Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Particle detection and tracking in fluorescence time-lapse imaging: a contrario approach

This paper proposes a probabilistic approach for the detection and the tracking of particles in fluorescent time-lapse imaging. In the presence of a very noised and poor-quality data, particles and trajectories can be characterized by an a contrario model, that estimates the probability of observing the structures of interest in random data. This approach, first introduced in the modeling of human visual perception and then successfully applied in many image processing tasks, leads to algorithms that neither require a previous learning stage, nor a tedious parameter tuning and are very robust to noise. Comparative evaluations against a well-established baseline show that the proposed approach outperforms the state of the art.Comment: Published in Journal of Machine Vision and Application

Total Variation as a local filter

International audienceIn the Rudin-Osher-Fatemi (ROF) image denoising model, Total Variation (TV) is used as a global regularization term. However, as we observe, the local interactions induced by Total Variation do not propagate much at long distances in practice, so that the ROF model is not far from being a local filter. In this paper, we propose to build a purely local filter by considering the ROF model in a given neighborhood of each pixel. We show that appropriate weights are required to avoid aliasing-like effects, and we provide an explicit convergence criterion for an associated dual minimization algorithm based on Chambolle's work. We study theoretical properties of the obtained local filter, and show that this localization of the ROF model brings an interesting optimization of the bias-variance trade-off, and a strong reduction a ROF drawback called "staircasing effect". We finally present a new denoising algorithm, TV-means, that efficiently combines the idea of local TV-filtering with the non-local means patch-based method

Point tracking: an a-contrario approach

In this work, we propose a new approach to recover trajectories from points previously detected in a sequence of images. In presence of spurious and missing detections, actual trajectories can be characterized by an a-contrario model, that estimates the probability of observing a similar trajectory in random data. This results in a single criterion combining trajectory characteristics (duration, number of points, smoothness) and data statistics (number of images and detected points), which can then be used to drive a dynamic programming algorithm able to extract sequentially the most meaningful trajectories. The performances obtained on synthetic and real-world data are studied in detail, and shown to compare favorably to the state-of-the-art ROADS algorithm

Fast and accurate evaluation of a generalized incomplete gamma function

We present a computational procedure to evaluate the integral ∫xy sp-1 e-μs ds, for 0 ≤ x 0, which generalizes the lower (x=0) and upper (y=+∞) incomplete gamma functions. To allow for large values of x, y, and p while avoiding under/overflow issues in the standard double precision floating point arithmetic, we use an explicit normalization that is much more efficient than the classical ratio with the complete gamma function. The generalized incomplete gamma function is estimated with continued fractions, integrations by parts, or, when x ≈ y, with the Romberg numerical integration algorithm. We show that the accuracy reached by our algorithm improves a recent state-of-the-art method by two orders of magnitude, and is essentially optimal considering the limitations imposed by the floating point arithmetic. Moreover, the admissible parameter range of our algorithm (0 ≤ p,x,y ≤ 1015) is much larger than competing algorithms and its robustness is assessed through massive usage in an image processing application

A Compact Representation of Random Phase and Gaussian Textures

In this paper, we are interested in the mathematical analysis of the micro-textures that have the property to be perceptually invariant under the randomization of the phases of their Fourier Transform. We propose a compact representation of these textures by considering a special instance of them: the one that has identically null phases, and we call it ''texton''. We show that this texton has many interesting properties, and in particular it is concentrated around the spatial origin. It appears to be a simple and useful tool for texture analysis and texture synthesis, and its definition can be extended to the case of color micro-textures

A New A Contrario Approach for the Robust Determination of the Fundamental Matrix

International audienceThe fundamental matrix is a two-view tensor that plays a central role in Computer Vision geometry. We address its robust estimation given correspondences between image features. We use a non-parametric estimate of the distribution of image features, and then follow a probabilistic approach to select the best possible set of inliers among the given feature correspondences. The use of this perception-based \acontrario principle allows us to avoid the selection of a precision threshold as in RANSAC, since we provide a decision criterion that integrates all data and method parameters (total number of points, precision threshold, number of inliers given this threshold). Our proposal is analyzed in simulated and real data experiments; it yields a significant improvement of the ORSA method proposed in 2004, in terms of reprojection error and relative motion estimation, especially in situations of low inlier ratios

The Billard Theorem for Multiple Random Fourier Series

International audienceWe propose a generalization of a classical result on random Fourier series, namely the Billard Theorem, for random Fourier series over the d-dimensional torus. We provide an investigation of the independence with respect to a choice of a sequence of partial sums (or method of summation). We also study some probabilistic properties of the resulting sum field such as stationarity and characteristics of the marginal distribution

Total Variation Restoration of Images Corrupted by Poisson Noise with Iterated Conditional Expectations

International audienceInterpreting the celebrated Rudin-Osher-Fatemi (ROF) model in a Bayesian framework has led to interesting new variants for Total Variation image denoising in the last decade. The Posterior Mean variant avoids the so-called staircasing artifact of the ROF model but is computationally very expensive. Another recent variant, called TV-ICE (for Iterated Conditional Expectation), delivers very similar images but uses a much faster fixed-point algorithm. In the present work, we consider the TV-ICE approach in the case of a Poisson noise model. We derive an explicit form of the recursion operator, and show linear convergence of the algorithm, as well as the absence of staircasing effect. We also provide a numerical algorithm that carefully handles precision and numerical overflow issues, and show experiments that illustrate the interest of this Poisson TV-ICE variant

Aggregated primary detectors for generic change detection in satellite images

International audienceDetecting changes between two satellite images of the same scene generally requires an accurate (and thus often uneasy to obtain) model discriminating relevant changes from irrelevant ones. We here present a generic method, based on the definition of four different a-contrario detection models (associated to arbitrary features), whose aggregation is then trained from specific examples with gradient boosting. The results we present are encouraging, and in particular the low false positive rate is noticeable