This dissertation develops new approaches for improving the performance of hyperspectral target detection. Different aspects of hyperspectral target detection are reviewed and studied to effectively distinguish target features from background interference. The contributions of this dissertation are detailed as follows. 1) Propose an adaptive background characterization method that integrates region segmentation with target detection. In the experiments, not only unstructured matched filter based detectors are considered, but also two hybrid detectors combining fully constrained least squared abundance estimation with statistic test (i.e., adaptive matched subspace detector and adaptive cosine/coherent detector) are investigated. The experimental results demonstrate that using local adaptive background characterization, background clutters can be better suppressed than the original algorithms with global characterization. 2) Propose a new approach to estimate abundance fractions based on the linear spectral mixture model for hybrid structured and unstructured detectors. The new approach utilizes the sparseness constraint to estimate abundance fractions, and achieves better performance than the popular non-negative and fully constrained methods in the situations when background endmember spectra are not accurately acquired or estimated, which is very common in practical applications. To improve the dictionary incoherence, the use of band selection is proposed to improve the sparseness constrained linear unmixing. 3) Propose random projection based dimensionality reduction and decision fusion approach for detection improvement. Such a data independent dimensionality reduction process has very low computational cost, and it is capable of preserving the original data structure. Target detection can be robustly improved by decision fusion of multiple runs of random projection. A graphics processing unit (GPU) parallel implementation scheme is developed to expedite the overall process. 4) Propose nonlinear dimensionality reduction approaches for target detection. Auto-associative neural network-based Nonlinear Principal Component Analysis (NLPCA) and Kernel Principal Component Analysis (KPCA) are applied to the original data to extract principal components as features for target detection. The results show that NLPCA and KPCA can efficiently suppress trivial spectral variations, and perform better than the traditional linear version of PCA in target detection. Their performance may be even better than the directly kernelized detectors.

Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2009. / The use of near infrared (NIR) hyperspectral imaging and hyperspectral image analysis for distinguishing between whole maize kernels of varying degrees of hardness and fungal infected and non-infected kernels have been investigated. Near infrared hyperspectral images of whole maize kernels of varying degrees of hardness were acquired using a Spectral Dimensions MatrixNIR camera with a spectral range of 960-1662 nm as well as a sisuChema SWIR (short wave infrared) hyperspectral pushbroom imaging system with a spectral range of 1000-2498 nm. Exploratory principal component analysis (PCA) on absorbance images was used to remove background, bad pixels and shading. On the cleaned images, PCA could be used effectively to find histological classes including glassy (hard) and floury (soft) endosperm. PCA illustrated a distinct difference between floury and glassy endosperm along principal component (PC) three. Interpreting the PC loading line plots important absorbance peaks responsible for the variation were 1215, 1395 and 1450 nm, associated with starch and moisture for both MatrixNIR images (12 and 24 kernels). The loading line plots for the sisuChema (24 kernels) illustrated peaks of importance at the aforementioned wavelengths as well as 1695, 1900 and 1940 nm, also associated with starch and moisture. Partial least squares-discriminant analysis (PLS-DA) was applied as a means to predict whether the different endosperm types observed, were glassy or floury. For the MatrixNIR image (12 kernels), the PLS-DA model exhibited a classification rate of up to 99% for the discrimination of both floury and glassy endosperm. The PLS-DA model for the second MatrixNIR image (24 kernels) yielded a classification rate of 82% for the discrimination of glassy and 73% for floury endosperm. The sisuChema image (24 kernels) yielded a classification rate of 95% for the discrimination of floury and 92% for glassy endosperm. The fungal infected and sound whole maize kernels were imaged using the same instruments. Background, bad pixels and shading were removed by applying PCA on absorbance images. On the cleaned images, PCA could be used effectively to find the infected regions, pedicle as well as non-infected regions. A distinct difference between infected and sound kernels was illustrated along PC1. Interpreting the PC loading line plots showed important absorbance peaks responsible for the variation and predominantly associated with starch and moisture: 1215, 1450, 1480, 1690, 1940 and 2136 nm for both MatrixNIR images (15 and 21 kernels). The MatrixNIR image (15 kernels) exhibited a PLS-DA classification rate of up to 96.1% for the discrimination of infected kernels and the sisuChema had a classification rate of 99% for the same region of interest. The The iv sisuChema image (21-kernels) had a classification rate for infected kernels of 97.6% without pre-processing, 97.7% with multiplicative scatter correction (MSC) and 97.4% with standard normal variate (SNV). Near infrared hyperspectral imaging is a promising technique, capable of distinguishing between maize kernels of varying hardness and between fungal infected and sound kernels. While there are still limitations with hardware and software, these results provide the platform which would greatly assist with the determination of maize kernel hardness in breeding programmes without having to destroy the kernel. Further, NIR hyperspectral imaging could serve as an objective, rapid tool for identification of fungal infected kernels.

Alzheimer's disease is a widespread disease that has devastating effects on the human brain and mind. Ultimately, it leads to death and there are currently no treatment methods available that can stop the disease progression. The mechanisms involved behind the disease are not fully understood although it is known that amyloid fibrils play an important role in the disease development. These fibrils are able to form plaques that can trigger neuronal death, by interacting with receptors on the cell surface and the synaptic cleft or by entering the cell and disturb important functions such as metabolic pathways. To study the plaque formation of amyloid proteins, both in vitro and in vivo methods are used to investigate the characteristics of the protein. Luminescent conjugated oligothiophene probes are able to bind in to amyloid beta fibrils and emit light when excited by an external light source. This way fibrillation properties of the protein can be studied. Developing probes that can serve as biomarkers for detection of amyloid fibrils could change the way Alzheimer's is treated. Being able to detect the disease in its early disease course, and start treatments early, is suggested to stop the progression of neural breakdown. In this project a software is developed to analyze fluorescent microscopy images, taken on tissue stained with these probes. The software is able to filter out background noise and capture parts of the picture that are of interest when studying the amyloid plaques. This software generates results similar to if the images were to be analyzed using any software where the regions to analyze are selected manually, suggesting that the software developed produce reliable results unbiased by background noise.

Single-cell bio-analytical techniques play a pivotal role in contemporary biological and biomedical research. Among current high-throughput single-cell imaging methods, coherent Raman imaging offers both high bio-compatibility and high-throughput information-rich capabilities, offering insights into cellular composition, dynamics, and function. Coherent Raman imaging finds its value in diverse applications, ranging from live cell dynamic imaging, high-throughput drug screening, fast antimicrobial susceptibility testing, etc. In this thesis, I first present a deep learning algorithm to solve the inverse problem of getting a chemically labeled image from a single-shot femtosecond stimulated Raman scattering (SRS) image. This method allows high-speed, high-throughput tracking of lipid droplet dynamics and drug response in live cells. Second, I provide image-based single-cell analysis in an engineered Escherichia coli (E. coli) population, confirming the chemical composition and subcellular structure organization of individual engineered E. coli cells. Additionally, I unveil metabolon formation in engineered E. coli by high-speed spectroscopic SRS and two-photon fluorescence imaging. Lastly, I present stimulated Raman-activated cell ejection (S-RACE) by integrating high-throughput SRS imaging, in situ image decomposition, and high-precision laser-induced cell ejection. I demonstrate the automatic imaging-identification-sorting workflow in S-RACE and advance its compatibility with versatile samples ranging from polymer particles, single live bacteria/fungus, and tissue sections. Collectively, these efforts demonstrate the valuable capability of SRS in high-throughput single-cell imaging and sorting, opening opportunities for a wide range of biological and biomedical applications.

En fournissant en plus de l'information spatiale une mesure spectrale en fonction des longueurs d'ondes, l'imagerie hyperspectrale s'enorgueillie d'atteindre une précision bien plus importante que l'imagerie couleur. Grâce à cela, elle a été utilisée en contrôle qualité, inspection de matériaux,… Cependant, pour exploiter pleinement ce potentiel, il est important de traiter la donnée spectrale comme une mesure, d'où la nécessité de la métrologie, pour laquelle exactitude, incertitude et biais doivent être maitrisés à tous les niveaux de traitement.Face à cet objectif, nous avons choisi de développer une approche non-linéaire, basée sur la morphologie mathématique et de l'étendre au domaine spectral par le biais d'une relation d'ordre spectral basée sur les fonctions de distance. Une nouvelle fonction de distance spectrale et une nouvelle relation d'ordonnancement sont ainsi proposées. De plus, un nouvel outil d'analyse du basé sur les histogrammes de différences spectrales a été développé.Afin d'assurer la validité des opérateurs, une validation théorique rigoureuse et une évaluation métrologique ont été mises en œuvre à chaque étage de développement. Des protocoles d'évaluation de la qualité des traitements morphologiques sont proposés, exploitant des jeux de données artificielles pour la validation théorique, des ensembles de données dont certaines caractéristiques sont connues pour évaluer la robustesse et la stabilité et des jeux de données de cas réel pour prouver l'intérêt des approches en contexte applicatif. Les applications sont développées dans le contexte du patrimoine culturel pour l'analyse de peintures et pigments. / Providing not only spatial information but also spectral measure as a function of wavelength, hyperspectral imaging boasts a much greater gain in accuracy than the traditional color imaging. And for this capability, hyperspectral imaging has been employed for quality control, inspection of materials in various fields. However, to fully exploit this potential, it is important to process the spectral data as a measure. This induces the need of metrology where accuracy, uncertainty, and bias are managed at every level of processing.Aiming at developing a metrological image processing framework for spectral data, we select to develop a nonlinear approach using the mathematical morphology framework and extended it to the spectral domain by means of a distance-based ordering relation. A novel spectral distance function and spectral ordering relation are proposed, in addition of a new analysis tools based on spectral differences. To ensure the validity of the spectral mathematical morphology framework, rigorous theoretical validation and metrological assessment are carried out at each development stages. So, protocols for quality assessment of spectral image processing tools are developed. These protocols consist of artificial datasets to validate completely the theoretical requirements, datasets with known characteristics to assess the robustness and stability, and datasets from real cases to proof the usefulness of the framework on applicative context. The application tasks themselves are within the cultural heritage domain, where the target images come from pigments and paintings. / Hyperspektral avbildning muliggjør mye mer nøyaktige målinger enn tradisjonelle gråskala og fargebilder, gjennom både høy romlig og spektral oppløsning (funksjon av bølgelengde). På grunn av dette har hyperspektral avbildning blitt anvendt i økende grad ulike applikasjoner som kvalitetskontroll og inspeksjon av materialer. Men for å fullt ut utnytte sitt potensiale, er det viktig å være i stand til å behandle spektrale bildedata som målinger på en gyldig måte. Dette induserer behovet for metrologi, der nøyaktighet, usikkerhet og skjevhet blir adressert og kontrollert på alle nivå av bildebehandlingen.Med sikte på å utvikle et metrologisk rammeverk for spektral bildebehandling valgte vi en ikke-lineær metodikk basert på det etablerte matematisk morfologi-rammeverket. Vi har utvidet dette rammeverket til det spektrale domenet ved hjelp av en avstandsbasert sorteringsrelasjon. En ny spektral avstandsfunksjon og nye spektrale sorteringsrelasjoner ble foreslått, samt nye verktøy for spektral bildeanalyse basert på histogrammer av spektrale forskjeller.For å sikre gyldigheten av det nye spektrale rammeverket for matematisk morfologi, har vi utført en grundig teoretisk validering og metrologisk vurde-ring på hvert trinn i utviklingen. Dermed er og-så nye protokoller for kvalitetsvurdering av spektrale bildebehandlingsverktøy utviklet. Disse protokollene består av kunstige datasett for å validere de teoretiske måletekniske kravene, bildedatasett med kjente egenskaper for å vurdere robustheten og stabiliteten, og datasett fra reelle anvendelser for å bevise nytten av rammeverket i en anvendt sammenheng. De valgte anvendelsene er innenfor kulturminnefeltet, hvor de analyserte bildene er av pigmenter og malerier.