The snow cover plays an important role not only for the whole climate system but also for tourism and economy in the Lapland winter (e.g. dog sledding, snow mobile, etc). Snow constitutes a shelter for animals and plants during the winter due to thermal isolation, but, on the range of this investigation, it can make grazing difficult for reindeers, if the conditions are not favorable. Different approaches to the study have been made; the first and most important part of the investigation was a campaign in Järämä, in Swedish Lapland. During 3 days (between the 3rd and 5th of March 2009), a series of snow pits were done, recording snow grain size, snow layers depth, snow hardness/compactness, density and temperature. The hardness in the snow was evaluated through ram penetration tests. It was additionally studied the correspondence between the snow layers found in situ and the Sámi terminology. Another approach of the study consisted of satellite observations during the winter season 2008/2009 with day light in the region. The type of imagery used was MODIS (The Moderate Resolution Imaging Spectroradiometer) daily snow albedo and 8-day surface reflectance products. Measurements of temperature, precipitation, snow depth were used to cover the polar night time when satellite images were missing. According to these weather observations some snow metamorphisms were also studied, and their influence on the snowpack conditions. Through the comparison between all these forms of data it was found that in the winter season 2008/2009 the conditions for reindeers grazing were not good due to the formation of ice encapsulating the lichens and grass. Additionally several hard snow layers have been found in the snowpack which increase the difficulty to dig in the snow and may cause problems to the reindeers’ digestion. Snow hardness measurements with a ram penetrometer, manual tests and visual grain size observation proved these discovers. Several periods of positive temperature may cause melting/refreezing cycles contributing to the formation of hard snow layers. These conclusions are supported by the snow albedo and surface reflectance satellite imagery. In these images is visible a period with snow albedo decreasing a lot in the beginning of autumn, after the first lasting snowfall. The weather conditions in early fall, when the first durable snow occurs, are of extreme importance for the reindeers’ grazing, and in the case of the studied winter season, the conditions were not favorable.

Potato ground cover and spectral data were measured in the Columbia Basin during the 1990 growing season. Three spectral were correlated with ground cover; normalized difference, near infrared-red ratio, and the first derivative of the spectral curve at 750 nm. All models were statistically significant at the 99% level. Normalized was most correlated followed by the near infrared-red ratio, and the first derivative of the spectral curve at 750 nm. / Graduation date: 1992

La réflectance de la neige est un paramètre climatique important qui suscite l'intérêt de plusieurs disciplines telles que la glaciologie, la climatologie, la météorologie, la prévision des risques d'avalanches. Le but de cette thèse est l'étude théorique et expérimentale de la réflectance de la neige sur la partie visible et proche infrarouge du spectre solaire. Une grande partie de ce travail de recherche a été consacrée à la modélisation des propriétés optiques de la neige en fonction de ses caractéristiques physiques (taille et forme des cristaux) et de sa pollution par le carbone suie. Le modèle développé fait appel a la théorie du transfert radiatif à l'aide de la méthode adding-doubling et fournit la polarisation du rayonnement réfléchi. Les limites de la théorie (forme des cristaux de neige dans le proche infrarouge) ont été mises en évidence lors de confrontations avec des mesures effectuées en laboratoire et sur le terrain. Cette étude s'inscrit aussi dans le cadre de la télédétection satellitaire et a pour but l'analyse des futures données du polarimètre-imageur P.O.L.D.E.R. (polarization and directionality of earth's reflectance) au dessus de l'Antarctique. Pour cela, un modèle prenant en compte la B.R.D.F. (bidirectional reflectance diffusion function) et les rugosités de surface (sastrugi) a été mis au point. Des mesures terrain de B.R.D.F. au pôle Sud nous ont été fournies et les résultats de comparaison avec le modèle sont prometteurs

A portable dual-camera video system was used to evaluate the potential for using total projected green cover as an indirect measure of weed infestations in a wheat crop during early growth stages. The video system would have applications in mapping weed infestations to assist precision farming operations. <p>The two cameras provided a real-time composite image of reflected light measured in red (640 nm), and near-infrared (860 nm) wavelengths. A simple ratio of reflected light intensity in each wavelength was used to isolate the growing plants from the background. Software was developed to automatically adjust for varying ambient light conditions and calculate the percentage of the image occupied by growing plants. Total green cover was measured at randomly selected sites prior to direct seeding wheat and at four growth stages following wheat emergence. The portion of green cover observed was compared to crop and weed dry matter at each location. Weed infestations at each location were estimated by measuring the total green cover and subtracting the projected green cover due to the crop alone. A minimum weed dry matter of 20 g/m2 and 30 g/m2 could be detected by the video system at the 3-leaf and 5-leaf growth stages, respectively. Weed dry matter less than 20 g/m2 could not be detected reliably due to the variability of the wheat crop. Detection of weeds within the crop beyond the 5-leaf stage using this method was difficult due to crop canopy closure.

Graduation date: 1993

<p>Breast conserving surgery (BCS) is a common treatment option for breast cancer patients. The goal of BCS is to remove the entire tumor from the breast while preserving as much normal tissue as possible for a better cosmetic outcome after surgery. Specifically, the excised specimen must have at least 2 mm of normal tissue surrounding the diseased mass. Unfortunately, a staggering 20-70% of patients undergoing BCS require repeated surgeries due to the incomplete removal of the tumor diagnosed post-operatively. Due to these high re-excision rates as well as limited post-operative histopathological sampling of the tumor specimen, there is an unmet clinical need for margin assessment. Quantitative diffuse reflectance spectral imaging has previously been explored as a promising, method for providing real-time visual maps of tissue composition to help surgeons determine breast tumor margins to ensure the complete removal of the disease during breast conserving surgery. We have leveraged the underlying sources of contrast in breast tissue, specifically total hemoglobin content, beta-carotene content, and tissue scattering, and developed various fiber optics based spectral imaging systems for this clinical application. Combined with a fast inverse Monte Carlo model of reflectance, previous studies have shown that this technology may be able to decrease re-excision rates for BCS. However, these systems, which all consist of a broadband source, fiber optics probes, an imaging spectrograph and a CCD, have severe limitations in system footprint, tumor area coverage, and speed for acquisition and analysis. The fiber based spectral imaging systems are not scalable to smaller designs that cover a large surveillance area at a very fast speed, which ultimately makes them impractical for use in the clinical environment. The objective of this dissertation was to design, develop, test, and show clinical feasibility of a novel wide field spectral imaging system that utilizes the same scientific principles of previously developed fiber optics based imaging systems, but improves upon the technical issues, such as size, complexity, and speed,to meet the demands of the intra-operative setting. </p><p>First, our simple re-design of the system completely eliminated the need for an imaging spectrograph and CCD by replacing them with an array of custom annular photodiodes. The geometry of the photodiodes were designed with the goal of minimizing optical crosstalk, maximizing SNR, and achieving the appropriate tissue sensing depth of up to 2 mm for tumor margin assessment. Without the imaging spectrograph and CCD, the system requires discrete wavelengths of light to launch into the tissue sample. A wavelength selection method that combines an inverse Monte Carlo model and a genetic algorithm was developed in order to optimize the wavelength choices specifically for the underlying breast tissue optical contrast. The final system design consisted of a broadband source with an 8-slot filter wheel containing the optimized set of wavelength choices, an optical light guide and quartz light delivery tube to send the 8 wavelengths of light in free space through the back apertures of each annular photodiode in the imaging array, an 8-channel integrating transimpedance amplifier circuit with a switch box and data acquisition card to collect the reflectance signal, and a laptop computer that controls all the components and analyzes the data.</p><p>This newly designed wide field spectral imaging system was tested in tissue-mimicking liquid phantoms and achieved comparable performance to previous clinically-validated fiber optics based systems in its ability to extract optical properties with high accuracy. The system was also tested in various biological samples, including a murine tumor model, porcine tissue, and human breast tissue, for the direct comparison with its fiber optics based counterparts. The photodiode based imaging system achieved comparable or better SNR, comparable extractions of optical properties extractions for all tissue types, and feasible improvements in speed and coverage for future iterations. We show proof of concept in performing fast, wide field spectral imaging with a simple, inexpensive design. With a reduction in size, cost, number of wavelengths used, and overall complexity, the system described by this dissertation allows for a more seamless scaling to higher pixel number and density in future iterations of the technology, which will help make this a clinically translatable tool for breast tumor margin assessment.</p> / Dissertation

The thesis presents an investigation of the potential of measuring plant condition from hyperspectral reflectance data. To do this, some linear methods for embedding the high dimensional hyperspectral data and to perform regression to a plant condition space have been compared. A preprocessing step that aims at normalized illumination intensity in the hyperspectral images has been conducted and some different methods for this purpose have also been compared.A large scale experiment has been conducted where tobacco plants have been grown and treated differently with respect to watering and nutrition. The treatment of the plants has served as ground truth for the plant condition. Four sets of plants have been grown one week apart and the plants have been measured at different ages up to the age of about five weeks. The thesis concludes that there is a relationship between plant treatment and their leaves' spectral reflectance, but the treatment has to be somewhat extreme for enabling a useful treatment approximation from the spectrum. CCA has been the proposed method for calculation of the hyperspectral basis that is used to embed the hyperspectral data to the plant condition (treatment) space. A preprocessing method that uses a weighted normalization of the spectrums for illumination intensity normalization is concluded to be the most powerful of the compared methods.

A portable dual-camera video system was used to evaluate the potential for using total projected green cover as an indirect measure of weed infestations in a wheat crop during early growth stages. The video system would have applications in mapping weed infestations to assist precision farming operations. <p>The two cameras provided a real-time composite image of reflected light measured in red (640 nm), and near-infrared (860 nm) wavelengths. A simple ratio of reflected light intensity in each wavelength was used to isolate the growing plants from the background. Software was developed to automatically adjust for varying ambient light conditions and calculate the percentage of the image occupied by growing plants. Total green cover was measured at randomly selected sites prior to direct seeding wheat and at four growth stages following wheat emergence. The portion of green cover observed was compared to crop and weed dry matter at each location. Weed infestations at each location were estimated by measuring the total green cover and subtracting the projected green cover due to the crop alone. A minimum weed dry matter of 20 g/m2 and 30 g/m2 could be detected by the video system at the 3-leaf and 5-leaf growth stages, respectively. Weed dry matter less than 20 g/m2 could not be detected reliably due to the variability of the wheat crop. Detection of weeds within the crop beyond the 5-leaf stage using this method was difficult due to crop canopy closure.

<p>Among women worldwide, cervical cancer is the third most common cancer with an incidence rate of 15.3 per 100,000 and a mortality rate of 7.8 per 100,000 women. This is largely attributed to the lack of infrastructure and resources in the developing countries to support the organized screening and diagnostic programs that are available to women in developed nations. Hence, there is a critical global need for a screening and diagnostic paradigm that is effective in low-resource settings. Various strategies are described to design an optical spectroscopic sensor capable of collecting reliable diffuse reflectance data to extract quantitative optical contrasts for cervical cancer screening and diagnosis. </p><p> A scalable Monte Carlo based optical toolbox can be used to extract absorption and scattering contrasts from diffuse reflectance acquired in the cervix in vivo. [Total Hb] was shown to increase significantly in high-grade cervical intraepithelial neoplasia (CIN 2+), clinically the most important tissue grade to identify, compared to normal and low-grade intraepithelial neoplasia (CIN 1). Scattering was not significantly decreased in CIN 2+ versus normal and CIN 1, but was significantly decreased in CIN relative to normal cervical tissues. </p><p> Immunohistochemistry via anti-CD34, which stains the endothelial cells that line blood vessels, was used to validate the observed absorption contrast. The concomitant increase in microvessel density and [total Hb] suggests that both are reactive to angiogenic forces from up-regulated expression of VEGF in CIN 2+. Masson's trichrome stain was used to assess collagen density changes associated with dysplastic transformation of the cervix, hypothesized as the dominant source of decreased scattering observed. Due to mismatch in optical and histological sampling, as well as the small sample size, collagen density and scattering did not change in a similar fashion with tissue grade. Dysplasia may also induce changes in cross-linking of collagen without altering the amount of collagen present. Further work would be required to elucidate the exact sources of scattering contrast observed. </p><p> Common confounding variables that limit the accuracy and clinical acceptability of optical spectroscopic systems are calibration requirements and variable probe-tissue contact pressures. Our results suggest that using a real-time self-calibration channel, as opposed to conventional post-experiment diffuse reflectance standard calibration measurements, significantly improved data integrity for the extraction of scattering contrast. Extracted [total Hb] and scattering were also significantly associated with applied contact probe pressure in colposcopically normal sites. Hence, future contact probe spectroscopy or imaging systems should incorporate a self-calibration channel and ensure spectral acquisition at a consistent contact pressure to collect reliable data with enhanced absorption and scattering contrasts. </p><p> Another method to enhance optical contrast is to selectively interrogate different depths in the dysplastic cervix. For instance, scattering has been shown to increase in the epithelium (increase in nuclear-to-cytoplasmic ratio) while decrease in the stroma (re-organization of the extra-cellular matrix and changes in of collagen fiber cross-links). A fiber-optic probe with 45° illumination and collection fibers with a separation distance of 330 &#956;m was designed and constructed to selectively interrogate the cervical epithelium. Mean extraction errors from liquid phantoms with optical properties mimicking the cervical epithelium for &#956;a and &#956;s' were 11.3 % and 12.7 %, respectively. Diffuse reflectance spectra from 9 sites in four loop electrosurgical excision procedure (LEEP) patients were analyzed. Preliminary data demonstrate the utility of the oblique fiber geometry in extracting scattering contrast in the cervical epithelium. Further work is needed to study the systematic error in optical property extraction and to incorporate simultaneous extraction of epithelial and stromal contrasts using both flat and oblique illumination and collection fibers. </p><p> Various strategies, namely self-calibration, consistent contact pressure, and the incorporation of depth-selective sensing, have been proposed to improve the data integrity of an optical spectroscopic system for maximal contrast. In addition to addressing field operation requirements (such as power and operator training requirement), these improvements should enable the collection of reliable spectral data to aid in the adoption of optical smart sensors in the screening and diagnosis of cervical precancer, especially in a global health setting.</p> / Dissertation

Reflectance anisotropy spectroscopy is a non-contact technique for surface detection. which means through the optical reflection from surface of the substrate measured. Because of its high sensitivity, RAS is used for in real-time control of semiconductor epitaxy. On our study, RAS is used to study the surface characteristics of liquid crystal alignment layer. We used rubbing for polyimide film to achieve alignment purposes. The rubbing strength is determined by adjusting the pile impress and the number of rubbed. We found that the anisotropy spectroscopy will appear after rubbing. And the strength of RA signals changes with photon energy of the probe beam. The pretile angle of the liquid crystal sandwiched in between rubbed PI show certain degree correlation with RA strength. In addition, using surface free energy measurement to explore the relationship with pretilt angle and try to connect three of them. We also tried to measure the reflection signal from the sample back. We found the signal of sample back would decay in UV region and it may be a result of UV absorption in the substrate.