Unmixing hyperspectral data: independent and dependent component analysis

The development of high spatial resolution airborne and spaceborne sensors has improved the capability of ground-based data collection in the fields of agriculture, geography, geology, mineral identification, detection [2, 3], and classification [4–8]. The signal read by the sensor from a given spatial element of resolution and at a given spectral band is a mixing of components originated by the constituent substances, termed endmembers, located at that element of resolution. This chapter addresses hyperspectral unmixing, which is the decomposition of the pixel spectra into a collection of constituent spectra, or spectral signatures, and their corresponding fractional abundances indicating the proportion of each endmember present in the pixel [9, 10]. Depending on the mixing scales at each pixel, the observed mixture is either linear or nonlinear [11, 12]. The linear mixing model holds when the mixing scale is macroscopic [13]. The nonlinear model holds when the mixing scale is microscopic (i.e., intimate mixtures) [14, 15]. The linear model assumes negligible interaction among distinct endmembers [16, 17]. The nonlinear model assumes that incident solar radiation is scattered by the scene through multiple bounces involving several endmembers [18]. Under the linear mixing model and assuming that the number of endmembers and their spectral signatures are known, hyperspectral unmixing is a linear problem, which can be addressed, for example, under the maximum likelihood setup [19], the constrained least-squares approach [20], the spectral signature matching [21], the spectral angle mapper [22], and the subspace projection methods [20, 23, 24]. Orthogonal subspace projection [23] reduces the data dimensionality, suppresses undesired spectral signatures, and detects the presence of a spectral signature of interest. The basic concept is to project each pixel onto a subspace that is orthogonal to the undesired signatures. As shown in Settle [19], the orthogonal subspace projection technique is equivalent to the maximum likelihood estimator. This projection technique was extended by three unconstrained least-squares approaches [24] (signature space orthogonal projection, oblique subspace projection, target signature space orthogonal projection). Other works using maximum a posteriori probability (MAP) framework [25] and projection pursuit [26, 27] have also been applied to hyperspectral data. In most cases the number of endmembers and their signatures are not known. Independent component analysis (ICA) is an unsupervised source separation process that has been applied with success to blind source separation, to feature extraction, and to unsupervised recognition [28, 29]. ICA consists in finding a linear decomposition of observed data yielding statistically independent components. Given that hyperspectral data are, in given circumstances, linear mixtures, ICA comes to mind as a possible tool to unmix this class of data. In fact, the application of ICA to hyperspectral data has been proposed in reference 30, where endmember signatures are treated as sources and the mixing matrix is composed by the abundance fractions, and in references 9, 25, and 31–38, where sources are the abundance fractions of each endmember. In the first approach, we face two problems: (1) The number of samples are limited to the number of channels and (2) the process of pixel selection, playing the role of mixed sources, is not straightforward. In the second approach, ICA is based on the assumption of mutually independent sources, which is not the case of hyperspectral data, since the sum of the abundance fractions is constant, implying dependence among abundances. This dependence compromises ICA applicability to hyperspectral images. In addition, hyperspectral data are immersed in noise, which degrades the ICA performance. IFA [39] was introduced as a method for recovering independent hidden sources from their observed noisy mixtures. IFA implements two steps. First, source densities and noise covariance are estimated from the observed data by maximum likelihood. Second, sources are reconstructed by an optimal nonlinear estimator. Although IFA is a well-suited technique to unmix independent sources under noisy observations, the dependence among abundance fractions in hyperspectral imagery compromises, as in the ICA case, the IFA performance. Considering the linear mixing model, hyperspectral observations are in a simplex whose vertices correspond to the endmembers. Several approaches [40–43] have exploited this geometric feature of hyperspectral mixtures [42]. Minimum volume transform (MVT) algorithm [43] determines the simplex of minimum volume containing the data. The MVT-type approaches are complex from the computational point of view. Usually, these algorithms first find the convex hull defined by the observed data and then fit a minimum volume simplex to it. Aiming at a lower computational complexity, some algorithms such as the vertex component analysis (VCA) [44], the pixel purity index (PPI) [42], and the N-FINDR [45] still find the minimum volume simplex containing the data cloud, but they assume the presence in the data of at least one pure pixel of each endmember. This is a strong requisite that may not hold in some data sets. In any case, these algorithms find the set of most pure pixels in the data. Hyperspectral sensors collects spatial images over many narrow contiguous bands, yielding large amounts of data. For this reason, very often, the processing of hyperspectral data, included unmixing, is preceded by a dimensionality reduction step to reduce computational complexity and to improve the signal-to-noise ratio (SNR). Principal component analysis (PCA) [46], maximum noise fraction (MNF) [47], and singular value decomposition (SVD) [48] are three well-known projection techniques widely used in remote sensing in general and in unmixing in particular. The newly introduced method [49] exploits the structure of hyperspectral mixtures, namely the fact that spectral vectors are nonnegative. The computational complexity associated with these techniques is an obstacle to real-time implementations. To overcome this problem, band selection [50] and non-statistical [51] algorithms have been introduced. This chapter addresses hyperspectral data source dependence and its impact on ICA and IFA performances. The study consider simulated and real data and is based on mutual information minimization. Hyperspectral observations are described by a generative model. This model takes into account the degradation mechanisms normally found in hyperspectral applications—namely, signature variability [52–54], abundance constraints, topography modulation, and system noise. The computation of mutual information is based on fitting mixtures of Gaussians (MOG) to data. The MOG parameters (number of components, means, covariances, and weights) are inferred using the minimum description length (MDL) based algorithm [55]. We study the behavior of the mutual information as a function of the unmixing matrix. The conclusion is that the unmixing matrix minimizing the mutual information might be very far from the true one. Nevertheless, some abundance fractions might be well separated, mainly in the presence of strong signature variability, a large number of endmembers, and high SNR. We end this chapter by sketching a new methodology to blindly unmix hyperspectral data, where abundance fractions are modeled as a mixture of Dirichlet sources. This model enforces positivity and constant sum sources (full additivity) constraints. The mixing matrix is inferred by an expectation-maximization (EM)-type algorithm. This approach is in the vein of references 39 and 56, replacing independent sources represented by MOG with mixture of Dirichlet sources. Compared with the geometric-based approaches, the advantage of this model is that there is no need to have pure pixels in the observations. The chapter is organized as follows. Section 6.2 presents a spectral radiance model and formulates the spectral unmixing as a linear problem accounting for abundance constraints, signature variability, topography modulation, and system noise. Section 6.3 presents a brief resume of ICA and IFA algorithms. Section 6.4 illustrates the performance of IFA and of some well-known ICA algorithms with experimental data. Section 6.5 studies the ICA and IFA limitations in unmixing hyperspectral data. Section 6.6 presents results of ICA based on real data. Section 6.7 describes the new blind unmixing scheme and some illustrative examples. Section 6.8 concludes with some remarks.

Blind hyperspectral unmixing

This paper introduces a new hyperspectral unmixing method called Dependent Component Analysis (DECA). This method decomposes a hyperspectral image into a collection of reflectance (or radiance) spectra of the materials present in the scene (endmember signatures) and the corresponding abundance fractions at each pixel. DECA models the abundance fractions as mixtures of Dirichlet densities, thus enforcing the constraints on abundance fractions imposed by the acquisition process, namely non-negativity and constant sum. The mixing matrix is inferred by a generalized expectation-maximization (GEM) type algorithm. This method overcomes the limitations of unmixing methods based on Independent Component Analysis (ICA) and on geometrical based approaches. DECA performance is illustrated using simulated and real data.

Blind hyperspectral unmixing

Hyperspectral unmixing methods aim at the decomposition of a hyperspectral image into a collection endmember signatures, i.e., the radiance or reflectance of the materials present in the scene, and the correspondent abundance fractions at each pixel in the image. This paper introduces a new unmixing method termed dependent component analysis (DECA). This method is blind and fully automatic and it overcomes the limitations of unmixing methods based on Independent Component Analysis (ICA) and on geometrical based approaches. DECA is based on the linear mixture model, i.e., each pixel is a linear mixture of the endmembers signatures weighted by the correspondent abundance fractions. These abundances are modeled as mixtures of Dirichlet densities, thus enforcing the non-negativity and constant sum constraints, imposed by the acquisition process. The endmembers signatures are inferred by a generalized expectation-maximization (GEM) type algorithm. The paper illustrates the effectiveness of DECA on synthetic and real hyperspectral images.

Downstream processing development of enveloped viruses for clinical applications: innovative tools for rational process optimization

Dissertation presented to obtain a Ph.D. degree in Engineering and Technology Sciences, Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Development of a system to monitor surfer’s balance and plantar pressure and surfboard’s movement

O uso da tecnologia tem crescido nas últimas décadas nas mais diversas áreas, seja na indústria ou no dia-a-dia, e é cada vez mais evidente os benefícios que traz. No desporto não é diferente. Cada dia surgem novos desenvolvimentos objetivando a melhoria do desempenho dos praticantes de atividades físicas, possibilitando atingir resultados nunca antes pensados. Além disto, a utilização da tecnologia no desporto permite a obtenção de dados biomecânicos que podem ser utilizados tanto no treinamento quando na melhoria da qualidade de vida dos atletas auxiliando na prevenção de lesões, por exemplo. Deste modo, o presente projeto se aplica na área do desporto, nomeadamente, na modalidade do surfe, onde a ausência de trabalhos científicos ainda é elevada, aliando a tecnologia eletrônica ao desporto para quantificar informações até então desconhecidas. Três fatores básicos de desempenho foram levantados, sendo eles: equilíbrio, posicionamento dos pés e movimentação da prancha de surfe. Estes fatores levaram ao desenvolvimento de um sistema capaz de medi-los dinamicamente através da medição das forças plantares e da rotação da prancha de surfe. Além da medição dos fatores, o sistema é capaz de armazenar os dados adquiridos localmente através de um cartão de memória, para posterior análise; e também enviá-los através de uma comunicação sem fio, permitindo a visualização do centro de pressões plantares; dos ângulos de rotação da prancha de surfe; e da ativação dos sensores; em tempo real. O dispositivo consiste em um sistema eletrônico embarcado composto por um microcontrolador ATMEGA1280; um circuito de aquisição e condicionamento de sinal analógico; uma central inercial; um módulo de comunicação sem fio RN131; e um conjunto de sensores de força Flexiforce. O firmware embarcado foi desenvolvido em linguagem C. O software Matlab foi utilizado para receção de dados e visualização em tempo real. Os testes realizados demostraram que o funcionamento do sistema atende aos requisitos propostos, fornecendo informação acerca do equilíbrio, através do centro de pressões; do posicionamento dos pés, através da distribuição das pressões plantares; e do movimento da prancha nos eixos pitch e roll, através da central inercial. O erro médio de medição de força verificado foi de -0.0012 ± 0.0064 N, enquanto a mínima distância alcançada na transmissão sem fios foi de 100 m. A potência medida do sistema foi de 330 mW.

Development of web services to help risk management of construction projects

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Development of Schistosoma mansoni in Biomphalaria tenagophila, Biomphalaria straminea and Biomphalaria glabrata

A comparative study of the development of Schistosoma mansoni during the intra-molluscan phase was made by means of histological sections of Biomphalaria tenagophila, B. straminea and B. glabrata from Brazil. Two hundred snails of each species were individually exposed to 50 miracidia of the S. mansoni, AL line. No larvae were observed in the snails fixed 72 h after exposure. In specimens shedding cercariae, 31 days after exposure tissue reactions encapsulating the larvae were seen in B. tenagophila and B. straminea, in the head-foot, mantle collar and renal ducts. No tissue reactions occurred in the digestive glands of these two species. In B. glabrata the presence of numerous sporocysts and cercariae without tissue reactions was observed in the digestive gland, and other organs. The levels of infection of the snails and the average numbers of cercariae shed per day were 32.6% and 79±90 respectively for B. tenagophila, 11.3% and 112±100 for B. straminea and 75.3% and 432±436 for B. glabrata. The lower levels of infection and average numbers of cercariae shed by B. tenagophila and B. straminea are thus related to their more potent internal defense systems.

Influence of temperature on development of Schistosoma mansoni female cercariae in Biomphalaria glabrata

In these experiments the ratio of male to female S. mansoni larvae in D. glabrata from Belo Horizonte and Ribeirão das Neves Minas Gerais, Brazil, either reared in laboratoty or collected in the field, varied from 1:1 to 1:1.3 or 1.4:1. Cercariae of LE strain of Schistosoma mansoni, shed by 39 snails maintained at 25±0.5ºC were used to infect mice on a weekly basis. Subsequent perfusion resulted in 76.6% male and 23.4% female worms. The cercariac produced by 32 infected snails maintained at 27+0.5°C were inoculated into mice and produced 43.4% male and 56.6% female worms (p<0.05). Cercariae eliminated by snails collected in Barreiro and Ressaca, Belo Horizonte, during hot months, produced 45.7 to 47.7% male and 52.3 to 54.3% female worms. A lower number of cercariae shed by snails collected in Gorduras, Belo Horizonte, at 20+3.0°C, produced 51.6% male and 48.4% female worms. Thus, in this region the infection of vertebrate hosts with S. mansoni cercariae would be more severe in the summer due to the higher level of parasites and the number of eggs.

HEMAGGLUTINATION TEST FOR THE DIAGNOSIS OF HUMAN NEUROCYSTICERCOSIS: DEVELOPMENT OF A STABLE REAGENT USING HOMOLOGOUS AND HETEROLOGOUS ANTIGENS

A hemagglutination (HA) test was standardized using formalin- and tannin-treated gander red blood cells sensitized with a total salt extract of C. cellulosae (HA-Cc) and an antigenic extract of Cysticercus longicollis (HA-Cl) vesicular fluid. A total of 61 cerebrospinal fluid (CSF) samples were assayed, 41 from patients with neurocysticercosis and 20 from a control group, which were, respectively, reactive and non-reactive to ELISA using C. cellulosae. The CSF samples from the control group did not react and 35 (85.4%) and 34 (82.9%) CSF samples from patients were reactive to the HA-Cc and HA-Cl tests, respectively. The reagents ready for use were stable up to 6 months when stored at 4°C in 50% glycerol. The present results confirm that the reagent using Cysticercus longicollis stabilized with glycerol can be used as an alternative in the immunological diagnosis of neurocysticercosis

Sex Determination and Female Reproductive Development in the Genus Schistosoma: A Review

Parasites of the genus Schistosoma were among the first metazoans to develop separate sexes, which is chromosomally determined in the fertilized egg. Despite the occurrence of specific sex chromosomes, the females of most Schistosomatidae species do not complete their somatic development and reach no sexual maturity without the presence of males. Indeed, the most controversial and at the same time most fascinating aspect about the sexual development of Schistosoma females lies on discover the nature of the stimulus produced by males that triggers and controls this process. Although the nature of the stimulus (physical or chemical) is a source of controversy, there is agreement that mating is a necessary requirement for maturation to occur and for migration of the female to a definitive final site of residence in the vascular system of the vertebrate host. It has also been proposed that the stimulus is not species-specific and, in some cases, not even genus-specific. Despite a vast literature on the subject, the process or processes underlying the meeting of males and females in the circulatory system have not been determined and as yet no consensus exists about the nature of the stimulus that triggers and maintains female development. In the studies about their role, Schistosoma males have been considered, at times pejoratively, the brother, the muscles or even the liver of females. Indeed, it still remains to be determined whether the stimulus responsible for female maturation involves the transfer of hormones, nutrients, neuromediators, mere tactile stimulation or a combination of chemotactic and thigmotactic factors

Development of Secondary Resistance to Fluconazole in Cryptococcus neoformans Isolated from a Patient with AIDS

Cryptococcus neoformans is the fifth most common opportunistic agent of infection in patients with AIDS in the USA, exceeded only by Candida species, Pneumocystis carinii, cytomegalovirus and Mycobacterium avium1, 2, 6, 10, 11. In Brazil is the sixth, exceeded by Candida species, P. carinii, Mycobacterium species, Toxoplasma gondii, and herpes simplex virus (AIDS, Boletim Epidemiológico, set/nov 96, Ministério da Saúde, Brasil). During 30 years, the treatment of C. neoformans meningitis was based on the use of amphotericin B with or without flucytosine13. Nowadays, with the immunodepression caused by human immunodeficiency virus (HIV) infection and the availability of new antifungal drugs as the triazoles, the concept related to cure and relapses of cryptococcosis has been altered7, 20. Patients are treated with amphotericin B with or without flucytosine as initial therapy, but maintenance therapy is always necessary in AIDS patients with C. neoformans infections

Valorization of traditional portuguese apples and cherries: biochemical characterization and development of functional ingredients

Dissertation presented to obtain a Ph.D degree in Engineering and Technology Sciences, Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

The role of molecular imaging in modern drug development

Drug development represents a highly complex, inefficient and costly process. Over the past decade, the widespread use of nuclear imaging, owing to its functional and molecular nature, has proven to be a determinant in improving the efficiency in selecting the candidate drugs that should either be abandoned or moved forward into clinical trials. This helps not only with the development of safer and effective drugs but also with the shortening of time-to-market. The modern concept and future trends concerning molecular imaging will assumedly be hybrid or multimodality imaging, including combinations between high sensitivity and functional (molecular) modalities with high spatial resolution and morphological techniques.

ELEVATED ALANINE AMINOTRANSFERASE (ALT) IN BLOOD DONORS: AN ASSESSMENT OF THE MAIN ASSOCIATED CONDITIONS AND ITS RELATIONSHIP TO THE DEVELOPMENT OF HEPATITIS C

The determination of aminotranferases levels is very useful in the diagnosis of hepatopathies. In recent years, an elevated serum ALT level in blood donors has been associated with an increased risk of post-transfusion hepatitis (PTH). The purpose of the study was to research the factors associated with elevated ALT levels in a cohort of voluntary blood donors and to evaluate the relationship between increased ALT levels and the development of hepatitis C (HCV) infection. 166 volunteer blood donors with elevated ALT at the time of their first donation were studied. All of the donors were questioned about previous hepatopathies, exposure to hepatitis, exposure to chemicals, use of medication or drugs, sexual behaviour, contact with blood or secretions and their intake of alcohol. Every three months, the serum levels of AST, ALT, alkaline phosphatase, gamma glutamyl transpeptidase, cholesterol, triglyceride and glycemia are assessed over a two year follow-up. The serum thyroid hormone levels as well as the presence of auto-antibodies were also measured. Abdominal ultrasound was performed in all patients with persistently elevated ALT or AST levels. A needle biopsy of liver was performed in 9 donors without definite diagnostic after medical investigation. The presence of anti-HCV antibodies in 116 donors were assayed again the first clinical evaluation. At the end of follow-up period (2 years later) 71 donors were tested again for the presence of anti-HCV antibodies. None of donors resulted positive for hepatitis B or hepatitis C markers during the follow-up. Of the 116 donors, 101 (87%) had persistently elevated ALT serum levels during the follow-up. Obesity and alcoholism were the principal conditions related to elevated ALT serum levels in 91/101 (90.1%) donors. Hypertriglyceridemia, hypercholesterolemia, hypothyroidism and diabetes mellitus also were associated with increased ALT levels. Only 1/101 (0.9%) had mild chronic active non A-G viral hepatitis and 3/101 (2.9%) had liver biopsy with non-specific reactive hepatitis. The determination of ALT levels was not useful to detect donors infected with HCV at donation in Brazil, including the initial seronegative anti-HCV phase.

Development of CO-releasing molecular for the treatment of inflammatory diseases

Dissertation presented to obtain a Ph.D. degree (Doutoramento) in Chemistry at the Instituto de Tecnologia Quimica e Biol6gica da Universidade Nova de Lisboa