [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria, 3122 (Australia); Bate, N. F. [Sydney Institute for Astronomy, School of Physics, A28, University of Sydney, NSW, 2006 (Australia)

2014-03-01

As synoptic all-sky surveys begin to discover new multiply lensed quasars, the flow of data will enable statistical cosmological microlensing studies of sufficient size to constrain quasar accretion disk and supermassive black hole properties. In preparation for this new era, we are undertaking the GPU-Enabled, High Resolution cosmological MicroLensing parameter survey (GERLUMPH). We present here the GERLUMPH Data Release 1, which consists of 12,342 high resolution cosmological microlensing magnification maps and provides the first uniform coverage of the convergence, shear, and smooth matter fraction parameter space. We use these maps to perform a comprehensive numerical investigation of the mass-sheet degeneracy, finding excellent agreement with its predictions. We study the effect of smooth matter on microlensing induced magnification fluctuations. In particular, in the minima and saddle-point regions, fluctuations are enhanced only along the critical line, while in the maxima region they are always enhanced for high smooth matter fractions (≈0.9). We describe our approach to data management, including the use of an SQL database with a Web interface for data access and online analysis, obviating the need for individuals to download large volumes of data. In combination with existing observational databases and online applications, the GERLUMPH archive represents a fundamental component of a new microlensing eResearch cloud. Our maps and tools are publicly available at http://gerlumph.swin.edu.au/.

Smartphones Based Mobile Mapping Systems

Directory of Open Access Journals (Sweden)

A. Al-Hamad

2014-06-01

Full Text Available The past 20 years have witnessed an explosive growth in the demand for geo-spatial data. This demand has numerous sources and takes many forms; however, the net effect is an ever-increasing thirst for data that is more accurate, has higher density, is produced more rapidly, and is acquired less expensively. For mapping and Geographic Information Systems (GIS projects, this has been achieved through the major development of Mobile Mapping Systems (MMS. MMS integrate various navigation and remote sensing technologies which allow mapping from moving platforms (e.g. cars, airplanes, boats, etc. to obtain the 3D coordinates of the points of interest. Such systems obtain accuracies that are suitable for all but the most demanding mapping and engineering applications. However, this accuracy doesn't come cheaply. As a consequence of the platform and navigation and mapping technologies used, even an "inexpensive" system costs well over 200 000 USD. Today's mobile phones are getting ever more sophisticated. Phone makers are determined to reduce the gap between computers and mobile phones. Smartphones, in addition to becoming status symbols, are increasingly being equipped with extended Global Positioning System (GPS capabilities, Micro Electro Mechanical System (MEMS inertial sensors, extremely powerful computing power and very high resolution cameras. Using all of these components, smartphones have the potential to replace the traditional land MMS and portable GPS/GIS equipment. This paper introduces an innovative application of smartphones as a very low cost portable MMS for mapping and GIS applications.

A high-resolution map of the three-dimensional chromatin interactome in human cells.

Science.gov (United States)

Jin, Fulai; Li, Yan; Dixon, Jesse R; Selvaraj, Siddarth; Ye, Zhen; Lee, Ah Young; Yen, Chia-An; Schmitt, Anthony D; Espinoza, Celso A; Ren, Bing

2013-11-14

A large number of cis-regulatory sequences have been annotated in the human genome, but defining their target genes remains a challenge. One strategy is to identify the long-range looping interactions at these elements with the use of chromosome conformation capture (3C)-based techniques. However, previous studies lack either the resolution or coverage to permit a whole-genome, unbiased view of chromatin interactions. Here we report a comprehensive chromatin interaction map generated in human fibroblasts using a genome-wide 3C analysis method (Hi-C). We determined over one million long-range chromatin interactions at 5-10-kb resolution, and uncovered general principles of chromatin organization at different types of genomic features. We also characterized the dynamics of promoter-enhancer contacts after TNF-α signalling in these cells. Unexpectedly, we found that TNF-α-responsive enhancers are already in contact with their target promoters before signalling. Such pre-existing chromatin looping, which also exists in other cell types with different extracellular signalling, is a strong predictor of gene induction. Our observations suggest that the three-dimensional chromatin landscape, once established in a particular cell type, is relatively stable and could influence the selection or activation of target genes by a ubiquitous transcription activator in a cell-specific manner.

destiny: diffusion maps for large-scale single-cell data in R.

Science.gov (United States)

Angerer, Philipp; Haghverdi, Laleh; Büttner, Maren; Theis, Fabian J; Marr, Carsten; Buettner, Florian

2016-04-15

: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming. destiny is an open-source R/Bioconductor package "bioconductor.org/packages/destiny" also available at www.helmholtz-muenchen.de/icb/destiny A detailed vignette describing functions and workflows is provided with the package. carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The MAPS-based vertex detector for the STAR experiment: Lessons learned and performance

Energy Technology Data Exchange (ETDEWEB)

Contin, Giacomo, E-mail: gcontin@lbl.gov

2016-09-21

The PiXeL detector (PXL) of the STAR experiment at RHIC is the first application of the state-of-the-art thin Monolithic Active Pixel Sensors (MAPS) technology in a collider environment. The PXL, together with the Intermediate Silicon Tracker (IST) and the Silicon Strip Detector (SSD), form the Heavy Flavor Tracker (HFT), which has been designed to improve the vertex resolution and extend the STAR measurement capabilities in the heavy flavor domain, providing a clean probe for studying the Quark–Gluon Plasma. The two PXL layers are placed at a radius of 2.8 and 8 cm from the beam line, respectively, and is based on ultra-thin high resolution MAPS sensors. The sensor features 20.7 μm pixel pitch, 185.6 μs readout time and 170 mW/cm{sup 2} power dissipation. The detector is air-cooled, allowing a global material budget of 0.4% radiation length on the innermost layer. A novel mechanical approach to detector insertion allows for fast installation and integration of the pixel sub detector. The HFT took data in Au+Au collisions at 200 GeV during the 2014 RHIC run. Modified during the RHIC shutdown to improve its reliability, material budget, and tracking capabilities, the HFT took data in p+p and p+Au collisions at √s{sub NN}=200 GeV in the 2015 RHIC run. In this paper we present detector specifications, experience from the construction and operations, and lessons learned. We also show preliminary results from 2014 Au+Au data analyses, demonstrating the capabilities of charm reconstruction with the HFT. - Highlights: • First MAPS-based vertex detector in a collider experiment. • Achieved low material budget of 0.39% of radiation length per detector layer. • Track pointing resolution to the primary vertex better than 10⊕24 GeV/p×c μm. • Gain in significance for the topological reconstruction of the D{sup 0}−>K+π decay in STAR. • Observed latch-up induced damage of MAPS sensors.

Superior cognitive mapping through single landmark-related learning than through boundary-related learning.

Science.gov (United States)

Zhou, Ruojing; Mou, Weimin

2016-08-01

Cognitive mapping is assumed to be through hippocampus-dependent place learning rather than striatum-dependent response learning. However, we proposed that either type of spatial learning, as long as it involves encoding metric relations between locations and reference points, could lead to a cognitive map. Furthermore, the fewer reference points to specify individual locations, the more accurate a cognitive map of these locations will be. We demonstrated that participants have more accurate representations of vectors between 2 locations and of configurations among 3 locations when locations are individually encoded in terms of a single landmark than when locations are encoded in terms of a boundary. Previous findings have shown that learning locations relative to a boundary involve stronger place learning and higher hippocampal activation whereas learning relative to a single landmark involves stronger response learning and higher striatal activation. Recognizing this, we have provided evidence challenging the cognitive map theory but favoring our proposal. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Landscape mapping MAV using single image perspective cues

CSIR Research Space (South Africa)

Tekane, YC

2015-01-01

Full Text Available in order to do mapping, our method does require a 3D model. Instead, our method first classifies the type of site the MAV is in, and the uses vision algorithms based on perspective cues to estimate the landscape location and the do mapping. We tested our...

High-resolution mapping reveals links of HP1 with active and inactive chromatin components.

Directory of Open Access Journals (Sweden)

Elzo de Wit

2007-03-01

Full Text Available Heterochromatin protein 1 (HP1 is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5' regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2, which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5' ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

High Resolution Tracking Devices Based on Capillaries Filled with Liquid Scintillator

CERN Multimedia

Bonekamper, D; Vassiltchenko, V; Wolff, T

2002-01-01

%RD46 %title\\\\ \\\\The aim of the project is to develop high resolution tracking devices based on thin glass capillary arrays filled with liquid scintillator. This technique provides high hit densities and a position resolution better than 20 $\\mu$m. Further, their radiation hardness makes them superior to other types of tracking devices with comparable performance. Therefore, the technique is attractive for inner tracking in collider experiments, microvertex devices, or active targets for short-lived particle detection. High integration levels in the read-out based on the use of multi-pixel photon detectors and the possibility of optical multiplexing allow to reduce considerably the number of output channels, and, thus, the cost for the detector.\\\\ \\\\New optoelectronic devices have been developed and tested: the megapixel Electron Bombarded CCD (EBCCD), a high resolution image-detector having an outstanding capability of single photo-electron detection; the Vacuum Image Pipeline (VIP), a high-speed gateable pi...

One arc-minute resolution maps of the Orion Nebula at 20, 50, and 100 microns

International Nuclear Information System (INIS)

Werner x , M.W.; Gatley, I.; Harper, D.A.; Becklin, E.E.; Loewenstein, R.F.; Telesco, C.M.; Thronson, H.A.

1976-01-01

The central 5' of the Orion Nebula has been mapped with 1' resolution at 50 μ and 100 μ, using the NASA 91 cm Airborne Infrared Telescope; a new 20 μ map with similar resolution is presented as well. At all three wavelengths a pronounced maximum in the surface brightness is observed at the infrared cluster, where the total 10 to 1000 μ luminosity into a 1' beam is approx.7 x 10 4 L/sub sun/. The spatial and temperature resolution of these data allow us to reach the following conclusions about the nature of the far-infrared emission from this source: The total luminosity of the infrared cluster is in excess of 1.2 x 10 5 L/sub sun/. Heating by both the infrared cluster and the Trapezium stars is important in producing far-infrared emission associated with the central ridge of the molecular cloud. The infrared cluster is located within the molecular ridge, and the Trapezium stars are probably no further than 0.1 pc from the molecular cloud. Far-infrared emission is seen from an optically prominent ionization front to the southeast of the Trapezium. The emission is produced by material at or near the H I--H II boundary which is heated directly by the Trapezium stars

Delineation of wetland areas from high resolution WorldView-2 data by object-based method

International Nuclear Information System (INIS)

Hassan, N; Hamid, J R A; Adnan, N A; Jaafar, M

2014-01-01

Various classification methods are available that can be used to delineate land cover types. Object-based is one of such methods for delineating the land cover from satellite imageries. This paper focuses on the digital image processing aspects of discriminating wetland areas via object-based method using high resolution satellite multispectral WorldView-2 image data taken over part of Penang Island region. This research is an attempt to improve the wetland area delineation in conjunction with a range of classification techniques which can be applied to satellite data with high spatial and spectral resolution such as World View 2. The intent is to determine a suitable approach to delineate and map these wetland areas more appropriately. There are common parameters to take into account that are pivotal in object-based method which are the spatial resolution and the range of spectral channels of the imaging sensor system. The preliminary results of the study showed object-based analysis is capable of delineating wetland region of interest with an accuracy that is acceptable to the required tolerance for land cover classification

Towards an EO-based Landslide Web Mapping and Monitoring Service

Science.gov (United States)

Hölbling, Daniel; Weinke, Elisabeth; Albrecht, Florian; Eisank, Clemens; Vecchiotti, Filippo; Friedl, Barbara; Kociu, Arben

2017-04-01

National and regional authorities and infrastructure maintainers in mountainous regions require accurate knowledge of the location and spatial extent of landslides for hazard and risk management. Information on landslides is often collected by a combination of ground surveying and manual image interpretation following landslide triggering events. However, the high workload and limited time for data acquisition result in a trade-off between completeness, accuracy and detail. Remote sensing data offers great potential for mapping and monitoring landslides in a fast and efficient manner. While facing an increased availability of high-quality Earth Observation (EO) data and new computational methods, there is still a lack in science-policy interaction and in providing innovative tools and methods that can easily be used by stakeholders and users to support their daily work. Taking up this issue, we introduce an innovative and user-oriented EO-based web service for landslide mapping and monitoring. Three central design components of the service are presented: (1) the user requirements definition, (2) the semi-automated image analysis methods implemented in the service, and (3) the web mapping application with its responsive user interface. User requirements were gathered during semi-structured interviews with regional authorities. The potential users were asked if and how they employ remote sensing data for landslide investigation and what their expectations to a landslide web mapping service regarding reliability and usability are. The interviews revealed the capability of our service for landslide documentation and mapping as well as monitoring of selected landslide sites, for example to complete and update landslide inventory maps. In addition, the users see a considerable potential for landslide rapid mapping. The user requirements analysis served as basis for the service concept definition. Optical satellite imagery from different high resolution (HR) and very high

A 30 m Resolution Surface Water Mask Including Estimation of Positional and Thematic Differences Using Landsat 8, SRTM and OpenStreetMap: A Case Study in the Murray-Darling Basin, Australia

Directory of Open Access Journals (Sweden)

Gennadii Donchyts

2016-05-01

Full Text Available Accurate maps of surface water are essential for many environmental applications. Surface water maps can be generated by combining measurements from multiple sources. Precise estimation of surface water using satellite imagery remains a challenging task due to the sensor limitations, complex land cover, topography, and atmospheric conditions. As a complementary dataset, in the case of hilly landscapes, a drainage network can be extracted from high-resolution digital elevation models. Additionally, Volunteered Geographic Information (VGI initiatives, such as OpenStreetMap, can also be used to produce high-resolution surface water masks. In this study, we derive a high-resolution water mask using Landsat 8 imagery and OpenStreetMap as well as (potential a drainage network using 30 m SRTM. Our approach to derive a surface water mask from Landsat 8 imagery comprises the use of a lower 15% percentile of Landsat 8 Top of Atmosphere (TOA reflectance from 2013 to 2015. We introduce a new non-parametric unsupervised method based on the Canny edge filter and Otsu thresholding to detect water in flat areas. For hilly areas, the method is extended with an additional supervised classification step used to refine the water mask. We applied the method across the Murray-Darling basin, Australia. Differences between our new Landsat-based water mask and the OpenStreetMap water mask regarding positional differences along the rivers and overall coverage were analyzed. Our results show that about 50% of the OpenStreetMap linear water features can be confirmed using the water mask extracted from Landsat 8 imagery and the drainage network derived from SRTM. We also show that the observed distances between river features derived from OpenStreetMap and Landsat 8 are mostly smaller than 60 m. The differences between the new water mask and SRTM-based linear features and hilly areas are slightly larger (110 m. The overall agreement between OpenStreetMap and Landsat 8 water

Method for mapping population-based case-control studies: an application using generalized additive models

Directory of Open Access Journals (Sweden)

Aschengrau Ann

2006-06-01

Full Text Available Abstract Background Mapping spatial distributions of disease occurrence and risk can serve as a useful tool for identifying exposures of public health concern. Disease registry data are often mapped by town or county of diagnosis and contain limited data on covariates. These maps often possess poor spatial resolution, the potential for spatial confounding, and the inability to consider latency. Population-based case-control studies can provide detailed information on residential history and covariates. Results Generalized additive models (GAMs provide a useful framework for mapping point-based epidemiologic data. Smoothing on location while controlling for covariates produces adjusted maps. We generate maps of odds ratios using the entire study area as a reference. We smooth using a locally weighted regression smoother (loess, a method that combines the advantages of nearest neighbor and kernel methods. We choose an optimal degree of smoothing by minimizing Akaike's Information Criterion. We use a deviance-based test to assess the overall importance of location in the model and pointwise permutation tests to locate regions of significantly increased or decreased risk. The method is illustrated with synthetic data and data from a population-based case-control study, using S-Plus and ArcView software. Conclusion Our goal is to develop practical methods for mapping population-based case-control and cohort studies. The method described here performs well for our synthetic data, reproducing important features of the data and adequately controlling the covariate. When applied to the population-based case-control data set, the method suggests spatial confounding and identifies statistically significant areas of increased and decreased odds ratios.

A system and method for online high-resolution mapping of gastric slow-wave activity.

Science.gov (United States)

Bull, Simon H; O'Grady, Gregory; Du, Peng; Cheng, Leo K

2014-11-01

High-resolution (HR) mapping employs multielectrode arrays to achieve spatially detailed analyses of propagating bioelectrical events. A major current limitation is that spatial analyses must currently be performed "off-line" (after experiments), compromising timely recording feedback and restricting experimental interventions. These problems motivated development of a system and method for "online" HR mapping. HR gastric recordings were acquired and streamed to a novel software client. Algorithms were devised to filter data, identify slow-wave events, eliminate corrupt channels, and cluster activation events. A graphical user interface animated data and plotted electrograms and maps. Results were compared against off-line methods. The online system analyzed 256-channel serosal recordings with no unexpected system terminations with a mean delay 18 s. Activation time marking sensitivity was 0.92; positive predictive value was 0.93. Abnormal slow-wave patterns including conduction blocks, ectopic pacemaking, and colliding wave fronts were reliably identified. Compared to traditional analysis methods, online mapping had comparable results with equivalent coverage of 90% of electrodes, average RMS errors of less than 1 s, and CC of activation maps of 0.99. Accurate slow-wave mapping was achieved in near real-time, enabling monitoring of recording quality and experimental interventions targeted to dysrhythmic onset. This work also advances the translation of HR mapping toward real-time clinical application.

4D super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues.

Directory of Open Access Journals (Sweden)

David Baddeley

Full Text Available BACKGROUND: Optical super-resolution imaging of fluorescently stained biological samples is rapidly becoming an important tool to investigate protein distribution at the molecular scale. It is therefore important to develop practical super-resolution methods that allow capturing the full three-dimensional nature of biological systems and also can visualize multiple protein species in the same sample. METHODOLOGY/PRINCIPAL FINDINGS: We show that the use of a combination of conventional near-infrared dyes, such as Alexa 647, Alexa 680 and Alexa 750, all excited with a 671 nm diode laser, enables 3D multi-colour super-resolution imaging of complex biological samples. Optically thick samples, including human tissue sections, cardiac rat myocytes and densely grown neuronal cultures were imaged with lateral resolutions of ∼15 nm (std. dev. while reducing marker cross-talk to <1%. Using astigmatism an axial resolution of ∼65 nm (std. dev. was routinely achieved. The number of marker species that can be distinguished depends on the mean photon number of single molecule events. With the typical photon yields from Alexa 680 of ∼2000 up to 5 markers may in principle be resolved with <2% crosstalk. CONCLUSIONS/SIGNIFICANCE: Our approach is based entirely on the use of conventional, commercially available markers and requires only a single laser. It provides a very straightforward way to investigate biological samples at the nanometre scale and should help establish practical 4D super-resolution microscopy as a routine research tool in many laboratories.

BaseMap

Data.gov (United States)

California Natural Resource Agency — The goal of this project is to provide a convenient base map that can be used as a starting point for CA projects. It's simple, but designed to work at a number of...

Spatiotemporal High-Resolution Cloud Mapping with a Ground-Based IR Scanner

NARCIS (Netherlands)

Brede, Benjamin; Thies, Boris; Bendix, Jörg; Feister, Uwe

2017-01-01

The high spatiotemporal variability of clouds requires automated monitoring systems. This study presents a retrieval algorithm that evaluates observations of a hemispherically scanning thermal infrared radiometer, the NubiScope, to produce georeferenced, spatially explicit cloud maps. The algorithm

Multi-resolution simulation of focused ultrasound propagation through ovine skull from a single-element transducer

Science.gov (United States)

Yoon, Kyungho; Lee, Wonhye; Croce, Phillip; Cammalleri, Amanda; Yoo, Seung-Schik

2018-05-01

Transcranial focused ultrasound (tFUS) is emerging as a non-invasive brain stimulation modality. Complicated interactions between acoustic pressure waves and osseous tissue introduce many challenges in the accurate targeting of an acoustic focus through the cranium. Image-guidance accompanied by a numerical simulation is desired to predict the intracranial acoustic propagation through the skull; however, such simulations typically demand heavy computation, which warrants an expedited processing method to provide on-site feedback for the user in guiding the acoustic focus to a particular brain region. In this paper, we present a multi-resolution simulation method based on the finite-difference time-domain formulation to model the transcranial propagation of acoustic waves from a single-element transducer (250 kHz). The multi-resolution approach improved computational efficiency by providing the flexibility in adjusting the spatial resolution. The simulation was also accelerated by utilizing parallelized computation through the graphic processing unit. To evaluate the accuracy of the method, we measured the actual acoustic fields through ex vivo sheep skulls with different sonication incident angles. The measured acoustic fields were compared to the simulation results in terms of focal location, dimensions, and pressure levels. The computational efficiency of the presented method was also assessed by comparing simulation speeds at various combinations of resolution grid settings. The multi-resolution grids consisting of 0.5 and 1.0 mm resolutions gave acceptable accuracy (under 3 mm in terms of focal position and dimension, less than 5% difference in peak pressure ratio) with a speed compatible with semi real-time user feedback (within 30 s). The proposed multi-resolution approach may serve as a novel tool for simulation-based guidance for tFUS applications.

Remote sensing of potential lunar resources. 2: High spatial resolution mapping of spectral reflectance ratios and implications for nearside mare TiO2 content`

Science.gov (United States)

Melendrez, David E.; Johnson, Jeffrey R.; Larson, Stephen M.; Singer, Robert B.

1994-01-01

High spatial resolution maps illustrating variations in spectral reflectance 400/560 nm ratio values have been generated for the following mare regions: (1) the border between southern Mare Serenitatis and northern Mare Tranquillitatis (including the MS-2 standard area and Apollo 17 landing site), (2) central Mare Tranquillitatis, (3) Oceanus Procellarum near Seleucus, and (4) southern Oceanus Procellarum and Flamsteed. We have also obtained 320-1000 nm reflectance spectra of several sites relative to MS-2 to facilitate scaling of the images and provide additional information on surface composition. Inferred TiO2 abundances for these mare regions have been determined using an empirical calibration which relates the weight percent TiO2 in mature mare regolith to the observed 400/560 nm ratio. Mare areas with high TiO2 abundances are probably rich in ilmenite (FeTiO3) a potential lunar resource. The highest potential TiO2 concentrations we have identified in the nearside maria occur in central Mare Tranquillitatis. Inferred TiO2 contents for these areas are greater than 9 wt% and are spatially consistent with the highest-TiO2 regions mapped previously at lower spatial resolution. We note that the morphology of surface units with high 400/560 nm ratio values increases in complexity at higher spatial resolutions. Comparisons have been made with previously published geologic maps, Lunar Orbiter IV, and ground-based images, and some possible morphologic correlatins have been found between our mapped 400/560 nm ratio values and volcanic landforms such as lava flows, mare domes, and collapse pits.

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

Science.gov (United States)

Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

2018-04-04

The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Evolution of dislocation structures following a change in loading conditions studied by in situ high resolution reciprocal space mapping