Automated tracking of colloidal clusters with sub-pixel accuracy and precision

Quantitative tracking of features from video images is a basic technique employed in many areas of science. Here, we present a method for the tracking of features that partially overlap, in order to be able to track so-called colloidal molecules. Our approach implements two improvements into existing particle tracking algorithms. Firstly, we use the history of previously identified feature locations to successfully find their positions in consecutive frames. Secondly, we present a framework for non-linear least-squares fitting to summed radial model functions and analyze the accuracy (bias) and precision (random error) of the method on artificial data. We find that our tracking algorithm correctly identifies overlapping features with an accuracy below 0.2% of the feature radius and a precision of 0.1 to 0.01 pixels for a typical image of a colloidal cluster. Finally, we use our method to extract the three-dimensional diffusion tensor from the Brownian motion of colloidal dimers.Comment: 20 pages, 8 figures. Non-revised preprint version, please refer to http://dx.doi.org/10.1088/1361-648X/29/4/04400

Image Segmentation Using Weak Shape Priors

The problem of image segmentation is known to become particularly challenging in the case of partial occlusion of the object(s) of interest, background clutter, and the presence of strong noise. To overcome this problem, the present paper introduces a novel approach segmentation through the use of "weak" shape priors. Specifically, in the proposed method, an segmenting active contour is constrained to converge to a configuration at which its geometric parameters attain their empirical probability densities closely matching the corresponding model densities that are learned based on training samples. It is shown through numerical experiments that the proposed shape modeling can be regarded as "weak" in the sense that it minimally influences the segmentation, which is allowed to be dominated by data-related forces. On the other hand, the priors provide sufficient constraints to regularize the convergence of segmentation, while requiring substantially smaller training sets to yield less biased results as compared to the case of PCA-based regularization methods. The main advantages of the proposed technique over some existing alternatives is demonstrated in a series of experiments.Comment: 27 pages, 8 figure

A framework for quantification and physical modeling of cell mixing applied to oscillator synchronization in vertebrate somitogenesis

In development and disease, cells move as they exchange signals. One example is found in vertebrate development, during which the timing of segment formation is set by a ‘segmentation clock’, in which oscillating gene expression is synchronized across a population of cells by Delta-Notch signaling. Delta-Notch signaling requires local cell-cell contact, but in the zebrafish embryonic tailbud, oscillating cells move rapidly, exchanging neighbors. Previous theoretical studies proposed that this relative movement or cell mixing might alter signaling and thereby enhance synchronization. However, it remains unclear whether the mixing timescale in the tissue is in the right range for this effect, because a framework to reliably measure the mixing timescale and compare it with signaling timescale is lacking. Here, we develop such a framework using a quantitative description of cell mixing without the need for an external reference frame and constructing a physical model of cell movement based on the data. Numerical simulations show that mixing with experimentally observed statistics enhances synchronization of coupled phase oscillators, suggesting that mixing in the tailbud is fast enough to affect the coherence of rhythmic gene expression. Our approach will find general application in analyzing the relative movements of communicating cells during development and disease.Fil: Uriu, Koichiro. Kanazawa University; JapónFil: Bhavna, Rajasekaran. Max Planck Institute of Molecular Cell Biology and Genetics; Alemania. Max Planck Institute for the Physics of Complex Systems; AlemaniaFil: Oates, Andrew C.. Francis Crick Institute; Reino Unido. University College London; Reino UnidoFil: Morelli, Luis Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires - Instituto Partner de la Sociedad Max Planck; Argentina. Max Planck Institute for Molecular Physiology; Alemania. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentin

An extension of min/max flow framework

In this paper, the min/max flow scheme for image restoration is revised. The novelty consists of the fol- 24 lowing three parts. The first is to analyze the reason of the speckle generation and then to modify the 25 original scheme. The second is to point out that the continued application of this scheme cannot result 26 in an adaptive stopping of the curvature flow. This is followed by modifications of the original scheme 27 through the introduction of the Gradient Vector Flow (GVF) field and the zero-crossing detector, so as 28 to control the smoothing effect. Our experimental results with image restoration show that the proposed 29 schemes can reach a steady state solution while preserving the essential structures of objects. The third is 30 to extend the min/max flow scheme to deal with the boundary leaking problem, which is indeed an 31 intrinsic shortcoming of the familiar geodesic active contour model. The min/max flow framework pro- 32 vides us with an effective way to approximate the optimal solution. From an implementation point of 33 view, this extended scheme makes the speed function simpler and more flexible. The experimental 34 results of segmentation and region tracking show that the boundary leaking problem can be effectively 35 suppressed

Efficient MRF Energy Propagation for Video Segmentation via Bilateral Filters

Segmentation of an object from a video is a challenging task in multimedia applications. Depending on the application, automatic or interactive methods are desired; however, regardless of the application type, efficient computation of video object segmentation is crucial for time-critical applications; specifically, mobile and interactive applications require near real-time efficiencies. In this paper, we address the problem of video segmentation from the perspective of efficiency. We initially redefine the problem of video object segmentation as the propagation of MRF energies along the temporal domain. For this purpose, a novel and efficient method is proposed to propagate MRF energies throughout the frames via bilateral filters without using any global texture, color or shape model. Recently presented bi-exponential filter is utilized for efficiency, whereas a novel technique is also developed to dynamically solve graph-cuts for varying, non-lattice graphs in general linear filtering scenario. These improvements are experimented for both automatic and interactive video segmentation scenarios. Moreover, in addition to the efficiency, segmentation quality is also tested both quantitatively and qualitatively. Indeed, for some challenging examples, significant time efficiency is observed without loss of segmentation quality.Comment: Multimedia, IEEE Transactions on (Volume:16, Issue: 5, Aug. 2014

Vessel tractography using an intensity based tensor model with branch detection

In this paper, we present a tubular structure seg- mentation method that utilizes a second order tensor constructed from directional intensity measurements, which is inspired from diffusion tensor image (DTI) modeling. The constructed anisotropic tensor which is fit inside a vessel drives the segmen- tation analogously to a tractography approach in DTI. Our model is initialized at a single seed point and is capable of capturing whole vessel trees by an automatic branch detection algorithm developed in the same framework. The centerline of the vessel as well as its thickness is extracted. Performance results within the Rotterdam Coronary Artery Algorithm Evaluation framework are provided for comparison with existing techniques. 96.4% average overlap with ground truth delineated by experts is obtained in addition to other measures reported in the paper. Moreover, we demonstrate further quantitative results over synthetic vascular datasets, and we provide quantitative experiments for branch detection on patient Computed Tomography Angiography (CTA) volumes, as well as qualitative evaluations on the same CTA datasets, from visual scores by a cardiologist expert