For several years, we have been developing vortex phase masks based on sub-wavelength gratings, known as Annular Groove Phase Masks. Etched onto diamond substrates, these AGPMs are currently designed to be used in the thermal infrared (ranging from 3 to 13 pm). Our AGPMs were first installed on VLT/NACO and VLT/VISIR in 2012, followed by LBT/LMIRCam in 2013 and Keck/NIRC2 in 2015. In this paper, we review the development, commissioning, on-sky performance, and early scientific results of these new coronagraphic modes and report on the lessons learned. We conclude with perspectives for future developments and applications.

Este trabalho explora as propriedades óticas das plantas no infravermelho termal para avaliar como esse tipo de dado poderia ser usado em estudos de ecossistemas, tanto no laboratório, quanto no campo, ou com sensoriamento remoto, e também, para analisar vários aspectos da química de diferentes espécies. Espectros de refletância total atenuada (ATR) das folhas mostram bandas de absorção devidas às vibrações moleculares de diferentes compostos, e quando ATR de folhas frescas foi comparado com espectros de compostos padrões selecionados, foi possível relacionar bandas das folhas com bandas de celulose, cutina, sílica ( quartzo microcristalino), água e triterpeno ácido. Usando um procedimento de busca foi possível localizar espécies com características químicas semelhantes, dentro de uma biblioteca espectral. Potenciais fontes de variações foram exploradas para compreender se o ATR poderia ser usado na identificação de espécies. Variações temporais, espaciais e posicionais. Por exemplo, folhas de sol mostraram diferenças espectrais de folhas de sombra. Espectros das superfícies adaxiais quase sempre eram diferentes das abaxiais. Indivíduos da mesma espécies quase sempre mostraram espectros muito similares. Numa simulação de um estudo ecológico de campo usando ATR como ferramenta para a identificação de espécies, 82% dos indivíduos foram corretamente identificados. Imagens de microscopia de varredura (SEM) das folhas foram usadas com medidas de refletância hemisférica direcional (DHR) para estudar os efeitos da tridimensionalidade estrutural sobre o comportamento espectral. Por exemplo, estruturas formadas pelas ceras na superfície foliar podem causar atenuação das características espectrais devidas ao efeito Holblaum (de cavidade). Medidas de DHR podem ser relacionadas à emissividade pela lei de Kirchhoff (ε=1-R), e por isso é importante compreende-las, pelas informações que podem estar disponíveis por sensoriamento remoto. Para explorar os efeitos da estrutura do dossel nos espectros, medidas de emissividade foram feitas usando um espectrômetro de campo. Os dados mostram, pela primeira vez, que é possível discriminar características de emissividade espectral de plantas daquelas do ambiente ao redor. Medidas espectrais feitas com distâncias horizontais crescentes de alguns dosséis de árvores mostraram uma atenuação progressiva das características de emissividade espectral, devido ao número crescente de cavidades no campo de visão, e problemas de correção atmosférica. Apesar disso, há potencial no estudo de plantas usando sensoriamento remoto no infravermelho termal. Um sensor em plataforma de avião operando na janela atmosférica entre 8-14 m teria que ter uma alta razão sinal-ruído, e um campo de visão pequeno que permittise medidas das folhas individualmente. Métodos de calibragem e algoritmos para análises espectrais precisariam ser refinados a fim de permitir a extração das características sutis de emissividade das plantas. / This work explores the thermal infrared spectral properties of plants to evaluate how such data might be used in laboratory, field, and remote sensing studies of ecosystems, and to analyze diverse chemical aspects of plant species. Attenuated total reflectance (ATR) spectra of plant leaves display absorption bands caused by the fundamental molecular vibrations of various compounds. By comparing ATR spectra of fresh leaves to reference spectra of selected pure compounds, it was possible to assign a number of leaf absorption bands related to cellulose, cutin, silica ( quartz micro-crystalline), water and acid triterpene. By using spectral search/match procedures it was possible to locate species within a database of leaf spectra that had similar chemical characteristics. Potential sources of spectral variation were explored, including temporal, spatial, and positional variations. For example, sun leaves showed spectral differences compared to shaded leaves. Spectra of adaxial leaf surfaces were commonly different from those of abaxial surfaces. Individuals of the same species consistently showed very similar spectra. In a simulated ecological study using field ATR measurements as a tool for species identification 82% of the individuals were correctly identified. Scanning electron microscope images were utilized in conjunction with directional hemispherical reflectance (DHR) measurements of leaves to study 3-dimensional structural effects on spectral behavior. For example, small-scale structures formed by waxes on a leaf surface can cause the attenuation of spectral features due to the Holblaum (cavity) effect. DHR measurements can be linked to emissivity using Kirchhoff’s law (ε=1-R), and therefore are relevant to understanding the kinds of information concerning plants that may be available via remote sensing. Finally, to explore the effects of canopy structure on spectra, direct emissivity measurements were made by using a field spectrometer. The data show, for the first time, that it is possible to discriminate spectral emissivity features of plants from those of the surrounding environment. Spectral measurements made at increasing horizontal distances from several tree canopies showed progressive attenuation of the spectral emissivity features. This attenuation is ascribed to the increasing proportion of canopy voids in the instrument field of view, and to increased surface scattering effects. Errors associated with removal of atmospheric features also contributed to the loss of spectral information at greater measurement distances. Despite these problems, there is untapped potential for using thermal infrared remote sensing measurements to study plants. To be effective an airborne sensor operating in the 8-14 m atmospheric window would need high signal-to-noise and a small instantaneous field of view to enable measurements of individual leaf surfaces. Data calibration methods and spectral analysis algorithms would also require refinement to permit the extraction of subtle plant emissivity features.

Este trabalho explora as propriedades óticas das plantas no infravermelho termal para avaliar como esse tipo de dado poderia ser usado em estudos de ecossistemas, tanto no laboratório, quanto no campo, ou com sensoriamento remoto, e também, para analisar vários aspectos da química de diferentes espécies. Espectros de refletância total atenuada (ATR) das folhas mostram bandas de absorção devidas às vibrações moleculares de diferentes compostos, e quando ATR de folhas frescas foi comparado com espectros de compostos padrões selecionados, foi possível relacionar bandas das folhas com bandas de celulose, cutina, sílica ( quartzo microcristalino), água e triterpeno ácido. Usando um procedimento de busca foi possível localizar espécies com características químicas semelhantes, dentro de uma biblioteca espectral. Potenciais fontes de variações foram exploradas para compreender se o ATR poderia ser usado na identificação de espécies. Variações temporais, espaciais e posicionais. Por exemplo, folhas de sol mostraram diferenças espectrais de folhas de sombra. Espectros das superfícies adaxiais quase sempre eram diferentes das abaxiais. Indivíduos da mesma espécies quase sempre mostraram espectros muito similares. Numa simulação de um estudo ecológico de campo usando ATR como ferramenta para a identificação de espécies, 82% dos indivíduos foram corretamente identificados. Imagens de microscopia de varredura (SEM) das folhas foram usadas com medidas de refletância hemisférica direcional (DHR) para estudar os efeitos da tridimensionalidade estrutural sobre o comportamento espectral. Por exemplo, estruturas formadas pelas ceras na superfície foliar podem causar atenuação das características espectrais devidas ao efeito Holblaum (de cavidade). Medidas de DHR podem ser relacionadas à emissividade pela lei de Kirchhoff (ε=1-R), e por isso é importante compreende-las, pelas informações que podem estar disponíveis por sensoriamento remoto. Para explorar os efeitos da estrutura do dossel nos espectros, medidas de emissividade foram feitas usando um espectrômetro de campo. Os dados mostram, pela primeira vez, que é possível discriminar características de emissividade espectral de plantas daquelas do ambiente ao redor. Medidas espectrais feitas com distâncias horizontais crescentes de alguns dosséis de árvores mostraram uma atenuação progressiva das características de emissividade espectral, devido ao número crescente de cavidades no campo de visão, e problemas de correção atmosférica. Apesar disso, há potencial no estudo de plantas usando sensoriamento remoto no infravermelho termal. Um sensor em plataforma de avião operando na janela atmosférica entre 8-14 m teria que ter uma alta razão sinal-ruído, e um campo de visão pequeno que permittise medidas das folhas individualmente. Métodos de calibragem e algoritmos para análises espectrais precisariam ser refinados a fim de permitir a extração das características sutis de emissividade das plantas. / This work explores the thermal infrared spectral properties of plants to evaluate how such data might be used in laboratory, field, and remote sensing studies of ecosystems, and to analyze diverse chemical aspects of plant species. Attenuated total reflectance (ATR) spectra of plant leaves display absorption bands caused by the fundamental molecular vibrations of various compounds. By comparing ATR spectra of fresh leaves to reference spectra of selected pure compounds, it was possible to assign a number of leaf absorption bands related to cellulose, cutin, silica ( quartz micro-crystalline), water and acid triterpene. By using spectral search/match procedures it was possible to locate species within a database of leaf spectra that had similar chemical characteristics. Potential sources of spectral variation were explored, including temporal, spatial, and positional variations. For example, sun leaves showed spectral differences compared to shaded leaves. Spectra of adaxial leaf surfaces were commonly different from those of abaxial surfaces. Individuals of the same species consistently showed very similar spectra. In a simulated ecological study using field ATR measurements as a tool for species identification 82% of the individuals were correctly identified. Scanning electron microscope images were utilized in conjunction with directional hemispherical reflectance (DHR) measurements of leaves to study 3-dimensional structural effects on spectral behavior. For example, small-scale structures formed by waxes on a leaf surface can cause the attenuation of spectral features due to the Holblaum (cavity) effect. DHR measurements can be linked to emissivity using Kirchhoff’s law (ε=1-R), and therefore are relevant to understanding the kinds of information concerning plants that may be available via remote sensing. Finally, to explore the effects of canopy structure on spectra, direct emissivity measurements were made by using a field spectrometer. The data show, for the first time, that it is possible to discriminate spectral emissivity features of plants from those of the surrounding environment. Spectral measurements made at increasing horizontal distances from several tree canopies showed progressive attenuation of the spectral emissivity features. This attenuation is ascribed to the increasing proportion of canopy voids in the instrument field of view, and to increased surface scattering effects. Errors associated with removal of atmospheric features also contributed to the loss of spectral information at greater measurement distances. Despite these problems, there is untapped potential for using thermal infrared remote sensing measurements to study plants. To be effective an airborne sensor operating in the 8-14 m atmospheric window would need high signal-to-noise and a small instantaneous field of view to enable measurements of individual leaf surfaces. Data calibration methods and spectral analysis algorithms would also require refinement to permit the extraction of subtle plant emissivity features.

Esta pesquisa tem como objetivo principal desenvolver uma rotina de procedimentos de coleta de dados espectrais utilizando um espectro radiômetro de campo portátil, μFTIR Model 102, desenvolvido pela empresa Design & Prototypes, o qual permite a aquisição de espectros infravermelhos de superfícies entre 2 e 14 μm. O equipamento foi utilizado para realizar leituras de radiância e calculo de emissividade, transmitância e refletância, utilizando uma amostra de quartzo, a qual apresenta uma curva de emissividade bem conhecida no infravermelho termal (região entre 8-14 μm). Foram realizadas leituras na amostra para diferentes condições de temperatura e umidade, tanto no campo como no laboratório com o fin de obter um completo protocolo para a calibração e coleta de dados. Embora o instrumento opere numa região mais ampla, este estudo apenas avalia os dados entre 7-14 μm onde a maioria dos instrumentos a bordo de plataformas aéreas e orbitais posiciona os detectores. / The main purpose of this research is to develop a routine procedure for data collection using a field spectral radiometer, μFTIR Model 102, developed by Design & Prototypes, which allows the acquisition of infrared spectra of surfaces between 2 and 14 μm. The instrument was used to perform lectures of radiances and calculation of emissivity, transmittance and reflectance, using a sample of quartz, which shows a very well-known curve of emissivity in the thermal infrared (region between 8-14 μm). Reading were taken in the sample for different conditions of temperature and humidity, both in the field and in the laboratory with the objective of get a complete protocol for calibration and data collection. Although the instrument operating in a wider region, this study evaluates the data between 7-14 μm where most of the instruments on board of airborne platforms and orbital detectors are positioned.

Esta pesquisa tem como objetivo principal desenvolver uma rotina de procedimentos de coleta de dados espectrais utilizando um espectro radiômetro de campo portátil, μFTIR Model 102, desenvolvido pela empresa Design & Prototypes, o qual permite a aquisição de espectros infravermelhos de superfícies entre 2 e 14 μm. O equipamento foi utilizado para realizar leituras de radiância e calculo de emissividade, transmitância e refletância, utilizando uma amostra de quartzo, a qual apresenta uma curva de emissividade bem conhecida no infravermelho termal (região entre 8-14 μm). Foram realizadas leituras na amostra para diferentes condições de temperatura e umidade, tanto no campo como no laboratório com o fin de obter um completo protocolo para a calibração e coleta de dados. Embora o instrumento opere numa região mais ampla, este estudo apenas avalia os dados entre 7-14 μm onde a maioria dos instrumentos a bordo de plataformas aéreas e orbitais posiciona os detectores. / The main purpose of this research is to develop a routine procedure for data collection using a field spectral radiometer, μFTIR Model 102, developed by Design & Prototypes, which allows the acquisition of infrared spectra of surfaces between 2 and 14 μm. The instrument was used to perform lectures of radiances and calculation of emissivity, transmittance and reflectance, using a sample of quartz, which shows a very well-known curve of emissivity in the thermal infrared (region between 8-14 μm). Reading were taken in the sample for different conditions of temperature and humidity, both in the field and in the laboratory with the objective of get a complete protocol for calibration and data collection. Although the instrument operating in a wider region, this study evaluates the data between 7-14 μm where most of the instruments on board of airborne platforms and orbital detectors are positioned.

Esta pesquisa tem como objetivo principal desenvolver uma rotina de procedimentos de coleta de dados espectrais utilizando um espectro radiômetro de campo portátil, μFTIR Model 102, desenvolvido pela empresa Design & Prototypes, o qual permite a aquisição de espectros infravermelhos de superfícies entre 2 e 14 μm. O equipamento foi utilizado para realizar leituras de radiância e calculo de emissividade, transmitância e refletância, utilizando uma amostra de quartzo, a qual apresenta uma curva de emissividade bem conhecida no infravermelho termal (região entre 8-14 μm). Foram realizadas leituras na amostra para diferentes condições de temperatura e umidade, tanto no campo como no laboratório com o fin de obter um completo protocolo para a calibração e coleta de dados. Embora o instrumento opere numa região mais ampla, este estudo apenas avalia os dados entre 7-14 μm onde a maioria dos instrumentos a bordo de plataformas aéreas e orbitais posiciona os detectores. / The main purpose of this research is to develop a routine procedure for data collection using a field spectral radiometer, μFTIR Model 102, developed by Design & Prototypes, which allows the acquisition of infrared spectra of surfaces between 2 and 14 μm. The instrument was used to perform lectures of radiances and calculation of emissivity, transmittance and reflectance, using a sample of quartz, which shows a very well-known curve of emissivity in the thermal infrared (region between 8-14 μm). Reading were taken in the sample for different conditions of temperature and humidity, both in the field and in the laboratory with the objective of get a complete protocol for calibration and data collection. Although the instrument operating in a wider region, this study evaluates the data between 7-14 μm where most of the instruments on board of airborne platforms and orbital detectors are positioned.

Master of Science / Department of Biological & Agricultural Engineering / Ronaldo G. Maghirang / Particulate matter (PM) emissions from open beef cattle feedlots depend heavily on the level of water on the pen surface. Wet pen surfaces are able to keep PM emissions low, while dry surfaces have much higher rates of emission. Current research shows that 20-25% surface water content is a critical threshold for minimizing PM emissions from open cattle feedlots. The amount of water on the pen surface will also dictate the level of gaseous emissions, such as ammonia, nitrous oxide, and hydrogen sulfide. Traditional methods of measuring pen surface water are not sufficient within a dense cattle feedlot and cannot provide a continuous method of measurement unattended. The process of using infrared thermometry and meteorological variables to remotely sense surface water provides an inexpensive, ground level approach. Testing in laboratory, outdoor, and feedlot conditions was conducted to analyze the potential of using the thermal inertia remote sensing approach. This approach involved continuous measurement of weighted soil water content, surface temperature of the soil, air temperature, solar radiation, wind speed, and relative humidity. Controlled laboratory testing performed the best at predicting soil water content from the difference in soil surface and air temperature, with the coefficient of determination (R2) at 0.91 for a Smolan silt loam and 0.83 for dry feedlot soil. Outdoor testing achieved mixed results with R2 values only as high as 0.38 for 10-cm soil layer and 0.67 for 5-cm soil layer. Testing in a cattle feedlot with dry, loose manure layer proved to be imprecise, but was able to differentiate surface water levels varying from 4.1% to 9.1% wet basis.

La température de surface terrestre (LST) est un paramètre important dans les systèmes climatiques. Les données infrarouge thermique (TIR) contiennent un nombre d'information de la surface terrestre et de l'atmosphère sont des sources de l'information important pour estimer la LST à l'aide de télédétection. / Land surface temperature (LST) is an important parameter in climate systems. Hyperspectral thermal infrared (TIR) data, containing large information about the surface and the atmosphere, is an important source of information for retrieving LST by remote-sensing.

Water temperature directly affects biological and chemical processes of fresh water ecosystems. Elevated instream temperatures are commonplace in the Virgin River of southwestern Utah during summer due to a hot desert climate and high water demands that result in low stream flows. This is of concern since the Virgin River is home to two endangered species, the Virgin River Chub (Gila seminuda) and Woundfin (Plagopterus argentissimus). Efforts to model instream temperatures within the Virgin River have been undertaken to help mitigate elevated instream temperatures including the development of a two-zone temperature and solute (TZTS) model. This model was developed to approximate the dominant processes that influence instream temperatures and used both temperature and solute data in parameter estimation. Past model applications highlighted two concerns: (1) how to confidently estimate the high number of parameters and (2) whether Rhodamine WT (RhWT) could be used as a conservative solute tracer within the Virgin River. To begin addressing these issues, spatially representative data were collected to facilitate the physical estimation of two previously calibrated parameters: total average channel width (BTOT) and the fraction of channel width associated with dead zones (β). Methods for analyzing multispectral and thermal infrared imagery were developed to provide estimates of these parameters at different resolutions. Three different TZTS model calibration cases were then evaluated to determine how decreasing the calibrated parameters and increasing the resolution and frequency at which these parameters are estimated improved model predictions and/or decreased parameter uncertainty. While temperature predictions did not change significantly in each of the calibrations, parameter uncertainty was reduced. The concern regarding the use of RhWT resulted in a series of studies to quantify the potential losses of RhWT within this system. A batch sorption study resulted in distribution coefficient values lower than those found in literature. A photodegradation study suggested possible photolysis; however, a dual tracer study conducted within the Virgin River comparing Br- (conservative tracer) with RhWT confirmed that there was insignificant RhWT loss within this system.

Anthropogenic influences and climate change are warming rivers in New Brunswick and threatening the cold water habitats of native salmonids. When ambient river temperatures in summer exceed the tolerance level of Atlantic salmon and brook trout, individuals behaviourally thermoregulate by seeking out cold water refugia. These critical thermal habitats are often created by tributaries and concentrated groundwater discharge. Thermal infrared imagery was used to map cold water anomalies along a 53 km reach of the Cains River on 23 July 2008. Although efficient and useful for mapping surface temperature of a continuous stream reach, the fish did not use all identified thermal anomalies as refugia. Overall, 100 % of observed large brook trout >35 cm in length were found in 30 % of the TIR-mapped cold water anomalies. Ninety eight percent of observed small brook trout 8 – 30 cm in length were found in 80 % of the mapped cold water anomalies and their densities within anomalies were significantly higher than densities outside of anomalies. Fifty nine percent of observed salmon parr were found in 65 % of the mapped anomalies; however, they were dispersed within study sites and their densities were not significantly different within anomalies compared to outside of the anomalies. No brook trout were observed at the seven noncold water study sites that were investigated. Preference curves for various habitat variables including velocity, temperature, depth, substrate, and deep water availability near cold water anomalies were developed based on field investigations during high temperature events (ambient river temperature >21 oC). Combined with thermal imagery, managers can use the physical descriptions of thermal refugia developed here as a tool to help conserve and restore critical thermal refugia for Atlantic salmon and brook trout on the Cains River, and potentially similar river systems.