Approximate Bayesian Computation, stochastic algorithms and non-local means for complex noise models

International audienceIn this paper, we present a stochastic NL-means-based denoising algorithm for generalized non-parametric noise models. First, we provide a statistical interpretation to current patch-based neighborhood filters and justify the Bayesian inference that needs to explicitly accounts for discrepancies between the model and the data. Furthermore, we investigate the Approximate Bayesian Computation (ABC) rejection method combined with density learning techniques for handling situations where the posterior is intractable or too prohibitive to calculate. We demonstrate our stochastic Gamma NL-means (SGNL) on real images corrupted by non-Gaussian noise

Lifetime estimation of moving vesicles in frequency-domain fluorescence lifetime imaging microscopy

International audienceWe propose a framework for correcting the effect of vesicles motion in frequency domain FLIM imaging. Estimation of movement and lifetime are decoupled and alternatively performed. Robust M-estimation is involved to improve the accuracy of our estimate. Our method has been evaluated with both simulated and real samples

3D Flow Field Estimation and Assessment for Live Cell Fluorescence Microscopy

International audienceMotivation: The revolution in light sheet microscopy enables the concurrent observation of thousands of dynamic processes, from single molecules to cellular organelles, with high spatiotemporal resolution. However, challenges in the interpretation of multidimensional data requires the fully automaticmeasurement of those motions to link local processes to cellular functions. This includes the design and the implementation of image processing pipelines able to deal with diverse motion types, and 3D visualization tools adapted to the human visual system.Results: Here, we describe a new method for 3D motion estimation that addresses the aforementioned issues. We integrate 3D matching and variational approach to handle a diverse range of motion without any prior on the shape of moving objects. We compare dierent similarity measures to cope with intensity ambiguities and demonstrate the eectiveness of the Census signature for both stages. Additionally, wepresent two intuitive visualization approaches to adapt complex 3D measures into an interpretable 2D view, and a novel way to assess the quality of flow estimates in absence of ground truth

Lifetime MAP reconstruction in frequency-domain fluorescence lifetime imaging microscopy

International audienceWe propose a robust statistical framework for reconstructing lifetime map corrupted by vesicle motion in frequency domain FLIM imaging. Instrumental noise is taken into account to improve lifetime estimation. Robust M-estimators and MLestimators allow to jointly estimate motion and lifetime. Performances are demonstrated on simulated and real samples

Lifetime estimation on moving sub-cellular objects in frequency domain FLIM imaging

International audienceFluorescence lifetime is usually defined as the average nanosecond-scale delay between excitation and emission of fluorescence. It has been established that lifetime measurement yields numerous indications on cellular processes such as inter-protein and intra-protein mechanisms through fluorescent tagging and Förster resonance energy transfer (FRET). In this area, frequency domain fluorescence lifetime imaging microscopy (FD FLIM) is particularly well appropriate to probe a sample non-invasively and quantify these interactions in living cells. The aim is then to measure fluorescence lifetime in the sample at each location in space from fluorescence variations observed in a temporal sequence of images obtained by phase modulation of the detection signal. This leads to a sensitivity of lifetime determination to other sources of fluorescence variations such as intracellular motion. In this paper, we propose a robust statistical method for lifetime estimation on both background and small moving structures with a focus on intracellular vesicle trafficking

A sparse-to-dense method for 3D optical flow estimation in 3D light microscopy image sequences

International audienceWe present a two-stage 3D optical flow estimation method for light microscopy image volumes. The method takes a pair of light microscopy image volumes as input, segments the 2D slices of the source volume in superpixels and sparsely estimates the 3D displacement vectors in the volume pair. A weighted interpolation is then introduced to get a dense 3D flow field. Edges and motion boundaries are considered during the interpolation. Our experimental results show good gain in execution speed, and accuracy evaluated in computer generated 3D data. Promising results on real 3D image sequences are reported

Piecewise-stationary motion modeling and iterative smoothing to track heterogeneous particle motions in dense environments

International audienceOne of the major challenges in multiple particle tracking is the capture of extremely heterogeneous movements of objects in crowded scenes. The presence of numerous assignment candidates in the expected range of particle motion makes the tracking ambiguous and induces false positives. Lowering the ambiguity by reducing the search range, on the other hand, is not an option, as this would increase the rate of false negatives. We propose here a piecewise-stationary motion model (PMM) for the particle transport along an iterative smoother that exploits recursive tracking in multiple rounds in forward and backward temporal directions. By fusing past and future information, our method, termed PMMS, can recover fast transitions from freely or confined diffusive to directed motions with linear time complexity. To avoid false positives we complemented recursive tracking with a robust inline estimator of the search radius for assignment (a.k.a. gating), where past and future information are exploited using only two frames at each optimization step. We demonstrate the improvement of our technique on simulated data – especially the impact of density, variation in frame to frame displacements, and motion switching probability. We evaluated our technique on the 2D particle tracking challenge dataset published by Chenouard et al in 2014. Using high SNR to focus on motion modeling challenges, we show superior performance at high particle density. On biological applications, our algorithm allows us to quantify the extremely small percentage of motor-driven movements of fluorescent particles along microtubules in a dense field of unbound, diffusing particles. We also show with virus imaging that our algorithm can cope with a strong reduction in recording frame rate while keeping the same performance relative to methods relying on fast sampling

Perancangan Sistem Dan Denah Bazaar Dengan Memanfaatkan Canvas HTML5 Berbasis Website Dan Android

At present, almost every organizers holds an attractive bazaar due to the growing number of enthusiasts who want to join bazaar. Bazaar can be an alternative place to sell new product and introduce the local product to the general society. Booking booth process in bazaar still using manual system, which tenant fills the order form and then the form is scanned to be sent to the organizer of the event via e-email. Once the booking is received, event organizer has to check and make a registration list of tenants whom will join the bazaar. Therefore there is a need to have an information system to help both eventorganizer and tenant to make a better booking process. Aplication Bazaar based on Android and website intends to help user do all booking process efficiently.Application based on mobile assist tenant in making reservation from fill form until payment order. It helps tenant to search for information about the bazaar which will be held in accordance with bazaar categories of interest and can follow event, so tenant will be easier to get bazaar information. In addition, application based on website helps event organizer to manage the whole process from booking to the payment which received from tenant order, then event organizer can edit event map in order to facilitate tenant when choose a booth at the bazaar.The test results which obatained have two modules, Mobile Application based on Android for tenant and application website for event organizer. Mobile Application can make a booking in bazaar, can get a notification, follow the event, displaying order data. Application website for the event organizer can manage the whole order and payment from tenant, and can edit map event to help tenant make an order. From the test of mobile application that have been done, 50% of respondents rate the app is overall good, and 42% of respondent rate the app overall very good. For Website Application, event organizer has satified with the existing features on the website

Community standards for open cell migration data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration

Glutathione Deficiency in Cardiac Patients Is Related to the Functional Status and Structural Cardiac Abnormalities

International audienceBACKGROUND: The tripeptide glutathione (L-gamma-glutamyl-cysteinyl-glycine) is essential to cell survival, and deficiency in cardiac and systemic glutathione relates to heart failure progression and cardiac remodelling in animal models. Accordingly, we investigated cardiac and blood glutathione levels in patients of different functional classes and with different structural heart diseases. METHODS: Glutathione was measured using standard enzymatic recycling method in venous blood samples obtained from 91 individuals, including 15 healthy volunteers and 76 patients of New York Heart Association (NYHA) functional class I to IV, undergoing cardiac surgery for coronary artery disease, aortic stenosis or terminal cardiomyopathy. Glutathione was also quantified in right atrial appendages obtained at the time of surgery. RESULTS: In atrial tissue, glutathione was severely depleted (-58%) in NYHA class IV patients compared to NYHA class I patients (P = 0.002). In patients with coronary artery disease, this depletion was related to the severity of left ventricular dysfunction (P = 0.006). Compared to healthy controls, blood glutathione was decreased by 21% in NYHA class I patients with structural cardiac disease (P<0.01), and by 40% in symptomatic patients of NYHA class II to IV (P<0.0001). According to the functional NYHA class, significant depletion in blood glutathione occurred before detectable elevation in blood sTNFR1, a marker of symptomatic heart failure severity, as shown by the exponential relationship between these two parameters in the whole cohort of patients (r = 0.88). CONCLUSIONS: This study provides evidence that cardiac and systemic glutathione deficiency is related to the functional status and structural cardiac abnormalities of patients with cardiac diseases. These data also suggest that blood glutathione test may be an interesting new biomarker to detect asymptomatic patients with structural cardiac abnormalities