Applications des graphes en traitement d'images

International audienceLes graphes sont des outils de représentation des données très puissants et universels, utiles dans divers domaines des sciences notamment le traitement d'images, la reconnaissance des formes ou la vision par ordinateur. Dans ces domaines, la mesure de similarité entre les objets est souvent une phase importante. Dans le cadre d'une représentation sous forme de graphe cette phase se traduit par un appariement des graphes. Dans cet article nous passons en revue un ensemble de travaux basé sur la théorie des graphes appliquée aux traitements d'images. Notamment les approches de représentation en graphe et les différentes mesures de similarité de graphes. Également, nous présentons quelques applications des graphes dans l'analyse d'images et la recherche par le contenu

Neuroimaging in Friedreich's ataxia : new approaches and clinical aplication

Orientadores: Marcondes Cavalcante França Junior, Andreia Vasconcellos FariaTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo: A ataxia de Friedreich (FRDA) é a ataxia autossômica recessiva mais comum no mundo. Clinicamente, é caracterizada por início precoce, alterações sensoriais e ataxia de lenta progressão. Os estudos de imagem têm focado somente em estruturas infratentoriais, desconsiderando o envolvimento de estruturas supratentoriais, diferenças fenotípicas e duração da doença, bem como a evolução do dano neurológico. Portanto, o objetivo deste trabalho é avaliar, por meio de imagens de ressonância magnética multimodal, pacientes com ataxia de Friedreich a fim de compreender a evolução do dano encefálico, identificar o padrão de dano encefálico entre os fenótipos da doença, os sítios de depósitos de ferro extra-cerebelares e as primeiras estruturas acometidas na doença. A fim de atingir todos os objetivos, foram recrutados 25 pacientes adultos com a forma clássica da doença, 13 pacientes com início tardio e 12 pacientes pediátricos. Para quantificar a gravidade da doença foi utilizada a escala FARS. O dano estrutural de substância cinza e branca foi avaliado via imagens de ressonância magnética ponderadas em T1, T2 e DTI. Para análise de tais imagens foram utilizadas as ferramentas FreeSurfer, T1 MultiAtlas, DTI Multiatlas, SPM, SpineSeg e TBSS. As comparações de grupos revelaram comprometimento microestrutural multifocal na substância branca encefálica na FRDA, com dano extenso nos pedúnculos cerebelares, corpo caloso e tratos piramidais. Encontramos também alterações na substância cinzenta no núcleo denteado do cerebelo, tronco e córtex motor. Nós não identificamos mudanças volumétricas longitudinais, porém análises prospectivas da substância branca identificaram anormalidades microestruturais progressivas no corpo caloso, tratos piramidais e pedúnculos cerebelares superiores após um ano de seguimento. A respeito do estudo comparando o tipo clássico e o tipo tardio (cFRDA vs. LOFA), nós mostramos que ambos os fenótipos possuem um padrão de anormalidades similares, mas não idênticas. Embora sutis, as diferenças estruturais encontradas ajudam a explicar a variabilidade fenotípica entre estas duas apresentações da doença. Por exemplo, o maior dano microestrutural no trato córtico-espinhal no grupo LOFA ajuda a explicar os sinais piramidais mais exuberantes neste grupo. Não fomos capazes de identificar depósitos de ferro cerebrais nos pacientes com FRDA. Neste sentido, tais depósitos ficariam restritos somente ao núcleo denteado do cerebelo. Por fim, fomos capazes de observar que a manifestação inicial da doença, vista em pacientes pediátricos, se concentra na medula espinhal e no pedúnculo cerebelar inferiorAbstract: Friedreich¿s ataxia (FRDA) is the most common autosomal-recessive ataxia worldwide; it is characterized by early onset, sensory abnormalities and slowly progressive ataxia. Besides that, most of neuroimaging studies have been focused only in infratentorial structures of adult patients. Furthermore, studies comparing different phenotypes of disease does not exist. Therefore, the objective of this study is to assess, using multimodal magnetic (MRI) resonance imaging, patients with Friedreich ataxia to better comprehend the progression of brain damage, to identify the pattern of damage across disease phenotypes, to identify areas with abnormal iron deposits in the brain and to characterize the structures initially damaged in early disease stages. To accomplish that, we enrolled 25 adult patients with classical FRDA, 13 patients with late-onset FRDA and 12 pediatric patients. The FARS scale was employed to quantify the disease severity. To assess the structural damage in gray and white matter, we acquired T1-weighted, T2-weighted and DTI images of the brain. To evaluate these images, we used the following tools: FreeSurfer, T1 MultiAtlas, SPM, DTI MultiAtlas, SpineSeg and TBSS. After group comparisons, there was widespread microstructural damage in the cerebral white matter, including cerebellar peduncles, corpus callosum and pyramidal tracts of patients with FRDA. We also found gray matter volumetric reduction in the dentate nuclei of the cerebellum, brainstem and motor cortex. We did not find volumetric reduction over time, but there was progressive white matter microstructural damage in the corpus callosum, pyramidal tracts and superior cerebellar peduncles after 1 year of follow-up. Regarding the disease phenotypes, we found that both classical FRDA and LOFA have similar, but not identical neuroimaging signatures. Although subtle, the structural differences might help to explain the phenotypic differences seen in both conditions. The corticospinal tracts are damaged in both conditions, but more severely in the late-onset FRDA group, which may explain why pyramidal signs are more evident in the latter subgroup. We failed to identify iron deposits in brain regions other than the dentate nuclei of patients with FRDA. Finally, we found that the spinal cord and inferior cerebellar peduncles are the structures compromised in pediatric patients with FRDADoutoradoFisiopatologia MédicaDoutor em Ciências2014/19786-7, 2015/09793-9FAPES

Spinal and encephalic structural damage in spinocerebellar ataxia type 1 : characterization and clinical correlates

Orientador: Marcondes Cavalcante França JuniorTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo: A ataxia espinocerebelar do tipo 1 (SCA1) é uma doença neurodegenerativa cuja expressão clínica predominante é a ataxia cerebelar progressiva associada à hiperreflexia profunda e às alterações sacádicas. Causada por expansão instável de uma sequência CAG no gene ATXN1 no cromossomo 6, foi a primeira ataxia espinocerebelar que teve seu substrato genético elucidado. Apesar disso, existem poucos estudos acerca de seus aspectos clínicos e morfológicos, principalmente no que diz respeito às manifestações não motoras e suas correlações estruturais. Desta forma, o objetivo deste trabalho é caracterizar, clínica e morfologicamente, os pacientes com SCA1, utilizando escalas clínicas bem estabelecidas e técnicas multimodais de ressonância magnética. Para tanto, foram recrutados 33 pacientes adultos com teste molecular positivo para SCA1 acompanhados nos serviços de neurologia da UNICAMP e UNIFESP. Os pacientes foram submetidos a exame neurológico pormenorizado, enfatizando aspectos motores e não-motores. Para a graduação da ataxia utilizou-se a Scale for the Assessment and Rating of Ataxia (SARA). Para avaliação de sintomas não-motores utilizou-se a Modified Fatigue Impact Scale (MFIS) para fadiga, Epworth Sleepiness Scale (ESS) para sonolência excessiva diurna, Beck Depression Inventory (BDI) para depressão e Addenbrooke¿s Cognitive Examination ¿ Revised (ACE-R) para cognição. O dano estrutural encefálico e medular foi avaliado por imagens de ressonância magnética ponderadas em T1 e DTI. Para análise, foram utilizadas as ferramentas FreeSurfer, T1 MultiAtlas, DTI MultiAtlas, CERES e SpineSeg. Com o objetivo de avaliar evolutivamente a SCA1, os pacientes foram divididos em três grupos de acordo com o tempo de doença. Variáveis clínicas e imaginológicas foram comparadas nesses grupos a fim de determinar, temporalmente, o padrão evolutivo das alterações no SNC. Os sintomas motores correlacionaram-se diretamente com o dano dos núcleos rubros, medular e cerebelar. Os níveis de fadiga foram significativamente maiores nos pacientes comparado aos controles e apresentaram relação direta com depressão e duração da doença. A depressão foi mais frequente nos pacientes e correlacionou-se com aspectos motores, entretanto, não houve correlação com áreas encefálicas. As alterações cognitivas foram importantes, principalmente nos domínios de memória e fluência, os quais correlacionaram-se diretamente com atrofia na amígdala e lóbulo VIII cerebelar, respectivamente. Evidenciou-se redução da área e aumento da excentricidade significativos na medula cervical dos pacientes quando comparados aos controles. A redução da área medular correlacionou-se diretamente com aspectos motores, apresentando duração e CAGn como possíveis determinantes. Avaliações transversais do encéfalo revelaram danos significativos em áreas primárias e associativas em córtex cerebral, substância cinzenta profunda, córtex cerebelar e subtância branca encefálica, principalmente em regiões infratentoriais. Do ponto de vista evolutivo, verificou-se padrão lesional em sentido caudo-cranial. Por fim, fomos capazes de caracterizar fenoticamente a SCA1 e correlacionar seus aspectos clínicos e estruturaisAbstract: Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease expressed clinically by progressive cerebellar ataxia associated with deep hyperreflexia and saccadic alterations. Caused by unstable expansions of a CAG sequence in the ATXN1 gene on chromosome 6, it was the first spinocerebellar ataxia that had its genetic substrate elucidated. Despite this, there are few studies about its clinical and morphological aspects, mainly regarding non-motor manifestations and their structural correlations. In this way, the objective of this study is to characterize, clinically and morphologically, patients with SCA1, using well-established clinical scales and multimodal magnetic resonance techniques. We have thus evaluated 33 consecutive adult patients regularly followed at UNICAMP and UNIFESP and 33 healthy age-and-sex matched controls. All patients had molecular confirmation of SCA1. The patients underwent detailed neurological examination, emphasizing motor and non-motor aspects. For ataxia quantification, the Scale for the Assessment and Rating of Ataxia (SARA) was used. For the evaluation of non-motor symptoms, we used the Modified Fatigue Impact Scale (MFIS) for fatigue, Epworth Sleepiness Scale (ESS) for excessive daytime sleepiness, Beck Depression Inventory (BDI) for depression and Addenbrooke's Cognitive Examination ¿ Revised (ACE-R) for cognition aspects. The encephalic and spinal structural damage were evaluated by DTI and T1-weighted magnetic resonance imaging. For MRI analyses, the tools FreeSurfer, T1 MultiAtlas, DTI MultiAtlas, CERES and SpineSeg were used. Attempting to analyse the evolution pattern, the patients were divided into three groups according to the disease duration. Clinical and imaging variables were compared in these groups to determine the evolutionary pattern of CNS changes. Motor symptoms correlated to damage of red nuclei, spinal cord and cerebellar cortex. Fatigue levels were significantly higher in patients compared to controls and were directly related to depression and disease duration. Depression was more frequent in patients and correlated to motor aspects, however, there was no association with brain areas. Cognitive alterations were important, especially in memory and fluency domains, which correlated directly to atrophy in the amygdala and cerebellar lobe VIII, respectively. Significant area reduction and eccentricity increase were observed in patients' cervical spinal cord when compared to controls. The reduction of the cord area correlated directly to motor aspects; and duration and CAGn were possible determinants. Cross-sectional brain evaluations revealed significant damage in primary and associative areas in cerebral cortex, deep gray matter, cerebellar cortex and encephalic white matter, especially in infratentorial regions. Analysis of disease course disclosed a caudal-cranial pattern of damage in the CNS. Finally, we were able to phenotypically characterize SCA1 and to correlate its clinical and structural aspectsDoutoradoFisiopatologia MédicaDoutor em Ciência

Supervised pattern classification using optimum path forest

Orientador: Alexandre Xavier FalcãoTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Padrões são geralmente representados por vetores de atributos obtidos através de amostras em uma base de dados, a qual pode estar totalmente, parcialmente ou não rotulada. Dependendo da quantidade de informação disponível dessa base de dados, podemos aplicar três tipos de técnicas para identificação desses padrões: supervisionadas, semisupervisionadas ou não-supervisionadas. No presente trabalho, estudamos técnicas supervisionadas, as quais caracterizam-se pelo total conhecimento dos rótulos das amostras da base de dados. Propusemos também um novo método para classificação supervisionada de padrões baseada em Floresta de Caminhos Ótimos (OPF - Optimum-Path Forest), a qual modela o problema de reconhecimento de padrões como sendo um grafo, onde os nós são as amostras e os arcos definidos por uma relação de adjacência. Amostras mais relevantes (protótipos) são identificadas e um processo de competição entre elas é iniciado, as quais tentam oferecer caminhos de custo ótimo para as demais amostras da base de dados. Apresentamos aqui duas abordagens, as quais diferem na relação de adjacência, função de custo de caminho e maneira de identificar os protótipos. A primeira delas utiliza como relação de adjacência o grafo completo e identifica os protótipos nas regiões de fronteira entre as classes, os quais oferecem caminhos de custo ótimo que são computados como sendo o valor do maior peso de arco do caminho entre esses protótipos e as demais amostras da base de dados, sendo o peso do arco entre duas amostras dado pela distância entre seus vetores de características. O algoritmo OPF tenta minimizar esses custos para todas as amostras. A outra abordagem utiliza como relação de adjacência um grafo k-nn e identifica os protótipos como sendo os máximos de uma função de densidade de probabilidade, a qual é computada utilizando os pesos dos arcos. O valor do custo do caminho é dado pelo menor valor de densidade ao longo do caminho. Neste caso, o algoritmo OPF tenta agora maximizar esses custos. Apresentamos também um algoritmo de aprendizado genérico, o qual ensina o classificador através de seus erros em um conjunto de validação, trocando amostras classificadas incorretamente por outras selecionadas através de certas restrições. Esse processo é repetido at'e um critério de erro ser estabelecido. Comparações com os classificadores SVM, ANN-MLP, k-NN e BC foram feitas, tendo o OPF demonstrado ser similar ao SVM, porém bem mais rápido, e superior aos restantes.Abstract: Patterns are usually represented by feature vectors obtained from samples of a dataset, which can be fully, partially or non labeled. Depending on the amount of available information of these datasets, three kinds of pattern identification techniques can be applied: supervised, semi-supervised or non supervised. In this work, we addressed the supervised ones, which are characterized by the fully knowledge of the labels from the dataset samples, and we also proposed a novel idea for supervised pattern recognition based on Optimum-Path Forest (OPF), which models the pattern recognition problem as a graph, where the nodes are the samples and the arcs are defined by some adjacency relation. The most relevant samples (prototypes) are identified and a competition process between them is started, which try to offer optimum-path costs to the remaining dataset samples. We presented here two approaches, which differ from each other in the adjacency relation, path-cost function and the prototypes identification procedure. The first ones uses as the adjacency relation the complete graph and identify the prototypes in the boundaries of the classes, which offer optimum-path costs that are computed as been the maximum path arc-weight between these prototypes and the other dataset samples, in which the arc-weight is given by the distance between their feature vectors. In this case, the OPF algorithm tries to minimize these costs for each sample of the dataset. The other approach uses as the adjacency relation a k-nn graph and identifies the prototypes as the maxima of a probability density function, which is computed using the arc-weigths. The path-cost value is given by the lowest density value among it. The OPF algorithm now tries to maximize these costs. We also presented a generic learning algorithm, which tries to teach a classifier through its erros in a validation set, replacing the misclassified samples by other selected using some constraints. This process is repeated until an error criterion is satisfied. Comparisons with SVM, ANN-MLP, k-NN and BC classifiers were also performed, being the OPF similar to SVM, but much faster, and superior to the remaining classifiers.DoutoradoMetodologia e Tecnicas da ComputaçãoDoutor em Ciência da Computaçã

Automatic Image Segmentation By Tree Pruning

The Image Foresting Transform (IFT) is a tool for the design of image processing operators based on connectivity, which reduces image processing problems into an optimum-path forest problem in a graph derived from the image. A new image operator is presented, which solves segmentation by pruning trees of the forest. An IFT is applied to create an optimum-path forest whose roots are seed pixels, selected inside a desired object. In this forest, object and background are connected by optimum paths (leaking paths), which cross the object's boundary through its "most weakly connected" parts (leaking pixels). These leaking pixels are automatically identified and their subtrees are eliminated, such that the remaining forest defines the object. Tree pruning runs in linear time, is extensible to multidimensional images, is free of ad hoc parameters, and requires only internal seeds, with little interference from the heterogeneity of the background. These aspects favor solutions for automatic segmentation. We present a formal definition of the obtained objects, algorithms, sufficient conditions for tree pruning, and two applications involving automatic segmentation: 3D MR-image segmentation of the human brain and image segmentation of license plates. Given that its most competitive approach is the watershed transform by markers, we also include a comparative analysis between them. © 2007 Springer Science+Business Media, LLC.2902/03/15141162Audigier, R., Lotufo, R.A., Falcão, A.X., 3D visualization to assist iterative object definition from medical images (2006) Comput. Med. 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Spineseg: A Segmentation And Measurement Tool For Evaluation Of Spinal Cord Atrophy

Spinal cord atrophy occurs in several pathologies. Measurement of atrophy patterns from magnetic resonance (MR) images improve the neurologists's understanding of these pathologies and provide reliable means to distinguish between pathologies with similar symptoms. Spinal cord measurements from MR are complicated by spinal cord curvature, patient movement, MR resolution, lack of reproducibility in interactive methods and the need of pathology-specific MR protocols. In this work we present SpineSeg, a tool that combines image analysis techniques to achieve reproducibility in spinal cord atrophy measurements without requiring pathology-specific MR protocols. © 2012 AISTI.Döhlinger, S., Hauser, T.K., Borkert, J., Luft, A., Schulz, J., Magnetic resonance imaging in spinocerebellar ataxias (2008) The Cerebellum, 7, pp. 204-214Losseff, N.A., Spinal cord atrophy and disability in multiple sclerosis (1996) Brain, 119 (3), pp. 701-708Klockgether, T., The natural history of degenerative ataxia: A retrospective study in 466 patients (1998) Brain, 121 (4), pp. 589-600Durr, A., Autosomal dominant cerebellar ataxias: Polyglutamine expansions and beyond (2010) The Lancet Neurology, 9 (9), pp. 885-894Bartels, R.H., Beatty, J.C., Barsky, B.A., (1987) An Introduction to Splines for Use in Computer Graphics and Geometric Modeling, , Morgan Kaufmann PublishersRomeny, B.M., Image processing on diagnostic workstations (2008) Image Processing in Radiology, pp. 123-134. , Edited by A.L. Baert et al, SpringerHanson, D.P., Robb, R.A., Three-dimensional visualization in Medicine and Biology (2009) Handbook of Medical Image Processing and Analysis, pp. 755-784. , (2 nd edition), Academic PressBergo, F.P.G., Falcão, A.X., Miranda, P.A.V., Rocha, L.M., Automatic image segmentation by tree pruning (2007) Journal of Mathemathical Imaging and Vision, 29 (2-3), pp. 141-162Dougherty, E., Lotufo, R.A., (2003) Hands-on Morphological Image Processing, , SPIE PressFalcão, A.X., Stolfi, J., Lotufo, R.A., The image foresting transform: Theory, algorithms and applications (2004) IEEE Trans. on Pattern Analysis and Machine Intelligence, 26, pp. 19-29Fitzgibbon, A., Pilu, M., Fisher, R.B., Direct least square fitting of ellipses (1999) IEEE Trans. On Pattern Analysis and Machine Intelligence, 21 (5), pp. 476-480Lukas, C., Spinal cord atrophy in spinocerebellar ataxia type 3 and 6 - Impact on clinical disability (2008) Journal of Neurology, 255 (8), pp. 1244-1249Liu, C., Edwards, S., Gong, Q., Roberts, N., Blumhardt, L.D., Three dimensional MRI estimates of brain and spinal cord atrophy in multiple sclerosis (1999) Journal of Neurology, Neurosurgery and Psychiatry, 66 (3), pp. 323-33

A Fast And Automatic Method For 3d Rigid Registration Of Mr Images Of The Human Brain

Image registration is an important problem with several applications in Medical Imaging. Intra-subject rigid registration requires a minimal set of parameters to be computed, and is sufficient for organs with no significant movement or deformation, such as the human brain. Rigid registration has also been used as the first step before inter-subject deformable registration. In this paper we present a fast and automatic method for 3D rigid registration of magnetic resonance images of the human brain. The method combines previous approaches for mid-sagittal plane location and brain segmentation with a greedy-search algorithm to find the best match between source and target images. We evaluated the method on 200 image pairs: 100 without structural abnormalities and 100 with artificially created lesions, such that it was possible to quantify the registration errors. The method achieved very accurate registration within a few seconds. © 2008 IEEE.121128Audette, M., Ferrie, F., Peters, T., An algorithmic overview of surface registration techniques for medical imaging (2000) Medical Image Analysis, 4 (3), pp. 201-217Bergo, F.P.G., Falcão, A.X., Miranda, P.A.V., Rocha, L.M., Automatic image segmentation by tree pruning (2007) J Math Imaging and Vision, 29 (2-3), pp. 141-162. , NovF. P. G. Bergo, G. C. S. Ruppert, L. F. Pinto, and A. X. Falcão. Fast and robust mid-sagittal plane location in 3D MR images of the brain. In Proc. BIOSIGNALS 2008 - Intl. Conf. on Bio-Inspired Syst. and Sig. Proc., pages 92-99, Jan 2008Besl, P.J., McKay, N.D., A method for registration of 3-d shapes (1992) IEEE Transactions on pattern analysis and machine intelligence, 14 (2), pp. 239-256Brown, L.G., A survey of image registration techniques (1992) ACM. 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L. Yasuda, C. C. Valise, A. V. Saúde, A. L. F. Costa, F. R. Pereira, M. Morita, L. E. Betting, H. Tedeschi, E. Oliveira, G. Castellano, and F. Cendes. Recovery of white matter atrophy (WMA) after successful surgery in mesial TLE. In Proc. 60th Annual Meeting of the American Academy of Neurology, page to appear, 2008Zhou, H., Liu, T., Lin, F., Pang, Y., Wu, J., Wu, J., Towards efficient registration of medical images (2007) Computerized Medical Imaging and Graphics, 31, pp. 374-382. , SepZivota, B., Flusser, J., Image registration methods: A survey (2003) Image and Vision Computing, 21, pp. 977-1000Zou, X., Zhao, X., Feng, Y., An efficient medical image registration algorithm based on gradient descent (2007) Complex Medical Engineering, pp. 636-639. , Ma

Fast, Accurate And Precise Mid-sagittal Plane Location In 3d Mr Images Of The Brain

Extraction of the mid-sagittal plane (MSP) is a key step for brain image registration and asymmetry analysis. We present a fast MSP extraction method for 3D MR images, based on automatic segmentation of the brain and on heuristic maximization of the cerebro-spinal fluid within the MSP. The method is robust to severe anatomical asymmetries between the hemispheres, caused by surgical procedures and lesions. The method is also accurate with respect to MSP delineations done by a specialist. The method was evaluated on 64 MR images (36 pathological, 20 healthy, 8 synthetic), and it found a precise and accurate approximation of the MSP in all of them with a mean time of 60.0 seconds per image, mean angular variation within a same image (precision) of 1.26° and mean angular difference from specialist delineations (accuracy) of 1.64°. © 2008 Springer-Verlag.25 CCIS278290Davidson, R.J., Hugdahl, K., (1996) Brain Asymmetry, , MIT Press/Bradford BooksCrow, T.J., Schizophrenia as an anomaly of cerebral asymmetry (1993) Imaging of the Brain in Psychiatry and Related Fields, pp. 3-17. , Maurer, K. (ed.) 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