Imaging Mass Spectrometry

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Parameters derived from remote sensing that can be used to assess fire danger include surface reflectance, live and dead biomass, canopy water content, species composition, and fuel state. Spectral bands and wavelength locations of traditional multispectral data make assessment of fire danger in Mediterranean shrublands difficult, although fire danger parameters have been derived from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data. We compare nearly simultaneous acquisition of Hyperion and AVIRIS to evaluate spaceborne monitoring potential of fire danger in Southern California chaparral. Field spectra were acquired to support reflectance retrieval and construct a spectral library for vegetation mapping. Reflectance spectra retrieved from Hyperion and AVIRIS had similar shape and albedo, but SNR was five times higher in AVIRIS. Fuel condition was assessed using the endmember fractions from spectral mixture analysis, with both Hyperion and AVIRIS imaging spectrometer data providing similar fractions and spatial distributions. Hyperion demonstrated good capability for separating spectral signals from bare soil and dry plant litter. Canopy water content was compared using the 980-and 1200-nm liquid water bands, the water index, and the normalized difference water index. Results showed that Hyperion is capable of retrieving canopy water at 1200 nm, but demonstrates poor performance at 980 nm. Sensor noise and instrumental artifacts account for poor performance in this spectral region. Overall, full-spectrum measures outperformed band ratios because of a lower sensitivity to sensor noise in individual bands. Species and community mapping showed similar patterns with better accuracy for AVIRIS relative to Hyperion, but with both instruments achieving only 79% and 50% overall accuracy, respectively.

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

The Parys Mountain mine on Anglesey, North Wales is a site of great importance both historically and mineralogically. Mining at the site dates back to the Bronze age and this has left a legacy of mine waste at the site. The main objectives of this study are to use hyperspectral imaging spectrometry to: characterise mine waste at, and map contamination transport around, the Parys Mountain mine site and; to map associated vegetation stress using SWIR Imaging Spectrometry. This work builds on the expertise gained during the MINEO project in which mine waste was mapped at various sites across Europe using advanced Earth observation techniques. In MINEO BGS used HyMap data to map an area of abandoned tin mining in Cornwall and so the skills learnt in contamination mapping have been applied to the HyMap data for Parys Mountain. Both HyMap and CASI (Compact Airborne Spectrographic Imager) SWIR (Short Wave Infrared) data have been acquired over Parys Mountain. Mine site characterization has been undertaken using SAM (Spectral Angle Mapper) classification techniques and the contamination at Parys Mountain has been mapped. This is being backed up with geochemical analysis for verification of the spectra observed both in the field and the image data. Historical geochemical and spectral data from the Parys mountain deposit is being used for comparison proposes. Mine waste at the mine site has been characterised and mapped and the resulting maps of contamination will be shown at the conference. These methods will now be applied to the HyMap data of Rheidol Valley, acquired by Vito during 2004.

The aim of this study was to define and compare the distributions of five trace elements (essential: Cu, Fe, Se, Zn ; non-essential: Cd) among cytosolic biomolecules of different molecular masses isolated from livers of European chub (Squalius cephalus) and brown trout (Salmo trutta). These two fish species are often applied as bioindicators of environmental contamination in different types of fluvial ecosystems. European chub were sampled in the lowland river Sutla and brown trout in the karstic river Krka in Croatia, in autumn seasons of 2009 and 2015, respectively. To obtain the elemental profiles, metals bound to cytosolic biomolecules were separated by size exclusion high performance-liquid chromatography and subsequently analysed by high resolution-inductively coupled plasma-mass spectrometry. Obtained profiles indicated certain differences between two species. Both Cd and Cu were associated to metallothioneins in both species, but only in trout their binding to high molecular...

The increasing quantity and sophistication of imaging spectroscopy applications have led to a higher demand on the quality of Earth observation data products. In particular, it is desired that data products be as consistent as possible (i.e., ideally uniform) in both spectral and spatial dimensions. Yet, data acquired from real (e.g., pushbroom) imaging spectrometers are adversely affected by various categories of artifacts and aberrations including as follows: singular and linear (e.g., bad pixels and missing lines), area (e.g., optical aberrations), and stability and degradation defects. Typically, the consumer of such data products is not aware of the magnitude of such inherent data uncertainties even as more uncertainty is introduced during higher level processing for any particular application. In this paper, it is shown that the impact of imaging spectrometry data product imperfections in currently available data products has an inherent uncertainty of 10%, even though worst case scenarios were excluded, state-of-the-art corrections were applied, and radiometric calibration uncertainties were excluded. Thereafter, it is demonstrated how this error can be reduced (< 5%) with appropriate available technology (onboard, scene, and laboratory calibration) and assimilation procedures during the preprocessing of the data. As a result, more accurate, i.e., uniform, imaging spectrometry data can be delivered to the user community. Hence, the term uniformity of imaging spectrometry data products is defined for enabling the quantitative means to assess the quality of imaging spectrometry data. It is argued that such rigor is necessary for calculating the error propagation of respective higher level processing results and products.

▪ Water mainly absorbs electromagnetic radiation in this domain and its retrieval using imaging spectrometry should be improved transmittance in the 0.4–2.5 m region as a function of biochemical content (photosynthetic▪ Water mainly absorbs electromagnetic radiation in this domain and its retrieval using imaging spectrometry should be improved▪ Vegetation emissivity seems to depend on leaf water status (Olioso et al., 2007) pigments, water and dry matter) and structure anatomy▪ Vegetation emissivity seems to depend on ...

Seed germination is the essential first step in crop establishment, and can be severely affected by salinity stress which can inhibit essential metabolic processes during the germination process. Salt stress during seed germination can trigger lipid-dependent signalling cascades that activate plant adaptation processes, lead to changes in membrane fluidity to help resist the stress, and cause secondary metabolite responses due to increased oxidative stress. In germinating barley (Hordeum vulgare), knowledge of the changes in spatial distribution of lipids and other small molecules at a cellular level in response to salt stress is limited. In this study, mass spectrometry imaging (MSI), liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS), inductively coupled plasma mass spectrometry (ICP-MS), and X-ray fluorescence (XRF) were used to determine the spatial distribution of metabolites, lipids and a range of elements, such as K + and Na + , in seeds of two barley genotypes with contrasting germination phenology (Australian barley varieties Mundah and Keel). We detected and tentatively identified more than 200 lipid species belonging to seven major lipid classes (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, prenol lipids, sterol lipids, and polyketides) that differed in their spatial distribution based on genotype (Mundah or Keel), time postimbibition (0 to 72 h), or treatment (control or salt). We found a tentative flavonoid was discriminant in post-imbibed Mundah embryos under saline conditions, and a delayed flavonoid response in Keel relative to Mundah. We further employed MSI-MS/MS and LC-QToF-MS/MS to explore the identity of the discriminant flavonoid and study the temporal pattern in five additional barley genotypes. ICP-MS was used to quantify the elemental composition of both Mundah and Keel seeds, showing a significant increase in Na + in salt treated samples. Spatial mapping of elements using µ-XRF localized the elements within the seeds. This study integrates data obtained from three mass

Drosophila melanogaster (fruit fly) has a relatively simple nervous system but possesses high order brain functions similar to humans. Therefore, it has been used as a common model system in biological studies, particularly drug addiction. Here, the spatial distribution of biomolecules in the brain of the fly was studied using time‐of‐flight SIMS. Fly brains were analyzed frozen to prevent molecular redistribution prior to analysis. Different molecules were found to distribute differently in the tissue, particularly the eye pigments, diacylglycerides, and phospholipids, and this is expected to be driven by their biological functions in the brain. Correlations in the localization of these molecules were also observed using principal components analysis of image data, and this was used to identify peaks for further analysis. Furthermore, consecutive analyses following 10 keV Ar2500+ sputtering showed that different biomolecules respond differently to Ar2500+ sputtering. Significant ch...

Perceiving abnormal regions in the images of different medical modalities plays a crucial role in diagnosis and subsequent treatment planning. In medical images to visually perceive abnormalities&#39; extent and boundaries requires substantial experience. Consequently, manually drawn region of interest (ROI) to outline boundaries of abnormalities suffers from limitations of human perception leading to inter-observer variability. As an alternative to human drawn ROI, it is proposed the use of a computer-based segmentation algorithm to segment digital medical image data.Hierarchical Clustering-based Segmentation (HCS) process is a generic unsupervised segmentation process that can be used to segment dissimilar regions in digital images. HCS process generates a hierarchy of segmented images by partitioning an image into its constituent regions at hierarchical levels of allowable dissimilarity between its different regions. The hierarchy represents the continuous merging of similar, spa...

Beam homogenization and spatially dynamic beam patterning optics have been combined to improve the imaging matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOFMS) experiment. The optical design was developed to improve upon the spatial resolution limit imposed by the laser beam profile (∼25-50 m) and to decrease the long analysis times associated with mechanical translation of the MALDI sample stage. This arrangement consists of: laser beam conditioning optics, laser beam shaping optics via a digital micromirror device (DMD), and an imaging lens system. Experimental results comparing traditional imaging MALDI-TOFMS and spatially dynamic imaging MALDI-TOFMS are discussed. The optical system has proven useful for patterning the MALDI laser beam into user defined beam shapes, can potentially decrease analysis times associated with mechanical movement of the sample stage, and may be capable of increasing the limits of detection by simultaneously irradiating multiple spots.

We use time of flight secondary ion mass spectrometry (ToF-SIMS) imaging to investigate the effects of orally administrated methylphenidate on lipids in the brain of Drosophila melanogaster (fruit fly), a major invertebrate model system in biological study and neuroscience. ToF-SIMS imaging was carried out using a recently designed high energy 40 keV Ar4000+ gas cluster ion gun which demonstrated improved sensitivity for intact lipids in the fly brain compared to the 40 keV C60+ primary ion gun. In addition, correlation of ToF-SIMS and SEM imaging on the same fly brain showed that there is specific localization that is related to biological functions of various biomolecules. Different lipids distribute in different parts of the brain - central brain, optical lobes, and proboscis - depending on the length of carbon chain and saturation level of fatty acid (FA) branches. Furthermore, data analysis using image principal components analysis (PCA) showed that methylphenidate dramatically...

Drosophila melanogaster (fruit fly) has a relatively simple nervous system but possesses high order brain functions similar to humans. Therefore, it has been used as a common model system in biological studies, particularly drug addiction. Here, the spatial distribution of biomolecules in the brain of the fly was studied using time‐of‐flight SIMS. Fly brains were analyzed frozen to prevent molecular redistribution prior to analysis. Different molecules were found to distribute differently in the tissue, particularly the eye pigments, diacylglycerides, and phospholipids, and this is expected to be driven by their biological functions in the brain. Correlations in the localization of these molecules were also observed using principal components analysis of image data, and this was used to identify peaks for further analysis. Furthermore, consecutive analyses following 10 keV Ar2500+ sputtering showed that different biomolecules respond differently to Ar2500+ sputtering. Significant ch...

Imaging mass spectrometry is an emerging technique of great potential for investigating the chemical architecture in biological matrices. Although the potential for studying neurobiological systems is evident, the relevance of the technique for application in neuroscience is still in its infancy. In the present Review, a principal overview of the different approaches, including matrix assisted laser desorption ionization and secondary ion mass spectrometry, is provided with particular focus on their strengths and limitations for studying different neurochemical species in situ and in vitro. The potential of the various approaches is discussed based on both fundamental and biomedical neuroscience research. This Review aims to serve as a general guide to familiarize the neuroscience community and other biomedical researchers with the technique, highlighting its great potential and suitability for comprehensive and specific chemical imaging.

An approach for the use of in-source fragmentation with electrospray ionization followed by product ion scan in a triple quadrupole mass spectrometer system is described. This approach is based on the elucidation of the various fragmentation pathways by further dissociation of each fragment ion in the ion spectrum. This can be achieved predominately, by combining fragmentor voltage induced dissociation (in-source fragmentation) with subsequent collision-induced dissociation; this process can be referred to as pseudo-MS3scan mode. This technique permitted unambiguous assignment and provided sufficient sensitivity and specificity. It is advantageous for structure elucidation of unknown compounds. We investigate the possibility of using in-source fragmentation with the diverse novel chemical entities encompassing different substituents. This process was intended to improve the qualitative capability of tandem mass spectrometry simulating the MS3of ion trap for studying fragmentation me...

Healthy vegetation function supports diverse biological communities and ecosystem processes, and provides crops, forest products, forage, and countless other benefits. Vegetation function can be assessed by examining dynamic processes and by evaluating plant traits, which themselves are dynamic. Using both trait-based and process-based approaches, spectroscopy can assess vegetation function at multiple scales using a variety of sensors and platforms ranging from proximal to airborne and satellite measurements. Since spectroscopic data are defined by the instruments and platforms available, along with their corresponding spatial, temporal and spectral scales, and since these scales may not always match those of the function of interest, consideration of scale is a necessary focus. For a full understanding of vegetation processes, combined (multi-scale) sampling methods using empirical and theoretical approaches are required, along with improved informatics.

Neurolipids are a class of bioactive lipids that are produced locally through specific biosynthetic pathways in response to extracellular stimuli. Neurolipids are important endogenous regulators of neural cell proliferation, differentiation, oxidative stress, inflammation and apoptosis. Endocannabinoids (eCBs) and lysophosphatidic acid (LPA) are examples of this type of molecule and are involved in neuroprotection. The present study analyzes a possible relationship of the main receptor subtypes for both neurolipid systems that are present in the central nervous system, the CB 1 and LPA 1 receptors, by using brain slices from CB 1 KO mice and LPA 1-null mice. Receptor-mediated G protein activation and glycerophospholipid regulation of potential precursors of their endogenous neurotransmitters were measured by two different in vitro imaging techniques, functional autoradiography and imaging mass spectrometry (IMS), respectively. Possible crosstalk between CB 1 and LPA 1 receptors was identified in specific areas of the brain, such as the amygdala, where LPA 1 receptor activity is upregulated in CB 1 KO mice. More evidence of an interaction between both systems was that the CB 1-mediated activity was clearly increased in the prefrontal cortex and cerebellum of LPA 1-null mice. The eCB system was specifically over-activated in regions where LPA 1 has an important signaling role during embryonic development. The modifications on phospholipids (PLs) observed in these genetically modified mice by using the IMS technique indicated the regulation of some of the PL precursors of both LPA and eCBs in specific brain areas. For example, phosphatidylcholine (PC) (36:1) was detected as a potential LPA precursor, and phosphatidylethanolamine (PE) (40:6) and PE (p18:0/22:6) as potential eCB precursors. The absence of the main cerebral receptors for LPA or eCB systems is able to induce modulation on the other at the levels of both signaling and synthesis of endogenous neurotransmitters, indicating adaptive responses between both systems during prenatal and/or postnatal development.

A new instrument has been setup at the Centre de Recherche Public-Gabriel Lippmann to measure spectral emissivity values of typical earth surface samples in the 8 to 12 μm range at a spectral resolution of up to 0.25 cm −1. The instrument is based on a Hyper-Cam-LW built by Telops with a modified fore-optic for vertical measurements at ground level and a platform for airborne acquisitions. A processing chain has been developed to convert calibrated radiances into emissivity spectra. Repeat measurements taken on samples of sandstone show a high repeatability of the system with a wavelength dependent standard deviation of less than 0.01 (1.25% of the mean emissivity). Evaluation of retrieved emissivity spectra indicates good agreement with reference measurements. The new instrument facilitates the assessment of the spatial variability of emissivity spectra of material surfaces-at present still largely unknown-at various scales from ground and airborne platforms and thus will provide new opportunities in environmental remote sensing.

The oxygen utilization and, therefore, the metabolic state, of a distinctive area of the retina may be calculated from the diameter of the supplying artery and vein, the haemoglobin oxygenation, and the velocity of the blood. The first two parameters can be determined by imaging spectrometry at the patients ocular fundus. However, the reflected light emerging from a vessel followed different pathways through the ocular fundus layers and the vessel embedded in the retina. The contribution of the single pathways to the vessel reflection profile is investigated by a Monte Carlo simulation. Considering retinal vessels with diameters of 25-200 m we found the reflection from a thin vessel to be determined by the single and double transmission of light at 560 nm. The backscattering from the blood column determines the reflectance in the case of a thick vessel. However, both components are in the same order of magnitude. This has to be considered in the calculation of the oxygen saturation of blood in retinal vessels from their reflection spectra.

The oxygen utilization and, therefore, the metabolic state, of a distinctive area of the retina may be calculated from the diameter of the supplying artery and vein, the haemoglobin oxygenation, and the velocity of the blood. The first two parameters can be determined by imaging spectrometry at the patients ocular fundus. However, the reflected light emerging from a vessel followed different pathways through the ocular fundus layers and the vessel embedded in the retina. The contribution of the single pathways to the vessel reflection profile is investigated by a Monte Carlo simulation. Considering retinal vessels with diameters of 25-200 m we found the reflection from a thin vessel to be determined by the single and double transmission of light at 560 nm. The backscattering from the blood column determines the reflectance in the case of a thick vessel. However, both components are in the same order of magnitude. This has to be considered in the calculation of the oxygen saturation of blood in retinal vessels from their reflection spectra.

High surface sensitivity and lateral resolution imaging make time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) a unique and powerful tool for biological analysis. However, with the leaps forward made in the capabilities of the ToF‐SIMS instrumentation, the data being recorded from these instruments has dramatically increased. Unfortunately, with these large, often complex, datasets, a bottleneck appears in their processing and interpretation. Here, an application of peak picking is described and applied to ToF‐SIMS images allowing for large compression of data, noise removal and improved contrast, while retaining a high percentage of the original signal. Peak picking is performed to locate peaks within ToF‐SIMS data. By using this information, signal arising from the same distribution can be summed and overlapping signals separated. As a result, the data size and complexity can be dramatically reduced. This method also acts as an effective noise filter, discarding unwanted n...

Matrix‐assisted laser desorption/ionization imaging mass spectrometry (MALDI‐IMS) is a well‐established technique for elucidating the location and relative abundance of a range of biomolecules. More recently, research into this technique has shifted from simple discovery and demonstration of utility to application in biomedical research. Here, we describe a protocol utilizing MALDI‐IMS for the spatial mapping of lipids in brain tissue from normal human brains and brains from patients with Alzheimer&#39;s disease, in the context of Alzheimer&#39;s disease. Improved accuracy calibration of the instrument from the tissue surface is emphasized, as this allows for significantly improved mass determination in time of flight (TOF)‐based instruments enabling more confident preliminary lipid identification. This improved initial result allows MALDI‐IMS data to be complemented with additional instrumentation, such as liquid chromatography mass spectrometry workflows or specialized non‐TOF sys...

Background-Wilms tumor (WT) is the most common childhood kidney cancer worldwide and arises in children of black African ancestry with greater frequency and severity than other race groups. A biologic basis for this pediatric cancer disparity has not been previously determined. We hypothesized that unique molecular fingerprints might underlie the variable incidence and distinct disease characteristics of WT observed between race groups. Study Design-To evaluate molecular disparities between WTs of different race groups, the Children's Oncology Group provided 80 favorable histology specimens divided evenly between black and white patients and matched for disease characteristics. As a surrogate of sub-Saharan African patients, we also analyzed 18 Kenyan WT specimens. Tissues were probed for peptide

This study integrates ground spectrometry, imaging spectrometry, and in-situ pavement condition surveys for asphalt road assessment. There is strong spectral evidence for asphalt aging and deterioration processes, hence field spectra showed that asphalt aging and deterioration produce measurable changes in spectra as these surfaces undergo a transition from hydrocarbon dominated new roads to mineral dominated older roads. Spectral measures derived from field and image spectra correlated well with pavement quality indicators. Spectral confusion between pavement material aging and asphalt mix erosion on the one hand, and structural road damages (e.g. cracking) on the other, poses some limits to remote sensing based mapping. Both the &quot;common practice&quot; methods (Pavement management systems-PMS, in-situ vehicle inspections), and analysis using imaging spectrometry are effective in identifying roads in good and very good condition. Variance and uncertainty in all survey data (PMS...

We integrate ground spectrometry, imaging spectrometry, and in situ pavement condition surveys for assessment of asphalt road infrastructure. There is strong spectral evidence for asphalt aging and deterioration. Several spectral measures derived from field and image spectra correlate well with pavement quality indicators (e.g., a pavement condition index). However, the potential for mapping is limited by fine spatial resolution requirements (as fine as 0.5 m) and by the spectral confusion between pavement material aging and asphalt mix erosion on the one hand and structural road damages (e.g., cracking) on the other.

Among the needs usually expressed by teams using mass spectrometry imaging, one that often arises is that for user-friendly software able to manage huge data volumes quickly and to provide efficient assistance for the interpretation of data. To answer this need, the Computis European project developed several complementary software tools to process mass spectrometry imaging data. Data Cube Explorer provides a simple spatial and spectral exploration for matrix-assisted laser desorption/ionisation–time of flight (MALDI-ToF) and time of flight–secondary-ion mass spectrometry (ToF-SIMS) data. SpectViewer offers visualisation functions, assistance to the interpretation of data, classification functionalities, peak list extraction to interrogate biological database and image overlay, and it can process data issued from MALDI-ToF, ToF-SIMS and desorption electrospray ionisation (DESI) equipment. EasyReg2D is able to register two images, in American Standard Code for Information Interchange...

Precise estimation of carotenoid (Car) content in crops, using remote sensing data, could be helpful for agricultural resources management. Conventional methods for Car content estimation were mostly based on reflectance data acquired from nadir direction. However, reflectance acquired at this direction is highly influenced by canopy structure and soil background reflectance. Off-nadir observation is less impacted, and multi-angle viewing data are proven to contain additional information rarely exploited for crop Car content estimation. The objective of this study was to explore the potential of multi-angle observation data for winter wheat canopy Car content estimation. Canopy spectral reflectance was measured from nadir as well as from a series of off-nadir directions during different growing stages of winter wheat, with concurrent canopy Car content measurements. Correlation analyses were performed between Car content and the original and continuum removed spectral reflectance. Spectral features and previously published indices were derived from data obtained at different viewing angles and were tested for Car content estimation. Results showed that spectral features and indices obtained from backscattering directions between 20°and 40°view zenith angle had a stronger correlation with Car content than that from the nadir direction, and the strongest correlation was observed from about 30°backscattering direction. Spectral absorption depth at 500 nm derived from spectral data obtained from 30°backscattering direction was found to reduce the difference induced by plant cultivars greatly. It was the most suitable for winter wheat canopy Car estimation, with a coefficient of determination 0.79 and a root mean square error of 19.03 mg/m 2. This work indicates the importance of taking viewing geometry effect into account when using spectral features/indices and provides new insight in the application of multi-angle remote sensing for the estimation of crop physiology.

Precise estimation of carotenoid (Car) content in crops, using remote sensing data, could be helpful for agricultural resources management. Conventional methods for Car content estimation were mostly based on reflectance data acquired from nadir direction. However, reflectance acquired at this direction is highly influenced by canopy structure and soil background reflectance. Off-nadir observation is less impacted, and multi-angle viewing data are proven to contain additional information rarely exploited for crop Car content estimation. The objective of this study was to explore the potential of multi-angle observation data for winter wheat canopy Car content estimation. Canopy spectral reflectance was measured from nadir as well as from a series of off-nadir directions during different growing stages of winter wheat, with concurrent canopy Car content measurements. Correlation analyses were performed between Car content and the original and continuum removed spectral reflectance. Spectral features and previously published indices were derived from data obtained at different viewing angles and were tested for Car content estimation. Results showed that spectral features and indices obtained from backscattering directions between 20°and 40°view zenith angle had a stronger correlation with Car content than that from the nadir direction, and the strongest correlation was observed from about 30°backscattering direction. Spectral absorption depth at 500 nm derived from spectral data obtained from 30°backscattering direction was found to reduce the difference induced by plant cultivars greatly. It was the most suitable for winter wheat canopy Car estimation, with a coefficient of determination 0.79 and a root mean square error of 19.03 mg/m 2. This work indicates the importance of taking viewing geometry effect into account when using spectral features/indices and provides new insight in the application of multi-angle remote sensing for the estimation of crop physiology.

• Fractured shales in New York State (NYS) naturally release gas to the surface. • Western NYS shale gas seeps contain high concentrations of ethane and propane. • Shales in other regions with less or older fracturing rarely show gas seepage. • Historical gas seeps in NYS diminished after nearby gas and oil production. • SCIAMACHY satellite data could not detect methane anomalies over western NYS.

The influence of laser focusing on the target in matrix-assisted laser desorptionlionizatlon (MALDI) has been studied. The emission of stable and metastable molecular ions of bovine insulin depends on both the laser energy and the distance between the target and the laser focal plane. The results clearly show that the laser fluence is the important parameter in MALDI. The fluence threshold of metastable-ion emission is higher than that of stableion emission. Beyond this threshold, the emission of stable ions reaches a plateau. This is due to the spatial inhomogeneity of the laser energy distribution. A phenomenological model including two fluence thresholds for the stable-and metastable-ion emission has been developed and compared to the experimental data.

Drosophila melanogaster (fruit fly) has a relatively simple nervous system but possesses high order brain functions similar to humans. Therefore, it has been used as a common model system in biological studies, particularly drug addiction. Here, the spatial distribution of biomolecules in the brain of the fly was studied using time‐of‐flight SIMS. Fly brains were analyzed frozen to prevent molecular redistribution prior to analysis. Different molecules were found to distribute differently in the tissue, particularly the eye pigments, diacylglycerides, and phospholipids, and this is expected to be driven by their biological functions in the brain. Correlations in the localization of these molecules were also observed using principal components analysis of image data, and this was used to identify peaks for further analysis. Furthermore, consecutive analyses following 10 keV Ar2500+ sputtering showed that different biomolecules respond differently to Ar2500+ sputtering. Significant ch...

Neurolipids are a class of bioactive lipids that are produced locally through specific biosynthetic pathways in response to extracellular stimuli. Neurolipids are important endogenous regulators of neural cell proliferation, differentiation, oxidative stress, inflammation and apoptosis. Endocannabinoids (eCBs) and lysophosphatidic acid (LPA) are examples of this type of molecule and are involved in neuroprotection. The present study analyzes a possible relationship of the main receptor subtypes for both neurolipid systems that are present in the central nervous system, the CB 1 and LPA 1 receptors, by using brain slices from CB 1 KO mice and LPA 1-null mice. Receptor-mediated G protein activation and glycerophospholipid regulation of potential precursors of their endogenous neurotransmitters were measured by two different in vitro imaging techniques, functional autoradiography and imaging mass spectrometry (IMS), respectively. Possible crosstalk between CB 1 and LPA 1 receptors was identified in specific areas of the brain, such as the amygdala, where LPA 1 receptor activity is upregulated in CB 1 KO mice. More evidence of an interaction between both systems was that the CB 1-mediated activity was clearly increased in the prefrontal cortex and cerebellum of LPA 1-null mice. The eCB system was specifically over-activated in regions where LPA 1 has an important signaling role during embryonic development. The modifications on phospholipids (PLs) observed in these genetically modified mice by using the IMS technique indicated the regulation of some of the PL precursors of both LPA and eCBs in specific brain areas. For example, phosphatidylcholine (PC) (36:1) was detected as a potential LPA precursor, and phosphatidylethanolamine (PE) (40:6) and PE (p18:0/22:6) as potential eCB precursors. The absence of the main cerebral receptors for LPA or eCB systems is able to induce modulation on the other at the levels of both signaling and synthesis of endogenous neurotransmitters, indicating adaptive responses between both systems during prenatal and/or postnatal development.

RATIONALE: Amphibians can produce a large amount of bioactive peptides over the skin. In order to map the precise tissue localization of these compounds and evaluate their functions, mass spectrometry imaging (MSI) and gene expression studies were used to investigate a possible correlation between molecules involved in the antimicrobial defense mechanisms and anti-predatory behavior by Physalaemus nattereri. METHODS: Total skin secretion of P. nattereri was analyzed by classical Protein Chemistry and proteomic techniques. Intact inguinal macroglands were dissected from the rest of the skin and both tissues were analyzed by MSI and real-time polymerase chain reaction (RT-PCR) experiments. Peptides were primarily identified by de novo sequencing, automatic Edman degradation and cDNA data. RESULTS: Fifteen bradykinin (BK)-related peptides and two antimicrobial peptides were sequenced and mapped by MSI on the inguinal macrogland and the rest of P. nattereri skin. RT-PCR results revealed that BK-related peptide levels of expression were about 30,000 times higher on the inguinal macroglands than on the any other region of the skin, whilst antimicrobial peptide ions appear to be evenly distributed in both investigated regions. CONCLUSIONS: The presence of antimicrobial peptides in all investigated tissue regions is in accordance with the defensive role against microorganisms thoroughly demonstrated in the literature, whereas BK-related molecules are largely found on the inguinal macroglands suggesting an intriguing link between their noxious activities against potential predators of P. nattereri and the frog's deimatic behavior.

There is a renewed awareness of the finite nature of the world's soil resources, growing concern about soil security and significant uncertainties about the carrying capacity of the planet. Regular assessments of soil conditions from local through to global scales are requested, and there is a clear demand for accurate, up-to-date and spatially referenced soil information by the modelling scientific community, farmers and land users, and policy-and decision-makers. Soil and imaging spectroscopy, based on visible-near-infrared and shortwave infrared (400-2500 nm) spectral reflectance, has been shown to be a proven method for the quantitative prediction of key soil surface properties. With the upcoming launch of the next generation of hyperspectral satellite sensors in the next years, a high potential to meet the demand for global soil mapping and monitoring is appearing. In this paper, we briefly review the basic concepts of soil spectroscopy with a special attention to the effects of soil roughness on reflectance and then provide a review of state of the art, achievements and perspectives in soil mapping and monitoring based on imaging spectroscopy from airand spaceborne sensors. Selected application cases are presented for the modelling of soil organic carbon, mineralogical composition, topsoil water content and characterization of soil crust, soil erosion and soil degradation stages based on airborne and simulated spaceborne imaging spectroscopy data. Further, current challenges, gaps and new directions toward enhanced soil properties modelling are presented. Overall, this paper highlights the potential and limitations of multiscale imaging spectroscopy nowadays for soil mapping and monitoring, and capabilities and requirements of upcoming spaceborne sensors as support for a more informed and sustainable use of our world's soil resources.

We designed a unique hyperspectral experiment from the Earth Observing One (EO-1) orbit change to evaluate solar illumination effects over tropical forests in Brazil. Ten nadir-viewing Hyperion images collected over a fixed site and period of the year (July to August) were selected for analysis. We evaluated variations in reflectance and in 16 narrowband vegetation indices (VIs) with increasing solar zenith angle (SZA) from the pre-drift (2004-2008) to the EO-1 drift period (2011-2016). To detect changes in reflectance and shadows, we applied spectral mixture analysis (SMA) and principal component analysis (PCA) and calculated the similarity spectral angle (θ) between the vegetation spectra measured with variable SZA. The magnitude of the illumination effects was also evaluated from change-point analysis and nonparametric Mann-Whitney U tests applied over the time series. Finally, we complemented our experiment using the PROSAIL model to simulate the VIs variation with increasing SZA resultant from satellite drift. The results showed significant changes in Hyperion reflectance and VIs, especially when the EO-1 crossed the study area at earlier times and larger SZA in 2015 (9:05 a.m.; SZA = 59°) and 2016 (8:30 a.m.; SZA = 67°). Compared to the pre-drift period (10:30 a.m.; SZA = 45°), the SZA differences of 14°(2015) and 22°(2016) increased the shade fractions and decreased the vegetation brightness. PCA separated the pre-drift and drift reflectance datasets, showing shifts in scores due to changes in brightness. θ increased with SZA, indicating changes in the shape of the vegetation spectra with drift. For most VIs, the change-point analysis indicated 2015 (SZA = 59°) as the predominant year of detected changes. Compared to the EO-1 original orbit, the Plant Senescence Reflectance Index (PSRI), Anthocyanin Reflectance Index (ARI) and Structure Insensitive Pigment Index (SIPI) presented the largest positive changes during drift, while the Photochemical Reflectance Index (PRI), Visible Atmospherically Resistant Index (VARI) and Enhanced Vegetation Index (EVI) had the largest negative changes. The effect size of the illumination geometry on these VIs was large, as indicated by increasing values of the Cohen's r metric toward 2016. The anisotropy of the Hyperion VIs was generally consistent with that from PROSAIL in the simulated pre-drift and drift periods. Focusing on structural indices, it affected the relationships between VIs and simulated leaf area index (LAI) at large SZA.

Neuropeptides are a diverse set of complex cell-cell signaling molecules that modulate behavior, learning and memory. Their spatially heterogeneous distributions, large number of post-translational modifications, and wide range of physiologically active concentrations make their characterization challenging. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging is well-suited to characterizing and mapping neuropeptides in the central nervous system. Because matrix application can cause peptide migration within tissue samples, application parameters for MALDI typically represent a compromise between attaining the highest signal quality and preserving native spatial distributions. The stretched sample approach minimizes this tradeoff by fragmenting the tissue section into thousands of spatially isolated islands, each ~40 microns in size. This inhibits analyte migration between the pieces and, at the same time, reduces analyte-salt adduct formation. Here we present methodological improvements that enable the imaging of stretched tissues and reveal neuropeptide distributions in nervous tissue from Aplysia californica. The distributions of known neuropeptides are shown to correspond with previous immunohistochemical results, demonstrating that the stretched imaging method is well-suited for working with easily redistributed molecules and heterogeneous tissues, and reduces adducts from physiological salts.

Mass spectrometry imaging (MSI) provides the ability to detect and identify a broad range of analytes and their spatial distributions from a variety of sample types, including tissue sections. Here we describe an approach for probing neuropeptides from sparse cell cultures using matrixassisted laser desorption/ionization time-of-flight (MALDI-TOF) MSI-at single cell spatial resolution-in both MS and tandem MS modes. Cultures of Aplysia californica neurons are grown on an array of glass beads embedded in a stretchable layer of Parafilm M. As the membrane is stretched, the beads/neurons are separated physically and the separated beads/ neurons analyzed via MALDI TOF MS. Compared with direct MS imaging of samples, the stretching procedure enhances analyte extraction and incorporation into the MALDI matrix, with negligible analyte spread between separated beads. MALDI tandem MSI using the stretched imaging approach yields localization maps of both parent and fragment ions from Aplysia pedal peptide, thereby confirming peptide identification. This methodology represents a flexible platform for MSI investigation of a variety of cell cultures, including functioning neuronal networks.

Soil reflectance spectroscopy has become a pioneering technique for quantifying soil properties that provide data for soil classification and digital soil mapping studies. This work was conducted with the aim to analyze the spatial variability of soil spectrometric properties between surface and subsurface soil under three land use patterns namely; pine, barren land and oak in Sherawa village, northeast Iraq. Soil samples were collected from the three land types at two depths: surface soil at 0–15 cm and subsurface soil at 15–30 cm in duplicates totaling 6 collected soil samples. The elemental composition and mineral phases of soils were determined by X-ray fluorescent XRF and X-ray diffraction (XRD) respectively for qualitative and quantitative characterization. Magnesium oxide (MgO) was highest detected concentration in the surface soil layer reaching 34.16%, 36.75%, and 33.63%, respectively for pine, barren land and oak compared to 41.57%, 38.54%, 33.94% of the respective concent...

An alternative secondary ion mass spectrometry utilizing laser preionization is introduced. The native Ag sample surface is first irradiated with laser pulse (100 fs duration, 10 10-10 11 W/cm 2 intensity, 1240 nm wavelength) and subsequently bombarded with primary ions (Bi 3 + , 10 ns duration, 25 keV energy). Multiple correlation patterns are observed in the mass spectra, confirming the mutual laser-secondary ion mass spectrometry (SIMS) interplay in the preionization mechanism.

Vegetation function and dynamics are key parameters in terrestrial carbon-cycle models. The strong linkages between biochemical constituents in foliage with photosynthetic capacity and ecosystem productivity makes the development of methods to characterise patterns of foliage biochemistry a potentially powerful approach for estimating leaf function and carbon fluxes at a variety of scales. Eucalypt foliage spectra were obtained over a range of species and locations in southern New South Wales, covering a significant productivity and climatic gradient. We applied a spectral decomposition technique, based on multivariate factor analysis, which allows inter-correlations of underlying factors affecting a set of variables to be assessed. A small number of factors capture virtually all of the variation observed in the foliage spectra and each factor contains significant information relating to species and plot variation over the region. Factor analysis indicated that key chlorophyll, nitr...

This paper presents the result of a work orientated to the spectral optimization of the acquisition devices in vascular biometrics systems. Spectral windows are proposed which will allow to design a multispectral system with a few and well defined bands, obtaining a more robust and reliable device, compared with the standard single band systems. This is in accordance to general trend of electro-optical and infrared acquisition systems in the field of the detection and remote sensing, where the work focus is on obtaining optimizedb ands. To carry out this work a Hyperespectral Imaging System (HIS) has been used as the acquisition system. In order to analyze the large amount of information and to select the spectral bands, a Principal Component Analysis (PCA) has been done. I.

There is a consensus about the necessity to achieve a quick soil spatial information with few human resources. Remote/proximal sensing and pedotransference are methods that can be integrated into this approach. On the other hand, there is still a lack of strategies indicating on how to put this in practice, especially in the tropics. Thus, the objective of this work was to suggest a strategy for the spatial prediction of soil classes by using soil spectroscopy from ground laboratory spectra to space images platform, as associated with terrain attributes and spectral libraries. The study area is located in São Paulo State, Brazil, which was covered by a regular grid (one per ha), with 473 boreholes collected at top and undersurface. All soil samples were analyzed in laboratory (granulometry and chemical), and scanned with a VIS-NIR-SWIR (400-2500 nm) spectroradiometer. We developed two traditional pedological maps with different detail levels for comparison: TFS-1 regarding orders and subgroups; and TFS-2 with additional information such as color, iron and fertility. Afterwards, we performed a digital soil map, generated by models, which used the following information: (i) predicted soil attributes from undersurface layer (diagnostic horizon), obtained by using a local spectral library; (ii) spectral reflectance of a bare soil surface obtained by Landsat image; and (iii) derivative of terrain attributes. Thus, the digital map was generated by a combination of three variables: remote sensing (Landsat data), proximal sensing (laboratory spectroscopy) and relief. Landsat image with bare soil was used as a first observation of surface. This strategy assisted on the location of topossequences to achieve soil variation in the area. Afterwards, spectral undersurface information from these locations was used to modelize soil attributes quantification (156 samples). The model was used to quantify samples in the entire area by spectra (other 317 samples). Since the surface was bare soil, it was sampled by image spectroscopy. Indeed, topsoil spectral laboratory information presented great similarity with satellite spectra. We observed angle variation on spectra from clayey to sandy soils as differentiated by intensity. Soil lines between bands 3/4 and 5/7 were helpful on the link between laboratory and satellite data. The spectral models of soil attributes (i.e., clay, sand, and iron) presented a high predictive performance (R 2 0.71 to 0.90) with low error. The spatial prediction of these attributes also presented a high performance (validations with R 2 > 0.78). The models increased spatial resolution of soil weathering information using a known spectral library. Elevation (altitude) improved mapping due to correlation with soil attributes

Chlorophyll is a good water quality indicator for determining other pollutants in inland water bodies. Chlorophyll concentrations can be measured by remote sensing techniques; howeve, studies show that the broad wavelength spectral data available on current satellites do not permit discrimination between chlorophyll and suspended sediments. Hyperspectral imaging by satellite and aircraft sensors provide significant relationships bettveen chlorophyll and radiance/reflectance measurements. This paper describes the identification of chlorophyll concentrations using hyperspectral imagery in inland water bodies. This hyperspectral study site is located in the Caballo Reservoir along the Rio Grande in the State of New Mexico. Run offfroin agricultural fields, failing septic tanks, and other sources of pollutants enter this water body. NASA 's Jet Propulsion Labo ratoryflew the flight line on June 30, 1999 and acquired the images in the study with an Advanced Visible infrared imaging Spectrometer (AVIRIS). No groundtruth measurements were available at the time of the A VIRIS flight mission to compare to the images of the flight line. The images were atmospherically corrected for distortions using the ACORN software. Hyperspectral image analysis techniques using ENVI software were used for identifying potential chlorophyll areas. The spectral matching signature method was used to identjfy chlorophyll near the shores of the Caballo Reservoir This method allows mapping of the chlorophyll constituent using the Spectral Angle Mapper (SAM) classification technique. The clean-up tasks afterwards are easier for eliminating any point or non-point pollutant sources because it reduces equipment and field sampling costs by obtaining water quality pollutant concentrations over a large geographical area.

Imaging mass spectrometry is an emerging technique of great potential for investigating the chemical architecture in biological matrices. Although the potential for studying neurobiological systems is evident, the relevance of the technique for application in neuroscience is still in its infancy. In the present Review, a principal overview of the different approaches, including matrix assisted laser desorption ionization and secondary ion mass spectrometry, is provided with particular focus on their strengths and limitations for studying different neurochemical species in situ and in vitro. The potential of the various approaches is discussed based on both fundamental and biomedical neuroscience research. This Review aims to serve as a general guide to familiarize the neuroscience community and other biomedical researchers with the technique, highlighting its great potential and suitability for comprehensive and specific chemical imaging.

Drosophila melanogaster (fruit fly) has a relatively simple nervous system but possesses high order brain functions similar to humans. Therefore, it has been used as a common model system in biological studies, particularly drug addiction. Here, the spatial distribution of biomolecules in the brain of the fly was studied using time‐of‐flight SIMS. Fly brains were analyzed frozen to prevent molecular redistribution prior to analysis. Different molecules were found to distribute differently in the tissue, particularly the eye pigments, diacylglycerides, and phospholipids, and this is expected to be driven by their biological functions in the brain. Correlations in the localization of these molecules were also observed using principal components analysis of image data, and this was used to identify peaks for further analysis. Furthermore, consecutive analyses following 10 keV Ar2500+ sputtering showed that different biomolecules respond differently to Ar2500+ sputtering. Significant ch...

Imaging mass spectrometry is an emerging technique of great potential for investigating the chemical architecture in biological matrices. Although the potential for studying neurobiological systems is evident, the relevance of the technique for application in neuroscience is still in its infancy. In the present Review, a principal overview of the different approaches, including matrix assisted laser desorption ionization and secondary ion mass spectrometry, is provided with particular focus on their strengths and limitations for studying different neurochemical species in situ and in vitro. The potential of the various approaches is discussed based on both fundamental and biomedical neuroscience research. This Review aims to serve as a general guide to familiarize the neuroscience community and other biomedical researchers with the technique, highlighting its great potential and suitability for comprehensive and specific chemical imaging.

Healthy vegetation function supports diverse biological communities and ecosystem processes, and provides crops, forest products, forage, and countless other benefits. Vegetation function can be assessed by examining dynamic processes and by evaluating plant traits, which themselves are dynamic. Using both trait-based and process-based approaches, spectroscopy can assess vegetation function at multiple scales using a variety of sensors and platforms ranging from proximal to airborne and satellite measurements. Since spectroscopic data are defined by the instruments and platforms available, along with their corresponding spatial, temporal and spectral scales, and since these scales may not always match those of the function of interest, consideration of scale is a necessary focus. For a full understanding of vegetation processes, combined (multi-scale) sampling methods using empirical and theoretical approaches are required, along with improved informatics.

We present a novel configuration for high spectral resolution multiplexing acquisition based on the Hadamard transform in stimulated Raman scattering (SRS) microscopy. The broadband tunable output of a dual-beam femtosecond laser is filtered by a fast, narrowband, and multi-channel acousto-optic tunable filter (AOTF). By turning on and off different subsets of its 8 independent channels, the AOTF generates the spectral masks given by the Hadamard matrix. We demonstrate a seamless and automated operation in the Raman fingerprint and CH-stretch regions. In the presence of additive noise, the spectral measurements using the multiplexed method show the same signal-to-noise ratio of conventional single-wavenumber acquisitions performed with 4 times longer integration time.