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6. A system for integrative and post-planned analysis of 2-DE/MS centered proteomics data

Author

Wang Juhui, Caron Christophe, He Xuefeng, Carpentier Audrey, Mistou Michel-Yves, Trubuil Alain, Gitton Christophe, Henry Céline, and Guillot Alain

Subjects
Biotechnology, TP248.13-248.65
Abstract

Proteomic analysis is intrinsically an iterative, incremental process. Information is usually acquired gradually by researchers, and in different projects. At the same time, there are relatively few examples of biological data management systems which take into account this reality, most of them usually treat the experiment generated data as static and unchangeable: data are never reconsidered, or seldom, whereas technology becomes more powerful or that other researchers have brought information on data correction. And yet, post-planned analysis [21] which involves multiple iterations and subsequent re-investigations of previously prepared data might bring tremendous benefits.

Published
2005
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7. Design and Evaluation of Three Selection Techniques for Tightly Packed 3D Objects in Cell Lineage Specification in Botany

Author

Hong, Jiayi, Argelaguet Sanz, Ferran, Trubuil, Alain, Isenberg, Tobias, Analysis and Visualization (AVIZ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Interaction avec l'Humain (IaH), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 3D interaction with virtual environments using body and mind (Hybrid), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-MEDIA ET INTERACTIONS (IRISA-D6), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Interaction avec l'Humain (IaH), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
000 computer science, object selection, 3D interaction, dense datasets, [INFO]Computer Science [cs]
Abstract

International audience; We report on a controlled user study in which we investigated and compared three selection techniques in discovering and traversing 3D objects in densely packed environments. We apply this to cell division history marking as required by plant biologists who study the development of embryos, for whom existing selection techniques do not work due to the occlusion and tight packing of the cells to be selected. We specifically compared a list-based technique with an additional 3D view, a 3D selection technique that relies on an exploded view, and a combination of both techniques. Our results indicate that the combination was most preferred. List selection has advantages for traversing cells, while we did not find differences for surface cells. Our participants appreciated the combination because it supports discovering 3D objects with the 3D explosion technique while using the lists to traverse 3D cells.

Published
2021

10. LineageD: An Interactive Visual System for Plant Cell Lineage Assignments based on Correctable Machine Learning.

Author

Hong, Jiayi, Trubuil, Alain, and Isenberg, Tobias

Subjects
*MACHINE learning, *ARTIFICIAL neural networks, *PLANT cells & tissues, *BOTANISTS, *CELL division, *DECISION making, *BIOLOGISTS
Abstract

We describe LineageD—a hybrid web‐based system to predict, visualize, and interactively adjust plant embryo cell lineages. Currently, plant biologists explore the development of an embryo and its hierarchical cell lineage manually, based on a 3D dataset that represents the embryo status at one point in time. This human decision‐making process, however, is time‐consuming, tedious, and error‐prone due to the lack of integrated graphical support for specifying the cell lineage. To fill this gap, we developed a new system to support the biologists in their tasks using an interactive combination of 3D visualization, abstract data visualization, and correctable machine learning to modify the proposed cell lineage. We use existing manually established cell lineages to obtain a neural network model. We then allow biologists to use this model to repeatedly predict assignments of a single cell division stage. After each hierarchy level prediction, we allow them to interactively adjust the machine learning based assignment, which we then integrate into the pool of verified assignments for further predictions. In addition to building the hierarchy this way in a bottom‐up fashion, we also offer users to divide the whole embryo and create the hierarchy tree in a top‐down fashion for a few steps, improving the ML‐based assignments by reducing the potential for wrong predictions. We visualize the continuously updated embryo and its hierarchical development using both 3D spatial and abstract tree representations, together with information about the model's confidence and spatial properties. We conducted case study validations with five expert biologists to explore the utility of our approach and to assess the potential for LineageD to be used in their daily workflow. We found that the visualizations of both 3D representations and abstract representations help with decision making and the hierarchy tree top‐down building approach can reduce assignments errors in real practice. [ABSTRACT FROM AUTHOR]

Published
2022
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11. An Interactive System for Analyzing Plant Embryo Cell Division

Author

Hong, Jiayi, Argelaguet, Ferran, Trubuil, Alain, Isenberg, Tobias, Analysis and Visualization (AVIZ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Recherche en Informatique (LRI), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 3D interaction with virtual environments using body and mind (Hybrid), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-MEDIA ET INTERACTIONS (IRISA-D6), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)

Subjects
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, [INFO]Computer Science [cs]
Abstract

International audience; We provide an interactive system for biologists to assist them in analyzing the development of plant embryos. With this tool they could reconstruct the development history of an embryo, based on a single segmented 3D image from the confocal microscopy. Compared to their traditional manual procedure, our approach supports reasoning about the development of both wild type and mutant plant embryos. For this purpose we use reconstructed surface models of the individual cells, allow the researchers to interactively assign sister cells per development cycle, and complete an inheritance tree. In addition to this manual assignment, we also add an automatic assignment based on the area of the cell interfaces (shared surfaces between cells). For the interactive assignment or correction, we explore different selection strategies of the cells in the dense dataset.

Published
2020

17. 3-D aggregated object detection and labeling from multivariate confocal microscopy images: a model validation approach

Author

Wang, Juhui, Trubuil, Alain, Graffigne, Christine, and Kaeffer, Bertrand

Subjects
Machine vision -- Research
Abstract

One essential assumption used in object detection and labeling by imaging is that the photometric properties of object are homogeneous. This homogeneousness requirement is often violated in microscopy imaging. Classical methods are usually of high computational cost and fail to give stable solution. This paper presents a low computational complexity and robust method for three-dimensional (3-D) biological object detection and labeling. The developed approach is based on a statistical, nonparametric framework. Image is first divided into regular nonoverlapped regions and each region is evaluated according to a general photometric variability model. The regions not consistent with this model are considered as aberration in the data and excluded from the analysis procedure. Simultaneously, the interior parts of the object are detected, they correspond to regions where the supposed model is valid. In the second stage, the valid regions from a same object are merged together depending on a set of hypotheses. These hypotheses are generated by taking into account photometric and geometric properties of objects of interest and the merging is achieved according to an iterative algorithm. The approach has been applied in investigations of spatial distribution of nuclei within colonic glands of rats observed with the help of confocal fluorescence microscopy. Index Terms--Cytometry, confocal microscopy, image analysis, intestinal crypts, multivariate statistics, model validation.

Published
2003

18. An inverse problem approach to the probabilistic reconstruction of particle tracks on a censored and closed surface

Author

Lu, Yunjiao, Hodara, Pierre, Kervrann, Charles, Trubuil, Alain, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), and Institut National de la Recherche Agronomique (INRA)

Subjects
[STAT]Statistics [stat], [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], [STAT.AP]Statistics [stat]/Applications [stat.AP], Image reconstruction, probabilistic modelling, stochastic processes, Multi object tracking, parametric estimation
Abstract

Investigation of dynamics processes in cell biology very often relies on the observation of sampled regions without considering re-entrance events. In the case of image-based observations of bacteria cell wall processes, a large amount of the cylinder-shaped wall is not observed. It follows that biomolecules may disappear for a period of time in a region of interest, and then reappear later. Assuming Brownian motion with drift, we address the mathematical problem of the connection of particle trajectories on a cylindrical surface. A subregion of the cylinder is typically observed during the observation period, and biomolecules may appear or disappear in any place of the 3D surface. The performance of the method is mainly demonstrated on simulation data that mimic MreB dynamics observed in 2D time-lapse fluorescence microscopy.

Published
2019

19. Probabilistic overall reconstruction of membrane-associated molecular dynamics from partial observations in rod-shaped bacteria

Author

Lu, Yunjiao, Hodara, Pierre, Kervrann, Charles, Trubuil, Alain, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Compartimentation et dynamique cellulaires (CDC), Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Kervrann, Charles, Institut Curie-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [INFO.INFO-TS] Computer Science [cs]/Signal and Image Processing, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Time-lapse microscopy, Multi object tracking, Total Internal Reflection (TIRF) Microscopy, parametric estimation, [INFO.INFO-TI] Computer Science [cs]/Image Processing [eess.IV], [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], Image reconstruction, probabilistic modelling, stochastic processes, [MATH.MATH-MP] Mathematics [math]/Mathematical Physics [math-ph], [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

20. Deciphering cell division patterns in plant early embryogenesis by combining 3D image analysis and computer modelling

Author

Laruelle, Elise, Moukhtar, Julien, Trubuil, Alain, Belcram, Katia, Legland, David, Khadir, Zhor, Palauqui, Jean-Christophe, Andrey, Philippe, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [MATH] Mathematics [math], [INFO] Computer Science [cs], [SDV.IDA] Life Sciences [q-bio]/Food engineering, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

21. Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos

Author

Moukhtar, Julien, Trubuil, Alain, Belcram, Katia, Legland, David, Khadir, Zhor, Urbain, Aurelie, Palauqui, Jean-Christophe, Andrey, Philippe, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Génie et Microbiologie des Procédés Alimentaires (GMPA), French State grant [ANR-10-LABX-0040-SPS, ANR-11-IDEX-0003-02], INRA fellowship, and Saclay Plant Sciences LabEx

Subjects
Embryology, Leaves, Arabidopsis, Plant Science, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Morphogenesis, polarity, Cell Cycle and Cell Division, lcsh:QH301-705.5, Cell Analysis, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], mechanisms, Simulation and Modeling, Plant Anatomy, Eukaryota, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Plants, organization, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Bioassays and Physiological Analysis, Cell Division Analysis, Experimental Organism Systems, Cell Processes, Cellular Types, Cell Division, Research Article, Arabidopsis Thaliana, Plant Cell Biology, [SCCO.COMP]Cognitive science/Computer science, Brassica, Research and Analysis Methods, microtubules, Model Organisms, Plant and Algal Models, Plant Cells, Cell Lineage, Computer Simulation, patterns, thaliana, Cell Shape, Cell Nucleus, Models, Statistical, Arabidopsis Proteins, software, Embryos, nucleus, Organisms, Biology and Life Sciences, tissue, Cell Biology, lcsh:Biology (General), manipulation, Animal Studies, Developmental Biology
Abstract

Plant tissue architecture and organ morphogenesis rely on the proper orientation of cell divisions. Previous attempts to predict division planes from cell geometry in plants mostly focused on 2D symmetric divisions. Using the stereotyped division patterns of Arabidopsis thaliana early embryogenesis, we investigated geometrical principles underlying plane selection in symmetric and in asymmetric divisions within complex 3D cell shapes. Introducing a 3D computational model of cell division, we show that area minimization constrained on passing through the cell centroid predicts observed divisions. Our results suggest that the positioning of division planes ensues from cell geometry and gives rise to spatially organized cell types with stereotyped shapes, thus underlining the role of self-organization in the developing architecture of the embryo. Our data further suggested the rule could be interpreted as surface minimization constrained by the nucleus position, which was validated using live imaging of cell divisions in the stomatal cell lineage., Author summary The proper positioning of division planes is key for correct development and morphogenesis of organs, in particular in plants were cellular walls prevent cell rearrangements. Elucidating how division planes are selected is therefore essential to decipher the cellular bases of plant morphogenesis. Previous attempts to identify geometrical rules relating cell shape and division plane positioning in plants mostly focused on symmetric divisions in tissues reduced to 2D geometries. Here, we combined 3D quantitative image analysis and a new 3D cell division model to evaluate the existence of geometrical rules in asymmetrical and symmetrical divisions of complex cell shapes. We show that in the early embryo of the model plant Arabidopsis thaliana, which presents stereotyped but complex cell division patterns, a single geometrical rule (area minimization constrained on passing through the cell centroid) recapitulates the complete sequence of division events. This new rule, valid for both symmetrical and asymmetrical divisions, generalizes previously proposed cell division rules and can be interpreted based on the dynamics of the cytoskeleton and on the positioning of the nucleus, a hypothesis that we validated using leaf cell division patterns. This work highlights the importance of self-organization in plant early morphogenesis and the emergence of robust cellular organizations based on geometrical feedback loops between cell geometry and division plane selection.

Published
2019

22. Toward a standardised annotation of morphokinetical parameters for an automatic early prediction of the in vitro development potential of bovine embryos

Author

De Paula Reis, Alline, Brocart, Guillaume, Belghiti, Mounya, Le Brusq, N., Messoudi, Soundouss, Le Guienne, B. M., Laffont, Ludivine, Ruffini, Sylvie, Canon, Eugénie, Adenot, Pierre, Duranthon, Véronique, Trubuil, Alain, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Recherche et Développement, LACTALIS (LACTALIS NUTRITION), and International Embryo Transfer Society (IETS). USA.

Subjects
[SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology
Abstract

International audience; In a previous work, we proposed an algorithm to select a subset of discriminant morphokinetical parameters within a larger predefined set (116 parameters) and to predict 6 major bovine embryo profiles of in vitro development. The algorithm relies on flexible combinations of the discriminant parameters selected within the four first cleavage cycles. The retained profiles were arrested embryos (embryos without mitotic activity, showing signs of life); dead embryos (embryos with all cells dead); anarchic embryos (embryos with abnormal morphological and/or kinetical development: some of these embryos can result in a blastocyst); not hatched blastocysts (blastocysts not hatching by 8 dpi); hatching blastocysts (blastocysts hatching in vitro from 7.3 to 8 dpi); and early hatching blastocysts (blastocysts hatching from 6 to 7.2 dpi) (Reis et al. 2018 Anim. Reprod.). The aim of the present work was to develop a ready-to-use software (EasyPickAndPredict) allowing the extension of this methodology to other embryologists. The software of high portability was built with the JAVA language and embedded with the classifier (R language, R Foundation for Statistical Computing, Vienna, Austria) and a user’s help for annotation (Adobe Premiere Pro CS5, San Jose, CA, USA). The predictive software is easy to handle, fast to load, and has high portability. The “manual annotation” function is based on click actions to annotate the discriminant parameters. The “prediction” function calls the embedded classifier. The “report” function creates customised reports including the embryo classification, the summary of the measures, and the accuracy of the prediction (vote system). The “help” function calls an audiovisual guideline with annotation specifications for all the morphokinetic parameters currently described (including the discriminant subset of parameters). This document includes help to produce a good time-lapse video (16 min 51 s); annotation specifications for the cleavage cycles 1 to 4 (36 min 26 s); and a summary with examples of the 6 major embryonic morphokinetical profiles (16 min 47 s). The predictive graphical interface is easy to manipulate and automatically extracts the value of each discriminant parameter on the time-lapse picture as validated by the user click. The functions “manual annotation”, “automatic prediction”, “help”, and “report” supply embryologists with a standard approach to predict and analyse morphokinetical profiles of their embryos. This standardised approach is necessary to improve the capacity of comparison of morphokinetical works in different laboratories and enhance knowledge about in vitro-produced bovine embryos.

Published
2019

23. 3D stochastic process simulation for better interpretation of molecular dynamics related to cell wall biogenesis observed with TIRF microscopy

Author

Lu, Yunjiao, Billaudeau, Cyrille, Carballlido-Lopez, Rut, Kervrann, Charles, Trubuil, Alain, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
[MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

24. Combining 3D image analysis and computer modeling to understand cell division patterns in plant early embryogenesis

Author

Moukhtar El Demerdache, Julien, Laruelle, Elise, Trubuil, Alain, Belcram, Katia, Legland, David, Khadir, Zhor, Palauqui, Jean-Christophe, Andrey, Philippe, ProdInra, Migration, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA)

Subjects
[SDV] Life Sciences [q-bio], [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [MATH] Mathematics [math], [MATH]Mathematics [math], [INFO] Computer Science [cs], [SDV.IDA] Life Sciences [q-bio]/Food engineering, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2019

25. Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos

Author

Moukhtar El Demerdache, Julien, Trubuil, Alain, Belcram, Katia, Legland, David, Khadir, Zhor, Urbain, Aurelie, Palauqui, Jean-Christophe, and Andrey, Philippe

Subjects
polarity, patterns, software, thaliana, mechanisms, organization, manipulation, microtubules, tissue, nucleus
Abstract

Plant tissue architecture and organ morphogenesis rely on the proper orientation of cell divisions. Previous attempts to predict division planes from cell geometry in plants mostly focused on 2D symmetric divisions. Using the stereotyped division patterns of Arabidopsis thaliana early embryogenesis, we investigated geometrical principles underlying plane selection in symmetric and in asymmetric divisions within complex 3D cell shapes. Introducing a 3D computational model of cell division, we show that area minimization constrained on passing through the cell centroid predicts observed divisions. Our results suggest that the positioning of division planes ensues from cell geometry and gives rise to spatially organized cell types with stereotyped shapes, thus underlining the role of self-organization in the developing architecture of the embryo. Our data further suggested the rule could be interpreted as surface minimization constrained by the nucleus position, which was validated using live imaging of cell divisions in the stomatal cell lineage.

Published
2019

28. Design and Evaluation of Three Selection Techniques for Tightly Packed 3D Objects in Cell Lineage Specification in Botany.

Author

Jiayi Hong, Argelaguet, Ferran, Trubuil, Alain, and Isenberg, Tobias

Subjects
CELL division, BOTANISTS, EMBRYOS, USER interfaces, BIOLOGISTS
Abstract

We report on a controlled user study in which we investigated and compared three selection techniques in discovering and traversing 3D objects in densely packed environments. We apply this to cell division history marking as required by plant biologists who study the development of embryos, for whom existing selection techniques do not work due to the occlusion and tight packing of the cells to be selected. We specifically compared a list-based technique with an additional 3D view, a 3D selection technique that relies on an exploded view, and a combination of both techniques. Our results indicate that the combination was most preferred. List selection has advantages for traversing cells, while we did not find differences for surface cells. Our participants appreciated the combination because it supports discovering 3D objects with the 3D explosion technique while using the lists to traverse 3D cells. [ABSTRACT FROM AUTHOR]

Published
2021

29. Identification and mathematical prediction of different morphokinetic profiles of in vitro developed bovine embryos

Author

De Paula Reis, Alline, Belghiti, Mounya, Messoudi, Soundouss, Marquant-Le Guienne, Brigitte, Laffont, Ludivine, Ruffini, Sylvie, Canon, Eugenie, Adenot, Pierre, Le Brusq, M, Duranthon, Veronique, Trubuil, Alain, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Recherche et Développement, LACTALIS (LACTALIS NUTRITION), and Association Européenne des Technologies et de l'Embryon (AETE) (AETE). FRA.

Subjects
expression cinétique, blastocyste, embryon, Biologie du développement, embryo, morphokinetics, prediction, in vitro, Development Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

30. PROBABILISTIC RECONSTRUCTION OF TRUNCATED PARTICLE TRAJECTORIES ON A CLOSED SURFACE.

Author

YUNJIAO LU, HODARA, PIERRE, KERVRANN, CHARLES, and TRUBUIL, ALAIN

Subjects
PARTICLE tracks (Nuclear physics), BACTERIAL cell walls, FLUORESCENCE microscopy, BROWNIAN motion, BACTERIAL proteins
Abstract

Investigation of dynamic processes in cell biology very often relies on the observation in two dimensions of three-dimensional (3D) biological processes. Consequently, the data are partial and statistical methods and models are required to recover the parameters describing the dynamical processes. In the case of molecules moving over the 3D surface, such as proteins on walls of bacteria cell, a large portion of the 3D surface is not observed in two-dimensional (2D)-time microscopy. It follows that biomolecules may disappear for a period of time in a region of interest, and then reappear later. Assuming Brownian motion with drift, we address the mathematical problem of the reconstruction of biomolecules trajectories on a cylindrical surface. A subregion of the cylinder is typically recorded during the observation period, and biomolecules may appear or disappear in any place of the 3D surface. The performance of the method is demonstrated on simulated particle trajectories that mimic MreB protein dynamics observed in 2D time-lapse fluorescence microscopy in rod-shaped bacteria. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
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31. Towards Automated Early Classification of Embryos

Author

Trubuil, Alain, Belghiti, Mounya, Duranthon, Véronique, Adenot, Pierre, Laffont, Ludivine, Ruffini, Sylvie, Le guienne, Brigitte, De Paula Reis, Alline, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), École nationale vétérinaire d'Alfort (ENVA), Université Paris Saclay (COmUE), Allice, and BioImage Informatics.

Subjects
[SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

32. Morphokinetic and transcriptomic characterisation of bovine embryos: towards an improvment of the use of embryos for population recovery

Author

De Paula Reis, Alline, Trubuil, Alain, Jouneau, Alice, Canon, Eugénie, Laffont, Ludivine, Ruffini, Sylvie, Adenot, Pierre, Le guienne, Brigitte, Richard, Christophe, Duranthon, Véronique, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), École nationale vétérinaire d'Alfort (ENVA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Allice, CRB Anim project 'Investissements d'Avenir' ANR-11-INBS-0003, and Centres de Ressources Biologiques pour les Animaux Domestiques (CRB-Anim). FRA.

Subjects
[SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

33. Towards the modelling of conceptus morphogenesis in ruminants

Author

Chettaoui, Chadha, Degrelle, Severine, Trubuil, Alain, Hue, Isabelle, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Nonlinear Analysis for Biology and Geophysical flows (BANG), Laboratoire Jacques-Louis Lions (LJLL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut National de la Santé et de la Recherche Médicale (INSERM), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Institut Thématique Multi-Organisme Biologie Cellulaire, Développement et Evolution (ITMO). FRA., and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)

Subjects
cell differentiation, embryonic structures, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, ruminant, trophoblast, [SDV.BDD]Life Sciences [q-bio]/Development Biology, cell shape
Abstract

Remerciements: Plateforme MIMA2, Inra Jouy en Josas; National audience; In ruminants, the elongation of the conceptus is marked by an anisotropic growth of the extra- embryonic tissues prior to implantation. This has not been related so far to processes such as cell deformation or specific cell organisation and could result from oriented cell divisions within the trophoblast [Wang, CRAS, 2009]. However, since the endoderm cells that underline the trophoblast display highly anisotropic features [Flechon, Genesis, 2007] it could be that this extra-embryonic layer drives the elongation process. To test these 2 hypotheses: oriented trophoblast division and endoderm driven process, we have started analysing these cells, their divisions and their interactions to extract biological and/or biophysical parameters. Once evaluated, we could integrate them and aim at the modelling of this ruminant specific morphogenesis.

Published
2015

34. Proteomic signature of Lactococcus lactis NCDO763 cultivated in milk

Author

Gitton, Christophe, Meyrand, Mickael, Wang, Juhui, Caron, Christophe, Trubuil, Alain, Guillot, Alain, and Mistou, Michel-Yves

Subjects
Lactococcus -- Genetic aspects, Proteomics -- Research, Glutamine metabolism -- Research, Glutamine metabolism -- Genetic aspects, Biological sciences
Abstract

A study is conducted to characterize the proteomic profile of Lactococcus lactis during its development in milk. The proteomic analysis provides the role of glutamine synthetase and further genetic experiments highlights the key role of this enzyme in the development of Lactococcus lactis in dairy environments.

Published
2005

35. Computational modelling of cell division patterns during plant early embryogenesis

Author

Moukhtar, Julien, Belcram, Katia, Trubuil, Alain, Legland, David, Palauqui, Jean-Christophe, Andrey, Philippe, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [INFO]Computer Science [cs], [MATH] Mathematics [math], [SDV.IDA] Life Sciences [q-bio]/Food engineering, [INFO] Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

36. Imaging and quantitative analysis of size and distribution of sperical bodies, e.g. embryonic oil bodies

Author

Trigui, Ghassen, Trubuil, Alain, Miquel, Martine, and Dubreucq, Bertrand

Subjects
plant, image processing
Abstract

Oil bodies (OBs) are seed-specific lipid storage organelles that allow the accumulation of neutral lipids that sustain plantlet development after the onset of germination. Using fluorescent dyes and confocal microscopy, we monitored the dynamics of OBs in living Arabidopsis (Arabidopsis thaliana) embryos at different stages of development (Miquel et al., 2014). Image acquisition was followed by a detailed statistical analysis of OB size and distribution during seed development in the four dimensions (x, y, z, and t).

Published
2015

37. Imaging and quantitative analysis of size and distribution of sperical bodies, [i]e.g[/i]. embryonic oil bodies

Author

Miquel, Martine, Trigui, Ghassen, Trubuil, Alain, Dubreucq, Bertrand, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], plant, image processing
Abstract

C'est article est un PROTOCOLE; Oil bodies (OBs) are seed-specific lipid storage organelles that allow the accumulation of neutral lipids that sustain plantlet development after the onset of germination. Using fluorescent dyes and confocal microscopy, we monitored the dynamics of OBs in living Arabidopsis (Arabidopsis thaliana) embryos at different stages of development (Miquel et al., 2014). Image acquisition was followed by a detailed statistical analysis of OB size and distribution during seed development in the four dimensions (x, y, z, and t).

Published
2015

38. Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos.

Author

Julien, Moukhtar, Trubuil, Alain, Belcram, Katia, Legland, David, Khadir, Zhor, Urbain, Aurélie, Palauqui, Jean-Christophe, and Andrey, Philippe

Subjects
*ARABIDOPSIS, *EMBRYOS, *PLANT cells & tissues, *EMBRYOLOGY, *CENTROID
Abstract

Plant tissue architecture and organ morphogenesis rely on the proper orientation of cell divisions. Previous attempts to predict division planes from cell geometry in plants mostly focused on 2D symmetric divisions. Using the stereotyped division patterns of Arabidopsis thaliana early embryogenesis, we investigated geometrical principles underlying plane selection in symmetric and in asymmetric divisions within complex 3D cell shapes. Introducing a 3D computational model of cell division, we show that area minimization constrained on passing through the cell centroid predicts observed divisions. Our results suggest that the positioning of division planes ensues from cell geometry and gives rise to spatially organized cell types with stereotyped shapes, thus underlining the role of self-organization in the developing architecture of the embryo. Our data further suggested the rule could be interpreted as surface minimization constrained by the nucleus position, which was validated using live imaging of cell divisions in the stomatal cell lineage. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

39. Specialization of oleosins in OB dynamics during seed development in Arabidopsis thaliana seeds

Author

Miquel, Martine, Trigui, Ghassen, D'Andrea, Sabine, Kelemen, Zsolt, Baud, Sebastien, Berger, Adeline, Deruyffelaere, Carine, Trubuil, Alain, Lepiniec, Loic, Dubreucq, Bertrand, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Mathématiques et Informatique Appliquées (MIA), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, arabidopsis, oil body, oleosin, seed development
Abstract

Oil bodies (OBs) are seed-specific lipid storage organelles that allow accumulation of neutral lipids that sustain plantlet development after the onset of germination. OBs are covered with specific proteins embedded in a single layer of phospholipids. Using fluorescent dyes and confocal microscopy, we monitored the dynamics of OBs in living arabidopsis embryos at different stages of development. Analyses were carried out with different genotypes i.e. the wild type and 3 mutants affected in the accumulation of various oleosins (OLE1, OLE2 and OLE4), three major OB proteins. Image acquisition was followed by a detailed statistical analysis of OB size and distribution during seed development in the 4 dimensions (X, Y, Z, T). Our results indicate that OB size increases sharply during seed maturation, in part by OB fusion, and then decreases until the end of the maturation process. In single, double and triple mutant backgrounds, the size and spatial distribution of OBs are modified, affecting in turn the total lipid content, which suggests that the oleosins studied have specific functions in the dynamics of lipid accumulation.

Published
2014

40. Some specific problems of dynamics recovery in cell biology

Author

Trubuil, Alain, Unité de biométrie et intelligence artificielle de jouy, and Institut National de la Recherche Agronomique (INRA)

Subjects
[INFO]Computer Science [cs], [MATH]Mathematics [math], biofilm
Abstract

International audience; In this talk, I will highlight several biological studies for which we are faced with dynamics recovery at the cell scale. I will start with early plant embryogenesis and explain how we can extract dynamical information despite the fact that no time lapse data is available but observations of a collection of embryos at different stages of development. In the second part of the talk, I will address a new study we are involved in and concerns the dynamics of swimmers bacteria inside biofilms. In this context two image channels could be combined in order to better understand the interaction between swimmers bacteria and biofilm.

Published
2014

41. Geometrical Analysis of early stage Arabidopsis thaliana embryos

Author

Trubuil, Alain, Unité de biométrie et intelligence artificielle de jouy, and Institut National de la Recherche Agronomique (INRA)

Subjects
algorithm, morphogenesis, plant, [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

42. Analysis of factors affecting the growth of oil bodies in A. Thaliana seeds: use of ordinary least squares and quantile regression

Author

Trigui, Ghassen, Miquel, Martine, Dubreucq, Bertrand, David, Olivier, Trubuil, Alain, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de biométrie et intelligence artificielle de jouy, and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [INFO]Computer Science [cs], [MATH]Mathematics [math], ordinary least squares, quantile regression, oil bodies, oleosin, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

43. On 3D reconstruction and lineage of Arabidopsis embryos from a collection of fixed samples

Author

Urbain, Aurelie, Palauqui, Jean-Christophe, Nikolaev, S.V., Kolchanov, N.A., Trubuil, Alain, Unité de recherche Mathématiques et Informatique Appliquées (MIA), Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, algorithm, morphogenesis, plant, cell lineage
Abstract

Development of plant embryo beginning from the very early stages is not fully studied yet. For example, detailed description of dynamics of cellular composition of embryo, and the cells growth are unknown. Herein we propose a quantitative description of the early Arabidopsis thaliana development. The description is quantitative with respect to cell shapes, division planes, dynamics though time lapse data are not available. We have designed three algorithms. The first one is devoted to 3D reconstruction from stacks of confocal images. The second algorithm builds a tree representation of the embryo. Each node of the tree corresponds to a set of related cells and each branch points towards a daughter cell. This representation is based on topological and geometrical rules applied on the 3D reconstructions. The third algorithm is devoted to embryos comparisons. Considering two embryos at different stages of development and their associated tree representations we propose to plug the younger embryo inside the older one. This is realized by tree explorations from the root. Results: 3D geometrical models of early stages of Arabidopsis embry development were constructed in meshes representation. Different features such as volumes, neighboring structure have been computed. For several embryos, the history of divisions has been reconstructed.Growth rates could be inferred from the plug-in of embryos. Conlusion: From a collection of Arabidopsis embryos observed iconfocal microscopy quantitative data such as volumes can be analyzed. Despite the fact that no time lapse is available dynamics information could be inferred. At least several rounds of divisions can be guess. Of course variability should be addressed and the plug-in algorithm we propose can be helpful. The 4D information we got can now be used for designing models for biomechanics and transport phenomena evaluation during early plant embryo development.

Published
2012

44. The dynamics of oil bodies in A. thaliana seeds :A mathematical model of biogenesis and coalescence

Author

Trigui, Ghassen, Laroche, Béatrice, Miquel, Martine, Dubreucq, Bertrand, Trubuil, Alain, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Mathématiques et Informatique Appliquées (MIA), Institut National de la Recherche Agronomique (INRA), and Labo/service de l'auteur, Ville service.

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, coalescence, population dynamics, dynamique des populations, échelle microscopique, oil body, biogenesis, coalescence, oil body, oleosin, population dynamics, biogenesis, oleosin
Abstract

The subcellular organelles called oil bodies (OBs) arelipid-filled quasi-spherical droplets produced from the endoplasmicreticulum (ER) and then released into the cytoplasm during seeddevelopment. It is believed that an OB grows by coalescence withother OBs and that its stability depends on the composition ofoleosins, major proteins inserted in the hemi membrane that coversOBs. In this study, we measured the OB-volume distribution fromdifferent genotypes of A. thaliana after 7, 8, 9, 10 and 11 days ofseed development. In order to test the hypothesis of OBs dynamics,we developed a simple mathematical model using non-linear differentialequations inspired from the theory of coagulation. The modeldescribes the evolution of OB-volume distribution during the firststeps of seed development by taking into consideration the productionof OBs, the increase of triacylglycerol volume to be stored, and thegrowth by coalescence of OBs. Fitted parameters values show anincrease in the OB production and coalescence rates in A. thalianaoleosin mutants compared to wild type.

Published
2012

45. Role of bacterial peptidase F inferred by statistical analysis and further experimental validation

Author

López Kleine, Liliana, Monnet, Veronique, Péchoux, Christine, Trubuil, Alain, Biochimie bactérienne (BIOBAC), Institut National de la Recherche Agronomique (INRA), Unité de recherche génomique et physiologie de la lactation (GPL), and Unité de biométrie et intelligence artificielle de jouy

Subjects
complete genome sequence, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

46. Retrieval of canopy biophysical variables from bidirectional reflectance using prior information to solve the ill-posed inverse problem

Author

Combal, B., Baret, Frédéric, Weiss, M., Trubuil, Alain, Mace, D., Pragnère, A., Myneni, R., Knyazikhin, Y., Wang, L., ProdInra, Migration, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), and Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SPI.OTHER]Engineering Sciences [physics]/Other, INFORMATION A PRIORI, [SPI.OTHER] Engineering Sciences [physics]/Other, RESEAU DE NEURONES, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2002

47. Optimal level curves and global minimizers of Cost functionals in image segmentation

Author

Kervrann, Charles, Trubuil, Alain, Unité de biométrie et intelligence artificielle de jouy, and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], METEOROLOGIE
Abstract

57 ref. *INRA Biométrie 78352 Jouy-en-Josas (FRA) Diffusion du document : INRA Biométrie 78352 Jouy-en-Josas (FRA); International audience

Published
2001

48. Precision of systematic counts

Author

Kiêu, Kiên, Xiong, W., Trubuil, Alain, Unité de recherche Biométrie (UB), Institut National de la Recherche Agronomique (INRA), and Unité de biométrie et intelligence artificielle de jouy

Subjects
[SDV]Life Sciences [q-bio]
Abstract

Rapport technique * INRA - Unité de Biométrie, Centre de Versailles (FRA) Diffusion du document : INRA - Unité de Biométrie, Centre de Versailles (FRA); International audience; In this paper, the estimation of a population size from counts in systematically distributed units is considered. The empirical estimator is unbiased if the sampling is uniform. A method for assessing the precision of the empirical estimator from the count data is described. Although the main part of the paper concerns one-dimensional sampling (events distributed along an axis), extensions to systematic counts in multidimensional spaces are available. Furthermore, the described methods also apply to particle counts with edge effect corrections.

Published
1998

49. Non-parametric segmentation for star-shaped objects

Author

Istas, J., Trubuil, Alain, Unité de biométrie et intelligence artificielle de jouy, and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], OBJET, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1995

50. Automatic analysis of unidimensional electrophoresis

Author

Trubuil, Alain, RODOLPHE, F., Unité de biométrie et intelligence artificielle de jouy, and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], STATION DE TRAVAIL, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
1990

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