Spectral Unmixing: Analysis of Performance in the Olfactory Bulb In Vivo

Background: The generation of transgenic mice expressing combinations of fluorescent proteins has greatly aided the reporting of activity and identification of specific neuronal populations. Methods capable of separating multiple overlapping fluorescence emission spectra, deep in the living brain, with high sensitivity and temporal resolution are therefore required. Here, we investigate to what extent spectral unmixing addresses these issues. Methodology/Principal Findings: Using fluorescence resonance energy transfer (FRET)-based reporters, and two-photon laser scanning microscopy with synchronous multichannel detection, we report that spectral unmixing consistently improved FRET signal amplitude, both in vitro and in vivo. Our approach allows us to detect odor-evoked FRET transients 180-250 mm deep in the brain, the first demonstration of in vivo spectral imaging and unmixing of FRET signals at depths greater than a few tens of micrometer. Furthermore, we determine the reporter efficiency threshold for which FRET detection is improved by spectral unmixing. Conclusions/Significance: Our method allows the detection of small spectral variations in depth in the living brain, which is essential for imaging efficiently transgenic animals expressing combination of multiple fluorescent proteins

Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images

International audienceAstrocytes regulate neuronal information processing through a variety of spatio-temporal calcium signals. Advances in calcium imaging started to reveal astrocytic activities, but the complexity of the recorded data strongly call for computational analysis tools. Their development is hindered by the lack of reliable annotations that are essential for their evaluation and for the design of learning-based methods. To overcome the labeling problem, we present a framework to simulate realistic astrocytic calcium signals in 3D+time lattice light sheet microscopy (LLSM) images by closely modeling calcium kinetics in real astrocytes

Approches intégrées de construction et d’analyse des modèles de systèmes pétroliers : apports pour l’exploration pétrolière

Numerical tools for petroleum system modeling and forward stratigraphic modeling were designed to account for complex processes responsible for hydrocarbon accumulations in petroleum reservoirs. These processes, which extended to new mechanisms and gained details with increasing understanding, involve several geoscience disciplines making difficult the building of models consistent with both data and knowledge. The work performed during this Ph.D. aims at making basin modeling more accessible to geoscientists first by making easier the integration of geological concepts and available data during the process of model building and then by improving quality of forecasts and of risk quantification through sensitivity and risk analysis on maps. In a first section, two methods designed for better and easier estimation of the thermal history and of the distribution of marine organic matter in sedimentary basins are presented. They are based on a similar procedure which uses local data and regional knowledge to assess these two key aspects of petroleum system exploration. An optimization loop is initially performed on input parameters to fit on local data before extrapolating the results to basin scale under the constraint of the regional geological information. Both approaches were patented (Ducros, 2012; Ducros et Chauveau, 2015). The basin of Berkine in Algeria, for which an important set of thermal data is available, was used as an application case study for the method designed for estimating thermal history. The Western Canadian Sedimentary Basin, known for its production of unconventionals, was used for illustrating the estimation of the distribution of organic matter. The second part of the work is dedicated to a new methodology for sensitivity and risk analysis on maps. It is built on a proxy-model of the simulator behavior in the uncertain space to save time during the sampling phase required for providing statistical results. It also uses a principal component analysis to reduce the space dimension when dealing with maps. The approach is illustrated on two case studies: one using a forward stratigraphic model for assessing the position of petroleum reservoirs and one on a petroleum system modeling tool for assessing the maturity of a source-rock in the Levant Basin. These new tools strengthen the integration of data coming from different disciplines to produce more consistent and robust results. They make easier the interpretation of risk analysis provided on a format compatible with classical methods of risk assessment in petroleum exploration such as CRS mapping. The results of this work emphasize the role of these tools for making the link between the different disciplines of geosciences to provide consistent and predictive results. They also give access to powerful risk mapping that can be part of a more general framework, called Common Risk Segment Mapping, used for risks assessment in petroleum exploration.Les outils numériques de modélisation des bassins sédimentaires et des systèmes pétroliers prennent en compte des processus naturels chaque fois plus nombreux et font intervenir une grande variété de disciplines des géosciences. C’est pourquoi il est ardu de construire des modèles qui soient cohérents avec l’ensemble des données disponibles et l’ensemble des connaissances géologiques. Les travaux réalisés dans cette thèse de doctorat visent à rendre ces outils de modélisation plus accessibles d’une part en facilitant la construction des modèles numériques par l’intégration simultanée et automatique des concepts géologiques et des données et d’autre part en donnant accès à l’interprétation des risques d’exploration sous forme de cartes. Pour répondre au premier objectif, deux méthodes ont été mises au point afin de faciliter et d’améliorer la détermination de l’histoire thermique des bassins sédimentaires et de la distribution régionale de la matière organique. Elles se basent sur une même procédure d’exploitation des mesures locales et de l’information géologique régionale pour mieux estimer ces aspects clés pour l’exploration des systèmes pétroliers. Une optimisation des paramètres de modélisation est d’abord réalisée afin de reproduire les données locales avant d’extrapoler les résultats à l’échelle du bassin via l’utilisation des données géologiques. Les deux approches ont été valorisées chacune par le dépôt d’un brevet (Ducros, 2012 ; Ducros et Chauveau, 2015). Elles sont illustrées pour l’une sur le cas du bassin de Berkine, où l’on dispose d’une importante base de données thermiques, et pour l’autre sur le bassin Ouest-Canadien, objet d’une intense exploration des hydrocarbures de roche-mère. La deuxième partie des travaux a porté sur la mise au point et l’application d’une méthode d’analyse de sensibilité et de risques sous forme de cartes. Elle s’appuie sur une approche d’approximation de la réponse d’un simulateur sur l’ensemble de l’espace d’incertitude afin de réduire le temps d’échantillonnage nécessaire à l’estimation des risques et sur une analyse en composantes principales permettant de réduire la dimension des résultats à traiter. La méthode est illustrée sur deux exemples d’application : le premier utilise un outil de modélisation stratigraphique pour l’estimation de la position des réservoirs pétroliers dans un bassin sédimentaire et le deuxième montre comment peut-être déterminé le risque sur la maturité de la roche-mère. Ces nouveaux outils renforcent les liens entre les différentes disciplines des géosciences afin de produire des résultats plus cohérents et plus prédictifs. Ils facilitent également l’accès à des analyses d’incertitudes et de risques qui permettent des interprétations cartographiques puissantes, en lien avec les techniques courantes d’appréciation des risques d’exploration (CRS mapping)

Integrated approach for building and analyzing petroleum system models : new insights for petroleum exploration

Les outils numériques de modélisation des bassins sédimentaires et des systèmes pétroliers prennent en compte des processus naturels chaque fois plus nombreux et font intervenir une grande variété de disciplines des géosciences. C’est pourquoi il est ardu de construire des modèles qui soient cohérents avec l’ensemble des données disponibles et l’ensemble des connaissances géologiques. Les travaux réalisés dans cette thèse de doctorat visent à rendre ces outils de modélisation plus accessibles d’une part en facilitant la construction des modèles numériques par l’intégration simultanée et automatique des concepts géologiques et des données et d’autre part en donnant accès à l’interprétation des risques d’exploration sous forme de cartes. Pour répondre au premier objectif, deux méthodes ont été mises au point afin de faciliter et d’améliorer la détermination de l’histoire thermique des bassins sédimentaires et de la distribution régionale de la matière organique. Elles se basent sur une même procédure d’exploitation des mesures locales et de l’information géologique régionale pour mieux estimer ces aspects clés pour l’exploration des systèmes pétroliers. Une optimisation des paramètres de modélisation est d’abord réalisée afin de reproduire les données locales avant d’extrapoler les résultats à l’échelle du bassin via l’utilisation des données géologiques. Les deux approches ont été valorisées chacune par le dépôt d’un brevet (Ducros, 2012 ; Ducros et Chauveau, 2015). Elles sont illustrées pour l’une sur le cas du bassin de Berkine, où l’on dispose d’une importante base de données thermiques, et pour l’autre sur le bassin Ouest-Canadien, objet d’une intense exploration des hydrocarbures de roche-mère. La deuxième partie des travaux a porté sur la mise au point et l’application d’une méthode d’analyse de sensibilité et de risques sous forme de cartes. Elle s’appuie sur une approche d’approximation de la réponse d’un simulateur sur l’ensemble de l’espace d’incertitude afin de réduire le temps d’échantillonnage nécessaire à l’estimation des risques et sur une analyse en composantes principales permettant de réduire la dimension des résultats à traiter. La méthode est illustrée sur deux exemples d’application : le premier utilise un outil de modélisation stratigraphique pour l’estimation de la position des réservoirs pétroliers dans un bassin sédimentaire et le deuxième montre comment peut-être déterminé le risque sur la maturité de la roche-mère. Ces nouveaux outils renforcent les liens entre les différentes disciplines des géosciences afin de produire des résultats plus cohérents et plus prédictifs. Ils facilitent également l’accès à des analyses d’incertitudes et de risques qui permettent des interprétations cartographiques puissantes, en lien avec les techniques courantes d’appréciation des risques d’exploration (CRS mapping).Numerical tools for petroleum system modeling and forward stratigraphic modeling were designed to account for complex processes responsible for hydrocarbon accumulations in petroleum reservoirs. These processes, which extended to new mechanisms and gained details with increasing understanding, involve several geoscience disciplines making difficult the building of models consistent with both data and knowledge. The work performed during this Ph.D. aims at making basin modeling more accessible to geoscientists first by making easier the integration of geological concepts and available data during the process of model building and then by improving quality of forecasts and of risk quantification through sensitivity and risk analysis on maps. In a first section, two methods designed for better and easier estimation of the thermal history and of the distribution of marine organic matter in sedimentary basins are presented. They are based on a similar procedure which uses local data and regional knowledge to assess these two key aspects of petroleum system exploration. An optimization loop is initially performed on input parameters to fit on local data before extrapolating the results to basin scale under the constraint of the regional geological information. Both approaches were patented (Ducros, 2012; Ducros et Chauveau, 2015). The basin of Berkine in Algeria, for which an important set of thermal data is available, was used as an application case study for the method designed for estimating thermal history. The Western Canadian Sedimentary Basin, known for its production of unconventionals, was used for illustrating the estimation of the distribution of organic matter. The second part of the work is dedicated to a new methodology for sensitivity and risk analysis on maps. It is built on a proxy-model of the simulator behavior in the uncertain space to save time during the sampling phase required for providing statistical results. It also uses a principal component analysis to reduce the space dimension when dealing with maps. The approach is illustrated on two case studies: one using a forward stratigraphic model for assessing the position of petroleum reservoirs and one on a petroleum system modeling tool for assessing the maturity of a source-rock in the Levant Basin. These new tools strengthen the integration of data coming from different disciplines to produce more consistent and robust results. They make easier the interpretation of risk analysis provided on a format compatible with classical methods of risk assessment in petroleum exploration such as CRS mapping. The results of this work emphasize the role of these tools for making the link between the different disciplines of geosciences to provide consistent and predictive results. They also give access to powerful risk mapping that can be part of a more general framework, called Common Risk Segment Mapping, used for risks assessment in petroleum exploration

Lattice light-sheet microscopy and photo-stimulation in brain slices

International audienceLattice light sheet (LLS) fluorescence microscopy is a powerful recent technique for in vivo imaging of single and multi-cellular samples at very high spatio-temporal resolutions. We built a LLS microscope in which we added a photo-stimulation path to perform all-optical neurophysiological studies in rodent hippocampal brain slices. Thanks to the photo-stimulation path we could achieve fluorescence recovery after photobleaching (FRAP) or glutamate uncaging at spatially and temporally controlled regions of interest. Several fluorescence labelling protocols were employed depending on the imaged structure. Sub-micrometric neuronal elements such as spines or dendritic vesicles could be imaged down to ~20 µm below the surface. We demonstrate the performances of LLS in several ongoing studies: measurement of AMPA receptor surface diffusion at single spines, vesicular transport in dendrites, spontaneous and stimulated local calcium activity in neurons and astrocytes

3D Numerical Modelling and Sensitivity Analysis of the Processes Controlling Organic Matter Distribution and Heterogeneity—A Case Study from the Toarcian of the Paris Basin

International audienceThe active debate about the processes governing the organic-rich sediment deposition generally involves the relative roles of elevated primary productivity and enhanced preservation related to anoxia. However, other less spotlighted factors could have a strong impact on such deposits, e.g., residence time into the water column (bathymetry), sedimentation rate, transport behavior of organo-mineral floccules on the sea floor. They are all strongly interrelated and may be obscured in the current conceptual models inspired from most representative modern analogues (i.e., upwelling zones and stratified basins). To improve our comprehension of organic matter distribution and heterogeneities, we conducted a sensitivity analysis on the processes involved in organic matter production and preservation that have been simulated within a 3D stratigraphic forward model. The Lower-Middle Toarcian of the Paris Basin was chosen as a case study as it represents one of the best documented example of marine organic matter accumulation. The relative influence of the critical parameters (bathymetry, diffusive transport, oxygen mixing rate and primary production) on the output parameters (Total Organic Carbon, and oxygen level), determined performing a Global Sensitivity Analysis, shows that, in the context of a shallow epicontinental basin, a moderate primary productivity (>175 gC·m −2 ·year −1) can led to local anoxia and organic matter accumulation. We argue that, regarding all the processes involved, the presence and distribution of organic-rich intervals is linked as a first-order parameter to the morphology of the basin (e.g., ramp slope, bottom topography). These interpretations are supported by very specific ranges of critical parameters that allowed to obtain output parameter values in accordance with the data. This quantitative approach and its conclusions open new perspectives about the understanding of global distribution and preservation of organic-rich sediments

Erratum to: 3D thermal history and maturity modelling of the Levant Basin and its eastern margin, offshore–onshore Lebanon

International audienceThe original version of this article, unfortunately, containederrors.The images of Figures 8 and 9 found in the online PDF did notmatch with the HTML version. In the PDF, continued imagesof Figs. 8 and 9 were duplication of panel "b" of each figure.The correct images are presented in this article.In addition, "Upper Triassic," which is found in the caption ofFigure 8 was corrected to "Lower Triassic" and is nowreflected in this paper.Lastly, the name Samer Bou Daher, though appearing correctlyin the published version, appears as S. B. Daher in indexingsites instead of S. Bou Daher. The metadata was updated todisplay the name correctly in indexing sites.The original version of this paper was updated to reflect thechanges stated on this erratum.The online version of the original article can be found at http://dx.doi.org/10.1007/s12517-016-2455-1

Integrated 3D forward stratigraphic and petroleum system modeling of the Levant Basin, Eastern Mediterranean

International audienceThe Eastern Mediterranean Levant Basin is a proven hydrocarbon province with recent major gas discoveries. To date, no exploration wells targeted its northern part, in particular the Lebanese offshore. The present study assesses the tectono‐stratigraphic evolution and related petroleum systems of the northern Levant Basin via an integrated approach that combines stratigraphic forward modeling and petroleum systems/basin modeling based on the previous published work. Stratigraphic modeling results provide a best‐fit realisation of the basin‐scale sedimentary filling, from the post‐rift Upper Jurassic until the Pliocene. Simulation results suggest dominant eastern marginal and Arabian Plate sources for Cenozoic siliciclastic sediments and a significant contribution from the southern Nilotic source mostly from Lower Oligocene to Lower Miocene. Basin modeling results suggest the presence of a working thermogenic petroleum system with mature source rocks localised in the deeper offshore. The generated hydrocarbons migrated through the deep basin within Jurassic and Cretaceous permeable layers towards the Latakia Ridge in the north and the Levant margin and offshore topographic highs. Furthermore, the basin model indicates a possibly significant influence of salt deposition during Messinian salinity crisis on formation fluids. Ultimately, the proposed integrated workflow provides a powerful tool for the assessment of petroleum systems in underexplored areas