Algae can be used to treat wastewater and manure while producing a feedstock for renewable energy. Algae require nutrients to achieve their maximum growth and manure could provide those nutrients, thereby reducing the cost of algae production and the impact of manure treatment. Algae concentration during cultivation is a critical variable that is difficult to measure due to the high concentration of suspended solids present in manure. This dissertation addresses methods to measure algae concentration in the presence of manure solids. Quantifying the algae concentration gravimetrically or by optical density was unreliable due to manure solids interfering with the measurement. Cell counting to determine algae concentration was accurate but time consuming, subjective, required dilution of concentrated samples and only small sample volumes could be measured. Chlorophyll extraction was a consistent method to determine algae concentration in manure based media, but the model had to be adjusted to account for solids interference. The proposed equation predicted chlorophyll concentration from Chlorella vulgaris in dairy manure better than the reference equation. Different algae strains (Chlorella vulgaris, Cylindrocystis sp, and Scenedesmus sp.) and manure sources (dairy, beef, swine, and sheep) were used to validate the proposed equation and all combinations had a linear relationship between actual and predicted chlorophyll concentration, but not all comparisons followed a 1:1 reference line. Even with chlorophyll extraction the manure solids interfered with the chlorophyll measurement and calibrations had to be developed based on manure type. A method based on spectral deconvolution was used to quantify algae concentration in the presence of manure without chlorophyll extraction. Various manure-algae mixtures were scanned with a spectrophotometer. Algae concentration was accurately determined with the four manure sources. Measuring algae concentration required absorbance spectra from 600 to 700 nm and manure solids concentration between 280 and 350 nm. Spectral deconvolution was able to differentiate algae concentration and manure solids concentration with a Pearson coefficient of 95.3% and 99.8% respectively. This method proved to be an accurate and efficient method for estimating algae and manure solids content in unprocessed samples. A critical factor was utilizing appropriate reference spectra.

The viability of using a slicer based integral field spectrograph (IFS) for high contrast observations has been under scrutiny due to the belief that the one dimensional coherence that persists along the slice to the point of sampling at the detector will cause the creation of secondary speckles that will not have the same characteristics as normal speckles, thus stopping us from calibrating them out. It has also been previously assumed that a suitably low differential wavefront error when moving slice to slice was not guaranteed by design. It was for these reasons that slicer based IFSs were not selected for the current generation of planet finding instruments. As part of the EPICS (Exo Planet Imaging Camera and Spectrograph for the E-ELT) design study it was decided that slicers should be re-investigated due to results from on sky observations suggesting these limitations did not exist. The purpose of this thesis was to determine whether there was validity to the concerns mentioned above and therefore to answer the question; Would implementing a slicer based integral field spectrograph limit the achievable contrast of an instrument designed for the direct detection of exoplanets? Chapter 1 gives a brief introduction into the field of exoplanet research. Charpter 2 describes the noise limiting direct detection of exoplanets and the ways to get around it. Chapter 3 gives an overview of the two types of IFS under investigation by the EPICS consortium. Chapter 4 looks into details of the EPICS instrument and the IFS design study that came about. Chapter 5 shows simulations performed for the aim of achieving better contrasts via post processing methods and accurate data reduction as well as simulations of slicer based integral field spectrographs. Experimental tests using a slicer and a preoptics setup designed to simulate the limiting noise are described in Chapter 6. Chapter 7 looks at using SINFONI for high contrast observations and Chapter 8 details the conclusions drawn from the work presented in this thesis, as well as possible extensions to it. The work performed in this thesis dispels the concerns about the continued one dimensional coherence up to the detecter and suggests that slicer based integral field spectrographs do not inherently limit the contrast achievable; Results from experiments fit well with the requirements for EPICS to achieve its goals. Simulations also supported the idea that secondary speckle noise should not be an issue for the slicer based IFS. This means that a slicer based IFS is a viable option for the EPICS instrument.

Aerosols are small, micrometer-sized particles, whose optical effects coupled with their impact on cloud properties is a source of large uncertainty in climate models. While their radiative forcing impact is largely of a cooling nature, there can be significant variations in the degree of their impact, depending on the size and the nature of the aerosols. The radiative and optical impact of aerosols are, first and foremost, dependent on their concentration or number density (an extensive parameter) and secondly on the size and nature of the aerosols (intensive, per particle, parameters). We employed passive (sunphotmetry) and active (backscatter lidar) measurements to retrieve extensive optical signals (aerosol optical depth or AOD and backscatter coefficient respectively) and semi-intensive optical signals (fine and coarse mode OD and fine and coarse mode backscatter coefficient respectively) and compared the optical coherency of these retrievals over a variety of aerosol and thin cloud events (pollution, dust, volcanic, smoke, thin cloud dominated). The retrievals were performed using an existing spectral deconvolution method applied to the sunphotometry data (SDA) and a new retrieval technique for the lidar based on a colour ratio thresholding technique. The validation of the lidar retrieval was accomplished by comparing the vertical integrations of the fine mode, coarse mode and total backscatter coefficients of the lidar with their sunphotometry analogues where lidar ratios (the intensive parameter required to transform backscatter coefficients into extinction coefficients) were (a) computed independently using the SDA retrievals for fine mode aerosols or prescribed for coarse mode aerosols and clouds or (b) computed by forcing the computed (fine, coarse and total) lidar ODs to be equal to their analog sunphotometry ODs. Comparisons between cases (a) and (b) as well as the semi-qualitative verification of the derived fine and coarse mode vertical profiles with the expected backscatter coefficient behavior of fine and coarse mode aerosols yielded satisfactory agreement (notably that the fine, coarse and total OD errors were <~ sunphotometry instrument errors). Comparisons between cases (a) and (b) also showed a degree of optical coherency between the fine mode lidar ratios.