A near real-time water surface detection method based on HSV transformation of MODIS multi-Spectral time series data

In the face of global population growth and the uneven distribution of water supply, a better knowledge of the spatial and temporal distribution of surface water resources is critical. Remote sensing provides a synoptic view of ongoing processes, which addresses the intricate nature of water surfaces and allows an assessment of the pressures placed on aquatic ecosystems. However, the main challenge in identifying water surfaces from remotely sensed data is the high variability of spectral signatures, both in space and time. In the last 10 years only a few operational methods have been proposed to map or monitor surface water at continental or global scale, and each of them show limitations. The objective of this study is to develop and demonstrate the adequacy of a generic multi-temporal and multi-spectral image analysis method to detect water surfaces automatically, and to monitor them in near-real-time. The proposed approach, based on a transformation of the RGB color space into HSV, provides dynamic information at the continental scale. The validation of the algorithm showed very few omission errors and no commission errors. It demonstrates the ability of the proposed algorithm to perform as effectively as human interpretation of the images. The validation of the permanent water surface product with an independent dataset derived from high resolution imagery, showed an accuracy of 91.5% and few commission errors. Potential applications of the proposed method have been identified and discussed. The methodology that has been developed 27 is generic: it can be applied to sensors with similar bands with good reliability, and minimal effort. Moreover, this experiment at continental scale showed that the methodology is efficient for a large range of environmental conditions. Additional preliminary tests over other continents indicate that the proposed methodology could also be applied at the global scale without too many difficulties

Spectral characteristics and thermal evolution of long-period gratings in photonic crystal fibers fabricated with a near-IR radiation femtosecond laser using point-by-point inscription

The spectral properties of long-period gratings (LPGs) fabricated in photonic crystal fibers using femtosecond laser pulses by the point-by-point technique, without oil-immersion of the fiber, are investigated in detail. Postfabrication spectral monitoring at room temperature showed significant long-term instability of the gratings and stable spectra only after 600 h. The stabilized spectral properties of the gratings improved with increasing annealing temperature. The observed changes in resonant wavelength, optical strength, and grating birefringence were correlated to the laser inscription energy and were further used to study the mechanism of femtosecond inscription. Furthermore, the femtosecond-laser inscribed LPGs were compared to electric-arc fabricated LPGs. Comparison of experimental results with theoretical models of LPGs and laser propagation during inscription indicate that the major processes responsible for the index change are permanent compaction and thermally induced strain, the latter can be significantly changed through annealing. © 2011 Optical Society of America.

Efficient lasing at near 3μm by a Dy-doped ZBLAN fiber laser pumped at ∼1.1 μm by an Yb fiber laser

Operation of a single-clad Dy 3+-doped ZrF 4-BaF 2-LaF 3-AlF 3-NaF (ZBLAN) fiber laser operating at mid-infrared near 3 μm is presented. The laser is pumped by an Yb 3+-doped silica fiber laser centered at 1088 nm. An output of near 0.1 W with a slope efficiency of up to 23% with respect to absorbed pump power was measured. The laser performance, theoretical modeling and laser spectrum of Dy fiber laser system with respect to various cavity losses are studied. The experimental slope efficiency is more than 4.5 times higher than the previous demonstration, and is 64% of the Stokes efficiency limit. The efficiency was improved by using cavity mirrors of reflectivities of 99 and 50%. The emission central wavelength and spectral width are found to be dependent on the pump power and output coupler, reflectivity. © 2011 by Astro Ltd., published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA.

Analysis Of The Dna Fourier Transform-infrared Microspectroscopic Signature Using An All-reflecting Objective.

The Fourier transform-infrared (FT-IR) signature of dry samples of DNA and DNA-polypeptide complexes, as studied by IR microspectroscopy using a diamond attenuated total reflection (ATR) objective, has revealed important discriminatory characteristics relative to the PO2(-) vibrational stretchings. However, DNA IR marks that provide information on the sample's richness in hydrogen bonds have not been resolved in the spectral profiles obtained with this objective. Here we investigated the performance of an all reflecting objective (ARO) for analysis of the FT-IR signal of hydrogen bonds in DNA samples differing in base richness types (salmon testis vs calf thymus). The results obtained using the ARO indicate prominent band peaks at the spectral region representative of the vibration of nitrogenous base hydrogen bonds and of NH and NH2 groups. The band areas at this spectral region differ in agreement with the DNA base richness type when using the ARO. A peak assigned to adenine was more evident in the AT-rich salmon DNA using either the ARO or the ATR objective. It is concluded that, for the discrimination of DNA IR hydrogen bond vibrations associated with varying base type proportions, the use of an ARO is recommended.

In situ infrared (FTIR) study of the mechanism of the borohydride oxidation reaction

Early reports stated that Au was a catalyst of choice for the BOR because it would yield a near complete faradaic efficiency. However, it has recently been suggested that gold could yield to some extent the heterogeneous hydrolysis of BH(4)(-),therefore lowering the electron count per BH(4)(-), especially at low potential. Actually, the blur will exist regarding the BOR mechanism on Au as long as no physical proof regarding the reaction intermediates is not put forward. In that frame, in situ physical techniques like FTIR exhibit some interest to study the BOR. Consequently, in situ infrared reflectance spectroscopy measurements (SPAIRS technique) have been performed in 1 M NaOH/1 M NaBH(4) on a gold electrode with the aim to detect the intermediate species. We monitored several bands in B-H ((nu) over bar similar to 1180,1080 and 972 cm(-1)) and B-O bond regions ((nu) over bar =1325 and similar to 1425cm(-1)), which appear sequentially as a function of the electrode polarization. These absorption bands are assigned to BH(3), BH(2) and BO(2)(-) species. At the light of the experimental results, possible initial elementary steps of the BOR on gold electrode have been proposed and discussed according to the relevant literature data.

Spectral tuning and the visual ecology of mantis shrimps

The compound eyes of mantis shrimps (stomatopod crustaceans) include an unparalleled diversity of visual pigments and spectral receptor classes in retinas of each species. We compared the visual pigment and spectral receptor classes of 12 species of gonodactyloid stomatopods from a variety of photo environments, from intertidal to deep water ( > 50 m), to learn how spectral tuning in the different photoreceptor types is modified within different photic environments. Results show that receptors of the peripheral photoreceptors, those outside the midband which are responsible for standard visual tasks such as spatial vision and motion detection, reveal the well-known pattern of decreasing lambda(max) with increasing depth. Receptors of midband rows 5 and 6, which are specialized for polarization vision, are similar in all species, having visual lambda(max)-values near 500 nm, independent of depth. Finally the spectral receptors of midband rows 1 to 4 are tuned for maximum coverage of the spectrum of irradiance available in the habitat of each species. The quality of the visual worlds experienced by each species we studied must vary considerably, but all appear to exploit the full capabilities offered by their complex visual systems.

Hydrofluoric acid pre-treatment for improving 13C CPMAS NMR spectral quality of forest soils in south-east Queensland, Australia

Hydrofluoric acid (HF) was used to pre-treat forest soils of south-east Queensland for assessing the effectiveness of iron (Fe) removal, carbon (C) composition using C-13 cross-polarisation (CP) with magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) before and after the HF pre-treatment, and the improvement of C-13 CPMAS NMR spectra. Soil samples were collected from 4 experimental sites of different soil types, harvest residue management or prescribed burning, and tree species. More than 86% of Fe was in all soil types removed by the HF treatment. The C-13 NMR spectral quality was improved with increased resolution, especially in the alkyl C and O-alkyl C regions, and reduced NMR run-time (1-5 h per sample compared with >20 h per sample without the pre-treatment). The C composition appeared to alter slightly after the pre-treatment, but this might be largely due to improved spectrometer conditions and increased resolution leading to more accurate NMR spectral integration. Organic C recovery after HF pre-treatment varied with soil types and forest management, and soluble soil organic matter (SOM) could be lost during the pre-treatment. The Fourier Transform-Infrared (FT-IR) spectra of HF extracts indicated the preferential removal of carboxylic C groups during the pre-treatment, but this could also be due to adsorbed water on the mineral matter. The NMR spectra revealed some changes in C composition and quality due to residue management and decomposition. Overall, the HF treatment was a useful pre-treatment for obtaining semi-quantitative C-13 CPMAS NMR spectra of subtropical Australian forest soils.

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Saturació tenar d’oxigen (StO2) mesurada de forma no invasiva mitjançant l’espectroscòpia (NIRS) durant la prova de respiració espontània com a predictor d’èxit de la retirada de la ventilació mecànica.

Es tracta d’un estudi unicèntric prospectiu amb 30 pacients sotmesos a ventilació mecànica i considerats candidats a la retirada del suport ventilatori per part del seu equip mèdic assistencial. L’objectiu de l’estudi és determinar si els canvis de la saturació tenar d’oxigen (StO2), així com les corves de desoxigenació i reoxigenació de StO2 derivades d’una maniobra d’isquèmia vascular transitòria, mesurades de forma no invasiva mitjançant l’espectroscòpia en el límit de la llum infrarroja (Near Infra Red Spectroscopy - NIRS), són útils com a predictors del fracàs de l’extubació en el procés de retirada de la ventilació mecànica.

Evaluation of a linear spectral mixture model and vegetation indices (NDVI and EVI) in a study of schistosomiasis mansoni and Biomphalaria glabrata distribution in the state of Minas Gerais, Brazil

This paper analyses the associations between Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) on the prevalence of schistosomiasis and the presence of Biomphalaria glabrata in the state of Minas Gerais (MG), Brazil. Additionally, vegetation, soil and shade fraction images were created using a Linear Spectral Mixture Model (LSMM) from the blue, red and infrared channels of the Moderate Resolution Imaging Spectroradiometer spaceborne sensor and the relationship between these images and the prevalence of schistosomiasis and the presence of B. glabrata was analysed. First, we found a high correlation between the vegetation fraction image and EVI and second, a high correlation between soil fraction image and NDVI. The results also indicate that there was a positive correlation between prevalence and the vegetation fraction image (July 2002), a negative correlation between prevalence and the soil fraction image (July 2002) and a positive correlation between B. glabrata and the shade fraction image (July 2002). This paper demonstrates that the LSMM variables can be used as a substitute for the standard vegetation indices (EVI and NDVI) to determine and delimit risk areas for B. glabrata and schistosomiasis in MG, which can be used to improve the allocation of resources for disease control.

Transmission Fourier transform infrared microspectroscopy allows simultaneous assessment of cutin and cell-wall polysaccharides of Arabidopsis petals.

A procedure for the simultaneous analysis of cell-wall polysaccharides, amides and aliphatic polyesters by transmission Fourier transform infrared microspectroscopy (FTIR) has been established for Arabidopsis petals. The combination of FTIR imaging with spectra derivatization revealed that petals, in contrast to other organs, have a characteristic chemical zoning with high amount of aliphatic compounds and esters in the lamina and of polysaccharides in the stalk of the petal. The hinge region of petals was particular rich in amides as well as in vibrations potentially associated with hemicellulose. In addition, a number of other distribution patterns have been identified. Analyses of mutants in cutin deposition confirmed that vibrations of aliphatic compounds and esters present in the lamina were largely associated with the cuticular polyester. Calculation of spectrotypes, including the standard deviation of intensities, allowed detailed comparison of the spectral features of various mutants. The spectrotypes not only revealed differences in the amount of polyesters in cutin mutants, but also changes in other compound classes. For example, in addition to the expected strong deficiencies in polyester content, the long-chain acyl CoA synthase 2 mutant showed increased intensities of vibrations in a wavelength range that is typical for polysaccharides. Identical spectral features were observed in quasimodo2, a cell-wall mutant of Arabidopsis with a defect in pectin formation that exhibits increased cellulose synthase activity. FTIR thus proved to be a convenient method for the identification and characterization of mutants affected in the deposition of cutin in petals.

Soil spectral library and its use in soil classification

Soil science has sought to develop better techniques for the classification of soils, one of which is the use of remote sensing applications. The use of ground sensors to obtain soil spectral data has enabled the characterization of these data and the advancement of techniques for the quantification of soil attributes. In order to do this, the creation of a soil spectral library is necessary. A spectral library should be representative of the variability of the soils in a region. The objective of this study was to create a spectral library of distinct soils from several agricultural regions of Brazil. Spectral data were collected (using a Fieldspec sensor, 350-2,500 nm) for the horizons of 223 soil profiles from the regions of Matão, Paraguaçu Paulista, Andradina, Ipaussu, Mirandópolis, Piracicaba, São Carlos, Araraquara, Guararapes, Valparaíso (SP); Naviraí, Maracajú, Rio Brilhante, Três Lagoas (MS); Goianésia (GO); and Uberaba and Lagoa da Prata (MG). A Principal Component Analysis (PCA) of the data was then performed and a graphic representation of the spectral curve was created for each profile. The reflectance intensity of the curves was principally influenced by the levels of Fe2O3, clay, organic matter and the presence of opaque minerals. There was no change in the spectral curves in the horizons of the Latossolos, Nitossolos, and Neossolos Quartzarênicos. Argissolos had superficial horizon curves with the greatest intensity of reflection above 2,200 nm. Cambissolos and Neossolos Litólicos had curves with greater reflectance intensity in poorly developed horizons. Gleisols showed a convex curve in the region of 350-400 nm. The PCA was able to separate different data collection areas according to the region of source material. Principal component one (PC1) was correlated with the intensity of reflectance samples and PC2 with the slope between the visible and infrared samples. The use of the Spectral Library as an indicator of possible soil classes proved to be an important tool in profile classification.

A new and simple variable-angle accessory for infrared specular reflectance

A simple, low-cost accessory (patent pending) with only two flat mirrors and a new variable-angle mechanism has been developed for infrared specular reflectance measurements. The system allows the angles of incidence to be varied continuously from 15° (near normal incidence) to 85° (near grazing angle) without losing the alignment of the accessory. The reflectivity of boron nitride thin films deposited on metallic substrates has been measured at different angles of incidence to demonstrate the utility of this accessory.