Search

Counting cells in culture is a common task in biotechnology research and production. This process should be automated to provide fast and objective quantification. Flow cytometry is adapted to count cells in suspension. However, the morphological information and the spatial organisation of adherent cells are lost when cells are removed from culture. This paper proposes a methodology based on image analysis to quantify stained nuclei in culture. The protocol is composed of several steps: cell staining, automatic microscopy imaging, segmentation by an automatic algorithm including a classification approach, and computation of quantitative data that characterizes the growth of cells. An evaluation shows that the automatic process of counting provides results similar to human manual counting. The major interests of the proposed approach are the fully automated processing and preservation of cell shapes and positions in culture. More than two thousand culture conditions have been measured by this tool for various applications including optimization of cell culture media, improvement of the culture processes and measurement of drug toxicity.

International audience; Defects in miRNA biogenesis or activity are associated to development abnormalities and diseases. In Drosophila, miRNAs are predominantly loaded in Argonaute-1, which they guide for silencing of target RNAs. The miRNA pathway overlaps the RNAi pathway in this organism, as miRNAs may also associate with Argonaute-2, the mediator of RNAi. We set up a gene construct in which a single inducible promoter directs the expression of the GFP protein as well as two miRNAs perfectly matching the GFP sequences. We show that self-silencing of the resulting automiG gene requires Drosha, Pasha, Dicer-1, Dicer-2 and Argonaute-2 loaded with the anti-GFP miRNAs. In contrast, self-silencing of the automiG gene does not involve Argonaute-1. Thus, automiG reports in vivo for both miRNA biogenesis and Ago-2 mediated silencing, providing a powerful biosensor to identify situations where miRNA or siRNA pathways are impaired. As a proof of concept, we used automiG as a biosensor to screen a chemical library and identified 29 molecules that strongly inhibit miRNA silencing, out of which 5 also inhibit RNAi triggered by long double-stranded RNA. Finally, the automiG sensor is also self-silenced by the anti-GFP miRNAs in HeLa cells and might be easily used to identify factors involved in miRNA biogenesis and silencing guided by perfect target complementarity in mammals.

International audience; We introduce a novel paradigm for statistical analysis of spatial signals, applied to colocalization studies in bioimag-ing. Quantitative assessment of the spatial colocalization of different molecules in microscopy provides important functional information on cellular processes. By reducing objects (molecules or cluster of molecules) to their position (points), existing methods are predominantly restricted to point-based analyses, and scale poorly to applications involving large, asymmetric and complex-in-shape objects. We address this issue, and propose a statistical model for shape-based colocalization analysis. Our solution is a generalization of the Ripley's K-function for arbitrary shapes, and provides a method to statistically interpret the coupling of molecules to biological objects which are implicitly represented via level set embedding. Compared to the state-of-the-art, our solution is efficient and generic, and establishes the theoretical basis for an one-fits-all approach to tackle the heterogeneous challenges in robust interpretation of molecular association in biology. The efficacy of our method is established via synthetic simulations, and a practical application is also described to measure the statistical accumulation of synaptic molecules' spots near the cell's boundary of cultured neurons.

SUMMARYAdvances in single cell RNA sequencing have allowed for the identification and characterization of cellular subtypes based on quantification of the number of transcripts in each cell. However, cells may differ not only in the number of mRNA transcripts that they exhibit, but also in their spatial and temporal distribution, intrinsic to the definition of their cellular state. Here we describe DypFISH, an approach to quantitatively investigate the spatial and temporal subcellular localization of RNA and protein, by combining micropatterning of cells with fluorescence microscopy at high resolution. We introduce a range of analytical techniques for quantitatively interrogating single molecule RNA FISH data in combination with protein immunolabeling over time. Strikingly, our results show that constraining cellular architecture reduces variation in subcellular mRNA and protein distributions, allowing the characterization of their localization and dynamics with high reproducibility. Many tissues contain cells that exist in similar constrained architectures. Thus DypFISH reveals reproducible patterns of clustering, strong correlative influences of mRNA-protein localization on MTOC orientation when they are present and interdependent dynamics globally and at specific subcellular locations which can be extended to physiological systems.

International audience; Abstract-In this work, we introduce an original strategy to apply the Compressed Sensing (CS) framework to a super-resolution Structured Illumination Microscopy (SIM) technique. We first define a framework for direct domain CS, that exploits the sparsity of fluorescence microscopy images in the Fourier domain. We then propose an application of this method to a fast 4-images SIM technique, which allows to reconstruct super-resolved fluorescence microscopy images using only 25% of the camera pixels for each acquisition..; Dans cet article, nous proposons une méthode pour appliquer la théorie de l'Acquisition Comprimée (Compressed Sensing-CS) à une technique de super-résolution : la microscopie à illumination structurée (SIM). Nous commençons par définir le cadre d'application du CS en domaine direct, en exploitant la parcimonie dans le domaine de Fourier d'images en microscopie à fluorescence. Ensuite, nous proposons d'appliquer cette méthode à la reconstruction SIM à 4 images, ce qui permet de reconstruire des images en microscopie à fluorescence super-résolues, en n'utilisant que 25% des pixels de la caméra pour chaque acquisition.

International audience; Super-resolution in Structured Illumination Microscopy (SIM) is obtained through de-aliasing of modulated raw images, in which high frequencies are measured indirectly inside the optical transfer function. Usual approaches that use 9 or 15 images are often too slow for dynamic studies. Moreover, as experimental conditions change with time, modulation parameters must be estimated within the images. This paper tackles the problem of image reconstruction for fast super resolution in SIM, where the number of available raw images is reduced to four instead of nine or fifteen. Within an optimization framework, the solution is inferred via a joint myopic criterion for image and modulation (or acquisition) parameters, leading to what is frequently called a myopic or semi-blind inversion problem. The estimate is chosen as the minimizer of the nonlinear criterion, numerically calculated by means of a block coordinate optimization algorithm. The effectiveness of the proposed method is demonstrated for simulated and experimental examples. The results show precise estimation of the modulation parameters jointly with the reconstruction of the super resolution image. The method also shows its effectiveness for thick biological samples.

International audience; Anisotropies that underlie organ morphogenesis have been quantified in 2D, taking advantage of a reference axis. However, morphogenesis is a 3D process and it remains a challenge to analyze cell polarities in 3D. Here, we have designed a novel procedure that integrates multidisciplinary tools, including image segmentation, statistical analyses, axial clustering and correlation analysis. The result is a sensitive and unbiased assessment of the significant alignment of cell orientations in 3D, compared with a random axial distribution. Taking the mouse heart as a model, we validate the procedure at the fetal stage, when cardiomyocytes are known to be aligned. At the embryonic stage, our study reveals that ventricular cells are already coordinated locally. The centrosome-nucleus axes and the cell division axes are biased in a plane parallel to the outer surface of the heart, with a minor transmural component. We show further alignment of these axes locally in the plane of the heart surface. Our method is generally applicable to other sets of vectors or axes in 3D tissues to map the regions where they show significant alignment.

Summary Intraflagellar transport (IFT) is necessary for the construction of cilia and flagella. IFT proteins are concentrated at the base of the flagellum but little is known about the actual role of this pool of proteins. Here, IFT was investigated in Trypanosoma brucei, an attractive model for flagellum studies, using GFP fusions with IFT52 or the IFT dynein heavy chain DHC2.1. Tracking analysis by a curvelet method allowing automated separation of forward and return transport demonstrated a uniform speed for retrograde IFT (5 µm s−1) but two distinct populations for anterograde movement that are sensitive to temperature. When they reach the distal tip, anterograde trains are split into three and converted to retrograde trains. When a fast anterograde train catches up with a slow one, it is almost twice as likely to fuse with it rather than to overtake it, implying that these trains travel on a restricted set of microtubules. Using photobleaching experiments, we show for the first time that IFT proteins coming back from the flagellum are mixed with those present at the flagellum base and can reiterate a full IFT cycle in the flagellum. This recycling is dependent on flagellum length and IFT velocities. Mathematical modelling integrating all parameters actually reveals the existence of two pools of IFT proteins at the flagellum base, but only one is actively engaged in IFT.

Ultrasonic vocalisation is a broadly used proxy to evaluate social communication in mouse models of neuropsychiatric disorders. The efficacy and robustness of testing these models suffer from limited knowledge of the structure and functions of these vocalisations as well as of the way to analyse the data. We created mouseTube, an open database with a web interface, to facilitate sharing and comparison of ultrasonic vocalisations data and metadata attached to a recording file. Metadata describe 1) the acquisition procedure, e.g., hardware, software, sampling frequency, bit depth; 2) the biological protocol used to elicit ultrasonic vocalisations; 3) the characteristics of the individual emitting ultrasonic vocalisations (e.g., strain, sex, age). To promote open science and enable reproducibility, data are made freely available. The website provides searching functions to facilitate the retrieval of recording files of interest. It is designed to enable comparisons of ultrasonic vocalisation emission between strains, protocols or laboratories, as well as to test different analysis algorithms and to search for protocols established to elicit mouse ultrasonic vocalisations. Over the long term, users will be able to download and compare different analysis results for each data file. Such application will boost the knowledge on mouse ultrasonic communication and stimulate sharing and comparison of automatic analysis methods to refine phenotyping techniques in mouse models of neuropsychiatric disorders.

International audience; Mice emit ultrasonic vocalizations in different contexts throughout development and in adulthood. These vocal signals are now currently used as proxies for modeling the genetic bases of vocal communication deficits. Characterizing the vocal behavior of mouse models carrying mutations in genes associated with neuropsychiatric disorders such as autism spectrum disorders will help to understand the mechanisms leading to social communication deficits. We provide here protocols to reliably elicit ultrasonic vocalizations in pups and in adult mice. This standardization will help reduce inter-study variability due to the experimental settings. Pup isolation calls are recorded throughout development from individual pups isolated from dam and littermates. In adulthood, vocalizations are recorded during same-sex interactions (without a sexual component) by exposing socially motivated males or females to an unknown same-sex conspecific. We also provide a protocol to record vocalizations from adult males exposed to an estrus female. In this context, there is a sexual component in the interaction. These protocols are established to elicit a large amount of ultrasonic vocalizations in laboratory mice. However, we point out the important inter-individual variability in the vocal behavior of mice, which should be taken into account by recording a minimal number of individuals (at least 12 in each condition). These recordings of ultrasonic vocalizations are used to evaluate the call rate, the vocal repertoire and the acoustic structure of the calls. Data are combined with the analysis of synchronous video recordings to provide a more complete view on social communication in mice. These protocols are used to characterize the vocal communication deficits in mice lacking ProSAP1/Shank2, a gene associated with autism spectrum disorders. More ultrasonic vocalizations recordings can also be found on the mouseTube database, developed to favor the exchange of such data.

Although in flies the atypical cadherin Fat is an upstream regulator of Hippo signalling, the closest mammalian homologue, Fat4, has been shown to regulate tissue polarity rather than growth. Here we show in the mouse heart that Fat4 modulates Hippo signalling to restrict growth. Fat4 mutant myocardium is thicker, with increased cardiomyocyte size and proliferation, and this is mediated by an upregulation of the transcriptional activity of Yap1, an effector of the Hippo pathway. Fat4 is not required for the canonical activation of Hippo kinases but it sequesters a partner of Yap1, Amotl1, out of the nucleus. The nuclear translocation of Amotl1 is accompanied by Yap1 to promote cardiomyocyte proliferation. We, therefore, identify Amotl1, which is not present in flies, as a mammalian intermediate for non-canonical Hippo signalling, downstream of Fat4. This work uncovers a mechanism for the restriction of heart growth at birth, a process which impedes the regenerative potential of the mammalian heart., Growth of the mammalian heart is controlled by Hippo signalling but how this is regulated is unclear. Here, the authors show that Fat4 (an atypical cadherin) acts upstream of Hippo signalling and Fat4 mutant mice have thicker myocardium, which is mediated by the scaffold Amot1 and transcription factor Yap1.

Icy is a collaborative platform for biological image analysis that extends reproducible research principles by facilitating and stimulating the contribution and sharing of algorithm-based tools and protocols between researchers. Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/ .

The multiscale variance stabilization Transform (MSVST) has recently been proposed for Poisson data denoising. This procedure, which is nonparametric, is based on thresholding wavelet coefficients. We present in this paper an extension of the MSVST to 3D data (in fact 2D-1D data) when the third dimension is not a spatial dimension, but the wavelength, the energy, or the time. We show that the MSVST can be used for detecting and characterizing astrophysical sources of high-energy gamma rays, using realistic simulated observations with the Large Area Telescope (LAT). The LAT was launched in June 2008 on the Fermi Gamma-ray Space Telescope mission. The MSVST algorithm is very fast relative to traditional likelihood model fitting, and permits efficient detection across the time dimension and immediate estimation of spectral properties. Astrophysical sources of gamma rays, especially active galaxies, are typically quite variable, and our current work may lead to a reliable method to quickly characterize the flaring properties of newly-detected sources., Accepted. Full paper will figures available at http://jstarck.free.fr/aa08_msvst.pdf

International audience; We have previously identified a new gene with sequence homology to the WASP-family of actin regulators denoted WAFL (WASP and FKBP-like). Here we report a possible biological function for WAFL, by demonstrating an association to early endosomes via its central coiled-coil domain. Further we show by functional and structural studies that WAFL is associated with both microtubules and the actin filament system, the two means of transport of early endosomes. In addition, WAFL interacts with WASP-interacting protein (WIP) and actin, thus linking WAFL to actin dynamics. The use of RNAi depletion of WAFL shows that WAFL-deficient cells display delayed transport of endosomal cargo. Our findings are compatible with a model whereby WAFL is involved in the transport of early endosomes at the level of transition between microfilament-based and microtubule-based movement.

International audience; Microscopy imaging, including fluorescence microscopy and electron microscopy, has taken a prominent role in life science research and medicine due to its ability to investigate the 3D interior of live cells and organisms. A long-term research in bio-imaging at the sub-cellular and cellular scales consists then in inferring the relationships between the dynamics of macromolecules and their functions. In this area, image processing and analysis methods are now essential to understand the dynamic organization of groups of interacting molecules inside molecular machineries and to address issues in fundamental biology driven by advances in molecular biology, optics and technology. In this paper, we present recent advances in fluorescence and electron microscopy and we focus on dedicated image processing and analysis methods required to quantify phenotypes for a limited number but typical studies in cell imaging.

Numerous clinical reports underscore the frequency of olfactory impairments in patients suffering from major depressive disorders (MDDs), yet the underlying physiopathological mechanisms remain poorly understood. We hypothesized that one key link between olfactory deficits and MDD lies in hypercortisolemia, a cardinal symptom of MDD. Corticosterone (CORT) is known to negatively correlate with hippocampal neurogenesis, yet its effects on olfactory neurogenesis and olfaction remain unknown. Here we used a rodent model of anxiety/depression-like states, which is based on chronic CORT administration and studied the effects of the antidepressant fluoxetine (FLX) on behavior, olfaction, and adult neurogenesis in the dentate gyrus (DG), olfactory bulb (OB), and the olfactory epithelium (OE). Chronic CORT had no effect on cell proliferation in the OE or on olfactory sensory neurons projecting to the OB, but induced pronounced deficits in olfactory acuity, fine discrimination of odorants and olfactory memory. These alterations were accompanied by a significant decrease in the number of adult-born neurons in both the DG and OB. Remarkably, FLX not only reversed depression-like states as expected, but also improved olfactory acuity, memory, and restored impaired adult neurogenesis. However, fine olfactory discrimination was not restored. Morphological analysis of adult-born neurons in both the DG and the OB showed that dendritic complexity was not significantly affected by CORT, but was increased by FLX. These findings demonstrate an essential role for glucocorticoids in triggering olfactory impairments in MDD and highlight a novel therapeutic effect of FLX.SIGNIFICANCE STATEMENTIncreasing clinical reports show that major depression is characterized by pronounced olfactory deficits, yet the underlying mechanisms remain unknown. In this work, we used an endocrine model of depression to study whether hypothalamic-pituitary-adrenal axis perturbation could be sufficient to provoke olfactory impairments. We found that chronic corticosterone not only induces marked deficits in olfactory acuity, fine discrimination and olfactory memory, but also significantly decreases bulbar and hippocampal neurogenesis. Importantly, the antidepressant fluoxetine restores both adult neurogenesis and depressive states, and improves most olfactory functions. Our data reveal that impairment of hypothalamic-pituitary-adrenal axis during depression can lead to olfactory deficits and that the neurogenic effects of selective serotonin reuptake inhibitor antidepressants can successfully restore certain olfactory functions.

International audience; Synucleinopathies such as Parkinson's disease are characterized by the pathological deposition of misfolded α-synuclein aggregates into inclusions throughout the central and peripheral nervous system. Mounting evidence suggests that intercellular propagation of α-synuclein aggregates may contribute to the neuropathology; however, the mechanism by which spread occurs is not fully understood. By using quantitative fluorescence microscopy with co-cultured neurons, here we show that α-synuclein fibrils efficiently transfer from donor to acceptor cells through tunneling nanotubes (TNTs) inside lysosomal vesicles. Following transfer through TNTs, α-synuclein fibrils are able to seed soluble α-synuclein aggregation in the cytosol of acceptor cells. We propose that donor cells overloaded with α-synuclein aggregates in lysosomes dispose of this material by hijacking TNT-mediated intercellular trafficking. Our findings thus reveal a possible novel role of TNTs and lysosomes in the progression of synucleinopathies.

Microscopy imaging, including fluorescence microscopy and electron microscopy, has a prominent role in life science and medical research. During the past two decades, biological imaging has undergone a revolution by way of the development of new microscopy techniques that allow the visualization of tissues, cells, proteins and macromolecular structures at all levels of resolution, physiological states, chemical composition and dynamic analysis. Thanks to recent advances in optics, digital sensing technologies and labeling probes (i.e., XFP—Colored Fluorescence Protein), we can now visualize subcellular components and organelles at the scale of a few nanometers to several hundreds of nanometers. As a result, fluorescent microscopy has become the workhorse of modern biology. Further technological advances include structured and coherent light sources, faster and more sensitive detectors, smaller and more specific molecular probes and automation processes for image acquisition. Additionally, there is a push towards multimodal imaging in order to gather complementary information such as the concentration of fluorophores at various wavelengths and the refractive index of a given sample (phase imaging).

International audience; Social communication is heavily affected in patients with neuropsychiatric disorders. Accordingly, mouse models designed to study the mechanisms leading to these disorders are tested for this phenotypic trait. Test conditions vary between different models, and the effect of these test conditions on the quantity and quality of social interactions and ultrasonic communication is unknown. The present study examines to which extent the habituation time to the test cage as well as the shape/size of the cage influence social communication in freely interacting mice. We tested 8 pairs of male mice in free dyadic social interactions, with two habituation times (20 min and 30 min) and three cage formats (rectangle, round, square). We tested the effect of these conditions on the different types of social contacts, approach-escape sequences, follow behavior, and the time each animal spent in the vision field of the other one, as well as on the emission of ultrasonic vocalizations and their contexts of emission. We provide for the first time an integrated analysis of the social interaction behavior and ultrasonic vocalizations. Surprisingly, we did not highlight any significant effect of habituation time and cage shape/size on the behavioral events examined. There was only a slight increase of social interactions with the longer habituation time in the round cage. Remarkably, we also showed that vocalizations were emitted during specific behavioral sequences especially during close contact or approach behaviors. The present study provides a protocol reliably eliciting social contacts and ultrasonic vocalizations in adult male mice. This protocol is therefore well adapted for standardized investigation of social interactions in mouse models of neuropsychiatric disorders.

International audience; Adult C57BL/6J mice are known to exhibit high level of social flexibility while mice lacking the β2 subunit of nicotinic receptors (β2(-/-) mice) present social rigidity. We asked ourselves what would be the consequences of a restraint acute stress (45 min) on social interactions in adult mice of both genotypes, hence the contribution of neuronal nicotinic receptors in this process. We therefore dissected social interaction complexity of stressed and not stressed dyads of mice in a social interaction task. We also measured plasma corticosterone levels in our experimental conditions. We showed that a single stress exposure occurring in adulthood reduced and disorganized social interaction complexity in both C57BL/6J and β2(-/-) mice. These stress-induced maladaptive social interactions involved alteration of distinct social categories and strategies in both genotypes, suggesting a dissociable impact of stress depending on the functioning of the cholinergic nicotinic system. In both genotypes, social behaviors under stress were coupled to aggressive reactions with no plasma corticosterone changes. Thus, aggressiveness appeared a general response independent of nicotinic function. We demonstrate here that a single stress exposure occurring in adulthood is sufficient to impoverish social interactions: stress impaired social flexibility in C57BL/6J mice whereas it reinforced β2(-/-) mice behavioral rigidity.

International audience; We propose a structured illumination microscopy method to combine super resolution and optical sectioning in three-dimensional (3D) samples that allows the use of two-dimensional (2D) data processing. Indeed, obtaining super-resolution images of thick samples is a difficult task if low spatial frequencies are present in the in-focus section of the sample, as these frequencies have to be distinguished from the out-of-focus background. A rigorous treatment would require a 3D reconstruction of the whole sample using a 3D point spread function and a 3D stack of structured illumination data. The number of raw images required, 15 per optical section in this case, limits the rate at which high-resolution images can be obtained. We show that by a succession of two different treatments of structured illumination data we can estimate the contrast of the illumination pattern and remove the out-of-focus content from the raw images. After this cleaning step, we can obtain super-resolution images of optical sections in thick samples using a two-beam harmonic illumination pattern and a limited number of raw images. This two-step processing makes it possible to obtain super resolved optical sections in thick samples as fast as if the sample was two-dimensional.

International audience; This paper presents a segmentation and tracking method for quantitative analysis of cell dynamics from in vitro videomicroscopy data. The method is based on parametric active contours and includes several adaptations that address important difficulties of cellular imaging, particularly the presence of low-contrast boundary deformations known as pseudopods, and the occurence of multiple contacts between cells. First, we use an edge map based on the average intensity dispersion that takes advantage of relative background homogeneity to facilitate the detection of both pseudopods and interfaces between adjacent cells. Second, we introduce a repulsive interaction between contours that allows correct segmentation of objects in contact and overcomes the shortcomings of previously reported techniques to enforce contour separation. Our tracking technique was validated on a realistic data set by comparison with a manually defined ground-truth and was successfully applied to study the motility of amoebae in a biological research project.

International audience; Subventricular zone (SVZ) neurogenesis continuously provides new GABA-and dopamine (DA)-containing interneurons for the olfac-tory bulb (OB) in most adult mammals. DAergic interneurons are located in the glomerular layer (GL) where they participate in the processing of sensory inputs. To examine whether adult neurogenesis might contribute to regeneration after circuit injury in mice, we induce DAergic neuronal loss by injecting 6-hydroxydopamine (6-OHDA) in the dorsal GL or in the right substantia nigra pars compacta. We found that a 6-OHDA treatment of the OB produces olfactory deficits and local inflammation and partially decreases the number of neurons expressing the enzyme tyrosine hydroxylase (TH) near the injected site. Blockade of inflammation by minocycline treatment immediately after the 6-OHDA administration rescued neither TH ϩ interneuron number nor the olfactory deficits, suggesting that the olfactory impairments are most likely linked to TH ϩ cell death and not to microglial activation. TH ϩ interneuron number was restored 1 month later. This rescue resulted at least in part from enhanced recruitment of immature neurons targeting the lesioned GL area. Seven days after 6-OHDA lesion in the OB, we found that the integration of lentivirus-labeled adult-born neurons was biased: newly formed neurons were preferentially incorporated into glomerular circuits of the lesioned area. Behavioral rehabilitation occurs 2 months after lesion. This study establishes a new model into which loss of DAergic cells could be compensated by recruiting newly formed neurons. We propose that adult neurogenesis not only replenishes the population of DAergic bulbar neurons but that it also restores olfactory sensory processing.

International audience; Chlamydia trachomatis is an obligate intracellular pathogen responsible for loss of eyesight through trachoma and for millions of cases annually of sexually transmitted diseases. The bacteria develop within a membrane-bounded inclusion. They lack enzymes for several biosynthetic pathways, including those to make some phospholipids, and exploit their host to compensate. Three-dimensional fluorescence microscopy demonstrates that small organelles of the host, peroxisomes, are translocated into the Chlamydia inclusion and are found adjacent to the bacteria. In cells deficient for peroxisome biogenesis the bacteria are able to multiply and give rise to infectious progeny, demonstrating that peroxisomes are not essential for bacterial development in vitro. Mass spectrometry-based lipidomics reveal the presence in C. trachomatis of plasmalogens, ether phospholipids whose synthesis begins in peroxisomes and have never been described in aerobic bacteria before. Some of the bacterial plasmalogens are novel structures containing bacteria-specific odd-chain fatty acids; they are not made in uninfected cells nor in peroxisome-deficient cells. Their biosynthesis is thus accomplished by the metabolic collaboration of peroxisomes and bacteria.

Social animals establish flexible behaviors and integrated decision-making processes to adapt to social environments. Such behaviors are impaired in all major neuropsychiatric disorders and depend on the prefrontal cortex (PFC). We previously showed that nicotinic acetylcholine receptors (nAChRs) and norepinephrine (NE) in the PFC are necessary for mice to show adapted social cognition. Here, we investigated how the cholinergic and NE systems converge within the PFC to modulate social behavior. We used a social interaction task (SIT) in C57BL/6 mice and mice lacking β2*nAChRs (β2−/− mice), making use of dedicated software to analyze >20 social sequences and pinpoint social decisions. We performed specific PFC NE depletions before SIT and measured monoamines and acetylcholine (ACh) levels in limbic corticostriatal circuitry. After PFC-NE depletion, C57BL/6 mice exhibited impoverished and more rigid social behavior and were 6-fold more aggressive than sham-lesioned animals, whereas β2−/− mice showed unimpaired social behavior. Our biochemical measures suggest a critical involvement of DA in SIT. In addition, we show that the balance between basal levels of monoamines and of ACh modulates aggressiveness and this modulation requires functional β2*nAChRs. These findings demonstrate the critical interplay between prefrontal NE and nAChRs for the development of adapted and nonaggressive social cognition.—Coura, R. S., Cressant, A., Xia, J., de Chaumont, F., Olivo-Marin, J. C., Pelloux, Y., Dalley, J. W., Granon, S. Nonaggressive and adapted social cognition is controlled by the interplay between noradrenergic and nicotinic receptor mechanisms in the prefrontal cortex.

Summary The neural cell-adhesion molecules contactin 4, contactin 5 and contactin 6 are involved in brain development, and disruptions in contactin genes may confer increased risk for autism spectrum disorders (ASD). We describe a co-culture of rat cortical neurons and HEK293 cells overexpressing and delivering the secreted forms of rat contactin 4–6. We quantified their effects on the length and branching of neurites. Contactin 4–6 effects were different depending on the contactin member and duration of co-culture. At 4 days in culture, contactin 4 and -6 increased the length of neurites, while contactin 5 increased the number of roots. Up to 8 days in culture, contactin 6 progressively increased the length of neurites while contactin 5 was more efficient on neurite branching. We studied the molecular sites of interaction between human contactin 4, -5 or -6 and the human Protein Tyrosine Phosphatase Receptor Gamma (PTPRG), a contactin partner, by modeling their 3D structures. As compared to contactin 4, we observed differences in the Ig2 and Ig3 domains of contactin 5 and -6 with the appearance of an omega loop that could adopt three distinct conformations. However, interactive residues between human contactin 4–6 and PTPRG were strictly conserved. We did not observe any differences in PTPRG binding on contactin 5 and -6 either. Our data suggest that the differential contactin effects on neurite outgrowth do not result from distinct interactions with PTPRG. A better understanding of the contactin cellular properties should help elucidate their roles in ASD.

Motivation: In developmental biology, quantitative tools to extract features from fluorescence microscopy images are becoming essential to characterize organ morphogenesis at the cellular level. However, automated image analysis in this context is a challenging task, owing to perturbations induced by the acquisition process, especially in organisms where the tissue is dense and opaque. Results: We propose an automated framework for the segmentation of 3D microscopy images of highly cluttered environments such as developing tissues. The approach is based on a partial differential equation framework that jointly takes advantage of the nuclear and cellular membrane information to enable accurate extraction of nuclei and cells in dense tissues. This framework has been used to study the developing mouse heart, allowing the extraction of quantitative information such as the cell cycle duration; the method also provides qualitative information on cell division and cell polarity through the creation of 3D orientation maps that provide novel insight into tissue organization during organogenesis. Availability: The proposed framework is free, open-source and available on the Icy platform (http://www.icy.bioimageanalysis.org/). Contact: adufour@pasteur.fr or jcolivo@pasteur.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Summary Receptor-mediated endocytosis is an essential process used by eukaryotic cells to internalise many molecules. Several clathrin-independent endocytic routes exist, but the molecular mechanism of each pathway remains to be uncovered. The present study focuses on a clathrin-independent dynamin-dependent pathway used by interleukin 2 receptors (IL-2R), essential players of the immune response. Ras-related C3 botulinum toxin substrate (Rac1) and its targets, the p21-activated kinases (Pak), are specific regulators of this pathway, acting on cortactin and actin polymerization. The present study reveals a dual and specific role of phosphatidylinositol 3-kinase (PI3K) in IL-2R endocytosis. Inhibition of the catalytic activity of PI3K strongly affects IL-2R endocytosis, in contrast to transferrin (Tf) uptake, a marker of the clathrin-mediated pathway. Moreover, Vav2, a GTPase exchange factor (GEF) induced upon PI3K activation, is specifically involved in IL-2R entry. The second action of PI3K is through its regulatory subunit, p85α, which binds to and recruits Rac1 during IL-2R internalisation. Indeed, the overexpression of a p85α mutant missing the Rac1 binding motif leads to the specific inhibition of IL-2R endocytosis. The inhibitory effect of this p85α mutant could be rescued by the overexpression of either Rac1 or the active form of Pak, indicating that p85α acts upstream of the Rac1-Pak cascade. Finally, biochemical and fluorescent microscopy techniques reveal an interaction between p85α, Rac1 and IL-2R that is enhanced by IL-2. In summary, our results indicate a key role of class I PI3K in IL-2R endocytosis that creates a link with IL-2 signalling.

Listeria monocytogenes (Lm) is a ubiquitous bacterium able to survive and thrive within the environment and readily colonizes a wide range of substrates, often as a biofilm. It is also a facultative intracellular pathogen, which actively invades diverse hosts and induces listeriosis. So far, these two complementary facets of Lm biology have been studied independently. Here we demonstrate that the major Lm virulence determinant ActA, a PrfA-regulated gene product enabling actin polymerization and thereby promoting its intracellular motility and cell-to-cell spread, is critical for bacterial aggregation and biofilm formation. We show that ActA mediates Lm aggregation via direct ActA-ActA interactions and that the ActA C-terminal region, which is not involved in actin polymerization, is essential for aggregation in vitro. In mice permissive to orally-acquired listeriosis, ActA-mediated Lm aggregation is not observed in infected tissues but occurs in the gut lumen. Strikingly, ActA-dependent aggregating bacteria exhibit an increased ability to persist within the cecum and colon lumen of mice, and are shed in the feces three order of magnitude more efficiently and for twice as long than bacteria unable to aggregate. In conclusion, this study identifies a novel function for ActA and illustrates that in addition to contributing to its dissemination within the host, ActA plays a key role in Lm persistence within the host and in transmission from the host back to the environment., Author Summary Listeria monocytogenes (Lm) is a ubiquitous bacterium that survives and thrives within the environment, and a facultative intracellular pathogen that induces listeriosis. So far, these two complementary facets of Lm biology have been studied independently. Here we identify ActA, which is a major Lm virulence determinant mediating actin-based motility, as critical for bacterial aggregation and biofilm formation. ActA promotes Lm aggregation via direct ActA-ActA interaction and ActA C-terminal region, which is not involved in actin polymerization, is essential for aggregation. Whereas ActA-mediated Lm aggregation is not observed in infected tissues, it occurs in the gut lumen. Strikingly, ActA-dependent aggregating bacteria exhibit an increased ability to persist within the gut lumen, and are shed in the feces three order of magnitude more and for twice as long than bacteria unable to aggregate. This study identifies a novel function for ActA, which plays a key role in Lm persistence within the host and transmission.

International audience; Histological renal lesions observed after liver transplantation are complex, multifactorial, and interrelated. The aims of this study were to determine whether kidney lesions observed at five yr after liver transplantation can predict long-term kidney function. Ninety-nine liver transplant patients receiving calcineurin inhibitor (CNI)-based immunosuppression, who had undergone a kidney biopsy at 60 ± 48 months post-transplant, were included in this follow-up study. Kidney biopsies were scored according to the Banff classification. Estimated glomerular filtration rate (eGFR) was assessed at last follow-up, that is, 109 ± 48 months after liver transplantation. eGFR decreased from 92 ± 33 mL/min at transplantation to 63 ± 19 mL/min after six months, to 57 ± 17 mL/min at the kidney biopsy, to 54 ± 24 mL/min at last follow-up (p < 0.0001). At last follow-up, only three patients required renal replacement therapy. After the kidney biopsy, 13 patients were converted from CNIs to mammalian target of rapamycin inhibitors, but no significant improvement in eGFR was observed after conversion. Elevated eGFR at six months post-transplant and a lower fibrous intimal thickening score (cv) observed at five yr post-transplant were the two independent predictive factors for eGFR ≥60 mL/min at nine yr post-transplant. Long-term kidney function seems to be predicted by the kidney vascular lesions.

To evaluate the reliability of quantitative ultrasonic measurement of renal allograft elasticity using supersonic shear imaging (SSI) and its relationship with parenchymal pathological changes.Forty-three kidney transplant recipients (22 women, 21 men) (mean age, 51 years; age range, 18-70 years) underwent SSI elastography, followed by biopsy. The quantitative measurements of cortical elasticity were performed by two radiologists and expressed in terms of Young's modulus (kPa). Intra- and inter-observer reproducibility was assessed (Kruskal-Wallis test and Bland-Altman analysis), as well as the correlation between elasticity values and clinical, biological and pathological data (semi-quantitative Banff scoring). Interstitial fibrosis was evaluated semi-quantitatively by the Banff score and measured by quantitative image analysis.Intra- and inter-observer variation coefficients of cortical elasticity were 20 % and 12 %, respectively. Renal cortical stiffness did not correlate with any clinical parameters, any single semi-quantitative Banff score or the level of interstitial fibrosis; however, a significant correlation was observed between cortical stiffness and the total Banff scores of chronic lesions and of all elementary lesions (R = 0.34, P = 0.05 and R = 0.41, P = 0.03,respectively).Quantitative measurement of renal cortical stiffness using SSI is a promising non-invasive tool to evaluate global histological deterioration.• Supersonic shear imaging elastography can measure cortical stiffness in renal transplants • The level of cortical stiffness is correlated with the global degree of tissue lesions • The global histological deterioration of transplanted kidneys can be quantified using elastography.

International audience; In this article, we characterize the lateral field distortions in a low numerical aperture and large field-of-view (FOV) fluorescence imaging system. To this end, we study a commercial fluorescence MACROscope setup, which is a zooming microscope. The versatility of this system lies in its ability to image at different zoom ranges, so that sample preparations can be examined in three-dimensions, at cellular, organ and whole body levels. Yet, we found that the imaging system's optics are optimized only for high magnifications where the observed FOV is small. When we studied the point-spread function (PSF) by using fluorescent polystyrene beads as "guide-stars", we noticed that the PSF is spatially varying due to field distortions. This variation was found to be laterally symmetrical and the distortions were found to increase with the distance from the center of the FOV. In this communication, we investigate the idea of using the field at the back focal plane of an optical system for characterizing distortions. As this field is unknown, we develop a theoretical framework to retrieve the amplitude and phase of the field at the back focal pupil plane, from the empirical bead images. By using the retrieved amplitude, we can understand and characterize the underlying cause of these distortions. We also propose a few approaches, before acquisition, to either avoid it or correct it at the optical design level.

International audience; The use of uncontrolled deceased donors after cardiac arrest (uDDCA) has been developed in France to compensate for organ shortage. The quality of these kidneys remains unclear. We analyzed kidney graft function and histology from 27 uDDCA and compared them with kidneys from 30 extended criteria donors (ECD) and from 24 simultaneous pancreas kidney (SPK) donors as a control group of optimal deceased donors. Kidneys from ECD and SPK donors were preserved by static cold storage while kidneys from uDDCA were preserved by pulsatile perfusion. The uDDCA graft function at 3 years posttransplantation (estimated with MDRD and measured with inulin clearance) did not differ from that of the ECD group (eGFR 44.1 vs. 37.4 mL/min/1.73 m2, p = 0.13; mGFR 44.6 vs. 36.1 mL/min/1.73 m2, p = 0.07 in the uDDCA and ECD groups, respectively). The histological assessment of 3-month and 1-year protocol biopsies did not show differences for interstitial lesions between the uDDCA and ECD grafts (IF score at M3 was 30 vs. 28% and at M12 36 vs. 33%, p = NS). In conclusion, the results at 3 years with carefully selected and machine-perfused uDDCA kidneys have been comparable to ECD kidneys and encourage continuation of this program and development of similar programs.

International audience; The study of social interactions in mice is used as a model for normal and pathological cognitive and emotional processes. But extracting comprehensive behavioral information from videos of interacting mice is still a challenge. We describe a computerized method and software, MiceProfiler, that uses geometrical primitives to model and track two mice without requiring any specific tagging. The program monitors a comprehensive repertoire of behavioral states and their temporal evolution, allowing the identification of key elements that trigger social contact. Using MiceProfiler we studied the role of neuronal nicotinic receptors in the establishment of social interactions and risk-prone postures. We found that the duration and type of social interactions with a conspecific evolves differently over time in mice lacking neuronal nicotinic receptors (Chrnb2-/-, here called β2(-/-)), compared to C57BL/6J mice, and identified a new type of coordinated posture, called back-to-back posture, that we rarely observed in β2(-/-) mice.

Item does not contain fulltext Enlarged early endosomes have been observed in neurons and fibroblasts in Down syndrome (DS). These endosome abnormalities have been implicated in the early development of Alzheimer's disease (AD) pathology in these subjects. Here, we show the presence of enlarged endosomes in blood mononuclear cells and lymphoblastoid cell lines (LCLs) from individuals with DS using immunofluorescence and confocal microscopy. Genotype-phenotype correlations in LCLs carrying partial trisomies 21 revealed that triplication of a 2.56 Mb locus in 21q22.11 is associated with the endosomal abnormalities. This locus contains the gene encoding the phosphoinositide phosphatase synaptojanin 1 (SYNJ1), a key regulator of the signalling phospholipid phosphatidylinositol-4,5-biphosphate that has been shown to regulate clathrin-mediated endocytosis. We found that SYNJ1 transcripts are increased in LCLs from individuals with DS and that overexpression of SYNJ1 in a neuroblastoma cell line as well as in transgenic mice leads to enlarged endosomes. Moreover, the proportion of enlarged endosomes in fibroblasts from an individual with DS was reduced after silencing SYNJ1 expression with RNA interference. In LCLs carrying amyloid precursor protein (APP) microduplications causing autosomal dominant early-onset AD, enlarged endosomes were absent, suggesting that APP overexpression alone is not involved in the modification of early endosomes in this cell type. These findings provide new insights into the contribution of SYNJ1 overexpression to the endosomal changes observed in DS and suggest an attractive new target for rescuing endocytic dysfunction and lipid metabolism in DS and in AD.

International audience; —Structured illumination microscopy is a recent imaging technique that aims at going beyond the classical optical resolution by reconstructing high-resolution (HR) images from low-resolution (LR) images acquired through modulation of the transfer function of the microscope. The classical implementation has a number of drawbacks, such as requiring a large number of images to be acquired and parameters to be manually set in an ad-hoc manner that have, until now, hampered its wide dissemination. Here, we present a new framework based on a Bayesian inverse problem formulation approach that enables the computation of one HR image from a reduced number of LR images and has no specific constraints on the modulation. Moreover, it permits to automatically estimate the optimal reconstruction hyperparameters and to compute an uncertainty bound on the estimated values. We demonstrate through numerical evaluations on simulated data and examples on real microscopy data that our approach represents a decisive advance for a wider use of HR microscopy through structured illumination.

International audience

International audience; Background. Chronic allograft injury, the primary cause of late allograft failure in renal transplantation, can be diagnosed early at a preclinical stage by histopathological changes such as interstitial fibrosis (IF). Currently, assessed by semiquantitative analysis in the Banff classification, IF quantification is limited by pathologist's subjective interpretation.Methods. We have designed algorithms dedicated to quantify IF by computerized color image analysis. This innovative and objective software automatically extracts the green areas characteristic of IF in Masson's trichrome based on color image segmentation followed by removal of nonspecific IF staining (capsula, sclerosis glomeruli and normal glomeruli, normal basement membrane) and computes an index. It also counts automatically the number of glomeruli. Sixty-seven Masson stained renal transplant biopsies at various IF stages were imaged using a digital color camera mounted on a microscope. We tested the robustness of the method against varying acquisition parameters.Results. We demonstrated that the parameters do not have an impact on this quantification and that the algorithm is able to handle biopsy color variations. The intra- and interobserver reproducibility was good (P

International audience; Organization of locomotor behavior is altered in mice knockout for the β2 subunit of the nicotinic receptor-β2-/- mice-during novelty exploration. We investigated the neuronal basis of this alteration by measuring activation of the immediate early gene c-fos in the brains of wild-type (WT) and β2-/- mice after exploration of a novel or a familiar environment. Results show 1) no constitutive difference between WT and β2-/- mice in c-fos gene expression in any brain region, 2) novelty exploration triggered activation of the hippocampus and the reward circuit while exploration of a familiar environment produced increased activation in the amygdala, and 3) in β2-/- mice, exploration of novelty, but not familiarity, induced an increase in activation in the prelimbic prefrontal cortex (PFC) compared with WT mice. c-Fos immunoreactivity after different stages of learning in a maze increased similarly in the prelimbic area of both WT and β2-/- mice, while their performance differed. In WT mice, exploration of a novel environment triggered an increase in c-Fos expression in the reward circuit and the hippocampus, while in β2-/- mice, the amygdala and the motor cortex were additionally activated. We also highlight the role of nicotinic receptors during activation of the PFC, specifically during free exploration of a novel environment.

International audience; An imbalance between inhibitory and excitatory neurotransmission has been proposed to contribute to altered brain function in individuals with Down syndrome (DS). Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system and accordingly treatment with GABA-A antagonists can efficiently restore cognitive functions of Ts65Dn mice, a genetic model for DS. However, GABA-A antagonists are also convulsant which preclude their use for therapeutic intervention in DS individuals. Here, we have evaluated safer strategies to release GABAergic inhibition using a GABA-A-benzodiazepine receptor inverse agonist selective for the α5-subtype (α5IA). We demonstrate that α5IA restores learning and memory functions of Ts65Dn mice in the novel-object recognition and in the Morris water maze tasks. Furthermore, we show that following behavioural stimulation, α5IA enhances learning-evoked immediate early gene products in specific brain regions involved in cognition. Importantly, acute and chronic treatments with α5IA do not induce any convulsant or anxiogenic effects that are associated with GABA-A antagonists or non-selective inverse agonists of the GABA-A-benzodiazepine receptors. Finally, chronic treatment with α5IA did not induce histological alterations in the brain, liver and kidney of mice. Our results suggest that non-convulsant α5-selective GABA-A inverse agonists could improve learning and memory deficits in DS individuals.

International audience; Social behavior is a defining mammalian feature that integrates emotional and motivational processes with external rewarding stimuli. It is thus an appropriate readout for complex behaviors, yet its neuronal and molecular bases remain poorly understood. In this study, we investigated the role of the mouse prefrontal area, particularly the involvement of β2-subunit nicotinic receptors (β2*-nAChRs) in a paradigm of social behavior with concurrent motivations. We previously observed that mice lacking β2*-nAChRs (β2(-/-)) display increased time in social contact and exaggerated approach movements toward the novel conspecific. Here, combining behavioral analysis, localized brain lesions, and lentiviral gene rescue, we found that c-Fos expression is specifically activated in the prelimbic (PrL) area of the prefrontal cortex (PFC) of mice exposed to a novel conspecific; lesions of the PrL area in wild-type mice produce the same social pattern as in β2(-/-) mice; and virally mediated reexpression of the β2-subunit in the PrL area of β2(-/-) mice rescues behavioral components in the social interaction task up to normal levels. Together, these data reveal that social interactions particularly mobilize the PrL area of the mouse PFC and that the presence of functional PrL β2*-nAChRs is necessary for this integrated behavior to emerge.

International audience; Variational deformable models have proven over the past decades a high efficiency for segmentation and tracking in 2-D sequences. Yet, their application to 3-D time-lapse images has been hampered by discretization issues, heavy computational loads and lack of proper user visualization and interaction, limiting their use for routine analysis of large data-sets. We propose here to address these limitations by reformulating the problem entirely in the discrete domain using 3-D active meshes, which express a surface as a discrete triangular mesh, and minimize the energy functional accordingly. By performing computations in the discrete domain, computational costs are drastically reduced, whilst the mesh formalism allows to benefit from real-time 3-D rendering and other GPU-based optimizations. Performance evaluations on both simulated and real biological data sets show that this novel framework outperforms current state-of-the-art methods, constituting a light and fast alternative to traditional variational models for segmentation and tracking applications.

International audience; Screening renal biopsies (RB) may assess early changes of interstitial fibrosis (IF) after transplantation. The aim of this study was to quantify IF by automatic color image analysis on sequential RB. We analyzed RB performed at day (D) 0, month (M) 3 and M12 from 140 renal transplant recipients with a program of color segmentation imaging. The mean IF score was 19 ± 9% at D0, 27 ± 11% at M3 and 32 ± 11% at M12 with a 8% progression during the first 3 months and 5% between M3 and M12. IF at M3 was correlated with estimated glomerular rate (eGFR) at M3, 12 and 24 (p < 0.02) and IF at M12 with eGFR at M12 and 48 (p < 0.05). Furthermore, IF evolution between D0 and M3 (ΔIFM3-D0) was correlated with eGFR at M24, 36 and 48 (p < 0.03). IF at M12 was significantly associated with male donor gender and tacrolimus dose (p = 0.03). ΔIFM3-D0 was significantly associated with male donor gender, acute rejection episodes (p = 0.04) and diabetes mellitus (p = 0.02). Thus, significant IF is already present before transplantation. IF evolution is more important during the first 3 months and has some predictive ability for change in GFR. Intervention to decrease IF should be applied early, i.e. before 3 months, after transplantation.

International audience; The Notch pathway is involved in cell-cell signaling during development and adulthood from invertebrates to higher eukaryotes. Activation of the Notch receptor by its ligands relies upon a multi-step processing. The extracellular part of the receptor is removed by a metalloprotease of the ADAM family and the remaining fragment is cleaved within its transmembrane domain by a presenilin-dependent γ-secretase activity. γ-Secretase processing of Notch has been shown to depend upon monoubiquitination as well as clathrin-mediated endocytosis (CME). We show here that AAK1, the adaptor-associated kinase 1, directly interacts with the membrane-tethered active form of Notch released by metalloprotease cleavage. Active AAK1 acts upstream of the γ-secretase cleavage by stabilizing both the membrane-tethered activated form of Notch and its monoubiquitinated counterpart. We propose that AAK1 acts as an adaptor for Notch interaction with components of the clathrin-mediated pathway such as Eps15b. Moreover, transfected AAK1 increases the localization of activated Notch to Rab5-positive endocytic vesicles, while AAK1 depletion or overexpression of Numb, an inhibitor of the pathway, interferes with this localization. These results suggest that after ligand-induced activation of Notch, the membrane-tethered form can be directed to different endocytic pathways leading to distinct fates.

Compressed sensing (CS) is a new sampling theory that was recently introduced for efficient acquisition of compressible signals. In this thesis, we have studied practical applications of the Fourier-based CS sampling theory for biological microscopy imaging, with two main contributions: (i) Image denoising: microscopic images suffer from complex artifacts associated with noise and non-perfect illumination conditions. In fluorescence microscopy, noise and photobleaching degrade the quality of the image. In this work, we have exploited the CS theory as an image denoising tool, using multiple random undersampling in the Fourier domain and the Total Variation as a spatial sparsity prior. Compounding of images reconstructed from multiple sets of random measurements enforce spatial coherence of meaningful signal components and decorrelate noisy components. We have studied the relation between signal sparsity and noise reduction performance under different noise conditions. We have demonstrated on simulated and practical experiments on fluorescence microscopy that the proposed denoising framework provide images with similar or increased signal-to-noise ratio (SNR) compared to state of the art denoising methods while relying on a limited number of samples. If Fourier-domain image point acquisitions were feasible, the proposed denoising could be used as a fast acquisition scheme which would enable to reduce exposition times, and reduce the photobleaching effects. (ii) Compressed digital holographic microscopy: high data throughput is becoming increasingly important in microscopy, with high-resolution cameras (i.e. large numbers of samples per acquisition) and long observation times. The com- pressed sensing theory provides a framework to reconstruct images from fewer samples than traditional acquisition approaches. However, the very few measurements must be spread over a large field of view, which is difficult to achieve in conventional microscopy. In a first experiment, we have proposed a computational scheme to perform fast temporal acquisitions of sequences of Fourier amplitude measures in optical Fourier imaging and estimate the missing phase information from spectra interpolation between few in-between complete keyframes. This approach was evaluated for high-frame rate imaging of moving cells. In a second experiment, we have implemented a real CS acquisition scheme for digital holographic microscopy, acquiring a diffraction map of the optical field and recovering high quality images from as little as 7% of random measurements. The CS acquisition setup was successfully extended to high speed low-light single-shot off-axis holography.; La technique d'acquisition compressée (compressed sensing, CS) est une nouvelle théorie pour l'échantillonnage qui fût introduite afin de permettre l'acquisition efficace de signaux compressibles. Dans cette thèse, nous avons étudié des applications pratiques de cette technique d'échantillonnage, où les acquisitions sont réalisées dans le domaine de Fourier, menant aux deux principales contributions suivantes : (i) Débruitage d'image : Les images microscopiques présentent souvent des dégradations dûs à des artefacts complexes, associés à du bruit ou encore des mauvaises conditions d'éclairage. En microscopie à fluorescence, le bruit et le photoblanchiment altèrent la qualité de l'image. Notre travail a consisté à exploiter la théorie d'acquisition compressée comme un outil de débruitage d'image. Nous avons utilisé plusieurs acquisitions aléatoires dans le domaine de Fourier, et la variation totale comme un a priori sur la parcimonie spatiale. La composition des différentes images de reconstruction correspondant aux différents ensembles de mesures aléatoires renforce la cohérence spatiale de composants du signal significatifs et per- met de décorréler les composants bruités. Nous avons étudié les relations entre la parcimonie d'un signal et les statistiques et la performance pour la réduction du bruit sous différentes conditions initiales de bruitage. Nous avons montré que la technique proposée, basée sur un a priori sur la parcimonie du signal et sur des échantillonnages aléatoires dans le domaine de Fourier, permet d'obtenir des im- ages avec un rapport signal/bruit (SNR) au pire égal à celui obtenu avec les méthodes de débruitage classiques, tout en utilisant un nombre limité d'échantillons. Sous réserve de pouvoir acquérir l'image dans le domaine de Fourier, le schéma de débruitage proposé fournirait une méthode d'acquisition rapide nécessitant un temps d'exposition moindre, réduisant les effets de photoblanchiment. (ii) Acquisition compressée en microscopie holographique : En microscopie, les données en sortie deviennent considérables, impliquant notamment l'utilisation de capteurs haute-définition (i.e. beaucoup d'échantillons par acquisition) et l'augmentation des temps d'acquisition. La théorie de l'acquisition compressée fournit des outils pour la reconstruction d'images, nécessitant moins d'échantillons que les approches classiques. Cependant, les quelques mesures nécessaires doivent être prises dans un domaine incohérent au domaine spatiale, ce qui est difficile à réaliser en microscopie conventionnelle. Nous avons tout d'abord proposé un schéma de calcul permettant l'acquisition de séquences temporelles de mesures d'amplitude dans le domaine de Fourier, et l'estimation de l'information manquante sur la phase par interpolation de spectre de quelques acquisitions complètes d'images. Cette approche a été mise en pratique dans le contexte de l'imagerie rapide, utilisée pour des cellules en mouvement. Dans un deuxième temps nous avons implanté un schéma d'acquisition compressée pratique, conçu pour l'holographie numérique. Ce schéma permet de mesurer une figure de diffraction du champ optique et reconstruire images de haute qualité à partir de seulement 7% de mesures aléatoires. L'expérience d'acquisition compressée a été étendue avec succès à l'holographie compressée rapide à acquisition unique et dans des conditions d'éclairage faible.

Compressed sensing (CS) is a new sampling theory that was recently introduced for efficient acquisition of compressible signals. In this thesis, we have studied practical applications of the Fourier-based CS sampling theory for biological microscopy imaging, with two main contributions: (i) Image denoising: microscopic images suffer from complex artifacts associated with noise and non-perfect illumination conditions. In fluorescence microscopy, noise and photobleaching degrade the quality of the image. In this work, we have exploited the CS theory as an image denoising tool, using multiple random undersampling in the Fourier domain and the Total Variation as a spatial sparsity prior. Compounding of images reconstructed from multiple sets of random measurements enforce spatial coherence of meaningful signal components and decorrelate noisy components. We have studied the relation between signal sparsity and noise reduction performance under different noise conditions. We have demonstrated on simulated and practical experiments on fluorescence microscopy that the proposed denoising framework provide images with similar or increased signal-to-noise ratio (SNR) compared to state of the art denoising methods while relying on a limited number of samples. If Fourier-domain image point acquisitions were feasible, the proposed denoising could be used as a fast acquisition scheme which would enable to reduce exposition times, and reduce the photobleaching effects. (ii) Compressed digital holographic microscopy: high data throughput is becoming increasingly important in microscopy, with high-resolution cameras (i.e. large numbers of samples per acquisition) and long observation times. The com- pressed sensing theory provides a framework to reconstruct images from fewer samples than traditional acquisition approaches. However, the very few measurements must be spread over a large field of view, which is difficult to achieve in conventional microscopy. In a first experiment, we have proposed a computational scheme to perform fast temporal acquisitions of sequences of Fourier amplitude measures in optical Fourier imaging and estimate the missing phase information from spectra interpolation between few in-between complete keyframes. This approach was evaluated for high-frame rate imaging of moving cells. In a second experiment, we have implemented a real CS acquisition scheme for digital holographic microscopy, acquiring a diffraction map of the optical field and recovering high quality images from as little as 7% of random measurements. The CS acquisition setup was successfully extended to high speed low-light single-shot off-axis holography.; La technique d'acquisition compressée (compressed sensing, CS) est une nouvelle théorie pour l'échantillonnage qui fût introduite afin de permettre l'acquisition efficace de signaux compressibles. Dans cette thèse, nous avons étudié des applications pratiques de cette technique d'échantillonnage, où les acquisitions sont réalisées dans le domaine de Fourier, menant aux deux principales contributions suivantes : (i) Débruitage d'image : Les images microscopiques présentent souvent des dégradations dûs à des artefacts complexes, associés à du bruit ou encore des mauvaises conditions d'éclairage. En microscopie à fluorescence, le bruit et le photoblanchiment altèrent la qualité de l'image. Notre travail a consisté à exploiter la théorie d'acquisition compressée comme un outil de débruitage d'image. Nous avons utilisé plusieurs acquisitions aléatoires dans le domaine de Fourier, et la variation totale comme un a priori sur la parcimonie spatiale. La composition des différentes images de reconstruction correspondant aux différents ensembles de mesures aléatoires renforce la cohérence spatiale de composants du signal significatifs et per- met de décorréler les composants bruités. Nous avons étudié les relations entre la parcimonie d'un signal et les statistiques et la performance pour la réduction du bruit sous différentes conditions initiales de bruitage. Nous avons montré que la technique proposée, basée sur un a priori sur la parcimonie du signal et sur des échantillonnages aléatoires dans le domaine de Fourier, permet d'obtenir des im- ages avec un rapport signal/bruit (SNR) au pire égal à celui obtenu avec les méthodes de débruitage classiques, tout en utilisant un nombre limité d'échantillons. Sous réserve de pouvoir acquérir l'image dans le domaine de Fourier, le schéma de débruitage proposé fournirait une méthode d'acquisition rapide nécessitant un temps d'exposition moindre, réduisant les effets de photoblanchiment. (ii) Acquisition compressée en microscopie holographique : En microscopie, les données en sortie deviennent considérables, impliquant notamment l'utilisation de capteurs haute-définition (i.e. beaucoup d'échantillons par acquisition) et l'augmentation des temps d'acquisition. La théorie de l'acquisition compressée fournit des outils pour la reconstruction d'images, nécessitant moins d'échantillons que les approches classiques. Cependant, les quelques mesures nécessaires doivent être prises dans un domaine incohérent au domaine spatiale, ce qui est difficile à réaliser en microscopie conventionnelle. Nous avons tout d'abord proposé un schéma de calcul permettant l'acquisition de séquences temporelles de mesures d'amplitude dans le domaine de Fourier, et l'estimation de l'information manquante sur la phase par interpolation de spectre de quelques acquisitions complètes d'images. Cette approche a été mise en pratique dans le contexte de l'imagerie rapide, utilisée pour des cellules en mouvement. Dans un deuxième temps nous avons implanté un schéma d'acquisition compressée pratique, conçu pour l'holographie numérique. Ce schéma permet de mesurer une figure de diffraction du champ optique et reconstruire images de haute qualité à partir de seulement 7% de mesures aléatoires. L'expérience d'acquisition compressée a été étendue avec succès à l'holographie compressée rapide à acquisition unique et dans des conditions d'éclairage faible.

Compressed sensing (CS) is a new sampling theory that was recently introduced for efficient acquisition of compressible signals. In this thesis, we have studied prac- tical applications of the Fourier-based CS sampling theory for biological microscopy imaging, with two main contributions: (i) Image denoising: microscopic images suffer from complex artifacts associated with noise and non-perfect illumination con- ditions. In fluorescence microscopy, noise and photobleaching degrade the quality of the image. In this work, we have exploited the CS theory as an image denoising tool, using multiple random undersampling in the Fourier domain and the Total Variation as a spatial sparsity prior. Compounding of images reconstructed from multiple sets of random measurements enforce spatial coherence of meaningful signal components and decorrelate noisy components. We have studied the relation between signal sparsity and noise reduction performance under different noise conditions. We have demonstrated on simulated and practical experiments on fluorescence microscopy that the proposed denoising framework provide images with similar or increased signal-to-noise ratio (SNR) compared to state of the art denoising methods while relying on a limited number of samples. If Fourier-domain image point acquisitions were feasible, the proposed denoising could be used as a fast acquisition scheme which would enable to reduce exposition times, and reduce the photobleaching ef- fects. (ii) Compressed digital holographic microscopy: high data throughput is becoming increasingly important in microscopy, with high-resolution cameras (i.e. large numbers of samples per acquisition) and long observation times. The com- pressed sensing theory provides a framework to reconstruct images from fewer sam- ples than traditional acquisition approaches. However, the very few measurements must be spread over a large field of view, which is difficult to achieve in conven- tional microscopy. In a first experiment, we have proposed a computational scheme to perform fast temporal acquisitions of sequences of Fourier amplitude measures in optical Fourier imaging and estimate the missing phase information from spectra interpolation between few in-between complete keyframes. This approach was eval- uated for high-frame rate imaging of moving cells. In a second experiment, we have implemented a real CS acquisition scheme for digital holographic microscopy, ac- quiring a diffraction map of the optical field and recovering high quality images from as little as 7% of random measurements. The CS acquisition setup was successfully extended to high speed low-light single-shot off-axis holography.; La technique d'acquisition compressée (compressed sensing, CS) est une nouvelle théorie pour l'échantillonnage qui fût introduite afin de permettre l'acquisition ef- ficace de signaux compressibles. Dans cette thèse, nous avons étudié des applica- tions pratiques de cette technique d'échantillonnage, où les acquisitions sont réal- isées dans le domaine de Fourier, menant aux deux principales contributions suiv- antes : (i) Débruitage d'image : Les images microscopiques présentent souvent des dégradations dûs à des artefacts complexes, associés à du bruit ou encore des mauvaises conditions d'éclairage. En microscopie à fluorescence, le bruit et le pho- toblanchiment altèrent la qualité de l'image. Notre travail a consisté à exploiter la théorie d'acquisition compressée comme un outil de débruitage d'image. Nous avons utilisé plusieurs acquisitions aléatoires dans le domaine de Fourier, et la variation totale comme un a priori sur la parcimonie spatiale. La composition des différentes images de reconstruction correspondant aux différents ensembles de mesures aléa- toires renforce la cohérence spatiale de composants du signal significatifs et per- met de décorréler les composants bruités. Nous avons étudié les relations entre la parcimonie d'un signal et les statistiques et la performance pour la réduction du bruit sous différentes conditions initiales de bruitage. Nous avons montré que la technique proposée, basée sur un a priori sur la parcimonie du signal et sur des échantillonnages aléatoires dans le domaine de Fourier, permet d'obtenir des im- ages avec un rapport signal/bruit (SNR) au pire égal à celui obtenu avec les méth- odes de débruitage classiques, tout en utilisant un nombre limité d'échantillons. Sous réserve de pouvoir acquérir l'image dans le domaine de Fourier, le schéma de débruitage proposé fournirait une méthode d'acquisition rapide nécessitant un temps d'exposition moindre, réduisant les effets de photoblanchiment. (ii) Acquisi- tion compressée en microscopie holographique : En microscopie, les données en sortie deviennent considérables, impliquant notamment l'utilisation de capteurs haute-définition (i.e. beaucoup d'échantillons par acquisition) et l'augmentation des temps d'acquisition. La théorie de l'acquisition compressée fournit des outils pour la reconstruction d'images, nécessitant moins d'échantillons que les approches clas- siques. Cependant, les quelques mesures nécessaires doivent être prises dans un domaine incohérent au domaine spatiale, ce qui est difficile à réaliser en microscopie conventionnelle. Nous avons tout d'abord proposé un schéma de calcul permettant l'acquisition de séquences temporelles de mesures d'amplitude dans le domaine de Fourier, et l'estimation de l'information manquante sur la phase par interpolation de spectre de quelques acquisitions complètes d'images. Cette approche a été mise en pratique dans le contexte de l'imagerie rapide, utilisée pour des cellules en mou- vement. Dans un deuxième temps nous avons implanté un schéma d'acquisition compressée pratique, conçu pour l'holographie numérique. Ce schéma permet de mesurer une figure de diffraction du champ optique et reconstruire images de haute qualité à partir de seulement 7% de mesures aléatoires. L'expérience d'acquisition compressée a été étendue avec succès à l'holographie compressée rapide à acquisition unique et dans des conditions d'éclairage faible.

International audience; In this paper, we present an approach to calculate the wavefront in the back pupil plane of an objective in a fluorescent MACROscope. We use the three-dimensional image of a fluorescent bead because it contains potential pupil information in the ‘far' out-of-focus planes for sensing the wavefront at the back focal plane of the objective. Wavefront sensing by phase retrieval technique is needed for several reasons. Firstly, the point-spread function of the imaging system can be calculated from the estimated pupil phase and used for image restoration. Secondly, the aberrations in the optics of the objective can be determined by studying this phase. Finally, the estimated wavefront can be used to correct the aberrated optical path with- out a wavefront sensor. In this paper, we estimate the wavefront of a MACROscope optical system by using Bayesian inferencing and derive the Gerchberg-Saxton algorithm as a special case.

International audience; Confocal fluorescence microscopy has become a standard tool to image thick 3D tissue samples, permitting the observation of cell behaviour, such as cell division within developing organs. However, robust and automatic extraction of nuclear shape and mitotic orientation may be hindered by a highly cluttered environment as for example in mammalian tissues. We propose a fast and automated framework for the segmentation of nuclei from cluttered 3D images, allowing robust quantification of various parameters such as number of cells, number of mitoses and mitotic orientation. We have applied this framework to scans of the developing mouse heart, and manual validation on three independent experiments indicates a detection rate of 93% in all cases. Moreover, the proposed tool permits fast, real-time 3D rendering of the data set during the analysis, and can be easily adapted to other applications related to dense tissue analysis.

International audience; This Letter reports a demonstration of off-axis compressed holography in low-light level imaging conditions. An acquisition protocol relying on a single exposure of a randomly undersampled diffraction map of the optical field, recorded in the high heterodyne gain regime, is proposed. The image acquisition scheme is based on compressed sensing, a theory establishing that near-exact recovery of an unknown sparse signal is possible from a small number of nonstructured measurements. Image reconstruction is further enhanced by introducing an off-axis spatial support constraint to the image estimation algorithm. We report accurate experimental recovering of holographic images of a resolution target in low-light conditions with a frame exposure of 5 μs, scaling down measurements to 9% of random pixels within the array detector.