Properties of seawater (pH total scale) from a Satlantic SeaFET instrument mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous pH measurements made during 2013 expedition with a Satlantic SeaFET instrument that was connected to the flowthrough system. Data calibration was performed according to Bresnahan et al. (2014) (using spectrophotometric pH measurements on discrete samples (Clayton and Byrne 1993). pH_internal values were taken to calibrate the data (rather than pH_external) because of the better calibration coefficient (there was no trend associated with it). The equations of Clayton and Byrne (1993) was used to compute pH from the measured absorbance values at the temperature of measurement. The data was converted to in situ temperature using the "CO2-sys" program which can be downloaded from http://cdiac.ornl.gov/ftp/co2sys/.

Properties of seawater and particulate matter from a FRRF instrument, operating in a flow-through mode on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with a FRRF instrument, operating in a flow-through mode during the 2009-2012 part of the expedition. It operates by exciting chlorophyll fluorescence using a series of short flashes of controlled energy and time intervals (Kolber et al, 1998). The fluorescence transients produced by this excitation signal were analysed in real-time to provide estimates of abundance of photosynthetic pigments, the photosynthetic yields (Fv/Fm), the functional absorption cross section (a proxy for efficiency of photosynthetic energy acquisition), the kinetics of photosynthetic electron transport between Photosystem II and Photosystem I, and the size of the PQ pool. These parameters were measured at excitation wavelength of 445 nm, 470nm, 505 nm, and 535 nm, allowing to assess the presence and the photosynthetic performance of different phytoplankton taxa based on the spectral composition of their light harvesting pigments. The FRRF-derived photosynthetic characteristics were used to calculate the initial slope, the half saturation, and the maximum level of Photosynthesis vs Irradiance relationship. FRRF data were acquired continuously, at 1-minute time intervals.

Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol.

Properties of seawater (partial pressure of carbon dioxide (pCO2)) from a ProOceanus CO2-Pro sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements of partial pressure of carbon dioxide (pCO2), using a ProOceanus CO2-Pro instrument mounted on the flowthrough system. This automatic sensor is fitted with an equilibrator made of gas permeable silicone membrane and an internal detection loop with a non-dispersive infrared detector of PPSystems SBA-4 CO2 analyzer. A zero-CO2 baseline is provided for the subsequent measurements circulating the internal gas through a CO2 absorption chamber containing soda lime or Ascarite. The frequency of this automatic zero point calibration was set to be 24 hours. All data recorded during zeroing processes were discarded with the 15-minute data after each calibration. The output of CO2-Pro is the mole fraction of CO2 in the measured water and the pCO2 is obtained using the measured total pressure of the internal wet gas. The fugacity of CO2 (fCO2) in the surface seawater, whose difference with the atmospheric CO2 fugacity is proportional to the air-sea CO2 fluxes, is obtained by correcting the pCO2 for non-ideal CO2 gas concentration according to Weiss (1974). The fCO2 computed using CO2-Pro measurements was corrected to the sea surface condition by considering the temperature effect on fCO2 (Takahashi et al., 1993). The surface seawater observations that were initially estimated with a 15 seconds frequency were averaged every 5-min cycle. The performance of CO2-Pro was adjusted by comparing the sensor outputs against the thermodynamic carbonate calculation of pCO2 using the carbonic system constants of Millero et al. (2006) from the determinations of total inorganic carbon (CT ) and total alkalinity (AT ) in discrete samples collected at sea surface. AT was determined using an automated open cell potentiometric titration (Haraldsson et al. 1997). CT was determined with an automated coulometric titration (Johnson et al. 1985; 1987), using the MIDSOMMA system (Mintrop, 2005). fCO2 data are flagged according to the WOCE guidelines following Pierrot et al. (2009) identifying recommended values and questionable measurements giving additional information about the reasons of the questionability.

Wave Statistics and Space-time Extremes via Stereo Imaging

We present an analysis of the space-time dynamics of oceanic sea states exploiting stereo imaging techniques. In particular, a novel Wave Acquisition Stereo System (WASS) has been developed and deployed at the oceanographic tower Acqua Alta in the Northern Adriatic Sea, off the Venice coast in Italy. The analysis of WASS video measurements yields accurate estimates of the oceanic sea state dynamics, the associated directional spectra and wave surface statistics that agree well with theoretical models. Finally, we show that a space-time extreme, defined as the expected largest surface wave height over an area, is considerably larger than the maximum crest observed in time at a point, in agreement with theoretical predictions.

Characterization and Test of a Data Acquisition System for PET

A small Positron Emission Tomography demonstrator based on LYSO slabs and Silicon Photomultiplier matrices is under construction at the University and INFN of Pisa. In this paper we present the characterization results of the read-out electronics and of the detection system. Two SiPM matrices, composed by 8 × 8 SiPM pixels, 1.5 mm pitch, have been coupled one to one to a LYSO crystals array. Custom Front-End ASICs were used to read the 64 channels of each matrix. Data from each Front-End were multiplexed and sent to a DAQ board for the digital conversion; a motherboard collects the data and communicates with a host computer through a USB port. Specific tests were carried out on the system in order to assess its performance. Futhermore we have measured some of the most important parameters of the system for PET application.

Aplicaciones de interés forestal de las imágenes obtenidas con el sensor Multi-angle Imaging SpectroRadiometer (MISR)

Las aplicaciones de la teledetección al seguimiento de lo que ocurre en la superficie terrestre se han ido multiplicando y afinando con el lanzamiento de nuevos sensores por parte de las diferentes agencias espaciales. La necesidad de tener información actualizada cada poco tiempo y espacialmente homogénea, ha provocado el desarrollo de nuevos programas como el Earth Observing System (EOS) de la National Aeronautics and Space Administration (NASA). Uno de los sensores que incorpora el buque insignia de ese programa, el satélite TERRA, es el Multi-angle Imaging SpectroRadiometer (MISR), diseñado para capturar información multiangular de la superficie terrestre. Ya desde los años 1970, se conocía que la reflectancia de las diversas ocupaciones y usos del suelo variaba en función del ángulo de observación y de iluminación, es decir, que eran anisotrópicas. Tal variación estaba además relacionada con la estructura tridimensional de tales ocupaciones, por lo que se podía aprovechar tal relación para obtener información de esa estructura, más allá de la que pudiera proporcionar la información meramente espectral. El sensor MISR incorpora 9 cámaras a diferentes ángulos para capturar 9 imágenes casi simultáneas del mismo punto, lo que permite estimar con relativa fiabilidad la respuesta anisotrópica de la superficie terrestre. Varios trabajos han demostrado que se pueden estimar variables relacionadas con la estructura de la vegetación con la información que proporciona MISR. En esta Tesis se ha realizado una primera aplicación a la Península Ibérica, para comprobar su utilidad a la hora de estimar variables de interés forestal. En un primer paso se ha analizado la variabilidad temporal que se produce en los datos, debido a los cambios en la geometría de captación, es decir, debido a la posición relativa de sensores y fuente de iluminación, que en este caso es el Sol. Se ha comprobado cómo la anisotropía es mayor desde finales de otoño hasta principios de primavera debido a que la posición del Sol es más cercana al plano de los sensores. También se ha comprobado que los valores máximo y mínimo se van desplazando temporalmente entre el centro y el extremo angular. En la caracterización multiangular de ocupaciones del suelo de CORINE Land Cover que se ha realizado, se puede observar cómo la forma predominante en las imágenes con el Sol más alto es convexa con un máximo en la cámara más cercana a la fuente de iluminación. Sin embargo, cuando el Sol se encuentra mucho más bajo, ese máximo es muy externo. Por otra parte, los datos obtenidos en verano son mucho más variables para cada ocupación que los de noviembre, posiblemente debido al aumento proporcional de las zonas en sombra. Para comprobar si la información multiangular tiene algún efecto en la obtención de imágenes clasificadas según ocupación y usos del suelo, se han realizado una serie de clasificaciones variando la información utilizada, desde sólo multiespectral, a multiangular y multiespectral. Los resultados muestran que, mientras para las clasificaciones más genéricas la información multiangular proporciona los peores resultados, a medida que se amplían el número de clases a obtener tal información mejora a lo obtenido únicamente con información multiespectral. Por otra parte, se ha realizado una estimación de variables cuantitativas como la fracción de cabida cubierta (Fcc) y la altura de la vegetación a partir de información proporcionada por MISR a diferentes resoluciones. En el valle de Alcudia (Ciudad Real) se ha estimado la fracción de cabida cubierta del arbolado para un píxel de 275 m utilizando redes neuronales. Los resultados muestran que utilizar información multiespectral y multiangular puede mejorar casi un 20% las estimaciones realizadas sólo con datos multiespectrales. Además, las relaciones obtenidas llegan al 0,7 de R con errores inferiores a un 10% en Fcc, siendo éstos mucho mejores que los obtenidos con el producto elaborado a partir de datos multiespectrales del sensor Moderate Resolution Imaging Spectroradiometer (MODIS), también a bordo de Terra, para la misma variable. Por último, se ha estimado la fracción de cabida cubierta y la altura efectiva de la vegetación para 700.000 ha de la provincia de Murcia, con una resolución de 1.100 m. Los resultados muestran la relación existente entre los datos espectrales y los multiangulares, obteniéndose coeficientes de Spearman del orden de 0,8 en el caso de la fracción de cabida cubierta de la vegetación, y de 0,4 en el caso de la altura efectiva. Las estimaciones de ambas variables con redes neuronales y diversas combinaciones de datos, arrojan resultados con R superiores a 0,85 para el caso del grado de cubierta vegetal, y 0,6 para la altura efectiva. Los parámetros multiangulares proporcionados en los productos elaborados con MISR a 1.100 m, no obtienen buenos resultados por sí mismos pero producen cierta mejora al incorporarlos a la información espectral. Los errores cuadráticos medios obtenidos son inferiores a 0,016 para la Fcc de la vegetación en tanto por uno, y 0,7 m para la altura efectiva de la misma. Regresiones geográficamente ponderadas muestran además que localmente se pueden obtener mejores resultados aún mejores, especialmente cuando hay una mayor variabilidad espacial de las variables estimadas. En resumen, la utilización de los datos proporcionados por MISR ofrece una prometedora vía de mejora de resultados en la media-baja resolución, tanto para la clasificación de imágenes como para la obtención de variables cuantitativas de la estructura de la vegetación. ABSTRACT Applications of remote sensing for monitoring what is happening on the land surface have been multiplied and refined with the launch of new sensors by different Space Agencies. The need of having up to date and spatially homogeneous data, has led to the development of new programs such as the Earth Observing System (EOS) of the National Aeronautics and Space Administration (NASA). One of the sensors incorporating the flagship of that program, the TERRA satellite, is Multi-angle Imaging Spectroradiometer (MISR), designed to capture the multi-angle information of the Earth's surface. Since the 1970s, it was known that the reflectance of various land covers and land uses varied depending on the viewing and ilumination angles, so they are anisotropic. Such variation was also related to the three dimensional structure of such covers, so that one could take advantage of such a relationship to obtain information from that structure, beyond which spectral information could provide. The MISR sensor incorporates 9 cameras at different angles to capture 9 almost simultaneous images of the same point, allowing relatively reliable estimates of the anisotropic response of the Earth's surface. Several studies have shown that we can estimate variables related to the vegetation structure with the information provided by this sensor, so this thesis has made an initial application to the Iberian Peninsula, to check their usefulness in estimating forest variables of interest. In a first step we analyzed the temporal variability that occurs in the data, due to the changes in the acquisition geometry, i.e. the relative position of sensor and light source, which in this case is the Sun. It has been found that the anisotropy is greater from late fall through early spring due to the Sun's position closer to the plane of the sensors. It was also found that the maximum and minimum values are displaced temporarily between the center and the ends. In characterizing CORINE Land Covers that has been done, one could see how the predominant form in the images with the highest sun is convex with a maximum in the camera closer to the light source. However, when the sun is much lower, the maximum is external. Moreover, the data obtained for each land cover are much more variable in summer that in November, possibly due to the proportional increase in shadow areas. To check whether the information has any effect on multi-angle imaging classification of land cover and land use, a series of classifications have been produced changing the data used, from only multispectrally, to multi-angle and multispectral. The results show that while for the most generic classifications multi-angle information is the worst, as there are extended the number of classes to obtain such information it improves the results. On the other hand, an estimate was made of quantitative variables such as canopy cover and vegetation height using information provided by MISR at different resolutions. In the valley of Alcudia (Ciudad Real), we estimated the canopy cover of trees for a pixel of 275 m by using neural networks. The results showed that using multispectral and multiangle information can improve by almost 20% the estimates that only used multispectral data. Furthermore, the relationships obtained reached an R coefficient of 0.7 with errors below 10% in canopy cover, which is much better result than the one obtained using data from the Moderate Resolution Imaging Spectroradiometer (MODIS), also onboard Terra, for the same variable. Finally we estimated the canopy cover and the effective height of the vegetation for 700,000 hectares in the province of Murcia, with a spatial resolution of 1,100 m. The results show a relationship between the spectral and the multi-angle data, and provide estimates of the canopy cover with a Spearman’s coefficient of 0.8 in the case of the vegetation canopy cover, and 0.4 in the case of the effective height. The estimates of both variables using neural networks and various combinations of data, yield results with an R coefficient greater than 0.85 for the case of the canopy cover, and 0.6 for the effective height. Multi-angle parameters provided in the products made from MISR at 1,100 m pixel size, did not produce good results from themselves but improved the results when included to the spectral information. The mean square errors were less than 0.016 for the canopy cover, and 0.7 m for the effective height. Geographically weighted regressions also showed that locally we can have even better results, especially when there is high spatial variability of estimated variables. In summary, the use of the data provided by MISR offers a promising way of improving remote sensing performance in the low-medium spatial resolution, both for image classification and for the estimation of quantitative variables of the vegetation structure.

Analytic design method for optimal imaging: coupling three ray sets using two free-form lens profiles

In this work, a new two-dimensional optics design method is proposed that enables the coupling of three ray sets with two lens surfaces. The method is especially important for optical systems designed for wide field of view and with clearly separated optical surfaces. Fermat’s principle is used to deduce a set of functional differential equations fully describing the entire optical system. The presented general analytic solution makes it possible to calculate the lens profiles. Ray tracing results for calculated 15th order Taylor polynomials describing the lens profiles demonstrate excellent imaging performance and the versatility of this new analytic design method.

Perfect imaging of three object points with only two analytic lens surfaces in two dimensions

In this work, a new two-dimensional analytic optics design method is presented that enables the coupling of three ray sets with two lens profiles. This method is particularly promising for optical systems designed for wide field of view and with clearly separated optical surfaces. However, this coupling can only be achieved if different ray sets will use different portions of the second lens profile. Based on a very basic example of a single thick lens, the Simultaneous Multiple Surfaces design method in two dimensions (SMS2D) will help to provide a better understanding of the practical implications on the design process by an increased lens thickness and a wider field of view. Fermat?s principle is used to deduce a set of functional differential equations fully describing the entire optical system. The transformation of these functional differential equations into an algebraic linear system of equations allows the successive calculation of the Taylor series coefficients up to an arbitrary order. The evaluation of the solution space reveals the wide range of possible lens configurations covered by this analytic design method. Ray tracing analysis for calculated 20th order Taylor polynomials demonstrate excellent performance and the versatility of this new analytical optics design concept.

Analysis of Super Imaging Properties of Spherical Geodesic Waveguide Using COMSOL Multyphisics

Negative Refractive Lens (NRL) has shown that an optical system can produce images with details below the classic Abbe diffraction limit using materials of negative dielectric and magnetic constants. Recently, two devices with positive refraction, the Maxwell Fish Eye lens (MFE) (Leonhardt et al 2000) and the Spherical Geodesic Waveguide (SGW)(Minano et all 2011) have been claimed to break the diffraction limit using positive refraction with a different meaning. In these cases, it has been considered the power transmission from a point source to a point receptor, which falls drastically when the receptor is displaced from the focus by a distance much smaller than the wavelength. Moreover, recent analysis of the SGW with defined object and image surfaces, which are both conical sections of the sphere, has shown that the system transmits images bellow diffraction limit. The key assumption is the use of a perfectly absorbing receptor called perfect drain. This receptor is capable to absorb all the radiation without reflection or scattering. Here, it is presented the COMSOL analysis of the SGW using a perfect drain that absorbs perfectly two modes. The design procedure for PD capable to absorb k modes is proposed, as well.

Perfect imaging analysis of the spherical geodesic waveguide

Negative Refractive Lens (NRL) has shown that an optical system can produce images with details below the classic Abbe diffraction limit. This optical system transmits the electromagnetic fields, emitted by an object plane, towards an image plane producing the same field distribution in both planes. In particular, a Dirac delta electric field in the object plane is focused without diffraction limit to the Dirac delta electric field in the image plane. Two devices with positive refraction, the Maxwell Fish Eye lens (MFE) and the Spherical Geodesic Waveguide (SGW) have been claimed to break the diffraction limit using positive refraction with a different meaning. In these cases, it has been considered the power transmission from a point source to a point receptor, which falls drastically when the receptor is displaced from the focus by a distance much smaller than the wavelength. Although these systems can detect displacements up to ?/3000, they cannot be compared to the NRL, since the concept of image is different. The SGW deals only with point source and drain, while in the case of the NRL, there is an object and an image surface. Here, it is presented an analysis of the SGW with defined object and image surfaces (both are conical surfaces), similarly as in the case of the NRL. The results show that a Dirac delta electric field on the object surface produces an image below the diffraction limit on the image surface.

Objective Assessment of Olfactory Function Using Functional Magnetic Resonance Imaging=Estudio objetivo del olfato mediante resonancia magnética funcional

Objective: To show the results of a device that generates automated olfactory stimuli suitable for functional magnetic resonance imaging (fMRI) experiments. Material and methods: Te n normal volunteers, 5 women and 5 men, were studied. The system allows the programming of several sequences, providing the capability to synchronise the onset of odour presentation with acquisition by a trigger signal of the MRI scanner. The olfactometer is a device that allows selection of the odour, the event paradigm, the time of stimuli and the odour concentration. The paradigm used during fMRI scanning consisted of 15-s blocks. The odorant event took 2 s with butanol, mint and coffee. Results: We observed olfactory activity in the olfactory bulb, entorhinal cortex (4%), amygdala (2.5%) and temporo-parietal cortex, especially in the areas related to emotional integration. Conclusions: The device has demonstrated its effectiveness in stimulating olfactory areas and its capacity to adapt to fMRI equipment.RESUMEN Objetivo: Mostrar los resultados del olfatómetro capaz de generar tareas olfativas en un equipo de resonancia magnética funcional (fMRI). Material y métodos: Estudiamos 10 sujetos normales: 5 varones y 5 mujeres. El olfatómetro está dise ̃ nado para que el estímulo que produce se sincronice con el equipo de fMRI mediante la se ̃ nal desencadenante que suministra el propio equipo. El olfatómetro es capaz de: selec- cionar el olor, secuenciar los distintos olores, programar la frecuencia y duración de los olores y controlar la intensidad del olor. El paradigma utilizado responde a un dise ̃ no de activación asociada a eventos, en el que la duración del bloque de activación y de reposo es de 15 s. La duración del estímulo olfativo (butanol, menta o café) es de 2 segundos, durante toda la serie que consta de 9 ciclos. Resultados: Se ha observado reactividad (contraste BOLD) en las diferentes áreas cerebrales involucradas en las tareas olfativas: bulbo olfatorio, córtex entorrinal (4%), amigdala (2,5%) y córtex temporoparietal. Las áreas relacionadas con integración de las emociones tienen una reactividad mayor. Conclusiones: El dispositivo propuesto nos permite controlar de forma automática y sincronizada los olores necesarios para estudiar la actividad de las áreas olfatorias cerebrales mediante fMRI.

Perfect imaging of point sources with positive refraction

The capability of a device called the Spherical Geodesic Waveguide (SGW) to produce images with details below the classic Abbe diffraction limit (super-resolution) is analyzed here. The SGW is an optical system equivalent (by means of Transformation Optics) to the Maxwell Fish Eye (MFE) refractive index distribution. Recently, it has been claimed that the necessary condition to get super-resolution in the MFE and the SGW is the use of a Perfect Point Drain (PPD). The PPD is a punctual receptor placed in the focal point that absorbs the incident wave, without reflection or scattering. A microwave circuit comprising three elements, the SGW, the source and the drain (two coaxial lines loaded with specific impedances) is designed and simulated in COMSOL. The super-resolution properties have been analyzed for different position of the source and drain and for two different load impedances: the PPD and the characteristic line impedance. The results show that in both cases super-resolution occurs only for discrete number of frequencies. Out of these frequencies, the SGW does not show SR in the analysis carried out.

Automated processing of zebrafish imaging data: a survey

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.