Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Since manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized, for the first time, an open competition, in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to important practical conclusions for users and developers.
In image processing, restoration is expected to improve the qualitative inspection of the image and the performance of quantitative image analysis techniques. In this paper, an adaptation of the nonlocal (NL)-means filter is proposed for speckle reduction in ultrasound (US) images. Originally developed for additive white Gaussian noise, we propose to use a Bayesian framework to derive a NL-means filter adapted to a relevant ultrasound noise model. Quantitative results on synthetic data show the performances of the proposed method compared to well-established and state-of-the-art methods. Results on real images demonstrate that the proposed method is able to preserve accurately edges and structural details of the image.
Abstract-A novel adaptive and patch-based approach is proposed for image denoising and representation. The method is based on a pointwise selection of small image patches of fixed size in the variable neighborhood of each pixel. Our contribution is to associate with each pixel the weighted sum of data points within an adaptive neighborhood, in a manner that it balances the accuracy of approximation and the stochastic error, at each spatial position. This method is general and can be applied under the assumption that there exists repetitive patterns in a local neighborhood of a point. By introducing spatial adaptivity, we extend the work earlier described by Buades et al. which can be considered as an extension of bilateral filtering to image patches. Finally, we propose a nearly parameter-free algorithm for image denoising. The method is applied to both artificially corrupted (white Gaussian noise) and real images and the performance is very close to, and in some cases even surpasses, that of the already published denoising methods.
Abstract-We present a non-parametric regression method for denoising 3D image sequences acquired via fluorescence microscopy. The proposed method exploits the redundancy of the 3D+time information to improve the signal-to-noise ratio of images corrupted by PoissonGaussian noise. A variance stabilization transform is first applied to the image-data to remove the dependence between the mean and variance of intensity values. This preprocessing requires the knowledge of parameters related to the acquisition system, also estimated in our approach. In a second step, we propose an original statistical patchbased framework for noise reduction and preservation of space-time discontinuities. In our study, discontinuities are related to small moving spots with high velocity observed in fluorescence video-microscopy. The idea is to minimize an objective non-local energy functional involving spatiotemporal image patches. The minimizer has a simple form and is defined as the weighted average of input data taken in spatially-varying neighborhoods. The size of each neighborhood is optimized to improve the performance of the pointwise estimator. The performance of the algorithm (which requires no motion estimation) is then evaluated on both synthetic and real image sequences using qualitative and quantitative criteria.Index Terms-Video-microscopy, fluorescence, image sequence denoising, patch-based approach, Poisson noise, variance stabilization, adaptive estimation, energy minimization.
Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000× below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.OMX | phototoxicity | image processing | denoising | yeast
a b s t r a c tOptical flow estimation is one of the oldest and still most active research domains in computer vision. In 35 years, many methodological concepts have been introduced and have progressively improved performances, while opening the way to new challenges. In the last decade, the growing interest in evaluation benchmarks has stimulated a great amount of work. In this paper, we propose a survey of optical flow estimation classifying the main principles elaborated during this evolution, with a particular concern given to recent developments. It is conceived as a tutorial organizing in a comprehensive framework current approaches and practices. We give insights on the motivations, interests and limitations of modeling and optimization techniques, and we highlight similarities between methods to allow for a clear understanding of their behavior.
A novel adaptive and exemplar-based approach is proposed for image restoration (denoising) and representation. The method is based on a pointwise selection of similar image patches of fixed size in the variable neighborhood of each pixel. The main idea is to associate with each pixel the weighted sum of data points within an adaptive neighborhood. We use small image patches (e.g. 7 × 7 or 9 × 9 patches) to compute these weights since they are able to capture local geometric patterns and texels seen in images. In this paper, we mainly focus on the problem of adaptive neighborhood selection in a manner that balances the accuracy of approximation and the stochastic error, at each spatial position. The proposed pointwise estimator is then iterative and automatically adapts to the degree of underlying smoothness with minimal a priori assumptions on the function to be recovered. The method is applied to artificially corrupted real images and the performance is very close, and in some cases even surpasses, to that of the already published denoising methods. The proposed algorithm is demonstrated on real images corrupted by non-Gaussian noise and is used for applications in bio-imaging.
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