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<p>In recent years, hyperspectral imaging technologies have been broadly applied to evaluate complex plant physiological features such as leaf moisture content, nutrient level and disease stress. A  critical  component  of  this  technique  is  white  referencing  used  to  remove  the  effect  of  non-uniform  lighting  intensity  in  different  wavelengths  on  raw  hyperspectral  images. Based  on  the  literature,  the leaf  geometry (e.g.,  tilt  angles)  and its interaction  with  the  illumination  severely impact  the  plant  reflectance  spectra  and vegetation  indices  such  as  the  normalized  difference  vegetation index (NDVI).  This thesis is  aimed to address the issues caused by the tilt angles across the leaf surface. To achieve this, two methods based on the fusion of the hyperspectral images and 3D  point  clouds  were  proposed.  The  first  method  was  to  build  a  3D  white  reference  library  in  which a point with almost the same tilt angle, height and position with the pixel on the plant leaf can be found, and then the white reference spectrum at that point can be used to calibrate the raw spectrum of the leaf pixel. The second method was to observe and summarize how the plant spectra and NDVI values changed with the leaf angles. Using the changing trends, the original NDVI and spectra  of  leaf  pixels  at  different  angles  can  be  calibrate  to  a  same  standard  as  if  the  leaf  was  imaged  at  a  flat  and  horizontal  surface.  The  approach  was  called  3D  calibration.  The  results  showed  that  the NDVI  values significantly  changed  with  leaf  angles  and  the  changing  trends differed  between  the  corn  and  soybean  species.  To evaluate the  performance  of  3D  calibration, 180 soybean plants with different genotypes, nitrogen (N), phosphorus (P) and water treatments were  grown  in  the  greenhouse. Each  plant  was  imaged  in three systems:  the high-throughput greenhouse hyperspectral imaging system, the indoor desktop imaging system with a visible-near infrared  (VINIR)  hyperspectral camera and  an  Intel  RealSense  depth  camera  and  the handheld device hyperspectral imaging system. In the greenhouse system, the whole canopy was captured. In the indoor desktop system, the partial canopy was captured because of the space limitation and the  top-matured  leaf  (the  middle  leaf  of  the  uppermost  matured  trifoliate)  was  focused.  The proposed  3D  calibration  was  applied  on  the  top-matured  leaf  to  remove  angle  impacts.  In  the  handheld device system, the flat top-matured leaf was captured. After done with imaging work, the plants were harvested to collect the ground truth data such as relative water content (RWC), N content and P content. Combined with the ground truth data, the NDVI values from three systems were  used  to  discriminate  different  genotypes  and  biochemical treatments,  whereas,  the  spectra from three systems were used to build partial least squares regression (PLSR) models for N, P and RWC. The results showed that the averaged tilt angles of top-matured leaves were impacted by different treatments. For instance, the low-nitrogen (LN) plants showed significantly higher leaf angles than high-nitrogen (HN) plants; the leaf angles on water-stressed (WS) plants were higher than those on well-watered (WW) plants. The leaf angles carried some signals that influenced not only the NDVI discrimination but also the PLSR modelling results. The signals were lost after 3D calibration.  For  the  top-matured  leaves,  the  discrimination  and  modelling  results  after  3D  calibration in the indoor desktop system were close to those from the flat leaves in the handheld device  system.  The  proposed  3D  calibration  approach  has  a  potential  to  eliminate  leaf  angle  impacts.</p>

The global temperature is at an all-time high, the polar ice is melting, the sea levels are rising and the associated disasters are a time bomb. These variations in temperature are thought to trace roots to anthropogenic sources. In order to mitigate these changes and slow down the rate of warming, several efforts have been made locally and internationally. One of the agreed up-on way to do this is by using forests as reservoirs for carbon since carbon is one of those greenhouses gasses responsible for the warming. Mau forest, in Kenya, is one of those ecosystems where degradation has happened tremendously, though still viewed as a potential site for reclamation. Using GIS and remote sensing analysis of Landsat images, the study sought to compare various change detection techniques, find the amount of biomass lost or gained in the forest and the possible income accrued in case the forest is placed under the Kyoto protocol’s Clean Development Mechanism (CDM). Various vegetation ratios were used in the study ranging from NDVI, NDII to RSR. The results obtained from these ratios were not quite convincing as setting threshold for the ratios to separate dense forest from other forms of vegetation was not straightforward. As a consequence, the three ratios NDVI, NDII and RSR were combined and substituted for RGB bands respectively. A classification was done using this combination and the results compared to classifications based on tasselled cap and principal component analysis (PCA). The results of the various methods showed that the forest has lost its biomass over time. The methods indicated that the section of the forest studied lost between 8088 ha and 9450 ha of dense forest land between 1986 and 2010. This is between 29% and 35% of forest cover lost depending on the various methods of change detection used. This acreage when converted into forest biomass at a rate of 236 Mg.ha-1 gives a value of between 1908768 tons and 2230200 tons of carbon. If the Mau forest were registered as Kyoto compliant, then in the carbon market, this would have been a loss of between $24.1m and $ 28.2m according to California carbon dashboard (28th, May 2015). This is a huge sum of money if paid to a rural community as benefits from carbon sequestration via forestry. Such are the amounts that a community can earn by protecting a forest for the purposes of carbon sequestration and trading.

Habitat degradation and hunting pose the most proximate threats to many primate species, while climate change is expected to exacerbate these threats (habitat and climate change combined henceforth as "global change") and present new challenges. Madagascar's lemurs are earth's most endangered primates, placing added urgency to their conservation in the face of global change. My dissertation focused on the critically endangered golden-crowned sifaka (Propithecus tattersalli; hereafter, "sifaka") which is endemic to fragmented forests across a gradient of dry, moderate, and wet forest types in northeastern Madagascar. I surveyed sifakas across their global range and investigated factors affecting their densities. I explored sifaka diets across different forest types and evaluated if nutritional factors influenced sifaka densities. Lastly, I investigated sifaka range-wide genetic diversity and conducted a connectivity analysis to prioritize corridor-restoration and other potential conservation efforts. Sifaka densities varied widely across forest fragments (6.8 (SE = 2.0-22.8) to 78.1 (SE = 53.1-114.8) sifakas/km²) and populations have declined by as much as 30-43% in 10 years, from ~18,000 to 10,222-12,631 individuals (95% CI: 8,230-15,966). Tree cutting, normalized difference vegetation index (NDVI) during the wet season, and Simpson's diversity index (1-D) predicted sifaka densities range-wide. Sifakas consumed over 101 plant species and spent 27.1% of their active time feeding on buds, flowers, fruits, seeds, and young and mature leaves. Feeding effort and plant part consumption varied by season, forest type, and sex. Minerals in sifaka food items (Mg (β = 0.62, SE = 0.19) and K (β = 0.58, SE = 0.20)) and wet season NDVI (β = 0.43, SE = 0.20) predicted sifaka densities. Genetic measures across forest fragments indicated that sifaka populations are becoming more isolated (moderate FIS values: mean = 0.27, range = 0.11-0.60; high M-ratios: mean = 0.59, range = 0.49-0.82; low overall effective population size: Ne = 139.8-144 sifakas). FST comparisons between fragments (mean = 0.12, range = 0.01-0.30) supported previous findings that sifakas still moved across the fragmented landscape. Further validation of these genetic results is needed. I identified critical corridors that conservation managers could protect and/or expand via active reforestation to ensure the continued existence of this critically-endangered lemur. / Doctor of Philosophy / Worldwide, many species of primates are threatened with extinction due to habitat degradation, hunting, and climate change (habitat and climate combined threats, henceforth, "global change"). These threats work at different time scales, with hunting being the most immediate and climate change likely to have its fullest impact experienced from the present to a longer time frame. Lemurs are a type of primate found only on Madagascar, an island experiencing rapid global change, which puts lemurs at a heightened risk of extinction. My dissertation research focused on the critically endangered golden-crowned sifaka (Propithecus tattersalli; hereafter, "sifaka"), a species of lemur found only in a few isolated forests across a dry to wet gradient in northeastern Madagascar. To better understand their extinction risk, I conducted surveys to estimate the number of sifakas remaining and investigated several factors that might determine how many sifakas can live in one place. I then explored how sifaka diets varied depending on the forest type that they inhabit and tested whether nutrients in their food might determine sifaka numbers. Lastly, I calculated sifaka genetic diversity to assess their ability to adapt to new environmental conditions and to determine whether sifakas can move across the landscape to find new mates and to potentially colonize new areas of habitat. Sifaka densities varied widely across their range (6.8-78.1 sifakas/km² ). Only 10,222-12,631 sifakas remain, which is 30-43% less than the range of estimates obtained 10 years ago (~18,000 sifakas). Tree cutting, normalized difference vegetation index (NDVI; a measure of plant health or "greenness" obtained from satellite data), and a tree species diversity index were useful measures to predict sifaka densities. Sifakas ate different plant parts (buds, flowers, fruits, seeds, and leaves) from over 101 plant species. The amount of time they spent eating each day varied by the time of year, forest type, and sex. On average, they spent a quarter of their day eating. Magnesium and potassium concentrations in sifaka food items also were useful nutrition-related measures to predict sifaka densities. Genetic analyses suggested that sifaka populations are becoming more isolated and inbred, meaning sifakas are breeding with other sifakas to which they are closely related. However, it appears that sifakas still can move between forest patches to find new mates and to potentially colonize new areas, if such areas are created. Further validation of these genetic results is needed. I also identified critical areas that will be important to protect and reforest to ensure that movements between populations can continue.

The Appalachian National Scenic Trail is a unit of the National Park System created by the National Trails Act of 1968. Commonly referred to as the Appalachian Trail, or the AT, this National Park has some of the longest boundaries of any park. The AT is routed more than 2000 miles along the mountains of the eastern United States. The land purchased for the protection of the AT creates a separate boundary on each side of the trail. Monitoring these boundaries for intrusions or encroachments is a difficult and time-consuming task when done totally by field methods. This thesis presents a more efficient and consistent monitoring process using remote sensing data and change detection algorithms. Using Landsat TM images, Normalized Difference Vegetation Index (NDVI), and image difference change detection, this research shows that major boundary encroachments can be detected. Detection of sub-pixel vegetation index decreases identifies specific locations for field inspection. Assuming low cost multispectral Landsat imagery is available, simple NDVI difference calculation allows this technique to be applied to the entire AT one or more times per year. This procedure would improve the response time for encroachment mediation. The producer's accuracy for finding possible encroachments was 100 percent and the consumer's accuracy for possible encroachments indicated was 78.3 percent. Due to limited image availability, this study only examines change between one pair of Landsat images. Further refinement of these techniques should investigate other Landsat images at other times. Use of other remote sensing systems and change detection algorithms could be the focus of further research. / Master of Science

Double cropping soybean after small grain harvest does not always allow sufficient canopy growth to maximize photosynthesis and seed yield. This is due to a shorter growing season and moisture deficits common to the Mid-Atlantic USA. Leaf area index (LAI) is the ratio of unit leaf area of a crop to unit ground area and is a reliable indicator of leaf area development and crop biomass. An LAI of 3.5 to 4.0 by flowering is required to maximize yield potential. Soybean LAI will vary within and between fields due to soil differences, cultivar selection, and other cultural practices. Site-specific management strategies such as varying plant population may be used to manipulate LAI and increase yield in leaf area-limited systems. Furthermore, methods to remotely sense leaf area are in order to facilitate such management strategies in large fields. The objectives of this research were to: i) determine the effect of plant population density on soybean LAI and yield; ii) determine the relationship between LAI measured at different reproductive stages and yield; iii) investigate and validate relationships between LAI and yield for two cultivars in three crop rotations across varying soil moisture regimes; iv) validate relationships found in previous work between soybean LAI and yield across soil moisture regimes in grower fields; and v) determine if normalized difference vegetation index (NDVI) values obtained from aerial infrared images can be used to estimate LAI and soybean yield variability. Increasing plant population increased LAI for cultivars at Suffolk in 2000 and 2001, but LAI increased with plant populations on soils with lower plant available water holding capacity (PAWHC) at Port Royal in 2001. In 2000 at Suffolk, seed yield increased quadratically with increasing population and cultivar did not affect the response. In 2001, no relationship occurred between yield and plant population at either Suffolk or Port Royal, but the relationship of yield and LAI depended on soybean development stage at both sites. However, this relationship was not consistent between sites or years. In another study, crop rotation affected LAI and yield one out of two years. However, LAI and yield in both study years were negatively impacted on soil types with lower PAWHC. Where significant, a linear relationship was observed between yield and LAI for all soil types. Studies on grower fields showed similar linear relationships between yield and LAI. Remote sensing techniques showed promise for estimation of LAI and yield. When obtained at an appropriate development stage, vegetation indices correlated to both LAI and yield, and were observed to be effective as a predictor of LAI until plants achieved LAI levels of 3.5 to 4.0. / Master of Science