Clustering algorithms and shape factor methods to discriminate among small GTPase phenotypes using DIC image analysis.

Naïvement perçu, le processus d’évolution est une succession d’événements de duplication et de mutations graduelles dans le génome qui mènent à des changements dans les fonctions et les interactions du protéome. La famille des hydrolases de guanosine triphosphate (GTPases) similaire à Ras constitue un bon modèle de travail afin de comprendre ce phénomène fondamental, car cette famille de protéines contient un nombre limité d’éléments qui diffèrent en fonctionnalité et en interactions. Globalement, nous désirons comprendre comment les mutations singulières au niveau des GTPases affectent la morphologie des cellules ainsi que leur degré d’impact sur les populations asynchrones. Mon travail de maîtrise vise à classifier de manière significative différents phénotypes de la levure Saccaromyces cerevisiae via l’analyse de plusieurs critères morphologiques de souches exprimant des GTPases mutées et natives. Notre approche à base de microscopie et d’analyses bioinformatique des images DIC (microscopie d’interférence différentielle de contraste) permet de distinguer les phénotypes propres aux cellules natives et aux mutants. L’emploi de cette méthode a permis une détection automatisée et une caractérisation des phénotypes mutants associés à la sur-expression de GTPases constitutivement actives. Les mutants de GTPases constitutivement actifs Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V ont été analysés avec succès. En effet, l’implémentation de différents algorithmes de partitionnement, permet d’analyser des données qui combinent les mesures morphologiques de population native et mutantes. Nos résultats démontrent que l’algorithme Fuzzy C-Means performe un partitionnement efficace des cellules natives ou mutantes, où les différents types de cellules sont classifiés en fonction de plusieurs facteurs de formes cellulaires obtenus à partir des images DIC. Cette analyse démontre que les mutations Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V induisent respectivement des phénotypes amorphe, allongé, rond et large qui sont représentés par des vecteurs de facteurs de forme distincts. Ces distinctions sont observées avec différentes proportions (morphologie mutante / morphologie native) dans les populations de mutants. Le développement de nouvelles méthodes automatisées d’analyse morphologique des cellules natives et mutantes s’avère extrêmement utile pour l’étude de la famille des GTPases ainsi que des résidus spécifiques qui dictent leurs fonctions et réseau d’interaction. Nous pouvons maintenant envisager de produire des mutants de GTPases qui inversent leur fonction en ciblant des résidus divergents. La substitution fonctionnelle est ensuite détectée au niveau morphologique grâce à notre nouvelle stratégie quantitative. Ce type d’analyse peut également être transposé à d’autres familles de protéines et contribuer de manière significative au domaine de la biologie évolutive.

Example Based Image Analysis and Synthesis

Image analysis and graphics synthesis can be achieved with learning techniques using directly image examples without physically-based, 3D models. In our technique: -- the mapping from novel images to a vector of "pose" and "expression" parameters can be learned from a small set of example images using a function approximation technique that we call an analysis network; -- the inverse mapping from input "pose" and "expression" parameters to output images can be synthesized from a small set of example images and used to produce new images using a similar synthesis network. The techniques described here have several applications in computer graphics, special effects, interactive multimedia and very low bandwidth teleconferencing.

Analysis and Simulation of Transverse Random Fracture of Long Fibre Reinforced Composites

La present tesi proposa una metodología per a la simulació probabilística de la fallada de la matriu en materials compòsits reforçats amb fibres de carboni, basant-se en l'anàlisi de la distribució aleatòria de les fibres. En els primers capítols es revisa l'estat de l'art sobre modelització matemàtica de materials aleatoris, càlcul de propietats efectives i criteris de fallada transversal en materials compòsits. El primer pas en la metodologia proposada és la definició de la determinació del tamany mínim d'un Element de Volum Representatiu Estadístic (SRVE) . Aquesta determinació es du a terme analitzant el volum de fibra, les propietats elàstiques efectives, la condició de Hill, els estadístics de les components de tensió i defromació, la funció de densitat de probabilitat i les funcions estadístiques de distància entre fibres de models d'elements de la microestructura, de diferent tamany. Un cop s'ha determinat aquest tamany mínim, es comparen un model periòdic i un model aleatori, per constatar la magnitud de les diferències que s'hi observen. Es defineix, també, una metodologia per a l'anàlisi estadístic de la distribució de la fibra en el compòsit, a partir d'imatges digitals de la secció transversal. Aquest anàlisi s'aplica a quatre materials diferents. Finalment, es proposa un mètode computacional de dues escales per a simular la fallada transversal de làmines unidireccionals, que permet obtenir funcions de densitat de probabilitat per a les variables mecàniques. Es descriuen algunes aplicacions i possibilitats d'aquest mètode i es comparen els resultats obtinguts de la simulació amb valors experimentals.

The use of image analysis to estimate population growth rate in Daphnia magna

1. Population growth rate (PGR) is central to the theory of population ecology and is crucial for projecting population trends in conservation biology, pest management and wildlife harvesting. Furthermore, PGR is increasingly used to assess the effects of stressors. Image analysis that can automatically count and measure photographed individuals offers a potential methodology for estimating PGR. 2. This study evaluated two ways in which the PGR of Daphnia magna, exposed to different stressors, can be estimated using an image analysis system. The first method estimated PGR as the ratio of counts of individuals obtained at two different times, while the second method estimated PGR as the ratio of population sizes at two different times, where size is measured by the sum of the individuals' surface areas, i.e. total population surface area. This method is attractive if surface area is correlated with reproductive value (RV), as it is for D. magna, because of the theoretical result that PGR is the rate at which the population RV increases. 3. The image analysis system proved reliable and reproducible in counting populations of up to 440 individuals in 5 L of water. Image counts correlated well with manual counts but with a systematic underestimate of about 30%. This does not affect accuracy when estimating PGR as the ratio of two counts. Area estimates of PGR correlated well with count estimates, but were systematically higher, possibly reflecting their greater accuracy in the study situation. 4. Analysis of relevant scenarios suggested the correlation between RV and body size will generally be good for organisms in which fecundity correlates with body size. In these circumstances, area estimation of PGR is theoretically better than count estimation. 5. Synthesis and applications. There are both theoretical and practical advantages to area estimation of population growth rate when individuals' reproductive values are consistently well correlated with their surface areas. Because stressors may affect both the number and quality of individuals, area estimation of population growth rate should improve the accuracy of predicting stress impacts at the population level.

Techniques for image analysis of movement of juveniles of root-knot nematodes encumbered with Pasteuria penetrans spores

Root-knot nematodes (Meloidogyne spp.) are the most significant plant-parasitic nematodes that damage many crops all over the world. The free-living second stage juvenile (J2) is the infective stage that enters plants. The J2s move in the soil water films to reach the root zone. The bacterium Pasteuria penetrans is an obligate parasite of root-knot nematodes, is cosmopolitan, frequently encountered in many climates and environmental conditions and is considered promising for the control of Meloidogyne spp. The infection potential of P. penetrans to nematodes is well studied but not the attachment effects on the movement of root-knot nematode juveniles, image analysis techniques were used to characterize movement of individual juveniles with or without P. penetrans spores attached to their cuticles. Methods include the study of nematode locomotion based on (a) the centroid body point, (b) shape analysis and (c) image stack analysis. All methods proved that individual J2s without P. penetrans spores attached have a sinusoidal forward movement compared with those encumbered with spores. From these separate analytical studies of encumbered and unencumbered nematodes, it was possible to demonstrate how the presence of P. penetrans spores on a nematode body disrupted the normal movement of the nematode.

A flow system for the on-line quantitative measurement of the retention of dosage forms on biological surfaces using spectroscopy and image analysis

Measuring the retention, or residence time, of dosage forms to biological tissue is commonly a qualitative measurement, where no real values to describe the retention can be recorded. The result of this is an assessment that is dependent upon a user's interpretation of visual observation. This research paper outlines the development of a methodology to quantitatively measure, both by image analysis and by spectrophotometric techniques, the retention of material to biological tissues, using the retention of polymer solutions to ocular tissue as an example. Both methods have been shown to be repeatable, with the spectrophotometric measurement generating data reliably and quickly for further analysis.

Performance evaluation of crowd image analysis using the PETS2009 dataset

This paper presents the PETS2009 outdoor crowd image analysis surveillance dataset and the performance evaluation of people counting, detection and tracking results using the dataset submitted to five IEEE Performance Evaluation of Tracking and Surveillance (PETS) workshops. The evaluation was carried out using well established metrics developed in the Video Analysis and Content Extraction (VACE) programme and the CLassification of Events, Activities, and Relationships (CLEAR) consortium. The comparative evaluation highlights the detection and tracking performance of the authors’ systems in areas such as precision, accuracy and robustness and provides a brief analysis of the metrics themselves to provide further insights into the performance of the authors’ systems.

Topological multi-contour decomposition for image analysis and image retrieval

Successful classification, information retrieval and image analysis tools are intimately related with the quality of the features employed in the process. Pixel intensities, color, texture and shape are, generally, the basis from which most of the features are Computed and used in such fields. This papers presents a novel shape-based feature extraction approach where an image is decomposed into multiple contours, and further characterized by Fourier descriptors. Unlike traditional approaches we make use of topological knowledge to generate well-defined closed contours, which are efficient signatures for image retrieval. The method has been evaluated in the CBIR context and image analysis. The results have shown that the multi-contour decomposition, as opposed to a single shape information, introduced a significant improvement in the discrimination power. (c) 2008 Elsevier B.V. All rights reserved,

Digital spiral analysis for objective assessment of fine motor timing variability in Parkinson's disease

OBJECTIVES: To develop a method for objective assessment of fine motor timing variability in Parkinson’s disease (PD) patients, using digital spiral data gathered by a touch screen device. BACKGROUND: A retrospective analysis was conducted on data from 105 subjects including65 patients with advanced PD (group A), 15 intermediate patients experiencing motor fluctuations (group I), 15 early stage patients (group S), and 10 healthy elderly subjects (HE) were examined. The subjects were asked to perform repeated upper limb motor tasks by tracing a pre-drawn Archimedes spiral as shown on the screen of the device. The spiral tracing test was performed using an ergonomic pen stylus, using dominant hand. The test was repeated three times per test occasion and the subjects were instructed to complete it within 10 seconds. Digital spiral data including stylus position (x-ycoordinates) and timestamps (milliseconds) were collected and used in subsequent analysis. The total number of observations with the test battery were as follows: Swedish group (n=10079), Italian I group (n=822), Italian S group (n = 811), and HE (n=299). METHODS: The raw spiral data were processed with three data processing methods. To quantify motor timing variability during spiral drawing tasks Approximate Entropy (APEN) method was applied on digitized spiral data. APEN is designed to capture the amount of irregularity or complexity in time series. APEN requires determination of two parameters, namely, the window size and similarity measure. In our work and after experimentation, window size was set to 4 and similarity measure to 0.2 (20% of the standard deviation of the time series). The final score obtained by APEN was normalized by total drawing completion time and used in subsequent analysis. The score generated by this method is hence on denoted APEN. In addition, two more methods were applied on digital spiral data and their scores were used in subsequent analysis. The first method was based on Digital Wavelet Transform and Principal Component Analysis and generated a score representing spiral drawing impairment. The score generated by this method is hence on denoted WAV. The second method was based on standard deviation of frequency filtered drawing velocity. The score generated by this method is hence on denoted SDDV. Linear mixed-effects (LME) models were used to evaluate mean differences of the spiral scores of the three methods across the four subject groups. Test-retest reliability of the three scores was assessed after taking mean of the three possible correlations (Spearman’s rank coefficients) between the three test trials. Internal consistency of the methods was assessed by calculating correlations between their scores. RESULTS: When comparing mean spiral scores between the four subject groups, the APEN scores were different between HE subjects and three patient groups (P=0.626 for S group with 9.9% mean value difference, P=0.089 for I group with 30.2%, and P=0.0019 for A group with 44.1%). However, there were no significant differences in mean scores of the other two methods, except for the WAV between the HE and A groups (P<0.001). WAV and SDDV were highly and significantly correlated to each other with a coefficient of 0.69. However, APEN was not correlated to neither WAV nor SDDV with coefficients of 0.11 and 0.12, respectively. Test-retest reliability coefficients of the three scores were as follows: APEN (0.9), WAV(0.83) and SD-DV (0.55). CONCLUSIONS: The results show that the digital spiral analysis-based objective APEN measure is able to significantly differentiate the healthy subjects from patients at advanced level. In contrast to the other two methods (WAV and SDDV) that are designed to quantify dyskinesias (over-medications), this method can be useful for characterizing Off symptoms in PD. The APEN was not correlated to none of the other two methods indicating that it measures a different construct of upper limb motor function in PD patients than WAV and SDDV. The APEN also had a better test-retest reliability indicating that it is more stable and consistent over time than WAV and SDDV.

Análise digital de imagem e estereologia da angiogênese em adenomas e no adenocarcinoma colorretal invasivo de submucosa

A angiogênese é essencial no desenvolvimento neoplásico, associando-se às metástases à distância e recorrência em diversas neoplasias malignas. Em carcinomas colorretais, os parâmetros da análise digital de imagem e estereologia da angiogênese foram pouco estudados. Objetivo: avaliar parâmetros tridimensionais e a quantificação microvascular bidimensional nas diferentes apresentações morfológicas dos adenomas colorretais e no adenocarcinoma colorretal restrito à submucosa, a fim de determinar o papel da angiogênese nas diferentes etapas da seqüência adenoma-carcinoma e sua relação com as diferentes apresentações das lesões precursoras do carcinoma colorretal. Material e métodos: foi realizado estudo histórico de delineamento transversal, incluindo 115 lesões neoplásicas colorretais, ressecadas endoscópica ou cirurgicamente no período de 1997 a 2001, obtidas de pacientes do Hospital de Clínicas de Porto Alegre e da Fundação Universitária de Gastroenterologia (FUGAST). Para análise da angiogênese foram utilizadas as técnicas de imuno-histoquímica, análise digital de imagem, quantificação microvascular e estereologia. Os resultados foram apresentados como mediana e intervalos interquartis. Resultados: a quantificação microvascular foi progressivamente mais elevada nas lesões polipóides com displasia de alto grau comparadas às de baixo grau. Quanto maior o grau de atipia observado, maior foi o número de microvasos (regressão linear, P < 0,05). O volume e extensão microvascular foram diferentes entre as fases evolutivas da neoplasia colorretal, resultando em aumento no volume 728 (416 - 1408) versus 178 (93 - 601) e extensão microvascular 242,4 (131,1 - 936,8) vs 24,0 (6,5 - 142,2) (P < 0,001) nas lesões polipóides com displasia de alto grau comparadas às de baixo grau, respectivamente. A quantificação microvascular foi progressivamente mais elevada, acompanhando a progressão neoplásica polipóide: displasia de baixo grau 41,8 (15,8 - 71,9), displasia de alto grau 60,0 (23,0 - 95,6) e carcinoma de submucosa 76,0 (37,5 - 132,6) (P < 0,001). Concomitante, o volume 956 (436 - 2188) vs 178 (93 - 601) e a extensão microvascular 534,6 (146,7 - 1262) vs 24,0 (6,5 - 142,2) foram mais elevados nos adenocarcinomas colorretais restritos à submucosa em relação às lesões polipóides com displasia de baixo grau, respectivamente (P < 0,001). Não foi encontrada diferença estatisticamente significativa na angiogênese entre os adenomas polipóides e não-polipóides através da quantificação 41,8 (15,8 - 71,9) vs 22 (16 - 40) e estimativa da extensão microvascular 24 (6,5-142,2) vs 17,5 (4,4-54,7), respectivamente. Conclusão: a utilização da análise digital de imagem e estereologia acrescentou maior objetividade e eficácia na metodologia de avaliação angiogênica, pois permitiu a precisa segmentação das áreas hipervasculares, a representação da morfologia tridimensional característica do suprimento vascular e a identificação de diferenças na microvascularização nas etapas evolutivas do câncer colorretal.

Automated system of seedling image analysis (SVIS) and electrical conductivity to assess sun hemp seed vigor

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Análise da imagem digital para estimativa da área foliar em plantas de laranja Pêra

Objetivou-se, com o trabalho, avaliar dois métodos de estimativa da área foliar, em plantas de laranja Pêra, pela análise da imagem digital obtida com scanner e câmera fotográfica digital. Para determinar a área das folhas, um grupo de discos foi colocado sobre um leitor de scanner, sendo que a imagem obtida foi armazenada. Os mesmos grupos de discos foram fixados sobre cartolina branca e fotografados com câmera fotográfica digital. As imagens obtidas da câmera fotográfica e do scanner foram processadas utilizando ferramentas de um editor de imagem que permite a contagem de pixels de determinada cor, no caso verde. Para a comparação dos métodos, os discos foram submetidos a integrador óptico de área foliar modelo LICOR-3100, utilizando os mesmos agrupamentos. Foram coletadas 20 folhas (cinco em cada quadrante da planta) por parcela de um experimento para comparação de fertilizantes comerciais e doses de zinco, aplicados via foliar, em plantas de sete anos de idade. O experimento foi composto de sete tratamentos e quatro repetições, num total de 28 parcelas. Os dois métodos apresentaram alta correlação com a área estimada pelo integrador óptico de área, considerado como método de referência. O método da análise da imagem obtida com câmera fotográfica, na resolução de 5.0 megapixel, foi mais precisa quando comparada à área estimada pelo integrador óptico de área.

Estado nutricional em nitrogênio da grama esmeralda avaliado por meio do teor foliar, clorofilômetro e imagem digital, em área adubada com lodo de esgoto

A intensidade da cor verde da folha pode ser alternativa para estimar a concentração de N na planta, devido à relação entre o teor de clorofila e o de N no tecido foliar. Objetivou-se neste trabalho avaliar índices da cor verde da grama esmeralda obtidos da análise da imagem digital e pelo uso do clorofilômetro para predizer o estado nutricional em N fornecido pelo lodo de esgoto. O experimento foi instalado e desenvolvido em uma propriedade comercial de grama esmeralda, localizada na cidade de Itapetininga (SP). O delineamento experimental foi em blocos casualizados, com quatro repetições e cinco doses de lodo de esgoto: 0, 10, 20, 30 e 40 Mg ha-1, base seca. As doses de lodo aplicadas correspondem a 100, 200, 300 e 400 kg ha-1 de nitrogênio disponível. Foram avaliadas as concentrações de N e a intensidade de coloração verde da folha pelo uso do clorofilômetro (ICV) e por meio da análise da imagem digital (G, H e ICVE) aos 45, 105 e 165 dias após a aplicação do lodo. Os valores de intensidade obtidos foram correlacionados com a concentração de N na lâmina foliar e com a taxa de cobertura do solo determinada nas mesmas épocas. A aplicação de doses de lodo de esgoto proporcionou aumento dos índices de cor verde e da concentração de N nas folhas da grama esmeralda. A concentração de N na lâmina foliar pode auxiliar a adubação nitrogenada em cobertura, pois proporcionou altas correlações com a taxa de cobertura do solo. O matiz (H) obtido com a imagem digital e a intensidade de cor verde da folha (ICV) obtida com o clorofilômetro correlacionaram-se com a concentração de N e com a taxa de cobertura do solo e, dessa forma, podem servir como índices na recomendação da adubação nitrogenada.

Quantitative fractography under light microscopy: A digital image processing approach

This work is an example of the improvement on quantitative fractography by means of digital image processing and light microscopy. Two techniques are presented to investigate the quantitative fracture behavior of Ti-4Al-4V heat-treated alloy specimens, under Charpy impact testing. The first technique is the Minkowski method for fractal dimension measurement from surface profiles, revealing the multifractal character of Ti-4Al-4V fracture. It was not observed a clear positive correlation of fractal values against Charpy energies for Ti-4Al-4V alloy specimens, due to their ductility, microstructural heterogeneities and the dynamic loading characteristics at region near the V-notch. The second technique provides an entire elevation map of fracture surface by extracting in-focus regions for each picture from a stack of images acquired at successive focus positions, then computing the surface roughness. Extended-focus reconstruction has been used to explain the behavior along fracture surface. Since these techniques are based on light microscopy, their inherent low cost is very interesting for failure investigations.