Tracking Level Set Representation Driven by a Stochastic Dynamics

International audienceWe introduce a non-linear stochastic filtering technique to track the state of a free curve from image data. The approach we propose is implemented through a particle filter, which includes color measurements characterizing the target and the background respectively. We design a continuous-time dynamics that allows us to infer inter-frame deformations. The curve is defined by an implicit level-set representation and the stochastic dynamics is expressed on the level-set function. It takes the form of a stochastic partial differential equation with a Brownian motion of low dimension. Specific noise models lead to the traditional level set evolution law based on mean curvature motions, while other forms lead to new evolution laws with different smoothing behaviors. In these evolution models, we propose to combine local photometric information, some velocity induced by the curve displacement and an uncertainty modeling of the dynamics. The associated filter capabilities are demonstrated on various sequences with highly deformable objects

Stochastic level set dynamics to track closed curves through image data

International audienceWe introduce a stochastic filtering technique for the tracking of closed curves from image sequence. For that purpose, we design a continuous-time dynamics that allows us to infer inter-frame deformations. The curve is defined by an implicit level-set representation and the stochastic dynamics is expressed on the level-set function. It takes the form of a stochastic partial differential equation with a Brownian motion of low dimension. The evolution model we propose combines local photometric information, deformations induced by the curve displacement and an uncertainty modeling of the dynamics. Specific choices of noise models and drift terms lead to an evolution law based on mean curvature as in classic level set methods, while other choices yield new evolution laws. The approach we propose is implemented through a particle filter, which includes color measurements characterizing the target and the background photometric probability densities respectively. The merit of this filter is demonstrated on various satellite image sequences depicting the evolution of complex geophysical flows

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Prostate cancer is a common cancer type in men, yet some of its traits are still under-explored. One reason for this is high molecular and morphological heterogeneity. The purpose of this study was to develop a method to gain new insights into the connection between morphological changes and underlying molecular patterns. We used artificial intelligence (AI) to analyze the morphology of seven hematoxylin and eosin (H&E)-stained prostatectomy slides from a patient with multi-focal prostate cancer. We also paired the slides with spatially resolved expression for thousands of genes obtained by a novel spatial transcriptomics (ST) technique. As both spaces are highly dimensional, we focused on dimensionality reduction before seeking associations between them. Consequently, we extracted morphological features from H&E images using an ensemble of pre-trained convolutional neural networks and proposed a workflow for dimensionality reduction. To summarize the ST data into genetic profiles, we used a previously proposed factor analysis. We found that the regions were automatically defined, outlined by unsupervised clustering, associated with independent manual annotations, in some cases, finding further relevant subdivisions. The morphological patterns were also correlated with molecular profiles and could predict the spatial variation of individual genes. This novel approach enables flexible unsupervised studies relating morphological and genetic heterogeneity using AI to be carried out

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Prostate cancer is a common cancer type in men, yet some of its traits are still under-explored. One reason for this is high molecular and morphological heterogeneity. The purpose of this study was to develop a method to gain new insights into the connection between morphological changes and underlying molecular patterns. We used artificial intelligence (AI) to analyze the morphology of seven hematoxylin and eosin (H&E)-stained prostatectomy slides from a patient with multi-focal prostate cancer. We also paired the slides with spatially resolved expression for thousands of genes obtained by a novel spatial transcriptomics (ST) technique. As both spaces are highly dimensional, we focused on dimensionality reduction before seeking associations between them. Consequently, we extracted morphological features from H&E images using an ensemble of pre-trained convolutional neural networks and proposed a workflow for dimensionality reduction. To summarize the ST data into genetic profiles, we used a previously proposed factor analysis. We found that the regions were automatically defined, outlined by unsupervised clustering, associated with independent manual annotations, in some cases, finding further relevant subdivisions. The morphological patterns were also correlated with molecular profiles and could predict the spatial variation of individual genes. This novel approach enables flexible unsupervised studies relating morphological and genetic heterogeneity using AI to be carried out

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Prostate cancer is a common cancer type in men, yet some of its traits are still under-explored. One reason for this is high molecular and morphological heterogeneity. The purpose of this study was to develop a method to gain new insights into the connection between morphological changes and underlying molecular patterns. We used artificial intelligence (AI) to analyze the morphology of seven hematoxylin and eosin (H&E)-stained prostatectomy slides from a patient with multi-focal prostate cancer. We also paired the slides with spatially resolved expression for thousands of genes obtained by a novel spatial transcriptomics (ST) technique. As both spaces are highly dimensional, we focused on dimensionality reduction before seeking associations between them. Consequently, we extracted morphological features from H&E images using an ensemble of pre-trained convolutional neural networks and proposed a workflow for dimensionality reduction. To summarize the ST data into genetic profiles, we used a previously proposed factor analysis. We found that the regions were automatically defined, outlined by unsupervised clustering, associated with independent manual annotations, in some cases, finding further relevant subdivisions. The morphological patterns were also correlated with molecular profiles and could predict the spatial variation of individual genes. This novel approach enables flexible unsupervised studies relating morphological and genetic heterogeneity using AI to be carried out

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Prostate cancer is a common cancer type in men, yet some of its traits are still under-explored. One reason for this is high molecular and morphological heterogeneity. The purpose of this study was to develop a method to gain new insights into the connection between morphological changes and underlying molecular patterns. We used artificial intelligence (AI) to analyze the morphology of seven hematoxylin and eosin (H&E)-stained prostatectomy slides from a patient with multi-focal prostate cancer. We also paired the slides with spatially resolved expression for thousands of genes obtained by a novel spatial transcriptomics (ST) technique. As both spaces are highly dimensional, we focused on dimensionality reduction before seeking associations between them. Consequently, we extracted morphological features from H&E images using an ensemble of pre-trained convolutional neural networks and proposed a workflow for dimensionality reduction. To summarize the ST data into genetic profiles, we used a previously proposed factor analysis. We found that the regions were automatically defined, outlined by unsupervised clustering, associated with independent manual annotations, in some cases, finding further relevant subdivisions. The morphological patterns were also correlated with molecular profiles and could predict the spatial variation of individual genes. This novel approach enables flexible unsupervised studies relating morphological and genetic heterogeneity using AI to be carried out

Suivi de courbes libres fermées déformables par processus stochastique

The joint analysis of movement and deformation is crucial in many computer vision applications. This thesis proposes a stochastic non-linear filter to track a free curve in time. The proposed approach is implemented through a particle filter including colorimetric measurements characterizing respectively the target and the background. The involved dynamics is formulated as a stochastic differential equation. This allows a continuous representation of the curve trajectory, and thus the possibility to deduce the deformation between images. The curve is defined by an implicit level set, on which the stochastic dynamics is expressed. This takes the form of a stochastic differential equation with a Brownian motion of small dimension. We combined in these evolution models a local motion information extracted from the images and a model of the uncertainty of the dynamics. The associated filter proposed for curve tracking thus belongs to the family of conditional particle filters. Its capabilities are tested on different sequences containing highly deformable objects.L'analyse conjointe du mouvement et des déformations est cruciale dans un grand nombre d'applications de vision par ordinateur. Cette thèse propose d'introduire un filtre stochastique non linéaire afin de suivre une courbe libre dans le temps. L'approche proposée est implémentée à travers un filtre particulaire incluant des mesures colorimétriques caractérisant respectivement la cible et le fond. La dynamique impliquée est formulée sous la forme d'une équation différentielle stochastique. Cela permet d'avoir une représentation continue de la trajectoire de la courbe, et d'être ainsi capable d'en déduire les déformations entre images. La courbe est définie par une courbe de niveau implicite, et la dynamique stochastique s'exprime sur cette dernière. Cela prend la forme d'une équation différentielle stochastique avec un mouvement Brownien de faible dimension. Dans ces modèles d'évolution sont combinés les informations de mouvement locales extraites des images et un modèle d'incertitude de la dynamique. Le filtrage associé proposé pour le suivi de courbes appartient ainsi à la famille des filtrages particulaires conditionnels. Ses capacités sont vérifiées sur différentes séquences contenant des objets fortement déformables

Suivi de courbes libres fermées déformables par processus stochastiques

L'analyse conjointe du mouvement et des déformations est cruciale dans un grand nombre d'applications de vision par ordinateur. Cette thèse propose d'introduire un filtre stochastique non linéaire afin de suivre une courbe libre dans le temps. L'approche proposée est implémentée à travers un filtre particulaire incluant des mesures colorimétriques caractérisant respectivement la cible et le fond. La dynamique impliquée est formulée sous la forme d'une équation différentielle stochastique. Cela permet d'avoir une représentation continue de la trajectoire de la courbe, et d'être ainsi capable d'en déduire les déformations entre images. La courbe est définie par une courbe de niveau implicite, et la dynamique stochastique s'exprime sur cette dernière. Cela prend la forme d'une équation différentielle stochastique avec un mouvement Brownien de faible dimension. Dans ces modèles d'évolution sont combinés les informations de mouvement locales extraites des images et un modèle d'incertitude de la dynamique. Le filtrage associé proposé pour le suivi de courbes appartient ainsi à la famille des filtrages particulaires conditionnels. Ses capacités sont vérifiées sur différentes séquences contenant des objets fortement déformables.The joint analysis of movement and deformation is crucial in many computer vision applications. This thesis proposes a stochastic non-linear filter to track a free curve in time. The proposed approach is implemented through a particle filter including colorimetric measurements characterizing respectively the target and the background. The involved dynamics is formulated as a stochastic differential equation. This allows a continuous representation of the curve trajectory, and thus the possibility to deduce the deformation between images. The curve is defined by an implicit level set, on which the stochastic dynamics is expressed. This takes the form of a stochastic differential equation with a Brownian motion of small dimension. We combined in these evolution models a local motion information extracted from the images and a model of the uncertainty of the dynamics. The associated filter proposed for curve tracking thus belongs to the family of conditional particle filters. Its capabilities are tested on different sequences containing highly deformable objects.RENNES1-BU Sciences Philo (352382102) / SudocSudocFranceF

Stochastic filtering of level sets for curve tracking

International audienceThis paper focuses on the tracking of free curves using non-linear stochastic filtering techniques. It relies on a particle filter which includes color measurements. The curve and its velocity are defined through two coupled implicit level set representations. The stochastic dynamics of the curve is expressed directly on the level set function associated to the curve representation and combines a velocity field captured from the additional second level set attached to the past curve's points location. The curve's dynamics combines a lowdimensional noise model and a data-driven local force. We demonstrate how this approach allows the tracking of highly and rapidly deforming objects, such as convective cells in infra-red satellite images, while providing a location-dependent assessment of the estimation confidence