Dissertations / Theses on the topic 'Image de microscopie'
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Toledo, Acosta Bertha Mayela. "Multimodal image registration in 2D and 3D correlative microscopy." Thesis, Rennes 1, 2018. http://www.theses.fr/2018REN1S054/document.
Full textThis thesis is concerned with the definition of an automated registration framework for 2D and 3D correlative microscopy images, in particular for correlative light and electron microscopy (CLEM) images. In recent years, CLEM has become an important and powerful tool in the bioimaging field. By using CLEM, complementary information can be collected from a biological sample. An overlay of the different microscopy images is commonly achieved using techniques involving manual assistance at several steps, which is demanding and time consuming for biologists. To facilitate and disseminate the CLEM process for biologists, the thesis work is focused on creating automatic registration methods that are reliable, easy to use and do not require parameter tuning or complex knowledge. CLEM registration has to deal with many issues due to the differences between electron microscopy and light microscopy images and their acquisition, both in terms of pixel resolution, image size, content, field of view and appearance. We have designed intensity-based methods to align CLEM images in 2D and 3D. They involved a common representation of the LM and EM images using the LoG transform, a pre-alignment step exploiting histogram-based similarities within an exhaustive search, and a fine mutual information-based registration. In addition, we have defined a robust motion model selection method, and a multiscale spot detection method which were exploited in the 2D CLEM registration. Our automated CLEM registration framework was successfully tested on several real 2D and 3D CLEM datasets and the results were validated by biologists, offering an excellent perspective in the usefulness of our methods
Denimal, Emmanuel. "Détection de formes compactes en imagerie : développement de méthodes cumulatives basées sur l'étude des gradients : Applications à l'agroalimentaire." Thesis, Bourgogne Franche-Comté, 2018. http://www.theses.fr/2018UBFCK006/document.
Full textThe counting cells (Malassez, Thoma ...) are designed to allow the enumeration of cells under a microscope and the determination of their concentration thanks to the calibrated volume of the grid appearing in the microscopic image. Manual counting has major disadvantages: subjectivity, non-repeatability ... There are commercial automatic counting solutions, the disadvantage of which is that a well-controlled environment is required which can’t be obtained in certain studies ( eg glycerol greatly affects the quality of the images ). The objective of the project is therefore twofold: an automated cell count and sufficiently robust to be feasible regardless of the acquisition conditions.In a first step, a method based on the Fourier transform has been developed to detect, characterize and erase the grid of the counting cell. The characteristics of the grid extracted by this method serve to determine an area of interest and its erasure makes it easier to detect the cells to count.To perform the count, the main problem is to obtain a cell detection method robust enough to adapt to the variable acquisition conditions. The methods based on gradient accumulations have been improved by the addition of structures allowing a finer detection of accumulation peaks. The proposed method allows accurate detection of cells and limits the appearance of false positives.The results obtained show that the combination of these two methods makes it possible to obtain a repeatable and representative count of a consensus of manual counts made by operators
Moisan, Frédéric. "Optimisation du contraste image en microscopie optique : application à l'inspection microélectronique." Grenoble 1, 1988. http://tel.archives-ouvertes.fr/tel-00331501.
Full textMoisan, Frédéric. "Optimisation du contraste image en microscopie optique application à l'inspection microélectronique /." Grenoble 2 : ANRT, 1988. http://catalogue.bnf.fr/ark:/12148/cb37616602c.
Full textMoisan, Frédéric Courtois Bernard. "Optimisation du contraste image en microscopie optique application à l'inspection microélectronique /." S.l. : Université Grenoble 1, 2008. http://tel.archives-ouvertes.fr/tel-00331501.
Full textJezierska, Anna Maria. "Image restoration in the presence of Poisson-Gaussian noise." Phd thesis, Université Paris-Est, 2013. http://tel.archives-ouvertes.fr/tel-00906718.
Full textLe, Floch Hervé. "Acquisition des images en microscopie electronique a balayage in situ." Toulouse 3, 1986. http://www.theses.fr/1986TOU30026.
Full textHenrot, Simon. "Déconvolution et séparation d'images hyperspectrales en microscopie." Electronic Thesis or Diss., Université de Lorraine, 2013. http://www.theses.fr/2013LORR0187.
Full textHyperspectral imaging refers to the acquisition of spatial images at many spectral bands, e.g. in microscopy. Processing such data is often challenging due to the blur caused by the observation system, mathematically expressed as a convolution. The operation of deconvolution is thus necessary to restore the original image. Image restoration falls into the class of inverse problems, as opposed to the direct problem which consists in modeling the image degradation process, treated in part 1 of the thesis. Another inverse problem with many applications in hyperspectral imaging consists in extracting the pure materials making up the image, called endmembers, and their fractional contribution to the data or abundances. This problem is termed spectral unmixing and its resolution accounts for the nonnegativity of the endmembers and abundances. Part 2 presents algorithms designed to efficiently solve the hyperspectral image restoration problem, formulated as the minimization of a composite criterion. The methods are based on a common framework allowing to account for several a priori assumptions on the solution, including a nonnegativity constraint and the preservation of edges in the image. The performance of the proposed algorithms are demonstrated on fluorescence confocal images of bacterial biosensors. Part 3 deals with the spectral unmixing problem from a geometrical viewpoint. A sufficient condition on abundance coefficients for the identifiability of endmembers is proposed. We derive and study a joint observation model and mixing model and demonstrate the interest of performing deconvolution as a prior step to spectral unmixing on confocal Raman microscopy data
Henrot, Simon. "Déconvolution et séparation d'images hyperspectrales en microscopie." Phd thesis, Université de Lorraine, 2013. http://tel.archives-ouvertes.fr/tel-00931579.
Full textSibarita, Jean-Baptiste. "Formation et restauration d'images en microscopie à rayons : application à l'observation d'échantillons biologiques." Phd thesis, Université Joseph Fourier (Grenoble), 1996. http://tel.archives-ouvertes.fr/tel-00345364.
Full textVuillemot, Rémi. "Molecular dynamics simulation based image analysis methods for structural studies of biological macromolecular complexesolecular complexes." Electronic Thesis or Diss., Sorbonne université, 2023. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2023SORUS328.pdf.
Full textCryo-Electron Microscopy (cryo-EM) allows conformational studies of macromolecular complexes in their close-to-native state, essential for understanding their working mechanisms and for structure-based drug development. Deciphering continuous conformational transitions of macromolecules, through the main cryo-EM processing techniques, Single Particle Analysis (SPA) and cryo-Electron Tomography (cryo-ET), is challenging partly due to the low signal-to-noise ratio and is currently an active field of research. During my Ph.D. thesis, I investigated new image processing methods based on Molecular Dynamics (MD) simulations that allow extracting continuous conformational variability from SPA and cryo-ET data. My work resulted in the development of MDSPACE and MDTOMO, the two first methods using MD simulations, empowered by Normal Mode Analysis (NMA), to extract the continuous conformational landscape from SPA and cryo-ET datasets, respectively. The developed methods were employed to investigate the conformational behavior of diverse systems such as 80S ribosome and AAA ATPase p97 (MDSPACE) and SARS-CoV2 spike protein in situ (MDTOMO)
Bertrand, Cédric. "Développement d'une nouvelle méthode d'imagerie cutanée in-vivo par microscopie confocale tandem." Saint-Etienne, 1994. http://www.theses.fr/1994STET4016.
Full textMartinez, Sandrine. "Contribution à la caractérisation des surfaces acquises en microscopie tridimensionnelle." Saint-Etienne, 1998. http://www.theses.fr/1998STET4023.
Full textBergher, Laurent Courtois Bernard. "Analyse de défaillances de circuits VLSI par microscopie électronique à balayage." S.l. : Université Grenoble 1, 2008. http://tel.archives-ouvertes.fr/tel-00315589.
Full textMarim, Marcio. "Applications du Compressed Sensing à l'imagerie biologique de microscopie." Phd thesis, Télécom ParisTech, 2011. http://pastel.archives-ouvertes.fr/pastel-00710395.
Full textKarathanou, Argyro. "Image processing for on-line analysis of electron microscope images : automatic Recognition of Reconstituted Membranes." Phd thesis, Université de Haute Alsace - Mulhouse, 2009. http://tel.archives-ouvertes.fr/tel-00559800.
Full textMercier, Michel. "Recherches sur l'image scientifique : génèse du sens et signification en microscopie électronique." Bordeaux 1, 1987. http://www.theses.fr/1987BOR10567.
Full textBouyrie, Mathieu. "Restauration d'images de noyaux cellulaires en microscopie 3D par l'introduction de connaissance a priori." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLA032/document.
Full textIn this this document, we present a method to denoise 3D images acquired by 2-photon microscopy and displaying cell nuclei of animal embryos. The specimens are observed in toto and in vivo during their early development. Image deterioration can be explained by the microscope optical flaws, the acquisition system limitations, and light absorption and diffusion through the tissue depth.The proposed method is a 3D adaptation of a 2D method so far applied to astronomical images and it also differs from state-of the of-the-art methods by the introduction of priors on the biological data. Our hypotheses include assuming that noise statistics are Mixed Poisson Gaussian (MPG) and that cell nuclei are quasi spherical.To implement our method in 3D, we had to take into account the sampling grid dimensions which are different in the x, y or z directions. A spherical object imaged on this grid loses this property. To deal with such a grid, we had to interpret the filtering process, which is a core element of the original theory, as a diffusion process
Angulo, López Jesús. "Morphologie mathématique et indexation d'image couleur : application à la microscopie en biomédecine." Paris, ENMP, 2003. https://pastel.archives-ouvertes.fr/tel-00007524.
Full textFernandez, Romain. "Reconstruction tridimensionnelle et suivi de lignées cellulaires à partir d'images de microscopie laser : application à des tissus végétaux." Phd thesis, Université Montpellier II - Sciences et Techniques du Languedoc, 2010. http://tel.archives-ouvertes.fr/tel-00845205.
Full textLouys, Mireille. "Traitement d'images de microscopie électronique appliqué à l'étude structurale de macromolécules biologiques." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13153.
Full textBouchama, Lyes. "Apport des techniques d'apprentissage (profond) à la microscopie holographique pour applications médicales." Electronic Thesis or Diss., Institut polytechnique de Paris, 2023. http://www.theses.fr/2023IPPAS022.
Full textThis research is part of the Télécom SudParis (TSP) and TRIBVN/T-life strategic partnership, dedicated to the development of new approaches in optical microscopy, coupled with artificial intelligence, to identify, predict and monitor hematological and parasitological pathologies.In this regard, we developed a prototype microscope based on a computational imaging principle with a synthetic aperture, based on the FPM (Fourier Ptychographic Microscopy) approach. This approach makes it possible to overcome conventional optics' resolution limits, or equivalently access very large fields of view (from 4 to 25 times larger) at fixed resolution. It also enables us to diversify the nature of the data acquired (with phase recording in addition to intensity data).However, despite its promise, the technology faces challenges in widespread adoption and commercialization within the microscopy field, primarily due to constraints such as the time-intensive process required for image acquisition and reconstruction to achieve optimal quality.The research conducted in this thesis has led to substantial advancements in overcoming certain limitations of this technology, leveraging models based on neural networks.We have proposed an efficient automatic refocusing of bimodal images over large fields of view, thanks to post-processing based on a U-Net. We have also proposed an original approach, combining statistical learning and physics-driven optimization to reduce image acquisition and reconstruction times.These frameworks have validated their efficacy by yielding more precise and discriminating diagnoses in the fields of parasitology and haematology.The potential applications of these contributions go far beyond the field of FPM, opening up perspectives in various other fields of computational imaging
Bechensteen, Arne. "Optimisation L2-L0 contrainte et application à la microscopie à molécule unique." Thesis, Université Côte d'Azur, 2020. http://www.theses.fr/2020COAZ4068.
Full textSparse optimization is crucial in today's society, as this is used in multiple domains, such as denoising, compression, machine learning, and variable selection. Sparse optimization is also vital in single-molecule localization microscopy, a microscopy method widely used in biology. However, obtaining a good sparse solution of a signal is computationally challenging. This thesis focuses on sparse optimization in the form of minimizing the least square loss function under a k-sparse constraint with an L0 pseudo-norm (the constrained L2-L0 problem). We also study the sum of the least square loss function and an L0 penalty term (the penalized L2-L0 problem). Both problems are non-convex, non-continuous, and NP-hard. We propose three new approaches to sparse optimization. We present first a continuous relaxation of the constrained problem and present a method to minimize the proposed relaxation. Secondly, we reformulate the L0 pseudo-norm as a convex minimization problem. This is done by introducing an auxiliary variable, and we present an exact biconvex reformulation of the constrained (CoBic) and penalized (PeBic) problems. Finally, we present a method to minimize the product of the data fidelity term and the regularization term. The latter is still an ongoing research work. We apply the three proposed methods (relaxation, CoBic, and PeBic) to single-molecule localization microscopy and compare them with other commonly used algorithms in sparse optimization. The proposed algorithms' results are as good as the state-of-the-art in grid-based methods. Furthermore, fixing the sparsity constraint constant is usually more intuitive than fixing the penalty parameter, making the constraint approach attractive for applications
Marim, Marcio. "L'Imagerie Compressé Appliqué a la Microscopie Biologique." Phd thesis, Telecom ParisTech, 2011. http://tel.archives-ouvertes.fr/tel-00586625.
Full textPonzio, Serge. "Etude d'un système de numérisation d'image haute définition : application au traitement d'images obtenues par microscopie électronique." Saint-Etienne, 1987. http://www.theses.fr/1987STET4013.
Full textShayan, Azad Seyed Ramtin. "Analyse structurale de la biogenèse de la petite sous-unité ribosomique eucaryote par cryo-microscopie électronique et analyse d'images." Thesis, Toulouse 3, 2019. http://www.theses.fr/2019TOU30128.
Full textRibosome assembly is a complex process that requires the intervention of more than 200 assembly factors (AFs). These proteins are essential for the processing and modification of ribosomal RNAs, as well as the structural assembly of ribosomal subunits. This mechanism, highly studied in yeast, generally conserved in eukaryotes, but has become more complex with evolution in higher eukaryotes. In addition, defects in ribosome synthesis have recently been associated with a list of human genetic diseases (called ribosomopathies) and cancers, via ribosome biogenesis disease. Numerous molecular and functional studies then made it possible to define several successive stages of cytoplasmic maturation of pre-40S particles in human and yeast. It is now crucial to incorporate these highly detailed molecular descriptions of ribosome maturation events into a three-dimensional view of ribosome assembly and to understand the structural remodeling of pre-ribosomal maturation particles. Using tandem purification methods, coupled with cryo-electron microscopy and isolated particle analysis, I have determined several high-resolution 3D structures of cytoplasmic pre-40S particles, in yeast and human, at different maturation steps. First, i determined the 3D structure of the pre-40S particles, purified using AF Tsr1-FPZ as a bait at 3.1 Å resolution. Structural heterogeneity tests indicated that the beak and platform domains are dynamic zones, and sheds new light on the structural remodeling events occurring during 40S subunit assembly. Moreover, in collaboration with the team of Dr. Brigitte Pertschy, we have determined the 3D structure of yeast cytoplasmic pre-40S particles carrying point mutations on Rps20. Our atomic models have allowed to highlight a close relationship between the correct assembly of Rps20 and the release of AFs Ltv1 and Rio2 from the maturing small ribosomal subunit. Finally, I also determined the 3D structures of human pre-40S particles trapped at a very late cytoplasmic maturation step, with a resolution of ~3 Å. This work was performed in collaboration with Prof. Ulrike Kutay's team (ETH Zurich). These data allowed us to uncover new steps in the cytoplasmic maturation of human pre-40S particles. This structural study allows us to propose new molecular mechanisms underlying the final steps of eukaryotic ribosomal assembly
Boussemaere, Luc. "Investigating off-axis digital holographic microscopy with a source of partial spatial coherence as a real-time sensor for cell cultures." Doctoral thesis, Universite Libre de Bruxelles, 2015. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209086.
Full textDoctorat en Sciences de l'ingénieur
info:eu-repo/semantics/nonPublished
Bigler, Emmanuel. "Detecteurs d'images x grand champ : applications a la microscopie x de contact et a la microanalyse d'absorption avec le rayonnement synchrotron." Phd thesis, Université Paris Sud - Paris XI, 1986. http://pastel.archives-ouvertes.fr/pastel-00713898.
Full textSouchay, Henri. "Microscopie électronique à transmission en haute résolution numérique et quantitative : développement d'un outil interactif d'acquisition, simulation et analyse d'images." Châtenay-Malabry, Ecole centrale de Paris, 1999. http://www.theses.fr/1999ECAP0625.
Full textBen, Romdhane Ferdaous. "Synthèse et caractérisation de nouvelles phases bidimensionnelles par microscopie électronique in-situ." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAE001/document.
Full textThe aim of this thesis is the synthesis and characterization of new two-dimensional phases in an in-situ transmission electron microscopy experiment. These studies concerned the nucleation and growth of three deferent materials: quasi-two-dimensional silica (SiO2), the smallest possible carbon cages with the size of C20, and two-dimensional chalcocite (β-Cu2S). The characterization of these structures has been performed using high resolution imaging (HRTEM) and electron energy-loss spectroscopy (EELS). The first part of this thesis is devoted to the study of the nucleation and growth of an ordered or disordered 2D crystalline phase of silica on different substrates (Co, Ru, Fe) and a 1D silica phase grown at atomic steps of a metal surface. The second part illustrates the in-situ growth of the smallest possible carbon cages with a diameter of about 0.36 nm on catalytically active metal surfaces such as Co, Fe, or Ru. The last part is devoted to the growth of the thinnest stable layer of β-Cu2S on a graphene surface. All these studies were accompanied by image simulations
Cottet‐Rousselle, Cécile. "Mesure par microscopie confocale du métabolisme mitochondrial et du niveau énergétique cellulaire au cours d’épisodes de carences en substrats et/ou en oxygène." Thesis, Paris, EPHE, 2016. http://www.theses.fr/2016EPHE3096/document.
Full textMitochondria form an information hub at the center of the cellular metabolism because of its physiological role consisting in the porduction of ATP from the degradation of porducts stemming from our food through the OXPHOS process. However, changes in the functionnig of the mitochondria can be responsible for numerous diseases. Among the different foms of metabolic stress leading to mitchondrial dysfunctions, ischemia-reperfusion can be found in numerous pathological situations. This work aims at developing a methodological approach based on confocal microscopy and image analysis to dissect –at cell level- the consequences of metabolic stress induced by episodes of deprivation in substrata associated or not with hypoxia or anoxia. Having developed the program of image analysis based on the « tophat » method, two approaches were designed to vizualize and quantify the mitochondrial function. The first one, combining TMRM labelling with NADH fluorescence made it possible to highlight some differences in the response to the stress caused by ischemia-reperfusion at the level of the respiratory chain or concerning the PTP opening in the four cellular types that were tested : HMEC-1, INS1, RT112 or pirmary heaptocyes. The second approach consisted in testing the use of biosensors designed to follow the variations of ATP concentration (ATeam) or the activation of AMPK (AMPKAR). The experimental conditions established in this work did not allow us to validate their use
Roudot, Philippe. "Image processing methods for dynamical intracellular processes analysis in quantitative fluorescence microscopy." Thesis, Rennes 1, 2014. http://www.theses.fr/2014REN1S025/document.
Full textWe propose in this manuscript a study of the instrumentation required for the quantification in frequency domain fluorescence lifetime imaging microscopy (FD FLIM). A FD FLIM measurement is defined as a series of images with sinusoidal intensity variations. The fluorescence lifetime is defined as the nanosecond-scale delay between excitation and emission of fluorescence. We propose two main contributions in the area: a modeling of the image process and noise introduced by the acquisition system (ICCD sensor); a robust statistical method for lifetime estimation on moving structures and intracellular vesicles. The second part presents a contribution to the tracking of multiple particles presenting heterogeneous transports in dense conditions. We focus here on the switching between confined diffusion in the cytosol and motor-mediated active transport in random directions. We show that current multiple model filtering and gating strategies fail at estimating unpredictable transitions between Brownian and directed displacements. We propose a new algorithm, based on the u-track algorithm [Jaqaman et al., 2008], based on a set of Kalman filters adapted to several motion types, for each tracked object. The algorithm has been evaluated on simulated and real data (vimentin, virus) data. We show that our method outperforms competing methods in the targeted scenario, but also on more homogeneous types of dynamics challenged by density
Pankajakshan, Praveen. "Déconvolution Aveugle en Imagerie de Microscopie Confocale À Balayage Laser." Phd thesis, Université de Nice Sophia-Antipolis, 2009. http://tel.archives-ouvertes.fr/tel-00474264.
Full textVercauteren, Tom. "Recalage et Mosaïques d'Images pour la Microscopie Confocale Fibrée Dynamique In Vivo." Phd thesis, Ecole Nationale Supérieure des Mines de Paris, 2008. http://tel.archives-ouvertes.fr/tel-00635297.
Full textMarak, Laszlo. "On continuous maximum flow image segmentation algorithm." Phd thesis, Université Paris-Est, 2012. http://tel.archives-ouvertes.fr/tel-00786914.
Full textClaveau, Rémy. "Caractérisation spectrale locale à l'aide de la microscopie interférométrique : simulations et mesures." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAD037/document.
Full textWhite light interference microscopy is a measurement method based on the acquisition and processing of the signal coming from the interaction between two wave fronts, known as the “object” and “reference” wave-fronts. These waves come from the reflection of the light on a reference mirror and the sample studied. Usually used for topographic or tomographic analysis of a sample, the interferometric data can be exploited for spectroscopic purposes. The resulting spectral characterizations are spatially resolved in the three directions of space. In this project, we have studied the performance of this technique, as well as the associated limitations when the sample becomes more complex (degradation of the interferometric signal). The analysis has been first applied to reflective materials for surface measurements and subsequently to transparent and scattering layers for probing within the depth of the medium and then extracting the individual spectral response of the buried structures
Basset, Antoine. "Détection et caractérisation par des approches statistiques locales d'évènements dynamiques dans des séquences d'images : application à la fusion membranaire en microscopie TIRF." Thesis, Rennes 1, 2015. http://www.theses.fr/2015REN1S096/document.
Full textIn this thesis, we investigate statistical methods to detect, estimate and characterize dynamical events in image sequences. Our main focus is on fluorescence microscopy images, which represent a fundamental tool for cell biology. There are two cases : 1. Studied objects do not interact, and individual dynamics can be independently analyzed ; 2. Studied objects interact, and group dynamics must be analyzed as a whole. In the case of individual dynamics, our primary focus is on biological image sequences showing proteins evolving in a cell, and more precisely at the cell frontier named plasma membrane. Proteins transported in the cell by vesicles, are observed in total internal reflection fluorescence microscopy (TIRFM), an observation technique well adapted to plasma membrane dynamics analysis. At the end of the exocytosis process, vesicles fuse to the plasma membrane and release proteins, which then diffuse. We first propose a new spot detection method aimed at localizing fusion events. Then, we model the protein dynamics and estimate the biophysical parameters in TIRFM image sequences for further biological analysis. We also address the processing of image sequences at lower magnifications, that is, depicting groups of cells, instead of an isolated cell. We propose a method to jointly estimate quantitative and qualitative motion measurements. It is used to classify the group motion, recover principal paths followed in the scene, and detect localized anomalies. Since they are free of appearance model, the developed methods are quite general and also applied to other applications including crowd motion analysis in videos. Whether it is for spot detection, protein dynamics estimation or group motion analysis, a common approach is ubiquitous, however. First, statistical arguments are used to automatically infer the method parameters. Secondly, we rely on local approaches, which have the advantage of being computationally efficient. Local modeling handles spatially varying image statistics much more easily and more accurately than global modeling. Local approaches also allow neglecting contextual variations such as spatially varying background contrast or, in fluorescence microscopy, temporal fading known as photobleaching
Pascal, Hubert, and Jean-Michel Martin. "Modification des surfaces par frottement : apport des techniques de microscopie à force atomique et à balayage électronique." Ecully, Ecole centrale de Lyon, 1994. http://www.theses.fr/1994ECDL0042.
Full textThe atomic force (AFM) and lateral force microscope (LFM) allow respectively to achieve, in the real space, topographic images and lateral images of various materials. The resolution is uncommon and reach the atomic scale. This study has two main purposes. The first is to locale the AFM in comparison with others techniques of surfaces observation. The second is to use at room temperature a LFM as a micro-tribometer with in order to investigate the friction and wear phenomenas at nano-scale. First, from wear macroscopic tracks made by classic tribologic test on a ceramic (the polycristalline silicon carbide) and on a sputtered film (the molybdenum disulphide), we show that AFM confirms and completes the observations achieved by optical or electronic beam microscopy. The restored contrast by a technique allow to alleviate the artefacts and the doubt of each others. To understand the origin of the very weak coefficient of friction (0. 001) of MoS2 deposits, the investigations has been continued at atomic scale. They confirm certain hypothesis built up from thin films observations (TEM, HRTEM. . . ) concerning the role of the crystalline structure in superlubricity of MoS2. Second, the literature having revealed that the information is dependent on the apparatus (tip, lever,. . . ) and the physics of contact, we model the LFM mechanical structure to understand and to reduce the apparatus influence on the measurements, in order to focus them on the physics distortion. The contact study exhibits role of the surface morphology in lateral force measurements. This force is made of one interfacial component induced by friction and a local one linked to topography. This distinction is the starting point of two suggested calibration procedure in lateral force. After, we are interested in the friction component influence on the image resolution. For that, we modify the surface physicochemistry of pure silica and cobalt metallic deposit by working in liquid environment (water, oil, alcohol. . . ). A friction consequence is a very weak wear at nano-scale. To investigate the wear process at this scale, we adapt to LFM a triboscopic method
Tseng, Qingzong. "Etude d'architecture multicellulaire avec le microenvironnement contrôlé." Phd thesis, Université de Grenoble, 2011. http://tel.archives-ouvertes.fr/tel-00622264.
Full textVurpillot, François. "Étude de la fonction de transfert pointe-image de la sonde atomique tomographique." Rouen, 2001. http://www.theses.fr/2001ROUES033.
Full textVerguet, Amandine. "Développements méthodologiques et informatiques pour la microscopie électronique en transmission appliqués à des échantillons biologiques Alignment of Tilt Series (Chapter 7 of the Book: Cellular Imaging: Electron Tomography and Related Techniques, Hanssen Eric) An ImageJ tool for simplified post-treatment of TEM phase contrast images (SPCI) Comparison of methods based on feature tracking for fiducial-less image alignment in electron tomography." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS487.
Full textTransmission Electron Microscopy is a major tool for performing structural studies in biology. Some methods used for image sampling and analysis need to be improved in order to observe electron dose sensitive samples with good contrast and good signal to noise ratio. During this thesis, various methodological and computational approaches have been studied which aim to improve image quality. First, I evaluated the relevance of combining energy filtered imaging with the STEM mode. I show that this allows an improvement of the signal to noise ratio of images. Then, I devised an algorithm that generates an image from phase data. This approach allows improving the image contrast over direct imaging. The use of a phase plate and focal tilt series are both efficient tools to achieve this goal. While working on the software approach for processing of tilt series, we found that a qualitative result can be obtained from a single image. I developped the SPCI plugin for the ImageJ software. It allows processing between one and three focal images. My work involves optimization of the tomographic reconstruction process, including working with both alignment algorithms and reconstruction algorithms. I expose my studies on image alignment methods used on tilt series. These methods do rely on the use of key points and associated local descriptors. They have proved to be efficient to process images lacking fiducial markers. Finally, I propose a new unified algorithmic approach for 3D reconstruction of tomographic tilt series acquired with sparse sampling. I then derived another novel method that integrates the image alignment step in the process. Studies and developments will continue on both methods in futur work
Moebel, Emmanuel. "New strategies for the identification and enumeration of macromolecules in 3D images of cryo electron tomography." Thesis, Rennes 1, 2019. http://www.theses.fr/2019REN1S007/document.
Full textCryo electron tomography (cryo-ET) is an imaging technique capable of producing 3D views of biological specimens. This technology enables to capture large field of views of vitrified cells at nanometer resolution. These features allow to combine several scales of understanding of the cellular machinery, from the interactions between groups of proteins to their atomic structure. Cryo-ET therefore has the potential to act as a link between in vivo cell imaging and atomic resolution techniques. However, cryo-ET images suffer from a high amount of noise and imaging artifacts, and the interpretability of these images heavily depends on computational image analysis methods. Existing methods allow to identify large macromolecules such as ribosomes, but there is evidence that the detections are incomplete. In addition, these methods are limited when searched objects are smaller and have more structural variability. The purpose of this thesis is to propose new image analysis methods, in order to enable a more robust identification of macromolecules of interest. We propose two computational methods to achieve this goal. The first aims at reducing the noise and imaging artifacts, and operates by iteratively adding and removing artificial noise to the image. We provide both mathematical and experimental evidence that this concept allows to enhance signal in cryo-ET images. The second method builds on recent advances in machine learning to improve macromolecule localization. The method is based on a convolutional neural network, and we show how it can be adapted to achieve better detection rates than the current state-of- the-art
Tibayrenc, Pierre. "Mesures d'états au sein d'une population de levures : application à l'étude de la réponse de S. cerevisiae à différents stress technologiques liés à la production de bioéthanol." Thesis, Montpellier 2, 2010. http://www.theses.fr/2010MON20027/document.
Full textFor bioprocess control and optimization, biomass monitoring and physiological state evaluation is an important issue. During this work, in situ and at-line measurements have been used to evaluate cell state and detect a phenotypic variability within a yeast population. Dielectric spectroscopy, based on the polarization of viable cell membranes exposed to an electrical field, has been selected to infer cell state on-line. In parallel with the use of a Coulter-type cell counter, a dedicated system of automated microscopy and image analysis has been developed to measure cell morphology and viability. Single-cell growth on agar medium was monitored to characterize individual cells with regard to lag-time and initial growth rate. Bioethanol production with S. cerevisiae has been chosen as a model process since the yeast cells are exposed to strong physicochemical stresses (temperature, acetate, furfural,?) which affect their physiological state and impair fermentation efficiency. The cell population, kinetically homogeneous during stress-free fermentations, became heterogeneous when a perturbation was applied. The mean and the variance of lag-time distributions were related to the stress severity. During the decline phase, cell death went along with a decrease in cell size and changes of their microscopy aspect. These changes were significant enough to infer the proportion of viable cells directly from the size distributions obtained with the cell counter or from microscopy image analysis. Dielectric spectroscopy gave reliable estimates of the viable cell volume fraction and enabled the measurements of membrane capacitance Cm and intracellular conductivity sin, parameters related to membrane and cytoplasm states. The Cm value remained constant as long as the cells were viable and dropped to zero at cell death, while sin varied significantly depending on the growth phase and in response to stress
Pasqualin, Côme. "Dynamique calcique dans les cardiomyocytes de veines pulmonaires de rat : une hétérogénéité source d'arythmie ?" Thesis, Tours, 2016. http://www.theses.fr/2016TOUR3808/document.
Full textEctopic foci leading to atrial fibrillation episodes might be due to abnormal calcium handling by the pulmonary vein (PV) cardiomyocytes (CM). Therefore, the calcium cycle of PV CM was characterized and compared to those of left atria (LA) and left ventricle (LV) CM. Some tools have been developed to measure the organization of transverse tubular networks and contractility of PV CM. Unlike LA and LV CM, the heterogeneous organization of the tubular networks in the PV CM population leads to wide ranges of calcium transient shapes and contraction amplitudes. Within the whole PV, these different types of CM are gathered in islets. The frequency of spontaneous calcium release is also higher in PV CM than in LA and LV CM. The special features of the calcium handling properties of the PV CM population could be a source of arrhythmias
Kouvahe, Amélé Eyram Florence. "Etude du remodelage vasculaire pathologique : de la caractérisation macroscopique en imagerie TDM à l’analyse en microscopie numérique." Electronic Thesis or Diss., Institut polytechnique de Paris, 2020. http://www.theses.fr/2020IPPAS019.
Full textThis research focuses on the study of the vascular network in general, in several imaging modalities and several anatomo-pathological configurations. Its objective is to discriminate vascular structures in image data and to detect and quantify the presence of morphological modifications (remodeling) related to a pathology. The proposed generic analysis framework exploits a priori knowledge of the geometry of blood vessels and their contrast with respect to the surrounding tissue. The originality of the developed approach consists in exploiting a multidirectional locally connected filter (LCF) adapted to the dimension of the data space (2D or 3D). This filter allows the selection of curvilinear structures in positive contrast in images whose cross-sectional size does not exceed the size of the filtering window. This selection remains effective even at the level of vessel subdivision. The multi-resolution approach makes it possible to overcome the difference in vascular calibers in the network and to segment the entire vascular structure, even in the presence of a local caliber change. The proposed segmentation approach is general. It can be easily adapted to different imaging modalities that preserve a contrast (positive or negative) between the vessels and their environment. This has been demonstrated in different types of imaging, such as thoracic CT with and without contrast agent injection, hepatic perfusion data, eye fundus imaging and infrared microscopy (for fiber segmentation in mouse brain).From an accurate and robust segmentation of the vascular network, it is possible to detect and characterize the presence of remodeling due to a pathology. This is achieved by analyzing the vessel caliber variation along the central axis which provides both a global view on the caliber distribution in the studied organ (to be compared with a "healthy" reference) and a local detection of shape remodeling. The latter case has been applied for the detection and quantification of pulmonary arteriovenous malformations (PAVM).Initially planned in a study of tumor angiogenesis, the segmentation method developed above was not applicable to infrared microscopy because of lack of vascular contrast in the spectral bands analyzed. Instead, it was exploited for the extraction of brain fibers as a support element for image interpolation aiming the 3D reconstruction of the brain volume from the 2D sub-sampled data. In this respect, a 2D-2D interpolation with realignment of the structures was developed as a second methodological contribution of the thesis. We proposed a geometric interpolation approach controlled by a prior mapping of the corresponding structures in the images, which in our case were the tumor region, the fibers, the brain ventricles and the contour of the brain. An atlas containing the unique labels of the structures to be matched is thus built up for each image. Labels of the same value are aligned using a field of directional vectors established at the level of their contours, in a higher dimensional space (3D here). The diffusion of this field of vectors results in a smooth directional flow from one image to the other, which represents the homeomorphic transformation between the two images. The proposed method has two advantages: it is general, which is demonstrated on different image modalities (microscopy, CT, MRI, atlas) and it allows controlling the alignment of structures whose correspondence is targeted in priority
Mignon, Simon. "Semi-unbalanced optimal transport for referenced-based image restoration and synthesis." Electronic Thesis or Diss., Orléans, 2024. http://www.theses.fr/2024ORLE1044.
Full textOptimal transport is widely used in image processing to align distributions, but in many contexts, it lacks flexibility by incorporating the entire target distribution. In this thesis, we introduce semi-unbalanced optimal transport, which, through a new parameter, allows the selection of the most relevant parts of the target distribution with respect to the processed distribution. We demonstrate the effectiveness of this new tool in applications of image restoration and synthesis in both discrete and semi-discrete settings, where it outperforms classical optimal transport
Luengo, Lydie. "Développement de méthodes d’analyse d’images dédiées à la caractérisation morphologique et nano structurale des noirs de carbone dans les matrices polymères." Thesis, Orléans, 2017. http://www.theses.fr/2017ORLE2038.
Full textIn the field of rubber material development, CB is the most commonly used reinforcing filler. The characterization of CB morphology and nanostructure is therefore crucial to understand the physicochemical properties induced by the introduction of CB in rubber materials. Classical analytical methods only allow indirect and incomplete access to these properties. This PhD offers an innovative method that allows the automatic identification of CB grades by coupling Scanning Transmission Electron Microscopy (STEM) detector and image processing chain. A thorough statistical investigation over a hundred of morphological and structural characteristics of CB was performed on a set of 6000 STEM images. This study has introduced 7 new features and selected the 37 most discriminating descriptors to create the final model. An unsupervised segmentation algorithm has been developed and evaluated in order to build an automatic process as efficient as possible. Then, five classifiers were trained and compared on a base of nearly 65,000 aggregates. It appears that the most suitable descriptor is the Neuron networks as it gives a perfect recognition. As the recognition model is based on 2D projections of CB aggregates, it is necessary to verify that the chosen descriptors are indeed able to correctly characterize the three dimensional structure of CB. The statistical comparison of the 2D descriptors with 3D descriptors extracted from electronic tomography images has been successful, and therefore demonstrates the relevance of the model. The proposed approach, starting from the sample preparation and STEM acquisitions to their classification and through the image analysis steps, offers a new and innovative method for the reliable characterization of CB. This method can be used routinely on raw CB or CB extracted from vulcanizes rubbers
Pascault, Alice. "Investigating Candida albicans epithelial infection using a high-throughput microscopy-based assay." Electronic Thesis or Diss., Sorbonne université, 2023. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2023SORUS277.pdf.
Full textFungal infections are an emerging threat to human health in developed countries. Candida albicans is a dimorphic yeast which colonizes the oral, genital and intestinal mucosa as part of the commensal flora of most of the healthy population. However, it can also lead to local infections such as oral and vaginal thrush and in susceptible patients to severe systemic infections. While much effort has been made in deciphering the interplay between C. albicans and the host at the immunological level, infection begins with invasion of the host epithelium, a process that is only partially understood. At the onset of infection, C. albicans transforms from a yeast to a filamentous hyphal form that can invade and damage epithelial cells, sometimes followed by translocation deeper into host tissues. Several fungal and host molecular factors have been shown to regulate epithelial invasion, including fungal adhesins, invasins and secreted factors such as the fungal toxin candidalysin, as well as host factors such as E-cadherin, which plays a role in C. albicans endocytic uptake. Recent work from our lab based on single cell, live imaging of early invasion into HeLa and Caco-2 cell lines revealed that two invasive lifestyles involving distinct host cellular niches can be exploited by the fungus: (1) Damaging invasion, in which host membranes are breached, leading most often to host cell death; (2) C. albicans trans-cellular tunnelling (CaTCT), in which hyphae extend within host membrane-derived transcellular tunnels without host damage. During CaTCT, hyphae can traverse through several host cells in sequence, leading to the formation of multi-layered tunnel structures. Currently, the molecular factors and cellular mechanisms regulating CaTCT from both the fungal and host sides remain almost entirely undescribed. The objective of my thesis project was to identify and characterize molecular factors and cellular processes regulating early Caco-2 infection by C. albicans, which occurs exclusively via CaTCT for up to 9 hours post-infection. For this purpose, I developed a novel quantitative, high-throughput and universal (i.e. applicable to a wide variety of fungal and host models) experimental imaging assay that uses an automated non-biased approach to provide single cell readouts pertaining to adhesion, hyphal formation, invasion and host damage in a single experiment. I then applied this assay to study several distinct aspects of CaTCT: (1) the function of the fungal Als3 protein in C. albicans adhesion and invasion; (2) the reservoir of host membranes implicated in trans-cellular tunnel formation and extension; (3) the function of the fungal toxin candidalysin and fungal secreted aspartyl proteases (Saps); (4) nutrient uptake and glycogen metabolism ; (5) the role of host secreted IgA in immune defence at the epithelial surface. In order to identify new potential virulence factors, I also employed the assay to screen for differences in epithelial infection between C. albicans clinical strains isolated from commensal and invasive origins. Overall, my work has provided several new insights into the mechanism of CaTCT, which act to further enhance our knowledge of this enigmatic process. Furthermore, the experimental assay developed in this project has important potential applications for future targeted studies and screens relating to C. albicans epithelial infection, as well as infection by other fungal pathogens
Tran, Thi Nhu Hoa. "Analyse et modélisation 3D de l’organisation spatiale des tissus dans des images biologiques." Electronic Thesis or Diss., Sorbonne université, 2018. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2018SORUS457.pdf.
Full textCells within the tissue preferentially form a network that works together to carry out a specific function. Thus, the role of a tissue is affected by its cell types as well as the architecture of cellular interactions. A question is to what degree the spatial organization of these cells affects the function of the tissue. We first propose a set of methodologies to analyze the multi-cellular structure of tissues at both local and global scale. The goal is to analyze, formalize, and model the spatial organization of the tissue captured by fluorescence microscopy images. At the local scale, we investigate the spatial relationship of several structures with both direct and indirect cellular interactions. At the global scale, we apply spatial statistic approaches to investigate the degree of randomness of the cell distribution. In addition, an open source toolbox is developed which allows researchers to perform investigations of the position of different cells within a 3D multicellular structure. We apply the toolbox to study of the spatial organization of the islet of Langerhans, a special kind of tissue that plays an important role in regulating the blood glucose level. With a good segmentation accuracy, we have been able to perform our analysis of the islets of Langerhans on several different species such as mouse and monkey. We also utilize our toolbox to explore the structural-functional mechanism of the delta cell, a specific kind of cell within the islet whose role has not yet been determined, but could potentially influence the islet function, in mouse and human. Our generic toolbox is implemented with unbiased analytical capabilities in software platform ImageJ
Bélaroui, Karima. "Compréhension des mécanismes de fragmentation par analyse granulométrique et morphologique." Vandoeuvre-les-Nancy, INPL, 1999. http://docnum.univ-lorraine.fr/public/INPL_T_1999_BELAROUI_K.pdf.
Full textComminution is an important process in powder technology, in which progress can still be made, to improve the operation of existing equipments or to design new systems. To understand better the phenomena taking place in the grinding chambers, the classical approach based on the examination of size distributions has been combined with the distributions of the shape of the fragments, observed by scanning electron microscopy and characterised by image analysis. The particle morphology has been assessed through the use of a set of seven parameters, six of them describing the 2D shape and one the pseudo 3D shape. In complement statistical tools (tests, principal component analysis) have been used. Comminution experiments have been run with different materials exhibiting either welldefined initial morphology (gibbsites obtained by crystallisation) or not (natural rocks) in a stirred bead-mill with different suspension concentrations, and beads diameters and filling rates. After a preliminary study of the particles before grinding, the analysis of the size reduction phenomena from the size distributions only has shawn its limits. The method finally proposed is based on a joint analysis of the shape and size parameters. If a better understanding of the phenomena can help to control the product quality, a possible pollution by fines produced by wear of the grinding bodies should be taken into account. A method based on the analysis of their surface by scanning electron microscopy is proposed to monitor this wear